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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https://aip.scitation.org/loi/jcp?af=R&feed=mostrecent

Chemical design by artificial intelligence
https://aip.scitation.org/doi/10.1063/5.0123281?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>
Chemical design by artificial intelligence
10.1063/5.0123281
The Journal of Chemical Physics
20220928T01:32:02Z
© 2022 Author(s).
Daniel H. Ess
Kim E. Jelfs
Heather J. Kulik

Computing chemical potentials of solutions from structure factors
https://aip.scitation.org/doi/10.1063/5.0107059?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>The chemical potential of a component in a solution is defined as the free energy change as the amount of that component changes. Computing this fundamental thermodynamic property from atomistic simulations is notoriously difficult because of the convergence issues involved in free energy methods and finite size effects. This Communication presents the socalled S0 method, which can be used to obtain chemical potentials from static structure factors computed from equilibrium molecular dynamics simulations under the isothermal–isobaric ensemble. This new method is demonstrated on the systems of binary LennardJones particles, urea–water mixtures, a NaCl aqueous solution, and a highpressure carbon–hydrogen mixture.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>The chemical potential of a component in a solution is defined as the free energy change as the amount of that component changes. Computing this fundamental thermodynamic property from atomistic simulations is notoriously difficult because of the convergence issues involved in free energy methods and finite size effects. This Communication presents the socalled S0 method, which can be used to obtain chemical potentials from static structure factors computed from equilibrium molecular dynamics simulations under the isothermal–isobaric ensemble. This new method is demonstrated on the systems of binary LennardJones particles, urea–water mixtures, a NaCl aqueous solution, and a highpressure carbon–hydrogen mixture.
Computing chemical potentials of solutions from structure factors
10.1063/5.0107059
The Journal of Chemical Physics
20220930T09:49:14Z
© 2022 Author(s).
Bingqing Cheng

Communication: Electronic transition of the l–C6+ cation at 417 nm
https://aip.scitation.org/doi/10.1063/5.0106183?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>A new electronic transition is reported for the linear C6+ cation with an origin at 416.8 nm. This spectrum can be compared to the matrix isolation spectra at lower energies reported previously by Fulara et al. [J. Chem. Phys. 123, 044305 (2005)], which assigned linear and cyclic isomers, and to the gas phase spectrum reported previously by Campbell and Dunk [Rev. Sci. Instrum. 90, 103101 (2019)], which detected the same cyclicisomer spectrum reported by Fulara. Comparisons to electronically excited states and vibrations predicted by various forms of theory allow assignment of the spectrum to a new electronic state of linear C6+. The spectrum consists of a strong origin band, two vibronic progression members at higher energy and four hot bands at lower energies. The hot bands provide the first gas phase information on ground state vibrational frequencies. The vibrational and electronic structure of C6+ provide a severe challenge to computational chemistry.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>A new electronic transition is reported for the linear C6+ cation with an origin at 416.8 nm. This spectrum can be compared to the matrix isolation spectra at lower energies reported previously by Fulara et al. [J. Chem. Phys. 123, 044305 (2005)], which assigned linear and cyclic isomers, and to the gas phase spectrum reported previously by Campbell and Dunk [Rev. Sci. Instrum. 90, 103101 (2019)], which detected the same cyclicisomer spectrum reported by Fulara. Comparisons to electronically excited states and vibrations predicted by various forms of theory allow assignment of the spectrum to a new electronic state of linear C6+. The spectrum consists of a strong origin band, two vibronic progression members at higher energy and four hot bands at lower energies. The hot bands provide the first gas phase information on ground state vibrational frequencies. The vibrational and electronic structure of C6+ provide a severe challenge to computational chemistry.
Communication: Electronic transition of the l–C6+ cation at 417 nm
10.1063/5.0106183
The Journal of Chemical Physics
20220930T09:49:10Z
© 2022 Author(s).
Jason E. Colley
Dylan S. Orr
Michael A. Duncan

Correction of residual errors in configuration interaction electronic structure calculations
https://aip.scitation.org/doi/10.1063/5.0098793?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>Methods for correcting residual energy errors of configuration interaction (CI) calculations of molecules and other electronic systems are discussed based on the assumption that the energy defect can be mapped onto atomic regions. The methods do not consider the detailed nature of excitations but instead define a defect energy per electron that is unique to a specific atom. Defect energy contributions are determined from calculations on diatomic and hydride molecules and then applied to other systems. Calculated energies are compared with experimental thermodynamic and spectroscopic data for a set of 41 mainly organic molecules representing a wide range of bonding environments. The most stringent test is based on a severely truncated virtual space in which higher spherical harmonic basis functions are removed. The errors of the initial CI calculations are large, but in each case, including defect corrections brings calculated CI energies into agreement with experimental values. The method is also applied to a NIST compilation of coupled cluster calculations that employ a larger basis set and no truncation of the virtual space. The corrections show excellent consistency with total energies in very good agreement with experimental values. An extension of the method is applied to dmsn states of Sc, Ti, V, Mn, Cr, Fe, Co, Ni, and Cu, significantly improving the agreement of calculated transition energies with spectroscopic values.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>Methods for correcting residual energy errors of configuration interaction (CI) calculations of molecules and other electronic systems are discussed based on the assumption that the energy defect can be mapped onto atomic regions. The methods do not consider the detailed nature of excitations but instead define a defect energy per electron that is unique to a specific atom. Defect energy contributions are determined from calculations on diatomic and hydride molecules and then applied to other systems. Calculated energies are compared with experimental thermodynamic and spectroscopic data for a set of 41 mainly organic molecules representing a wide range of bonding environments. The most stringent test is based on a severely truncated virtual space in which higher spherical harmonic basis functions are removed. The errors of the initial CI calculations are large, but in each case, including defect corrections brings calculated CI energies into agreement with experimental values. The method is also applied to a NIST compilation of coupled cluster calculations that employ a larger basis set and no truncation of the virtual space. The corrections show excellent consistency with total energies in very good agreement with experimental values. An extension of the method is applied to dmsn states of Sc, Ti, V, Mn, Cr, Fe, Co, Ni, and Cu, significantly improving the agreement of calculated transition energies with spectroscopic values.
Correction of residual errors in configuration interaction electronic structure calculations
10.1063/5.0098793
The Journal of Chemical Physics
20220922T10:07:02Z
© 2022 Author(s).
Jerry L. Whitten

Franck–Condon spectra of unbound and imaginaryfrequency vibrations via correlation functions: A branchcut free, numerically stable derivation
https://aip.scitation.org/doi/10.1063/5.0112217?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>Molecular electronic spectra can be represented in the time domain as autocorrelation functions of the initial vibrational wavepacket. We present a derivation of the harmonic vibrational autocorrelation function that is valid for both real and imaginary harmonic frequencies. The derivation rests on Lie algebra techniques that map otherwise complicated exponential operator arithmetic to simpler matrix formulas. The expressions for the zero and finitetemperature harmonic autocorrelation functions have been carefully structured both to be free of branchcut discontinuities and to remain numerically stable with finiteprecision arithmetic. Simple extensions correct the harmonic Franck–Condon approximation for the lowestorder anharmonic and Herzberg–Teller effects. Quantitative simulations are shown for several examples, including the electronic absorption spectra of F2, HOCl, CH2NH, and NO2.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>Molecular electronic spectra can be represented in the time domain as autocorrelation functions of the initial vibrational wavepacket. We present a derivation of the harmonic vibrational autocorrelation function that is valid for both real and imaginary harmonic frequencies. The derivation rests on Lie algebra techniques that map otherwise complicated exponential operator arithmetic to simpler matrix formulas. The expressions for the zero and finitetemperature harmonic autocorrelation functions have been carefully structured both to be free of branchcut discontinuities and to remain numerically stable with finiteprecision arithmetic. Simple extensions correct the harmonic Franck–Condon approximation for the lowestorder anharmonic and Herzberg–Teller effects. Quantitative simulations are shown for several examples, including the electronic absorption spectra of F2, HOCl, CH2NH, and NO2.
Franck–Condon spectra of unbound and imaginaryfrequency vibrations via correlation functions: A branchcut free, numerically stable derivation
10.1063/5.0112217
The Journal of Chemical Physics
20220922T10:07:35Z
© 2022 Author(s).
P. Bryan Changala
Nadav Genossar
Joshua H. Baraban

Theoretical quantum model of twodimensional propagating plexcitons
https://aip.scitation.org/doi/10.1063/5.0103383?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>When plasmonic excitations of metallic interfaces and nanostructures interact with electronic excitations in semiconductors, new states emerge that hybridize the characteristics of the uncoupled states. The engendered properties make these hybrid states appealing for a broad range of applications, ranging from photovoltaic devices to integrated circuitry for quantum devices. Here, through quantum modeling, the coupling of surface plasmon polaritons and mobile twodimensional excitons such as those in atomically thin semiconductors is examined with emphasis on the case of strong coupling. Our model shows that at around the energy crossing of the dispersion relationships of the uncoupled species, they strongly interact and polariton states—propagating plexcitons—emerge. The temporal evolution of the system where surface plasmon polaritons are continuously injected into the system is simulated to gain initial insight on potential experimental realizations of these states. The results show a steady state that is dominated by the lowerenergy polariton. The study theoretically further establishes the possible existence of propagating plexcitons in atomically thin semiconductors and provides important guidance for the experimental detection and characterization of such states for a wide range of optoelectronic technologies.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>When plasmonic excitations of metallic interfaces and nanostructures interact with electronic excitations in semiconductors, new states emerge that hybridize the characteristics of the uncoupled states. The engendered properties make these hybrid states appealing for a broad range of applications, ranging from photovoltaic devices to integrated circuitry for quantum devices. Here, through quantum modeling, the coupling of surface plasmon polaritons and mobile twodimensional excitons such as those in atomically thin semiconductors is examined with emphasis on the case of strong coupling. Our model shows that at around the energy crossing of the dispersion relationships of the uncoupled species, they strongly interact and polariton states—propagating plexcitons—emerge. The temporal evolution of the system where surface plasmon polaritons are continuously injected into the system is simulated to gain initial insight on potential experimental realizations of these states. The results show a steady state that is dominated by the lowerenergy polariton. The study theoretically further establishes the possible existence of propagating plexcitons in atomically thin semiconductors and provides important guidance for the experimental detection and characterization of such states for a wide range of optoelectronic technologies.
Theoretical quantum model of twodimensional propagating plexcitons
10.1063/5.0103383
The Journal of Chemical Physics
20220922T10:07:09Z
© 2022 Author(s).
Martín A. Mosquera
Juan M. MarmolejoTejada
Nicholas J. Borys

