1
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Carter-Fenk K, Liu M, Pujal L, Loipersberger M, Tsanai M, Vernon RM, Forman-Kay JD, Head-Gordon M, Heidar-Zadeh F, Head-Gordon T. The Energetic Origins of Pi-Pi Contacts in Proteins. J Am Chem Soc 2023; 145. [PMID: 37917924 PMCID: PMC10655088 DOI: 10.1021/jacs.3c09198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023]
Abstract
Accurate potential energy models of proteins must describe the many different types of noncovalent interactions that contribute to a protein's stability and structure. Pi-pi contacts are ubiquitous structural motifs in all proteins, occurring between aromatic and nonaromatic residues and play a nontrivial role in protein folding and in the formation of biomolecular condensates. Guided by a geometric criterion for isolating pi-pi contacts from classical molecular dynamics simulations of proteins, we use quantum mechanical energy decomposition analysis to determine the molecular interactions that stabilize different pi-pi contact motifs. We find that neutral pi-pi interactions in proteins are dominated by Pauli repulsion and London dispersion rather than repulsive quadrupole electrostatics, which is central to the textbook Hunter-Sanders model. This results in a notable lack of variability in the interaction profiles of neutral pi-pi contacts even with extreme changes in the dielectric medium, explaining the prevalence of pi-stacked arrangements in and between proteins. We also find interactions involving pi-containing anions and cations to be extremely malleable, interacting like neutral pi-pi contacts in polar media and like typical ion-pi interactions in nonpolar environments. Like-charged pairs such as arginine-arginine contacts are particularly sensitive to the polarity of their immediate surroundings and exhibit canonical pi-pi stacking behavior only if the interaction is mediated by environmental effects, such as aqueous solvation.
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Affiliation(s)
- Kevin Carter-Fenk
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Meili Liu
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Leila Pujal
- Department
of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Matthias Loipersberger
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Maria Tsanai
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Robert M. Vernon
- Molecular
Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Julie D. Forman-Kay
- Molecular
Medicine Program, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
- Department
of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Martin Head-Gordon
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Farnaz Heidar-Zadeh
- Department
of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
- Center
for Molecular Modeling (CMM), Ghent University, 9052 Zwijnaarde, Belgium
| | - Teresa Head-Gordon
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California, Berkeley, California 94720, United States
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2
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Heindel JP, Herman KM, Xantheas SS. Many-Body Effects in Aqueous Systems: Synergies Between Interaction Analysis Techniques and Force Field Development. Annu Rev Phys Chem 2023; 74:337-360. [PMID: 37093659 DOI: 10.1146/annurev-physchem-062422-023532] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Interaction analysis techniques, including the many-body expansion (MBE), symmetry-adapted perturbation theory, and energy decomposition analysis, allow for an intuitive understanding of complex molecular interactions. We review these methods by first providing a historical context for the study of many-body interactions and discussing how nonadditivities emerge from Hamiltonians containing strictly pairwise-additive interactions. We then elaborate on the synergy between these interaction analysis techniques and the development of advanced force fields aimed at accurately reproducing the Born-Oppenheimer potential energy surface. In particular, we focus on ab initio-based force fields that aim to explicitly reproduce many-body terms and are fitted to high-level electronic structure results. These force fields generally incorporate many-body effects through (a) parameterization of distributed multipoles, (b) explicit fitting of the MBE, (c) inclusion of many-atom features in a neural network, and (d) coarse-graining of many-body terms into an effective two-body term. We also discuss the emerging use of the MBE to improve the accuracy and speed of ab initio molecular dynamics.
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Affiliation(s)
- Joseph P Heindel
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Kristina M Herman
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Sotiris S Xantheas
- Department of Chemistry, University of Washington, Seattle, Washington, USA
- Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, Richland, Washington, USA; ,
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3
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Aldossary A, Gimferrer M, Mao Y, Hao H, Das AK, Salvador P, Head-Gordon T, Head-Gordon M. Force Decomposition Analysis: A Method to Decompose Intermolecular Forces into Physically Relevant Component Contributions. J Phys Chem A 2023; 127:1760-1774. [PMID: 36753558 DOI: 10.1021/acs.jpca.2c08061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Computational quantum chemistry can be more than just numerical experiments when methods are specifically adapted to investigate chemical concepts. One important example is the development of energy decomposition analysis (EDA) to reveal the physical driving forces behind intermolecular interactions. In EDA, typically the interaction energy from a good-quality density functional theory (DFT) calculation is decomposed into multiple additive components that unveil permanent and induced electrostatics, Pauli repulsion, dispersion, and charge-transfer contributions to noncovalent interactions. Herein, we formulate, implement, and investigate decomposing the forces associated with intermolecular interactions into the same components. The resulting force decomposition analysis (FDA) is potentially useful as a complement to the EDA to understand chemistry, while also providing far more information than an EDA for data analysis purposes such as training physics-based force fields. We apply the FDA based on absolutely localized molecular orbitals (ALMOs) to analyze interactions of water with sodium and chloride ions as well as in the water dimer. We also analyze the forces responsible for geometric changes in carbon dioxide upon adsorption onto (and activation by) gold and silver anions. We also investigate how the force components of an EDA-based force field for water clusters, namely MB-UCB, compare to those from force decomposition analysis.
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Affiliation(s)
- Abdulrahman Aldossary
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
| | - Martí Gimferrer
- Institut de Química Computacional i Catàlsi and Departament de Química, Universitat de Girona, 17003 Girona, Catalonia Spain
| | - Yuezhi Mao
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182, United States
| | - Hongxia Hao
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
| | - Akshaya K Das
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
| | - Pedro Salvador
- Institut de Química Computacional i Catàlsi and Departament de Química, Universitat de Girona, 17003 Girona, Catalonia Spain
| | - Teresa Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
| | - Martin Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley California 94720, United States
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4
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Kumar A, DeGregorio N, Ricard T, Iyengar SS. Graph-Theoretic Molecular Fragmentation for Potential Surfaces Leads Naturally to a Tensor Network Form and Allows Accurate and Efficient Quantum Nuclear Dynamics. J Chem Theory Comput 2022; 18:7243-7259. [PMID: 36332133 DOI: 10.1021/acs.jctc.2c00484] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Molecular fragmentation methods have revolutionized quantum chemistry. Here, we use a graph-theoretically generated molecular fragmentation method, to obtain accurate and efficient representations for multidimensional potential energy surfaces and the quantum time-evolution operator, which plays a critical role in quantum chemical dynamics. In doing so, we find that the graph-theoretic fragmentation approach naturally reduces the potential portion of the time-evolution operator into a tensor network that contains a stream of coupled lower-dimensional propagation steps to potentially achieve quantum dynamics with reduced complexity. Furthermore, the fragmentation approach used here has previously been shown to allow accurate and efficient computation of post-Hartree-Fock electronic potential energy surfaces, which in many cases has been shown to be at density functional theory cost. Thus, by combining the advantages of molecular fragmentation with the tensor network formalism, the approach yields an on-the-fly quantum dynamics scheme where both the electronic potential calculation and nuclear propagation portion are enormously simplified through a single stroke. The method is demonstrated by computing approximations to the propagator and to potential surfaces for a set of coupled nuclear dimensions within a protonated water wire problem exhibiting the Grotthuss mechanism of proton transport. In all cases, our approach has been shown to reduce the complexity of representing the quantum propagator, and by extension action of the propagator on an initial wavepacket, by several orders, with minimal loss in accuracy.
