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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Inverse molecular design from first principles: Tailoring organic chromophore spectra for optoelectronic applications
https://aip.scitation.org/doi/10.1063/5.0082311?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>The discovery of molecules with tailored optoelectronic properties, such as specific frequency and intensity of absorption or emission, is a major challenge in creating nextgeneration organic lightemitting diodes (OLEDs) and photovoltaics. This raises the following question: How can we predict a potential chemical structure from these properties? Approaches that attempt to tackle this inverse design problem include virtual screening, active machine learning, and genetic algorithms. However, these approaches rely on a molecular database or many electronic structure calculations, and significant computational savings could be achieved if there was prior knowledge of (i) whether the optoelectronic properties of a parent molecule could easily be improved and (ii) what morphing operations on a parent molecule could improve these properties. In this Perspective, we address both of these challenges from first principles. We first adapt the Thomas–Reiche–Kuhn sum rule to organic chromophores and show how this indicates how easily the absorption and emission of a molecule can be improved. We then show how by combining electronic structure theory and intensity borrowing perturbation theory we can predict whether or not the proposed morphing operations will achieve the desired spectral alteration, and thereby derive widely applicable design rules. We go on to provide proofofconcept illustrations of this approach to optimizing the visible absorption of acenes and the emission of radical OLEDs. We believe that this approach can be integrated into genetic algorithms by biasing morphing operations in favor of those that are likely to be successful, leading to faster molecular discovery and greener chemistry.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>The discovery of molecules with tailored optoelectronic properties, such as specific frequency and intensity of absorption or emission, is a major challenge in creating nextgeneration organic lightemitting diodes (OLEDs) and photovoltaics. This raises the following question: How can we predict a potential chemical structure from these properties? Approaches that attempt to tackle this inverse design problem include virtual screening, active machine learning, and genetic algorithms. However, these approaches rely on a molecular database or many electronic structure calculations, and significant computational savings could be achieved if there was prior knowledge of (i) whether the optoelectronic properties of a parent molecule could easily be improved and (ii) what morphing operations on a parent molecule could improve these properties. In this Perspective, we address both of these challenges from first principles. We first adapt the Thomas–Reiche–Kuhn sum rule to organic chromophores and show how this indicates how easily the absorption and emission of a molecule can be improved. We then show how by combining electronic structure theory and intensity borrowing perturbation theory we can predict whether or not the proposed morphing operations will achieve the desired spectral alteration, and thereby derive widely applicable design rules. We go on to provide proofofconcept illustrations of this approach to optimizing the visible absorption of acenes and the emission of radical OLEDs. We believe that this approach can be integrated into genetic algorithms by biasing morphing operations in favor of those that are likely to be successful, leading to faster molecular discovery and greener chemistry.
Inverse molecular design from first principles: Tailoring organic chromophore spectra for optoelectronic applications
10.1063/5.0082311
The Journal of Chemical Physics
20220510T10:12:55Z
© 2022 Author(s).
James D. Green
Eric G. Fuemmeler
Timothy J. H. Hele

Concerning the stability of biexcitons in hybrid HJ aggregates of πconjugated polymers
https://aip.scitation.org/doi/10.1063/5.0090515?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>Frenkel excitons are the primary photoexcitations in organic semiconductors and are ultimately responsible for the optical properties of such materials. They are also predicted to form bound exciton pairs, termed biexcitons, which are consequential intermediates in a wide range of photophysical processes. Generally, we think of bound states as arising from an attractive interaction. However, here, we report on our recent theoretical analysis, predicting the formation of stable biexciton states in a conjugated polymer material arising from both attractive and repulsive interactions. We show that in Jaggregate systems, 2Jbiexcitons can arise from repulsive dipolar interactions with energies E2J > 2EJ, while in Haggregates, 2Hbiexciton states with energies E2H < 2EH can arise corresponding to attractive dipole exciton/exciton interactions. These predictions are corroborated by using ultrafast doublequantum coherence spectroscopy on a [poly(2,5bis(3hexadecylthiophene2yl)thieno[3,2b]thiophene)] material that exhibits both J and Hlike excitonic behavior.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>Frenkel excitons are the primary photoexcitations in organic semiconductors and are ultimately responsible for the optical properties of such materials. They are also predicted to form bound exciton pairs, termed biexcitons, which are consequential intermediates in a wide range of photophysical processes. Generally, we think of bound states as arising from an attractive interaction. However, here, we report on our recent theoretical analysis, predicting the formation of stable biexciton states in a conjugated polymer material arising from both attractive and repulsive interactions. We show that in Jaggregate systems, 2Jbiexcitons can arise from repulsive dipolar interactions with energies E2J > 2EJ, while in Haggregates, 2Hbiexciton states with energies E2H < 2EH can arise corresponding to attractive dipole exciton/exciton interactions. These predictions are corroborated by using ultrafast doublequantum coherence spectroscopy on a [poly(2,5bis(3hexadecylthiophene2yl)thieno[3,2b]thiophene)] material that exhibits both J and Hlike excitonic behavior.
Concerning the stability of biexcitons in hybrid HJ aggregates of πconjugated polymers
10.1063/5.0090515
The Journal of Chemical Physics
20220510T09:43:22Z
© 2022 Author(s).
Eric R. Bittner
Carlos Silva

Fully periodic, computationally efficient constant potential molecular dynamics simulations of ionic liquid supercapacitors
https://aip.scitation.org/doi/10.1063/5.0086986?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>Molecular dynamics (MD) simulations of complex electrochemical systems, such as ionic liquid supercapacitors, are increasingly including the constant potential method (CPM) to model conductive electrodes at a specified potential difference, but the inclusion of CPM can be computationally expensive. We demonstrate the computational savings available in CPM MD simulations of ionic liquid supercapacitors when the usual nonperiodic slab geometry is replaced with fully periodic boundary conditions. We show how a doubled cell approach, previously used in nonCPM MD simulations of charged interfaces, can be used to enable fully periodic CPM MD simulations. Using either a doubled cell approach or a finite field approach previously reported by others, fully periodic CPM MD simulations produce comparable results to the traditional slab geometry simulations with a nearly double speedup in computational time. Indeed, these savings can offset the additional cost of the CPM algorithm, resulting in periodic CPM MD simulations that are computationally competitive with the nonperiodic, fixed charge equivalent simulations for the ionic liquid supercapacitors studied here.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>Molecular dynamics (MD) simulations of complex electrochemical systems, such as ionic liquid supercapacitors, are increasingly including the constant potential method (CPM) to model conductive electrodes at a specified potential difference, but the inclusion of CPM can be computationally expensive. We demonstrate the computational savings available in CPM MD simulations of ionic liquid supercapacitors when the usual nonperiodic slab geometry is replaced with fully periodic boundary conditions. We show how a doubled cell approach, previously used in nonCPM MD simulations of charged interfaces, can be used to enable fully periodic CPM MD simulations. Using either a doubled cell approach or a finite field approach previously reported by others, fully periodic CPM MD simulations produce comparable results to the traditional slab geometry simulations with a nearly double speedup in computational time. Indeed, these savings can offset the additional cost of the CPM algorithm, resulting in periodic CPM MD simulations that are computationally competitive with the nonperiodic, fixed charge equivalent simulations for the ionic liquid supercapacitors studied here.
Fully periodic, computationally efficient constant potential molecular dynamics simulations of ionic liquid supercapacitors
10.1063/5.0086986
The Journal of Chemical Physics
20220509T10:27:27Z
© 2022 Author(s).
Shern R. Tee
Debra J. Searles

Cooperative molecular structure in polaritonic and dark states
https://aip.scitation.org/doi/10.1063/5.0090047?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>An ensemble of identical, intrinsically noninteracting molecules exposed to quantum light is discussed. Their interaction with the quantum light induces interactions between the molecules. The resulting hybrid light–matter states exhibit a complex structure even if only a single vibrational coordinate per molecule is considered. Since all molecules are identical, it is appealing to start from the uniform situation where all molecules possess the same value of this vibrational coordinate. Then, polaritons and dark states follow like in atoms but are functions of this coordinate, and this vibrational degree of freedom makes the physics different from that of atoms. However, despite all molecules being identical, each molecule does have its own vibrational coordinate. It is thus a vital issue to understand the meaning of the uniform situation and how to depart from it and enable one to realistically investigate the ensemble. A rigorous and physically relevant meaning of the polariton energy curves in the uniform situation has been found. It is proven that any point on a polariton energy curve is a (local) minimum or maximum for departing from the uniform situation. It is shown how to explicitly compute the energetic impact of departing from the uniform situation using solely properties of a single free molecule in the absence of the quantum light. The structure of the dark states and their behavior upon departing from the uniform situation are analyzed as well. Useful techniques not used in this topical domain are introduced, and general results on, for example, minimum energy path and symmetry breaking and restoration are obtained. It is shown how to transfer the findings to include several or even many nuclear degrees of freedom per molecule and thus to address the problem of quantum light interacting with many complex molecules. It is demonstrated that the interplay of several vibrational degrees of freedom in a single molecule of the ensemble is expected to lead to additional and, in part, qualitatively different physics. General consequences are discussed.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>An ensemble of identical, intrinsically noninteracting molecules exposed to quantum light is discussed. Their interaction with the quantum light induces interactions between the molecules. The resulting hybrid light–matter states exhibit a complex structure even if only a single vibrational coordinate per molecule is considered. Since all molecules are identical, it is appealing to start from the uniform situation where all molecules possess the same value of this vibrational coordinate. Then, polaritons and dark states follow like in atoms but are functions of this coordinate, and this vibrational degree of freedom makes the physics different from that of atoms. However, despite all molecules being identical, each molecule does have its own vibrational coordinate. It is thus a vital issue to understand the meaning of the uniform situation and how to depart from it and enable one to realistically investigate the ensemble. A rigorous and physically relevant meaning of the polariton energy curves in the uniform situation has been found. It is proven that any point on a polariton energy curve is a (local) minimum or maximum for departing from the uniform situation. It is shown how to explicitly compute the energetic impact of departing from the uniform situation using solely properties of a single free molecule in the absence of the quantum light. The structure of the dark states and their behavior upon departing from the uniform situation are analyzed as well. Useful techniques not used in this topical domain are introduced, and general results on, for example, minimum energy path and symmetry breaking and restoration are obtained. It is shown how to transfer the findings to include several or even many nuclear degrees of freedom per molecule and thus to address the problem of quantum light interacting with many complex molecules. It is demonstrated that the interplay of several vibrational degrees of freedom in a single molecule of the ensemble is expected to lead to additional and, in part, qualitatively different physics. General consequences are discussed.
Cooperative molecular structure in polaritonic and dark states
10.1063/5.0090047
The Journal of Chemical Physics
20220509T10:28:27Z
© 2022 Author(s).
Lorenz S. Cederbaum

GraphVAMPNet, using graph neural networks and variational approach to Markov processes for dynamical modeling of biomolecules
https://aip.scitation.org/doi/10.1063/5.0085607?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>Finding a low dimensional representation of data from longtimescale trajectories of biomolecular processes, such as protein folding or ligand–receptor binding, is of fundamental importance, and kinetic models, such as Markov modeling, have proven useful in describing the kinetics of these systems. Recently, an unsupervised machine learning technique called VAMPNet was introduced to learn the low dimensional representation and the linear dynamical model in an endtoend manner. VAMPNet is based on the variational approach for Markov processes and relies on neural networks to learn the coarsegrained dynamics. In this paper, we combine VAMPNet and graph neural networks to generate an endtoend framework to efficiently learn highlevel dynamics and metastable states from the longtimescale molecular dynamics trajectories. This method bears the advantages of graph representation learning and uses graph message passing operations to generate an embedding for each datapoint, which is used in the VAMPNet to generate a coarsegrained dynamical model. This type of molecular representation results in a higher resolution and a more interpretable Markov model than the standard VAMPNet, enabling a more detailed kinetic study of the biomolecular processes. Our GraphVAMPNet approach is also enhanced with an attention mechanism to find the important residues for classification into different metastable states.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>Finding a low dimensional representation of data from longtimescale trajectories of biomolecular processes, such as protein folding or ligand–receptor binding, is of fundamental importance, and kinetic models, such as Markov modeling, have proven useful in describing the kinetics of these systems. Recently, an unsupervised machine learning technique called VAMPNet was introduced to learn the low dimensional representation and the linear dynamical model in an endtoend manner. VAMPNet is based on the variational approach for Markov processes and relies on neural networks to learn the coarsegrained dynamics. In this paper, we combine VAMPNet and graph neural networks to generate an endtoend framework to efficiently learn highlevel dynamics and metastable states from the longtimescale molecular dynamics trajectories. This method bears the advantages of graph representation learning and uses graph message passing operations to generate an embedding for each datapoint, which is used in the VAMPNet to generate a coarsegrained dynamical model. This type of molecular representation results in a higher resolution and a more interpretable Markov model than the standard VAMPNet, enabling a more detailed kinetic study of the biomolecular processes. Our GraphVAMPNet approach is also enhanced with an attention mechanism to find the important residues for classification into different metastable states.
GraphVAMPNet, using graph neural networks and variational approach to Markov processes for dynamical modeling of biomolecules
10.1063/5.0085607
The Journal of Chemical Physics
20220509T10:27:55Z
© 2022 Author(s).
Mahdi Ghorbani
Samarjeet Prasad
Jeffery B. Klauda
Bernard R. Brooks

