1
|
Sami S, LaCour RA, Heindel JP, Head-Gordon T. Simple and Accurate One-Body Energy and Dipole Moment Surfaces for Water and Beyond. J Phys Chem Lett 2024:6712-6721. [PMID: 38900596 DOI: 10.1021/acs.jpclett.4c00587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Water is often the testing ground for new, advanced force fields. While advanced functional forms for intermolecular interactions have been integral to the development of accurate water models, less attention has been paid to a transferable model for intramolecular valence terms. In this work, we present a one-body energy and dipole moment surface model, named 1B-UCB, that is simple yet accurate and can be feasibly adapted for both standard and advanced potentials. 1B-UCB for water is comparable in accuracy to those with much more complex functional forms, despite having drastically fewer parameters. The parametrization protocol has been implemented as part of the Q-Force automated workflow and requires only a quantum mechanical Hessian calculation as reference data, hence allowing it to be easily extended to a variety of molecular systems beyond water, which we demonstrate on a selection of small molecules with different symmetries.
Collapse
Affiliation(s)
- Selim Sami
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - R Allen LaCour
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Joseph P Heindel
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Theory Center and Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| |
Collapse
|
2
|
Chen G, Jaffrelot Inizan T, Plé T, Lagardère L, Piquemal JP, Maday Y. Advancing Force Fields Parameterization: A Directed Graph Attention Networks Approach. J Chem Theory Comput 2024. [PMID: 38875012 DOI: 10.1021/acs.jctc.3c01421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
Force fields (FFs) are an established tool for simulating large and complex molecular systems. However, parametrizing FFs is a challenging and time-consuming task that relies on empirical heuristics, experimental data, and computational data. Recent efforts aim to automate the assignment of FF parameters using pre-existing databases and on-the-fly ab initio data. In this study, we propose a graph-based force field (GB-FFs) model to directly derive parameters for the Generalized Amber Force Field (GAFF) from chemical environments and research into the influence of functional forms. Our end-to-end parametrization approach predicts parameters by aggregating the basic information in directed molecular graphs, eliminating the need for expert-defined procedures and enhances the accuracy and transferability of GAFF across a broader range of molecular complexes. Simulation results are compared to the original GAFF parametrization. In practice, our results demonstrate an improved transferability of the model, showcasing its improved accuracy in modeling intermolecular and torsional interactions, as well as improved solvation free energies. The optimization approach developed in this work is fully applicable to other nonpolarizable FFs as well as to polarizable ones.
Collapse
Affiliation(s)
- Gong Chen
- Sorbonne Université, CNRS, Université Paris Cité, Laboratoire Jacques-Louis Lions (LJLL), UMR 7598 CNRS, 75005 Paris, France
| | - Théo Jaffrelot Inizan
- Sorbonne Université, Laboratoire de Chimie Théorique (LCT), UMR 7616 CNRS, 75005 Paris, France
| | - Thomas Plé
- Sorbonne Université, Laboratoire de Chimie Théorique (LCT), UMR 7616 CNRS, 75005 Paris, France
| | - Louis Lagardère
- Sorbonne Université, Laboratoire de Chimie Théorique (LCT), UMR 7616 CNRS, 75005 Paris, France
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique (LCT), UMR 7616 CNRS, 75005 Paris, France
| | - Yvon Maday
- Sorbonne Université, CNRS, Université Paris Cité, Laboratoire Jacques-Louis Lions (LJLL), UMR 7598 CNRS, 75005 Paris, France
| |
Collapse
|
3
|
Hartke B. On the brink of self-hydration: the water heptadecamer. Phys Chem Chem Phys 2024; 26:15445-15451. [PMID: 38747364 DOI: 10.1039/d4cp00816b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
For pure, neutral, isolated molecular clusters, (H2O)17 marks the transition from structures with all water molecules on the cluster surface to water self-hydration, i.e., cluster structures around one central water molecule. Getting this right with water model potentials turns out to be challenging. Even the best water potentials currently available, which reproduce collective properties very well, still deliver contradicting results for (H2O)17, when different low-energy isomers from global structure optimizations are examined. Interestingly, ab initio quantum chemistry also struggles with the only seemingly simple question if (H2O)17 is all-surface or water-centered. Hence, although the long history of water potential development may be entering its final phase, it is not quite finished yet.
Collapse
Affiliation(s)
- Bernd Hartke
- Institute for Physical Chemistry, Kiel University, 24118 Kiel, Germany.
| |
Collapse
|
4
|
Mikkelsen JES, Jensen F. Ambiguities in Decomposing Molecular Polarizability into Atomic Charge Flow and Induced Dipole Contributions. J Phys Chem A 2024; 128:4168-4175. [PMID: 38743593 DOI: 10.1021/acs.jpca.4c01890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The molecular dipole polarizability can be decomposed into components corresponding to the charge flow between atoms and changes in atomic dipole moments. Such decompositions are recognized to depend on how atoms are defined within a molecule, as, for example, by Hirshfeld, iterative Stockholder, or quantum topology partitioning of the electron density. For some of these, however, there are significant differences between the numerical results obtained by analytical response methods and finite field calculations. We show that this difference is due to analytical response methods accounting for (only) the change in electron density by a perturbation, while finite field methods may also include a component corresponding to a perturbation-dependent change in the definition of an atom within a molecule. For some atom-in-molecule definitions, such as the iterative Hirshfeld, iterative Stockholder, and quantum topology methods, the latter effect significantly increases the charge flow component. The decomposition of molecular polarizability into atomic charge flow and induced dipole components thus depends on whether the atom-in-molecule definition is taken to be perturbation-dependent.
Collapse
Affiliation(s)
- Jonas E S Mikkelsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
| | - Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
| |
Collapse
|
5
|
Chung MKJ, Ponder JW. Beyond isotropic repulsion: Classical anisotropic repulsion by inclusion of p orbitals. J Chem Phys 2024; 160:174118. [PMID: 38748037 PMCID: PMC11078554 DOI: 10.1063/5.0203678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/15/2024] [Indexed: 05/19/2024] Open
Abstract
Accurate modeling of intermolecular repulsion is an integral component in force field development. Although repulsion can be explicitly calculated by applying the Pauli exclusion principle, this approach is computationally viable only for systems of limited sizes. Instead, it has previously been shown that repulsion can be reformulated in a "classical" picture: the Pauli exclusion principle prohibits electrons from occupying the same state, leading to a depletion of electronic charge between atoms, giving rise to an enhanced nuclear-nuclear electrostatic repulsion. This classical picture is called the isotropic S2/R approximation, where S is the overlap and R is the interatomic distance. This approximation accurately captures the repulsion of isotropic atoms such as noble gas dimers; however, a key deficiency is that it fails to capture the angular dependence of the repulsion of anisotropic molecules. To include directionality, the wave function must at least be a linear combination of s and p orbitals. We derive a new anisotropic S2/R repulsion model through the inclusion of the anisotropic p orbital term in the total wave function. Because repulsion is pairwise and decays rapidly, it can be truncated at a short range, making it amenable for efficient calculation of energy and forces in complex biomolecular systems. We present a parameterization of the S101 dimer database against the ab initio benchmark symmetry-adapted perturbation theory, which yields an rms error of only 0.9 kcal/mol. The importance of the anisotropic term is demonstrated through angular scans of water-water dimers and dimers involving halobenzene. Simulation of liquid water shows that the model can be computed efficiently for realistic system sizes.
Collapse
Affiliation(s)
| | - Jay W. Ponder
- Author to whom correspondence should be addressed: . Tel.: 314-935-4275
| |
Collapse
|
6
|
Xiong X, Friedman R, Wu W, Su P. QM/MM-Based Energy Decomposition Analysis Method for Large Systems. J Phys Chem A 2024. [PMID: 38687960 DOI: 10.1021/acs.jpca.4c00183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
In this work, a QM/MM-based EDA method, called GKS-EDA(QM/MM), is proposed. As an extension of GKS-EDA, this scheme divides the total interaction energy into electrostatic, exchange-repulsion, polarization, and correlation/dispersion terms. GKS-EDA(QM/MM) can be applied to describe the interactions of large-scale systems combined with various QM/MM platforms. By using the examples of a hydrated hydronium ion complex in water solution, the barnase-barstar complex, and MMP-13-pyrimidinetrione in a metalloprotein, the capability of GKS-EDA(QM/MM) for various interactions in large systems is validated.
Collapse
Affiliation(s)
- Xuewei Xiong
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnaeus University, 39182 Kalmar, Sweden
| | - Wei Wu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Peifeng Su
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| |
Collapse
|
7
|
Wang Y, Inizan TJ, Liu C, Piquemal JP, Ren P. Incorporating Neural Networks into the AMOEBA Polarizable Force Field. J Phys Chem B 2024; 128:2381-2388. [PMID: 38445577 PMCID: PMC10985787 DOI: 10.1021/acs.jpcb.3c08166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Neural network potentials (NNPs) offer significant promise to bridge the gap between the accuracy of quantum mechanics and the efficiency of molecular mechanics in molecular simulation. Most NNPs rely on the locality assumption that ensures the model's transferability and scalability and thus lack the treatment of long-range interactions, which are essential for molecular systems in the condensed phase. Here we present an integrated hybrid model, AMOEBA+NN, which combines the AMOEBA potential for the short- and long-range noncovalent atomic interactions and an NNP to capture the remaining local covalent contributions. The AMOEBA+NN model was trained on the conformational energy of the ANI-1x data set and tested on several external data sets ranging from small molecules to tetrapeptides. The hybrid model demonstrated substantial improvements over the baseline models in term of accuracy as the molecule size increased, suggesting its potential as a next-generation approach for chemically accurate molecular simulations.
Collapse
Affiliation(s)
- Yanxing Wang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Théo Jaffrelot Inizan
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, Paris 75005, France
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, Paris 75005, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
8
|
Valle JVL, Mendonça BHS, Barbosa MC, Chacham H, de Moraes EE. Accuracy of TIP4P/2005 and SPC/Fw Water Models. J Phys Chem B 2024; 128:1091-1097. [PMID: 38253517 DOI: 10.1021/acs.jpcb.3c07044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Water is used as the main solvent in model systems containing bioorganic molecules. Choosing the right water model is an important step in the study of the biophysical and biochemical processes that occur in cells. In the present work, we perform molecular dynamics simulations using two distinct force fields for water: the rigid model TIP4P/2005, where only intermolecular interactions are considered, and the flexible model SPC/Fw, where intramolecular interactions are also taken into account. The simulations aim to determine the effect of the inclusion of intramolecular interactions on the accuracy of calculated properties of bulk water (density and thermal expansion coefficient, self-diffusion coefficients, shear viscosity, radial distribution functions, and dielectric constant), as compared to experimental results, over a temperature range between 250 and 370 K. We find that the results of the rigid model present the smallest deviations relative to experiments for most of the calculated quantities, except for the shear viscosity of supercooled water and the water dielectric constant, where the flexible model presents better agreement with experiments.
