American Institute of Physics: The Journal of Chemical Physics: Table of Contents
Table of Contents for The Journal of Chemical Physics. List of articles from both the latest and ahead of print issues.
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American Institute of Physics: The Journal of Chemical Physics: Table of Contents
American Institute of Physics
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The Journal of Chemical Physics
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A perspective on the microscopic pressure (stress) tensor: History, current understanding, and future challenges
https://aip.scitation.org/doi/10.1063/5.0132487?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>The pressure tensor (equivalent to the negative stress tensor) at both microscopic and macroscopic levels is fundamental to many aspects of engineering and science, including fluid dynamics, solid mechanics, biophysics, and thermodynamics. In this Perspective, we review methods to calculate the microscopic pressure tensor. Connections between different pressure forms for equilibrium and nonequilibrium systems are established. We also point out several challenges in the field, including the historical controversies over the definition of the microscopic pressure tensor; the difficulties with manybody and longrange potentials; the insufficiency of software and computational tools; and the lack of experimental routes to probe the pressure tensor at the nanoscale. Possible future directions are suggested.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>The pressure tensor (equivalent to the negative stress tensor) at both microscopic and macroscopic levels is fundamental to many aspects of engineering and science, including fluid dynamics, solid mechanics, biophysics, and thermodynamics. In this Perspective, we review methods to calculate the microscopic pressure tensor. Connections between different pressure forms for equilibrium and nonequilibrium systems are established. We also point out several challenges in the field, including the historical controversies over the definition of the microscopic pressure tensor; the difficulties with manybody and longrange potentials; the insufficiency of software and computational tools; and the lack of experimental routes to probe the pressure tensor at the nanoscale. Possible future directions are suggested.
A perspective on the microscopic pressure (stress) tensor: History, current understanding, and future challenges
10.1063/5.0132487
The Journal of Chemical Physics
20230130T11:48:52Z
© 2023 Author(s).
Kaihang Shi
Edward R. Smith
Erik E. Santiso
Keith E. Gubbins

Kineticenhanced carbon fiber for rechargeable zinc–air batteries
https://aip.scitation.org/doi/10.1063/5.0135513?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Metalfree catalysts are made by the elements with infinite reserve in nature and, therefore, show the potential for largescale applications in energy devices including metal–air batteries. The construction of metal–air batteries prefers using selfsupporting catalysts with favorable activity as well as fast kinetics. However, it is challenging due to the limited electropositivity of metalfree catalysts for O–O bond formation in oxygen evolution reaction (OER), scaling relationship restrictions between OER and oxygen reduction reaction, and difficulty in porosity construction on the monolith electrode surface. In this contribution, through developing a facile methodology of quenching hightemperature carbon clothes in liquid nitrogen, a selfsupported carbon cloth with bifunctional active graphene skin and fast kinetics is well constructed to serve as the air cathode in metal–air batteries. Regulated oxygen species and threedimensionally hierarchical porosity are well constructed on the carbon fiber surfaces, contributing high intrinsic activity and prominently enhanced kinetics, which leads to favorable performances in aqueous as well as flexible rechargeable zinc–air batteries. The work proposed a promising strategy in the rational design and smart synthesis of fastkinetic monolith electrodes, which refreshes concepts and strategies of advanced material fabrication, and also bridges material science and practical energy devices.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Metalfree catalysts are made by the elements with infinite reserve in nature and, therefore, show the potential for largescale applications in energy devices including metal–air batteries. The construction of metal–air batteries prefers using selfsupporting catalysts with favorable activity as well as fast kinetics. However, it is challenging due to the limited electropositivity of metalfree catalysts for O–O bond formation in oxygen evolution reaction (OER), scaling relationship restrictions between OER and oxygen reduction reaction, and difficulty in porosity construction on the monolith electrode surface. In this contribution, through developing a facile methodology of quenching hightemperature carbon clothes in liquid nitrogen, a selfsupported carbon cloth with bifunctional active graphene skin and fast kinetics is well constructed to serve as the air cathode in metal–air batteries. Regulated oxygen species and threedimensionally hierarchical porosity are well constructed on the carbon fiber surfaces, contributing high intrinsic activity and prominently enhanced kinetics, which leads to favorable performances in aqueous as well as flexible rechargeable zinc–air batteries. The work proposed a promising strategy in the rational design and smart synthesis of fastkinetic monolith electrodes, which refreshes concepts and strategies of advanced material fabrication, and also bridges material science and practical energy devices.
Kineticenhanced carbon fiber for rechargeable zinc–air batteries
10.1063/5.0135513
The Journal of Chemical Physics
20230124T11:08:37Z
© 2023 Author(s).
Yang Li
Bin Wang
HaoFan Wang
Cheng Tang

Correlated Dirac–Coulomb–Breit multiconfigurational selfconsistentfield methods
https://aip.scitation.org/doi/10.1063/5.0133741?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>The fully correlated frequencyindependent Dirac–Coulomb–Breit Hamiltonian provides the most accurate description of electron–electron interaction before going to a genuine relativistic quantum electrodynamics theory of manyelectron systems. In this work, we introduce a correlated Dirac–Coulomb–Breit multiconfigurational selfconsistentfield method within the frameworks of complete active space and density matrix renormalization group. In this approach, the Dirac–Coulomb–Breit Hamiltonian is included variationally in both the meanfield and correlated electron treatment. We also analyze the importance of the Breit operator in electron correlation and the rotation between the positive and negativeorbital space in the novirtualpair approximation. Atomic finestructure splittings and lanthanide contraction in diatomic fluorides are used as benchmark studies to understand the contribution from the Breit correlation.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>The fully correlated frequencyindependent Dirac–Coulomb–Breit Hamiltonian provides the most accurate description of electron–electron interaction before going to a genuine relativistic quantum electrodynamics theory of manyelectron systems. In this work, we introduce a correlated Dirac–Coulomb–Breit multiconfigurational selfconsistentfield method within the frameworks of complete active space and density matrix renormalization group. In this approach, the Dirac–Coulomb–Breit Hamiltonian is included variationally in both the meanfield and correlated electron treatment. We also analyze the importance of the Breit operator in electron correlation and the rotation between the positive and negativeorbital space in the novirtualpair approximation. Atomic finestructure splittings and lanthanide contraction in diatomic fluorides are used as benchmark studies to understand the contribution from the Breit correlation.
Correlated Dirac–Coulomb–Breit multiconfigurational selfconsistentfield methods
10.1063/5.0133741
The Journal of Chemical Physics
20230123T10:54:53Z
© 2023 Author(s).
Chad E. Hoyer
Lixin Lu
Hang Hu
Kirill D. Shumilov
Shichao Sun
Stefan Knecht
Xiaosong Li

Oneelectron selfinteraction error and its relationship to geometry and higher orbital occupation
https://aip.scitation.org/doi/10.1063/5.0129820?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Density Functional Theory (DFT) sees prominent use in computational chemistry and physics; however, problems due to the selfinteraction error (SIE) pose additional challenges to obtaining qualitatively correct results. As an unphysical energy an electron exerts on itself, the SIE impacts most practical DFT calculations. We conduct an indepth analysis of the oneelectron SIE in which we replicate delocalization effects for simple geometries. We present a simple visualization of such effects, which may help in future qualitative analysis of the oneelectron SIE. By increasing the number of nuclei in a linear arrangement, the SIE increases dramatically. We also show how molecular shape impacts the SIE. Two and threedimensional shapes show an even greater SIE stemming mainly from the exchange functional with some error compensation from the oneelectron error, which we previously defined [D. R. Lonsdale and L. Goerigk, Phys. Chem. Chem. Phys. 22, 15805 (2020)]. Most tested geometries are affected by the functional error, while some suffer from the density error. For the latter, we establish a potential connection with electrons being unequally delocalized by the DFT methods. We also show how the SIE increases if electrons occupy higherlying atomic orbitals; seemingly oneelectron SIE free methods in a ground are no longer SIE free in excited states, which is an important insight for some popular, nonempirical density functional approximations (DFAs). We conclude that the erratic behavior of the SIE in even the simplest geometries shows that robust DFAs are needed. Our test systems can be used as a future benchmark or contribute toward DFT development.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Density Functional Theory (DFT) sees prominent use in computational chemistry and physics; however, problems due to the selfinteraction error (SIE) pose additional challenges to obtaining qualitatively correct results. As an unphysical energy an electron exerts on itself, the SIE impacts most practical DFT calculations. We conduct an indepth analysis of the oneelectron SIE in which we replicate delocalization effects for simple geometries. We present a simple visualization of such effects, which may help in future qualitative analysis of the oneelectron SIE. By increasing the number of nuclei in a linear arrangement, the SIE increases dramatically. We also show how molecular shape impacts the SIE. Two and threedimensional shapes show an even greater SIE stemming mainly from the exchange functional with some error compensation from the oneelectron error, which we previously defined [D. R. Lonsdale and L. Goerigk, Phys. Chem. Chem. Phys. 22, 15805 (2020)]. Most tested geometries are affected by the functional error, while some suffer from the density error. For the latter, we establish a potential connection with electrons being unequally delocalized by the DFT methods. We also show how the SIE increases if electrons occupy higherlying atomic orbitals; seemingly oneelectron SIE free methods in a ground are no longer SIE free in excited states, which is an important insight for some popular, nonempirical density functional approximations (DFAs). We conclude that the erratic behavior of the SIE in even the simplest geometries shows that robust DFAs are needed. Our test systems can be used as a future benchmark or contribute toward DFT development.
Oneelectron selfinteraction error and its relationship to geometry and higher orbital occupation
10.1063/5.0129820
The Journal of Chemical Physics
20230123T10:55:14Z
© 2023 Author(s).
Dale R. Lonsdale
Lars Goerigk

Douglas–Kroll and infinite order twocomponent transformations of Dirac–Fock operator
https://aip.scitation.org/doi/10.1063/5.0131926?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>We extended the conventional Douglas–Kroll (DK) and infinite order twocomponent (IOTC) methods to a technique applicable to Fock matrices, called extended DK (EDK) and extended IOTC (EIOTC), respectively. First, we defined a strategy to divide the Dirac–Fock operator into zero and firstorder terms. We then demonstrated that the firstorder extended DK transformation, which is the Foldy–Wouthuysen transformation for the zeroorder term, as well as the second and thirdorder EDK and EIOTC, could be well defined. The EDK and EIOTCtransformed Fock matrix, kinetic energy operator, nuclear attraction operator, and density matrix were derived. These equations were numerically evaluated, and it was found that these methods were accurate. In particular, EIOTC was consistent with the fourcomponent approach. Fourcomponent and extended twocomponent calculations are more expensive than nonrelativistic calculations due to smallcomponenttype twoelectron integrals. We developed a new approximation formula, RISV, for smallcomponenttype twoelectron integrals, including the spin–orbit interaction between electrons. These results suggest that the RISV formula effectively accelerates the fourcomponent and extended twocomponent methods.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>We extended the conventional Douglas–Kroll (DK) and infinite order twocomponent (IOTC) methods to a technique applicable to Fock matrices, called extended DK (EDK) and extended IOTC (EIOTC), respectively. First, we defined a strategy to divide the Dirac–Fock operator into zero and firstorder terms. We then demonstrated that the firstorder extended DK transformation, which is the Foldy–Wouthuysen transformation for the zeroorder term, as well as the second and thirdorder EDK and EIOTC, could be well defined. The EDK and EIOTCtransformed Fock matrix, kinetic energy operator, nuclear attraction operator, and density matrix were derived. These equations were numerically evaluated, and it was found that these methods were accurate. In particular, EIOTC was consistent with the fourcomponent approach. Fourcomponent and extended twocomponent calculations are more expensive than nonrelativistic calculations due to smallcomponenttype twoelectron integrals. We developed a new approximation formula, RISV, for smallcomponenttype twoelectron integrals, including the spin–orbit interaction between electrons. These results suggest that the RISV formula effectively accelerates the fourcomponent and extended twocomponent methods.
Douglas–Kroll and infinite order twocomponent transformations of Dirac–Fock operator
10.1063/5.0131926
The Journal of Chemical Physics
20230123T10:55:11Z
© 2023 Author(s).
Nobuki Inoue
Takahito Nakajima