Describing the photoisomerization of a retinal chromophore model with coupled and quantum trajectories
https://aip.scitation.org/doi/10.1063/5.0089415?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>The exact factorization of the electron–nuclear wavefunction is applied to the study of photoisomerization of a retinal chromophore model. We describe such an ultrafast nonadiabatic process by analyzing the timedependent potentials of the theory and by mimicking nuclear dynamics with quantum and coupled trajectories. The timedependent vector and scalar potentials are the signature of the exact factorization, as they guide nuclear dynamics by encoding the complete electronic dynamics and including excitedstate effects. Analysis of the potentials is, thus, essential—when possible—to predict the timedependent behavior of the system of interest. In this work, we employ the exact timedependent potentials, available for the numerically exactly solvable model used here, to propagate quantum nuclear trajectories representing the isomerization reaction of the retinal chromophore. The quantum trajectories are the best possible trajectorybased description of the reaction when using the exactfactorization formalism and, thus, allow us to assess the performance of the coupledtrajectory, fully approximate schemes derived from the exactfactorization equations.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>The exact factorization of the electron–nuclear wavefunction is applied to the study of photoisomerization of a retinal chromophore model. We describe such an ultrafast nonadiabatic process by analyzing the timedependent potentials of the theory and by mimicking nuclear dynamics with quantum and coupled trajectories. The timedependent vector and scalar potentials are the signature of the exact factorization, as they guide nuclear dynamics by encoding the complete electronic dynamics and including excitedstate effects. Analysis of the potentials is, thus, essential—when possible—to predict the timedependent behavior of the system of interest. In this work, we employ the exact timedependent potentials, available for the numerically exactly solvable model used here, to propagate quantum nuclear trajectories representing the isomerization reaction of the retinal chromophore. The quantum trajectories are the best possible trajectorybased description of the reaction when using the exactfactorization formalism and, thus, allow us to assess the performance of the coupledtrajectory, fully approximate schemes derived from the exactfactorization equations.
Describing the photoisomerization of a retinal chromophore model with coupled and quantum trajectories
10.1063/5.0089415
The Journal of Chemical Physics
20220509T10:27:37Z
© 2022 Author(s).
Francesco Talotta
David Lauvergnat
Federica Agostini

Quantum dynamics of the photoinduced charge separation in a symmetric donor–acceptor–donor triad: The role of vibronic couplings, symmetry and temperature
https://aip.scitation.org/doi/10.1063/5.0089887?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>The photoinduced charge separation in a symmetric donor–acceptor–donor (D–A–D) triad is studied quantum mechanically using a realistic diabatic vibronic coupling model. The model includes a locally excited DA*D state and two chargetransfer states D+A−D and DA−D+ and is constructed according to a procedure generally applicable to semirigid D–A–D structures and based on energies, forces, and force constants obtained by quantum chemical calculations. In this case, the electronic structure is described by timedependent density functional theory, and the corrected linear response is used in conjunction with the polarizable continuum model to account for statespecific solvent effects. The multimode dynamics following the photoexcitation to the locally excited state are simulated by the hybrid Gaussianmulticonfigurational timedependent Hartree method, and temperature effects are included using thermo field theory. The dynamics are connected to the transient absorption spectrum obtained in recent experiments, which is simulated and fully assigned from first principles. It is found that the charge separation is mediated by symmetrybreaking vibrations of relatively low frequency, which implies that temperature should be accounted for to obtain reliable estimates of the charge transfer rate.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>The photoinduced charge separation in a symmetric donor–acceptor–donor (D–A–D) triad is studied quantum mechanically using a realistic diabatic vibronic coupling model. The model includes a locally excited DA*D state and two chargetransfer states D+A−D and DA−D+ and is constructed according to a procedure generally applicable to semirigid D–A–D structures and based on energies, forces, and force constants obtained by quantum chemical calculations. In this case, the electronic structure is described by timedependent density functional theory, and the corrected linear response is used in conjunction with the polarizable continuum model to account for statespecific solvent effects. The multimode dynamics following the photoexcitation to the locally excited state are simulated by the hybrid Gaussianmulticonfigurational timedependent Hartree method, and temperature effects are included using thermo field theory. The dynamics are connected to the transient absorption spectrum obtained in recent experiments, which is simulated and fully assigned from first principles. It is found that the charge separation is mediated by symmetrybreaking vibrations of relatively low frequency, which implies that temperature should be accounted for to obtain reliable estimates of the charge transfer rate.
Quantum dynamics of the photoinduced charge separation in a symmetric donor–acceptor–donor triad: The role of vibronic couplings, symmetry and temperature
10.1063/5.0089887
The Journal of Chemical Physics
20220509T10:27:58Z
© 2022 Author(s).
David Picconi

Natural range separation of the Coulomb hole
https://aip.scitation.org/doi/10.1063/5.0085284?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>A natural range separation of the Coulomb hole into two components, one of them being predominant at long interelectronic separations [math] and the other at short distances [math], is exhaustively analyzed throughout various examples that put forward the most relevant features of this approach and how they can be used to develop efficient ways to capture electron correlation. We show that [math], which only depends on the firstorder reduced density matrix, can be used to identify molecules with a predominant nondynamic correlation regime and differentiate between two types of nondynamic correlation, types A and B. Through the asymptotic properties of the hole components, we explain how [math] can retrieve the longrange part of electron correlation. We perform an exhaustive analysis of the hydrogen molecule in a minimal basis set, dissecting the hole contributions into spin components. We also analyze the simplest molecule presenting a dispersion interaction and how [math] helps identify it. The study of several atoms in different spin states reveals that the Coulomb hole components distinguish correlation regimes that are not apparent from the entire hole. The results of this work hold out the promise to aid in developing new electronic structure methods that efficiently capture electron correlation.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>A natural range separation of the Coulomb hole into two components, one of them being predominant at long interelectronic separations [math] and the other at short distances [math], is exhaustively analyzed throughout various examples that put forward the most relevant features of this approach and how they can be used to develop efficient ways to capture electron correlation. We show that [math], which only depends on the firstorder reduced density matrix, can be used to identify molecules with a predominant nondynamic correlation regime and differentiate between two types of nondynamic correlation, types A and B. Through the asymptotic properties of the hole components, we explain how [math] can retrieve the longrange part of electron correlation. We perform an exhaustive analysis of the hydrogen molecule in a minimal basis set, dissecting the hole contributions into spin components. We also analyze the simplest molecule presenting a dispersion interaction and how [math] helps identify it. The study of several atoms in different spin states reveals that the Coulomb hole components distinguish correlation regimes that are not apparent from the entire hole. The results of this work hold out the promise to aid in developing new electronic structure methods that efficiently capture electron correlation.
Natural range separation of the Coulomb hole
10.1063/5.0085284
The Journal of Chemical Physics
20220510T09:42:55Z
© 2022 Author(s).
Mireia ViaNadal
Mauricio RodríguezMayorga
Eloy RamosCordoba
Eduard Matito

Piecewise interaction picture density matrix quantum Monte Carlo
https://aip.scitation.org/doi/10.1063/5.0094290?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>The density matrix quantum Monte Carlo (DMQMC) set of methods stochastically samples the exact Nbody density matrix for interacting electrons at finite temperature. We introduce a simple modification to the interaction picture DMQMC (IPDMQMC) method that overcomes the limitation of only sampling one inverse temperature point at a time, instead allowing for the sampling of a temperature range within a single calculation, thereby reducing the computational cost. At the target inverse temperature, instead of ending the simulation, we incorporate a change of picture away from the interaction picture. The resulting equations of motion have piecewise functions and use the interaction picture in the first phase of a simulation, followed by the application of the Bloch equation once the target inverse temperature is reached. We find that the performance of this method is similar to or better than the DMQMC and IPDMQMC algorithms in a variety of molecular test systems.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>The density matrix quantum Monte Carlo (DMQMC) set of methods stochastically samples the exact Nbody density matrix for interacting electrons at finite temperature. We introduce a simple modification to the interaction picture DMQMC (IPDMQMC) method that overcomes the limitation of only sampling one inverse temperature point at a time, instead allowing for the sampling of a temperature range within a single calculation, thereby reducing the computational cost. At the target inverse temperature, instead of ending the simulation, we incorporate a change of picture away from the interaction picture. The resulting equations of motion have piecewise functions and use the interaction picture in the first phase of a simulation, followed by the application of the Bloch equation once the target inverse temperature is reached. We find that the performance of this method is similar to or better than the DMQMC and IPDMQMC algorithms in a variety of molecular test systems.
Piecewise interaction picture density matrix quantum Monte Carlo
10.1063/5.0094290
The Journal of Chemical Physics
20220510T09:42:46Z
© 2022 Author(s).
William Z. Van Benschoten
James J. Shepherd

Brownian bridges for stochastic chemical processes—An approximation method based on the asymptotic behavior of the backward Fokker–Planck equation
https://aip.scitation.org/doi/10.1063/5.0080540?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>A Brownian bridge is a continuous random walk conditioned to end in a given region by adding an effective drift to guide paths toward the desired region of phase space. This idea has many applications in chemical science where one wants to control the endpoint of a stochastic process—e.g., polymer physics, chemical reaction pathways, heat/mass transfer, and Brownian dynamics simulations. Despite its broad applicability, the biggest limitation of the Brownian bridge technique is that it is often difficult to determine the effective drift as it comes from a solution of a Backward Fokker–Planck (BFP) equation that is infeasible to compute for complex or highdimensional systems. This paper introduces a fast approximation method to generate a Brownian bridge process without solving the BFP equation explicitly. Specifically, this paper uses the asymptotic properties of the BFP equation to generate an approximate drift and determine ways to correct (i.e., reweight) any errors incurred from this approximation. Because such a procedure avoids the solution of the BFP equation, we show that it drastically accelerates the generation of conditioned random walks. We also show that this approach offers reasonable improvement compared to other sampling approaches using simple bias potentials.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>A Brownian bridge is a continuous random walk conditioned to end in a given region by adding an effective drift to guide paths toward the desired region of phase space. This idea has many applications in chemical science where one wants to control the endpoint of a stochastic process—e.g., polymer physics, chemical reaction pathways, heat/mass transfer, and Brownian dynamics simulations. Despite its broad applicability, the biggest limitation of the Brownian bridge technique is that it is often difficult to determine the effective drift as it comes from a solution of a Backward Fokker–Planck (BFP) equation that is infeasible to compute for complex or highdimensional systems. This paper introduces a fast approximation method to generate a Brownian bridge process without solving the BFP equation explicitly. Specifically, this paper uses the asymptotic properties of the BFP equation to generate an approximate drift and determine ways to correct (i.e., reweight) any errors incurred from this approximation. Because such a procedure avoids the solution of the BFP equation, we show that it drastically accelerates the generation of conditioned random walks. We also show that this approach offers reasonable improvement compared to other sampling approaches using simple bias potentials.
Brownian bridges for stochastic chemical processes—An approximation method based on the asymptotic behavior of the backward Fokker–Planck equation
10.1063/5.0080540
The Journal of Chemical Physics
20220510T09:42:41Z
© 2022 Author(s).
Shiyan Wang
Anirudh Venkatesh
Doraiswami Ramkrishna
Vivek Narsimhan