Collapse
Affiliation(s)
- João V L Valle
- Instituto de Física, Universidade Federal da Bahia, Campus Universitário de Ondina, Salvador 40210-340, BA, Brazil
| | - Bruno H S Mendonça
- Departamento de Física, ICEX, Universidade Federal de Minas Gerais, CP 702, Belo Horizonte 30123-970, MG, Brazil
| | - Marcia C Barbosa
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
| | - Helio Chacham
- Departamento de Física, ICEX, Universidade Federal de Minas Gerais, CP 702, 30123-970 Belo Horizonte, MG, Brazil
| | - Elizane E de Moraes
- Instituto de Física, Universidade Federal da Bahia, Campus Universitário de Ondina, Salvador 40210-340, BA, Brazil
| |
Collapse
|
9
|
Demir Gİ, Tekin A. NICE-FF: A non-empirical, intermolecular, consistent, and extensible force field for nucleic acids and beyond. J Chem Phys 2023; 159:244117. [PMID: 38153156 DOI: 10.1063/5.0176641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023] Open
Abstract
A new non-empirical ab initio intermolecular force field (NICE-FF in buffered 14-7 potential form) has been developed for nucleic acids and beyond based on the dimer interaction energies (IEs) calculated at the spin component scaled-MI-second order Møller-Plesset perturbation theory. A fully automatic framework has been implemented for this purpose, capable of generating well-polished computational grids, performing the necessary ab initio calculations, conducting machine learning (ML) assisted force field (FF) parametrization, and extending existing FF parameters by incorporating new atom types. For the ML-assisted parametrization of NICE-FF, interaction energies of ∼18 000 dimer geometries (with IE < 0) were used, and the best fit gave a mean square deviation of about 0.46 kcal/mol. During this parametrization, atom types apparent in four deoxyribonucleic acid (DNA) bases have been first trained using the generated DNA base datasets. Both uracil and hypoxanthine, which contain the same atom types found in DNA bases, have been considered as test molecules. Three new atom types have been added to the DNA atom types by using IE datasets of both pyrazinamide and 9-methylhypoxanthine. Finally, the last test molecule, theophylline, has been selected, which contains already-fitted atom-type parameters. The performance of NICE-FF has been investigated on the S22 dataset, and it has been found that NICE-FF outperforms the well-known FFs by generating the most consistent IEs with the high-level ab initio ones. Moreover, NICE-FF has been integrated into our in-house developed crystal structure prediction (CSP) tool [called FFCASP (Fast and Flexible CrystAl Structure Predictor)], aiming to find the experimental crystal structures of all considered molecules. CSPs, which were performed up to 4 formula units (Z), resulted in NICE-FF being able to locate almost all the known experimental crystal structures with sufficiently low RMSD20 values to provide good starting points for density functional theory optimizations.
Collapse
Affiliation(s)
- Gözde İniş Demir
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Türkiye
| | - Adem Tekin
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Türkiye
- Research Institute for Fundamental Sciences (TÜBİTAK-TBAE), Kocaeli, Türkiye
| |
Collapse
|
10
|
Zhu JY, Liu Q, Jiang XN, Zheng XH, Wang L, Hao Q, Wang CS. From bonds to interactions: comprehensive molecular characterization via polarizable bond-dipole approach. Phys Chem Chem Phys 2023; 25:29867-29880. [PMID: 37888898 DOI: 10.1039/d3cp04060g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Accurately characterizing molecular interactions stands as a pivotal requirement for ensuring the reliability of molecular dynamics simulations. In line with our bond-dipole-based interaction model proposed by Gao et al. [X.-C. Gao, Q. Hao and C.-S. Wang, J. Chem. Theory Comput., 2017, 13, 2730-2741.], we have implemented an efficient and concise approach to compute electrostatic potential. This methodology capitalizes on the polarizable nature of chemical bond dipoles, resulting in a model of remarkable simplicity. In this study, we have revised the polarizable bond-dipole-based force field (PBFF) through the meticulous curation of quantum chemical data sets. These data sets encompass a comprehensive collection of 40 000 conformations, including those of water, methylamine, methanol, and N-methylacetamide. Additionally, we incorporate 520 hydrogen-bonded dimers into our data sets. In pursuit of enhanced accuracy in molecular dynamics simulations and a more faithful representation of potential energy landscapes, we undertook the re-optimization of the nonbonded parameters within the PBFF framework. Concurrently, we intricately fine-tuned the bonded parameters. The results of our comprehensive evaluation denote that this newly optimized force field method adeptly and efficiently computes structural characteristics, harmonic frequencies, and interaction energies. Overall, this study provides further validation for the applicability of PBFF in molecular dynamics simulations.
Collapse
Affiliation(s)
- Jia-Yi Zhu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, China.
| | - Qi Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, China.
| | - Xiao-Nan Jiang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, China.
| | - Xiao-Han Zheng
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, China.
| | - Lei Wang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, China.
| | - Qiang Hao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, China.
| | - Chang-Sheng Wang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, China.
| |
Collapse
|
11
|
Mendonça BHS, de Moraes EE, Kirch A, Batista RJC, de Oliveira AB, Barbosa MC, Chacham H. Flow through Deformed Carbon Nanotubes Predicted by Rigid and Flexible Water Models. J Phys Chem B 2023; 127:8634-8643. [PMID: 37754781 DOI: 10.1021/acs.jpcb.3c02889] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
In this study, using nonequilibrium molecular dynamics simulation, the flow of water in deformed carbon nanotubes is studied for two water models TIP4P/2005 and simple point charge/FH (SPC/FH). The results demonstrated a nonuniform dependence of the flow on the tube deformation and the flexibility imposed on the water molecules, leading to an unexpected increase in the flow in some cases. The effects of the tube diameter and pressure gradient are investigated to explain the abnormal flow behavior with different degrees of structural deformation.
Collapse
Affiliation(s)
- Bruno H S Mendonça
- Departamento de Física, ICEX, Universidade Federal de Minas Gerais, CP 702, Belo Horizonte 30123-970, MG, Brazil
| | - Elizane E de Moraes
- Instituto de Física, Universidade Federal da Bahia, Campus Universitário de Ondina, Salvador 40210-340, BA, Brazil
| | - Alexsandro Kirch
- Instituto de Física, Universidade de São Paulo, CP 66318, São Paulo 05315-970, SP, Brazil
| | - Ronaldo J C Batista
- Departamento de Física, Universidade Federal de Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto 35400-000, MG, Brazil
| | - Alan B de Oliveira
- Departamento de Física, Universidade Federal de Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto 35400-000, MG, Brazil
| | - Marcia C Barbosa
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
| | - Hélio Chacham
- Departamento de Física, ICEX, Universidade Federal de Minas Gerais, CP 702, Belo Horizonte 30123-970, MG, Brazil
| |
Collapse
|
12
|
Herman KM, Stone AJ, Xantheas SS. Accurate Calculation of Many-Body Energies in Water Clusters Using a Classical Geometry-Dependent Induction Model. J Chem Theory Comput 2023; 19:6805-6815. [PMID: 37703063 DOI: 10.1021/acs.jctc.3c00575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
We incorporate geometry-dependent distributed multipole and polarizability surfaces into an induction model that is used to describe the 3- and 4-body terms of the interaction between water molecules. The moment expansion is carried out up to the hexadecapole with the multipoles distributed on the atom sites. Dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole distributed polarizabilities are used to represent the response of the multipoles to an electric field. We compare the model against two large databases consisting of 43,844 3-body terms and 3,603 4-body terms obtained from high level ab initio calculations previously used to fit the MB-pol and q-AQUA classical interaction potentials for water. The classical induction model with no adjustable parameters reproduces the ab initio 3-/4-body terms contained in these two databases with a root-mean-square error (RMSE) of 0.104/0.058 and a mean-absolute error (MAE) of 0.054/0.026 kcal/mol, respectively. These results are on par with the ones obtained by fitting the same data using over 14,000 (for the 3-body) and 200 (for the 4-body) parameters via Permutationally Invariant Polynomials (PIPs). This demonstrates the accuracy of this physically motivated model in describing the 3- and 4-body terms in the interactions between water molecules with no adjustable parameters. The triple-dipole-dispersion energy, included in the calculation of the 3-body energy, was found to be small but not quite negligible. The model represents a practical, efficient, and transferable approach for obtaining accurate nonadditive interactions for multicomponent systems without the need to perform tens of thousands of high level electronic structure calculations and fitting them with PIPs.
Collapse
Affiliation(s)
- Kristina M Herman
- Department of Chemistry, University of Washington, Seattle, Washington 98185, United States
| | - Anthony J Stone
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Sotiris S Xantheas
- Department of Chemistry, University of Washington, Seattle, Washington 98185, United States
- Advanced Computing Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MSIN J7-10, Richland, Washington 99352, United States
| |
Collapse
|
13
|
Kostal V, Jungwirth P, Martinez-Seara H. Nonaqueous Ion Pairing Exemplifies the Case for Including Electronic Polarization in Molecular Dynamics Simulations. J Phys Chem Lett 2023; 14:8691-8696. [PMID: 37733610 PMCID: PMC10561266 DOI: 10.1021/acs.jpclett.3c02231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023]
Abstract
The inclusion of electronic polarization is of crucial importance in molecular simulations of systems containing charged moieties. When neglected, as often done in force field simulations, charge-charge interactions in solution may become severely overestimated, leading to unrealistically strong bindings of ions to biomolecules. The electronic continuum correction introduces electronic polarization in a mean-field way via scaling of charges by the reciprocal of the square root of the high-frequency dielectric constant of the solvent environment. Here, we use ab initio molecular dynamics simulations to quantify the effect of electronic polarization on pairs of like-charged ions in a model nonaqueous environment where electronic polarization is the only dielectric response. Our findings confirm the conceptual validity of this approach, underlining its applicability to complex aqueous biomolecular systems. Simultaneously, the results presented here justify the potential employment of weaker charge scaling factors in force field development.