Accurate analytical calculation of the rate coefficient for the diffusioncontrolled reactions due to hyperbolic diffusion
https://aip.scitation.org/doi/10.1063/5.0134727?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Using an approach based on the diffusion analog of the Cattaneo–Vernotte differential model, we find the exact analytical solution to the corresponding timedependent linear hyperbolic initial boundary value problem, describing irreversible diffusioncontrolled reactions under Smoluchowski’s boundary condition on a spherical sink. By means of this solution, we extend exact analytical calculations for the timedependent classical Smoluchowski rate coefficient to the case that includes the socalled inertial effects, occurring in the host media with finite relaxation times. We also present a brief survey of Smoluchowski’s theory and its various subsequent refinements, including works devoted to the description of the shorttime behavior of Brownian particles. In this paper, we managed to show that a known Rice’s formula, commonly recognized earlier as an exact reaction rate coefficient for the case of hyperbolic diffusion, turned out to be only its approximation being a uniform upper bound of the exact value. Here, the obtained formula seems to be of great significance for bridging a known gap between an analytically estimated rate coefficient on the one hand and molecular dynamics simulations together with experimentally observed results for the short times regime on the other hand. A particular emphasis has been placed on the rigorous mathematical treatment and important properties of the relevant initial boundary value problems in parabolic and hyperbolic diffusion theories.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Using an approach based on the diffusion analog of the Cattaneo–Vernotte differential model, we find the exact analytical solution to the corresponding timedependent linear hyperbolic initial boundary value problem, describing irreversible diffusioncontrolled reactions under Smoluchowski’s boundary condition on a spherical sink. By means of this solution, we extend exact analytical calculations for the timedependent classical Smoluchowski rate coefficient to the case that includes the socalled inertial effects, occurring in the host media with finite relaxation times. We also present a brief survey of Smoluchowski’s theory and its various subsequent refinements, including works devoted to the description of the shorttime behavior of Brownian particles. In this paper, we managed to show that a known Rice’s formula, commonly recognized earlier as an exact reaction rate coefficient for the case of hyperbolic diffusion, turned out to be only its approximation being a uniform upper bound of the exact value. Here, the obtained formula seems to be of great significance for bridging a known gap between an analytically estimated rate coefficient on the one hand and molecular dynamics simulations together with experimentally observed results for the short times regime on the other hand. A particular emphasis has been placed on the rigorous mathematical treatment and important properties of the relevant initial boundary value problems in parabolic and hyperbolic diffusion theories.
Accurate analytical calculation of the rate coefficient for the diffusioncontrolled reactions due to hyperbolic diffusion
10.1063/5.0134727
The Journal of Chemical Physics
20230123T10:55:46Z
© 2023 Author(s).
Sergey D. Traytak

Excitation energies of polycylic aromatic hydrocarbons by doublehybrid functionals: Assessing the PBE0DH and PBEQIDH models and their rangeseparated versions
https://aip.scitation.org/doi/10.1063/5.0134946?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>A family of nonempirical doublehybrid (DH) density functionals, such as Perdew–Burke–Ernzerhof (PBE)0DH, PBEQIDH, and their rangeseparated exchange (RSX) versions RSX0DH and RSXQIDH, all using PerdewBurkeErnzerhof(PBE) exchange and correlationfunctionals, is applied here to calculate the excitation energies for increasingly longer linear and cyclic acenes as part of their intense benchmarking for excited states of all types. The energies for the two lowestlying singlet 1La and 1Lb states of linear oligoacenes as well as the triplet 3La and 3Lb states, are calculated and compared with experimental results. These functionals clearly outperform the results obtained from hybrid functionals and favorably compare with other doublehybrid expressions also tested here, such as B2PLYP, B2GPPLYP, ωB2PLYP, and ωB2GPPLYP. The study is complemented by the computation of adiabatic S0–T1 singlettriplet energy difference for linear acenes as well as the extension of the study to strained cyclic oligomers, showing how the family of nonempirical expressions robustly leads to competitive results.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>A family of nonempirical doublehybrid (DH) density functionals, such as Perdew–Burke–Ernzerhof (PBE)0DH, PBEQIDH, and their rangeseparated exchange (RSX) versions RSX0DH and RSXQIDH, all using PerdewBurkeErnzerhof(PBE) exchange and correlationfunctionals, is applied here to calculate the excitation energies for increasingly longer linear and cyclic acenes as part of their intense benchmarking for excited states of all types. The energies for the two lowestlying singlet 1La and 1Lb states of linear oligoacenes as well as the triplet 3La and 3Lb states, are calculated and compared with experimental results. These functionals clearly outperform the results obtained from hybrid functionals and favorably compare with other doublehybrid expressions also tested here, such as B2PLYP, B2GPPLYP, ωB2PLYP, and ωB2GPPLYP. The study is complemented by the computation of adiabatic S0–T1 singlettriplet energy difference for linear acenes as well as the extension of the study to strained cyclic oligomers, showing how the family of nonempirical expressions robustly leads to competitive results.
Excitation energies of polycylic aromatic hydrocarbons by doublehybrid functionals: Assessing the PBE0DH and PBEQIDH models and their rangeseparated versions
10.1063/5.0134946
The Journal of Chemical Physics
20230123T10:55:43Z
© 2023 Author(s).
M. E. SandovalSalinas
E. Brémond
A. J. PérezJiménez
C. Adamo
J. C. SanchoGarcía

Calculation of exciton couplings based on density functional tightbinding coupled to stateinteraction stateaveraged ensemblereferenced Kohn–Sham approach
https://aip.scitation.org/doi/10.1063/5.0132361?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>We introduce the combination of the density functional tight binding (DFTB) approach, including onsite correction (OC) and longrange corrected (LC) functional and the stateinteraction stateaveraged spinrestricted ensemblereferenced Kohn–Sham (SISAREKS or SSR) method with extended active space involving four electrons and four orbitals [LCOCDFTB/SSR(4,4)], to investigate exciton couplings in multichromophoric systems, such as organic crystals and molecular aggregates. We employ the LCOCDFTB/SSR(4,4) method to calculate the excitonic coupling in anthracene and tetracene. As a result, the LCOCDFTB/SSR(4,4) method provides a reliable description of the locally excited (LE) state in a single chromophore and the excitonic couplings between chromophores with reasonable accuracy compared to the experiment and the conventional SSR(4,4) method. In addition, the thermal fluctuation of excitonic couplings from dynamic nuclear motion in an anthracene crystal with LCOCDFTB/SSR(4,4) shows a similar fluctuation of excitonic coupling and spectral density with those of firstprinciple calculations. We conclude that LCOCDFTB/SSR(4,4) is capable of providing reasonable features related to LE states, such as Frenkel exciton with efficient computational cost.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>We introduce the combination of the density functional tight binding (DFTB) approach, including onsite correction (OC) and longrange corrected (LC) functional and the stateinteraction stateaveraged spinrestricted ensemblereferenced Kohn–Sham (SISAREKS or SSR) method with extended active space involving four electrons and four orbitals [LCOCDFTB/SSR(4,4)], to investigate exciton couplings in multichromophoric systems, such as organic crystals and molecular aggregates. We employ the LCOCDFTB/SSR(4,4) method to calculate the excitonic coupling in anthracene and tetracene. As a result, the LCOCDFTB/SSR(4,4) method provides a reliable description of the locally excited (LE) state in a single chromophore and the excitonic couplings between chromophores with reasonable accuracy compared to the experiment and the conventional SSR(4,4) method. In addition, the thermal fluctuation of excitonic couplings from dynamic nuclear motion in an anthracene crystal with LCOCDFTB/SSR(4,4) shows a similar fluctuation of excitonic coupling and spectral density with those of firstprinciple calculations. We conclude that LCOCDFTB/SSR(4,4) is capable of providing reasonable features related to LE states, such as Frenkel exciton with efficient computational cost.
Calculation of exciton couplings based on density functional tightbinding coupled to stateinteraction stateaveraged ensemblereferenced Kohn–Sham approach
10.1063/5.0132361
The Journal of Chemical Physics
20230123T10:55:35Z
© 2023 Author(s).
Tae In Kim
In Seong Lee
Hwon Kim
Seung Kyu Min

Geometries and vibrational frequencies with Kohn–Sham methods using σfunctionals for the correlation energy
https://aip.scitation.org/doi/10.1063/5.0129524?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Recently, Kohn–Sham (KS) methods with new correlation functionals, called σfunctionals, have been introduced. Technically, σfunctionals are closely related to the wellknown random phase approximation (RPA); formally, σfunctionals are rooted in perturbation theory along the adiabatic connection. If employed in a postselfconsistent field manner in a Gaussian basis set framework, then, σfunctional methods are computationally very efficient. Moreover, for main group chemistry, σfunctionals are highly accurate and can compete with highlevel wavefunction methods. For reaction and transition state energies, e.g., chemical accuracy of 1 kcal/mol is reached. Here, we show how to calculate first derivatives of the total energy with respect to nuclear coordinates for methods using σfunctionals and then carry out geometry optimizations for test sets of main group molecules, transition metal compounds, and noncovalently bonded systems. For main group molecules, we additionally calculate vibrational frequencies. σFunctional methods are found to yield very accurate geometries and vibrational frequencies for main group molecules superior not only to those from conventional KS methods but also to those from RPA methods. For geometries of transition metal compounds, not surprisingly, best geometries are found for RPA methods, while σfunctional methods yield somewhat less good results. This is attributed to the fact that in the optimization of σfunctionals, transition metal compounds could not be represented well due to the lack of reliable reference data. For noncovalently bonded systems, σfunctionals yield geometries of the same quality as the RPA or as conventional KS schemes combined with dispersion corrections.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Recently, Kohn–Sham (KS) methods with new correlation functionals, called σfunctionals, have been introduced. Technically, σfunctionals are closely related to the wellknown random phase approximation (RPA); formally, σfunctionals are rooted in perturbation theory along the adiabatic connection. If employed in a postselfconsistent field manner in a Gaussian basis set framework, then, σfunctional methods are computationally very efficient. Moreover, for main group chemistry, σfunctionals are highly accurate and can compete with highlevel wavefunction methods. For reaction and transition state energies, e.g., chemical accuracy of 1 kcal/mol is reached. Here, we show how to calculate first derivatives of the total energy with respect to nuclear coordinates for methods using σfunctionals and then carry out geometry optimizations for test sets of main group molecules, transition metal compounds, and noncovalently bonded systems. For main group molecules, we additionally calculate vibrational frequencies. σFunctional methods are found to yield very accurate geometries and vibrational frequencies for main group molecules superior not only to those from conventional KS methods but also to those from RPA methods. For geometries of transition metal compounds, not surprisingly, best geometries are found for RPA methods, while σfunctional methods yield somewhat less good results. This is attributed to the fact that in the optimization of σfunctionals, transition metal compounds could not be represented well due to the lack of reliable reference data. For noncovalently bonded systems, σfunctionals yield geometries of the same quality as the RPA or as conventional KS schemes combined with dispersion corrections.
Geometries and vibrational frequencies with Kohn–Sham methods using σfunctionals for the correlation energy
10.1063/5.0129524
The Journal of Chemical Physics
20230124T11:08:24Z
© 2023 Author(s).
Christian Neiss
Steffen Fauser
Andreas Görling

Fermionicpropagator and alternatingbasis quantum Monte Carlo methods for correlated electrons on a lattice
https://aip.scitation.org/doi/10.1063/5.0133597?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Ultracoldatom simulations of the Hubbard model provide insights into the character of charge and spin correlations in and out of equilibrium. The corresponding numerical simulations, on the other hand, remain a significant challenge. We build on recent progress in the quantum Monte Carlo (QMC) simulation of electrons in continuous space and apply similar ideas to the squarelattice Hubbard model. We devise and benchmark two discretetime QMC methods, namely the fermionicpropagator QMC (FPQMC) and the alternatingbasis QMC (ABQMC). In FPQMC, the time evolution is represented by snapshots in real space, whereas the snapshots in ABQMC alternate between real and reciprocal space. The methods may be applied to study equilibrium properties within the grandcanonical or canonical ensemble, external field quenches, and even the evolution of pure states. Various realspace/reciprocalspace correlation functions are also within their reach. Both methods deal with matrices of size equal to the number of particles (thus independent of the number of orbitals or time slices), which allows for cheap updates. We benchmark the methods in relevant setups. In equilibrium, the FPQMC method is found to have an excellent average sign and, in some cases, yields correct results even with poor imaginarytime discretization. ABQMC has a significantly worse average sign, but also produces good results. Out of equilibrium, FPQMC suffers from a strong dynamical sign problem. On the contrary, in ABQMC, the sign problem is not timedependent. Using ABQMC, we compute survival probabilities for several experimentally relevant pure states.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Ultracoldatom simulations of the Hubbard model provide insights into the character of charge and spin correlations in and out of equilibrium. The corresponding numerical simulations, on the other hand, remain a significant challenge. We build on recent progress in the quantum Monte Carlo (QMC) simulation of electrons in continuous space and apply similar ideas to the squarelattice Hubbard model. We devise and benchmark two discretetime QMC methods, namely the fermionicpropagator QMC (FPQMC) and the alternatingbasis QMC (ABQMC). In FPQMC, the time evolution is represented by snapshots in real space, whereas the snapshots in ABQMC alternate between real and reciprocal space. The methods may be applied to study equilibrium properties within the grandcanonical or canonical ensemble, external field quenches, and even the evolution of pure states. Various realspace/reciprocalspace correlation functions are also within their reach. Both methods deal with matrices of size equal to the number of particles (thus independent of the number of orbitals or time slices), which allows for cheap updates. We benchmark the methods in relevant setups. In equilibrium, the FPQMC method is found to have an excellent average sign and, in some cases, yields correct results even with poor imaginarytime discretization. ABQMC has a significantly worse average sign, but also produces good results. Out of equilibrium, FPQMC suffers from a strong dynamical sign problem. On the contrary, in ABQMC, the sign problem is not timedependent. Using ABQMC, we compute survival probabilities for several experimentally relevant pure states.
Fermionicpropagator and alternatingbasis quantum Monte Carlo methods for correlated electrons on a lattice
10.1063/5.0133597
The Journal of Chemical Physics
20230124T11:08:40Z
© 2023 Author(s).
Veljko Janković
Jakša Vučičević