Organic photoredox catalysts for CO2 reduction: Driving discovery with genetic algorithms
https://aip.scitation.org/doi/10.1063/5.0088353?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>This work implements a genetic algorithm (GA) to discover organic catalysts for photoredox CO2 reduction that are both highly active and resistant to degradation. The lowest unoccupied molecular orbital energy of the ground state catalyst is chosen as the activity descriptor and the average Mulliken charge on all ring carbons is chosen as the descriptor for resistance to degradation via carboxylation (both obtained using density functional theory) to construct the fitness function of the GA. We combine the results of multiple GA runs, each based on different relative weighting of the two descriptors, and rigorously assess GA performance by calculating electron transfer barriers to CO2 reduction. A large majority of GA predictions exhibit improved performance relative to experimentally studied o, m, and pterphenyl catalysts. Based on stringent cutoffs imposed on the average charge, barrier to electron transfer to CO2, and excitation energy, we recommend 25 catalysts for further experimental investigation of viability toward photoredox CO2 reduction.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>This work implements a genetic algorithm (GA) to discover organic catalysts for photoredox CO2 reduction that are both highly active and resistant to degradation. The lowest unoccupied molecular orbital energy of the ground state catalyst is chosen as the activity descriptor and the average Mulliken charge on all ring carbons is chosen as the descriptor for resistance to degradation via carboxylation (both obtained using density functional theory) to construct the fitness function of the GA. We combine the results of multiple GA runs, each based on different relative weighting of the two descriptors, and rigorously assess GA performance by calculating electron transfer barriers to CO2 reduction. A large majority of GA predictions exhibit improved performance relative to experimentally studied o, m, and pterphenyl catalysts. Based on stringent cutoffs imposed on the average charge, barrier to electron transfer to CO2, and excitation energy, we recommend 25 catalysts for further experimental investigation of viability toward photoredox CO2 reduction.
Organic photoredox catalysts for CO2 reduction: Driving discovery with genetic algorithms
10.1063/5.0088353
The Journal of Chemical Physics
20220510T09:43:09Z
© 2022 Author(s).
Kareesa J. Kron
Andres RodriguezKatakura
Pranesh Regu
Maria N. Reed
Rachelle Elhessen
Shaama Mallikarjun Sharada

The factorization ansatz for nonlocal approximations to the exchange–correlation hole
https://aip.scitation.org/doi/10.1063/5.0077287?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>Among the various types of approximations to the exchange–correlation energy (EXC), the completely nonlocal approach is one of the lesser explored approximation schemes. It has not yet reached the predictive power of the widely used generalized gradient approximations, metageneralized gradient approximations, hybrids, etc. In nonlocal functionals pursued here, the electron density at every point in space is employed to express the exchange–correlation energy per particle ϵXC(r) at a given position r. Here, we use the nonlocal, sphericalaveraged density [math] as a starting point to construct approximate exchange–correlation holes through the factorization ansatz ρXC(r, u) = f(r, u)ρ(r, u). We present upper and lower bounds to the exchange energy per particle ϵX(r) in terms of ρ(r, u). The factor f(r, u) is then designed to satisfy various conditions that represent important exchange and correlation effects. We assess the resulting approximations and find that the complex, oscillatory structure of ρ(r, u) makes the construction of a corresponding f(r, u) very challenging. This conclusion, identifying the main issue of the nonlocal approximation, is supported by a detailed analysis of the resulting exchange–correlation holes.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>Among the various types of approximations to the exchange–correlation energy (EXC), the completely nonlocal approach is one of the lesser explored approximation schemes. It has not yet reached the predictive power of the widely used generalized gradient approximations, metageneralized gradient approximations, hybrids, etc. In nonlocal functionals pursued here, the electron density at every point in space is employed to express the exchange–correlation energy per particle ϵXC(r) at a given position r. Here, we use the nonlocal, sphericalaveraged density [math] as a starting point to construct approximate exchange–correlation holes through the factorization ansatz ρXC(r, u) = f(r, u)ρ(r, u). We present upper and lower bounds to the exchange energy per particle ϵX(r) in terms of ρ(r, u). The factor f(r, u) is then designed to satisfy various conditions that represent important exchange and correlation effects. We assess the resulting approximations and find that the complex, oscillatory structure of ρ(r, u) makes the construction of a corresponding f(r, u) very challenging. This conclusion, identifying the main issue of the nonlocal approximation, is supported by a detailed analysis of the resulting exchange–correlation holes.
The factorization ansatz for nonlocal approximations to the exchange–correlation hole
10.1063/5.0077287
The Journal of Chemical Physics
20220510T09:43:33Z
© 2022 Author(s).
Etienne Cuierrier
PierreOlivier Roy
Matthias Ernzerhof

Slip and stress from low shear rate nonequilibrium molecular dynamics: The transienttime correlation function technique
https://aip.scitation.org/doi/10.1063/5.0088127?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>We derive the transienttime correlation function (TTCF) expression for the computation of phase variables of inhomogenous confined atomistic fluids undergoing boundarydriven planar shear (Couette) flow at constant pressure. Using nonequilibrium molecular dynamics simulations, we then apply the TTCF formalism to the computation of the shear stress and the slip velocity for atomistic fluids at realistic low shear rates, in systems under constant pressure and constant volume. We show that, compared to direct averaging of multiple trajectories, the TTCF method dramatically improves the accuracy of the results at low shear rates and that it is suitable to investigate the tribology and rheology of atomistically detailed confined fluids at realistic flow rates.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>We derive the transienttime correlation function (TTCF) expression for the computation of phase variables of inhomogenous confined atomistic fluids undergoing boundarydriven planar shear (Couette) flow at constant pressure. Using nonequilibrium molecular dynamics simulations, we then apply the TTCF formalism to the computation of the shear stress and the slip velocity for atomistic fluids at realistic low shear rates, in systems under constant pressure and constant volume. We show that, compared to direct averaging of multiple trajectories, the TTCF method dramatically improves the accuracy of the results at low shear rates and that it is suitable to investigate the tribology and rheology of atomistically detailed confined fluids at realistic flow rates.
Slip and stress from low shear rate nonequilibrium molecular dynamics: The transienttime correlation function technique
10.1063/5.0088127
The Journal of Chemical Physics
20220510T09:42:24Z
© 2022 Author(s).
Luca Maffioli
Edward R. Smith
James P. Ewen
Peter J. Daivis
Daniele Dini
B. D. Todd

Molecular orbital projectors in nonempirical jmDFT recover exact conditions in transitionmetal chemistry
https://aip.scitation.org/doi/10.1063/5.0089460?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>Lowcost, nonempirical corrections to semilocal density functional theory are essential for accurately modeling transitionmetal chemistry. Here, we demonstrate the judiciously modified density functional theory (jmDFT) approach with nonempirical U and J parameters obtained directly from frontier orbital energetics on a series of transitionmetal complexes. We curate a set of nine representative Ti(III) and V(IV) d1 transitionmetal complexes and evaluate their flatplane errors along the fractional spin and charge lines. We demonstrate that while jmDFT improves upon both DFT+U and semilocal DFT with the standard atomic orbital projectors (AOPs), it does so inefficiently. We rationalize these inefficiencies by quantifying hybridization in the relevant frontier orbitals. To overcome these limitations, we introduce a procedure for computing a molecular orbital projector (MOP) basis for use with jmDFT. We demonstrate this single set of d1 MOPs to be suitable for nearly eliminating all energetic delocalization and static correlation errors. In all cases, MOP jmDFT outperforms AOP jmDFT, and it eliminates most flatplane errors at nonempirical values. Unlike DFT+U or hybrid functionals, jmDFT nearly eliminates energetic delocalization and static correlation errors within a nonempirical framework.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>Lowcost, nonempirical corrections to semilocal density functional theory are essential for accurately modeling transitionmetal chemistry. Here, we demonstrate the judiciously modified density functional theory (jmDFT) approach with nonempirical U and J parameters obtained directly from frontier orbital energetics on a series of transitionmetal complexes. We curate a set of nine representative Ti(III) and V(IV) d1 transitionmetal complexes and evaluate their flatplane errors along the fractional spin and charge lines. We demonstrate that while jmDFT improves upon both DFT+U and semilocal DFT with the standard atomic orbital projectors (AOPs), it does so inefficiently. We rationalize these inefficiencies by quantifying hybridization in the relevant frontier orbitals. To overcome these limitations, we introduce a procedure for computing a molecular orbital projector (MOP) basis for use with jmDFT. We demonstrate this single set of d1 MOPs to be suitable for nearly eliminating all energetic delocalization and static correlation errors. In all cases, MOP jmDFT outperforms AOP jmDFT, and it eliminates most flatplane errors at nonempirical values. Unlike DFT+U or hybrid functionals, jmDFT nearly eliminates energetic delocalization and static correlation errors within a nonempirical framework.
Molecular orbital projectors in nonempirical jmDFT recover exact conditions in transitionmetal chemistry
10.1063/5.0089460
The Journal of Chemical Physics
20220511T09:55:12Z
© 2022 Author(s).
Akash Bajaj
Chenru Duan
Aditya Nandy
Michael G. Taylor
Heather J. Kulik

Understanding the chemical bonding of ground and excited states of HfO and HfB with correlated wavefunction theory and density functional approximations
https://aip.scitation.org/doi/10.1063/5.0090128?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>Knowledge of the chemical bonding of HfO and HfB ground and lowlying electronic states provides essential insights into a range of catalysts and materials that contain Hf–O or Hf–B moieties. Here, we carry out highlevel multireference configuration interaction theory and coupled cluster quantum chemical calculations on these systems. We compute full potential energy curves, excitation energies, ionization energies, electronic configurations, and spectroscopic parameters with large quadrupleζ and quintupleζ quality correlation consistent basis sets. We also investigate equilibrium chemical bonding patterns and effects of correlating core electrons on property predictions. Differences in the ground state electron configuration of HfB(X4[math]−) and HfO(X1[math]+) lead to a significantly stronger bond in HfO than HfB, as judged by both dissociation energies and equilibrium bond distances. We extend our analysis to the chemical bonding patterns of the isovalent HfX (X = O, S, Se, Te, and Po) series and observe similar trends. We also note a linear trend between the decreasing value of the dissociation energy (De) from HfO to HfPo and the singlet–triplet energy gap ([math]ES–T) of the molecule. Finally, we compare these benchmark results to those obtained using density functional theory (DFT) with 23 exchange–correlation functionals spanning multiple rungs of “Jacob’s ladder.” When comparing DFT errors to coupled cluster reference values on dissociation energies, excitation energies, and ionization energies of HfB and HfO, we observe semilocal generalized gradient approximations to significantly outperform more complex and highcost functionals.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>Knowledge of the chemical bonding of HfO and HfB ground and lowlying electronic states provides essential insights into a range of catalysts and materials that contain Hf–O or Hf–B moieties. Here, we carry out highlevel multireference configuration interaction theory and coupled cluster quantum chemical calculations on these systems. We compute full potential energy curves, excitation energies, ionization energies, electronic configurations, and spectroscopic parameters with large quadrupleζ and quintupleζ quality correlation consistent basis sets. We also investigate equilibrium chemical bonding patterns and effects of correlating core electrons on property predictions. Differences in the ground state electron configuration of HfB(X4[math]−) and HfO(X1[math]+) lead to a significantly stronger bond in HfO than HfB, as judged by both dissociation energies and equilibrium bond distances. We extend our analysis to the chemical bonding patterns of the isovalent HfX (X = O, S, Se, Te, and Po) series and observe similar trends. We also note a linear trend between the decreasing value of the dissociation energy (De) from HfO to HfPo and the singlet–triplet energy gap ([math]ES–T) of the molecule. Finally, we compare these benchmark results to those obtained using density functional theory (DFT) with 23 exchange–correlation functionals spanning multiple rungs of “Jacob’s ladder.” When comparing DFT errors to coupled cluster reference values on dissociation energies, excitation energies, and ionization energies of HfB and HfO, we observe semilocal generalized gradient approximations to significantly outperform more complex and highcost functionals.
Understanding the chemical bonding of ground and excited states of HfO and HfB with correlated wavefunction theory and density functional approximations
10.1063/5.0090128
The Journal of Chemical Physics
20220511T09:55:00Z
© 2022 Author(s).
Isuru R. Ariyarathna
Chenru Duan
Heather J. Kulik