Collapse
Affiliation(s)
- Vojtech Kostal
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| |
Collapse
|
14
|
Wang X, Wang Y, Guo M, Wang X, Li Y, Zhang JZH. Assessment of an Electrostatic Energy-Based Charge Model for Modeling the Electrostatic Interactions in Water Solvent. J Chem Theory Comput 2023; 19:6294-6312. [PMID: 37656610 DOI: 10.1021/acs.jctc.3c00467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
The protein force field based on the restrained electrostatic potential (RESP) charges has limitations in accurately describing hydrogen bonding interactions in proteins. To address this issue, we propose an alternative approach called the electrostatic energy-based charges (EEC) model, which shows improved performance in describing electrostatic interactions (EIs) of hydrogen bonds in proteins. In this study, we further investigate the performance of the EEC model in modeling EIs in water solvent. Our findings demonstrate that the fixed EEC model can effectively reproduce the quantum mechanics/molecular mechanics (QM/MM)-calculated EIs between a water molecule and various water solvent environments. However, to achieve the same level of computational accuracy, the electrostatic potential (ESP) charge model needs to fluctuate according to the electrostatic environment. Our analysis indicates that the requirement for charge adjustments depends on the specific mathematical and physical representation of EIs as a function of the environment for deriving charges. By comparing with widely used empirical water models calibrated to reproduce experimental properties, we confirm that the performance of the EEC model in reproducing QM/MM EIs is similar to that of general purpose TIP4P-like water models such as TIP4P-Ew and TIP4P/2005. When comparing the computed 10,000 distinct EI values within the range of -40 to 0 kcal/mol with the QM/MM results calculated at the MP2/aug-cc-pVQZ/TIP3P level, we noticed that the mean unsigned error (MUE) for the EEC model is merely 0.487 kcal/mol, which is remarkably similar to the MUE values of the TIP4P-Ew (0.63 kcal/mol) and TIP4P/2005 (0.579 kcal/mol) models. However, both the RESP method and the TIP3P model exhibit a tendency to overestimate the EIs, as evidenced by their higher MUE values of 1.761 and 1.293 kcal/mol, respectively. EEC-based molecular dynamics simulations have demonstrated that, when combined with appropriate van der Waals parameters, the EEC model can closely reproduce oxygen-oxygen radial distribution function and density of water, showing a remarkable similarity to the well-established TIP4P-like empirical water models. Our results demonstrate that the EEC model has the potential to build force fields with comparable accuracy to more sophisticated empirical TIP4P-like water models.
Collapse
Affiliation(s)
- Xianwei Wang
- College of Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310023, China
| | - Yiying Wang
- College of Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310023, China
| | - Man Guo
- College of Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310023, China
| | - Xuechao Wang
- College of Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310023, China
| | - Yang Li
- College of Information Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - John Z H Zhang
- Shenzhen Institute of Synthetic Biology, Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| |
Collapse
|
15
|
Lanjan A, Moradi Z, Srinivasan S. Computational Framework Combining Quantum Mechanics, Molecular Dynamics, and Deep Neural Networks to Evaluate the Intrinsic Properties of Materials. J Phys Chem A 2023; 127:6603-6613. [PMID: 37497552 DOI: 10.1021/acs.jpca.3c02887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
The design and evaluation of future nanomaterials with specific properties is a challenging task as the current traditional methods rely on trial and error approaches that are time-consuming and expensive. On the computational front, design tools such as molecular dynamics (MD) simulations help us reduce the costs and times. However, nonbonded potential parameters, the key input parameters for an MD simulation, are usually not available for designing and studying new materials. Resolving this, quantum mechanics (QM) calculations could be used to evaluate the system's energy as a function of the nonbonded distances, and the resulting data set could be fit to a generic potential equation to obtain the fitting constants (potential parameters). However, fitting this massive data set containing thousands of unknown parameters using traditional mathematical formulations is not feasible. Hence, most computational frameworks in the literature utilize several simplifications, leading to a severe loss of accuracy. Addressing this deficiency, in this work, we propose a multi-scale framework that couples QM calculations and MD with advanced deep neural networks to determine the potential parameters. This advanced framework has been extensively validated by employing it to predict properties such as the density, boiling point, and melting point of five different types of molecules that are well-understood, namely, the polar molecule H2O, ionic compound LiPF6, ethanol (C2H5OH), long-chain molecule C8H18, and the complex molecular system ethylene carbonate (EC).
Collapse
Affiliation(s)
- Amirmasoud Lanjan
- Department of Mechanical Engineering, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Zahra Moradi
- W Booth School of Engineering Practice and Technology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Seshasai Srinivasan
- Department of Mechanical Engineering, McMaster University, Hamilton, Ontario L8S 4K1, Canada
- W Booth School of Engineering Practice and Technology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| |
Collapse
|
16
|
Arabzadeh H, Sperling JM, Acevedo O, Albrecht-Schönzart TE. Free Energy Calculations and Conformational Analysis of Dibenzo-30-crown-10 with Sm 2+, Eu 2+, and Three Halide Salts in THF Using the AMOEBA Force Field. J Phys Chem B 2023. [PMID: 37311109 DOI: 10.1021/acs.jpcb.3c01800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Crown ether complexes have been tailored for use in industrial separations of lanthanides (Ln) as a part of rare earth mining and refining. Dibenzo-30-crown-10 (DB30C10) is one of the most efficient complexants for the separation of rare earth mixtures based on the cation size. To understand the origin of this complexation, molecular dynamics (MD) simulations of DB30C10 have been performed using different combinations of divalent Sm and Eu and three halide salts Cl-, Br-, and I- in tetrahydrofuran (THF) solvent. DB30C10 was parameterized here for the polarizable atomic multipole optimized energetics for biomolecular simulation (AMOEBA) force field, and the existing parameters of THF, Sm2+, and Eu2+ were employed from our previous efforts. The large conformational fluctuations present in the DB30C10 systems were found to be dependent both on the identity of the lanthanide and halide complexes. For Cl- and Br- systems, there were no observed conformational changes at 200 ns, while in I- systems, there were two conformational changes with Sm2+ and one with Eu2+ within that same timeframe. In SmI2-DB30C10, there were three stages of conformational changes. In the first stage, the molecule is unfolded, in the second stage, the molecule is partly folded, and finally, in the third stage, the molecule is completely folded. Lastly, the Gibbs binding free energies of DB30C10 with SmBr2 and EuBr2 have been computed, which resulted in nearly identical ΔGcomp values for each lanthanide with Sm2+ being slightly more favorable. Considering the folding mechanism of the SmI2 system with DB30C10, the Gibbs binding free energies of DB30C10 and dicyclohexano-18-crown-6 (DCH18C6) with SmI2 were calculated separately and compared to probe their complexation affinities, in which the former was found to be more favorable.
Collapse
Affiliation(s)
- Hesam Arabzadeh
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Joseph M Sperling
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Orlando Acevedo
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Thomas E Albrecht-Schönzart
- Department of Chemistry and Nuclear Science & Engineering Center, Colorado School of Mines, Golden, Colorado 80401, United States
| |
Collapse
|
17
|
Yan S, Ji X, Peng W, Wang B. Evaluating the Transition State Stabilization/Destabilization Effects of the Electric Fields from Scaffold Residues by a QM/MM Approach. J Phys Chem B 2023; 127:4245-4253. [PMID: 37155960 DOI: 10.1021/acs.jpcb.3c01054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The protein scaffolds of enzymes not only provide structural support for the catalytic center but also exert preorganized electric fields for electrostatic catalysis. In recent years, uniform oriented external electric fields (OEEFs) have been widely applied to enzymatic reactions to mimic the electrostatic effects of the environment. However, the electric fields exerted by individual residues in proteins may be quite heterogeneous across the active site, with varying directions and strengths at different positions of the active site. Here, we propose a QM/MM-based approach to evaluate the effects of the electric fields exerted by individual residues in the protein scaffold. In particular, the heterogeneity of the residue electric fields and the effect of the native protein environment can be properly accounted for by this QM/MM approach. A case study of the O-O heterolysis reaction in the catalytic cycle of TyrH shows that (1) for scaffold residues that are relatively far from the active site, the heterogeneity of the residue electric field in the active site is not very significant and the electrostatic stabilization/destabilization due to each residue can be well approximated with the interaction energy between a uniform electric field and the QM region dipole; (2) for scaffold residues near the active site, the residue electric fields can be highly heterogeneous along the breaking O-O bond. In such a case, approximating the residue electric fields as uniform fields may misrepresent the overall electrostatic effect of the residue. The present QM/MM approach can be applied to evaluate the residues' electrostatic impact on enzymatic reactions, which also can be useful in computational optimization of electric fields to boost the enzyme catalysis.
Collapse
Affiliation(s)
- Shengheng Yan
- 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 and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Xinwei Ji
- 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 and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| | - Wei Peng
- 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 and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), 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 and Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen 361005, P. R. China
| |
Collapse
|
18
|
Wang W, Yan D, Cai Y, Xu D, Ma J, Wang Q. General Charge Transfer Dipole Model for AMOEBA-Like Force Fields. J Chem Theory Comput 2023; 19:2518-2534. [PMID: 37125725 DOI: 10.1021/acs.jctc.2c01084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The development of highly accurate force fields is always an importance aspect in molecular modeling. In this work, we introduce a general damping-based charge transfer dipole (D-CTD) model to describe the charge transfer energy and the corresponding charge flow for H, C, N, O, P, S, F, Cl, and Br elements in common bio-organic systems. Then, two effective schemes to evaluate the charge flow from the corresponding induced dipole moment between the interacting molecules were also proposed and discussed. The potential applicability of the D-CTD model in ion-containing systems was also demonstrated in a series of ion-water complexes including Li+, Na+, K+, Mg2+, Ca2+, Fe2+, Zn2+, Pt2+, F-, Cl-, Br-, and I- ions. In general, the D-CTD model demonstrated good accuracy and good transferability in both charge transfer energy and the corresponding charge flow for a wide range of model systems. By distinguishing the intermolecular charge redistribution (charge transfer) under the influence of an external electric field from the accompanying intramolecular charge redistribution (polarization), the D-CTD model is theoretically consistent with current induced dipole-based polarizable dipole models and hence can be easily implemented and parameterized. Along with our previous work in charge penetration-corrected electrostatics, a bottom-up approach constructed water model was also proposed and demonstrated. The structure-maker and structure-breaker roles of cations and anions were also correctly reproduced using Na+, K+, Cl-, and I- ions in the new water model, respectively. This work demonstrates a cost-effective approach to describe the charge transfer phenomena. The water and ion models also show the feasibility of a modulated development approach for future force fields.