Prediction of correlation energies using variational subspace valence bond
https://aip.scitation.org/doi/10.1063/5.0098146?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>In the variational subspace valence bond (VSVB) [G. D. Fletcher, J. Chem. Phys. 142, 134112 (2015)] method, the electronic orbitals comprising the wave function correspond to chemically meaningful objects, such as bonds, lone pairs, atomic cores, and so on. Selected regions of a molecule (for example, a single chemical bond, as opposed to all the bonds) can be modeled with different levels of basis set and possible methods for modeling correlation from the other regions. The interactions between the components of a molecule (say, a bond and a neighboring orbital) can then be studied in detail for their impact on a chemical phenomenon while avoiding the expense of necessarily applying the higher levels and methods to the entire molecule. This work presents the theoretical basis for modeling correlation effects between specific electron pairs by incorporating terms in the interelectronic coordinates (“r12”) into VSVB. The approach is validated with calculations on small systems using singlereference wave functions.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>In the variational subspace valence bond (VSVB) [G. D. Fletcher, J. Chem. Phys. 142, 134112 (2015)] method, the electronic orbitals comprising the wave function correspond to chemically meaningful objects, such as bonds, lone pairs, atomic cores, and so on. Selected regions of a molecule (for example, a single chemical bond, as opposed to all the bonds) can be modeled with different levels of basis set and possible methods for modeling correlation from the other regions. The interactions between the components of a molecule (say, a bond and a neighboring orbital) can then be studied in detail for their impact on a chemical phenomenon while avoiding the expense of necessarily applying the higher levels and methods to the entire molecule. This work presents the theoretical basis for modeling correlation effects between specific electron pairs by incorporating terms in the interelectronic coordinates (“r12”) into VSVB. The approach is validated with calculations on small systems using singlereference wave functions.
Prediction of correlation energies using variational subspace valence bond
10.1063/5.0098146
The Journal of Chemical Physics
20220923T10:13:04Z
© 2022 Author(s).
Graham D. Fletcher
Colleen Bertoni
Murat Keceli
Michael J. D’Mello

Development of efficient computational analysis of difference infrared and Raman spectroscopies
https://aip.scitation.org/doi/10.1063/5.0108934?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>Computational analysis of difference spectra between two analogous systems is a challenging issue, as reliable estimation of a tiny difference spectrum requires an extraordinary precision of the two original spectra. We have developed an alternative new method to calculate the difference spectra under backgroundfree conditions, which greatly improved the efficiency of computation. In this paper, we report further improvement by using efficient parallel implementation and the time correlation formula based on time derivative quantities. As a consequence, the present work achieved further remarkable acceleration in the calculations of difference infrared and Raman spectra in the order of magnitude and thereby allowed us by analyzing these difference spectra at a practical cost of computation.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>Computational analysis of difference spectra between two analogous systems is a challenging issue, as reliable estimation of a tiny difference spectrum requires an extraordinary precision of the two original spectra. We have developed an alternative new method to calculate the difference spectra under backgroundfree conditions, which greatly improved the efficiency of computation. In this paper, we report further improvement by using efficient parallel implementation and the time correlation formula based on time derivative quantities. As a consequence, the present work achieved further remarkable acceleration in the calculations of difference infrared and Raman spectra in the order of magnitude and thereby allowed us by analyzing these difference spectra at a practical cost of computation.
Development of efficient computational analysis of difference infrared and Raman spectroscopies
10.1063/5.0108934
The Journal of Chemical Physics
20220926T10:34:56Z
© 2022 Author(s).
Tomonori Hirano
Naoya Yazawa
Lin Wang
Akihiro Morita

A new framework for frequencydependent polarizable force fields
https://aip.scitation.org/doi/10.1063/5.0115151?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>A frequencydependent extension of the polarizable force field “AtomCondensed Kohn–Sham density functional theory approximated to the secondorder” (ACKS2) [Verstraelen et al., J. Chem. Phys. 141, 194114 (2014)] is proposed, referred to as ACKS2ω. The method enables theoretical predictions of dynamical response properties of finite systems after partitioning of the frequencydependent molecular response function. Parameters in this model are computed simply as expectation values of an electronic wavefunction, and the hardness matrix is entirely reused from ACKS2 as an adiabatic approximation is used. A numerical validation shows that accurate models can already be obtained with atomic monopoles and dipoles. Absorption spectra of 42 organic and inorganic molecular monomers are evaluated using ACKS2ω, and our results agree well with the timedependent DFT calculations. Also for the calculation of C6 dispersion coefficients, ACKS2ω closely reproduces its TDDFT reference. When parameters for ACKS2ω are derived from a PBE/augccpVDZ ground state, it reproduces experimental values for 903 organic and inorganic intermolecular pairs with an MAPE of 3.84%. Our results confirm that ACKS2ω offers a solid connection between the quantummechanical description of frequencydependent response and computationally efficient forcefield models.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>A frequencydependent extension of the polarizable force field “AtomCondensed Kohn–Sham density functional theory approximated to the secondorder” (ACKS2) [Verstraelen et al., J. Chem. Phys. 141, 194114 (2014)] is proposed, referred to as ACKS2ω. The method enables theoretical predictions of dynamical response properties of finite systems after partitioning of the frequencydependent molecular response function. Parameters in this model are computed simply as expectation values of an electronic wavefunction, and the hardness matrix is entirely reused from ACKS2 as an adiabatic approximation is used. A numerical validation shows that accurate models can already be obtained with atomic monopoles and dipoles. Absorption spectra of 42 organic and inorganic molecular monomers are evaluated using ACKS2ω, and our results agree well with the timedependent DFT calculations. Also for the calculation of C6 dispersion coefficients, ACKS2ω closely reproduces its TDDFT reference. When parameters for ACKS2ω are derived from a PBE/augccpVDZ ground state, it reproduces experimental values for 903 organic and inorganic intermolecular pairs with an MAPE of 3.84%. Our results confirm that ACKS2ω offers a solid connection between the quantummechanical description of frequencydependent response and computationally efficient forcefield models.
A new framework for frequencydependent polarizable force fields
10.1063/5.0115151
The Journal of Chemical Physics
20220926T10:34:50Z
© 2022 Author(s).
YingXing Cheng
Toon Verstraelen

A robust and memoryefficient transition state search method for complex energy landscapes
https://aip.scitation.org/doi/10.1063/5.0102145?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>Locating transition states is crucial for investigating transition mechanisms in wideranging phenomena, from atomistic to macroscale systems. Existing methods, however, can struggle in problems with a large number of degrees of freedom, onthefly adaptive remeshing and coarsegraining, and energy landscapes that are locally flat or discontinuous. To resolve these challenges, we introduce a new doubleended method, the BinaryImage Transition State Search (BITSS). It uses just two states that converge to the transition state, resulting in a fast, flexible, and memoryefficient method. We also show that it is more robust compared to existing bracketing methods that use only two states. We demonstrate its versatility by applying BITSS to three very different classes of problems: LennardJones clusters, shell buckling, and multiphase phasefield models.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>Locating transition states is crucial for investigating transition mechanisms in wideranging phenomena, from atomistic to macroscale systems. Existing methods, however, can struggle in problems with a large number of degrees of freedom, onthefly adaptive remeshing and coarsegraining, and energy landscapes that are locally flat or discontinuous. To resolve these challenges, we introduce a new doubleended method, the BinaryImage Transition State Search (BITSS). It uses just two states that converge to the transition state, resulting in a fast, flexible, and memoryefficient method. We also show that it is more robust compared to existing bracketing methods that use only two states. We demonstrate its versatility by applying BITSS to three very different classes of problems: LennardJones clusters, shell buckling, and multiphase phasefield models.
A robust and memoryefficient transition state search method for complex energy landscapes
10.1063/5.0102145
The Journal of Chemical Physics
20220927T10:19:37Z
© 2022 Author(s).
Samuel J. Avis
Jack R. Panter
Halim Kusumaatmaja