PESPIP: Software to fit complex molecular and manybody potential energy surfaces with permutationally invariant polynomials
https://aip.scitation.org/doi/10.1063/5.0134442?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>We wish to describe a potential energy surface by using a basis of permutationally invariant polynomials whose coefficients will be determined by numerical regression so as to smoothly fit a dataset of electronic energies as well as, perhaps, gradients. The polynomials will be powers of transformed internuclear distances, usually either Morse variables, exp(−ri,j/λ), where λ is a constant range hyperparameter, or reciprocals of the distances, 1/ri,j. The question we address is how to create the most efficient basis, including (a) which polynomials to keep or discard, (b) how many polynomials will be needed, (c) how to make sure the polynomials correctly reproduce the zero interaction at a large distance, (d) how to ensure special symmetries, and (e) how to calculate gradients efficiently. This article discusses how these questions can be answered by using a set of programs to choose and manipulate the polynomials as well as to write efficient Fortran programs for the calculation of energies and gradients. A userfriendly interface for access to monomial symmetrization approach results is also described. The software for these programs is now publicly available.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>We wish to describe a potential energy surface by using a basis of permutationally invariant polynomials whose coefficients will be determined by numerical regression so as to smoothly fit a dataset of electronic energies as well as, perhaps, gradients. The polynomials will be powers of transformed internuclear distances, usually either Morse variables, exp(−ri,j/λ), where λ is a constant range hyperparameter, or reciprocals of the distances, 1/ri,j. The question we address is how to create the most efficient basis, including (a) which polynomials to keep or discard, (b) how many polynomials will be needed, (c) how to make sure the polynomials correctly reproduce the zero interaction at a large distance, (d) how to ensure special symmetries, and (e) how to calculate gradients efficiently. This article discusses how these questions can be answered by using a set of programs to choose and manipulate the polynomials as well as to write efficient Fortran programs for the calculation of energies and gradients. A userfriendly interface for access to monomial symmetrization approach results is also described. The software for these programs is now publicly available.
PESPIP: Software to fit complex molecular and manybody potential energy surfaces with permutationally invariant polynomials
10.1063/5.0134442
The Journal of Chemical Physics
20230124T11:08:33Z
© 2023 Author(s).
Paul L. Houston
Chen Qu
Qi Yu
Riccardo Conte
Apurba Nandi
Jeffrey K. Li
Joel M. Bowman

Extending multilayer energybased fragment method for excitedstate calculations of large covalently bonded fragment systems
https://aip.scitation.org/doi/10.1063/5.0129458?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Recently, we developed a lowscaling MultiLayer EnergyBased Fragment (MLEBF) method for accurate excitedstate calculations and nonadiabatic dynamics simulations of nonbonded fragment systems. In this work, we extend the MLEBF method to treat covalently bonded fragment ones. The main idea is cutting a target system into many fragments according to chemical properties. Fragments with dangling bonds are first saturated by chemical groups; then, saturated fragments, together with the original fragments without dangling bonds, are grouped into different layers. The accurate total energy expression is formulated with the manybody energy expansion theory, in combination with the inclusion–exclusion principle that is used to delete the contribution of chemical groups introduced to saturate dangling bonds. Specifically, in a twolayer MLEBF model, the photochemically active and inert layers are calculated with highlevel and efficient electronic structure methods, respectively. Intralayer and interlayer energies can be truncated at the two or threebody interaction level. Subsequently, through several systems, including neutral and charged covalently bonded fragment systems, we demonstrate that MLEBF can provide accurate ground and excitedstate energies and gradients. Finally, we realize the structure, conical intersection, and path optimizations by combining our MLEBF program with commercial and free packages, e.g., ASE and SciPy. These developments make MLEBF a practical and reliable tool for studying complex photochemical and photophysical processes of large nonbonded and bonded fragment systems.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Recently, we developed a lowscaling MultiLayer EnergyBased Fragment (MLEBF) method for accurate excitedstate calculations and nonadiabatic dynamics simulations of nonbonded fragment systems. In this work, we extend the MLEBF method to treat covalently bonded fragment ones. The main idea is cutting a target system into many fragments according to chemical properties. Fragments with dangling bonds are first saturated by chemical groups; then, saturated fragments, together with the original fragments without dangling bonds, are grouped into different layers. The accurate total energy expression is formulated with the manybody energy expansion theory, in combination with the inclusion–exclusion principle that is used to delete the contribution of chemical groups introduced to saturate dangling bonds. Specifically, in a twolayer MLEBF model, the photochemically active and inert layers are calculated with highlevel and efficient electronic structure methods, respectively. Intralayer and interlayer energies can be truncated at the two or threebody interaction level. Subsequently, through several systems, including neutral and charged covalently bonded fragment systems, we demonstrate that MLEBF can provide accurate ground and excitedstate energies and gradients. Finally, we realize the structure, conical intersection, and path optimizations by combining our MLEBF program with commercial and free packages, e.g., ASE and SciPy. These developments make MLEBF a practical and reliable tool for studying complex photochemical and photophysical processes of large nonbonded and bonded fragment systems.
Extending multilayer energybased fragment method for excitedstate calculations of large covalently bonded fragment systems
10.1063/5.0129458
The Journal of Chemical Physics
20230124T11:08:12Z
© 2023 Author(s).
WenKai Chen
WeiHai Fang
Ganglong Cui

The loss of the property of locality of the kernel in highdimensional Gaussian process regression on the example of the fitting of molecular potential energy surfaces
https://aip.scitation.org/doi/10.1063/5.0136156?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Kernelbased methods, including Gaussian process regression (GPR) and generally kernel ridge regression, have been finding increasing use in computational chemistry, including the fitting of potential energy surfaces and density functionals in highdimensional feature spaces. Kernels of the Matern family, such as Gaussianlike kernels (basis functions), are often used which allow imparting to them the meaning of covariance functions and formulating GPR as an estimator of the mean of a Gaussian distribution. The notion of locality of the kernel is critical for this interpretation. It is also critical to the formulation of multizeta type basis functions widely used in computational chemistry. We show, on the example of fitting of molecular potential energy surfaces of increasing dimensionality, the practical disappearance of the property of locality of a Gaussianlike kernel in high dimensionality. We also formulate a multizeta approach to the kernel and show that it significantly improves the quality of regression in low dimensionality but loses any advantage in high dimensionality, which is attributed to the loss of the property of locality.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Kernelbased methods, including Gaussian process regression (GPR) and generally kernel ridge regression, have been finding increasing use in computational chemistry, including the fitting of potential energy surfaces and density functionals in highdimensional feature spaces. Kernels of the Matern family, such as Gaussianlike kernels (basis functions), are often used which allow imparting to them the meaning of covariance functions and formulating GPR as an estimator of the mean of a Gaussian distribution. The notion of locality of the kernel is critical for this interpretation. It is also critical to the formulation of multizeta type basis functions widely used in computational chemistry. We show, on the example of fitting of molecular potential energy surfaces of increasing dimensionality, the practical disappearance of the property of locality of a Gaussianlike kernel in high dimensionality. We also formulate a multizeta approach to the kernel and show that it significantly improves the quality of regression in low dimensionality but loses any advantage in high dimensionality, which is attributed to the loss of the property of locality.
The loss of the property of locality of the kernel in highdimensional Gaussian process regression on the example of the fitting of molecular potential energy surfaces
10.1063/5.0136156
The Journal of Chemical Physics
20230124T11:08:20Z
© 2023 Author(s).
Sergei Manzhos
Manabu Ihara

Dynamic correlations in lipid bilayer membranes over finite time intervals
https://aip.scitation.org/doi/10.1063/5.0129130?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Recent singlemolecule measurements [Schoch et al., Proc. Natl. Acad. Sci. U. S. A. 118, e2113202118 (2021)] have observed dynamic lipid–lipid correlations in membranes with submicrometer spatial resolution and submillisecond temporal resolution. While short from an instrumentation standpoint, these length and time scales remain long compared to microscopic molecular motions. Theoretical expressions are derived to infer experimentally measurable correlations from the twobody diffusion matrix appropriate for membranebound bodies coupled by hydrodynamic interactions. The temporal (and associated spatial) averaging resulting from finite acquisition times has the effect of washing out correlations as compared to naive predictions (i.e., the bare elements of the diffusion matrix), which would be expected to hold for instantaneous measurements. The theoretical predictions are shown to be in excellent agreement with Brownian dynamics simulations of experimental measurements. Numerical results suggest that the experimental measurement of membrane protein diffusion, in complement to lipid diffusion measurements, might help to resolve the experimental ambiguities encountered for certain black lipid membranes.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Recent singlemolecule measurements [Schoch et al., Proc. Natl. Acad. Sci. U. S. A. 118, e2113202118 (2021)] have observed dynamic lipid–lipid correlations in membranes with submicrometer spatial resolution and submillisecond temporal resolution. While short from an instrumentation standpoint, these length and time scales remain long compared to microscopic molecular motions. Theoretical expressions are derived to infer experimentally measurable correlations from the twobody diffusion matrix appropriate for membranebound bodies coupled by hydrodynamic interactions. The temporal (and associated spatial) averaging resulting from finite acquisition times has the effect of washing out correlations as compared to naive predictions (i.e., the bare elements of the diffusion matrix), which would be expected to hold for instantaneous measurements. The theoretical predictions are shown to be in excellent agreement with Brownian dynamics simulations of experimental measurements. Numerical results suggest that the experimental measurement of membrane protein diffusion, in complement to lipid diffusion measurements, might help to resolve the experimental ambiguities encountered for certain black lipid membranes.
Dynamic correlations in lipid bilayer membranes over finite time intervals
10.1063/5.0129130
The Journal of Chemical Physics
20230124T11:08:16Z
© 2023 Author(s).
Rafael L. Schoch
Gilad Haran
Frank L. H. Brown

Learning pair potentials using differentiable simulations
https://aip.scitation.org/doi/10.1063/5.0126475?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Learning pair interactions from experimental or simulation data is of great interest for molecular simulations. We propose a general stochastic method for learning pair interactions from data using differentiable simulations (DiffSim). DiffSim defines a loss function based on structural observables, such as the radial distribution function, through molecular dynamics (MD) simulations. The interaction potentials are then learned directly by stochastic gradient descent, using backpropagation to calculate the gradient of the structural loss metric with respect to the interaction potential through the MD simulation. This gradientbased method is flexible and can be configured to simulate and optimize multiple systems simultaneously. For example, it is possible to simultaneously learn potentials for different temperatures or for different compositions. We demonstrate the approach by recovering simple pair potentials, such as LennardJones systems, from radial distribution functions. We find that DiffSim can be used to probe a wider functional space of pair potentials compared with traditional methods like iterative Boltzmann inversion. We show that our methods can be used to simultaneously fit potentials for simulations at different compositions and temperatures to improve the transferability of the learned potentials.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Learning pair interactions from experimental or simulation data is of great interest for molecular simulations. We propose a general stochastic method for learning pair interactions from data using differentiable simulations (DiffSim). DiffSim defines a loss function based on structural observables, such as the radial distribution function, through molecular dynamics (MD) simulations. The interaction potentials are then learned directly by stochastic gradient descent, using backpropagation to calculate the gradient of the structural loss metric with respect to the interaction potential through the MD simulation. This gradientbased method is flexible and can be configured to simulate and optimize multiple systems simultaneously. For example, it is possible to simultaneously learn potentials for different temperatures or for different compositions. We demonstrate the approach by recovering simple pair potentials, such as LennardJones systems, from radial distribution functions. We find that DiffSim can be used to probe a wider functional space of pair potentials compared with traditional methods like iterative Boltzmann inversion. We show that our methods can be used to simultaneously fit potentials for simulations at different compositions and temperatures to improve the transferability of the learned potentials.
Learning pair potentials using differentiable simulations
10.1063/5.0126475
The Journal of Chemical Physics
20230125T12:38:50Z
© 2023 Author(s).
Wujie Wang
Zhenghao Wu
Johannes C. B. Dietschreit
Rafael GómezBombarelli

Dense random packing with a powerlaw size distribution: The structure factor, mass–radius relation, and pair distribution function
https://aip.scitation.org/doi/10.1063/5.0134813?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>We consider a dense random packing of disks with a powerlaw distribution of radii and investigate their correlation properties. We study the corresponding structure factor, mass–radius relation, and pair distribution function of the disk centers. A toy model of dense segments in one dimension (1D) is solved exactly. It is shown theoretically in 1D and numerically in 1D and 2D that such a packing exhibits fractal properties. It is found that the exponent of the powerlaw distribution and the fractal dimension coincide. An approximate relation for the structure factor in arbitrary dimensions is derived, which can be used as a fitting formula in smallangle scattering. These findings can be useful for understanding the microstructural properties of various systems such as ultrahigh performance concrete, highinternalphaseratio emulsions, or biological systems.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>We consider a dense random packing of disks with a powerlaw distribution of radii and investigate their correlation properties. We study the corresponding structure factor, mass–radius relation, and pair distribution function of the disk centers. A toy model of dense segments in one dimension (1D) is solved exactly. It is shown theoretically in 1D and numerically in 1D and 2D that such a packing exhibits fractal properties. It is found that the exponent of the powerlaw distribution and the fractal dimension coincide. An approximate relation for the structure factor in arbitrary dimensions is derived, which can be used as a fitting formula in smallangle scattering. These findings can be useful for understanding the microstructural properties of various systems such as ultrahigh performance concrete, highinternalphaseratio emulsions, or biological systems.
Dense random packing with a powerlaw size distribution: The structure factor, mass–radius relation, and pair distribution function
10.1063/5.0134813
The Journal of Chemical Physics
20230125T12:38:48Z
© 2023 Author(s).
Alexander Yu. Cherny
Eugen M. Anitas
Vladimir A. Osipov