Collapse
Affiliation(s)
- Wei Wang
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, China
| | - Dengjie Yan
- 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, China
| | - Yao Cai
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Dingguo Xu
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Jianyi Ma
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, 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, China
| |
Collapse
|
19
|
Plé T, Mauger N, Adjoua O, Inizan TJ, Lagardère L, Huppert S, Piquemal JP. Routine Molecular Dynamics Simulations Including Nuclear Quantum Effects: From Force Fields to Machine Learning Potentials. J Chem Theory Comput 2023; 19:1432-1445. [PMID: 36856658 DOI: 10.1021/acs.jctc.2c01233] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
We report the implementation of a multi-CPU and multi-GPU massively parallel platform dedicated to the explicit inclusion of nuclear quantum effects (NQEs) in the Tinker-HP molecular dynamics (MD) package. The platform, denoted Quantum-HP, exploits two simulation strategies: the Ring-Polymer Molecular Dynamics (RPMD) that provides exact structural properties at the cost of a MD simulation in an extended space of multiple replicas and the adaptive Quantum Thermal Bath (adQTB) that imposes the quantum distribution of energy on a classical system via a generalized Langevin thermostat and provides computationally affordable and accurate (though approximate) NQEs. We discuss some implementation details, efficient numerical schemes, and parallelization strategies and quickly review the GPU acceleration of our code. Our implementation allows an efficient inclusion of NQEs in MD simulations for very large systems, as demonstrated by scaling tests on water boxes with more than 200,000 atoms (simulated using the AMOEBA polarizable force field). We test the compatibility of the approach with Tinker-HP's recently introduced Deep-HP machine learning potentials module by computing water properties using the DeePMD potential with adQTB thermostatting. Finally, we show that the platform is also compatible with the alchemical free energy estimation capabilities of Tinker-HP and fast enough to perform simulations. Therefore, we study how NQEs affect the hydration free energy of small molecules solvated with the recently developed Q-AMOEBA water force field. Overall, the Quantum-HP platform allows users to perform routine quantum MD simulations of large condensed-phase systems and will help to shed new light on the quantum nature of important interactions in biological matter.
Collapse
Affiliation(s)
- Thomas Plé
- Sorbonne Université, LCT, UMR 7616 CNRS, F-75005 Paris, France
| | - Nastasia Mauger
- Sorbonne Université, LCT, UMR 7616 CNRS, F-75005 Paris, France
| | - Olivier Adjoua
- Sorbonne Université, LCT, UMR 7616 CNRS, F-75005 Paris, France
| | | | - Louis Lagardère
- Sorbonne Université, LCT, UMR 7616 CNRS, F-75005 Paris, France
| | - Simon Huppert
- Institut des Nanosciences de Paris (INSP), CNRS UMR 7588, and Sorbonne Université, F-75005 Paris, France
| | - Jean-Philip Piquemal
- Sorbonne Université, LCT, UMR 7616 CNRS, F-75005 Paris, France.,Institut Universitaire de France, 75005 Paris, France.,Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
20
|
Herman KM, Xantheas SS. An extensive assessment of the performance of pairwise and many-body interaction potentials in reproducing ab initio benchmark binding energies for water clusters n = 2-25. Phys Chem Chem Phys 2023; 25:7120-7143. [PMID: 36853239 DOI: 10.1039/d2cp03241d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We assess the performance of 7 pairwise additive (TIP3P, TIP4P, TIP4P-ice, TIP5P, OPC, SPC, SPC/E) and 8 families of many-body potentials (q-AQUA, HIPPO, AMOEBA, EFP, TTM, WHBB, MB-pol, MB-UCB) in reproducing high-level ab initio benchmark values, CCSD(T) or MP2 at the complete basis set (CBS) limit for the binding energy and the many-body expansion (MBE) of water clusters n = 2-11, 16-17, 20, 25. By including a large range of cluster sizes having dissimilar hydrogen bonding networks, we obtain an understanding of how these potentials perform for different hydrogen bonding arrangements that are mostly outside of their parameterization range. While it is appropriate to compare the results of ab initio based many-body potentials directly to the electronic binding energies (De's), the pairwise additive ones are compared to the enthalpies at T = 298 K, ΔH(298 K), as the latter class of force fields are parametrized to reproduce enthalpies (implicitly accounting for zero-point energy corrections) rather than binding energies. We find that all pairwise additive potentials considered overestimate the reference ΔH values for the n = 2-25 clusters by >13%. For the water dimer (n = 2) in particular, the errors are in the range 83-119% for the pairwise additive potentials studied since these are based on an effective rather than the true 2-body interaction specifically designed as a means of partially accounting for the missing many-body terms. This stronger 2-body interaction is achieved by an enhanced monomer dipole moment that mimics its increase from the gas phase monomer to the condensed phase value. Indeed, for cluster sizes n ≥ 4 the percent deviations become slightly smaller (albeit all exceeding 13%). In contrast, we find that the many-body potentials perform more accurately in reproducing the electronic binding energies (De's) throughout the entire cluster range (n = 2-25), all reproducing the ab initio benchmark binding energies within ±7% of the respective CBS values. We further assess the ability of a subset of the many-body potentials (MB-UCB, q-AQUA, MB-pol, and TTM2.1-F) to also reproduce the magnitude of the ab initio many-body energy terms for water cluster sizes n = 7, 10, 16 and 17. The potentials show an overall good agreement with the available benchmark values. However, we identify characteristic differences upon comparing the many-body terms at both the ab initio-optimized geometries and the respective potential-optimized geometries to the reference ab initio values. Additionally, by applying this analysis to a wide range of cluster sizes, trends in the MBE of the potentials with increasing cluster size can be identified. Finally, in an attempt to draw a parallel between the pairwise additive and many-body potentials, we report the analysis of the individual molecular dipole moments for water clusters with 1 to ∼4 solvation shells with the TTM2.1-F potential. We find that the internally solvated water molecules have in general a larger molecular dipole moment ranging from 2.6-3.0 D. This justifies the use of an enhanced, with respect to the gas-phase value, molecular dipole moment for the pairwise additive potentials, which is intended to fold in the many body terms into an effective (enhanced) pairwise interaction through the choice of the charges. These results have important implications for the development of future generations of efficient, transferable, and highly accurate classical interaction potentials in both the pairwise additive and many-body categories.
Collapse
Affiliation(s)
- Kristina M Herman
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - Sotiris S Xantheas
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA. .,Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, WA, 99352, USA.
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Janicki TD, Van Vleet MJ, Schmidt JR. Development and Implementation of Atomically Anisotropic First-Principles Force Fields: A Benzene Case Study. J Phys Chem A 2023; 127:1736-1749. [PMID: 36780209 DOI: 10.1021/acs.jpca.2c07244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
π-interactions are an important motif in chemical and biochemical systems. However, due to their anisotropic electron densities and complex balance of intermolecular interactions, aromatic molecules represent an ongoing challenge for accurate and transferable force field development. Historically, ab initio force fields for aromatics have not exhibited good accuracy with respect to bulk properties or have only been used to study gas-phase dimers. Using benzene as a proof of concept, herein we show how our own ab initio MASTIFF force field incorporates an atomically anisotropic description of intermolecular interactions to yield an accurate and robust model for aromatic interactions irrespective of phase. Compared to existing models, the MASTIFF benzene force field not only is accurate for liquid phase properties but also offers transferability to the gas and solid phases. Additionally, we introduce a computationally efficient OpenMM plugin which enables customizable anisotropic intermolecular functional forms and which can be generically used in any MD simulation where a model for nonspherical atomic features is required. Overall, our results demonstrate the importance of atomic-level anisotropy in enabling next-generation ab initio force field development.
Collapse
Affiliation(s)
- Tesia D Janicki
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Mary J Van Vleet
- Department of Chemistry and Biochemistry, Spelman College, 350 Spelman Ln SW, Atlanta, Georgia 30314, United States
| | - J R Schmidt
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| |
Collapse
|
23
|
Wait EE, Gourary J, Liu C, Spoerke ED, Rempe SB, Ren P. Development of AMOEBA Polarizable Force Field for Rare-Earth La 3+ Interaction with Bioinspired Ligands. J Phys Chem B 2023; 127:1367-1375. [PMID: 36735638 PMCID: PMC9957963 DOI: 10.1021/acs.jpcb.2c07237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Rare-earth metals (REMs) are crucial for many important industries, such as power generation and storage, in addition to cancer treatment and medical imaging. One promising new REM refinement approach involves mimicking the highly selective and efficient binding of REMs observed in relatively recently discovered proteins. However, realizing any such bioinspired approach requires an understanding of the biological recognition mechanisms. Here, we developed a new classical polarizable force field based on the AMOEBA framework for modeling a lanthanum ion (La3+) interacting with water, acetate, and acetamide, which have been found to coordinate the ion in proteins. The parameters were derived by comparing to high-level ab initio quantum mechanical (QM) calculations that include relativistic effects. The AMOEBA model, with advanced atomic multipoles and electronic polarization, is successful in capturing both the QM distance-dependent La3+-ligand interaction energies and experimental hydration free energy. A new scheme for pairwise polarization damping (POLPAIR) was developed to describe the polarization energy in La3+ interactions with both charged and neutral ligands. Simulations of La3+ in water showed water coordination numbers and ion-water distances consistent with previous experimental and theoretical findings. Water residence time analysis revealed both fast and slow kinetics in water exchange around the ion. This new model will allow investigation of fully solvated lanthanum ion-protein systems using GPU-accelerated dynamics simulations to gain insights on binding selectivity, which may be applied to the design of synthetic analogues.