A neural networkassisted open boundary molecular dynamics simulation method
https://aip.scitation.org/doi/10.1063/5.0083198?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>A neural networkassisted molecular dynamics method is developed to reduce the computational cost of open boundary simulations. Particle influxes and neural networkderived forces are applied at the boundaries of an open domain consisting of explicitly modeled LennardJones atoms in order to represent the effects of the unmodeled surrounding fluid. Canonical ensemble simulations with periodic boundaries are used to train the neural network and to sample boundary fluxes. The method, as implemented in the LAMMPS, yields temperature, kinetic energy, potential energy, and pressure values within 2.5% of those calculated using periodic molecular dynamics and runs two orders of magnitude faster than a comparable grand canonical molecular dynamics system.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>A neural networkassisted molecular dynamics method is developed to reduce the computational cost of open boundary simulations. Particle influxes and neural networkderived forces are applied at the boundaries of an open domain consisting of explicitly modeled LennardJones atoms in order to represent the effects of the unmodeled surrounding fluid. Canonical ensemble simulations with periodic boundaries are used to train the neural network and to sample boundary fluxes. The method, as implemented in the LAMMPS, yields temperature, kinetic energy, potential energy, and pressure values within 2.5% of those calculated using periodic molecular dynamics and runs two orders of magnitude faster than a comparable grand canonical molecular dynamics system.
A neural networkassisted open boundary molecular dynamics simulation method
10.1063/5.0083198
The Journal of Chemical Physics
20220512T12:44:42Z
© 2022 Author(s).
J. E. Floyd
J. R. Lukes

Vibronic resonance along effective modes mediates selective energy transfer in excitonically coupled aggregates
https://aip.scitation.org/doi/10.1063/5.0088855?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>We recently proposed effective normal modes for excitonically coupled aggregates that exactly transform the energy transfer Hamiltonian into a sum of onedimensional Hamiltonians along the effective normal modes. Identifying physically meaningful vibrational motions that maximally promote vibronic mixing suggested an interesting possibility of leveraging vibrationalelectronic resonance for mediating selective energy transfer. Here, we expand on the effective mode approach, elucidating its iterative nature for successively larger aggregates, and extend the idea of mediated energy transfer to larger aggregates. We show that energy transfer between electronically uncoupled but vibronically resonant donor–acceptor sites does not depend on the intermediate site energy or the number of intermediate sites. The intermediate sites simply mediate electronic coupling such that vibronic coupling along specific promoter modes leads to direct donor–acceptor energy transfer, bypassing any intermediate uphill energy transfer steps. We show that the interplay between the electronic Hamiltonian and the effective mode transformation partitions the linear vibronic coupling along specific promoter modes to dictate the selectivity of mediated energy transfer with a vital role of interference between vibronic couplings and multiparticle basis states. Our results suggest a general design principle for enhancing energy transfer through synergistic effects of vibronic resonance and weak mediated electronic coupling, where both effects individually do not promote efficient energy transfer. The effective mode approach proposed here paves a facile route toward fourwavemixing spectroscopy simulations of larger aggregates without severely approximating resonant vibronic coupling.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>We recently proposed effective normal modes for excitonically coupled aggregates that exactly transform the energy transfer Hamiltonian into a sum of onedimensional Hamiltonians along the effective normal modes. Identifying physically meaningful vibrational motions that maximally promote vibronic mixing suggested an interesting possibility of leveraging vibrationalelectronic resonance for mediating selective energy transfer. Here, we expand on the effective mode approach, elucidating its iterative nature for successively larger aggregates, and extend the idea of mediated energy transfer to larger aggregates. We show that energy transfer between electronically uncoupled but vibronically resonant donor–acceptor sites does not depend on the intermediate site energy or the number of intermediate sites. The intermediate sites simply mediate electronic coupling such that vibronic coupling along specific promoter modes leads to direct donor–acceptor energy transfer, bypassing any intermediate uphill energy transfer steps. We show that the interplay between the electronic Hamiltonian and the effective mode transformation partitions the linear vibronic coupling along specific promoter modes to dictate the selectivity of mediated energy transfer with a vital role of interference between vibronic couplings and multiparticle basis states. Our results suggest a general design principle for enhancing energy transfer through synergistic effects of vibronic resonance and weak mediated electronic coupling, where both effects individually do not promote efficient energy transfer. The effective mode approach proposed here paves a facile route toward fourwavemixing spectroscopy simulations of larger aggregates without severely approximating resonant vibronic coupling.
Vibronic resonance along effective modes mediates selective energy transfer in excitonically coupled aggregates
10.1063/5.0088855
The Journal of Chemical Physics
20220512T12:44:47Z
© 2022 Author(s).
Sanjoy Patra
Vivek Tiwari

Sample size dependence of tagged molecule dynamics in steadystate networks with bimolecular reactions: Cycle times of a lightdriven pump
https://aip.scitation.org/doi/10.1063/5.0089695?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>Here, steadystate reaction networks are inspected from the viewpoint of individual tagged molecules jumping among their chemical states upon the occurrence of reactive events. Such an agentbased viewpoint is useful for selectively characterizing the behavior of functional molecules, especially in the presence of bimolecular processes. We present the tools for simulating the jump dynamics both in the macroscopic limit and in the smallvolume sample where the numbers of reactive molecules are of the order of few units with an inherently stochastic kinetics. The focus is on how an ideal spatial “compartmentalization” may affect the dynamical features of the tagged molecule. Our general approach is applied to a synthetic lightdriven supramolecular pump composed of ringlike and axlelike molecules that dynamically assemble and disassemble, originating an average ringthroughaxle directed motion under constant irradiation. In such an example, the dynamical feature of interest is the completion time of direct/inverse cycles of tagged rings and axles. We find a surprisingly strong robustness of the average cycle times with respect to the system’s size. This is explained in the presence of ratedetermining unimolecular processes, which may, therefore, play a crucial role in stabilizing the behavior of small chemical systems against strong fluctuations in the number of molecules.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>Here, steadystate reaction networks are inspected from the viewpoint of individual tagged molecules jumping among their chemical states upon the occurrence of reactive events. Such an agentbased viewpoint is useful for selectively characterizing the behavior of functional molecules, especially in the presence of bimolecular processes. We present the tools for simulating the jump dynamics both in the macroscopic limit and in the smallvolume sample where the numbers of reactive molecules are of the order of few units with an inherently stochastic kinetics. The focus is on how an ideal spatial “compartmentalization” may affect the dynamical features of the tagged molecule. Our general approach is applied to a synthetic lightdriven supramolecular pump composed of ringlike and axlelike molecules that dynamically assemble and disassemble, originating an average ringthroughaxle directed motion under constant irradiation. In such an example, the dynamical feature of interest is the completion time of direct/inverse cycles of tagged rings and axles. We find a surprisingly strong robustness of the average cycle times with respect to the system’s size. This is explained in the presence of ratedetermining unimolecular processes, which may, therefore, play a crucial role in stabilizing the behavior of small chemical systems against strong fluctuations in the number of molecules.
Sample size dependence of tagged molecule dynamics in steadystate networks with bimolecular reactions: Cycle times of a lightdriven pump
10.1063/5.0089695
The Journal of Chemical Physics
20220512T12:44:41Z
© 2022 Author(s).
Daniele Asnicar
Emanuele Penocchio
Diego Frezzato

Quantum computing of Hückel molecular orbitals of πelectron systems
https://aip.scitation.org/doi/10.1063/5.0086489?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>In order to demonstrate an applicability of quantum computing to fundamental electronic structure problems of molecules, we describe the Hückel Hamiltonian matrix in terms of quantum gates and obtain the orbital energies of fundamental πelectron molecules (C2H4, C3H4, C4H4, C4H6, and C6H6) using a superconductingqubittype quantum computer (ibm_kawasaki) with a postselection error mitigation method. We show that the orbital energies are obtained with sufficiently high accuracy and small uncertainties and that characteristic features of the electronic structure of the πelectron molecules can be extracted by quantum computing in a straightforward manner.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>In order to demonstrate an applicability of quantum computing to fundamental electronic structure problems of molecules, we describe the Hückel Hamiltonian matrix in terms of quantum gates and obtain the orbital energies of fundamental πelectron molecules (C2H4, C3H4, C4H4, C4H6, and C6H6) using a superconductingqubittype quantum computer (ibm_kawasaki) with a postselection error mitigation method. We show that the orbital energies are obtained with sufficiently high accuracy and small uncertainties and that characteristic features of the electronic structure of the πelectron molecules can be extracted by quantum computing in a straightforward manner.
Quantum computing of Hückel molecular orbitals of πelectron systems
10.1063/5.0086489
The Journal of Chemical Physics
20220513T02:45:05Z
© 2022 Author(s).
Ryuhei Yoshida
Erik Lötstedt
Kaoru Yamanouchi

Systematic bottomup molecular coarsegraining via force and torque matching using anisotropic particles
https://aip.scitation.org/doi/10.1063/5.0085006?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>We derive a systematic and general method for parameterizing coarsegrained molecular models consisting of anisotropic particles from finegrained (e.g., allatom) models for condensedphase molecular dynamics simulations. The method, which we call anisotropic forcematching coarsegraining (AFMCG), is based on rigorous statistical mechanical principles, enforcing consistency between the coarsegrained and finegrained phasespace distributions to derive equations for the coarsegrained forces, torques, masses, and moments of inertia in terms of properties of a condensedphase finegrained system. We verify the accuracy and efficiency of the method by coarsegraining liquidstate systems of two different anisotropic organic molecules, benzene and perylene, and show that the parameterized coarsegrained models more accurately describe properties of these systems than previous anisotropic coarsegrained models parameterized using other methods that do not account for finitetemperature and manybody effects on the condensedphase coarsegrained interactions. The AFMCG method will be useful for developing accurate and efficient dynamical simulation models of condensedphase systems of molecules consisting of large, rigid, anisotropic fragments, such as liquid crystals, organic semiconductors, and nucleic acids.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>We derive a systematic and general method for parameterizing coarsegrained molecular models consisting of anisotropic particles from finegrained (e.g., allatom) models for condensedphase molecular dynamics simulations. The method, which we call anisotropic forcematching coarsegraining (AFMCG), is based on rigorous statistical mechanical principles, enforcing consistency between the coarsegrained and finegrained phasespace distributions to derive equations for the coarsegrained forces, torques, masses, and moments of inertia in terms of properties of a condensedphase finegrained system. We verify the accuracy and efficiency of the method by coarsegraining liquidstate systems of two different anisotropic organic molecules, benzene and perylene, and show that the parameterized coarsegrained models more accurately describe properties of these systems than previous anisotropic coarsegrained models parameterized using other methods that do not account for finitetemperature and manybody effects on the condensedphase coarsegrained interactions. The AFMCG method will be useful for developing accurate and efficient dynamical simulation models of condensedphase systems of molecules consisting of large, rigid, anisotropic fragments, such as liquid crystals, organic semiconductors, and nucleic acids.
Systematic bottomup molecular coarsegraining via force and torque matching using anisotropic particles
10.1063/5.0085006
The Journal of Chemical Physics
20220513T10:35:43Z
© 2022 Author(s).
Huong T. L. Nguyen
David M. Huang

A matrix completion algorithm for efficient calculation of quantum and variational effects in chemical reactions
https://aip.scitation.org/doi/10.1063/5.0091155?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>This work examines the viability of matrix completion methods as costeffective alternatives to full nuclear Hessians for calculating quantum and variational effects in chemical reactions. The harmonic varietybased matrix completion (HVMC) algorithm, developed in a previous study [S. J. Quiton et al., J. Chem. Phys. 153, 054122 (2020)], exploits the lowrank character of the polynomial expansion of potential energy to recover vibrational frequencies (square roots of eigenvalues of nuclear Hessians) constituting the reaction path using a small sample of its entities. These frequencies are essential for calculating rate coefficients using variational transition state theory with multidimensional tunneling (VTSTMT). HVMC performance is examined for four SN2 reactions and five hydrogen transfer reactions, with each Htransfer reaction consisting of at least one vibrational mode strongly coupled to the reaction coordinate. HVMC is robust and captures zeropoint energies, vibrational free energies, zerocurvature tunneling, and adiabatic ground state and free energy barriers as well as their positions on the reaction coordinate. For medium to large reactions involving Htransfer, with the sole exception of the most complex Ir catalysis system, less than 35% of total eigenvalue information is necessary for accurate recovery of key VTSTMT observables.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>This work examines the viability of matrix completion methods as costeffective alternatives to full nuclear Hessians for calculating quantum and variational effects in chemical reactions. The harmonic varietybased matrix completion (HVMC) algorithm, developed in a previous study [S. J. Quiton et al., J. Chem. Phys. 153, 054122 (2020)], exploits the lowrank character of the polynomial expansion of potential energy to recover vibrational frequencies (square roots of eigenvalues of nuclear Hessians) constituting the reaction path using a small sample of its entities. These frequencies are essential for calculating rate coefficients using variational transition state theory with multidimensional tunneling (VTSTMT). HVMC performance is examined for four SN2 reactions and five hydrogen transfer reactions, with each Htransfer reaction consisting of at least one vibrational mode strongly coupled to the reaction coordinate. HVMC is robust and captures zeropoint energies, vibrational free energies, zerocurvature tunneling, and adiabatic ground state and free energy barriers as well as their positions on the reaction coordinate. For medium to large reactions involving Htransfer, with the sole exception of the most complex Ir catalysis system, less than 35% of total eigenvalue information is necessary for accurate recovery of key VTSTMT observables.
A matrix completion algorithm for efficient calculation of quantum and variational effects in chemical reactions
10.1063/5.0091155
The Journal of Chemical Physics
20220513T10:35:51Z
© 2022 Author(s).
Selin Bac
Stephen Jon Quiton
Kareesa J. Kron
Jeongmin Chae
Urbashi Mitra
Shaama Mallikarjun Sharada