Efficient and improved prediction of the band offsets at semiconductor heterojunctions from metaGGA density functionals: A benchmark study
https://aip.scitation.org/doi/10.1063/5.0111693?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>Accurate theoretical prediction of the band offsets at interfaces of semiconductor heterostructures can often be quite challenging. Although density functional theory has been reasonably successful to carry out such calculations, efficient, accurate semilocal functionals are desirable to reduce the computational cost. In general, the semilocal functionals based on the generalized gradient approximation (GGA) significantly underestimate the bulk bandgaps. This, in turn, results in inaccurate estimates of the band offsets at the heterointerfaces. In this paper, we investigate the performance of several advanced metaGGA functionals in the computational prediction of band offsets at semiconductor heterojunctions. In particular, we investigate the performance of r2SCAN (two times revised strongly constrained and appropriately normed functional), rMGGAC (revised semilocal functional based on cuspless hydrogen model and Pauli kinetic energy density functional), mTASK (modified Aschebrock and Kümmel metaGGA functional), and local modified Becke–Johnson exchangecorrelation functionals. Our results strongly suggest that these metaGGA functionals for supercell calculations perform quite well, especially, when compared to computationally more demanding GW calculations. We also present band offsets calculated using ionization potentials and electron affinities, as well as band alignment via the branch point energies. Overall, our study shows that the aforementioned metaGGA functionals can be used within the density functional theory framework to estimate the band offsets in semiconductor heterostructures with predictive accuracy.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>Accurate theoretical prediction of the band offsets at interfaces of semiconductor heterostructures can often be quite challenging. Although density functional theory has been reasonably successful to carry out such calculations, efficient, accurate semilocal functionals are desirable to reduce the computational cost. In general, the semilocal functionals based on the generalized gradient approximation (GGA) significantly underestimate the bulk bandgaps. This, in turn, results in inaccurate estimates of the band offsets at the heterointerfaces. In this paper, we investigate the performance of several advanced metaGGA functionals in the computational prediction of band offsets at semiconductor heterojunctions. In particular, we investigate the performance of r2SCAN (two times revised strongly constrained and appropriately normed functional), rMGGAC (revised semilocal functional based on cuspless hydrogen model and Pauli kinetic energy density functional), mTASK (modified Aschebrock and Kümmel metaGGA functional), and local modified Becke–Johnson exchangecorrelation functionals. Our results strongly suggest that these metaGGA functionals for supercell calculations perform quite well, especially, when compared to computationally more demanding GW calculations. We also present band offsets calculated using ionization potentials and electron affinities, as well as band alignment via the branch point energies. Overall, our study shows that the aforementioned metaGGA functionals can be used within the density functional theory framework to estimate the band offsets in semiconductor heterostructures with predictive accuracy.
Efficient and improved prediction of the band offsets at semiconductor heterojunctions from metaGGA density functionals: A benchmark study
10.1063/5.0111693
The Journal of Chemical Physics
20220927T10:19:23Z
© 2022 Author(s).
Arghya Ghosh
Subrata Jana
Tomáš Rauch
Fabien Tran
Miguel A. L. Marques
Silvana Botti
Lucian A. Constantin
Manish K. Niranjan
Prasanjit Samal

Multilevel simulation of hardsphere mixtures
https://aip.scitation.org/doi/10.1063/5.0102875?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>We present a multilevel Monte Carlo simulation method for analyzing multiscale physical systems via a hierarchy of coarsegrained representations, to obtain numerically exact results, at the most detailed level. We apply the method to a mixture of sizeasymmetric hard spheres, in the grand canonical ensemble. A threelevel version of the method is compared with a previously studied twolevel version. The extra level interpolates between the full mixture and a coarsegrained description where only the large particles are present—this is achieved by restricting the small particles to regions close to the large ones. The threelevel method improves the performance of the estimator, at fixed computational cost. We analyze the asymptotic variance of the estimator and discuss the mechanisms for the improved performance.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>We present a multilevel Monte Carlo simulation method for analyzing multiscale physical systems via a hierarchy of coarsegrained representations, to obtain numerically exact results, at the most detailed level. We apply the method to a mixture of sizeasymmetric hard spheres, in the grand canonical ensemble. A threelevel version of the method is compared with a previously studied twolevel version. The extra level interpolates between the full mixture and a coarsegrained description where only the large particles are present—this is achieved by restricting the small particles to regions close to the large ones. The threelevel method improves the performance of the estimator, at fixed computational cost. We analyze the asymptotic variance of the estimator and discuss the mechanisms for the improved performance.
Multilevel simulation of hardsphere mixtures
10.1063/5.0102875
The Journal of Chemical Physics
20220927T10:19:10Z
© 2022 Author(s).
Paul B. Rohrbach
Hideki Kobayashi
Robert Scheichl
Nigel B. Wilding
Robert L. Jack

Capabilities and limits of the unitary coupledcluster approach with generalized twobody cluster operators
https://aip.scitation.org/doi/10.1063/5.0104815?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>Unitary cluster expansions of the electronic wavefunction have recently gained much interest because of their use in conjunction with quantum algorithms. In this contribution, we investigate some aspects of an ansatz, using generalized twobody excitation operators, which have been considered in some recent studies on quantum algorithms for quantum chemistry. Our numerical results show that, in particular, twobody operators with effective particle–hole excitation level of one in connection with the usual particle–hole double excitation operators lead to a very accurate, yet compact representation of the wavefunction. Generalized twobody operators with effective excitation rank zero have a considerably less pronounced effect. We compare with standard and unitary coupledcluster expansions and show that the above mentioned approach matches or even surpasses the accuracy of expansions with threebody particle–hole excitations, in particular at the onset of strong correlation. A downside of the approach is that it is rather difficult to rigorously converge it to its variational minimum.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>Unitary cluster expansions of the electronic wavefunction have recently gained much interest because of their use in conjunction with quantum algorithms. In this contribution, we investigate some aspects of an ansatz, using generalized twobody excitation operators, which have been considered in some recent studies on quantum algorithms for quantum chemistry. Our numerical results show that, in particular, twobody operators with effective particle–hole excitation level of one in connection with the usual particle–hole double excitation operators lead to a very accurate, yet compact representation of the wavefunction. Generalized twobody operators with effective excitation rank zero have a considerably less pronounced effect. We compare with standard and unitary coupledcluster expansions and show that the above mentioned approach matches or even surpasses the accuracy of expansions with threebody particle–hole excitations, in particular at the onset of strong correlation. A downside of the approach is that it is rather difficult to rigorously converge it to its variational minimum.
Capabilities and limits of the unitary coupledcluster approach with generalized twobody cluster operators
10.1063/5.0104815
The Journal of Chemical Physics
20220928T01:31:56Z
© 2022 Author(s).
Andreas Köhn
Jeppe Olsen

Importancesampling FCIQMC: Solving weak signproblem systems
https://aip.scitation.org/doi/10.1063/5.0107317?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>We investigate the exact full configuration interaction quantum Monte Carlo algorithm (without the initiator approximation) applied to weak signproblem fermionic systems, namely, systems in which the energy gap to the corresponding signfree or “stoquastized” state is small. We show that the minimum number of walkers required to exactly overcome the sign problem can be significantly reduced via an importancesampling similarity transformation even though the similaritytransformed Hamiltonian has the same stoquastic gap as the untransformed one. Furthermore, we show that in the offhalffilling Hubbard model at U/t = 8, the realspace (site) representation has a much weaker sign problem compared to the momentum space representation. By applying importance sampling using a Gutzwillerlike guiding wavefunction, we are able to substantially reduce the minimum number of walkers in the case of 2 × ℓ Hubbard ladders, enabling us to get exact energies for sizable ladders. With these results, we calculate the fundamental charge gap ΔEfund = E(N + 1) + E(N − 1) − 2E(N) for the ladder systems compared to strictly onedimensional Hubbard chains and show that the ladder systems have a reduced fundamental gap compared to the 1D chains.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>We investigate the exact full configuration interaction quantum Monte Carlo algorithm (without the initiator approximation) applied to weak signproblem fermionic systems, namely, systems in which the energy gap to the corresponding signfree or “stoquastized” state is small. We show that the minimum number of walkers required to exactly overcome the sign problem can be significantly reduced via an importancesampling similarity transformation even though the similaritytransformed Hamiltonian has the same stoquastic gap as the untransformed one. Furthermore, we show that in the offhalffilling Hubbard model at U/t = 8, the realspace (site) representation has a much weaker sign problem compared to the momentum space representation. By applying importance sampling using a Gutzwillerlike guiding wavefunction, we are able to substantially reduce the minimum number of walkers in the case of 2 × ℓ Hubbard ladders, enabling us to get exact energies for sizable ladders. With these results, we calculate the fundamental charge gap ΔEfund = E(N + 1) + E(N − 1) − 2E(N) for the ladder systems compared to strictly onedimensional Hubbard chains and show that the ladder systems have a reduced fundamental gap compared to the 1D chains.
Importancesampling FCIQMC: Solving weak signproblem systems
10.1063/5.0107317
The Journal of Chemical Physics
20220930T12:11:25Z
© 2022 Author(s).
Niklas Liebermann
Khaldoon Ghanem
Ali Alavi

Molecular photothermal effects on timeresolved IR spectroscopy
https://aip.scitation.org/doi/10.1063/5.0108826?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>Timeresolved IR pump–probe (IRPP) and twodimensional IR (2DIR) spectroscopy are valuable techniques for studying various ultrafast chemical and biological processes in solutions. The timedependent changes of nonlinear IR signals reflecting fast molecular processes such as vibrational energy transfer and chemical exchange provide invaluable information on the rates and mechanisms of solvation dynamics and structural transitions of multispecies vibrationally interacting molecular systems. However, due to the intrinsic difficulties in distinguishing the contributions of moleculespecific processes to the timeresolved IR signals from those resulting from local heating, it becomes challenging to interpret timeresolved IRPP and 2DIR spectra exhibiting transient growingin spectral components and crosspeaks unambiguously. Here, theoretical considerations of various effects of vibrational coupling, energy transfer, chemical exchange, the generation of hot ground states, molecular photothermal process, and their combinations on the line shapes and timedependent intensities of IRPP spectra and 2DIR diagonal peaks and crosspeaks are presented. We anticipate that the present work will help researchers using IR pump–probe and 2DIR techniques to distinguish local heatinginduced photothermal signals from genuine nonlinear IR signals.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>Timeresolved IR pump–probe (IRPP) and twodimensional IR (2DIR) spectroscopy are valuable techniques for studying various ultrafast chemical and biological processes in solutions. The timedependent changes of nonlinear IR signals reflecting fast molecular processes such as vibrational energy transfer and chemical exchange provide invaluable information on the rates and mechanisms of solvation dynamics and structural transitions of multispecies vibrationally interacting molecular systems. However, due to the intrinsic difficulties in distinguishing the contributions of moleculespecific processes to the timeresolved IR signals from those resulting from local heating, it becomes challenging to interpret timeresolved IRPP and 2DIR spectra exhibiting transient growingin spectral components and crosspeaks unambiguously. Here, theoretical considerations of various effects of vibrational coupling, energy transfer, chemical exchange, the generation of hot ground states, molecular photothermal process, and their combinations on the line shapes and timedependent intensities of IRPP spectra and 2DIR diagonal peaks and crosspeaks are presented. We anticipate that the present work will help researchers using IR pump–probe and 2DIR techniques to distinguish local heatinginduced photothermal signals from genuine nonlinear IR signals.
Molecular photothermal effects on timeresolved IR spectroscopy
10.1063/5.0108826
The Journal of Chemical Physics
20220928T01:32:00Z
© 2022 Author(s).
Minhaeng Cho