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Affiliation(s)
- Anup Kumar
- Department of Chemistry, and the Indiana University Quantum Science and Engineering Center (IU-QSEC), Indiana University, Bloomington, Indiana 47405, United States
| | - Nicole DeGregorio
- Department of Chemistry, and the Indiana University Quantum Science and Engineering Center (IU-QSEC), Indiana University, Bloomington, Indiana 47405, United States
| | - Timothy Ricard
- Department of Chemistry, and the Indiana University Quantum Science and Engineering Center (IU-QSEC), Indiana University, Bloomington, Indiana 47405, United States
| | - Srinivasan S Iyengar
- Department of Chemistry, and the Indiana University Quantum Science and Engineering Center (IU-QSEC), Indiana University, Bloomington, Indiana 47405, United States
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5
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Qu X, Dong L, Si Y, Zhao Y, Wang Q, Su P, Wang B. Reliable Prediction of the Protein-Ligand Binding Affinity Using a Charge Penetration Corrected AMOEBA Force Field: A Case Study of Drug Resistance Mutations in Abl Kinase. J Chem Theory Comput 2022; 18:1692-1700. [PMID: 35107298 DOI: 10.1021/acs.jctc.1c01005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein mutations that directly impair drug binding are related to therapeutic resistance, and accurate prediction of their impact on drug binding would benefit drug design and clinical practice. Here, we have developed a scoring strategy that predicts the effect of the mutations on the protein-ligand binding affinity. In view of the critical importance of electrostatics in protein-ligand interactions, the charge penetration corrected AMOEBA force field (AMOEBA_CP model) was employed to improve the accuracy of the calculated electrostatic energy. We calculated the electrostatic energy using an energy decomposition analysis scheme based on the generalized Kohn-Sham (GKS-EDA). The AMOEBA_CP model was validated by a protein-fragment-ligand complex data set (Abl236) constructed from the co-crystal structures of the cancer target Abl kinase with six inhibitors. To predict ligand binding affinity changes upon protein mutation of Abl kinase, we used sampling protocol with multistep simulated annealing to search conformations of mutant proteins. The scoring strategy based on AMOEBA_CP model has achieved considerable performance in predicting resistance for 8 kinase inhibitors across 144 clinically identified point mutations. Overall, this study illustrates that the AMOEBA_CP model, which accurately treats electrostatics through penetration correction, enables the accurate prediction of the mutation-induced variation of protein-ligand binding affinity.
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Affiliation(s)
- Xiaoyang Qu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Lina Dong
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Yubing Si
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Yuan Zhao
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, P. R. China
| | - Qiantao Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, P. R. China
| | - Peifeng Su
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
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6
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Rackers JA, Silva RR, Wang Z, Ponder JW. Polarizable Water Potential Derived from a Model Electron Density. J Chem Theory Comput 2021; 17:7056-7084. [PMID: 34699197 DOI: 10.1021/acs.jctc.1c00628] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new empirical potential for efficient, large scale molecular dynamics simulation of water is presented. The HIPPO (Hydrogen-like Intermolecular Polarizable POtential) force field is based upon the model electron density of a hydrogen-like atom. This framework is used to derive and parametrize individual terms describing charge penetration damped permanent electrostatics, damped polarization, charge transfer, anisotropic Pauli repulsion, and damped dispersion interactions. Initial parameter values were fit to Symmetry Adapted Perturbation Theory (SAPT) energy components for ten water dimer configurations, as well as the radial and angular dependence of the canonical dimer. The SAPT-based parameters were then systematically refined to extend the treatment to water bulk phases. The final HIPPO water model provides a balanced representation of a wide variety of properties of gas phase clusters, liquid water, and ice polymorphs, across a range of temperatures and pressures. This water potential yields a rationalization of water structure, dynamics, and thermodynamics explicitly correlated with an ab initio energy decomposition, while providing a level of accuracy comparable or superior to previous polarizable atomic multipole force fields. The HIPPO water model serves as a cornerstone around which similarly detailed physics-based models can be developed for additional molecular species.
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Affiliation(s)
- Joshua A Rackers
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States.,Center for Computing Research, Sandia National Laboratories, Albuquerque, New Mexico 87123, United States
| | - Roseane R Silva
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Zhi Wang
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Jay W Ponder
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States.,Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
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7
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Kumar A, DeGregorio N, Iyengar SS. Graph-Theory-Based Molecular Fragmentation for Efficient and Accurate Potential Surface Calculations in Multiple Dimensions. J Chem Theory Comput 2021; 17:6671-6690. [PMID: 34623129 DOI: 10.1021/acs.jctc.1c00065] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We present a multitopology molecular fragmentation approach, based on graph theory, to calculate multidimensional potential energy surfaces in agreement with post-Hartree-Fock levels of theory but at the density functional theory cost. A molecular assembly is coarse-grained into a set of graph-theoretic nodes that are then connected with edges to represent a collection of locally interacting subsystems up to an arbitrary order. Each of the subsystems is treated at two levels of electronic structure theory, the result being used to construct many-body expansions that are embedded within an ONIOM scheme. These expansions converge rapidly with the many-body order (or graphical rank) of subsystems and capture many-body interactions accurately and efficiently. However, multiple graphs, and hence multiple fragmentation topologies, may be defined in molecular configuration space that may arise during conformational sampling or from reactive, bond breaking and bond formation, events. Obtaining the resultant potential surfaces is an exponential scaling proposition, given the number of electronic structure computations needed. We utilize a family of graph-theoretic representations within a variational scheme to obtain multidimensional potential surfaces at a reduced cost. The fast convergence of the graph-theoretic expansion with increasing order of many-body interactions alleviates the exponential scaling cost for computing potential surfaces, with the need to only use molecular fragments that contain a fewer number of quantum nuclear degrees of freedom compared to the full system. This is because the dimensionality of the conformational space sampled by the fragment subsystems is much smaller than the full molecular configurational space. Additionally, we also introduce a multidimensional clustering algorithm, based on physically defined criteria, to reduce the number of energy calculations by orders of magnitude. The molecular systems benchmarked include coupled proton motion in protonated water wires. The potential energy surfaces and multidimensional nuclear eigenstates obtained are shown to be in very good agreement with those from explicit post-Hartree-Fock calculations that become prohibitive as the number of quantum nuclear dimensions grows. The developments here provide a rigorous and efficient alternative to this important chemical physics problem.
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Affiliation(s)
- Anup Kumar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Nicole DeGregorio
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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8
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Heindel JP, Xantheas SS. Molecular Dynamics Driven by the Many-Body Expansion (MBE-MD). J Chem Theory Comput 2021; 17:7341-7352. [PMID: 34723531 DOI: 10.1021/acs.jctc.1c00780] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a protocol for classical and nuclear quantum dynamics, in which the energies and forces are generated by the many-body expansion (MBE), and apply it to water clusters using the TTM2.1-F and MB-Pol interaction potentials at various temperatures. We carry out MBE-molecular dynamics (MD) classical and nuclear quantum dynamical simulations, in which the energies and forces of the full system are approximated by the two-, three-, and four-body terms of the MBE, and compare the average potential and the vibrational density of states with the full simulation, i.e., the one for which no MBE is used. Our results indicate that the thermally averaged potential energy from the MBE up to the four-body term converges with near-identical behavior to the one from the full simulation. The three-body makes a substantial contribution (∼20%) to the energy, whereas the four-body is necessary for obtaining quantitatively accurate energetics and forces, albeit making a small contribution to each (∼2%). We further show that the harmonic frequencies are reproduced to within a few wavenumbers (cm-1) at the four-body level and that the slowest modes to converge with the MBE rank are those involving the strongest hydrogen bonds. Anharmonicity exacerbates this effect, so that a four-body description of the energies and forces is needed to achieve accurate anharmonic vibrational frequencies in the hydrogen-bonded OH-stretching region. We also discuss the asymptotic scaling of the MBE-MD protocol with respect to the cost of the underlying potential energy evaluation, suggesting that electronic structure methods that scale at least as N4, N being the size of the system, are needed to result in savings over the traditional full MD simulation. We anticipate that the MBE-MD protocol can evolve into a powerful and practical method, which will allow for highly accurate ab initio MD simulations on a much broader range of molecular systems than can be currently handled.