Collapse
Affiliation(s)
- Elizabeth E. Wait
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Justin Gourary
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Erik D. Spoerke
- Electronic, Optical, and Nano Materials Department, Sandia National Laboratories, Albuquerque, NM 87185, USA
| | - Susan B. Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| |
Collapse
|
24
|
Li XL, Li CM, Zhu JY, Zhou Z, Hao Q, Wang CS. A scheme for rapid evaluation of the intermolecular three-body polarization effect in water clusters. J Comput Chem 2023; 44:677-686. [PMID: 36408852 DOI: 10.1002/jcc.27032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/22/2022] [Accepted: 10/24/2022] [Indexed: 11/22/2022]
Abstract
The ability to accurately and rapidly evaluate the intermolecular many-body polarization effect of the water system is very important for computer simulations of biomolecule in aqueous. In this paper, a scheme is proposed based on the polarizable dipole-dipole interaction model and used to rapidly estimate the intermolecular many-body polarization effect in water clusters. We use a bond-dipole-based polarization function to evaluate the polarization energy. We regard two OH bonds of a water molecule as two bond-dipoles and set the permanent OH bond-dipole moment of a water molecule to be 1.51 Debye. We estimate the induced OH bond-dipole moment via a simple formula in which only one correction factor is needed. This scheme is then applied to tens of water clusters to calculate the three- and four-body interaction energies. The three-body interaction energies of 93 water clusters produced by our scheme are compared with those produced by the counterpoise-corrected CCSD(T)/aug-cc-pVDZ, MP2/aug-cc-pVDZ, M06-2X/jul-cc-pVTZ methods, by the AMOEBApro13, iAMOEBA, AMOEBA+, AMOEBA+(CF) methods, and by the MB-pol method. The four-body interaction energies of 47 water clusters yielded by our scheme are compared with those yielded by the counterpoise-corrected MP2/aug-cc-pVDZ and M06-2X/ jul-cc-pVTZ methods, by the AMOEBApro13, AMOEBA+, AMOEBA+(CF) methods, and by the MB-pol method. The comparison results show that the scheme proposed in this paper can reproduce the counterpoise-corrected CCSD(T)/aug-cc-pVDZ three-body interaction energies and reproduce the counterpoise-corrected MP2/aug-cc-pVDZ four-body interaction energies both accurately and efficiently. We anticipate the scheme proposed here can be useful for computer simulations of liquid water and aqueous solutions.
Collapse
Affiliation(s)
- Xiao-Lei Li
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| | - Chao-Ming Li
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| | - Jia-Yi Zhu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| | - Zhan Zhou
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| | - Qiang Hao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| | - Chang-Sheng Wang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| |
Collapse
|
25
|
Brown M, Skelton JM, Popelier PLA. Construction of a Gaussian Process Regression Model of Formamide for Use in Molecular Simulations. J Phys Chem A 2023; 127:1702-1714. [PMID: 36756842 PMCID: PMC9969515 DOI: 10.1021/acs.jpca.2c06566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
FFLUX, a novel force field based on quantum chemical topology, can perform molecular dynamics simulations with flexible multipole moments that change with geometry. This is enabled by Gaussian process regression machine learning models, which accurately predict atomic energies and multipole moments up to the hexadecapole. We have constructed a model of the formamide monomer at the B3LYP/aug-cc-pVTZ level of theory capable of sub-kJ mol-1 accuracy, with the maximum prediction error for the molecule being 0.8 kJ mol-1. This model was used in FFLUX simulations along with Lennard-Jones parameters to successfully optimize the geometry of formamide dimers with errors smaller than 0.1 Å compared to those obtained with D3-corrected B3LYP/aug-cc-pVTZ. Comparisons were also made to a force field constructed with static multipole moments and Lennard-Jones parameters. FFLUX recovers the expected energy ranking of dimers compared to the literature, and changes in C═O and C-N bond lengths associated with hydrogen bonding were found to be consistent with density functional theory.
Collapse
|
26
|
Ignatov SK, Masunov AE. Unexpected polarization properties of sub-nanosized magnesium clusters. RSC Adv 2023; 13:4065-4076. [PMID: 36756583 PMCID: PMC9890678 DOI: 10.1039/d2ra08086a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 01/20/2023] [Indexed: 01/29/2023] Open
Abstract
The isotropic electrostatic polarizability (IEP) of sub-nanosized magnesium clusters Mg2-Mg32 was studied in an extensive set comprising 1237 structurally unique isomers. These isomers were found in the course of the global search for the potential energy surface minima of the magnesium clusters at the BP86/6-31G(d) level. The calculation of the polarizability at the same DFT level reveals an unexpected property of the IEP: the linear correlation between the polarizability of the most favorable isomers (and only them) and the cluster nuclearity n. Moreover, for each n, the most stable cluster isomer demonstrates nearly minimal IEP value among all found isomers of a given nuclearity. Surprisingly, these observed features are independent of the cluster structures which are quite different. We hypothesize that the energetic favorability of a cluster structure is related to their low polarizability. Apparently, the atoms forming the cluster tend to arrange themselves in such a way as to provide the most compact distribution of the cluster electron density. A possible explanation of the observed trends, their significance for cluster structure prediction, and the practical applications are discussed.
Collapse
Affiliation(s)
| | - Artëm E. Masunov
- NanoScience Technology Center, University of Central FloridaOrlandoFlorida 32826USA,School of Modeling, Simulations and Training, University of Central FloridaOrlandoFlorida 32826USA,South Ural State University (National Research University)ChelyabinskRussia
| |
Collapse
|
27
|
Thürlemann M, Böselt L, Riniker S. Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactions. J Chem Theory Comput 2023; 19:562-579. [PMID: 36633918 PMCID: PMC9878731 DOI: 10.1021/acs.jctc.2c00661] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Indexed: 01/13/2023]
Abstract
Simulations of molecular systems using electronic structure methods are still not feasible for many systems of biological importance. As a result, empirical methods such as force fields (FF) have become an established tool for the simulation of large and complex molecular systems. The parametrization of FF is, however, time-consuming and has traditionally been based on experimental data. Recent years have therefore seen increasing efforts to automatize FF parametrization or to replace FF with machine-learning (ML) based potentials. Here, we propose an alternative strategy to parametrize FF, which makes use of ML and gradient-descent based optimization while retaining a functional form founded in physics. Using a predefined functional form is shown to enable interpretability, robustness, and efficient simulations of large systems over long time scales. To demonstrate the strength of the proposed method, a fixed-charge and a polarizable model are trained on ab initio potential-energy surfaces. Given only information about the constituting elements, the molecular topology, and reference potential energies, the models successfully learn to assign atom types and corresponding FF parameters from scratch. The resulting models and parameters are validated on a wide range of experimentally and computationally derived properties of systems including dimers, pure liquids, and molecular crystals.
Collapse
Affiliation(s)
- Moritz Thürlemann
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Lennard Böselt
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| |
Collapse
|
28
|
Arabzadeh H, Walker B, Sperling JM, Acevedo O, Ren P, Yang W, Albrecht-Schönzart TE. Molecular Dynamics and Free Energy Calculations of Dicyclohexano-18-crown-6 Diastereoisomers with Sm 2+, Eu 2+, Dy 2+, Yb 2+, Cf 2+, and Three Halide Salts in Tetrahydrofuran and Acetonitrile Using the AMOEBA Force Field. J Phys Chem B 2022; 126:10721-10731. [PMID: 36508277 PMCID: PMC9999210 DOI: 10.1021/acs.jpcb.2c04613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
With the continual development of lanthanides (Ln) in current technological devices, an efficient separation process is needed that can recover greater amounts of these rare elements. Dicyclohexano-18-crown-6 (DCH18C6) is a crown ether that may be a promising candidate for Ln separation, but additional research is required. As such, molecular dynamics (MD) simulations have been performed on four divalent lanthanide halide salts (Sm2+, Eu2+, Dy2+, and Yb2+) and one divalent actinide halide salt (Cf2+) bound to three diastereoisomers of DCH18C6. Dy2+, Yb2+, Cf2+, DCH18C6, and tetrahydrofuran (THF) solvent were parameterized for the AMOEBA polarizable force field for the first time, whereas existing parameters for Sm2+ and Eu2+ were utilized from our previous efforts. A coordination number (CN) of six for Ln2+/An2+-O solvated in THF indicated that the cations interacted almost entirely with the oxygens of the polyether ring. A CN of one for Ln2+/An2+-N solvated in acetonitrile for systems containing iodide suggested that the N atom of acetonitrile was competitive with I- for cation interactions. Fluctuation between five and six CNs for Dy2+ and Yb2+ suggested that although the cations remained in the polyether ring, the size of the ring may not be an ideal fit as these cations possess comparatively smaller ionic radii. Gibbs binding free energies of Sm2+ in all DCH18C6 diastereoisomers solvated in THF were calculated. The binding free energy of the cis-syn-cis diastereoisomer was the most favorable, followed by cis-anti-cis, and then trans-anti-trans. Finally, two major types of conformation were observed for each diastereoisomer that were related to the electrostatic interactions and charge density of the cations.
Collapse
Affiliation(s)
- Hesam Arabzadeh
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Brandon Walker
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Joseph M. Sperling
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Orlando Acevedo
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Wei Yang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | | |
Collapse
|
29
|
Wang X, Tse YLS. Flexible Polarizable Water Model Parameterized via Gaussian Process Regression. J Chem Theory Comput 2022; 18:7155-7165. [PMID: 36374554 DOI: 10.1021/acs.jctc.2c00529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Water is one of the most common components in molecular dynamics (MD) simulations. Using Gaussian process regression for predicting the properties of a water model without the need of running a simulation whenever the parameters are changed, we obtained a flexible polarizable water model, named SWM4/Fw, that is able to reproduce many reference water properties. The added flexibility is critical for modeling chemical reactions in which chemical bonds can be stretched or even broken and for directly calculating vibrational spectra. In addition to being one of the few water models that are both flexible and polarizable, SWM4/Fw is also efficient thanks to the extended Lagrangian scheme with Drude oscillators. The overall accuracy is on par with or better than the related SWM4-NDP model.