Discretized hierarchical equations of motion in mixed Liouville–Wigner space for twodimensional vibrational spectroscopies of liquid water
https://aip.scitation.org/doi/10.1063/5.0135725?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>A model of a bulk water system describing the vibrational motion of intramolecular and intermolecular modes is constructed, enabling analysis of its linear and nonlinear vibrational spectra as well as the energy transfer processes between the vibrational modes. The model is described as a system of four interacting anharmonic oscillators nonlinearly coupled to their respective heat baths. To perform a rigorous numerical investigation of the nonMarkovian and nonperturbative quantum dissipative dynamics of the model, we derive discretized hierarchical equations of motion in mixed Liouville–Wigner space, with Lagrange–Hermite mesh discretization being employed in the Liouville space of the intramolecular modes and Lagrange–Hermite mesh discretization and Hermite discretization in the Wigner space of the intermolecular modes. Onedimensional infrared and Raman spectra and twodimensional terahertz–infrared–visible and infrared–infrared–Raman spectra are computed as demonstrations of the quantum dissipative description provided by our model.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>A model of a bulk water system describing the vibrational motion of intramolecular and intermolecular modes is constructed, enabling analysis of its linear and nonlinear vibrational spectra as well as the energy transfer processes between the vibrational modes. The model is described as a system of four interacting anharmonic oscillators nonlinearly coupled to their respective heat baths. To perform a rigorous numerical investigation of the nonMarkovian and nonperturbative quantum dissipative dynamics of the model, we derive discretized hierarchical equations of motion in mixed Liouville–Wigner space, with Lagrange–Hermite mesh discretization being employed in the Liouville space of the intramolecular modes and Lagrange–Hermite mesh discretization and Hermite discretization in the Wigner space of the intermolecular modes. Onedimensional infrared and Raman spectra and twodimensional terahertz–infrared–visible and infrared–infrared–Raman spectra are computed as demonstrations of the quantum dissipative description provided by our model.
Discretized hierarchical equations of motion in mixed Liouville–Wigner space for twodimensional vibrational spectroscopies of liquid water
10.1063/5.0135725
The Journal of Chemical Physics
20230125T12:38:45Z
© 2023 Author(s).
Hideaki Takahashi
Yoshitaka Tanimura

Exciton dispersion and exciton–phonon interaction in solids by timedependent density functional theory
https://aip.scitation.org/doi/10.1063/5.0137326?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Understanding, predicting, and ultimately controlling exciton band structure and exciton dynamics are central to diverse chemical and materials problems. Here, we have developed a firstprinciples method to determine exciton dispersion and exciton–phonon interaction in semiconducting and insulating solids based on timedependent density functional theory. The firstprinciples method is formulated in planewave bases and pseudopotentials and can be used to compute exciton band structures, exciton charge density, ionic forces, the nonadiabatic coupling matrix between excitonic states, and the exciton–phonon coupling matrix. Based on the spinor formulation, the method enables selfconsistent noncollinear calculations to capture spinorbital coupling. Hybrid exchangecorrelation functionals are incorporated to deal with longrange electron–hole interactions in solids. A subHilbert space approximation is introduced to reduce the computational cost without loss of accuracy. For validations, we have applied the method to compute the exciton band structure and exciton–phonon coupling strength in transition metal dichalcogenide monolayers; both agree very well with the previous GWBethe–Salpeter equation and experimental results. This development paves the way for accurate determinations of exciton dynamics in a wide range of solidstate materials.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Understanding, predicting, and ultimately controlling exciton band structure and exciton dynamics are central to diverse chemical and materials problems. Here, we have developed a firstprinciples method to determine exciton dispersion and exciton–phonon interaction in semiconducting and insulating solids based on timedependent density functional theory. The firstprinciples method is formulated in planewave bases and pseudopotentials and can be used to compute exciton band structures, exciton charge density, ionic forces, the nonadiabatic coupling matrix between excitonic states, and the exciton–phonon coupling matrix. Based on the spinor formulation, the method enables selfconsistent noncollinear calculations to capture spinorbital coupling. Hybrid exchangecorrelation functionals are incorporated to deal with longrange electron–hole interactions in solids. A subHilbert space approximation is introduced to reduce the computational cost without loss of accuracy. For validations, we have applied the method to compute the exciton band structure and exciton–phonon coupling strength in transition metal dichalcogenide monolayers; both agree very well with the previous GWBethe–Salpeter equation and experimental results. This development paves the way for accurate determinations of exciton dynamics in a wide range of solidstate materials.
Exciton dispersion and exciton–phonon interaction in solids by timedependent density functional theory
10.1063/5.0137326
The Journal of Chemical Physics
20230126T11:09:03Z
© 2023 Author(s).
Junyi Liu
Gang Lu
Xu Zhang

Predicting the structures and vibrational spectra of molecular crystals containing large molecules with the generalized energybased fragmentation approach
https://aip.scitation.org/doi/10.1063/5.0137072?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>The generalized energybased fragmentation (GEBF) approach under periodic boundary conditions (PBCs) has been developed to facilitate calculations of molecular crystals containing large molecules. The PBCGEBF approach can help predict structures and properties of molecular crystals at different theory levels by performing molecular quantum chemistry calculations on a series of nonperiodic subsystems constructed from the studied systems. A more rigorous formula of the forces on translational vectors of molecular crystals was proposed and implemented, enabling more reliable predictions of crystal structures. Our benchmark results on several typical molecular crystals show that the PBCGEBF approach could reproduce the forces on atoms and the translational vectors and the optimized crystal structures from the corresponding conventional periodic methods. The improved PBCGEBF approach is then applied to predict the crystal structures and vibrational spectra of two molecular crystals containing large molecules. The PBCGEBF approach can provide a satisfactory description on the crystal structure of a molecular crystal containing 312 atoms in a unit cell at densityfitting secondorder Møller–Plesset perturbation theory and density functional theory (DFT) levels and the infrared vibrational spectra of another molecular crystal containing 864 atoms in a unit cell at the DFT level. The PBCGEBF approach is expected to be a promising theoretical tool for electronic structure calculations on molecular crystals containing large molecules.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>The generalized energybased fragmentation (GEBF) approach under periodic boundary conditions (PBCs) has been developed to facilitate calculations of molecular crystals containing large molecules. The PBCGEBF approach can help predict structures and properties of molecular crystals at different theory levels by performing molecular quantum chemistry calculations on a series of nonperiodic subsystems constructed from the studied systems. A more rigorous formula of the forces on translational vectors of molecular crystals was proposed and implemented, enabling more reliable predictions of crystal structures. Our benchmark results on several typical molecular crystals show that the PBCGEBF approach could reproduce the forces on atoms and the translational vectors and the optimized crystal structures from the corresponding conventional periodic methods. The improved PBCGEBF approach is then applied to predict the crystal structures and vibrational spectra of two molecular crystals containing large molecules. The PBCGEBF approach can provide a satisfactory description on the crystal structure of a molecular crystal containing 312 atoms in a unit cell at densityfitting secondorder Møller–Plesset perturbation theory and density functional theory (DFT) levels and the infrared vibrational spectra of another molecular crystal containing 864 atoms in a unit cell at the DFT level. The PBCGEBF approach is expected to be a promising theoretical tool for electronic structure calculations on molecular crystals containing large molecules.
Predicting the structures and vibrational spectra of molecular crystals containing large molecules with the generalized energybased fragmentation approach
10.1063/5.0137072
The Journal of Chemical Physics
20230126T11:09:20Z
© 2023 Author(s).

How well do semiempirical QM methods describe the structure of proteins?
https://aip.scitation.org/doi/10.1063/5.0135091?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Semiempirical quantummechanical (QM) computational methods are an increasingly popular tool for the study of biomolecular systems. They were, however, developed and tested mostly on small model molecules. In this work, we explore one topic fundamental to these applications: the ability of the methods to describe the structure of proteins. In a set of 19 proteins for which a crystal structure with very high resolution is available, we analyze the properties of the protein geometries optimized using several semiempirical QM methods including PM6D3H4, PM7, and GFN2xTB. Some of the methods provide a very good description of the general structural features of the protein, yielding results better than or comparable to the AMBER ff03 force field. However, PM7 and PM6D3H4 optimizations introduce artificial close contacts in the structure, which is partially remediated by reparameterization.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Semiempirical quantummechanical (QM) computational methods are an increasingly popular tool for the study of biomolecular systems. They were, however, developed and tested mostly on small model molecules. In this work, we explore one topic fundamental to these applications: the ability of the methods to describe the structure of proteins. In a set of 19 proteins for which a crystal structure with very high resolution is available, we analyze the properties of the protein geometries optimized using several semiempirical QM methods including PM6D3H4, PM7, and GFN2xTB. Some of the methods provide a very good description of the general structural features of the protein, yielding results better than or comparable to the AMBER ff03 force field. However, PM7 and PM6D3H4 optimizations introduce artificial close contacts in the structure, which is partially remediated by reparameterization.
How well do semiempirical QM methods describe the structure of proteins?
10.1063/5.0135091
The Journal of Chemical Physics
20230126T11:09:33Z
© 2023 Author(s).
J. Řezáč
J. J. P. Stewart

Timereversal symmetry adaptation in relativistic density matrix renormalization group algorithm
https://aip.scitation.org/doi/10.1063/5.0127621?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>In the nonrelativistic Schrödinger equation, the total spin S and spin projection M are good quantum numbers. In contrast, spin symmetry is lost in the presence of spindependent interactions, such as spin–orbit couplings in relativistic Hamiltonians. Therefore, the relativistic density matrix renormalization group algorithm (RDMRG) only employing particle number symmetry is much more expensive than nonrelativistic DMRG. In addition, artificial breaking of Kramers degeneracy can happen in the treatment of systems with an odd number of electrons. To overcome these issues, we propose timereversal symmetry adaptation for RDMRG. Since the timereversal operator is antiunitary, this cannot be simply achieved in the usual way. We introduce a timereversal symmetryadapted renormalized basis and present strategies to maintain the structure of basis functions during the sweep optimization. With timereversal symmetry adaptation, only half of the renormalized operators are needed, and the computational costs of Hamiltonianwavefunction multiplication and renormalization are reduced by half. The present construction of the timereversal symmetryadapted basis also directly applies to other tensor network states without loops.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>In the nonrelativistic Schrödinger equation, the total spin S and spin projection M are good quantum numbers. In contrast, spin symmetry is lost in the presence of spindependent interactions, such as spin–orbit couplings in relativistic Hamiltonians. Therefore, the relativistic density matrix renormalization group algorithm (RDMRG) only employing particle number symmetry is much more expensive than nonrelativistic DMRG. In addition, artificial breaking of Kramers degeneracy can happen in the treatment of systems with an odd number of electrons. To overcome these issues, we propose timereversal symmetry adaptation for RDMRG. Since the timereversal operator is antiunitary, this cannot be simply achieved in the usual way. We introduce a timereversal symmetryadapted renormalized basis and present strategies to maintain the structure of basis functions during the sweep optimization. With timereversal symmetry adaptation, only half of the renormalized operators are needed, and the computational costs of Hamiltonianwavefunction multiplication and renormalization are reduced by half. The present construction of the timereversal symmetryadapted basis also directly applies to other tensor network states without loops.
Timereversal symmetry adaptation in relativistic density matrix renormalization group algorithm
10.1063/5.0127621
The Journal of Chemical Physics
20230126T11:09:14Z
© 2023 Author(s).
Zhendong Li

Spin–orbit coupling corrections for the GFNxTB method
https://aip.scitation.org/doi/10.1063/5.0129071?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Spin–orbit coupling (SOC) is crucial for correct electronic structure analysis in molecules and materials, for example, in large molecular systems such as superatoms, for understanding the role of transition metals in enzymes, and when investigating the energy transfer processes in metal–organic frameworks. We extend the GFNxTB method, popular to treat extended systems, by including SOC into the hamiltonian operator. We followed the same approach as previously reported for the density–functional tightbinding method and provide and validate the necessary parameters for all elements throughout the Periodic Table. The parameters have been obtained consistently from atomic SOC calculations using the density–functional theory. We tested them for reference structures where SOC is decisive, as in the transition metal containing heme moiety, chromophores in metal–organic frameworks, and in superatoms. Our parameterization paves the path for incorporation of SOC in the GFNxTB based electronic structure calculations of computationally expensive molecular systems.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Spin–orbit coupling (SOC) is crucial for correct electronic structure analysis in molecules and materials, for example, in large molecular systems such as superatoms, for understanding the role of transition metals in enzymes, and when investigating the energy transfer processes in metal–organic frameworks. We extend the GFNxTB method, popular to treat extended systems, by including SOC into the hamiltonian operator. We followed the same approach as previously reported for the density–functional tightbinding method and provide and validate the necessary parameters for all elements throughout the Periodic Table. The parameters have been obtained consistently from atomic SOC calculations using the density–functional theory. We tested them for reference structures where SOC is decisive, as in the transition metal containing heme moiety, chromophores in metal–organic frameworks, and in superatoms. Our parameterization paves the path for incorporation of SOC in the GFNxTB based electronic structure calculations of computationally expensive molecular systems.
Spin–orbit coupling corrections for the GFNxTB method
10.1063/5.0129071
The Journal of Chemical Physics
20230127T11:05:38Z
© 2023 Author(s).
Gautam Jha
Thomas Heine