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Affiliation(s)
- Joseph P Heindel
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Sotiris S Xantheas
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States.,Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States
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9
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Abstract
Cooperative or nonadditive effects contribute to the pairwise noncovalent interaction of two molecules in a cluster or the condensed phase in ways that depend on the specific arrangements and interactions of the other surrounding molecules that constitute their environment. General expressions for an effective two-body interaction are presented, which are correct to increasing orders in the many-body expansion. The simplest result, correct through third order, requires only seven individual calculations, in contrast to a linear number of three-body contributions. Two applications are presented. First, an error analysis is performed on a model (H2O)8 cluster which completes the first solvation shell of a central water-water hydrogen bond. Energy decomposition analysis is performed to show that the largest effects of cooperativity on the central hydrogen bond arise from electrical polarization. Second, the nature of cooperative effects on proton transfer in an HCl + (H2O)4 cluster is characterized.
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Affiliation(s)
- Cameron Mackie
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Alexander Zech
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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10
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Epifanovsky E, Gilbert ATB, Feng X, Lee J, Mao Y, Mardirossian N, Pokhilko P, White AF, Coons MP, Dempwolff AL, Gan Z, Hait D, Horn PR, Jacobson LD, Kaliman I, Kussmann J, Lange AW, Lao KU, Levine DS, Liu J, McKenzie SC, Morrison AF, Nanda KD, Plasser F, Rehn DR, Vidal ML, You ZQ, Zhu Y, Alam B, Albrecht BJ, Aldossary A, Alguire E, Andersen JH, Athavale V, Barton D, Begam K, Behn A, Bellonzi N, Bernard YA, Berquist EJ, Burton HGA, Carreras A, Carter-Fenk K, Chakraborty R, Chien AD, Closser KD, Cofer-Shabica V, Dasgupta S, de Wergifosse M, Deng J, Diedenhofen M, Do H, Ehlert S, Fang PT, Fatehi S, Feng Q, Friedhoff T, Gayvert J, Ge Q, Gidofalvi G, Goldey M, Gomes J, González-Espinoza CE, Gulania S, Gunina AO, Hanson-Heine MWD, Harbach PHP, Hauser A, Herbst MF, Hernández Vera M, Hodecker M, Holden ZC, Houck S, Huang X, Hui K, Huynh BC, Ivanov M, Jász Á, Ji H, Jiang H, Kaduk B, Kähler S, Khistyaev K, Kim J, Kis G, Klunzinger P, Koczor-Benda Z, Koh JH, Kosenkov D, Koulias L, Kowalczyk T, Krauter CM, Kue K, Kunitsa A, Kus T, Ladjánszki I, Landau A, Lawler KV, Lefrancois D, Lehtola S, Li RR, Li YP, Liang J, Liebenthal M, Lin HH, Lin YS, Liu F, Liu KY, Loipersberger M, Luenser A, Manjanath A, Manohar P, Mansoor E, Manzer SF, Mao SP, Marenich AV, Markovich T, Mason S, Maurer SA, McLaughlin PF, Menger MFSJ, Mewes JM, Mewes SA, Morgante P, Mullinax JW, Oosterbaan KJ, Paran G, Paul AC, Paul SK, Pavošević F, Pei Z, Prager S, Proynov EI, Rák Á, Ramos-Cordoba E, Rana B, Rask AE, Rettig A, Richard RM, Rob F, Rossomme E, Scheele T, Scheurer M, Schneider M, Sergueev N, Sharada SM, Skomorowski W, Small DW, Stein CJ, Su YC, Sundstrom EJ, Tao Z, Thirman J, Tornai GJ, Tsuchimochi T, Tubman NM, Veccham SP, Vydrov O, Wenzel J, Witte J, Yamada A, Yao K, Yeganeh S, Yost SR, Zech A, Zhang IY, Zhang X, Zhang Y, Zuev D, Aspuru-Guzik A, Bell AT, Besley NA, Bravaya KB, Brooks BR, Casanova D, Chai JD, Coriani S, Cramer CJ, Cserey G, DePrince AE, DiStasio RA, Dreuw A, Dunietz BD, Furlani TR, Goddard WA, Hammes-Schiffer S, Head-Gordon T, Hehre WJ, Hsu CP, Jagau TC, Jung Y, Klamt A, Kong J, Lambrecht DS, Liang W, Mayhall NJ, McCurdy CW, Neaton JB, Ochsenfeld C, Parkhill JA, Peverati R, Rassolov VA, Shao Y, Slipchenko LV, Stauch T, Steele RP, Subotnik JE, Thom AJW, Tkatchenko A, Truhlar DG, Van Voorhis T, Wesolowski TA, Whaley KB, Woodcock HL, Zimmerman PM, Faraji S, Gill PMW, Head-Gordon M, Herbert JM, Krylov AI. Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package. J Chem Phys 2021; 155:084801. [PMID: 34470363 PMCID: PMC9984241 DOI: 10.1063/5.0055522] [Citation(s) in RCA: 480] [Impact Index Per Article: 160.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.