Spectroscopic characterization of singlet–triplet doorway states of aluminum monofluoride
https://aip.scitation.org/doi/10.1063/5.0088288?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>Aluminum monofluoride (AlF) possesses highly favorable properties for laser cooling, both via the A1Π and a3Π states. Determining efficient pathways between the singlet and the triplet manifold of electronic states will be advantageous for future experiments at ultralow temperatures. The lowest rotational levels of the A1Π, v = 6 and b3Σ+, v = 5 states of AlF are nearly isoenergetic and interact via spin–orbit coupling. These levels thus have a strongly mixed spincharacter and provide a singlet–triplet doorway. We here present a hyperfine resolved spectroscopic study of the A1Π, v = 6//b3Σ+, v = 5 perturbed system in a jetcooled, pulsed molecular beam. From a fit to the observed energies of the hyperfine levels, the fine and hyperfine structure parameters of the coupled states and their relative energies as well as the spin–orbit interaction parameter are determined. The standard deviation of the fit is about 15 MHz. We experimentally determine the radiative lifetimes of selected hyperfine levels by timedelayed ionization, Lamb dip spectroscopy, and accurate measurements of the transition lineshapes. The measured lifetimes range between 2 and 200 ns, determined by the degree of singlet–triplet mixing for each level.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>Aluminum monofluoride (AlF) possesses highly favorable properties for laser cooling, both via the A1Π and a3Π states. Determining efficient pathways between the singlet and the triplet manifold of electronic states will be advantageous for future experiments at ultralow temperatures. The lowest rotational levels of the A1Π, v = 6 and b3Σ+, v = 5 states of AlF are nearly isoenergetic and interact via spin–orbit coupling. These levels thus have a strongly mixed spincharacter and provide a singlet–triplet doorway. We here present a hyperfine resolved spectroscopic study of the A1Π, v = 6//b3Σ+, v = 5 perturbed system in a jetcooled, pulsed molecular beam. From a fit to the observed energies of the hyperfine levels, the fine and hyperfine structure parameters of the coupled states and their relative energies as well as the spin–orbit interaction parameter are determined. The standard deviation of the fit is about 15 MHz. We experimentally determine the radiative lifetimes of selected hyperfine levels by timedelayed ionization, Lamb dip spectroscopy, and accurate measurements of the transition lineshapes. The measured lifetimes range between 2 and 200 ns, determined by the degree of singlet–triplet mixing for each level.
Spectroscopic characterization of singlet–triplet doorway states of aluminum monofluoride
10.1063/5.0088288
The Journal of Chemical Physics
20220509T10:27:12Z
© 2022 Author(s).
N. Walter
J. Seifert
S. Truppe
H. C. Schewe
B. G. Sartakov
G. Meijer

Collision excitation of cC3H−(X1A1) by He
https://aip.scitation.org/doi/10.1063/5.0089458?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>Accurate modeling of anionic abundances in the interstellar and circumstellar media requires calculations of collisional data with the most abundant species that are usually He atoms and H2 molecules. In this paper, we focus on smaller cyclic molecular anion, cC3H−, an astrophysical candidate, following the detection of larger CnH− carbon chains. From a new threedimensional potential energy surface, the rotational (de)excitation of the cC3H−(X1A1) anion by collision with He is investigated. The surface is obtained in the supermolecular approach at the CCSD(T)F12/augccpVTZ level of theory. Fully quantum closecoupling calculations of inelastic integral cross sections are performed on a grid of collisional energies large enough to ensure the convergence of the statetostate rate coefficients for the 34 first rotational levels up to [math] = 77,0 of cC3H− and temperatures ranging from 5 to 100 K. For this collisional system, rate coefficients exhibit a strong dominance in favor of 21,2 → l1,1 downward transition. This transition was previously used for the detection of the cyclic parent cC3H. The cC3H−–He rate coefficients (∼10−11 cm3 s−1) are of the same order of magnitude as those of the detected anions CnH− (as C2H−, C4H−, and C6H−) in collision with He and one order of magnitude smaller than those with H2. The critical densities of H2 were also estimated, and a discussion on the validity of the local thermodynamic equilibrium conditions is carried out. This work represents the contribution to understanding and modeling abundances and chemistry of hydrocarbon radicals, CnH, in astrophysical media.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>Accurate modeling of anionic abundances in the interstellar and circumstellar media requires calculations of collisional data with the most abundant species that are usually He atoms and H2 molecules. In this paper, we focus on smaller cyclic molecular anion, cC3H−, an astrophysical candidate, following the detection of larger CnH− carbon chains. From a new threedimensional potential energy surface, the rotational (de)excitation of the cC3H−(X1A1) anion by collision with He is investigated. The surface is obtained in the supermolecular approach at the CCSD(T)F12/augccpVTZ level of theory. Fully quantum closecoupling calculations of inelastic integral cross sections are performed on a grid of collisional energies large enough to ensure the convergence of the statetostate rate coefficients for the 34 first rotational levels up to [math] = 77,0 of cC3H− and temperatures ranging from 5 to 100 K. For this collisional system, rate coefficients exhibit a strong dominance in favor of 21,2 → l1,1 downward transition. This transition was previously used for the detection of the cyclic parent cC3H. The cC3H−–He rate coefficients (∼10−11 cm3 s−1) are of the same order of magnitude as those of the detected anions CnH− (as C2H−, C4H−, and C6H−) in collision with He and one order of magnitude smaller than those with H2. The critical densities of H2 were also estimated, and a discussion on the validity of the local thermodynamic equilibrium conditions is carried out. This work represents the contribution to understanding and modeling abundances and chemistry of hydrocarbon radicals, CnH, in astrophysical media.
Collision excitation of cC3H−(X1A1) by He
10.1063/5.0089458
The Journal of Chemical Physics
20220510T09:42:32Z
© 2022 Author(s).
Muneerah Mogren Al Mogren
Driss Ben Abdallah
Sarah Dhaif Allah Al Harbi
Maria Luisa Senent

Assessment of XC functionals for the study of organic molecules with superhalogen substitution. A systematic comparison between DFT and CCSD(T)
https://aip.scitation.org/doi/10.1063/5.0089672?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>A systematic density functional theory study, including 17 exchange–correlation functionals, was performed on 22 composite structures consisting of organic molecules, e.g., ethylene, ethane, and benzene, and superhalogen substitutions arising from [MgX3]− and [Mg2X5]− (X = F, Cl). Rangeseparated hybrid functionals [math]B97MV, [math]B97XD3(BJ), [math]B97XD, [math]B97X, and CAMB3LYP, as well as doublehybrid functionals B2PLYP and DSDPBEP86D3(BJ), are verified to provide reliable results with accuracy approaching that at the coupledcluster single double triple [CCSD(T)] level. The basis set effect of density functional theory calculation is usually moderate, and tripleξ quality, e.g., Def2TZVP, is enough in most cases. In addition, the average values from HF and MP2 method, indicated as (MP2 + HF)/2, are also quite close to those of CCSD(T).
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>A systematic density functional theory study, including 17 exchange–correlation functionals, was performed on 22 composite structures consisting of organic molecules, e.g., ethylene, ethane, and benzene, and superhalogen substitutions arising from [MgX3]− and [Mg2X5]− (X = F, Cl). Rangeseparated hybrid functionals [math]B97MV, [math]B97XD3(BJ), [math]B97XD, [math]B97X, and CAMB3LYP, as well as doublehybrid functionals B2PLYP and DSDPBEP86D3(BJ), are verified to provide reliable results with accuracy approaching that at the coupledcluster single double triple [CCSD(T)] level. The basis set effect of density functional theory calculation is usually moderate, and tripleξ quality, e.g., Def2TZVP, is enough in most cases. In addition, the average values from HF and MP2 method, indicated as (MP2 + HF)/2, are also quite close to those of CCSD(T).
Assessment of XC functionals for the study of organic molecules with superhalogen substitution. A systematic comparison between DFT and CCSD(T)
10.1063/5.0089672
The Journal of Chemical Physics
20220510T09:42:14Z
© 2022 Author(s).
JinFeng Li
JiaHui Wang
Bing Yin

Efficient force field and energy emulation through partition of permutationally equivalent atoms
https://aip.scitation.org/doi/10.1063/5.0088017?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>Gaussian process (GP) emulator has been used as a surrogate model for predicting force field and molecular potential, to overcome the computational bottleneck of ab initio molecular dynamics simulation. Integrating both atomic force and energy in predictions was found to be more accurate than using energy alone, yet it requires O((NM)3) computational operations for computing the likelihood function and making predictions, where N is the number of atoms and M is the number of simulated configurations in the training sample due to the inversion of a large covariance matrix. The high computational cost limits its applications to the simulation of small molecules. The computational challenge of using both gradient information and function values in GPs was recently noticed in machine learning communities, whereas conventional approximation methods may not work well. Here, we introduce a new approach, the atomized force field model, that integrates both force and energy in the emulator with many fewer computational operations. The drastic reduction in computation is achieved by utilizing the naturally sparse covariance structure that satisfies the constraints of the energy conservation and permutation symmetry of atoms. The efficient machine learning algorithm extends the limits of its applications on larger molecules under the same computational budget, with nearly no loss of predictive accuracy. Furthermore, our approach contains an uncertainty assessment of predictions of atomic forces and energies, useful for developing a sequential design over the chemical input space.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>Gaussian process (GP) emulator has been used as a surrogate model for predicting force field and molecular potential, to overcome the computational bottleneck of ab initio molecular dynamics simulation. Integrating both atomic force and energy in predictions was found to be more accurate than using energy alone, yet it requires O((NM)3) computational operations for computing the likelihood function and making predictions, where N is the number of atoms and M is the number of simulated configurations in the training sample due to the inversion of a large covariance matrix. The high computational cost limits its applications to the simulation of small molecules. The computational challenge of using both gradient information and function values in GPs was recently noticed in machine learning communities, whereas conventional approximation methods may not work well. Here, we introduce a new approach, the atomized force field model, that integrates both force and energy in the emulator with many fewer computational operations. The drastic reduction in computation is achieved by utilizing the naturally sparse covariance structure that satisfies the constraints of the energy conservation and permutation symmetry of atoms. The efficient machine learning algorithm extends the limits of its applications on larger molecules under the same computational budget, with nearly no loss of predictive accuracy. Furthermore, our approach contains an uncertainty assessment of predictions of atomic forces and energies, useful for developing a sequential design over the chemical input space.
Efficient force field and energy emulation through partition of permutationally equivalent atoms
10.1063/5.0088017
The Journal of Chemical Physics
20220510T10:13:02Z
© 2022 Author(s).
Hao Li
Musen Zhou
Jessalyn Sebastian
Jianzhong Wu
Mengyang Gu