Longrange corrected fragment molecular orbital density functional tightbinding method for excited states in large molecular systems
https://aip.scitation.org/doi/10.1063/5.0136844?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Herein, we present a new method to efficiently calculate electronically excited states in large molecular assemblies, consisting of hundreds of molecules. For this purpose, we combine the longrange corrected tightbinding density functional fragment molecular orbital method (FMOLCDFTB) with an excitonic Hamiltonian, which is constructed in the basis of locally excited and chargetransfer configuration state functions calculated for embedded monomers and dimers and accounts explicitly for the electronic coupling between all types of excitons. We first evaluate both the accuracy and efficiency of our fragmentation approach for molecular dimers and aggregates by comparing it with the full LCTDDFTB method. The comparison of the calculated spectra of an anthracene cluster shows a very good agreement between our method and the LCTDDFTB reference. The effective computational scaling of our method has been explored for anthracene clusters and for perylene bisimide aggregates. We demonstrate the applicability of our method by the calculation of the excited state properties of pentacene crystal models consisting of up to 319 molecules. Furthermore, the participation ratio of the monomer fragments to the excited states is analyzed by the calculation of natural transition orbital participation numbers, which are verified by the hole and particle density for a chosen pentacene cluster. The use of our FMOLCTDDFTB method will allow for future studies of excitonic dynamics and charge transport to be performed on complex molecular systems consisting of thousands of atoms.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Herein, we present a new method to efficiently calculate electronically excited states in large molecular assemblies, consisting of hundreds of molecules. For this purpose, we combine the longrange corrected tightbinding density functional fragment molecular orbital method (FMOLCDFTB) with an excitonic Hamiltonian, which is constructed in the basis of locally excited and chargetransfer configuration state functions calculated for embedded monomers and dimers and accounts explicitly for the electronic coupling between all types of excitons. We first evaluate both the accuracy and efficiency of our fragmentation approach for molecular dimers and aggregates by comparing it with the full LCTDDFTB method. The comparison of the calculated spectra of an anthracene cluster shows a very good agreement between our method and the LCTDDFTB reference. The effective computational scaling of our method has been explored for anthracene clusters and for perylene bisimide aggregates. We demonstrate the applicability of our method by the calculation of the excited state properties of pentacene crystal models consisting of up to 319 molecules. Furthermore, the participation ratio of the monomer fragments to the excited states is analyzed by the calculation of natural transition orbital participation numbers, which are verified by the hole and particle density for a chosen pentacene cluster. The use of our FMOLCTDDFTB method will allow for future studies of excitonic dynamics and charge transport to be performed on complex molecular systems consisting of thousands of atoms.
Longrange corrected fragment molecular orbital density functional tightbinding method for excited states in large molecular systems
10.1063/5.0136844
The Journal of Chemical Physics
20230127T11:05:42Z
© 2023 Author(s).
Richard Einsele
Joscha Hoche
Roland Mitrić

Analytical derivative couplings within the framework of timedependent density functional theory coupled with conductorlike polarizable continuum model: Formalism, implementation, and applications
https://aip.scitation.org/doi/10.1063/5.0130617?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>The nonadiabatic phenomena, which are characterized by a strong coupling between electronic and nuclear motions, are ubiquitous. The nonadiabatic effect of the studied system can be significantly affected by the surrounding environment, such as solvents, in which such nonadiabatic process takes place. It is essential to develop the theoretical models to simulate these processes while accurately modeling the solvent environment. The timedependent density functional theory (TDDFT) is currently the most efficient approach to describe the electronic structures and dynamics of complex systems, while the polarizable continuum model (PCM) represents one of the most successful examples among continuum solvation models. Here, we formulate the firstorder derivative couplings (DCs) between the ground and excited states as well as between two excited states by utilizing timeindependent equation of motion formalism within the framework of both linear response and spin flip formulations of TDDFT/CPCM (the conductorlike PCM), and implement the analytical DCs into the QCHEM electronic structure software package. The analytic implementation is validated by the comparison of the analytical and finitedifference results, and reproducing geometric phase effect in the protonated formaldimine test case. Taking 4(N,Ndimethylamino)benzonitrile and uracil in the gas phase and solution as an example, we demonstrate that the solvent effect is essential not only for the excitation energies of the lowlying excitedstates but also for the DCs between these states. Finally, we calculate the internal conversion rate of benzophenone in a solvent with DC being used. The current implementation of analytical DCs together with the existing analytical gradient and Hessian of TDDFT/PCM excited states allows one to study the nonadiabatic effects of relatively large systems in solutions with low computational cost.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>The nonadiabatic phenomena, which are characterized by a strong coupling between electronic and nuclear motions, are ubiquitous. The nonadiabatic effect of the studied system can be significantly affected by the surrounding environment, such as solvents, in which such nonadiabatic process takes place. It is essential to develop the theoretical models to simulate these processes while accurately modeling the solvent environment. The timedependent density functional theory (TDDFT) is currently the most efficient approach to describe the electronic structures and dynamics of complex systems, while the polarizable continuum model (PCM) represents one of the most successful examples among continuum solvation models. Here, we formulate the firstorder derivative couplings (DCs) between the ground and excited states as well as between two excited states by utilizing timeindependent equation of motion formalism within the framework of both linear response and spin flip formulations of TDDFT/CPCM (the conductorlike PCM), and implement the analytical DCs into the QCHEM electronic structure software package. The analytic implementation is validated by the comparison of the analytical and finitedifference results, and reproducing geometric phase effect in the protonated formaldimine test case. Taking 4(N,Ndimethylamino)benzonitrile and uracil in the gas phase and solution as an example, we demonstrate that the solvent effect is essential not only for the excitation energies of the lowlying excitedstates but also for the DCs between these states. Finally, we calculate the internal conversion rate of benzophenone in a solvent with DC being used. The current implementation of analytical DCs together with the existing analytical gradient and Hessian of TDDFT/PCM excited states allows one to study the nonadiabatic effects of relatively large systems in solutions with low computational cost.
Analytical derivative couplings within the framework of timedependent density functional theory coupled with conductorlike polarizable continuum model: Formalism, implementation, and applications
10.1063/5.0130617
The Journal of Chemical Physics
20230130T11:48:29Z
© 2023 Author(s).
Xunkun Huang
Zheng Pei
WanZhen Liang

Nonadiabatic ring polymer molecular dynamics in the phase space of the SU(N) Lie group
https://aip.scitation.org/doi/10.1063/5.0133970?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>We derive the nonadiabatic ring polymer molecular dynamics (RPMD) approach in the phase space of the SU(N) Lie Group. This method, which we refer to as the spin mapping nonadiabatic RPMD (SMNRPMD), is based on the spinmapping formalism for the electronic degrees of freedom (DOFs) and ring polymer pathintegral description for the nuclear DOFs. Using the Stratonovich–Weyl transform for the electronic DOFs and the Wigner transform for the nuclear DOFs, we derived an exact expression of the Kubotransformed timecorrelation function (TCF). We further derive the spin mapping nonadiabatic Matsubara dynamics using the Matsubara approximation that removes the high frequency nuclear normal modes in the TCF and derive the SMNRPMD approach from the nonadiabatic Matsubara dynamics by discarding the imaginary part of the Liouvillian. The SMNRPMD method has numerical advantages compared to the original NRPMD method based on the Meyer–Miller–Stock–Thoss (MMST) mapping formalism due to a more natural mapping using the SU(N) Lie Group that preserves the symmetry of the original system. We numerically compute the Kubotransformed position autocorrelation function and electronic population correlation function for threestate model systems. The numerical results demonstrate the accuracy of the SMNRPMD method, which outperforms the original MMSTbased NRPMD. We envision that the SMNRPMD method will be a powerful approach to simulate electronic nonadiabatic dynamics and nuclear quantum effects accurately.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>We derive the nonadiabatic ring polymer molecular dynamics (RPMD) approach in the phase space of the SU(N) Lie Group. This method, which we refer to as the spin mapping nonadiabatic RPMD (SMNRPMD), is based on the spinmapping formalism for the electronic degrees of freedom (DOFs) and ring polymer pathintegral description for the nuclear DOFs. Using the Stratonovich–Weyl transform for the electronic DOFs and the Wigner transform for the nuclear DOFs, we derived an exact expression of the Kubotransformed timecorrelation function (TCF). We further derive the spin mapping nonadiabatic Matsubara dynamics using the Matsubara approximation that removes the high frequency nuclear normal modes in the TCF and derive the SMNRPMD approach from the nonadiabatic Matsubara dynamics by discarding the imaginary part of the Liouvillian. The SMNRPMD method has numerical advantages compared to the original NRPMD method based on the Meyer–Miller–Stock–Thoss (MMST) mapping formalism due to a more natural mapping using the SU(N) Lie Group that preserves the symmetry of the original system. We numerically compute the Kubotransformed position autocorrelation function and electronic population correlation function for threestate model systems. The numerical results demonstrate the accuracy of the SMNRPMD method, which outperforms the original MMSTbased NRPMD. We envision that the SMNRPMD method will be a powerful approach to simulate electronic nonadiabatic dynamics and nuclear quantum effects accurately.
Nonadiabatic ring polymer molecular dynamics in the phase space of the SU(N) Lie group
10.1063/5.0133970
The Journal of Chemical Physics
20230131T11:00:17Z
© 2023 Author(s).
Duncan Bossion
Sutirtha N. Chowdhury
Pengfei Huo

Silver nanostructuremodified graphite electrode for inoperando SERRS investigation of iron porphyrins during highpotential electrocatalysis
https://aip.scitation.org/doi/10.1063/5.0136333?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Inoperando spectroscopic observation of the intermediates formed during various electrocatalytic oxidation and reduction reactions is crucial to propose the mechanism of the corresponding reaction. Surfaceenhanced resonance Raman spectroscopy coupled to rotating disk electrochemistry (SERRSRDE), developed about a decade ago, proved to be an excellent spectroscopic tool to investigate the mechanism of heterogeneous oxygen reduction reaction (ORR) catalyzed by synthetic iron porphyrin complexes under steadystate conditions in water. The information about the formation of the intermediates accumulated during the course of the reaction at the electrode interface helped to develop better ORR catalysts with second sphere residues in the porphyrin rings. To date, the application of this SERRSRDE setup is limited to ORR only because the thiol selfassembled monolayer (SAM)modified Ag electrode, used as the working electrode in these experiments, suffers from stability issues at more cathodic and anodic potential, where H2O oxidation, CO2 reduction, and H+ reduction reactions occur. The current investigation shows the development of a secondgeneration SERRSRDE setup consisting of an Ag nanostructure (AgNS)modified graphite electrode as the working electrode. These electrodes show higher stability (compared to the conventional thiol SAMmodified Ag electrode) upon exposure to very high cathodic and anodic potential with a good signaltonoise ratio in the Raman spectra. The behavior of this modified electrode toward ORR is found to be the same as the SAMmodified Ag electrode, and the same ORR intermediates are observed during electrochemical ORR. At higher cathodic potential, the signatures of Fe(0) porphyrin, an important intermediate in H+ and CO2 reduction reactions, was observed at the electrode–water interface.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Inoperando spectroscopic observation of the intermediates formed during various electrocatalytic oxidation and reduction reactions is crucial to propose the mechanism of the corresponding reaction. Surfaceenhanced resonance Raman spectroscopy coupled to rotating disk electrochemistry (SERRSRDE), developed about a decade ago, proved to be an excellent spectroscopic tool to investigate the mechanism of heterogeneous oxygen reduction reaction (ORR) catalyzed by synthetic iron porphyrin complexes under steadystate conditions in water. The information about the formation of the intermediates accumulated during the course of the reaction at the electrode interface helped to develop better ORR catalysts with second sphere residues in the porphyrin rings. To date, the application of this SERRSRDE setup is limited to ORR only because the thiol selfassembled monolayer (SAM)modified Ag electrode, used as the working electrode in these experiments, suffers from stability issues at more cathodic and anodic potential, where H2O oxidation, CO2 reduction, and H+ reduction reactions occur. The current investigation shows the development of a secondgeneration SERRSRDE setup consisting of an Ag nanostructure (AgNS)modified graphite electrode as the working electrode. These electrodes show higher stability (compared to the conventional thiol SAMmodified Ag electrode) upon exposure to very high cathodic and anodic potential with a good signaltonoise ratio in the Raman spectra. The behavior of this modified electrode toward ORR is found to be the same as the SAMmodified Ag electrode, and the same ORR intermediates are observed during electrochemical ORR. At higher cathodic potential, the signatures of Fe(0) porphyrin, an important intermediate in H+ and CO2 reduction reactions, was observed at the electrode–water interface.
Silver nanostructuremodified graphite electrode for inoperando SERRS investigation of iron porphyrins during highpotential electrocatalysis
10.1063/5.0136333
The Journal of Chemical Physics
20230130T11:48:24Z
© 2023 Author(s).
Samir Chattopadhyay
Soumya Samanta
Ankita Sarkar
Aishik Bhattacharya
Suman Patra
Abhishek Dey