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Affiliation(s)
- Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Joonho Lee
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yuezhi Mao
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Pavel Pokhilko
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alec F. White
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marc P. Coons
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Adrian L. Dempwolff
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zhengting Gan
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Diptarka Hait
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Paul R. Horn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Leif D. Jacobson
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Jörg Kussmann
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Adrian W. Lange
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ka Un Lao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Daniel S. Levine
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Simon C. McKenzie
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Kaushik D. Nanda
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Dirk R. Rehn
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Marta L. Vidal
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | - Ying Zhu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Bushra Alam
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Benjamin J. Albrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | - Ethan Alguire
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Josefine H. Andersen
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | - Vishikh Athavale
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Dennis Barton
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Khadiza Begam
- Department of Physics, Kent State University, Kent, Ohio 44242, USA
| | - Andrew Behn
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Nicole Bellonzi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yves A. Bernard
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Hugh G. A. Burton
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Abel Carreras
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | - Kevin Carter-Fenk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Alan D. Chien
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Vale Cofer-Shabica
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Marc de Wergifosse
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jia Deng
- Research School of Chemistry, Australian National University, Canberra, Australia
| | | | - Hainam Do
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Beringstr. 4, 53115 Bonn, Germany
| | - Po-Tung Fang
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Qingguo Feng
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Triet Friedhoff
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - James Gayvert
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Qinghui Ge
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gergely Gidofalvi
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, Washington 99258, USA
| | - Matthew Goldey
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Joe Gomes
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Sahil Gulania
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Anastasia O. Gunina
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Phillip H. P. Harbach
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Andreas Hauser
- Institute of Experimental Physics, Graz University of Technology, Graz, Austria
| | | | - Mario Hernández Vera
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Manuel Hodecker
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Zachary C. Holden
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Shannon Houck
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Xunkun Huang
- Department of Chemistry, Xiamen University, Xiamen 361005, China
| | - Kerwin Hui
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Bang C. Huynh
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Maxim Ivanov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Ádám Jász
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Hyunjun Ji
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hanjie Jiang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Benjamin Kaduk
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sven Kähler
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Kirill Khistyaev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Jaehoon Kim
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Gergely Kis
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | | | - Zsuzsanna Koczor-Benda
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Joong Hoon Koh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Dimitri Kosenkov
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Laura Koulias
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | | | - Caroline M. Krauter
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Karl Kue
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Alexander Kunitsa
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Thomas Kus
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | | | - Arie Landau
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Keith V. Lawler
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Daniel Lefrancois
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | | | - Run R. Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Yi-Pei Li
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Jiashu Liang
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Marcus Liebenthal
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Hung-Hsuan Lin
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - You-Sheng Lin
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Fenglai Liu
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | | | - Arne Luenser
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Aaditya Manjanath
- Institute of Chemistry, Academia Sinica, 128, Academia Road Section 2, Nangang District, Taipei 11529, Taiwan
| | - Prashant Manohar
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Erum Mansoor
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Sam F. Manzer
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Shan-Ping Mao
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | | | - Thomas Markovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Stephen Mason
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Simon A. Maurer
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - Peter F. McLaughlin
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | | | - Jan-Michael Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Stefanie A. Mewes
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Pierpaolo Morgante
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - J. Wayne Mullinax
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | | | | | - Alexander C. Paul
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Suranjan K. Paul
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fabijan Pavošević
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Zheng Pei
- School of Electrical and Computer Engineering, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Stefan Prager
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Emil I. Proynov
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Ádám Rák
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Eloy Ramos-Cordoba
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Bhaskar Rana
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Alan E. Rask
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Adam Rettig
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Ryan M. Richard
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Fazle Rob
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Elliot Rossomme
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Tarek Scheele
- Institute for Physical and Theoretical Chemistry, University of Bremen, Bremen, Germany
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Matthias Schneider
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Nickolai Sergueev
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Shaama M. Sharada
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Wojciech Skomorowski
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - David W. Small
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Christopher J. Stein
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yu-Chuan Su
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Eric J. Sundstrom
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Zhen Tao
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Jonathan Thirman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Gábor J. Tornai
- Stream Novation Ltd., Práter utca 50/a, H-1083 Budapest, Hungary
| | - Takashi Tsuchimochi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Norm M. Tubman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - Oleg Vydrov
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jan Wenzel
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Jon Witte
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Atsushi Yamada
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Kun Yao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Sina Yeganeh
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Shane R. Yost
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Alexander Zech
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Igor Ying Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xing Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Yu Zhang
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Dmitry Zuev
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Alán Aspuru-Guzik
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Alexis T. Bell
- Department of Chemical Engineering, University of California, Berkeley, California 94720, USA
| | - Nicholas A. Besley
- School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Ksenia B. Bravaya
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Bernard R. Brooks
- Laboratory of Computational Biophysics, National Institute of Health, Bethesda, Maryland 20892, USA
| | - David Casanova
- Donostia International Physics Center, 20080 Donostia, Euskadi, Spain
| | | | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kgs Lyngby, Denmark
| | | | | | - A. Eugene DePrince
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Robert A. DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Barry D. Dunietz
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44240, USA
| | - Thomas R. Furlani
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - William A. Goddard
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, USA
| | | | - Teresa Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | | | | | | | - Yousung Jung
- Graduate School of Energy, Environment, Water and Sustainability (EEWS), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Andreas Klamt
- COSMOlogic GmbH & Co. KG, Imbacher Weg 46, D-51379 Leverkusen, Germany
| | - Jing Kong
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Daniel S. Lambrecht
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | | | | | - C. William McCurdy
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Jeffrey B. Neaton
- Department of Physics, University of California, Berkeley, California 94720, USA
| | - Christian Ochsenfeld
- Department of Chemistry, Ludwig Maximilian University, Butenandtstr. 7, D-81377 München, Germany
| | - John A. Parkhill
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Roberto Peverati
- Department of Chemistry, Florida Institute of Technology, Melbourne, Florida 32901, USA
| | - Vitaly A. Rassolov
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
| | | | | | | | - Ryan P. Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Joseph E. Subotnik
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Alex J. W. Thom
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Donald G. Truhlar
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tomasz A. Wesolowski
- Department of Physical Chemistry, University of Geneva, 30, Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - K. Birgitta Whaley
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, USA
| | - Paul M. Zimmerman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, 9774AG Groningen, The Netherlands
| | | | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA,Author to whom correspondence should be addressed:
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11
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Abraham V, Mayhall NJ. Cluster many-body expansion: A many-body expansion of the electron correlation energy about a cluster mean field reference. J Chem Phys 2021; 155:054101. [PMID: 34364343 DOI: 10.1063/5.0057752] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The many-body expansion (MBE) is an efficient tool that has a long history of use for calculating interaction energies, binding energies, lattice energies, and so on. In the past, applications of MBE to correlation energy have been unfeasible for large systems, but recent improvements to computing resources have sparked renewed interest in capturing the correlation energy using the generalized nth order Bethe-Goldstone equation. In this work, we extend this approach, originally proposed for a Slater determinant, to a tensor product state (TPS) based wavefunction. By partitioning the active space into smaller orbital clusters, our approach starts from a cluster mean field reference TPS configuration and includes the correlation contribution of the excited TPSs using the MBE. This method, named cluster MBE (cMBE), improves the convergence of MBE at lower orders compared to directly doing a block-based MBE from a RHF reference. We present numerical results for strongly correlated systems, such as the one- and two-dimensional Hubbard models and the chromium dimer. The performance of the cMBE method is also tested by partitioning the extended π space of several large π-conjugated systems, including a graphene nano-sheet with a very large active space of 114 electrons in 114 orbitals, which would require 1066 determinants for the exact FCI solution.
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Affiliation(s)
- Vibin Abraham
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24060, USA
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12
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Błasiak B, Bednarska JD, Chołuj M, Góra RW, Bartkowiak W. Ab initio effective one-electron potential operators: Applications for charge-transfer energy in effective fragment potentials. J Comput Chem 2021; 42:398-411. [PMID: 33349929 DOI: 10.1002/jcc.26462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 12/19/2022]
Abstract
The concept of effective one-electron potentials (EOPs) has proven to be extremely useful in efficient description of electronic structure of chemical systems, especially extended molecular aggregates such as interacting molecules in condensed phases. Here, a general method for EOP-based elimination of electron repulsion integrals is presented, that is tuned toward the fragment-based calculation methodologies such as the second generation of the effective fragment potentials (EFP2) method. Two general types of the EOP operator matrix elements are distinguished and treated either via the distributed multipole expansion or the extended density fitting (DF) schemes developed in this work. The EOP technique is then applied to reduce the high computational costs of the effective fragment charge-transfer (CT) terms being the bottleneck of EFP2 potentials. The alternative EOP-based CT energy model is proposed, derived within the framework of intermolecular perturbation theory with Hartree-Fock noninteracting reference wavefunctions, compatible with the original EFP2 formulation. It is found that the computational cost of the EFP2 total interaction energy calculation can be reduced by up to 38 times when using the EOP-based formulation of CT energy, as compared to the original EFP2 scheme, without compromising the accuracy for a wide range of weakly interacting neutral and ionic molecular fragments. The proposed model can thus be used routinely within the EFP2 framework.