Rovibrational investigation of a new highlying [math] state of Cu2 by using twocolor resonant fourwavemixing spectroscopy
https://aip.scitation.org/doi/10.1063/5.0087743?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>A highly excited electronic state of dicopper is observed and characterized for the first time. The [math][math] system is measured at rotational resolution by using degenerate and twocolor resonant fourwavemixing, as well as laser induced fluorescence spectroscopy. Doubleresonance experiments are performed by labeling selected rotational levels of the ground state by tuning the probe laser wavelength to transitions in the wellknown (10) band of the [math][math] electronic system. Spectra obtained by scans of the pump laser in the UV wavelength range were then assigned unambiguously by the stringent doubleresonance selection rules. The absence of a Qband suggests a parallel transition (ΔΩ = 0) and determines the term symbol of the state as [math] in Hund’s case (c) notation. The equilibrium constants for 63Cu2 are Te = 39 559.921(92) cm−1, ωe = 277.70(14) cm−1, Be = 0.104 942(66) cm−1, and re = 2.2595(11) Å. These findings are supported by highlevel ab initio calculations at the MRCI+Q level, which clearly identifies this state as resulting from a 4p ← 3d transition. In addition, three dark perturber states are found in the v = 1 and v = 2 vibrational levels of the new state. A deperturbation analysis characterizes the interaction and rationalizes the anomalous dips in the excitation spectrum of the [math][math] system.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>A highly excited electronic state of dicopper is observed and characterized for the first time. The [math][math] system is measured at rotational resolution by using degenerate and twocolor resonant fourwavemixing, as well as laser induced fluorescence spectroscopy. Doubleresonance experiments are performed by labeling selected rotational levels of the ground state by tuning the probe laser wavelength to transitions in the wellknown (10) band of the [math][math] electronic system. Spectra obtained by scans of the pump laser in the UV wavelength range were then assigned unambiguously by the stringent doubleresonance selection rules. The absence of a Qband suggests a parallel transition (ΔΩ = 0) and determines the term symbol of the state as [math] in Hund’s case (c) notation. The equilibrium constants for 63Cu2 are Te = 39 559.921(92) cm−1, ωe = 277.70(14) cm−1, Be = 0.104 942(66) cm−1, and re = 2.2595(11) Å. These findings are supported by highlevel ab initio calculations at the MRCI+Q level, which clearly identifies this state as resulting from a 4p ← 3d transition. In addition, three dark perturber states are found in the v = 1 and v = 2 vibrational levels of the new state. A deperturbation analysis characterizes the interaction and rationalizes the anomalous dips in the excitation spectrum of the [math][math] system.
Rovibrational investigation of a new highlying [math] state of Cu2 by using twocolor resonant fourwavemixing spectroscopy
10.1063/5.0087743
The Journal of Chemical Physics
20220510T09:43:29Z
© 2022 Author(s).
Jiaye Jin
Qiang Zhang
Peter Bornhauser
Gregor Knopp
Roberto Marquardt
Peter P. Radi

Unconventional SN2 retention pathways induced by complex formation: Highlevel dynamics investigation of the NH2− + CH3I polyatomic reaction
https://aip.scitation.org/doi/10.1063/5.0091789?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>Investigations on the dynamics of chemical reactions have been a hot topic for experimental and theoretical studies over the last few decades. Here, we carry out the first highlevel dynamical characterization for the polyatom–polyatom reaction between NH2− and CH3I. A global analytical potential energy surface is developed to describe the possible pathways with the quasiclassical trajectory method at several collision energies. In addition to SN2 and proton abstraction, a significant iodine abstraction is identified, leading to the CH3 + [NH2⋯I]− products. For SN2, our computations reveal an indirect character as well, promoting the formation of [CH3⋯NH2] complexes. Two novel dominant SN2 retention pathways are uncovered induced by the rotation of the CH3 fragment in these latter [CH3⋯NH2] complexes. Moreover, these uncommon routes turn out to be the most dominant retention paths for the NH2− + CH3I SN2 reaction.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>Investigations on the dynamics of chemical reactions have been a hot topic for experimental and theoretical studies over the last few decades. Here, we carry out the first highlevel dynamical characterization for the polyatom–polyatom reaction between NH2− and CH3I. A global analytical potential energy surface is developed to describe the possible pathways with the quasiclassical trajectory method at several collision energies. In addition to SN2 and proton abstraction, a significant iodine abstraction is identified, leading to the CH3 + [NH2⋯I]− products. For SN2, our computations reveal an indirect character as well, promoting the formation of [CH3⋯NH2] complexes. Two novel dominant SN2 retention pathways are uncovered induced by the rotation of the CH3 fragment in these latter [CH3⋯NH2] complexes. Moreover, these uncommon routes turn out to be the most dominant retention paths for the NH2− + CH3I SN2 reaction.
Unconventional SN2 retention pathways induced by complex formation: Highlevel dynamics investigation of the NH2− + CH3I polyatomic reaction
10.1063/5.0091789
The Journal of Chemical Physics
20220512T10:20:37Z
© 2022 Author(s).
Domonkos A. Tasi
Gábor Czakó

Barely fluorescent molecules. I. Twindischarge jet laserinduced fluorescence spectroscopy of HSnCl and DSnCl
https://aip.scitation.org/doi/10.1063/5.0090628?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>The divalent tin transient molecules HSnCl and DSnCl have been detected for the first time by laserinduced fluorescence (LIF) spectroscopy. HSnCl/DSnCl were produced in a twindischarge jet using separate precursor streams of SnH4/SnD4 and the discharge products from HCl/DCl, both diluted in high pressure argon. The [math]1A″–[math]1A′ spectrum of HSnCl consists of a single vibronic [math] band with a very short fluorescence lifetime (∼30 ns). In contrast, the LIF spectrum of DSnCl exhibits three bands ([math]), whose fluorescence lifetimes decrease from 393 ns (00) to less than 10 ns (22). Single vibronic level emission spectra have been recorded, providing information on all three vibrational modes in the ground state. Previous detailed ab initio studies indicate that these molecules dissociate into SnCl + H on the excited state potential surface and this is the cause of the short fluorescence lifetimes and breaking off of the fluorescence. It is fortunate that the HSnCl excited state zeropoint level is still fluorescent or it would not be detectable by LIF spectroscopy.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>The divalent tin transient molecules HSnCl and DSnCl have been detected for the first time by laserinduced fluorescence (LIF) spectroscopy. HSnCl/DSnCl were produced in a twindischarge jet using separate precursor streams of SnH4/SnD4 and the discharge products from HCl/DCl, both diluted in high pressure argon. The [math]1A″–[math]1A′ spectrum of HSnCl consists of a single vibronic [math] band with a very short fluorescence lifetime (∼30 ns). In contrast, the LIF spectrum of DSnCl exhibits three bands ([math]), whose fluorescence lifetimes decrease from 393 ns (00) to less than 10 ns (22). Single vibronic level emission spectra have been recorded, providing information on all three vibrational modes in the ground state. Previous detailed ab initio studies indicate that these molecules dissociate into SnCl + H on the excited state potential surface and this is the cause of the short fluorescence lifetimes and breaking off of the fluorescence. It is fortunate that the HSnCl excited state zeropoint level is still fluorescent or it would not be detectable by LIF spectroscopy.
Barely fluorescent molecules. I. Twindischarge jet laserinduced fluorescence spectroscopy of HSnCl and DSnCl
10.1063/5.0090628
The Journal of Chemical Physics
20220513T10:35:27Z
© 2022 Author(s).
Gretchen Rothschopf
Tony C. Smith
Dennis J. Clouthier

Barely fluorescent molecules. II. Twindischarge jet laserinduced fluorescence spectroscopy of HSnBr and DSnBr
https://aip.scitation.org/doi/10.1063/5.0090629?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>HSnBr and DSnBr have been detected for the first time by a combination of laserinduced fluorescence (LIF), fluorescence holeburning, and wavelength resolved emission spectroscopies. The transient molecules were produced in a twindischarge jet using separate precursor streams of SnH4/SnD4 and HBr/DBr, both diluted in high pressure argon. The [math]1A″–[math]1A′ spectrum of HSnBr only consists of the [math] and [math] cold bands that show clearly resolved subband structure with fluorescence lifetimes varying from 526 to 162 ns. The DSnBr LIF spectrum exhibits four bands ([math], [math], [math], and [math]) whose fluorescence lifetimes decrease from 525 ns (00) to 175 ns (11). Single vibronic level emission spectra have provided extensive information on the ground state vibrations, including all the anharmonicities and the harmonic frequencies. Fluorescence holeburning experiments have shown that a few higher HSnBr nonfluorescent levels are very shortlived but still detectable. The ab initio studies of Tarroni and Clouthier [J. Chem. Phys. 156, 064304 (2022)] show that these molecules dissociate into SnBr + H on the excited state potential surface and this is the cause of the short fluorescence lifetimes and breaking off of the LIF spectra. HSnBr is a barely fluorescent molecule in the sense that only vibrational levels less than or equal to 317 cm−1 in the excited state emit detectable photons down to the ground state.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>HSnBr and DSnBr have been detected for the first time by a combination of laserinduced fluorescence (LIF), fluorescence holeburning, and wavelength resolved emission spectroscopies. The transient molecules were produced in a twindischarge jet using separate precursor streams of SnH4/SnD4 and HBr/DBr, both diluted in high pressure argon. The [math]1A″–[math]1A′ spectrum of HSnBr only consists of the [math] and [math] cold bands that show clearly resolved subband structure with fluorescence lifetimes varying from 526 to 162 ns. The DSnBr LIF spectrum exhibits four bands ([math], [math], [math], and [math]) whose fluorescence lifetimes decrease from 525 ns (00) to 175 ns (11). Single vibronic level emission spectra have provided extensive information on the ground state vibrations, including all the anharmonicities and the harmonic frequencies. Fluorescence holeburning experiments have shown that a few higher HSnBr nonfluorescent levels are very shortlived but still detectable. The ab initio studies of Tarroni and Clouthier [J. Chem. Phys. 156, 064304 (2022)] show that these molecules dissociate into SnBr + H on the excited state potential surface and this is the cause of the short fluorescence lifetimes and breaking off of the LIF spectra. HSnBr is a barely fluorescent molecule in the sense that only vibrational levels less than or equal to 317 cm−1 in the excited state emit detectable photons down to the ground state.
Barely fluorescent molecules. II. Twindischarge jet laserinduced fluorescence spectroscopy of HSnBr and DSnBr
10.1063/5.0090629
The Journal of Chemical Physics
20220513T11:37:08Z
© 2022 Author(s).
Gretchen Rothschopf
Joseph M. Cardon
Tony C. Smith
Dennis J. Clouthier

Temperature induced change of TMAO effects on hydrophobic hydration
https://aip.scitation.org/doi/10.1063/5.0088388?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>The effect of trimethylamineNoxide (TMAO) on hydrophobic solvation and hydrophobic interactions of methane has been studied with Molecular Dynamics simulations in the temperature range between 280 and 370 K at 1 bar ambient pressure. We observe a temperature transition in the effect of TMAO on the aqueous solubility of methane. At low temperature (280 K), methane is preferentially hydrated, causing TMAO to reduce its solubility in water, while above 320 K, methane preferentially interacts with TMAO, causing TMAO to promote its solubility in water. Based on a statisticalmechanical analysis of the excess chemical potential of methane, we find that the reversible work of creating a repulsive methane cavity opposes the solubility of methane in TMAO/water solution more than in pure water. Below 320 K, this solventexcluded volume effect overcompensates the contribution of methane–TMAO van der Waals interactions, which promote the solvation of methane and are observed at all temperatures. These van der Waals interactions with the methyl groups of TMAO tip the balance above 320 K where the effect of TMAO on solventexcluded volume is smaller. We furthermore find that the effective attraction between dissolved methane solutes increases with the increasing TMAO concentration. This observation correlates with a reduction in the methane solubility below 320 K but with an increase in methane solubility at higher temperatures.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>The effect of trimethylamineNoxide (TMAO) on hydrophobic solvation and hydrophobic interactions of methane has been studied with Molecular Dynamics simulations in the temperature range between 280 and 370 K at 1 bar ambient pressure. We observe a temperature transition in the effect of TMAO on the aqueous solubility of methane. At low temperature (280 K), methane is preferentially hydrated, causing TMAO to reduce its solubility in water, while above 320 K, methane preferentially interacts with TMAO, causing TMAO to promote its solubility in water. Based on a statisticalmechanical analysis of the excess chemical potential of methane, we find that the reversible work of creating a repulsive methane cavity opposes the solubility of methane in TMAO/water solution more than in pure water. Below 320 K, this solventexcluded volume effect overcompensates the contribution of methane–TMAO van der Waals interactions, which promote the solvation of methane and are observed at all temperatures. These van der Waals interactions with the methyl groups of TMAO tip the balance above 320 K where the effect of TMAO on solventexcluded volume is smaller. We furthermore find that the effective attraction between dissolved methane solutes increases with the increasing TMAO concentration. This observation correlates with a reduction in the methane solubility below 320 K but with an increase in methane solubility at higher temperatures.
Temperature induced change of TMAO effects on hydrophobic hydration
10.1063/5.0088388
The Journal of Chemical Physics
20220509T10:26:57Z
© 2022 Author(s).
Angelina Folberth
Nico F. A. van der Vegt