Collapse
Affiliation(s)
- Xinyan Wang
- Department of Chemistry, The Chinese University of Hong Kong, Sha Tin, Hong Kong000000, China
| | - Ying-Lung Steve Tse
- Department of Chemistry, The Chinese University of Hong Kong, Sha Tin, Hong Kong000000, China
| |
Collapse
|
30
|
Mauger N, Plé T, Lagardère L, Huppert S, Piquemal JP. Improving Condensed-Phase Water Dynamics with Explicit Nuclear Quantum Effects: The Polarizable Q-AMOEBA Force Field. J Phys Chem B 2022; 126:8813-8826. [PMID: 36270033 DOI: 10.1021/acs.jpcb.2c04454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We introduce a new parametrization of the AMOEBA polarizable force field for water denoted Q-AMOEBA, for use in simulations that explicitly account for nuclear quantum effects (NQEs). This study is made possible thanks to the recently introduced adaptive Quantum Thermal Bath (adQTB) simulation technique which computational cost is comparable to classical molecular dynamics. The flexible Q-AMOEBA model conserves the initial AMOEBA functional form, with an intermolecular potential including an atomic multipole description of electrostatic interactions (up to quadrupole), a polarization contribution based on the Thole interaction model and a buffered 14-7 potential to model van der Waals interactions. It has been obtained by using a ForceBalance fitting strategy including high-level quantum chemistry reference energies and selected condensed-phase properties targets. The final Q-AMOEBA model is shown to accurately reproduce both gas-phase and condensed-phase properties, notably improving the original AMOEBA water model. This development allows the fine study of NQEs on water liquid phase properties such as the average H-O-H angle compared to its gas-phase equilibrium value, isotope effects, and so on. Q-AMOEBA also provides improved infrared spectroscopy prediction capabilities compared to AMOEBA03. Overall, we show that the impact of NQEs depends on the underlying model functional form and on the associated strength of hydrogen bonds. Since adQTB simulations can be performed at near classical computational cost using the Tinker-HP package, Q-AMOEBA can be extended to organic molecules, proteins, and nucleic acids opening the possibility for the large-scale study of the importance of NQEs in biophysics.
Collapse
Affiliation(s)
- Nastasia Mauger
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, 75005 Paris, France
| | - Thomas Plé
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, 75005 Paris, France
| | - Louis Lagardère
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, 75005 Paris, France
| | - Simon Huppert
- Sorbonne Université, Institut des NanoSciences de Paris, UMR 7588 CNRS, 75005 Paris, France
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, 75005 Paris, France
| |
Collapse
|
31
|
Strunge K, Madzharova F, Jensen F, Weidner T, Nagata Y. Theoretical Sum Frequency Generation Spectra of Protein Amide with Surface-Specific Velocity-Velocity Correlation Functions. J Phys Chem B 2022; 126:8571-8578. [PMID: 36194760 DOI: 10.1021/acs.jpcb.2c04321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Vibrational sum frequency generation (vSFG) spectroscopy is widely used to probe the protein structure at interfaces. Because protein vSFG spectra are complex, they can only provide detailed structural information if combined with computer simulations of protein molecular dynamics and spectra calculations. We show how vSFG spectra can be accurately modeled using a surface-specific velocity-velocity scheme based on ab initio normal modes. Our calculated vSFG spectra show excellent agreement with the experimental sum frequency spectrum of LTα14 peptide and provide insight into the origin of the characteristic α-helical amide I peak. Analysis indicates that the peak shape can be explained largely by two effects: (1) the uncoupled response of amide groups located on opposite sides of the α-helix will have different orientations with respect to the interface and therefore different local environments affecting the local mode vibrations and (2) vibrational splitting from nearest neighbor coupling evaluated as inter-residue vibrational correlation. The conclusion is consistent with frequency mapping techniques with an empirically based ensemble of peptide structures, thus showing how time correlation approaches and frequency mapping techniques can give independent yet complementary molecular descriptions of protein vSFG. These models reveal the sensitive relationship between protein structure and their amide I response, allowing exploitation of the complicated molecular vibrations and their interference to derive the structures of proteins under native conditions at interfaces.
Collapse
Affiliation(s)
- Kris Strunge
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Fani Madzharova
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| |
Collapse
|
32
|
Abstract
Simulating water accurately has been a major challenge in atomistic simulations for decades. Inclusion of electronic polarizability effects holds considerable promise, yet existing approaches suffer from significant computational overheads compared to the widely used nonpolarizable water models. We have developed a globally optimal polarizable water model, OPC3-pol, that explicitly accounts for electronic polarizability with minimal impact on the computational efficiency. OPC3-pol reproduces five key bulk water properties at room temperature with an average relative error of 0.6%. In atomistic simulations, OPC3-pol's computational efficiency is in between that of 3- and 4-point nonpolarizable models; the model supports increased (4 fs) integration time step. OPC3-pol is tested in simulations of globular protein ubiquitin and a B-DNA dodecamer with several AMBER force fields, ff99SB, ff14SB, ff19SB, and OL15, demonstrating structure stability close to reference on multi-microsecond time scale. Simulation of an intrinsically disordered amyloid β-peptide yields an ensemble with the radius of gyration of a random coil. The proposed water model can be trivially adopted by any package that supports standard nonpolarizable force fields and water models; its intended use is in long classical atomistic simulations where water polarization effects are expected to be important.
Collapse
Affiliation(s)
- Yeyue Xiong
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg24061, United States
| | - Saeed Izadi
- Pharmaceutical Development Department, Genentech, South San Francisco94080, United States
| | - Alexey V Onufriev
- Department of Computer Science, Virginia Tech, Blacksburg24061, United States
- Department of Physics, Virginia Tech, Blacksburg24061, United States
- Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg24061, United States
| |
Collapse
|
33
|
Witek J, Heindel JP, Guan X, Leven I, Hao H, Naullage P, LaCour A, Sami S, Menger MFSJ, Cofer-Shabica DV, Berquist E, Faraji S, Epifanovsky E, Head-Gordon T. M-Chem: a Modular Software Package for Molecular Simulation that Spans Scientific Domains. Mol Phys 2022; 121:e2129500. [PMID: 37470065 PMCID: PMC10353727 DOI: 10.1080/00268976.2022.2129500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/06/2022] [Indexed: 10/10/2022]
Abstract
We present a new software package called M-Chem that is designed from scratch in C++ and parallelized on shared-memory multi-core architectures to facilitate efficient molecular simulations. Currently, M-Chem is a fast molecular dynamics (MD) engine that supports the evaluation of energies and forces from two-body to many-body all-atom potentials, reactive force fields, coarse-grained models, combined quantum mechanics molecular mechanics (QM/MM) models, and external force drivers from machine learning, augmented by algorithms that are focused on gains in computational simulation times. M-Chem also includes a range of standard simulation capabilities including thermostats, barostats, multi-timestepping, and periodic cells, as well as newer methods such as fast extended Lagrangians and high quality electrostatic potential generation. At present M-Chem is a developer friendly environment in which we encourage new software contributors from diverse fields to build their algorithms, models, and methods in our modular framework. The long-term objective of M-Chem is to create an interdisciplinary platform for computational methods with applications ranging from biomolecular simulations, reactive chemistry, to materials research.
Collapse
Affiliation(s)
- Jagna Witek
- Kenneth S. Pitzer Theory Center and Department of Chemistry
| | - Joseph P Heindel
- Kenneth S. Pitzer Theory Center and Department of Chemistry
- Chemical Sciences Division, Lawrence Berkeley National Laboratory
| | - Xingyi Guan
- Kenneth S. Pitzer Theory Center and Department of Chemistry
- Chemical Sciences Division, Lawrence Berkeley National Laboratory
| | - Itai Leven
- Kenneth S. Pitzer Theory Center and Department of Chemistry
| | - Hongxia Hao
- Kenneth S. Pitzer Theory Center and Department of Chemistry
| | | | - Allen LaCour
- Kenneth S. Pitzer Theory Center and Department of Chemistry
- Chemical Sciences Division, Lawrence Berkeley National Laboratory
| | - Selim Sami
- Kenneth S. Pitzer Theory Center and Department of Chemistry
| | - M F S J Menger
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - D Vale Cofer-Shabica
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19128 USA
| | - Eric Berquist
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Shirin Faraji
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Theory Center and Department of Chemistry
- Chemical Sciences Division, Lawrence Berkeley National Laboratory
- Department of Bioengineering and Chemical and Biomolecular Engineering University of California, Berkeley, CA, USA
| |
Collapse
|
34
|
Walker B, Liu C, Wait E, Ren P. Automation of AMOEBA polarizable force field for small molecules: Poltype 2. J Comput Chem 2022; 43:1530-1542. [PMID: 35778723 PMCID: PMC9329217 DOI: 10.1002/jcc.26954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/02/2022] [Accepted: 06/09/2022] [Indexed: 11/10/2022]
Abstract
A next-generation protocol (Poltype 2) has been developed which automatically generates AMOEBA polarizable force field parameters for small molecules. Both features and computational efficiency have been drastically improved. Notable advances include improved database transferability using SMILES, robust torsion fitting, non-aromatic ring torsion parameterization, coupled torsion-torsion parameterization, Van der Waals parameter refinement using ab initio dimer data and an intelligent fragmentation scheme that produces parameters with dramatically reduced ab initio computational cost. Additional improvements include better local frame assignment for atomic multipoles, automated formal charge assignment, Zwitterion detection, smart memory resource defaults, parallelized fragment job submission, incorporation of Psi4 quantum package, ab initio error handling, ionization state enumeration, hydration free energy prediction and binding free energy prediction. For validation, we have applied Poltype 2 to ~1000 FDA approved drug molecules from DrugBank. The ab initio molecular dipole moments and electrostatic potential values were compared with Poltype 2 derived AMOEBA counterparts. Parameters were further substantiated by calculating hydration free energy (HFE) on 40 small organic molecules and were compared with experimental data, resulting in an RMSE error of 0.59 kcal/mol. The torsion database has expanded to include 3543 fragments derived from FDA approved drugs. Poltype 2 provides a convenient utility for applications including binding free energy prediction for computational drug discovery. Further improvement will focus on automated parameter refinement by experimental liquid properties, expansion of the Van der Waals parameter database and automated parametrization of modified bio-fragments such as amino and nucleic acids.