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Affiliation(s)
- Bartosz Błasiak
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Joanna D Bednarska
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Marta Chołuj
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Robert W Góra
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Wojciech Bartkowiak
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
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13
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Mao Y, Loipersberger M, Horn PR, Das A, Demerdash O, Levine DS, Prasad Veccham S, Head-Gordon T, Head-Gordon M. From Intermolecular Interaction Energies and Observable Shifts to Component Contributions and Back Again: A Tale of Variational Energy Decomposition Analysis. Annu Rev Phys Chem 2021; 72:641-666. [PMID: 33636998 DOI: 10.1146/annurev-physchem-090419-115149] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Quantum chemistry in the form of density functional theory (DFT) calculations is a powerful numerical experiment for predicting intermolecular interaction energies. However, no chemical insight is gained in this way beyond predictions of observables. Energy decomposition analysis (EDA) can quantitatively bridge this gap by providing values for the chemical drivers of the interactions, such as permanent electrostatics, Pauli repulsion, dispersion, and charge transfer. These energetic contributions are identified by performing DFT calculations with constraints that disable components of the interaction. This review describes the second-generation version of the absolutely localized molecular orbital EDA (ALMO-EDA-II). The effects of different physical contributions on changes in observables such as structure and vibrational frequencies upon complex formation are characterized via the adiabatic EDA. Example applications include red- versus blue-shifting hydrogen bonds; the bonding and frequency shifts of CO, N2, and BF bound to a [Ru(II)(NH3)5]2 + moiety; and the nature of the strongly bound complexes between pyridine and the benzene and naphthalene radical cations. Additionally, the use of ALMO-EDA-II to benchmark and guide the development of advanced force fields for molecular simulation is illustrated with the recent, very promising, MB-UCB potential.
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Affiliation(s)
- Yuezhi Mao
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Matthias Loipersberger
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Paul R Horn
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Akshaya Das
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA; .,Department of Bioengineering and Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
| | - Omar Demerdash
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA; .,Department of Bioengineering and Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
| | - Daniel S Levine
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Srimukh Prasad Veccham
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
| | - Teresa Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA; .,Department of Bioengineering and Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA;
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14
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Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions. Nat Commun 2021; 12:1085. [PMID: 33597515 PMCID: PMC7889641 DOI: 10.1038/s41467-021-21181-9] [Citation(s) in RCA: 220] [Impact Index Per Article: 73.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 01/08/2021] [Indexed: 01/31/2023] Open
Abstract
Liquid-liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.
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15
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Krainer G, Welsh TJ, Joseph JA, Espinosa JR, Wittmann S, de Csilléry E, Sridhar A, Toprakcioglu Z, Gudiškytė G, Czekalska MA, Arter WE, Guillén-Boixet J, Franzmann TM, Qamar S, George-Hyslop PS, Hyman AA, Collepardo-Guevara R, Alberti S, Knowles TPJ. Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions. Nat Commun 2021; 12:1085. [PMID: 33597515 DOI: 10.1101/2020.05.04.076299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 01/08/2021] [Indexed: 05/26/2023] Open
Abstract
Liquid-liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.
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Affiliation(s)
- Georg Krainer
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Timothy J Welsh
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Jerelle A Joseph
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Jorge R Espinosa
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Sina Wittmann
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - Ella de Csilléry
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Akshay Sridhar
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Zenon Toprakcioglu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Giedre Gudiškytė
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Magdalena A Czekalska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka, 44/52 01-224, Warsaw, Poland
| | - William E Arter
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Jordina Guillén-Boixet
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - Titus M Franzmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - Seema Qamar
- Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Peter St George-Hyslop
- Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
- Division of Neurology, Department of Medicine, University of Toronto and University Health Network, Toronto, Ontario, Canada.
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.
| | - Rosana Collepardo-Guevara
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK.
- Department of Genetics, University of Cambridge, Cambridge, UK.
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
| | - Simon Alberti
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany.
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, UK.
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16
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Kwapien K, Gavara L, Docquier J, Berthomieu D, Hernandez J, Gresh N. Intermolecular interactions of the extended recognition site of
VIM
‐2
metallo‐β‐lactamase
with 1,2,4‐triazole‐3‐thione inhibitors. Validations of a polarizable molecular mechanics potential by ab initio
QC. J Comput Chem 2020; 42:86-106. [DOI: 10.1002/jcc.26437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Karolina Kwapien
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques Université de Paris UMR 8601 Paris France
- Laboratoire de Chimie Théorique Paris France
- Institut Charles Gerhardt, UMR 5253, CNRS, Université de Montpellier, ENSCM Montpellier France
| | - Laurent Gavara
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM, Faculté de Pharmacie Montpellier France
| | | | - Dorothée Berthomieu
- Institut Charles Gerhardt, UMR 5253, CNRS, Université de Montpellier, ENSCM Montpellier France
| | - Jean‐François Hernandez
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM, Faculté de Pharmacie Montpellier France
| | - Nohad Gresh
- Laboratoire de Chimie Théorique Paris France
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17
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Heindel JP, Xantheas SS. The Many-Body Expansion for Aqueous Systems Revisited: I. Water–Water Interactions. J Chem Theory Comput 2020; 16:6843-6855. [DOI: 10.1021/acs.jctc.9b00749] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Joseph P. Heindel
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Sotiris S. Xantheas
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box
999, MS K1-83, Richland, Washington 99352, United States
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18
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Clabaut P, Staub R, Galiana J, Antonetti E, Steinmann SN. Water adlayers on noble metal surfaces: Insights from energy decomposition analysis. J Chem Phys 2020; 153:054703. [DOI: 10.1063/5.0013040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Paul Clabaut
- Univ Lyon, Ecole Normale Supérieure de Lyon, CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182, 46 allée d’Italie, F-69364 Lyon, France
| | - Ruben Staub
- Univ Lyon, Ecole Normale Supérieure de Lyon, CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182, 46 allée d’Italie, F-69364 Lyon, France
| | - Joachim Galiana
- Univ Lyon, Ecole Normale Supérieure de Lyon, CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182, 46 allée d’Italie, F-69364 Lyon, France
| | - Elise Antonetti
- Univ Lyon, Ecole Normale Supérieure de Lyon, CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182, 46 allée d’Italie, F-69364 Lyon, France
| | - Stephan N. Steinmann
- Univ Lyon, Ecole Normale Supérieure de Lyon, CNRS Université Lyon 1, Laboratoire de Chimie UMR 5182, 46 allée d’Italie, F-69364 Lyon, France
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19
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Ricard TC, Iyengar SS. Efficient and Accurate Approach To Estimate Hybrid Functional and Large Basis-Set Contributions to Condensed-Phase Systems and Molecule–Surface Interactions. J Chem Theory Comput 2020; 16:4790-4812. [DOI: 10.1021/acs.jctc.9b01089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Timothy C. Ricard
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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20
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Egan CK, Bizzarro BB, Riera M, Paesani F. Nature of Alkali Ion–Water Interactions: Insights from Many-Body Representations and Density Functional Theory. II. J Chem Theory Comput 2020; 16:3055-3072. [DOI: 10.1021/acs.jctc.0c00082] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Colin K. Egan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Brandon B. Bizzarro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Marc Riera
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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21
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Jing Z, Qi R, Thibonnier M, Ren P. Molecular Dynamics Study of the Hybridization between RNA and Modified Oligonucleotides. J Chem Theory Comput 2019; 15:6422-6432. [PMID: 31553600 PMCID: PMC6889957 DOI: 10.1021/acs.jctc.9b00519] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) are attractive drug candidates for many diseases as they can modulate the expression of gene networks. Recently, we discovered that DNAs targeting microRNA-22-3p (miR-22-3p) hold the potential for treating obesity and related metabolic disorders (type 2 diabetes mellitus, hyperlipidemia, and nonalcoholic fatty liver disease (NAFLD)) by turning fat-storing white adipocytes into fat-burning adipocytes. In this work, we explored the effects of chemical modifications, including phosphorothioate (PS), locked nucleic acid (LNA), and peptide nucleic acid (PNA), on the structure and energy of DNA analogs by using molecular dynamics (MD) simulations. To achieve a reliable prediction of the hybridization free energy, the AMOEBA polarizable force field and the free energy perturbation technique were employed. The calculated hybridization free energies are generally compatible with previous experiments. For LNA and PNA, the enhanced duplex stability can be explained by the preorganization mechanism, i.e., the single strands adopt stable helical structures similar to those in the duplex. For PS, the S and R isomers (Sp and Rp) have preferences for C2'-endo and C3'-endo sugar puckering conformations, respectively, and therefore Sp is less stable than Rp in DNA/RNA hybrids. In addition, the solvation penalty of Rp accounts for its destabilization effect. PS-LNA is similar to LNA as the sugar puckering is dominated by the locked sugar ring. This work demonstrated that MD simulations with polarizable force fields are useful for the understanding and design of modified nucleic acids.