Spin–phonon coupling in ferrimagnet spinel CoMn2O4
https://aip.scitation.org/doi/10.1063/5.0087770?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>Coupling of material properties provides new fundamental insights and possibilities toward multifunctional devices. The spinel structures display strong coupling between different order parameters, as a consequence, exhibiting many fascinating properties, such as multiferroicity and superconductivity. Here, we have investigated the structural, magnetic, and vibrational properties of mixedspinel CoMn2O4 stabilized in distorted tetragonal structures as evidenced from xray diffraction measurements. Magnetization measurements reveal two ferrimagnetic phase transitions at 185 and 90 K. Raman scattering measurements reveal the renormalization of phonon parameters for a few phonon modes at low temperatures, arising from spin–phonon coupling. The obtained value for λS2 is ∼2 cm−1. The strength of spin–phonon coupling (λ) is estimated according to the spins involved in the corresponding lattice vibrations and discussed.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>Coupling of material properties provides new fundamental insights and possibilities toward multifunctional devices. The spinel structures display strong coupling between different order parameters, as a consequence, exhibiting many fascinating properties, such as multiferroicity and superconductivity. Here, we have investigated the structural, magnetic, and vibrational properties of mixedspinel CoMn2O4 stabilized in distorted tetragonal structures as evidenced from xray diffraction measurements. Magnetization measurements reveal two ferrimagnetic phase transitions at 185 and 90 K. Raman scattering measurements reveal the renormalization of phonon parameters for a few phonon modes at low temperatures, arising from spin–phonon coupling. The obtained value for λS2 is ∼2 cm−1. The strength of spin–phonon coupling (λ) is estimated according to the spins involved in the corresponding lattice vibrations and discussed.
Spin–phonon coupling in ferrimagnet spinel CoMn2O4
10.1063/5.0087770
The Journal of Chemical Physics
20220509T10:27:20Z
© 2022 Author(s).
Bommareddy Poojitha
Aswin Shaji
Shalini Badola
Surajit Saha

Transfer learning using attentions across atomic systems with graph neural networks (TAAG)
https://aip.scitation.org/doi/10.1063/5.0088019?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>Recent advances in Graph Neural Networks (GNNs) have transformed the space of molecular and catalyst discovery. Despite the fact that the underlying physics across these domains remain the same, most prior work has focused on building domainspecific models either in small molecules or in materials. However, building large datasets across all domains is computationally expensive; therefore, the use of transfer learning (TL) to generalize to different domains is a promising but underexplored approach to this problem. To evaluate this hypothesis, we use a model that is pretrained on the Open Catalyst Dataset (OC20), and we study the model’s behavior when finetuned for a set of different datasets and tasks. This includes MD17, the *CO adsorbate dataset, and OC20 across different tasks. Through extensive TL experiments, we demonstrate that the initial layers of GNNs learn a more basic representation that is consistent across domains, whereas the final layers learn more taskspecific features. Moreover, these wellknown strategies show significant improvement over the nonpretrained models for indomain tasks with improvements of 53% and 17% for the *CO dataset and across the Open Catalyst Project (OCP) task, respectively. TL approaches result in up to 4× speedup in model training depending on the target data and task. However, these do not perform well for the MD17 dataset, resulting in worse performance than the nonpretrained model for few molecules. Based on these observations, we propose transfer learning using attentions across atomic systems with graph Neural Networks (TAAG), an attentionbased approach that adapts to prioritize and transfer important features from the interaction layers of GNNs. The proposed method outperforms the best TL approach for outofdomain datasets, such as MD17, and gives a mean improvement of 6% over a model trained from scratch.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>Recent advances in Graph Neural Networks (GNNs) have transformed the space of molecular and catalyst discovery. Despite the fact that the underlying physics across these domains remain the same, most prior work has focused on building domainspecific models either in small molecules or in materials. However, building large datasets across all domains is computationally expensive; therefore, the use of transfer learning (TL) to generalize to different domains is a promising but underexplored approach to this problem. To evaluate this hypothesis, we use a model that is pretrained on the Open Catalyst Dataset (OC20), and we study the model’s behavior when finetuned for a set of different datasets and tasks. This includes MD17, the *CO adsorbate dataset, and OC20 across different tasks. Through extensive TL experiments, we demonstrate that the initial layers of GNNs learn a more basic representation that is consistent across domains, whereas the final layers learn more taskspecific features. Moreover, these wellknown strategies show significant improvement over the nonpretrained models for indomain tasks with improvements of 53% and 17% for the *CO dataset and across the Open Catalyst Project (OCP) task, respectively. TL approaches result in up to 4× speedup in model training depending on the target data and task. However, these do not perform well for the MD17 dataset, resulting in worse performance than the nonpretrained model for few molecules. Based on these observations, we propose transfer learning using attentions across atomic systems with graph Neural Networks (TAAG), an attentionbased approach that adapts to prioritize and transfer important features from the interaction layers of GNNs. The proposed method outperforms the best TL approach for outofdomain datasets, such as MD17, and gives a mean improvement of 6% over a model trained from scratch.
Transfer learning using attentions across atomic systems with graph neural networks (TAAG)
10.1063/5.0088019
The Journal of Chemical Physics
20220512T10:20:48Z
© 2022 Author(s).
Adeesh Kolluru
Nima Shoghi
Muhammed Shuaibi
Siddharth Goyal
Abhishek Das
C. Lawrence Zitnick
Zachary Ulissi

Computer simulation investigation of the adsorption of acetamide on low density amorphous ice. An astrochemical perspective
https://aip.scitation.org/doi/10.1063/5.0093561?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>The adsorption of acetamide on low density amorphous (LDA) ice is investigated by grand canonical Monte Carlo computer simulations at the temperatures 50, 100, and 200 K, characteristic of certain domains of the interstellar medium (ISM). We found that the relative importance of the acetamide–acetamide Hbonds with respect to the acetamide–water ones increases with decreasing temperature. Thus, with decreasing temperature, the existence of the stable monolayer, characterizing the adsorption at 200 K, is gradually replaced by the occurrence of marked multilayer adsorption, preceding even the saturation of the first layer at 50 K. While isolated acetamide molecules prefer to lay parallel to the ice surface to maximize their Hbonding with the surface water molecules, this orientational preference undergoes a marked change upon saturation of the first layer due to increasing competition of the adsorbed molecules for Hbonds with water and to the possibility of their Hbond formation with each other. As a result, molecules stay preferentially perpendicular to the ice surface in the saturated monolayer. The chemical potential value corresponding to the point of condensation is found to decrease linearly with increasing temperature. We provide, in analogy with the Clausius–Clapeyron equation, a thermodynamic explanation of this behavior and estimate the molar entropy of condensed phase acetamide to be 34.0 J/mol K. For the surface concentration of the saturated monolayer, we obtain the value 9.1 ± 0.8 µmol/m2, while the heat of adsorption at infinitely low surface coverage is estimated to be −67.8 ± 3.0 kJ/mol. Our results indicate that the interstellar formation of peptide chains through acetamide molecules, occurring at the surface of LDA ice, might well be a plausible process in the cold (i.e., below 50 K) domains of the ISM; however, it is a rather unlikely scenario in its higher temperature (i.e., 100–200 K) domains.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>The adsorption of acetamide on low density amorphous (LDA) ice is investigated by grand canonical Monte Carlo computer simulations at the temperatures 50, 100, and 200 K, characteristic of certain domains of the interstellar medium (ISM). We found that the relative importance of the acetamide–acetamide Hbonds with respect to the acetamide–water ones increases with decreasing temperature. Thus, with decreasing temperature, the existence of the stable monolayer, characterizing the adsorption at 200 K, is gradually replaced by the occurrence of marked multilayer adsorption, preceding even the saturation of the first layer at 50 K. While isolated acetamide molecules prefer to lay parallel to the ice surface to maximize their Hbonding with the surface water molecules, this orientational preference undergoes a marked change upon saturation of the first layer due to increasing competition of the adsorbed molecules for Hbonds with water and to the possibility of their Hbond formation with each other. As a result, molecules stay preferentially perpendicular to the ice surface in the saturated monolayer. The chemical potential value corresponding to the point of condensation is found to decrease linearly with increasing temperature. We provide, in analogy with the Clausius–Clapeyron equation, a thermodynamic explanation of this behavior and estimate the molar entropy of condensed phase acetamide to be 34.0 J/mol K. For the surface concentration of the saturated monolayer, we obtain the value 9.1 ± 0.8 µmol/m2, while the heat of adsorption at infinitely low surface coverage is estimated to be −67.8 ± 3.0 kJ/mol. Our results indicate that the interstellar formation of peptide chains through acetamide molecules, occurring at the surface of LDA ice, might well be a plausible process in the cold (i.e., below 50 K) domains of the ISM; however, it is a rather unlikely scenario in its higher temperature (i.e., 100–200 K) domains.
Computer simulation investigation of the adsorption of acetamide on low density amorphous ice. An astrochemical perspective
10.1063/5.0093561
The Journal of Chemical Physics
20220513T10:35:33Z
© 2022 Author(s).
Mirjam Balbisi
Réka A. Horváth
Milán Szőri
Pál Jedlovszky

Alchemical geometry relaxation
https://aip.scitation.org/doi/10.1063/5.0085817?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>We propose the relaxation of geometries throughout chemical compound space using alchemical perturbation density functional theory (APDFT). APDFT refers to perturbation theory involving changes in nuclear charges within approximate solutions to Schrödinger’s equation. We give an analytical formula to calculate the mixed second order energy derivatives with respect to both nuclear charges and nuclear positions (named “alchemical force”) within the restricted Hartree–Fock case. We have implemented and studied the formula for its use in geometry relaxation of various reference and target molecules. We have also analyzed the convergence of the alchemical force perturbation series as well as basis set effects. Interpolating alchemically predicted energies, forces, and Hessian to a Morse potential yields more accurate geometries and equilibrium energies than when performing a standard Newton–Raphson step. Our numerical predictions for small molecules including BF, CO, N2, CH4, NH3, H2O, and HF yield mean absolute errors of equilibrium energies and bond lengths smaller than 10 mHa and 0.01 bohr for fourth order APDFT predictions, respectively. Our alchemical geometry relaxation still preserves the combinatorial efficiency of APDFT: Based on a single coupled perturbed Hartree–Fock derivative for benzene, we provide numerical predictions of equilibrium energies and relaxed structures of all 17 isoelectronic chargeneutral BNdoped mutants with averaged absolute deviations of ∼27 mHa and ∼0.12 bohr, respectively.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>We propose the relaxation of geometries throughout chemical compound space using alchemical perturbation density functional theory (APDFT). APDFT refers to perturbation theory involving changes in nuclear charges within approximate solutions to Schrödinger’s equation. We give an analytical formula to calculate the mixed second order energy derivatives with respect to both nuclear charges and nuclear positions (named “alchemical force”) within the restricted Hartree–Fock case. We have implemented and studied the formula for its use in geometry relaxation of various reference and target molecules. We have also analyzed the convergence of the alchemical force perturbation series as well as basis set effects. Interpolating alchemically predicted energies, forces, and Hessian to a Morse potential yields more accurate geometries and equilibrium energies than when performing a standard Newton–Raphson step. Our numerical predictions for small molecules including BF, CO, N2, CH4, NH3, H2O, and HF yield mean absolute errors of equilibrium energies and bond lengths smaller than 10 mHa and 0.01 bohr for fourth order APDFT predictions, respectively. Our alchemical geometry relaxation still preserves the combinatorial efficiency of APDFT: Based on a single coupled perturbed Hartree–Fock derivative for benzene, we provide numerical predictions of equilibrium energies and relaxed structures of all 17 isoelectronic chargeneutral BNdoped mutants with averaged absolute deviations of ∼27 mHa and ∼0.12 bohr, respectively.
Alchemical geometry relaxation
10.1063/5.0085817
The Journal of Chemical Physics
20220509T10:28:11Z
© 2022 Author(s).
Giorgio Domenichini
O. Anatole von Lilienfeld