Vibrationally excited states of 1H and 2H1,2,3triazole isotopologues analyzed by millimeterwave and highresolution infrared spectroscopy with approximate statespecific quartic distortion constants
https://aip.scitation.org/doi/10.1063/5.0137340?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>In this work, we present the spectral analysis of 1H and 2H1,2,3triazole vibrationally excited states alongside provisional and practical computational predictions of the excitedstate quartic centrifugal distortion constants. The lowenergy fundamental vibrational states of 1H1,2,3triazole and five of its deuteriated isotopologues ([12H], [42H], [52H], [4,52H], and [1,4,52H]1H1,2,3triazole), as well as those of 2H1,2,3triazole and five of its deuteriated isotopologues ([22H], [42H], [2,42H], [4,52H], and [2,4,52H]2H1,2,3triazole), are studied using millimeterwave spectroscopy in the 130–375 GHz frequency region. The normal and [22H]isotopologues of 2H1,2,3triazole are also analyzed using highresolution infrared spectroscopy, determining the precise energies of three of their lowenergy fundamental states. The resulting spectroscopic constants for each of the vibrationally excited states are reported for the first time. Coupledcluster vibration–rotation interaction constants are compared with each of their experimentally determined values, often showing agreement within 500 kHz. Newly available coupledcluster predictions of the excitedstate quartic centrifugal distortion constants based on fourthorder vibrational perturbation theory are benchmarked using a large number of the 1,2,3triazole tautomer isotopologues and vibrationally excited states studied.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>In this work, we present the spectral analysis of 1H and 2H1,2,3triazole vibrationally excited states alongside provisional and practical computational predictions of the excitedstate quartic centrifugal distortion constants. The lowenergy fundamental vibrational states of 1H1,2,3triazole and five of its deuteriated isotopologues ([12H], [42H], [52H], [4,52H], and [1,4,52H]1H1,2,3triazole), as well as those of 2H1,2,3triazole and five of its deuteriated isotopologues ([22H], [42H], [2,42H], [4,52H], and [2,4,52H]2H1,2,3triazole), are studied using millimeterwave spectroscopy in the 130–375 GHz frequency region. The normal and [22H]isotopologues of 2H1,2,3triazole are also analyzed using highresolution infrared spectroscopy, determining the precise energies of three of their lowenergy fundamental states. The resulting spectroscopic constants for each of the vibrationally excited states are reported for the first time. Coupledcluster vibration–rotation interaction constants are compared with each of their experimentally determined values, often showing agreement within 500 kHz. Newly available coupledcluster predictions of the excitedstate quartic centrifugal distortion constants based on fourthorder vibrational perturbation theory are benchmarked using a large number of the 1,2,3triazole tautomer isotopologues and vibrationally excited states studied.
Vibrationally excited states of 1H and 2H1,2,3triazole isotopologues analyzed by millimeterwave and highresolution infrared spectroscopy with approximate statespecific quartic distortion constants
10.1063/5.0137340
The Journal of Chemical Physics
20230125T12:38:32Z
© 2023 Author(s).
Maria A. Zdanovskaia
Peter R. Franke
Brian J. Esselman
Brant E. Billinghurst
Jianbao Zhao
John F. Stanton
R. Claude Woods
Robert J. McMahon

Vibrational relaxation by methylated xanthines in solution: Insights from 2D IR spectroscopy and calculations
https://aip.scitation.org/doi/10.1063/5.0135412?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Twodimensional infrared (2D IR) spectroscopy, infrared pump–infrared probe spectroscopy, and density functional theory calculations were used to study vibrational relaxation by ring and carbonyl stretching modes in a series of methylated xanthine derivatives in acetonitrile and deuterium oxide (heavy water). Isotropic signals from the excited symmetric and asymmetric carbonyl stretch modes decay biexponentially in both solvents. Coherent energy transfer between the symmetric and asymmetric carbonyl stretching modes gives rise to a quantum beat in the timedependent anisotropy signals. The damping time of the coherent oscillation agrees with the fast decay component of the carbonyl bleach recovery signals, indicating that this time constant reflects intramolecular vibrational redistribution (IVR) to other solute modes. Despite their similar frequencies, the excited ring modes decay monoexponentially with a time constant that matches the slow decay component of the carbonyl modes. The slow decay times, which are faster in heavy water than in acetonitrile, approximately match the ones observed in previous UV pump–IR probe measurements on the same compounds. The slow component is assigned to intermolecular energy transfer to solvent bath modes from lowfrequency solute modes, which are populated by IVR and are anharmonically coupled to the carbonyl and ring stretch modes. 2D IR measurements indicate that the carbonyl stretching modes are weakly coupled to the delocalized ring modes, resulting in slow exchange that cannot explain the common solventdependence. IVR is suggested to occur at different rates for the carbonyl vs ring modes due to differences in modespecific couplings and not to differences in the density of accessible states.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Twodimensional infrared (2D IR) spectroscopy, infrared pump–infrared probe spectroscopy, and density functional theory calculations were used to study vibrational relaxation by ring and carbonyl stretching modes in a series of methylated xanthine derivatives in acetonitrile and deuterium oxide (heavy water). Isotropic signals from the excited symmetric and asymmetric carbonyl stretch modes decay biexponentially in both solvents. Coherent energy transfer between the symmetric and asymmetric carbonyl stretching modes gives rise to a quantum beat in the timedependent anisotropy signals. The damping time of the coherent oscillation agrees with the fast decay component of the carbonyl bleach recovery signals, indicating that this time constant reflects intramolecular vibrational redistribution (IVR) to other solute modes. Despite their similar frequencies, the excited ring modes decay monoexponentially with a time constant that matches the slow decay component of the carbonyl modes. The slow decay times, which are faster in heavy water than in acetonitrile, approximately match the ones observed in previous UV pump–IR probe measurements on the same compounds. The slow component is assigned to intermolecular energy transfer to solvent bath modes from lowfrequency solute modes, which are populated by IVR and are anharmonically coupled to the carbonyl and ring stretch modes. 2D IR measurements indicate that the carbonyl stretching modes are weakly coupled to the delocalized ring modes, resulting in slow exchange that cannot explain the common solventdependence. IVR is suggested to occur at different rates for the carbonyl vs ring modes due to differences in modespecific couplings and not to differences in the density of accessible states.
Vibrational relaxation by methylated xanthines in solution: Insights from 2D IR spectroscopy and calculations
10.1063/5.0135412
The Journal of Chemical Physics
20230126T11:09:37Z
© 2023 Author(s).
Alex T. Hanes
Christopher Grieco
Remy F. Lalisse
Christopher M. Hadad
Bern Kohler

Finestructure excitation of CCS by He: Potential energy surface and scattering calculations
https://aip.scitation.org/doi/10.1063/5.0138470?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>The fine structure excitation of the interstellar CCS radical induced by collisions with He is investigated. The first potential energy surface (PES) for the CCS–He van der Waals complex is presented. It was obtained from a highly correlated spin unrestricted coupled cluster approach with single double and perturbative triple excitations. The PES presents two shallow minima of 31.85 and 37.12 cm−1 for the linear (He facing S) and the nearly Tshaped geometries, respectively. The dissociation energy of the complex was calculated and found to be D0 = 14.183 cm−1. Inelastic scattering calculations were performed using the closecoupling approach. Crosssections for transitions between the 61 first fine structure levels of CCS were obtained for energy up to 600 cm−1 and rate coefficients for the 5–50 K temperature range were derived. This set of collisional data can be used to model CCS emission spectra in dark molecular interstellar clouds and circumstellar envelopes and enable an accurate determination of CCS abundance in these astrophysical media.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>The fine structure excitation of the interstellar CCS radical induced by collisions with He is investigated. The first potential energy surface (PES) for the CCS–He van der Waals complex is presented. It was obtained from a highly correlated spin unrestricted coupled cluster approach with single double and perturbative triple excitations. The PES presents two shallow minima of 31.85 and 37.12 cm−1 for the linear (He facing S) and the nearly Tshaped geometries, respectively. The dissociation energy of the complex was calculated and found to be D0 = 14.183 cm−1. Inelastic scattering calculations were performed using the closecoupling approach. Crosssections for transitions between the 61 first fine structure levels of CCS were obtained for energy up to 600 cm−1 and rate coefficients for the 5–50 K temperature range were derived. This set of collisional data can be used to model CCS emission spectra in dark molecular interstellar clouds and circumstellar envelopes and enable an accurate determination of CCS abundance in these astrophysical media.
Finestructure excitation of CCS by He: Potential energy surface and scattering calculations
10.1063/5.0138470
The Journal of Chemical Physics
20230130T11:48:15Z
© 2023 Author(s).
A. Godard Palluet
F. Lique

Physical mechanisms of the Soret effect in binary LennardJones liquids elucidated with thermalresponse calculations
https://aip.scitation.org/doi/10.1063/5.0135244?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>The Soret effect is the tendency of fluid mixtures to exhibit concentration gradients in the presence of a temperature gradient. Using moleculardynamics simulation of twocomponent LennardJones liquids, it is demonstrated that spatially sinusoidal heat pulses generate both temperature and pressure gradients. Over short timescales, the dominant effect is the generation of compressional waves, which dissipate over time as the system approaches mechanical equilibrium. The approach to mechanical equilibrium is also characterized by a decrease in particle density in the hightemperature region and an increase in particle density in the lowtemperature region. It is demonstrated that concentration gradients develop rapidly during the propagation of compressional waves through the liquid. Over longer timescales, heat conduction occurs to return the system to thermal equilibrium, with the particle current acting to restore a more uniform particle density. It is shown that the Soret effect arises due to the fact that the two components of the fluid exhibit different responses to pressure gradients. First, the socalled isotope effect occurs because light atoms tend to respond more rapidly to evolving conditions. In this case, there appears to be a connection to previous observations of “fast sound” in binary fluids. Second, it is shown that the partial pressures of the two components in equilibrium, and more directly, the relative magnitudes of their derivatives with respect to temperature and density, determine which species accumulate in the high and lowtemperature regions. In the conditions simulated here, the dependence of the partial pressure on density gradients is larger than the dependence on temperature gradients. This is directly connected to the accumulation of the species with the largest partial pressure in the hightemperature region and the accumulation of the species with the smallest partial pressure in the lowtemperature region. The results suggest that further development of theoretical descriptions of the Soret effect might begin with hydrodynamical equations in twocomponent liquids. Finally, it is suggested that the recently proposed concept of “thermophobicity” may be related to the sensitivity of partial pressures in a multicomponent fluid to changes in temperature and density.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>The Soret effect is the tendency of fluid mixtures to exhibit concentration gradients in the presence of a temperature gradient. Using moleculardynamics simulation of twocomponent LennardJones liquids, it is demonstrated that spatially sinusoidal heat pulses generate both temperature and pressure gradients. Over short timescales, the dominant effect is the generation of compressional waves, which dissipate over time as the system approaches mechanical equilibrium. The approach to mechanical equilibrium is also characterized by a decrease in particle density in the hightemperature region and an increase in particle density in the lowtemperature region. It is demonstrated that concentration gradients develop rapidly during the propagation of compressional waves through the liquid. Over longer timescales, heat conduction occurs to return the system to thermal equilibrium, with the particle current acting to restore a more uniform particle density. It is shown that the Soret effect arises due to the fact that the two components of the fluid exhibit different responses to pressure gradients. First, the socalled isotope effect occurs because light atoms tend to respond more rapidly to evolving conditions. In this case, there appears to be a connection to previous observations of “fast sound” in binary fluids. Second, it is shown that the partial pressures of the two components in equilibrium, and more directly, the relative magnitudes of their derivatives with respect to temperature and density, determine which species accumulate in the high and lowtemperature regions. In the conditions simulated here, the dependence of the partial pressure on density gradients is larger than the dependence on temperature gradients. This is directly connected to the accumulation of the species with the largest partial pressure in the hightemperature region and the accumulation of the species with the smallest partial pressure in the lowtemperature region. The results suggest that further development of theoretical descriptions of the Soret effect might begin with hydrodynamical equations in twocomponent liquids. Finally, it is suggested that the recently proposed concept of “thermophobicity” may be related to the sensitivity of partial pressures in a multicomponent fluid to changes in temperature and density.
Physical mechanisms of the Soret effect in binary LennardJones liquids elucidated with thermalresponse calculations
10.1063/5.0135244
The Journal of Chemical Physics
20230123T10:55:00Z
Patrick K. Schelling

Effect of particle anisotropy on the thermodynamics and kinetics of ordering transitions in hard faceted particles
https://aip.scitation.org/doi/10.1063/5.0135461?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Monte Carlo simulations were used to study the influence of particle aspect ratio on the kinetics and phase behavior of hard gyrobifastigia (GBF). First, the formation of a highly anisotropic nucleus shape in the isotropictocrystal transition in regular GBF is explained by the differences in interfacial free energies of various crystal planes and the nucleus geometry predicted by the Wulff construction. GBFrelated shapes with various aspect ratios were then studied, mapping their equations of state, determining phase coexistence conditions via interfacial pinning, and computing nucleation freeenergy barriers via umbrella sampling using suitable order parameters. Our simulations reveal a reduction of the kinetic barrier for isotropic–crystal transition upon an increase in aspect ratio, and that for highly oblate and prolate aspect ratios, an intermediate nematic phase is stabilized. Our results and observations also support two conjectures for the formation of the crystalline state from the isotropic phase: that low phase free energies at the ordering phase transition correlate with low transition barriers and that the emergence of a mesophase provides a steppingstone that expedites crystallization.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Monte Carlo simulations were used to study the influence of particle aspect ratio on the kinetics and phase behavior of hard gyrobifastigia (GBF). First, the formation of a highly anisotropic nucleus shape in the isotropictocrystal transition in regular GBF is explained by the differences in interfacial free energies of various crystal planes and the nucleus geometry predicted by the Wulff construction. GBFrelated shapes with various aspect ratios were then studied, mapping their equations of state, determining phase coexistence conditions via interfacial pinning, and computing nucleation freeenergy barriers via umbrella sampling using suitable order parameters. Our simulations reveal a reduction of the kinetic barrier for isotropic–crystal transition upon an increase in aspect ratio, and that for highly oblate and prolate aspect ratios, an intermediate nematic phase is stabilized. Our results and observations also support two conjectures for the formation of the crystalline state from the isotropic phase: that low phase free energies at the ordering phase transition correlate with low transition barriers and that the emergence of a mesophase provides a steppingstone that expedites crystallization.
Effect of particle anisotropy on the thermodynamics and kinetics of ordering transitions in hard faceted particles
10.1063/5.0135461
The Journal of Chemical Physics
20230125T12:38:41Z
© 2023 Author(s).
Abhishek K. Sharma
Fernando A. Escobedo