Quantitative dynamics of paradigmatic SN2 reaction OH− + CH3F on accurate fulldimensional potential energy surface
https://aip.scitation.org/doi/10.1063/5.0112228?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>The bimolecular reaction between OH− and CH3F is not just a prototypical SN2 process, but it has three other product channels. Here, we develop an accurate fulldimensional potential energy surface (PES) based on 191 193 points calculated at the level CCSD(T)F12a/augccpVTZ. A detailed dynamics and mechanism analysis was carried out on this potential energy surface using the quasiclassical trajectory approach. It is verified that the trajectories do not follow the minimum energy path (MEP), but directly dissociate to F− and CH3OH. In addition, a new transition state for proton exchange and a new product complex CH2F−⋯H2O for proton abstraction were discovered. The trajectories avoid the transition state or this complex, instead dissociate to H2O and CH2F− directly through the ridge regions of the minimum energy path before the transition state. These nonMEP dynamics become more pronounced at high collision energies. Detailed dynamic simulations provide new insights into the atomiclevel mechanisms of the title reaction, thanks to the new chemically accurate PES, with the aid of machine learning.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>The bimolecular reaction between OH− and CH3F is not just a prototypical SN2 process, but it has three other product channels. Here, we develop an accurate fulldimensional potential energy surface (PES) based on 191 193 points calculated at the level CCSD(T)F12a/augccpVTZ. A detailed dynamics and mechanism analysis was carried out on this potential energy surface using the quasiclassical trajectory approach. It is verified that the trajectories do not follow the minimum energy path (MEP), but directly dissociate to F− and CH3OH. In addition, a new transition state for proton exchange and a new product complex CH2F−⋯H2O for proton abstraction were discovered. The trajectories avoid the transition state or this complex, instead dissociate to H2O and CH2F− directly through the ridge regions of the minimum energy path before the transition state. These nonMEP dynamics become more pronounced at high collision energies. Detailed dynamic simulations provide new insights into the atomiclevel mechanisms of the title reaction, thanks to the new chemically accurate PES, with the aid of machine learning.
Quantitative dynamics of paradigmatic SN2 reaction OH− + CH3F on accurate fulldimensional potential energy surface
10.1063/5.0112228
The Journal of Chemical Physics
20220922T10:07:15Z
© 2022 Author(s).
Jie Qin
Yang Liu
Jun Li

Longlived quantum coherent dynamics of a Λsystem driven by a thermal environment
https://aip.scitation.org/doi/10.1063/5.0102808?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>We present a theoretical study of quantum coherent dynamics of a threelevel Λsystem driven by a thermal environment (such as blackbody radiation), which serves as an essential building block of photosynthetic lightharvesting models and quantum heat engines. By solving nonsecular Bloch–Redfield master equations, we obtain analytical results for the groundstate population and coherence dynamics and classify the dynamical regimes of the incoherently driven Λsystem as underdamped and overdamped depending on whether the ratio Δ/[rf(p)] is greater or less than one, where Δ is the groundstate energy splitting, r is the incoherent pumping rate, and f(p) is a function of the transition dipole alignment parameter p. In the underdamped regime, we observe longlived coherent dynamics that lasts for τc ≃ 1/r, even though the initial state of the Λsystem contains no coherences in the energy basis. In the overdamped regime for p = 1, we observe the emergence of coherent quasisteady states with the lifetime τc = 1.34(r/Δ2), which have a low von Neumann entropy compared to conventional thermal states. We propose an experimental scenario for observing noiseinduced coherent dynamics in metastable He* atoms driven by xpolarized incoherent light. Our results suggest that thermal excitations can generate experimentally observable longlived quantum coherent dynamics in the groundstate subspace of atomic and molecular Λsystems in the absence of coherent driving.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>We present a theoretical study of quantum coherent dynamics of a threelevel Λsystem driven by a thermal environment (such as blackbody radiation), which serves as an essential building block of photosynthetic lightharvesting models and quantum heat engines. By solving nonsecular Bloch–Redfield master equations, we obtain analytical results for the groundstate population and coherence dynamics and classify the dynamical regimes of the incoherently driven Λsystem as underdamped and overdamped depending on whether the ratio Δ/[rf(p)] is greater or less than one, where Δ is the groundstate energy splitting, r is the incoherent pumping rate, and f(p) is a function of the transition dipole alignment parameter p. In the underdamped regime, we observe longlived coherent dynamics that lasts for τc ≃ 1/r, even though the initial state of the Λsystem contains no coherences in the energy basis. In the overdamped regime for p = 1, we observe the emergence of coherent quasisteady states with the lifetime τc = 1.34(r/Δ2), which have a low von Neumann entropy compared to conventional thermal states. We propose an experimental scenario for observing noiseinduced coherent dynamics in metastable He* atoms driven by xpolarized incoherent light. Our results suggest that thermal excitations can generate experimentally observable longlived quantum coherent dynamics in the groundstate subspace of atomic and molecular Λsystems in the absence of coherent driving.
Longlived quantum coherent dynamics of a Λsystem driven by a thermal environment
10.1063/5.0102808
The Journal of Chemical Physics
20220923T10:12:59Z
© 2022 Author(s).
Suyesh Koyu
Timur V. Tscherbul

Structural prediction of anion thiolate protected gold clusters of [Au28+7n(SR)17+3n]− (n = 0–4)
https://aip.scitation.org/doi/10.1063/5.0105226?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>Structural prediction of thiolateprotected gold nanoclusters (AuNCs) with diverse charge states can enrich the understanding of this species. Untill now, the number of anion AuNCs is still deficient. In this work, a series of gold nanoclusters with negative total charge, including [Au28(SR)17]−, [Au35(SR)20]−, [Au42(SR)23]−, [Au49(SR)26]−, and [Au56(SR)29]−, are designed. Following a crystallized [Au23(SR)16]− prototype structure, the inner core of the newly predicted clusters is obtained through packing crossed Au7. Next, proper protecting thiolate ligands are arranged to fulfill the duet rule to obtain Au3(2e) and Au4(2e). Extensive analysis indicates that these clusters own high stabilities. Molecular orbital analysis shows that the orbitals for the populations of the valence electron locate at each Au3(2e) and Au4(2e), which demonstrates the reliability of the grand unified model. This work should be helpful for enriching the structural diversity of AuNCs.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>Structural prediction of thiolateprotected gold nanoclusters (AuNCs) with diverse charge states can enrich the understanding of this species. Untill now, the number of anion AuNCs is still deficient. In this work, a series of gold nanoclusters with negative total charge, including [Au28(SR)17]−, [Au35(SR)20]−, [Au42(SR)23]−, [Au49(SR)26]−, and [Au56(SR)29]−, are designed. Following a crystallized [Au23(SR)16]− prototype structure, the inner core of the newly predicted clusters is obtained through packing crossed Au7. Next, proper protecting thiolate ligands are arranged to fulfill the duet rule to obtain Au3(2e) and Au4(2e). Extensive analysis indicates that these clusters own high stabilities. Molecular orbital analysis shows that the orbitals for the populations of the valence electron locate at each Au3(2e) and Au4(2e), which demonstrates the reliability of the grand unified model. This work should be helpful for enriching the structural diversity of AuNCs.
Structural prediction of anion thiolate protected gold clusters of [Au28+7n(SR)17+3n]− (n = 0–4)
10.1063/5.0105226
The Journal of Chemical Physics
20220923T10:12:56Z
© 2022 Author(s).
Endong Wang
Junxia Ding
Wenhua Han
Shixia Luan

Ultraviolet photodissociation of Mg+–NO complex: Ion imaging of a reaction branching in the excited states
https://aip.scitation.org/doi/10.1063/5.0104744?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>Ultraviolet photodissociation processes of gas phase Mg+–NO complex were studied by photofragment ion imaging experiments and theoretical calculations for excited electronic states. At 355 nm excitation, both Mg+ and NO+ photofragment ions were observed with positive anisotropy parameters, and theoretical calculations revealed that the two dissociation channels originate from an electronic transition from a bonding orbital consisting of Mg+ 3s and NO π* orbitals to an antibonding counterpart. For the NO+ channel, the photofragment image exhibited a high anisotropy (β = 1.53 ± 0.07), and a relatively large fraction (∼40%) of the available energy was partitioned into translational energy. These observations are rationalized by proposing a rapid dissociation process on a repulsive potential energy surface correlated to the Mg(1S) + NO+(1Σ) dissociation limit. In contrast, for the Mg+ channel, the angular distribution was more isotropic (β = 0.48 ± 0.03) and only ∼25% of the available energy was released into translational energy. The differences in the recoil distribution for these competing channels imply a reaction branching on the excited state surface. On the theoretical potential surface of the excited state, we found a deep well facilitating an isomerization from bent geometry in the Franck–Condon region to linear and/or Tshaped isomer. As a result, the Mg+ fragment was formed via the structural change followed by further relaxation to lower electronic states correlated to the Mg+(2S) + NO(2Π) exit channel.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>Ultraviolet photodissociation processes of gas phase Mg+–NO complex were studied by photofragment ion imaging experiments and theoretical calculations for excited electronic states. At 355 nm excitation, both Mg+ and NO+ photofragment ions were observed with positive anisotropy parameters, and theoretical calculations revealed that the two dissociation channels originate from an electronic transition from a bonding orbital consisting of Mg+ 3s and NO π* orbitals to an antibonding counterpart. For the NO+ channel, the photofragment image exhibited a high anisotropy (β = 1.53 ± 0.07), and a relatively large fraction (∼40%) of the available energy was partitioned into translational energy. These observations are rationalized by proposing a rapid dissociation process on a repulsive potential energy surface correlated to the Mg(1S) + NO+(1Σ) dissociation limit. In contrast, for the Mg+ channel, the angular distribution was more isotropic (β = 0.48 ± 0.03) and only ∼25% of the available energy was released into translational energy. The differences in the recoil distribution for these competing channels imply a reaction branching on the excited state surface. On the theoretical potential surface of the excited state, we found a deep well facilitating an isomerization from bent geometry in the Franck–Condon region to linear and/or Tshaped isomer. As a result, the Mg+ fragment was formed via the structural change followed by further relaxation to lower electronic states correlated to the Mg+(2S) + NO(2Π) exit channel.
Ultraviolet photodissociation of Mg+–NO complex: Ion imaging of a reaction branching in the excited states
10.1063/5.0104744
The Journal of Chemical Physics
20220926T10:35:00Z
© 2022 Author(s).
Yuri Ito
Yuji Nakashima
Kenichi Okutsu
Motoyoshi Nakano
Fuminori Misaizu