Quantum Gaussian process model of potential energy surface for a polyatomic molecule
https://aip.scitation.org/doi/10.1063/5.0088821?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>With gates of a quantum computer designed to encode multidimensional vectors, projections of quantum computer states onto specific qubit states can produce kernels of reproducing kernel Hilbert spaces. We show that quantum kernels obtained with a fixed ansatz implementable on current quantum computers can be used for accurate regression models of global potential energy surfaces (PESs) for polyatomic molecules. To obtain accurate regression models, we apply Bayesian optimization to maximize marginal likelihood by varying the parameters of the quantum gates. This yields Gaussian process models with quantum kernels. We illustrate the effect of qubit entanglement in the quantum kernels and explore the generalization performance of quantum Gaussian processes by extrapolating global sixdimensional PESs in the energy domain.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>With gates of a quantum computer designed to encode multidimensional vectors, projections of quantum computer states onto specific qubit states can produce kernels of reproducing kernel Hilbert spaces. We show that quantum kernels obtained with a fixed ansatz implementable on current quantum computers can be used for accurate regression models of global potential energy surfaces (PESs) for polyatomic molecules. To obtain accurate regression models, we apply Bayesian optimization to maximize marginal likelihood by varying the parameters of the quantum gates. This yields Gaussian process models with quantum kernels. We illustrate the effect of qubit entanglement in the quantum kernels and explore the generalization performance of quantum Gaussian processes by extrapolating global sixdimensional PESs in the energy domain.
Quantum Gaussian process model of potential energy surface for a polyatomic molecule
10.1063/5.0088821
The Journal of Chemical Physics
20220511T09:55:07Z
© 2022 Author(s).
J. Dai
R. V. Krems

Entropic surface segregation from athermal polymer blends: Polymer flexibility vs bulkiness
https://aip.scitation.org/doi/10.1063/5.0087587?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>We examine athermal binary blends composed of conformationally asymmetric polymers of equal molecular volume next to a surface of width ξ. The selfconsistent field theory (SCFT) of Gaussian chains predicts that the more compact polymer with the shorter average endtoend length, R0, is entropically favored at the surface. Here, we extend the SCFT to wormlike chains with small persistence lengths, ℓp, relative to their contour lengths, ℓc, for which [math]. In the limit of ℓp ≪ ξ, we recover the Gaussianchain prediction where the segregation depends only on the product ℓpℓc, but for realistic polymer/air surfaces with ξ ∼ ℓp, the segregation depends separately on the two quantities. Although the surface continues to favor flexible polymers with smaller ℓp and bulky polymers with shorter ℓc, the effect of bulkiness is more pronounced. This imbalance can, under specific conditions, lead to anomalous surface segregation of the more extended polymer. For this to happen, the polymer must be bulkier and stiffer, with a stiffness that is sufficient to produce a larger R0 yet not so rigid as to reverse the surface affinity that favors bulky polymers.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>We examine athermal binary blends composed of conformationally asymmetric polymers of equal molecular volume next to a surface of width ξ. The selfconsistent field theory (SCFT) of Gaussian chains predicts that the more compact polymer with the shorter average endtoend length, R0, is entropically favored at the surface. Here, we extend the SCFT to wormlike chains with small persistence lengths, ℓp, relative to their contour lengths, ℓc, for which [math]. In the limit of ℓp ≪ ξ, we recover the Gaussianchain prediction where the segregation depends only on the product ℓpℓc, but for realistic polymer/air surfaces with ξ ∼ ℓp, the segregation depends separately on the two quantities. Although the surface continues to favor flexible polymers with smaller ℓp and bulky polymers with shorter ℓc, the effect of bulkiness is more pronounced. This imbalance can, under specific conditions, lead to anomalous surface segregation of the more extended polymer. For this to happen, the polymer must be bulkier and stiffer, with a stiffness that is sufficient to produce a larger R0 yet not so rigid as to reverse the surface affinity that favors bulky polymers.
Entropic surface segregation from athermal polymer blends: Polymer flexibility vs bulkiness
10.1063/5.0087587
The Journal of Chemical Physics
20220509T10:28:01Z
© 2022 Author(s).
M. W. Matsen

The rheology of confined colloidal hard disks
https://aip.scitation.org/doi/10.1063/5.0087444?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>Colloids may be treated as “big atoms” so that they are good models for atomic and molecular systems. Colloidal hard disks are, therefore, good models for 2d materials, and although their phase behavior is well characterized, rheology has received relatively little attention. Here, we exploit a novel, particleresolved, experimental setup and complementary computer simulations to measure the shear rheology of quasiharddisk colloids in extreme confinement. In particular, we confine quasi2d hard disks in a circular “corral” comprised of 27 particles held in optical traps. Confinement and shear suppress hexagonal ordering that would occur in the bulk and create a layered fluid. We measure the rheology of our system by balancing drag and driving forces on each layer. Given the extreme confinement, it is remarkable that our system exhibits rheological behavior very similar to unconfined 2d and 3d hard particle systems, characterized by a dynamic yield stress and shearthinning of comparable magnitude. By quantifying particle motion perpendicular to shear, we show that particles become more tightly confined to their layers with no concomitant increase in density upon increasing the shear rate. Shear thinning is, therefore, a consequence of a reduction in dissipation due to weakening in interactions between layers as the shear rate increases. We reproduce our experiments with Brownian dynamics simulations with Hydrodynamic Interactions (HI) included at the level of the Rotne–Prager tensor. That the inclusion of HI is necessary to reproduce our experiments is evidence of their importance in transmission of momentum through the system.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>Colloids may be treated as “big atoms” so that they are good models for atomic and molecular systems. Colloidal hard disks are, therefore, good models for 2d materials, and although their phase behavior is well characterized, rheology has received relatively little attention. Here, we exploit a novel, particleresolved, experimental setup and complementary computer simulations to measure the shear rheology of quasiharddisk colloids in extreme confinement. In particular, we confine quasi2d hard disks in a circular “corral” comprised of 27 particles held in optical traps. Confinement and shear suppress hexagonal ordering that would occur in the bulk and create a layered fluid. We measure the rheology of our system by balancing drag and driving forces on each layer. Given the extreme confinement, it is remarkable that our system exhibits rheological behavior very similar to unconfined 2d and 3d hard particle systems, characterized by a dynamic yield stress and shearthinning of comparable magnitude. By quantifying particle motion perpendicular to shear, we show that particles become more tightly confined to their layers with no concomitant increase in density upon increasing the shear rate. Shear thinning is, therefore, a consequence of a reduction in dissipation due to weakening in interactions between layers as the shear rate increases. We reproduce our experiments with Brownian dynamics simulations with Hydrodynamic Interactions (HI) included at the level of the Rotne–Prager tensor. That the inclusion of HI is necessary to reproduce our experiments is evidence of their importance in transmission of momentum through the system.
The rheology of confined colloidal hard disks
10.1063/5.0087444
The Journal of Chemical Physics
20220509T10:28:03Z
© 2022 Author(s).
Ian Williams
Erdal C. Oğuz
Hartmut Löwen
Wilson C. K. Poon
C. Patrick Royall

Information flow and allosteric communication in proteins
https://aip.scitation.org/doi/10.1063/5.0088522?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>Based on Schreiber’s work on transfer entropy, a molecular theory of nonlinear information transfer between residue pairs in proteins is developed. The joint distribution function for residue fluctuations required by the theory is expressed in terms of tensor Hermite polynomials that conveniently separate harmonic and nonlinear contributions to information transfer. The harmonic part of information transfer is expressed as the difference between time dependent and independent mutual information. Third order nonlinearities are discussed in detail. The amount and speed of information transfer between residues, which are important for understanding allosteric activity in proteins, are discussed. Mutual information between two residues is commonly used for information transfer. While mutual information shows the maximum amount of information that may be transferred between two residues, it does not explain the actual amount of transfer nor the transfer rate of information. For this, dynamic equations of the system are needed. The solution of the Langevin equation and molecular dynamics trajectories are used in the present work for this purpose. Allosteric communication in human NADdependent isocitrate dehydrogenase is studied as an example. Calculations show that several paths contribute collectively to information transfer. Important residues on these paths are identified. Time resolved information transfer between these residues, their amplitudes, and transfer rates, which are in agreement with time resolved ultraviolet resonance Raman measurements in general, are estimated. Peak values of calculated information transfer, ∼0.01–0.04 bits, are about two orders of magnitude smaller than the information content of residues. They are comparable to mutual information values, however. Estimated transfer rates are in the order of 1–20 megabits per second, and sustained transfer during the activity timespan of proteins may be significant. Information transfer from third order contributions is one to two orders of magnitude smaller than the harmonic terms, showing that harmonic analysis is a good approximation to information transfer.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>Based on Schreiber’s work on transfer entropy, a molecular theory of nonlinear information transfer between residue pairs in proteins is developed. The joint distribution function for residue fluctuations required by the theory is expressed in terms of tensor Hermite polynomials that conveniently separate harmonic and nonlinear contributions to information transfer. The harmonic part of information transfer is expressed as the difference between time dependent and independent mutual information. Third order nonlinearities are discussed in detail. The amount and speed of information transfer between residues, which are important for understanding allosteric activity in proteins, are discussed. Mutual information between two residues is commonly used for information transfer. While mutual information shows the maximum amount of information that may be transferred between two residues, it does not explain the actual amount of transfer nor the transfer rate of information. For this, dynamic equations of the system are needed. The solution of the Langevin equation and molecular dynamics trajectories are used in the present work for this purpose. Allosteric communication in human NADdependent isocitrate dehydrogenase is studied as an example. Calculations show that several paths contribute collectively to information transfer. Important residues on these paths are identified. Time resolved information transfer between these residues, their amplitudes, and transfer rates, which are in agreement with time resolved ultraviolet resonance Raman measurements in general, are estimated. Peak values of calculated information transfer, ∼0.01–0.04 bits, are about two orders of magnitude smaller than the information content of residues. They are comparable to mutual information values, however. Estimated transfer rates are in the order of 1–20 megabits per second, and sustained transfer during the activity timespan of proteins may be significant. Information transfer from third order contributions is one to two orders of magnitude smaller than the harmonic terms, showing that harmonic analysis is a good approximation to information transfer.
Information flow and allosteric communication in proteins
10.1063/5.0088522
The Journal of Chemical Physics
20220509T10:27:46Z
© 2022 Author(s).
Aysima Hacisuleyman
Burak Erman

Fluorographene with impurities as a biomimetic lightharvesting medium
https://aip.scitation.org/doi/10.1063/5.0089794?af=R&feed=mostrecent
The Journal of Chemical Physics, <a href="https://aip.scitation.org/toc/jcp/156/18">Volume 156, Issue 18</a>, May 2022. <br/>We investigate the prospect of using a twodimensional material, fluorographene, to mimic the lightharvesting function of natural photosynthetic antennas. We show by quantum chemical calculations that isles of graphene in a fluorographene sheet can act as quasimolecules similar to natural pigments from which the structures similar in function to photosynthetic antennas can be built. The graphene isles retain enough identity so that they can be used as building blocks to which intuitive design principles of natural photosynthetic antennas can be applied. We examine the excited state properties, stability, and interactions of these building blocks. Constraints put on the antenna structure by the twodimensionality of the material as well as the discrete nature of fluorographene sheet are studied. We construct a hypothetical energetic funnel out of two types of quasimolecules to show how a limited number of building blocks can be arranged to bridge the energy gap and spatial separation in excitation energy transfer. Energy transfer rates for a wide range of the system–environment interaction strengths are predicted. We conclude that conditions for the near unity quantum efficiency of energy transfer are likely to be fulfilled in fluorographene with the controlled arrangement of quasimolecules.
The Journal of Chemical Physics, Volume 156, Issue 18, May 2022. <br/>We investigate the prospect of using a twodimensional material, fluorographene, to mimic the lightharvesting function of natural photosynthetic antennas. We show by quantum chemical calculations that isles of graphene in a fluorographene sheet can act as quasimolecules similar to natural pigments from which the structures similar in function to photosynthetic antennas can be built. The graphene isles retain enough identity so that they can be used as building blocks to which intuitive design principles of natural photosynthetic antennas can be applied. We examine the excited state properties, stability, and interactions of these building blocks. Constraints put on the antenna structure by the twodimensionality of the material as well as the discrete nature of fluorographene sheet are studied. We construct a hypothetical energetic funnel out of two types of quasimolecules to show how a limited number of building blocks can be arranged to bridge the energy gap and spatial separation in excitation energy transfer. Energy transfer rates for a wide range of the system–environment interaction strengths are predicted. We conclude that conditions for the near unity quantum efficiency of energy transfer are likely to be fulfilled in fluorographene with the controlled arrangement of quasimolecules.
Fluorographene with impurities as a biomimetic lightharvesting medium
10.1063/5.0089794
The Journal of Chemical Physics
20220512T11:59:27Z
© 2022 Author(s).
Vladislav Sláma
Sayeh Rajabi
Tomáš Mančal