Diffusion and dynamics of noble gases in hydroquinone clathrate channels
https://aip.scitation.org/doi/10.1063/5.0137734?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>In the present work, we study the behavior of the noble gases He, Ne, Ar, and Kr inside a hydroquinone clathrate (HQC) by using allatom molecular dynamics. Larger elements of the same group were not considered due to their inability to fit inside the HQC cavities. By using the umbrella sampling technique, we have obtained the following intercage transition barriers—which are arguably the main factor determining the type of diffusion of the gases—at 310 K and 0.1 MPa: 1192; 2204; 6450; 10 730 kJ mol−1 for the guests He, Ne, Ar, and Kr, respectively. These energy barriers were found to have a linear relation with atomic radii (σ). We have tested this tendency with CH4, due to its intermediate size between Ar and Kr, obtaining a barrier of 8926 kJ mol−1, in excellent agreement with the results for noble gases.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>In the present work, we study the behavior of the noble gases He, Ne, Ar, and Kr inside a hydroquinone clathrate (HQC) by using allatom molecular dynamics. Larger elements of the same group were not considered due to their inability to fit inside the HQC cavities. By using the umbrella sampling technique, we have obtained the following intercage transition barriers—which are arguably the main factor determining the type of diffusion of the gases—at 310 K and 0.1 MPa: 1192; 2204; 6450; 10 730 kJ mol−1 for the guests He, Ne, Ar, and Kr, respectively. These energy barriers were found to have a linear relation with atomic radii (σ). We have tested this tendency with CH4, due to its intermediate size between Ar and Kr, obtaining a barrier of 8926 kJ mol−1, in excellent agreement with the results for noble gases.
Diffusion and dynamics of noble gases in hydroquinone clathrate channels
10.1063/5.0137734
The Journal of Chemical Physics
20230130T11:48:43Z
© 2023 Author(s).
Brais RodríguezGarcía
Manuel M. Piñeiro
Martín PérezRodríguez

Homogeneous nucleation of crystalline methane hydrate in molecular dynamics transition paths sampled under realistic conditions
https://aip.scitation.org/doi/10.1063/5.0124852?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Methane hydrates are important from a scientific and industrial perspective, and form by nucleation and growth from a supersaturated aqueous solution of methane. Molecular simulation is able to shed light on the process of homogeneous nucleation of hydrates, using straightforward molecular dynamics or rare event enhanced sampling techniques with atomistic and coarse grained force fields. In our previous work [Arjun, T. A. Berendsen, and P. G. Bolhuis, Proc. Natl. Acad. Sci. U. S. A. 116, 19305 (2019)], we performed transition path sampling (TPS) simulations using all atom force fields under moderate driving forces at high pressure, which enabled unbiased atomistic insight into the formation of methane hydrates. The supersaturation in these simulations was influenced by the Laplace pressure induced by the spherical gas reservoir. Here, we investigate the effect of removing this influence. Focusing on the supercooled, supersaturated regime to keep the system size tractable, our TPS simulations indicate that nuclei form amorphous structures below roughly 260 K and crystalline sI structures above 260 K. For these temperatures, the average transition path lengths are significantly longer than in our previous study, pushing the boundaries of what can be achieved with TPS. The temperature to observe a critical nucleus of certain size was roughly 20 K lower compared to a spherical reservoir due to the lower concentration of methane in the solution, yielding a reduced driving force. We analyze the TPS results using a model based on classical nucleation theory. The corresponding free energy barriers are estimated and found to be consistent with previous predictions, thus adding to the overall picture of the hydrate formation process.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Methane hydrates are important from a scientific and industrial perspective, and form by nucleation and growth from a supersaturated aqueous solution of methane. Molecular simulation is able to shed light on the process of homogeneous nucleation of hydrates, using straightforward molecular dynamics or rare event enhanced sampling techniques with atomistic and coarse grained force fields. In our previous work [Arjun, T. A. Berendsen, and P. G. Bolhuis, Proc. Natl. Acad. Sci. U. S. A. 116, 19305 (2019)], we performed transition path sampling (TPS) simulations using all atom force fields under moderate driving forces at high pressure, which enabled unbiased atomistic insight into the formation of methane hydrates. The supersaturation in these simulations was influenced by the Laplace pressure induced by the spherical gas reservoir. Here, we investigate the effect of removing this influence. Focusing on the supercooled, supersaturated regime to keep the system size tractable, our TPS simulations indicate that nuclei form amorphous structures below roughly 260 K and crystalline sI structures above 260 K. For these temperatures, the average transition path lengths are significantly longer than in our previous study, pushing the boundaries of what can be achieved with TPS. The temperature to observe a critical nucleus of certain size was roughly 20 K lower compared to a spherical reservoir due to the lower concentration of methane in the solution, yielding a reduced driving force. We analyze the TPS results using a model based on classical nucleation theory. The corresponding free energy barriers are estimated and found to be consistent with previous predictions, thus adding to the overall picture of the hydrate formation process.
Homogeneous nucleation of crystalline methane hydrate in molecular dynamics transition paths sampled under realistic conditions
10.1063/5.0124852
The Journal of Chemical Physics
20230131T11:00:08Z
© 2023 Author(s).
A. Arjun
Peter G. Bolhuis

On the Fresnel factor correction of sumfrequency generation spectra of interfacial water
https://aip.scitation.org/doi/10.1063/5.0133428?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Insights into the microscopic structure of aqueous interfaces are essential for understanding the chemical and physical processes on the water surface, including chemical synthesis, atmospheric chemistry, and events in biomolecular systems. These aqueous interfaces have been probed by heterodynedetected sumfrequency generation (HDSFG) spectroscopy. To obtain the molecular response from the measured HDSFG spectra, one needs to correct the measured ssp spectra for local electromagnetic field effects at the interface due to a spatially varying dielectric function. This socalled Fresnel factor correction can change the inferred response substantially, and different ways of performing this correction lead to different conclusions about the interfacial water response. Here, we compare the simulated and experimental spectra at the air/water interface. We use three previously developed models to compare the experiment with theory: an advanced approach taking into account the detailed inhomogeneous interfacial dielectric profile and the Lorentz and slab models to approximate the interfacial dielectric function. Using the advanced model, we obtain an excellent quantitative agreement between theory and experiment, in both spectral shape and amplitude. Remarkably, we find that for the Fresnel factor correction of the ssp spectra, the Lorentz model for the interfacial dielectric function is equally accurate in the hydrogen (H)bonded region of the response, while the slab model underestimates this response significantly. The Lorentz model, thus, provides a straightforward method to obtain the molecular response from the measured spectra of aqueous interfaces in the Hbonded region.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Insights into the microscopic structure of aqueous interfaces are essential for understanding the chemical and physical processes on the water surface, including chemical synthesis, atmospheric chemistry, and events in biomolecular systems. These aqueous interfaces have been probed by heterodynedetected sumfrequency generation (HDSFG) spectroscopy. To obtain the molecular response from the measured HDSFG spectra, one needs to correct the measured ssp spectra for local electromagnetic field effects at the interface due to a spatially varying dielectric function. This socalled Fresnel factor correction can change the inferred response substantially, and different ways of performing this correction lead to different conclusions about the interfacial water response. Here, we compare the simulated and experimental spectra at the air/water interface. We use three previously developed models to compare the experiment with theory: an advanced approach taking into account the detailed inhomogeneous interfacial dielectric profile and the Lorentz and slab models to approximate the interfacial dielectric function. Using the advanced model, we obtain an excellent quantitative agreement between theory and experiment, in both spectral shape and amplitude. Remarkably, we find that for the Fresnel factor correction of the ssp spectra, the Lorentz model for the interfacial dielectric function is equally accurate in the hydrogen (H)bonded region of the response, while the slab model underestimates this response significantly. The Lorentz model, thus, provides a straightforward method to obtain the molecular response from the measured spectra of aqueous interfaces in the Hbonded region.
On the Fresnel factor correction of sumfrequency generation spectra of interfacial water
10.1063/5.0133428
The Journal of Chemical Physics
20230123T10:55:06Z
© 2023 Author(s).
Xiaoqing Yu
KuoYang Chiang
ChunChieh Yu
Mischa Bonn
Yuki Nagata

TeraChem protocol buffers (TCPB): Accelerating QM and QM/MM simulations with a client–server model
https://aip.scitation.org/doi/10.1063/5.0130886?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>The routine use of electronic structures in many chemical simulation applications calls for efficient and easy ways to access electronic structure programs. We describe how the graphics processing unit (GPU) accelerated electronic structure program TeraChem can be set up as an electronic structure server, to be easily accessed by thirdparty client programs. We exploit Google’s protocol buffer framework for data serialization and communication. The client interface, called TeraChem protocol buffers (TCPB), has been designed for ease of use and compatibility with multiple programming languages, such as C++, Fortran, and Python. To demonstrate the ease of coupling thirdparty programs with electronic structures using TCPB, we have incorporated the TCPB client into Amber for quantum mechanics/molecular mechanics (QM/MM) simulations. The TCPB interface saves time with GPU initialization and I/O operations, achieving a speedup of more than 2× compared to a prior filebased implementation for a QM region with ∼250 basis functions. We demonstrate the practical application of TCPB by computing the free energy profile of phydroxybenzylidene2,3dimethylimidazolinone (pHBDI−)—a model chromophore in green fluorescent proteins—on the first excited singlet state using Hamiltonian replica exchange for enhanced sampling. All calculations in this work have been performed with the noncommercial freelyavailable version of TeraChem, which is sufficient for many QM region sizes in common use.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>The routine use of electronic structures in many chemical simulation applications calls for efficient and easy ways to access electronic structure programs. We describe how the graphics processing unit (GPU) accelerated electronic structure program TeraChem can be set up as an electronic structure server, to be easily accessed by thirdparty client programs. We exploit Google’s protocol buffer framework for data serialization and communication. The client interface, called TeraChem protocol buffers (TCPB), has been designed for ease of use and compatibility with multiple programming languages, such as C++, Fortran, and Python. To demonstrate the ease of coupling thirdparty programs with electronic structures using TCPB, we have incorporated the TCPB client into Amber for quantum mechanics/molecular mechanics (QM/MM) simulations. The TCPB interface saves time with GPU initialization and I/O operations, achieving a speedup of more than 2× compared to a prior filebased implementation for a QM region with ∼250 basis functions. We demonstrate the practical application of TCPB by computing the free energy profile of phydroxybenzylidene2,3dimethylimidazolinone (pHBDI−)—a model chromophore in green fluorescent proteins—on the first excited singlet state using Hamiltonian replica exchange for enhanced sampling. All calculations in this work have been performed with the noncommercial freelyavailable version of TeraChem, which is sufficient for many QM region sizes in common use.
TeraChem protocol buffers (TCPB): Accelerating QM and QM/MM simulations with a client–server model
10.1063/5.0130886
The Journal of Chemical Physics
20230125T12:38:54Z
© 2023 Author(s).
Vinícius Wilian D. Cruzeiro
Yuanheng Wang
Elisa Pieri
Edward G. Hohenstein
Todd J. Martínez