Collapse
Affiliation(s)
- Brandon Walker
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Elizabeth Wait
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
35
|
Symons BCB, Popelier PLA. Application of Quantum Chemical Topology Force Field FFLUX to Condensed Matter Simulations: Liquid Water. J Chem Theory Comput 2022; 18:5577-5588. [PMID: 35939826 PMCID: PMC9476653 DOI: 10.1021/acs.jctc.2c00311] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
We present here the first application of the quantum
chemical topology
force field FFLUX to condensed matter simulations. FFLUX offers many-body
potential energy surfaces learnt exclusively from ab initio data using Gaussian process regression. FFLUX also includes high-rank,
polarizable multipole moments (up to quadrupole moments in this work)
that are learnt from the same ab initio calculations
as the potential energy surfaces. Many-body effects (where a body
is an atom) and polarization are captured by the machine learning
models. The choice to use machine learning in this way allows the
force field’s representation of reality to be improved (e.g., by including higher order many-body effects) with
little detriment to the computational scaling of the code. In this
manner, FFLUX is inherently future-proof. The “plug and play”
nature of the machine learning models also ensures that FFLUX can
be applied to any system of interest, not just liquid water. In this
work we study liquid water across a range of temperatures and compare
the predicted bulk properties to experiment as well as other state-of-the-art
force fields AMOEBA(+CF), HIPPO, MB-Pol and SIBFA21. We find that
FFLUX finds a place amongst these.
Collapse
Affiliation(s)
- Benjamin C B Symons
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great Britain
| | - Paul L A Popelier
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, Great Britain
| |
Collapse
|
36
|
Arabzadeh H, Liu C, Acevedo O, Ren P, Yang W, Albrecht-Schönzart T. Hydration of divalent lanthanides, Sm 2+ and Eu 2+ : A molecular dynamics study with polarizable AMOEBA force field. J Comput Chem 2022; 43:1286-1297. [PMID: 35648124 PMCID: PMC10052752 DOI: 10.1002/jcc.26933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/31/2022] [Accepted: 05/08/2022] [Indexed: 11/06/2022]
Abstract
The chemistry of divalent lanthanides, Ln2+ , is a growing sub-field of heavy element chemistry owing to new synthetic approaches. However, some theoretical aspects of these unusual cations are currently underdeveloped, especially as they relate to their dynamic properties in solution. In this work, we address the hydration of two of the classical Ln2+ cations, Sm2+ and Eu2+ , using atomic multipole optimized energetic for biomolecular applications (AMOEBA) force fields. These cations have not been parameterized to date with AMOEBA, and few studies are available because of their instability with respect to oxidation in aqueous media. Coordination numbers (CN's) of 8.2 and 8.1 respectively for Sm2+ and Eu2+ , and 8.8 for both Sm3+ and Eu3+ have been obtained and are in good agreement with the few available AIMD and X-ray absorption fine structures studies. The decreased CN of Ln2+ compared with Ln3+ arises from progressive water exchange events that indicates the gradual stabilization of 8-coordinate structures with respect to 9-coordinate geometries. Moreover, the effects of the chloride counter anions on the coordination of Ln2+ cations have been studied at different chloride concentrations in this work. Lastly, water exchange times of Ln2+ cations have been calculated to provide a comprehensive understanding of the behavior of Eu2+ and Sm2+ in aqueous chloride media.
Collapse
Affiliation(s)
- Hesam Arabzadeh
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Chengwen Liu
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Orlando Acevedo
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Pengyu Ren
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Wei Yang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | | |
Collapse
|
37
|
Symons BCB, Popelier PLA. Flexible multipole moments in smooth particle mesh Ewald. J Chem Phys 2022; 156:244107. [DOI: 10.1063/5.0095581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The smooth particle mesh Ewald sum is extended with additional force terms that arise from the so-called flexible multipole moments. These are multipole moments (of any rank) that depend explicitly on atomic positions in some local environment that can be made arbitrarily large. By introducing explicit dependence on atomic positions, flexible multipole moments are polarized by their local environment, allowing both intramolecular and intermolecular polarizations to be captured. Multipolar torques are discussed in detail, and it is shown that they arise naturally in the presented framework. Furthermore, we give details of how we validated our implementation of the flexible smooth particle mesh Ewald sum by considering two mathematical limits of the smooth particle mesh Ewald summation.
Collapse
Affiliation(s)
- Benjamin C. B. Symons
- Department of Chemistry, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Paul L. A. Popelier
- Department of Chemistry, The University of Manchester, Manchester M13 9PL, United Kingdom
| |
Collapse
|
38
|
Naseem-Khan S, Lagardère L, Narth C, Cisneros GA, Ren P, Gresh N, Piquemal JP. Development of the Quantum-Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed-Phase Molecular Dynamics Simulations. J Chem Theory Comput 2022; 18:3607-3621. [PMID: 35575306 PMCID: PMC10851344 DOI: 10.1021/acs.jctc.2c00029] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present the extension of the Sum of Interactions Between Fragments Ab initio Computed (SIBFA) many-body polarizable force field to condensed-phase molecular dynamics (MD) simulations. The quantum-inspired SIBFA procedure is grounded on simplified integrals obtained from localized molecular orbital theory and achieves full separability of its intermolecular potential. It embodies long-range multipolar electrostatics (up to quadrupole) coupled to a short-range penetration correction (up to charge-quadrupole), exchange repulsion, many-body polarization, many-body charge transfer/delocalization, exchange dispersion, and dispersion (up to C10). This enables the reproduction of all energy contributions of ab initio symmetry-adapted perturbation theory (SAPT(DFT)) gas-phase reference computations. The SIBFA approach has been integrated within the Tinker-HP massively parallel MD package. To do so, all SIBFA energy gradients have been derived and the approach has been extended to enable periodic boundary conditions simulations using smooth particle mesh Ewald. This novel implementation also notably includes a computationally tractable simplification of the many-body charge transfer/delocalization contribution. As a proof of concept, we perform a first computational experiment defining a water model fitted on a limited set of SAPT(DFT) data. SIBFA is shown to enable a satisfactory reproduction of both gas-phase energetic contributions and condensed-phase properties highlighting the importance of its physically motivated functional form.
Collapse
Affiliation(s)
- Sehr Naseem-Khan
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Louis Lagardère
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- IP2CT, FR 2622, CNRS, Sorbonne Université, 75005 Paris, France
| | | | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Nohad Gresh
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
| | - Jean-Philip Piquemal
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Institut Universitaire de France, 75005 Paris, France
| |
Collapse
|
39
|
Yang X, Liu C, Ren P. High Order Ab Initio Valence Force Field with Chemical Pattern Based Parameter Assignment. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2022; 21:431-447. [PMID: 35784097 PMCID: PMC9248749 DOI: 10.1142/s2737416521420047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Bonded (or valence) interactions, which directly determine the local structures of the molecules, are fundamental parts of molecular mechanics force fields (FFs). Most popular classical FFs adopt the simple harmonic models for bond stretching and angle bending and ignore cross-coupling effects among the valence terms. This may lead to less accurate vibrational properties and configurations in molecular dynamics (MD) simulations. AMOEBA models utilize an MM3(MM4)-style bonded interaction model, in which the vibrational anharmonicity, the coupling effects among different energy terms, and the out-of-plane bending for sp2-hybridized atoms are considered. In this work, we report the development of bonded interaction parameters for a wide range of chemistry based on quantum mechanics (QM). About 270 atomic types defined by SMARTS strings were used to model the valence interactions. Our results indicate that the resulting valence parameters produce accurate vibrational frequencies (RMSD from QM is less than ~36.6 cm-1) over a large set of molecules with diverse functional groups (445 molecules). By contrast, the harmonic models usually give an RMS error greater than 60 cm-1. Meanwhile, this model accurately reflects the potential energy surface of the out-of-plane bending. Our model can generally be applied to the AMOEBA family and any MM3(MM4)-based molecular mechanics FFs.
Collapse
|
40
|
Barcza B, Szirmai ÁB, Szántó KJ, Tajti A, Szalay PG. Comparison of approximate intermolecular potentials for ab initio fragment calculations on medium sized N-heterocycles. J Comput Chem 2022; 43:1079-1093. [PMID: 35478353 PMCID: PMC9321956 DOI: 10.1002/jcc.26866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/26/2022] [Accepted: 03/29/2022] [Indexed: 01/15/2023]
Abstract
The ground state intermolecular potential of bimolecular complexes of N‐heterocycles is analyzed for the impact of individual terms in the interaction energy as provided by various, conceptually different theories. Novel combinations with several formulations of the electrostatic, Pauli repulsion, and dispersion contributions are tested at both short‐ and long‐distance sides of the potential energy surface, for various alignments of the pyrrole dimer as well as the cytosine–uracil complex. The integration of a DFT/CCSD density embedding scheme, with dispersion terms from the effective fragment potential (EFP) method is found to provide good agreement with a reference CCSD(T) potential overall; simultaneously, a quantum mechanics/molecular mechanics approach using CHELPG atomic point charges for the electrostatic interaction, augmented by EFP dispersion and Pauli repulsion, comes also close to the reference result. Both schemes have the advantage of not relying on predefined force fields; rather, the interaction parameters can be determined for the system under study, thus being excellent candidates for ab initio modeling.
Collapse
Affiliation(s)
- Bónis Barcza
- Institute of Chemistry, Laboratory of Theoretical Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ádám B Szirmai
- Institute of Chemistry, Laboratory of Theoretical Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Katalin J Szántó
- Institute of Chemistry, Laboratory of Theoretical Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Attila Tajti
- Institute of Chemistry, Laboratory of Theoretical Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Péter G Szalay
- Institute of Chemistry, Laboratory of Theoretical Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| |
Collapse
|
41
|
Benda RV, Cancès E, Ehrlacher V, Stamm B. Multi-center decomposition of molecular densities: a mathematical perspective. J Chem Phys 2022; 156:164107. [DOI: 10.1063/5.0076630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The aim of this article is to analyze from a mathematical perspective some existing schemes to partition a molecular density into several atomic contributions, with a specific focus on Iterative Stockholder Atom (ISA) methods. We provide a unified mathematical framework to describe the latter family of methods and propose a new scheme, named L-ISA (for linear approximation of ISA), which generalizes the so-called Additive Variational Hirshfeld method. We prove several important mathematical properties of the ISA and L-ISA minimization problems and show that the so-called ISA algorithms can be viewed as alternating minimization schemes, which in turn enables us to obtain new convergence results for these numerical methods. Specific mathematical properties of the ISA decomposition for diatomic systems are also presented. Different schemes are numerically compared on different molecules and we discuss the advantages and drawbacks of each approach. Numerical results on diatomic systems illustrate the proven mathematical properties.