A variational model for the hyperfine resolved spectrum of VO in its ground electronic state
https://aip.scitation.org/doi/10.1063/5.0105965?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>A variational model for the infrared spectrum of vanadium monoxide (VO) is presented, which aims to accurately predict the hyperfine structure within the VO [math] electronic ground state. To give the correct electron spin splitting of the [math] state, electron spin dipolar interaction within the ground state and the spin–orbit coupling between [math] and two excited states, [math] and [math], are calculated ab initio alongside hyperfine interaction terms. Four hyperfine coupling terms are explicitly considered: Fermicontact interaction, electron spinnuclear spin dipolar interaction, nuclear spinrotation interaction, and nuclear electric quadrupole interaction. These terms are included as part of a full variational solution of the nuclearmotion Schrödinger equation performed using program Duo, which is used to generate both hyperfineresolved energy levels and spectra. To improve the accuracy of the model, ab initio curves are subject to small shifts. The energy levels generated by this model show good agreement with the recently derived empirical term values. This and other comparisons validate both our model and the recently developed hyperfine modules in Duo.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>A variational model for the infrared spectrum of vanadium monoxide (VO) is presented, which aims to accurately predict the hyperfine structure within the VO [math] electronic ground state. To give the correct electron spin splitting of the [math] state, electron spin dipolar interaction within the ground state and the spin–orbit coupling between [math] and two excited states, [math] and [math], are calculated ab initio alongside hyperfine interaction terms. Four hyperfine coupling terms are explicitly considered: Fermicontact interaction, electron spinnuclear spin dipolar interaction, nuclear spinrotation interaction, and nuclear electric quadrupole interaction. These terms are included as part of a full variational solution of the nuclearmotion Schrödinger equation performed using program Duo, which is used to generate both hyperfineresolved energy levels and spectra. To improve the accuracy of the model, ab initio curves are subject to small shifts. The energy levels generated by this model show good agreement with the recently derived empirical term values. This and other comparisons validate both our model and the recently developed hyperfine modules in Duo.
A variational model for the hyperfine resolved spectrum of VO in its ground electronic state
10.1063/5.0105965
The Journal of Chemical Physics
20220927T10:19:14Z
© 2022 Author(s).
Qianwei Qu
Sergei N. Yurchenko
Jonathan Tennyson

Electronic state influence on selective bond breaking of coreexcited nitrosyl chloride (ClNO)
https://aip.scitation.org/doi/10.1063/5.0106642?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>The potential for selective bond breaking of a small molecule was investigated with electron spectroscopy and electron–ion coincidence experiments on ClNO. The electron spectra were measured upon direct valence photoionization and resonant core excitation at the N 1s and O 1sedges, followed by the emission of resonantAuger (RA) electrons. The RA spectra were analyzed with particular emphasis on the assignment of the participator and spectator states. The states are of special relevance for investigating how distinct electronic configurations influence selective bond breaking. The electron–ion coincidence measurements provided branching fractions of the produced ion fragments as a function of electron binding energy. They explicitly demonstrate how the final electronic states created after photoionization and RA decay influence fragmentation. In particular, we observed a significantly different branching fraction for spectator states compared with participator states. In addition, it was also observed that the bonds broken for the spectator states correlate with the antibonding nature of the spectator–electron orbital.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>The potential for selective bond breaking of a small molecule was investigated with electron spectroscopy and electron–ion coincidence experiments on ClNO. The electron spectra were measured upon direct valence photoionization and resonant core excitation at the N 1s and O 1sedges, followed by the emission of resonantAuger (RA) electrons. The RA spectra were analyzed with particular emphasis on the assignment of the participator and spectator states. The states are of special relevance for investigating how distinct electronic configurations influence selective bond breaking. The electron–ion coincidence measurements provided branching fractions of the produced ion fragments as a function of electron binding energy. They explicitly demonstrate how the final electronic states created after photoionization and RA decay influence fragmentation. In particular, we observed a significantly different branching fraction for spectator states compared with participator states. In addition, it was also observed that the bonds broken for the spectator states correlate with the antibonding nature of the spectator–electron orbital.
Electronic state influence on selective bond breaking of coreexcited nitrosyl chloride (ClNO)
10.1063/5.0106642
The Journal of Chemical Physics
20220930T12:11:22Z
© 2022 Author(s).
Peter Salén
Luca Schio
Robert Richter
Michele Alagia
Stefano Stranges
Stefano Falcinelli
Vitali Zhaunerchyk

Ground state spectroscopy and photochemistry of HAlOH
https://aip.scitation.org/doi/10.1063/5.0105814?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>Ab initio calculations were carried out in order to study the electronic structure and spectroscopy of cisHAlOH, transHAlOH, H2AlO, and AlOH2. The cis structure is more stable than the trans, and both are thermodynamically stable relative to the AlOH + H dissociation limit. A set of spectroscopic constants were generated for the lowest stable isomers to help with their detection in the laboratory and in the interstellar medium. The first excited state absorbs strongly in the visible region (λ = 460 nm), with a predicted transition dipole moment of 2.07 D. The electronic structures of the first excited state were calculated, including the lifetime, adiabatic excitation energy, rotational constants, and frequencies. We have shown that both isomers may be suitable for laserinduced fluorescence detection. Finally, photodissociation of the cis and transHAlOH isomers is a plausible mechanism for the production of AlOH and H.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>Ab initio calculations were carried out in order to study the electronic structure and spectroscopy of cisHAlOH, transHAlOH, H2AlO, and AlOH2. The cis structure is more stable than the trans, and both are thermodynamically stable relative to the AlOH + H dissociation limit. A set of spectroscopic constants were generated for the lowest stable isomers to help with their detection in the laboratory and in the interstellar medium. The first excited state absorbs strongly in the visible region (λ = 460 nm), with a predicted transition dipole moment of 2.07 D. The electronic structures of the first excited state were calculated, including the lifetime, adiabatic excitation energy, rotational constants, and frequencies. We have shown that both isomers may be suitable for laserinduced fluorescence detection. Finally, photodissociation of the cis and transHAlOH isomers is a plausible mechanism for the production of AlOH and H.
Ground state spectroscopy and photochemistry of HAlOH
10.1063/5.0105814
The Journal of Chemical Physics
20220930T12:11:11Z
© 2022 Author(s).
Tarek Trabelsi
Joseph S. Francisco

Fragility in glassy liquids: A structural approach based on machine learning
https://aip.scitation.org/doi/10.1063/5.0099071?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>The rapid rise of viscosity or relaxation time upon supercooling is a universal hallmark of glassy liquids. The temperature dependence of viscosity, however, is quite nonuniversal for glassy liquids and is characterized by the system’s “fragility,” with liquids with nearly Arrhenius temperaturedependent relaxation times referred to as strong liquids and those with superArrhenius behavior referred to as fragile liquids. What makes some liquids strong and others fragile is still not well understood. Here, we explore this question in a family of harmonic spheres that range from extremely strong to extremely fragile, using “softness,” a structural order parameter identified by machine learning to be highly correlated with dynamical rearrangements. We use a support vector machine to identify softness as the same linear combination of structural quantities across the entire family of liquids studied. We then use softness to identify the factors controlling fragility.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>The rapid rise of viscosity or relaxation time upon supercooling is a universal hallmark of glassy liquids. The temperature dependence of viscosity, however, is quite nonuniversal for glassy liquids and is characterized by the system’s “fragility,” with liquids with nearly Arrhenius temperaturedependent relaxation times referred to as strong liquids and those with superArrhenius behavior referred to as fragile liquids. What makes some liquids strong and others fragile is still not well understood. Here, we explore this question in a family of harmonic spheres that range from extremely strong to extremely fragile, using “softness,” a structural order parameter identified by machine learning to be highly correlated with dynamical rearrangements. We use a support vector machine to identify softness as the same linear combination of structural quantities across the entire family of liquids studied. We then use softness to identify the factors controlling fragility.
Fragility in glassy liquids: A structural approach based on machine learning
10.1063/5.0099071
The Journal of Chemical Physics
20220927T10:19:32Z
© 2022 Author(s).
Indrajit Tah
Sean A. Ridout
Andrea J. Liu