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712
| | - Rui Qi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712
| | | | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712
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22
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Das AK, Urban L, Leven I, Loipersberger M, Aldossary A, Head-Gordon M, Head-Gordon T. Development of an Advanced Force Field for Water Using Variational Energy Decomposition Analysis. J Chem Theory Comput 2019; 15:5001-5013. [DOI: 10.1021/acs.jctc.9b00478] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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23
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Andrés J, Ayers PW, Boto RA, Carbó-Dorca R, Chermette H, Cioslowski J, Contreras-García J, Cooper DL, Frenking G, Gatti C, Heidar-Zadeh F, Joubert L, Martín Pendás Á, Matito E, Mayer I, Misquitta AJ, Mo Y, Pilmé J, Popelier PLA, Rahm M, Ramos-Cordoba E, Salvador P, Schwarz WHE, Shahbazian S, Silvi B, Solà M, Szalewicz K, Tognetti V, Weinhold F, Zins ÉL. Nine questions on energy decomposition analysis. J Comput Chem 2019; 40:2248-2283. [PMID: 31251411 DOI: 10.1002/jcc.26003] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 05/16/2019] [Indexed: 01/05/2023]
Abstract
The paper collects the answers of the authors to the following questions: Is the lack of precision in the definition of many chemical concepts one of the reasons for the coexistence of many partition schemes? Does the adoption of a given partition scheme imply a set of more precise definitions of the underlying chemical concepts? How can one use the results of a partition scheme to improve the clarity of definitions of concepts? Are partition schemes subject to scientific Darwinism? If so, what is the influence of a community's sociological pressure in the "natural selection" process? To what extent does/can/should investigated systems influence the choice of a particular partition scheme? Do we need more focused chemical validation of Energy Decomposition Analysis (EDA) methodology and descriptors/terms in general? Is there any interest in developing common benchmarks and test sets for cross-validation of methods? Is it possible to contemplate a unified partition scheme (let us call it the "standard model" of partitioning), that is proper for all applications in chemistry, in the foreseeable future or even in principle? In the end, science is about experiments and the real world. Can one, therefore, use any experiment or experimental data be used to favor one partition scheme over another? © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Juan Andrés
- Departament de Ciències Experimentals Universitat Jaume I, 12080, Castelló, Spain
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, L8S 4M1, Hamilton, Ontario, Canada
| | | | - Ramon Carbó-Dorca
- Institut de Química Computational i Catàlisi, Universitat de Girona, C/M Aurelia Capmany 69, 17003, Girona, Spain
| | - Henry Chermette
- Université Lyon 1 et UMR CNRS 5280 Institut Sciences Analytiques, Université de Lyon, 69622, Paris, France
| | - Jerzy Cioslowski
- Institute of Physics, University of Szczecin, Wielkopolska, 15, 70-451, Szczecin, Poland
| | | | - David L Cooper
- Department of Chemistry, University of Liverpool, Liverpool, L69 7ZD, United Kingdom
| | - Gernot Frenking
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerweinstr. 4, 35032, Marburg, Germany
| | - Carlo Gatti
- CNR-ISTM Istituto di Scienze e Tecnologie Molecolari, via Golgi 19, 20133, Milan, Italy and Istituto Lombardo Accademia di Scienze e Lettere, via Brera 28, 20121, Milan, Italy
| | - Farnaz Heidar-Zadeh
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg and Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Laurent Joubert
- COBRA UMR 6014 & FR 3038, INSA Rouen, CNRS, Université de Rouen Normandie, Mont-St-Aignan, France
| | - Ángel Martín Pendás
- Departamento de Química Física y Analítica, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Eduard Matito
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), and Donostia International Physics Center (DIPC), P.K. 1072, 20080, Donostia, Euskadi, Spain.,IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Euskadi, Spain
| | - István Mayer
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, 1117, Hungary
| | - Alston J Misquitta
- School of Physics and Astronomy, Queen Mary University of London, Mile End Road, London, E1 4NS, United Kingdom
| | - Yirong Mo
- Chemistry Department, Western Michigan University, Kalamazoo, Michigan, 49008
| | - Julien Pilmé
- Sorbonne Université, CNRS, LCT, UMR 7616, 4 place Jussieu, 75005, Paris, France
| | - Paul L A Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, United Kingdom.,School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Martin Rahm
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Eloy Ramos-Cordoba
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), and Donostia International Physics Center (DIPC), P.K. 1072, 20080, Donostia, Euskadi, Spain
| | - Pedro Salvador
- Institut de Química Computacional i Catàlisi, Universitat de Girona, C/M Aurelia Capmany 69, 17003, Girona, Spain
| | - W H Eugen Schwarz
- Theoretical Chemistry Center at Tsinghua University, Beijing, 100084, China.,Physical and Theoretical Chemistry Laboratory, Faculty of Science and Engineering, University of Siegen, Siegen, 57068, Germany
| | - Shant Shahbazian
- Department of Physics, Shahid Beheshti University, P.O. Box 19395-4716, G. C., Evin, 19839, Tehran, Iran
| | - Bernard Silvi
- Sorbonne Université, CNRS, LCT, UMR 7616, 4 place Jussieu, 75005, Paris, France
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi, Universitat de Girona, C/M Aurelia Capmany 69, 17003, Girona, Spain
| | - Krzysztof Szalewicz
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware
| | - Vincent Tognetti
- COBRA UMR 6014 & FR 3038, INSA Rouen, CNRS, Université de Rouen Normandie, Mont-St-Aignan, France
| | - Frank Weinhold
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Émilie-Laure Zins
- Sorbonne Université, UPMC Univ. Paris 06, MONARIS, UMR 8233, Université Pierre et Marie Curie, 4 Place Jussieu, Case Courrier 49, 75252, Paris, France
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24
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Jing Z, Liu C, Cheng SY, Qi R, Walker BD, Piquemal JP, Ren P. Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications. Annu Rev Biophys 2019; 48:371-394. [PMID: 30916997 DOI: 10.1146/annurev-biophys-070317-033349] [Citation(s) in RCA: 217] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Realistic modeling of biomolecular systems requires an accurate treatment of electrostatics, including electronic polarization. Due to recent advances in physical models, simulation algorithms, and computing hardware, biomolecular simulations with advanced force fields at biologically relevant timescales are becoming increasingly promising. These advancements have not only led to new biophysical insights but also afforded opportunities to advance our understanding of fundamental intermolecular forces. This article describes the recent advances and applications, as well as future directions, of polarizable force fields in biomolecular simulations.