Estimating random close packing in polydisperse and bidisperse hard spheres via an equilibrium model of crowding
https://aip.scitation.org/doi/10.1063/5.0137111?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>We show that an analogy between crowding in fluid and jammed phases of hard spheres captures the density dependence of the kissing number for a family of numerically generated jammed states. We extend this analogy to jams of mixtures of hard spheres in d = 3 dimensions and, thus, obtain an estimate of the random close packing volume fraction, ϕRCP, as a function of size polydispersity. We first consider mixtures of particle sizes with discrete distributions. For binary systems, we show agreement between our predictions and simulations using both our own results and results reported in previous studies, as well as agreement with recent experiments from the literature. We then apply our approach to systems with continuous polydispersity using three different particle size distributions, namely, the lognormal, Gamma, and truncated powerlaw distributions. In all cases, we observe agreement between our theoretical findings and numerical results up to rather large polydispersities for all particle size distributions when using as reference our own simulations and results from the literature. In particular, we find ϕRCP to increase monotonically with the relative standard deviation, sσ, of the distribution and to saturate at a value that always remains below 1. A perturbative expansion yields a closedform expression for ϕRCP that quantitatively captures a distributionindependent regime for sσ < 0.5. Beyond that regime, we show that the gradual loss in agreement is tied to the growth of the skewness of size distributions.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>We show that an analogy between crowding in fluid and jammed phases of hard spheres captures the density dependence of the kissing number for a family of numerically generated jammed states. We extend this analogy to jams of mixtures of hard spheres in d = 3 dimensions and, thus, obtain an estimate of the random close packing volume fraction, ϕRCP, as a function of size polydispersity. We first consider mixtures of particle sizes with discrete distributions. For binary systems, we show agreement between our predictions and simulations using both our own results and results reported in previous studies, as well as agreement with recent experiments from the literature. We then apply our approach to systems with continuous polydispersity using three different particle size distributions, namely, the lognormal, Gamma, and truncated powerlaw distributions. In all cases, we observe agreement between our theoretical findings and numerical results up to rather large polydispersities for all particle size distributions when using as reference our own simulations and results from the literature. In particular, we find ϕRCP to increase monotonically with the relative standard deviation, sσ, of the distribution and to saturate at a value that always remains below 1. A perturbative expansion yields a closedform expression for ϕRCP that quantitatively captures a distributionindependent regime for sσ < 0.5. Beyond that regime, we show that the gradual loss in agreement is tied to the growth of the skewness of size distributions.
Estimating random close packing in polydisperse and bidisperse hard spheres via an equilibrium model of crowding
10.1063/5.0137111
The Journal of Chemical Physics
20230123T10:55:29Z
© 2023 Author(s).
Carmine Anzivino
Mathias Casiulis
Tom Zhang
Amgad Salah Moussa
Stefano Martiniani
Alessio Zaccone

The BKT transition and its dynamics in a spin fluid
https://aip.scitation.org/doi/10.1063/5.0129663?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>We study the effect of particle mobility on phase transitions in a spin fluid in two dimensions. The presence of a phase transition of the BKT universality class is shown in an offlattice model of particles with purely repulsive interaction employing computer simulations. A critical spin wave region 0 < T < TBKT is found with a nonuniversal exponent η(T) that follows the shape suggested by BKT theory, including a critical value consistent with ηBKT = 1/4. One can observe a transition from powerlaw decay to exponential decay in the static correlation functions at the transition temperature TBKT, which is supported by finitesize scaling analysis. A critical temperature TBKT = 0.17(1) is suggested. Investigations into the dynamic aspects of the phase transition are carried out. The shorttime behavior of the incoherent spin autocorrelation function agrees with the Nelson–Fisher prediction, whereas the longtime behavior differs from the finitesize scaling known for the static XY model. Analysis of coherent spin wave dynamics shows that the spin wave peak is a propagating mode that can be reasonably well fitted by hydrodynamic theory. The mobility of the particles strongly enhances damping of the spin waves, but the model still lies within the dynamic universality class of the standard XY model.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>We study the effect of particle mobility on phase transitions in a spin fluid in two dimensions. The presence of a phase transition of the BKT universality class is shown in an offlattice model of particles with purely repulsive interaction employing computer simulations. A critical spin wave region 0 < T < TBKT is found with a nonuniversal exponent η(T) that follows the shape suggested by BKT theory, including a critical value consistent with ηBKT = 1/4. One can observe a transition from powerlaw decay to exponential decay in the static correlation functions at the transition temperature TBKT, which is supported by finitesize scaling analysis. A critical temperature TBKT = 0.17(1) is suggested. Investigations into the dynamic aspects of the phase transition are carried out. The shorttime behavior of the incoherent spin autocorrelation function agrees with the Nelson–Fisher prediction, whereas the longtime behavior differs from the finitesize scaling known for the static XY model. Analysis of coherent spin wave dynamics shows that the spin wave peak is a propagating mode that can be reasonably well fitted by hydrodynamic theory. The mobility of the particles strongly enhances damping of the spin waves, but the model still lies within the dynamic universality class of the standard XY model.
The BKT transition and its dynamics in a spin fluid
10.1063/5.0129663
The Journal of Chemical Physics
20230123T10:55:40Z
© 2023 Author(s).
Thomas Bissinger
Matthias Fuchs

Ionic environment effects on collagen type II persistence length and assembly
https://aip.scitation.org/doi/10.1063/5.0131792?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Collagen type II is a main structural protein in cartilage and forms fibrils. The radius of the fibrils ranges from 50 nm to a few hundred nm, and previous theoretical studies point to electrostatics and collagen elasticity (measured as the persistence length, lp) as the main origin for the selflimiting size scales. In this study, we have investigated the collagen triple helical structure and fibril size scales in pH 2 solutions with varying NaCl concentrations from 10−4 to 100 mM, at which collagen is positively charged, and in pH 7.4 solutions, with varying ionic strengths from 100 to 250 mM, at which collagen is both positively and negatively charged. Using static and dynamic light scattering, the radius of gyration (Rg), hydrodynamic radius (Rh), and second virial coefficient (A2) of collagen triple helices are determined, and lp is calculated. With increasing ionic strength, triple helical lp decreases in pH 2 solutions and increases in pH 7.4 solutions. The value ranges from 60 to 100 nm depending on the ionic environment, but at the salt concentration at which A2 is near zero, there are no net backbone interactions in solution, and the intrinsic collagen triple helix lp is determined to be 90–95 nm. Electron microscopy is used to determine the diameter of fibrils assembled in pH 7.4 conditions, and we compare lp of the collagen triple helices and fibril diameter using recent theory on fibril assembly. By better understanding collagen lp and fibril assembly, we can further understand mechanisms of biomacromolecule selfassembly.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Collagen type II is a main structural protein in cartilage and forms fibrils. The radius of the fibrils ranges from 50 nm to a few hundred nm, and previous theoretical studies point to electrostatics and collagen elasticity (measured as the persistence length, lp) as the main origin for the selflimiting size scales. In this study, we have investigated the collagen triple helical structure and fibril size scales in pH 2 solutions with varying NaCl concentrations from 10−4 to 100 mM, at which collagen is positively charged, and in pH 7.4 solutions, with varying ionic strengths from 100 to 250 mM, at which collagen is both positively and negatively charged. Using static and dynamic light scattering, the radius of gyration (Rg), hydrodynamic radius (Rh), and second virial coefficient (A2) of collagen triple helices are determined, and lp is calculated. With increasing ionic strength, triple helical lp decreases in pH 2 solutions and increases in pH 7.4 solutions. The value ranges from 60 to 100 nm depending on the ionic environment, but at the salt concentration at which A2 is near zero, there are no net backbone interactions in solution, and the intrinsic collagen triple helix lp is determined to be 90–95 nm. Electron microscopy is used to determine the diameter of fibrils assembled in pH 7.4 conditions, and we compare lp of the collagen triple helices and fibril diameter using recent theory on fibril assembly. By better understanding collagen lp and fibril assembly, we can further understand mechanisms of biomacromolecule selfassembly.
Ionic environment effects on collagen type II persistence length and assembly
10.1063/5.0131792
The Journal of Chemical Physics
20230124T11:08:46Z
© 2023 Author(s).
Kathryn G. Wilcox
Grace M. Kemerer
Svetlana Morozova

Accounting for the ultraviolet divergence in fieldtheoretic simulations of block copolymer melts
https://aip.scitation.org/doi/10.1063/5.0134890?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>This study examines the ultraviolet (UV) divergence in fieldtheoretic simulations (FTSs) of block copolymer melts, which causes an unphysical dependence on the grid resolution, Δ, used to represent the fields. Our FTSs use the discrete Gaussian–chain model and a partial saddlepoint approximation to enforce incompressibility. Previous work has demonstrated that the UV divergence can be accounted for by defining an effective interaction parameter, [math], in terms of the bare interaction parameter, χb, used in the FTSs, where the coefficients of the expansion are determined by a Morse calibration. However, the need to use different grid resolutions for different ordered phases generally restricts the calibration to the linear approximation, χ ≈ z∞χb, and prevents the calculation of order–order transitions. Here, we resolve these two issues by showing how the nonlinear calibration can be translated between different grids and how the UV divergence can be removed from free energy calculations. By doing so, we confirm previous observations from particlebased simulations. In particular, we show that the free energy closely matches selfconsistent field theory (SCFT) predictions, even in the region where fluctuations disorder the periodic morphologies, and similarly, the periods of the ordered phases match SCFT predictions, provided the SCFT is evaluated with the nonlinear χ.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>This study examines the ultraviolet (UV) divergence in fieldtheoretic simulations (FTSs) of block copolymer melts, which causes an unphysical dependence on the grid resolution, Δ, used to represent the fields. Our FTSs use the discrete Gaussian–chain model and a partial saddlepoint approximation to enforce incompressibility. Previous work has demonstrated that the UV divergence can be accounted for by defining an effective interaction parameter, [math], in terms of the bare interaction parameter, χb, used in the FTSs, where the coefficients of the expansion are determined by a Morse calibration. However, the need to use different grid resolutions for different ordered phases generally restricts the calibration to the linear approximation, χ ≈ z∞χb, and prevents the calculation of order–order transitions. Here, we resolve these two issues by showing how the nonlinear calibration can be translated between different grids and how the UV divergence can be removed from free energy calculations. By doing so, we confirm previous observations from particlebased simulations. In particular, we show that the free energy closely matches selfconsistent field theory (SCFT) predictions, even in the region where fluctuations disorder the periodic morphologies, and similarly, the periods of the ordered phases match SCFT predictions, provided the SCFT is evaluated with the nonlinear χ.
Accounting for the ultraviolet divergence in fieldtheoretic simulations of block copolymer melts
10.1063/5.0134890
The Journal of Chemical Physics
20230124T11:08:18Z
© 2023 Author(s).
M. W. Matsen
T. M. Beardsley
J. D. Willis

Sequencespecific binding behavior of coralyne toward triplex DNA: An ultrafast timeresolved fluorescence spectroscopy study
https://aip.scitation.org/doi/10.1063/5.0133913?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/158/4">Volume 158, Issue 4</a>, January 2023. <br/>Triplex DNA structure has potential therapeutic application in inhibiting the expression of genes involved in cancer and other diseases. As a DNAtargeting antitumor and antibiotic drug, coralyne shows a remarkable binding propensity to triplex over canonical duplex and thus can modulate the stability of triplex structure, providing a prospective gene targeting strategy. Much less is known, however, about coralynebinding interactions with triplex. By combining multiple steadystate spectroscopy with ultrafast fluorescence spectroscopy, we have investigated the binding behaviors of coralyne with typical triplexes. Upon binding with a Gcontaining triplex, the fluorescence of coralyne is markedly quenched owing to the photoinduced electron transfer (PET) of coralyne with the G base. Systematic studies show that the PET rates are sensitive to the binding configuration and local microenvironment, from which the coexisting binding modes of monomeric (full and partial) intercalation and aggregate stacking along the sugarphosphate backbone are distinguished and their respective contributions are determined. It shows that coralyne has preferences for monomeric intercalation within CGG triplex and pure TAT triplex, whereas CGC+ triplex adopts mainly backbone binding of coralyne aggregates due to charge repulsion, revealing the sequencespecific binding selectivity. The triplexDNAinduced aggregation of coralyne could be used as a probe for recognizing the water content in local DNA structures. The strong π–π stacking of intercalated coralyne monomer with basetriplets plays an important role in stabilizing the triplex structure. These results provide mechanistic insights for understanding the remarkable propensity of coralyne in selective binding to triplex DNA and shed light on the prospective applications of coralynetriplex targeted antigene therapeutics.
The Journal of Chemical Physics, Volume 158, Issue 4, January 2023. <br/>Triplex DNA structure has potential therapeutic application in inhibiting the expression of genes involved in cancer and other diseases. As a DNAtargeting antitumor and antibiotic drug, coralyne shows a remarkable binding propensity to triplex over canonical duplex and thus can modulate the stability of triplex structure, providing a prospective gene targeting strategy. Much less is known, however, about coralynebinding interactions with triplex. By combining multiple steadystate spectroscopy with ultrafast fluorescence spectroscopy, we have investigated the binding behaviors of coralyne with typical triplexes. Upon binding with a Gcontaining triplex, the fluorescence of coralyne is markedly quenched owing to the photoinduced electron transfer (PET) of coralyne with the G base. Systematic studies show that the PET rates are sensitive to the binding configuration and local microenvironment, from which the coexisting binding modes of monomeric (full and partial) intercalation and aggregate stacking along the sugarphosphate backbone are distinguished and their respective contributions are determined. It shows that coralyne has preferences for monomeric intercalation within CGG triplex and pure TAT triplex, whereas CGC+ triplex adopts mainly backbone binding of coralyne aggregates due to charge repulsion, revealing the sequencespecific binding selectivity. The triplexDNAinduced aggregation of coralyne could be used as a probe for recognizing the water content in local DNA structures. The strong π–π stacking of intercalated coralyne monomer with basetriplets plays an important role in stabilizing the triplex structure. These results provide mechanistic insights for understanding the remarkable propensity of coralyne in selective binding to triplex DNA and shed light on the prospective applications of coralynetriplex targeted antigene therapeutics.
Sequencespecific binding behavior of coralyne toward triplex DNA: An ultrafast timeresolved fluorescence spectroscopy study
10.1063/5.0133913
The Journal of Chemical Physics
20230123T10:55:50Z
© 2023 Author(s).
Zeqing Jiao
Chunfan Yang
Qian Zhou
Zheng Hu
Jialong Jie
Xianwang Zhang
Hongmei Su