Anomalous properties in the potential energy landscape of a monatomic liquid across the liquid–gas and liquid–liquid phase transitions
https://aip.scitation.org/doi/10.1063/5.0106923?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>As a liquid approaches the gas state, the properties of the potential energy landscape (PEL) sampled by the system become anomalous. Specifically, (i) the mechanically stable local minima of the PEL [inherent structures (IS)] can exhibit cavitation above the socalled Sastry volume, vS, before the liquid enters the gas phase. In addition, (ii) the pressure of the liquid at the sampled IS [i.e., the PEL equation of state, PIS(v)] develops a spinodallike minimum at vS. We perform molecular dynamics simulations of a monatomic waterlike liquid and verify that points (i) and (ii) hold at high temperatures. However, at low temperatures, cavitation in the liquid and the corresponding IS occurs simultaneously and a Sastry volume cannot be defined. Remarkably, at intermediate/high temperatures, the IS of the liquid can exhibit crystallization, i.e., the liquid regularly visits the regions of the PEL that belong to the crystal state. The model liquid considered also exhibits a liquid–liquid phase transition (LLPT) between a lowdensity and a highdensity liquid (LDL and HDL). By studying the behavior of PIS(v) during the LLPT, we identify a Sastry volume for both LDL and HDL. The HDL Sastry volume marks the onset above which IS are heterogeneous (composed of LDL and HDL particles), analogous to points (i) and (ii) above. However, the relationship between the LDL Sastry volume and the onset of heterogeneous IS is less evident. We conclude by presenting a thermodynamic argument that can explain the behavior of the PEL equation of state PIS(v) across both the liquid–gas phase transition and LLPT.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>As a liquid approaches the gas state, the properties of the potential energy landscape (PEL) sampled by the system become anomalous. Specifically, (i) the mechanically stable local minima of the PEL [inherent structures (IS)] can exhibit cavitation above the socalled Sastry volume, vS, before the liquid enters the gas phase. In addition, (ii) the pressure of the liquid at the sampled IS [i.e., the PEL equation of state, PIS(v)] develops a spinodallike minimum at vS. We perform molecular dynamics simulations of a monatomic waterlike liquid and verify that points (i) and (ii) hold at high temperatures. However, at low temperatures, cavitation in the liquid and the corresponding IS occurs simultaneously and a Sastry volume cannot be defined. Remarkably, at intermediate/high temperatures, the IS of the liquid can exhibit crystallization, i.e., the liquid regularly visits the regions of the PEL that belong to the crystal state. The model liquid considered also exhibits a liquid–liquid phase transition (LLPT) between a lowdensity and a highdensity liquid (LDL and HDL). By studying the behavior of PIS(v) during the LLPT, we identify a Sastry volume for both LDL and HDL. The HDL Sastry volume marks the onset above which IS are heterogeneous (composed of LDL and HDL particles), analogous to points (i) and (ii) above. However, the relationship between the LDL Sastry volume and the onset of heterogeneous IS is less evident. We conclude by presenting a thermodynamic argument that can explain the behavior of the PEL equation of state PIS(v) across both the liquid–gas phase transition and LLPT.
Anomalous properties in the potential energy landscape of a monatomic liquid across the liquid–gas and liquid–liquid phase transitions
10.1063/5.0106923
The Journal of Chemical Physics
20220929T10:36:52Z
© 2022 Author(s).
Yang Zhou
Gustavo E. Lopez
Nicolas Giovambattista

The thermodynamics of pressurized methanol: A simple hydrogenbonded liquid as a touchstone for experiment and computer simulations
https://aip.scitation.org/doi/10.1063/5.0116083?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>Methanol as a basic liquid and the simplest alcohol is widely used in industry and scientific experiments. However, there are still no reliable data on the thermodynamic properties of methanol at high pressure. Here, we present an experimental and computational study of the thermodynamic properties of liquid methanol under high pressure up to 15 kbar, which significantly exceeds previously reported pressures. A temperature response to a small adiabatic change in pressure has been measured using a piston–cylinder apparatus. We have compared our experimental results with the literature data for lower pressures and NIST approximations. We find that all existing experimental data do not agree with each other and with our experiments. The NIST approximations are mainly based on low pressure data and appear to be unreliable in the high pressure region, giving even qualitatively wrong results. OPLS and COMPASS force field models have been used in the method of molecular dynamics. The agreement of molecular simulation with our experimental data is definitely unsatisfactory, which means that the most common computational models of methanol are not sufficiently good. We hope that these experimental data and approximations will help in developing better computational models.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>Methanol as a basic liquid and the simplest alcohol is widely used in industry and scientific experiments. However, there are still no reliable data on the thermodynamic properties of methanol at high pressure. Here, we present an experimental and computational study of the thermodynamic properties of liquid methanol under high pressure up to 15 kbar, which significantly exceeds previously reported pressures. A temperature response to a small adiabatic change in pressure has been measured using a piston–cylinder apparatus. We have compared our experimental results with the literature data for lower pressures and NIST approximations. We find that all existing experimental data do not agree with each other and with our experiments. The NIST approximations are mainly based on low pressure data and appear to be unreliable in the high pressure region, giving even qualitatively wrong results. OPLS and COMPASS force field models have been used in the method of molecular dynamics. The agreement of molecular simulation with our experimental data is definitely unsatisfactory, which means that the most common computational models of methanol are not sufficiently good. We hope that these experimental data and approximations will help in developing better computational models.
The thermodynamics of pressurized methanol: A simple hydrogenbonded liquid as a touchstone for experiment and computer simulations
10.1063/5.0116083
The Journal of Chemical Physics
20220930T12:11:06Z
© 2022 Author(s).
Yu. D. Fomin
L. N. Dzhavadov
E. N. Tsiok
V. N. Ryzhov
V. V. Brazhkin

Effect of nitrogen molecules on the growth kinetics at the interface between a (111) plane of cubic ice and water
https://aip.scitation.org/doi/10.1063/5.0106842?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>The molecularscale growth kinetics of ice from water in the presence of air molecules are still poorly understood, despite their importance for understanding ice particle formation in nature. In this study, a molecular dynamics simulation is conducted to elucidate the molecularscale growth kinetics at the interface between a (111) plane of cubic ice and water in the presence of N2 molecules. Two potential models of N2 molecules with and without atomic charges are examined. For both models, N2 molecules bind stably to the interface for a period of 1 ns or longer, and the stability of the binding is higher for the charged model than for the noncharged model. Freeenergy surfaces of an N2 molecule along the interface and along an ideal (111) plane surface of cubic ice suggest that for both models, the position where an N2 molecule binds stably is different at the interface and on the ideal plane surface, and the stability of the binding is much higher for the interface than for the ideal plane surface. For both models, stackingdisordered ice grows at the interface, and the formation probability of a hexagonal ice layer in the stackingdisordered ice is higher for the charged model than for the uncharged model. The formation probability for the hexagonal ice layer in the stackingdisordered ice depends not only on the stability of binding but also on the positions where N2 molecules bind to the underlying ice and the number of N2 molecules that bind stably to the underlying ice.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>The molecularscale growth kinetics of ice from water in the presence of air molecules are still poorly understood, despite their importance for understanding ice particle formation in nature. In this study, a molecular dynamics simulation is conducted to elucidate the molecularscale growth kinetics at the interface between a (111) plane of cubic ice and water in the presence of N2 molecules. Two potential models of N2 molecules with and without atomic charges are examined. For both models, N2 molecules bind stably to the interface for a period of 1 ns or longer, and the stability of the binding is higher for the charged model than for the noncharged model. Freeenergy surfaces of an N2 molecule along the interface and along an ideal (111) plane surface of cubic ice suggest that for both models, the position where an N2 molecule binds stably is different at the interface and on the ideal plane surface, and the stability of the binding is much higher for the interface than for the ideal plane surface. For both models, stackingdisordered ice grows at the interface, and the formation probability of a hexagonal ice layer in the stackingdisordered ice is higher for the charged model than for the uncharged model. The formation probability for the hexagonal ice layer in the stackingdisordered ice depends not only on the stability of binding but also on the positions where N2 molecules bind to the underlying ice and the number of N2 molecules that bind stably to the underlying ice.
Effect of nitrogen molecules on the growth kinetics at the interface between a (111) plane of cubic ice and water
10.1063/5.0106842
The Journal of Chemical Physics
20220922T10:07:19Z
© 2022 Author(s).
Hiroki Nada

Interfacial properties of binary azeotropic mixtures of simple fluids: Molecular dynamics simulation and density gradient theory
https://aip.scitation.org/doi/10.1063/5.0100728?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>Interfacial properties of binary azeotropic mixtures of LennardJones truncated and shifted fluids were studied by molecular dynamics (MD) simulation and density gradient theory (DGT) in combination with an equation of state. Three binary mixtures were investigated, which differ in the energetic cross interaction parameter that yields different types of azeotropic behavior. This study covers a wide temperature and composition range. Mixture A exhibits a heteroazeotrope at low temperatures, which changes to a lowboiling azeotrope at high temperatures, mixture B exhibits a lowboiling azeotrope, and mixture C exhibits a highboiling azeotrope. The phase behavior and fluid interfacial properties as well as their relation were studied. Vapor–liquid, liquid–liquid, and vapor–liquid–liquid equilibria and interfaces were considered. Density profiles, the surface tension, the interfacial thickness, as well as the relative adsorption and enrichment of the components at the interface were studied. The results obtained from the two independent methods (MD and DGT) are overall in good agreement. The results provide insights into the relation of the phase behavior, particularly the azeotropic behavior, of simple fluid mixtures and the corresponding interfacial properties. Strong enrichment was found for the mixture with a heteroazeotrope in the vicinity of the threephase equilibrium, which is related to a wetting transition.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>Interfacial properties of binary azeotropic mixtures of LennardJones truncated and shifted fluids were studied by molecular dynamics (MD) simulation and density gradient theory (DGT) in combination with an equation of state. Three binary mixtures were investigated, which differ in the energetic cross interaction parameter that yields different types of azeotropic behavior. This study covers a wide temperature and composition range. Mixture A exhibits a heteroazeotrope at low temperatures, which changes to a lowboiling azeotrope at high temperatures, mixture B exhibits a lowboiling azeotrope, and mixture C exhibits a highboiling azeotrope. The phase behavior and fluid interfacial properties as well as their relation were studied. Vapor–liquid, liquid–liquid, and vapor–liquid–liquid equilibria and interfaces were considered. Density profiles, the surface tension, the interfacial thickness, as well as the relative adsorption and enrichment of the components at the interface were studied. The results obtained from the two independent methods (MD and DGT) are overall in good agreement. The results provide insights into the relation of the phase behavior, particularly the azeotropic behavior, of simple fluid mixtures and the corresponding interfacial properties. Strong enrichment was found for the mixture with a heteroazeotrope in the vicinity of the threephase equilibrium, which is related to a wetting transition.
Interfacial properties of binary azeotropic mixtures of simple fluids: Molecular dynamics simulation and density gradient theory
10.1063/5.0100728
The Journal of Chemical Physics
20220922T10:07:25Z
© 2022 Author(s).
Jens Staubach
Simon Stephan