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Sara Y Cheng
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Rui Qi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Brandon D Walker
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Jean-Philip Piquemal
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA; .,Sorbonne Université, CNRS, Laboratoire de Chimie Theórique, 75252 Paris CEDEX 05, France.,Institut Universitaire de France, 75005 Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
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25
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Dziedzic J, Head-Gordon T, Head-Gordon M, Skylaris CK. Mutually polarizable QM/MM model with in situ optimized localized basis functions. J Chem Phys 2019; 150:074103. [PMID: 30795653 DOI: 10.1063/1.5080384] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We extend our recently developed quantum-mechanical/molecular mechanics (QM/MM) approach [Dziedzic et al., J. Chem. Phys. 145, 124106 (2016)] to enable in situ optimization of the localized orbitals. The quantum subsystem is described with onetep linear-scaling density functional theory and the classical subsystem - with the AMOEBA polarizable force field. The two subsystems interact via multipolar electrostatics and are fully mutually polarizable. A total energy minimization scheme is employed for the Hamiltonian of the coupled QM/MM system. We demonstrate that, compared to simpler models using fixed basis sets, the additional flexibility offered by in situ optimized basis functions improves the accuracy of the QM/MM interface, but also poses new challenges, making the QM subsystem more prone to overpolarization and unphysical charge transfer due to increased charge penetration. We show how these issues can be efficiently solved by replacing the classical repulsive van der Waals term for QM/MM interactions with an interaction of the electronic density with a fixed, repulsive MM potential that mimics Pauli repulsion, together with a modest increase in the damping of QM/MM polarization. We validate our method, with particular attention paid to the hydrogen bond, in tests on water-ion pairs, the water dimer, first solvation shells of neutral and charged species, and solute-solvent interaction energies. As a proof of principle, we determine suitable repulsive potential parameters for water, K+, and Cl-. The mechanisms we employed to counteract the unphysical overpolarization of the QM subsystem are demonstrated to be adequate, and our approach is robust. We find that the inclusion of explicit polarization in the MM part of QM/MM improves agreement with fully QM calculations. Our model permits the use of minimal size QM regions and, remarkably, yields good energetics across the well-balanced QM/MM interface.
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Affiliation(s)
- Jacek Dziedzic
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Teresa Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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26
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Staub R, Iannuzzi M, Khaliullin RZ, Steinmann SN. Energy Decomposition Analysis for Metal Surface-Adsorbate Interactions by Block Localized Wave Functions. J Chem Theory Comput 2018; 15:265-275. [PMID: 30462497 DOI: 10.1021/acs.jctc.8b00957] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The energy decomposition analysis based on block localized wave functions (BLW-EDA) allows one to gain physical insight into the nature of chemical bonding, decomposing the interaction energy in (1) a "frozen" term, accounting for the attraction due to electrostatic and dispersion interactions, modulated by Pauli repulsion, (2) the variationally assessed polarization energy, and (3) the charge transfer. This method has so far been applied to gas- and condensed-phase molecular systems. However, its standard version is not compatible with fractionally occupied orbitals (i.e., electronic smearing) and, as a consequence, cannot be applied to metallic surfaces. In this work, we propose a simple and practical extension of BLW-EDA to fractionally occupied orbitals, termed Ensemble BLW-EDA. As illustrative examples, we have applied the developed method to analyze the nature of the interaction of various adsorbates on Pt(111), ranging from physisorbed water to strongly chemisorbed ethylene. Our results show that polarization and charge transfer both contribute significantly at the adsorption minimum for all studied systems. The energy decomposition analysis provides details with respect to competing adsorption sites (e.g., CO on atop vs hollow sites) and elucidates the respective importance of polarization and charge transfer for the increased adsorption energy of H2S compared to H2O. Our development will enable a deeper understanding of the impact of charge transfer on catalytic processes in general.
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Affiliation(s)
- Ruben Staub
- Univ Lyon, Ecole Normale Supérieure de Lyon, CNRS Université Lyon 1 , Laboratoire de Chimie UMR 5182 , 46 allée d'Italie , Lyon , F-69364 , France
| | - Marcella Iannuzzi
- Institut für Chemie , University of Zurich , Winterthurerstrasse 190 , Zurich , CH-8057 , Switzerland
| | - Rustam Z Khaliullin
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Québec H3A 0B8 , Canada
| | - Stephan N Steinmann
- Univ Lyon, Ecole Normale Supérieure de Lyon, CNRS Université Lyon 1 , Laboratoire de Chimie UMR 5182 , 46 allée d'Italie , Lyon , F-69364 , France
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27
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Saranya V, Shankar R, Vijayakumar S. Structural exploration of viral matrix protein 40 interaction with the transition metal ions (Ag+ and Cu2+). J Biomol Struct Dyn 2018; 37:2875-2896. [DOI: 10.1080/07391102.2018.1498803] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- V. Saranya
- Department of Physics, Bharathiar University, Coimbatore, India
| | - R. Shankar
- Department of Physics, Bharathiar University, Coimbatore, India
| | - S. Vijayakumar
- Department of Medical Physics, Bharathiar University, Coimbatore, India
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28
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Das AK, Demerdash ON, Head-Gordon T. Improvements to the AMOEBA Force Field by Introducing Anisotropic Atomic Polarizability of the Water Molecule. J Chem Theory Comput 2018; 14:6722-6733. [DOI: 10.1021/acs.jctc.8b00978] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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29
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Rackers JA, Liu C, Ren P, Ponder JW. A physically grounded damped dispersion model with particle mesh Ewald summation. J Chem Phys 2018; 149:084115. [PMID: 30193468 DOI: 10.1063/1.5030434] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Accurate modeling of dispersion is critical to the goal of predictive biomolecular simulations. To achieve this accuracy, a model must be able to correctly capture both the short-range and asymptotic behavior of dispersion interactions. We present here a damped dispersion model based on the overlap of charge densities that correctly captures both regimes. The overlap damped dispersion model represents a classical physical interpretation of dispersion: the interaction between the instantaneous induced dipoles of two distinct charge distributions. This model is shown to be an excellent fit with symmetry adapted perturbation theory dispersion energy calculations, yielding an RMS error on the S101x7 database of 0.5 kcal/mol. Moreover, the damping function used in this model is wholly derived and parameterized from the electrostatic dipole-dipole interaction, making it not only physically grounded but transferable as well.
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Affiliation(s)
- Joshua A Rackers
- Program in Computational and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jay W Ponder
- Program in Computational and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
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30
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Pereyaslavets L, Kurnikov I, Kamath G, Butin O, Illarionov A, Leontyev I, Olevanov M, Levitt M, Kornberg RD, Fain B. On the importance of accounting for nuclear quantum effects in ab initio calibrated force fields in biological simulations. Proc Natl Acad Sci U S A 2018; 115:8878-8882. [PMID: 30127031 PMCID: PMC6130346 DOI: 10.1073/pnas.1806064115] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
In many important processes in chemistry, physics, and biology the nuclear degrees of freedom cannot be described using the laws of classical mechanics. At the same time, the vast majority of molecular simulations that employ wide-coverage force fields treat atomic motion classically. In light of the increasing desire for and accelerated development of quantum mechanics (QM)-parameterized interaction models, we reexamine whether the classical treatment is sufficient for a simple but crucial chemical species: alkanes. We show that when using an interaction model or force field in excellent agreement with the "gold standard" QM data, even very basic simulated properties of liquid alkanes, such as densities and heats of vaporization, deviate significantly from experimental values. Inclusion of nuclear quantum effects via techniques that treat nuclear degrees of freedom using the laws of classical mechanics brings the simulated properties much closer to reality.