Collapse
|
42
|
López R, Díaz N, Francisco E, Martín-Pendás A, Suárez D. QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach. J Chem Inf Model 2022; 62:1510-1524. [PMID: 35212531 PMCID: PMC8965874 DOI: 10.1021/acs.jcim.1c01372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interacting quantum atoms (IQA) method decomposes the quantum mechanical (QM) energy of a molecular system in terms of one- and two-center (atomic) contributions within the context of the quantum theory of atoms in molecules. Here, we demonstrate that IQA, enhanced with molecular mechanics (MM) and Poisson-Boltzmann surface-area (PBSA) solvation methods, is naturally extended to the realm of hybrid QM/MM methodologies, yielding intra- and inter-residue energy terms that characterize all kinds of covalent and noncovalent bonding interactions. To test the robustness of this approach, both metal-water interactions and QM/MM boundary artifacts are characterized in terms of the IQA descriptors derived from QM regions of varying size in Zn(II)- and Mg(II)-water clusters. In addition, we analyze a homologous series of inhibitors in complex with a matrix metalloproteinase (MMP-12) by carrying out QM/MM-PBSA calculations on their crystallographic structures followed by IQA energy decomposition. Overall, these applications not only show the advantages of the IQA QM/MM approach but also address some of the challenges lying ahead for expanding the QM/MM methodology.
Collapse
Affiliation(s)
- Roberto López
- Departamento de Química y Física Aplicadas, Universidad de León, Facultad de Biología, Campus de Vegazana s/n, 24071 León (Castilla y León), Spain
| | - Natalia Díaz
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
| | - Evelio Francisco
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
| | - Angel Martín-Pendás
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
| | - Dimas Suárez
- Departamento de Química Física y Analítica, Universidad de Oviedo, Facultad de Química, Julián Clavería 8, 33006 Oviedo (Asturias), Spain
| |
Collapse
|
43
|
Abstract
We review different models for introducing electric polarization in force fields, with special focus on methods where polarization is modelled at the atomic charge level. While electric polarization has been included in several force fields, the common approach has been to focus on atomic dipole polarizability. Several approaches allow modelling electric polarization by using charge-flow between charge sites instead, but this has been less exploited, despite that atomic charges and charge-flow is expected to be more important than atomic dipoles and dipole polarizability. A number of challenges are required to be solved for charge-flow models to be incorporated into polarizable force fields, for example how to parameterize the models and how to make them computational efficient.
Collapse
Affiliation(s)
- Frank Jensen
- Department of Chemistry, Aarhus University, Denmark.
| |
Collapse
|
44
|
Das AK, Liu M, Head-Gordon T. Development of a Many-Body Force Field for Aqueous Alkali Metal and Halogen Ions: An Energy Decomposition Analysis Guided Approach. J Chem Theory Comput 2022; 18:953-967. [DOI: 10.1021/acs.jctc.1c00537] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Akshaya Kumar Das
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Meili Liu
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Teresa Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| |
Collapse
|
45
|
Torii H. Singular value decomposition analysis of the electron density changes occurring upon electrostatic polarization of water. RSC Adv 2022; 12:2564-2573. [PMID: 35425301 PMCID: PMC8979083 DOI: 10.1039/d1ra06649h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 01/12/2022] [Indexed: 12/31/2022] Open
Abstract
In-depth elucidation of how molecules are electrically polarized would be one key factor for understanding the properties of those molecules under various thermodynamic and/or spatial conditions. Here this problem is tackled for the case of hydrogen-bonded water by conducting singular value decomposition of the electron density changes that occur upon electrostatic polarization. It is shown that all those electron density changes are approximately described as linear combinations of ten orthonormal basis “vectors”. One main component is the interatomic charge transfer through each OH bond, while some others are characterized as the atomic dipolar polarizations, meaning that both of these components are important for the electrostatic polarization of water. The interaction parameters that reasonably well reproduce the induced dipole moments are derived, which indicate the extent of mixing of the two components in electrostatic polarization. The main features of the electron density changes that occur upon electrostatic polarization of water are elucidated by conducting singular value decomposition analysis of those changes.![]()
Collapse
Affiliation(s)
- Hajime Torii
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University 3-5-1 Johoku, Naka-ku Hamamatsu 432-8561 Japan +81-53-478-1624 +81-53-478-1624.,Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University 3-5-1 Johoku, Naka-ku Hamamatsu 432-8561 Japan
| |
Collapse
|
46
|
Bodo E. Perspectives in the Computational Modeling of New Generation, Biocompatible Ionic Liquids. J Phys Chem B 2022; 126:3-13. [PMID: 34978449 PMCID: PMC8762658 DOI: 10.1021/acs.jpcb.1c09476] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/15/2021] [Indexed: 12/11/2022]
Abstract
In this Perspective, I review the current state of computational simulations on ionic liquids with an emphasis on the recent biocompatible variants. These materials are used here as an example of relatively complex systems that highlights the limits of some of the approaches commonly used to study their structure and dynamics. The source of these limits consists of the coexistence of nontrivial electrostatic, many-body quantum effects, strong hydrogen bonds, and chemical processes affecting the mutual protonation state of the constituent molecular ions. I also provide examples on how it is possible to overcome these problems using suitable simulation paradigms and recently improved techniques that, I expect, will be gradually introduced in the state-of-the-art of computational simulations of ionic liquids.
Collapse
Affiliation(s)
- Enrico Bodo
- Chemistry Department, University of Rome “La Sapienza”, P. A. Moro 5, 00185 Rome, Italy
| |
Collapse
|
47
|
Abstract
Thole-style mutual induction models for molecular polarization have been adopted by several popular polarizable force fields (FFs) for their simplicity and transferability. The atomic polarizability parameters of these models are typically derived by fitting to ab initio or/and experimental molecular polarizabilities. In this work, we improve upon Thole polarizability parameters by employing both high-level quantum mechanics molecular polarizabilities and electrostatic potential (ESP) responses on three-dimensional grids. Our results indicate that the two approaches to derive atomic polarizability parameters are both effective, while the ESP approaches can also capture the polarization for the atoms with lone pair electrons. The resulting polarizability parameters have been validated on a set of over 7200 molecules covering the most common elements found in organic molecules (C, H, O, N, P, S, F, Cl, Br, and I). These parameters have also been tested on the experimentally measured molecular polarizabilities of 422 molecules. The final set of parameters derived in this work show notable improvement over the current AMOEBA set. The result is a highly transferable, expanded set of atomic polarizabilities defined by the local chemical environment in the form of SMARTS patterns. These parameters can be used directly in molecular mechanics polarizable potential energy functions such as AMOEBA, AMOEBA+, and other Thole-style models.
Collapse
Affiliation(s)
| | | | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
48
|
Zhang C, Zhao DX, Feng Y, Wang J, Yang ZZ. Energetics and J-coupling constants for Ala, Gly, and Val peptides demonstrated using ABEEM polarizable force field in vacuo and an aqueous solution. Phys Chem Chem Phys 2022; 24:4232-4250. [DOI: 10.1039/d1cp05676j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of an atom-bond electronegativity equalisation method at the σπ-level (ABEEM) polarisable force field (PFF) for peptides is presented. ABEEM PFF utilises a fluctuating charge model to explicitly describe...
Collapse
|
49
|
Fan D, Chen L, Wang C, Yin S, Mo Y. Inter-anion chalcogen bonds: Are they anti-electrostatic in nature? J Chem Phys 2021; 155:234302. [PMID: 34937369 DOI: 10.1063/5.0076872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Inter-anion hydrogen and halogen bonds have emerged as counterintuitive linkers and inspired us to expand the range of this unconventional bonding pattern. Here, the inter-anion chalcogen bond (IAChB) was proposed and theoretically analyzed in a series of complexes formed by negatively charged bidentate chalcogen bond donors with chloride anions. The kinetic stability of IAChB was evidenced by the minima on binding energy profiles and further supported by ab initio molecular dynamic simulations. The block-localized wave function (BLW) method and its subsequent energy decomposition (BLW-ED) approach were employed to elucidate the physical origin of IAChB. While all other energy components vary monotonically as anions get together, the electrostatic interaction behaves exceptionally as it experiences a Coulombic repulsion barrier. Before reaching the barrier, the electrostatic repulsion increases with the shortening Ch⋯Cl- distance as expected from classical electrostatics. However, after passing the barrier, the electrostatic repulsion decreases with the Ch⋯Cl- distance shortening and subsequently turns into the most favorable trend among all energy terms at short ranges, representing a dominating force for the kinetic stability of inter-anions. For comparison, all energy components exhibit the same trends and vary monotonically in the conventional counterparts where donors are neutral. By comparing inter-anions and their conventional counterparts, we found that only the electrostatic energy term is affected by the extra negative charge. Remarkably, the distinctive (nonmonotonic) electrostatic energy profiles were reproduced using quantum mechanical-based atomic multipoles, suggesting that the crucial electrostatic interaction in IAChB can be rationalized within the classical electrostatic theory just like conventional non-covalent interactions.
Collapse
Affiliation(s)
- Dan Fan
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Li Chen
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Changwei Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Shiwei Yin
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Yirong Mo
- Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, USA
| |
Collapse
|
50
|
Schuitemaker A, Aufort J, Koziara KB, Demichelis R, Raiteri P, Gale JD. Simulating the binding of key organic functional groups to aqueous calcium carbonate species. Phys Chem Chem Phys 2021; 23:27253-27265. [PMID: 34870292 DOI: 10.1039/d1cp04226b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction of organic molecules with mineral systems is relevant to a wide variety of scientific problems both in the environment and minerals processing. In this study, the coordination of small organics that contain the two most relevant functional groups for biomineralisation of calcium carbonate, namely carboxylate and ammonium, with the corresponding mineral ions are examined in aqueous solution. Specifically, two force fields have been examined based on rigid-ion or polarisable models, with the latter being within the AMOEBA formalism. Here the parameters for the rigid-ion model are determined to target the accurate reproduction of the hydration structure and solvation thermodynamics, while both force fields are designed to be compatible with the corresponding recently published models for aqueous calcium carbonate. The application of these force fields to ion pairing in aqueous solution is studied in order to quantitatively determine the extent of association.
Collapse
Affiliation(s)
- Alicia Schuitemaker
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| | - Julie Aufort
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| | - Katarzyna B Koziara
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| | - Raffaella Demichelis
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| | - Paolo Raiteri
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| | - Julian D Gale
- Curtin Institute for Computation, The Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, GPO Box U1987, 6845 Perth, Western Australia, Australia.
| |
Collapse
|