Spin and alignment effects in O2 chemisorption on Fe(110), Ni(111), and Co(0001) films grown on W(110)
https://aip.scitation.org/doi/10.1063/5.0111934?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>O2 has a spin triplet multiplicity in its ground state, while the effect of its electron spin on O2surface interaction is not well understood. In this study, the spin and/or alignment effects in O2 chemisorption on surfaces of Fe(110), Ni(111), and Co(0001) films grown on W(110) have been investigated with the use of a single spinrotational stateselected O2 beam. The results indicate that the spin effects for the Fe and Ni films are similar in that the initial sticking probability (S0) of O2 is higher when the spins of O2 and the film are antiparallel, and the spin dependence in S0, which amounts to 30%–40% at thermal energy, decays with increasing the O2 kinetic energy (E0). In the case of the Fe/O2 system, however, considerable spin dependence was found to remain even at E0 > 0.2 eV and on the oxidized surface. It has also been shown that the barrier for O2 chemisorption increases in the order of Fe(110) [math] Ni(111) [math] Co(0001), and the difference in the observed alignment effect among the samples can be understood based on the difference in the barrier.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>O2 has a spin triplet multiplicity in its ground state, while the effect of its electron spin on O2surface interaction is not well understood. In this study, the spin and/or alignment effects in O2 chemisorption on surfaces of Fe(110), Ni(111), and Co(0001) films grown on W(110) have been investigated with the use of a single spinrotational stateselected O2 beam. The results indicate that the spin effects for the Fe and Ni films are similar in that the initial sticking probability (S0) of O2 is higher when the spins of O2 and the film are antiparallel, and the spin dependence in S0, which amounts to 30%–40% at thermal energy, decays with increasing the O2 kinetic energy (E0). In the case of the Fe/O2 system, however, considerable spin dependence was found to remain even at E0 > 0.2 eV and on the oxidized surface. It has also been shown that the barrier for O2 chemisorption increases in the order of Fe(110) [math] Ni(111) [math] Co(0001), and the difference in the observed alignment effect among the samples can be understood based on the difference in the barrier.
Spin and alignment effects in O2 chemisorption on Fe(110), Ni(111), and Co(0001) films grown on W(110)
10.1063/5.0111934
The Journal of Chemical Physics
20220927T10:19:30Z
© 2022 Author(s).
Mitsunori Kurahashi

Computational prediction of new magnetic materials
https://aip.scitation.org/doi/10.1063/5.0113745?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>The discovery of new magnetic materials is a big challenge in the field of modern materials science. We report the development of a new extension of the evolutionary algorithm USPEX, enabling the search for halfmetals (materials that are metallic only in one spin channel) and hard magnetic materials. First, we enabled the simultaneous optimization of stoichiometries, crystal structures, and magnetic structures of stable phases. Second, we developed a new fitness function for halfmetallic materials that can be used for predicting halfmetals through an evolutionary algorithm. We used this extended technique to predict new, potentially hard magnets and rediscover known halfmetals. In total, we report five promising hard magnets with high energy product (BHMAX), anisotropy field (Ha), and magnetic hardness (κ) and a few halfmetal phases in the Cr–O system. A comparison of our predictions with experimental results, including the synthesis of a newly predicted antiferromagnetic material (WMnB2), shows the robustness of our technique.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>The discovery of new magnetic materials is a big challenge in the field of modern materials science. We report the development of a new extension of the evolutionary algorithm USPEX, enabling the search for halfmetals (materials that are metallic only in one spin channel) and hard magnetic materials. First, we enabled the simultaneous optimization of stoichiometries, crystal structures, and magnetic structures of stable phases. Second, we developed a new fitness function for halfmetallic materials that can be used for predicting halfmetals through an evolutionary algorithm. We used this extended technique to predict new, potentially hard magnets and rediscover known halfmetals. In total, we report five promising hard magnets with high energy product (BHMAX), anisotropy field (Ha), and magnetic hardness (κ) and a few halfmetal phases in the Cr–O system. A comparison of our predictions with experimental results, including the synthesis of a newly predicted antiferromagnetic material (WMnB2), shows the robustness of our technique.
Computational prediction of new magnetic materials
10.1063/5.0113745
The Journal of Chemical Physics
20220929T10:36:56Z
© 2022 Author(s).
Saeed Rahmanian Koshkaki
Zahed Allahyari
Artem R. Oganov
Vladimir L. Solozhenko
Ilya B. Polovov
Alexander. S. Belozerov
Andrey A. Katanin
Vladimir I. Anisimov
Evgeny V. Tikhonov
GuangRui Qian
Konstantin V. Maksimtsev
Andrey S. Mukhamadeev
Andrey V. Chukin
Aleksandr V. Korolev
Nikolay V. Mushnikov
Hao Li

Vacancy diffusion on a brominated Si(100) surface: Critical effect of the dangling bond charge state
https://aip.scitation.org/doi/10.1063/5.0102546?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>Silicon dangling bonds (DBs) on an adsorbatecovered Si(100) surface can be created in a scanning tunneling microscope (STM) with high precision required for a number of applications. However, vacancies containing DBs can diffuse, disrupting precisely created structures. In this work, we study the diffusion of Br vacancies on a Si(100)2 × 1Br surface in an STM under typical imaging conditions. In agreement with previous work, Br vacancies diffuse at a positive sample bias voltage. Here, we demonstrated that only vacancies containing a positively charged DB hop across the two atoms of a single Si dimer, while vacancies containing neutral and negatively charged DBs do not. Calculations based on density functional theory confirmed that positively charged Br (and Cl) vacancies have a minimum activation barrier. We propose that diffusion operates by both oneelectron and twoelectron mechanisms depending on the applied voltage. Our results show that the DB charge has a critical effect on the vacancy diffusion. This effect should be taken into account when imaging surface structures with charged DBs as well as when studying the diffusion of other atoms and molecules on the Si(100) surface with vacancies in an adsorbate layer.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>Silicon dangling bonds (DBs) on an adsorbatecovered Si(100) surface can be created in a scanning tunneling microscope (STM) with high precision required for a number of applications. However, vacancies containing DBs can diffuse, disrupting precisely created structures. In this work, we study the diffusion of Br vacancies on a Si(100)2 × 1Br surface in an STM under typical imaging conditions. In agreement with previous work, Br vacancies diffuse at a positive sample bias voltage. Here, we demonstrated that only vacancies containing a positively charged DB hop across the two atoms of a single Si dimer, while vacancies containing neutral and negatively charged DBs do not. Calculations based on density functional theory confirmed that positively charged Br (and Cl) vacancies have a minimum activation barrier. We propose that diffusion operates by both oneelectron and twoelectron mechanisms depending on the applied voltage. Our results show that the DB charge has a critical effect on the vacancy diffusion. This effect should be taken into account when imaging surface structures with charged DBs as well as when studying the diffusion of other atoms and molecules on the Si(100) surface with vacancies in an adsorbate layer.
Vacancy diffusion on a brominated Si(100) surface: Critical effect of the dangling bond charge state
10.1063/5.0102546
The Journal of Chemical Physics
20220930T09:49:06Z
© 2022 Author(s).
T. V. Pavlova
V. M. Shevlyuga

Structure and dynamics of a 1,4polybutadiene melt in an alumina nanopore: A molecular dynamics simulation
https://aip.scitation.org/doi/10.1063/5.0105313?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>We present results of molecular dynamics simulations of a chemically realistic model of 1,4polybutadiene confined in a cylindrical alumina nanopore of diameter 10 nm. The simulations are done at three different temperatures above the glass transition temperature Tg. We investigate the density layering across the nanopore as well as the orientational ordering in the polymer melt, brought about by the confinement, on both the segmental and chain scales. For the chain scale ordering, the magnitude and orientation of the axes of the gyration tensor ellipsoid of single chains are studied and are found to prefer to align parallel to the pore axis. Even though double bonds near the wall are preferentially oriented along the pore walls, studying the nematic order parameter indicates that there is no nematic ordering at the melt–wall interface. As for the dynamics in the melt, we focus here on the meansquaredisplacement of the monomers for several layers across the nanopore as well as the movement of the chain center of mass both of which display a slowing down of the dynamics in the layer at the wall. We also show the strong adsorption of the monomers to the pore wall at lower temperatures.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>We present results of molecular dynamics simulations of a chemically realistic model of 1,4polybutadiene confined in a cylindrical alumina nanopore of diameter 10 nm. The simulations are done at three different temperatures above the glass transition temperature Tg. We investigate the density layering across the nanopore as well as the orientational ordering in the polymer melt, brought about by the confinement, on both the segmental and chain scales. For the chain scale ordering, the magnitude and orientation of the axes of the gyration tensor ellipsoid of single chains are studied and are found to prefer to align parallel to the pore axis. Even though double bonds near the wall are preferentially oriented along the pore walls, studying the nematic order parameter indicates that there is no nematic ordering at the melt–wall interface. As for the dynamics in the melt, we focus here on the meansquaredisplacement of the monomers for several layers across the nanopore as well as the movement of the chain center of mass both of which display a slowing down of the dynamics in the layer at the wall. We also show the strong adsorption of the monomers to the pore wall at lower temperatures.
Structure and dynamics of a 1,4polybutadiene melt in an alumina nanopore: A molecular dynamics simulation
10.1063/5.0105313
The Journal of Chemical Physics
20220927T10:19:34Z
© 2022 Author(s).
L. Tannoury
M. Solar
W. Paul