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Affiliation(s)
| | | | | | | | | | | | | | - Michael Levitt
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
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31
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Marefat Khah A, Karbalaei Khani S, Hättig C. Analytic Excited State Gradients for the QM/MM Polarizable Embedded Second-Order Algebraic Diagrammatic Construction for the Polarization Propagator PE-ADC(2). J Chem Theory Comput 2018; 14:4640-4650. [PMID: 30040882 DOI: 10.1021/acs.jctc.8b00396] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
An implementation of a QM/MM embedding in a polarizable environment is presented for second-order Møller-Plesset perturbation theory, MP2, for ground state energies and molecular gradients and for the second-order Algebraic Diagrammatic Construction, ADC(2), for excitation energies and excited state molecular gradients. In this implementation of PE-MP2 and PE-ADC(2), the polarizable embedded Hartree-Fock wave function is used as uncorrelated reference state. The polarization-correlation cross terms for the ground and excited states are included in this model via an approximate coupling density. A Lagrangian formulation is used to derive the relaxed electron densities and molecular gradients. The resolution-of-the-identity approximation speeds up the calculation of four-index electron repulsion integrals in the molecular orbital basis. As a first application, the method is used to study the photophysical properties of host-guest complexes where the accuracy and weaknesses of the model are also critically examined. It is demonstrated that the ground state geometries of the full quantum mechanical calculation for the supermolecule can be well reproduced. For excited state geometries, the deviations from the supermolecular calculation are slightly larger, but still the environment effects are captured qualitatively correctly, and energy gaps between the ground and excited states are obtained with sufficient accuracy.
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Affiliation(s)
- Alireza Marefat Khah
- Arbeitsgruppe Quantenchemie , Ruhr-Universität Bochum , Bochum D-44801 , Germany
| | | | - Christof Hättig
- Arbeitsgruppe Quantenchemie , Ruhr-Universität Bochum , Bochum D-44801 , Germany
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32
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Piquemal JP, Jordan KD. Preface: Special Topic: From Quantum Mechanics to Force Fields. J Chem Phys 2018; 147:161401. [PMID: 29096449 DOI: 10.1063/1.5008887] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This Special Topic issue entitled "From Quantum Mechanics to Force Fields" is dedicated to the ongoing efforts of the theoretical chemistry community to develop a new generation of accurate force fields based on data from high-level electronic structure calculations and to develop faster electronic structure methods for testing and designing force fields as well as for carrying out simulations. This issue includes a collection of 35 original research articles that illustrate recent theoretical advances in the field. It provides a timely snapshot of recent developments in the generation of approaches to enable more accurate molecular simulations of processes important in chemistry, physics, biophysics, and materials science.
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Affiliation(s)
- Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, UMR 7616 CNRS, UPMC, Sorbonne Universités, 75252 Paris Cedex 05, France
| | - Kenneth D Jordan
- Department of Chemistry, The University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, USA
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33
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Mao Y, Ge Q, Horn PR, Head-Gordon M. On the Computational Characterization of Charge-Transfer Effects in Noncovalently Bound Molecular Complexes. J Chem Theory Comput 2018; 14:2401-2417. [PMID: 29614855 DOI: 10.1021/acs.jctc.7b01256] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Charge-transfer (CT) is an important binding force in the formation of intermolecular complexes, and there have been a variety of theoretical models proposed to quantify this effect. These approaches, which typically rely on a definition of a "CT-free" state based on a partition of the system, sometimes yield significantly different results for a given intermolecular complex. Two widely used definitions of the "CT-free" state, the absolutely localized molecular orbitals (ALMO) method (where only on-fragment orbital mixings are permitted) and the constrained density functional theory (CDFT) approach (where fragment electron populations are fixed), are carefully examined in this work. Natural bond orbital (NBO) and the regularized symmetry-adapted perturbation theory (SAPT) are also briefly considered. Results for the ALMO and CDFT definitions of CT are compared on a broad range of model systems, including hydrogen-bonding systems, borane complexes, metal-carbonyl complexes, and complexes formed by water and metal cations. For most of these systems, CDFT yields a much smaller equilibrium CT energy compared to that given by the ALMO-based definition. This is mainly because the CDFT population constraint does not fully inhibit CT, which means that the CDFT "CT-free" state is in fact CT-contaminated. Examples of this contamination include (i) matching forward and backward donation (e.g., formic acid dimer) and (ii) unidirectional CT without changing fragment populations. The magnitude of the latter effect is quantified in systems such as the water dimer by employing a 3-space density constraint in addition to the orbital constraint. Furthermore, by means of the adiabatic EDA, it is shown that several observable effects of CT, such as the "pyramidalization" of the planar BH3 molecule upon the complexation with Lewis bases, already appear on the "CT-free" CDFT surface. These results reveal the essential distinctions between the ALMO and CDFT definitions of CT and suggest that the former is more consistent with accepted understanding of the role of CT in intermolecular binding.
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Affiliation(s)
- Yuezhi Mao
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California at Berkeley , Berkeley , California 94720 , United States
| | - Qinghui Ge
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California at Berkeley , Berkeley , California 94720 , United States.,Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Paul R Horn
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California at Berkeley , Berkeley , California 94720 , United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry , University of California at Berkeley , Berkeley , California 94720 , United States.,Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
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34
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McKinley JL, Beran GJO. Identifying pragmatic quasi-harmonic electronic structure approaches for modeling molecular crystal thermal expansion. Faraday Discuss 2018; 211:181-207. [PMID: 30027972 DOI: 10.1039/c8fd00048d] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Quasi-harmonic approaches provide an economical route to modeling the temperature dependence of molecular crystal structures and properties. Several studies have demonstrated good performance of these models, at least for rigid molecules, when using fragment-based approaches with correlated wavefunction techniques. Many others have found success employing dispersion-corrected density functional theory (DFT). Here, a hierarchy of models in which the energies, geometries, and phonons are computed either with correlated methods or DFT are examined to identify which combinations produce useful predictions for properties such as the molar volume, enthalpy, and entropy as a function of temperature. The results demonstrate that refining DFT geometries and phonons with single-point energies based on dispersion-corrected second-order Møller-Plesset perturbation theory can provide clear improvements in the molar volumes and enthalpies compared to those obtained from DFT alone. Predicted entropies, which are governed by vibrational contributions, benefit less clearly from the hybrid schemes. Using these hybrid techniques, the room-temperature thermochemistry of acetaminophen (paracetamol) is predicted to address the discrepancy between two experimental sublimation enthalpy measurements.
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Affiliation(s)
- Jessica L McKinley
- Department of Chemistry, University of California, Riverside, California 92521, USA.
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35
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Demerdash O, Wang L, Head‐Gordon T. Advanced models for water simulations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1355] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Omar Demerdash
- Kenneth S. Pitzer Center for Theoretical Chemistry University of California Berkeley CA USA
- Department of Chemistry University of California Berkeley CA USA
| | - Lee‐Ping Wang
- Department of Chemistry University of California, Davis Davis CA USA
| | - Teresa Head‐Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry University of California Berkeley CA USA
- Department of Chemistry University of California Berkeley CA USA
- Department of Bioengineering University of California Berkeley CA USA
- Department of Chemical and Biomolecular Engineering University of California Berkeley CA USA
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