Configurational entropy, transition rates, and optimal interactions for rapid folding in coarsegrained model proteins
https://aip.scitation.org/doi/10.1063/5.0098612?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>Under certain conditions, the dynamics of coarsegrained models of solvated proteins can be described using a Markov state model, which tracks the evolution of populations of configurations. The transition rates among states that appear in the Markov model can be determined by computing the relative entropy of states and their mean first passage times. In this paper, we present an adaptive method to evaluate the configurational entropy and the mean first passage times for linear chain models with discontinuous potentials. The approach is based on eventdriven dynamical sampling in a massively parallel architecture. Using the fact that the transition rate matrix can be calculated for any choice of interaction energies at any temperature, it is demonstrated how each state’s energy can be chosen such that the average time to transition between any two states is minimized. The methods are used to analyze the optimization of the folding process of two protein systems: the crambin protein and a model with frustration and misfolding. It is shown that the folding pathways for both systems are comprised of two regimes: first, the rapid establishment of local bonds, followed by the subsequent formation of more distant contacts. The state energies that lead to the most rapid folding encourage multiple pathways, and they either penalize folding pathways through kinetic traps by raising the energies of trapping states or establish an escape route from the trapping states by lowering free energy barriers to other states that rapidly reach the native state.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>Under certain conditions, the dynamics of coarsegrained models of solvated proteins can be described using a Markov state model, which tracks the evolution of populations of configurations. The transition rates among states that appear in the Markov model can be determined by computing the relative entropy of states and their mean first passage times. In this paper, we present an adaptive method to evaluate the configurational entropy and the mean first passage times for linear chain models with discontinuous potentials. The approach is based on eventdriven dynamical sampling in a massively parallel architecture. Using the fact that the transition rate matrix can be calculated for any choice of interaction energies at any temperature, it is demonstrated how each state’s energy can be chosen such that the average time to transition between any two states is minimized. The methods are used to analyze the optimization of the folding process of two protein systems: the crambin protein and a model with frustration and misfolding. It is shown that the folding pathways for both systems are comprised of two regimes: first, the rapid establishment of local bonds, followed by the subsequent formation of more distant contacts. The state energies that lead to the most rapid folding encourage multiple pathways, and they either penalize folding pathways through kinetic traps by raising the energies of trapping states or establish an escape route from the trapping states by lowering free energy barriers to other states that rapidly reach the native state.
Configurational entropy, transition rates, and optimal interactions for rapid folding in coarsegrained model proteins
10.1063/5.0098612
The Journal of Chemical Physics
20220923T10:13:01Z
© 2022 Author(s).
Margarita Colberg
Jeremy Schofield

Explicit models of motions to analyze NMR relaxation data in proteins
https://aip.scitation.org/doi/10.1063/5.0095910?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>Nuclear Magnetic Resonance (NMR) is a tool of choice to characterize molecular motions. In biological macromolecules, pico to nanosecond motions, in particular, can be probed by nuclear spin relaxation rates, which depend on the time fluctuations of the orientations of spin interaction frames. For the past 40 years, relaxation rates have been successfully analyzed using the ModelFree (MF) approach, which makes no assumption on the nature of motions and reports on the effective amplitude and timescale of the motions. However, obtaining a mechanistic picture of motions from this type of analysis is difficult at best, unless complemented with molecular dynamics (MD) simulations. In spite of their limited accuracy, such simulations can be used to obtain the information necessary to build explicit models of motions designed to analyze NMR relaxation data. Here, we present how to build such models, suited in particular to describe motions of methylbearing protein side chains and compare them with the MF approach. We show on synthetic data that explicit models of motions are more robust in the presence of rotamer jumps which dominate the relaxation in methyl groups of protein side chains. We expect this work to motivate the use of explicit models of motion to analyze MD and NMR data.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>Nuclear Magnetic Resonance (NMR) is a tool of choice to characterize molecular motions. In biological macromolecules, pico to nanosecond motions, in particular, can be probed by nuclear spin relaxation rates, which depend on the time fluctuations of the orientations of spin interaction frames. For the past 40 years, relaxation rates have been successfully analyzed using the ModelFree (MF) approach, which makes no assumption on the nature of motions and reports on the effective amplitude and timescale of the motions. However, obtaining a mechanistic picture of motions from this type of analysis is difficult at best, unless complemented with molecular dynamics (MD) simulations. In spite of their limited accuracy, such simulations can be used to obtain the information necessary to build explicit models of motions designed to analyze NMR relaxation data. Here, we present how to build such models, suited in particular to describe motions of methylbearing protein side chains and compare them with the MF approach. We show on synthetic data that explicit models of motions are more robust in the presence of rotamer jumps which dominate the relaxation in methyl groups of protein side chains. We expect this work to motivate the use of explicit models of motion to analyze MD and NMR data.
Explicit models of motions to analyze NMR relaxation data in proteins
10.1063/5.0095910
The Journal of Chemical Physics
20220930T11:40:46Z
© 2022 Author(s).
Nicolas BolikCoulon
Fabien Ferrage

Simulating the lowtemperature, metastable electrochromism of Photosystem I: Applications to Thermosynechococcus vulcanus and Chroococcidiopsis thermalis
https://aip.scitation.org/doi/10.1063/5.0100431?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>Lowtemperature, metastable electrochromism has been used as a tool to assign pigments in Photosystem I (PS I) from Thermosynechococcus vulcanus and both the white light and farred light (FRL) forms of Chroococcidiopsis thermalis. We find that a minimum of seven pigments is required to satisfactorily model the electrochromism of PS I. Using our model, we provide a short list of candidates for the chlorophyll f pigment in FRL C. thermalis that absorbs at 756 nm, whose identity, to date, has proven to be controversial. Specifically, we propose the linker pigments A40 and B39 and two antenna pigments A26 and B24 as defined by crystal structure 1JB0. The pros and cons of these assignments are discussed, and we propose further experiments to better understand the functioning of FRL C. thermalis.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>Lowtemperature, metastable electrochromism has been used as a tool to assign pigments in Photosystem I (PS I) from Thermosynechococcus vulcanus and both the white light and farred light (FRL) forms of Chroococcidiopsis thermalis. We find that a minimum of seven pigments is required to satisfactorily model the electrochromism of PS I. Using our model, we provide a short list of candidates for the chlorophyll f pigment in FRL C. thermalis that absorbs at 756 nm, whose identity, to date, has proven to be controversial. Specifically, we propose the linker pigments A40 and B39 and two antenna pigments A26 and B24 as defined by crystal structure 1JB0. The pros and cons of these assignments are discussed, and we propose further experiments to better understand the functioning of FRL C. thermalis.
Simulating the lowtemperature, metastable electrochromism of Photosystem I: Applications to Thermosynechococcus vulcanus and Chroococcidiopsis thermalis
10.1063/5.0100431
The Journal of Chemical Physics
20220930T12:11:09Z
© 2022 Author(s).
J. Langley
R. Purchase
S. Viola
A. Fantuzzi
G. A. Davis
JianRen Shen
A. W. Rutherford
E. Krausz
N. Cox

Atomic isotropic hyperfine properties for second row elements (Al–Cl)
https://aip.scitation.org/doi/10.1063/5.0114858?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>Isotropic hyperfine properties have been obtained for the second row elements Al–Cl using a systematic composite approach consisting of a sequence of core/valence correlation consistent basis sets, up through augccpCV7Z, along with configuration interaction and coupled cluster methods. The best nonrelativistic final values for the atomic ground states (in MHz) are −1.80 27Al (2Po1/2), −24.31 29Si (3P0), 63.70 31P (4So3/2), 20.77 33S (3P2), and 35.42 35Cl (2Po3/2). We find a large K shell contribution to the spin density at the nucleus that is almost canceled by the L and M shell contributions. The spin density in atomic units is approximately linear with respect to the atomic number.
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>Isotropic hyperfine properties have been obtained for the second row elements Al–Cl using a systematic composite approach consisting of a sequence of core/valence correlation consistent basis sets, up through augccpCV7Z, along with configuration interaction and coupled cluster methods. The best nonrelativistic final values for the atomic ground states (in MHz) are −1.80 27Al (2Po1/2), −24.31 29Si (3P0), 63.70 31P (4So3/2), 20.77 33S (3P2), and 35.42 35Cl (2Po3/2). We find a large K shell contribution to the spin density at the nucleus that is almost canceled by the L and M shell contributions. The spin density in atomic units is approximately linear with respect to the atomic number.
Atomic isotropic hyperfine properties for second row elements (Al–Cl)
10.1063/5.0114858
The Journal of Chemical Physics
20220922T10:07:28Z
© 2022 Author(s).
David Feller
John F. Stanton
Ernest R. Davidson

Publisher’s Note: “The manybody expansion for metals. I. The alkaline earth metals Be, Mg, and Ca” [J. Chem. Phys. 157, 084313 (2022)]
https://aip.scitation.org/doi/10.1063/5.0123916?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>
Publisher’s Note: “The manybody expansion for metals. I. The alkaline earth metals Be, Mg, and Ca” [J. Chem. Phys. 157, 084313 (2022)]
10.1063/5.0123916
The Journal of Chemical Physics
20220922T11:21:21Z
© 2022 Author(s).
Joani Mato
Demeter Tzeli
Sotiris S. Xantheas

Publisher’s Note: “Breaking covalent bonds in the context of the manybody expansion (MBE). I. The purported “first row anomaly” in XHn (X = C, Si, Ge, Sn; n = 1–4)” [J. Chem. Phys. 156, 244303 (2022)]
https://aip.scitation.org/doi/10.1063/5.0123913?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>
Publisher’s Note: “Breaking covalent bonds in the context of the manybody expansion (MBE). I. The purported “first row anomaly” in XHn (X = C, Si, Ge, Sn; n = 1–4)” [J. Chem. Phys. 156, 244303 (2022)]
10.1063/5.0123913
The Journal of Chemical Physics
20220922T11:21:20Z
© 2022 Author(s).
Demeter Tzeli
Sotiris S. Xantheas

Publisher’s Note: “A classical model for threebody interactions in aqueous ionic systems” [J. Chem. Phys. 157, 024101 (2022)]
https://aip.scitation.org/doi/10.1063/5.0123910?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/157/12">Volume 157, Issue 12</a>, September 2022. <br/>
The Journal of Chemical Physics, Volume 157, Issue 12, September 2022. <br/>
Publisher’s Note: “A classical model for threebody interactions in aqueous ionic systems” [J. Chem. Phys. 157, 024101 (2022)]
10.1063/5.0123910
The Journal of Chemical Physics
20220923T10:12:58Z
© 2022 Author(s).
Kristina M. Herman
Anthony J. Stone
Sotiris S. Xantheas