1
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Tu NTP, Williamson S, Johnson ER, Rowley CN. Modeling Intermolecular Interactions with Exchange-Hole Dipole Moment Dispersion Corrections to Neural Network Potentials. J Phys Chem B 2024; 128:8290-8302. [PMID: 39166778 DOI: 10.1021/acs.jpcb.4c02882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Neural network potentials (NNPs) are an innovative approach for calculating the potential energy and forces of a chemical system. In principle, these methods are capable of modeling large systems with an accuracy approaching that of a high-level ab initio calculation, but with a much smaller computational cost. Due to their training to density-functional theory (DFT) data and neglect of long-range interactions, some classes of NNPs require an additional term to include London dispersion physics. In this Perspective, we discuss the requirements for a dispersion model for use with an NNP, focusing on the MLXDM (Machine Learned eXchange-Hole Dipole Moment) model developed by our groups. This model is based on the DFT-based XDM dispersion correction, which calculates interatomic dispersion coefficients in terms of atomic moments and polarizabilities, both of which can be approximated effectively using neural networks.
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Affiliation(s)
| | - Siri Williamson
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4J3, Canada
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2
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Macaya L, González D, Vöhringer-Martinez E. Nonbonded Force Field Parameters from MBIS Partitioning of the Molecular Electron Density Improve Binding Affinity Predictions of the T4-Lysozyme Double Mutant. J Chem Inf Model 2024; 64:3269-3277. [PMID: 38546407 DOI: 10.1021/acs.jcim.3c01912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The use of computer simulation for binding affinity prediction is growing in drug discovery. However, its wider use is constrained by the accuracy of the free energy calculations. The key sources of error are the force fields used to depict molecular interactions and insufficient sampling of the configurational space. To improve the quality of the force field, we developed a Python-based computational workflow. The workflow described here uses the minimal basis iterative stockholder (MBIS) method to determine atomic charges and Lennard-Jones parameters from the polarized molecular density. This is done by performing electronic structure calculations on various configurations of the ligand when it is both bound and unbound. In addition, we validated a simulation procedure that accounts for the protein and ligand degrees of freedom to precisely calculate binding free energies. This was achieved by comparing the self-adjusted mixture sampling and nonequilibrium thermodynamic integration methods using various protein and ligand conformations. The accuracy of predicting binding affinity is improved by using MBIS-derived force field parameters and a validated simulation procedure. This improvement surpasses the chemical precision for the eight aromatic ligands, reaching a root-mean-square error of 0.7 kcal/mol.
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Affiliation(s)
- Luis Macaya
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070386 Concepción, Chile
| | - Duván González
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070386 Concepción, Chile
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070386 Concepción, Chile
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3
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Horton JT, Boothroyd S, Behara PK, Mobley DL, Cole DJ. A transferable double exponential potential for condensed phase simulations of small molecules. DIGITAL DISCOVERY 2023; 2:1178-1187. [PMID: 38013814 PMCID: PMC10408570 DOI: 10.1039/d3dd00070b] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/07/2023] [Indexed: 11/29/2023]
Abstract
The Lennard-Jones potential is the most widely-used function for the description of non-bonded interactions in transferable force fields for the condensed phase. This is not because it has an optimal functional form, but rather it is a legacy resulting from when computational expense was a major consideration and this potential was particularly convenient numerically. At present, it persists because the effort that would be required to re-write molecular modelling software and train new force fields has, until now, been prohibitive. Here, we present Smirnoff-plugins as a flexible framework to extend the Open Force Field software stack to allow custom force field functional forms. We deploy Smirnoff-plugins with the automated Open Force Field infrastructure to train a transferable, small molecule force field based on the recently-proposed double exponential functional form, on over 1000 experimental condensed phase properties. Extensive testing of the resulting force field shows improvements in transfer free energies, with acceptable conformational energetics, run times and convergence properties compared to state-of-the-art Lennard-Jones based force fields.
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Affiliation(s)
- Joshua T Horton
- School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | | | - Pavan Kumar Behara
- Department of Pharmaceutical Sciences, University of California Irvine California 92697 USA
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California Irvine California 92697 USA
- Department of Chemistry, University of California Irvine California 92697 USA
| | - Daniel J Cole
- School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne NE1 7RU UK
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4
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Csizi K, Reiher M. Universal
QM
/
MM
approaches for general nanoscale applications. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2023. [DOI: 10.1002/wcms.1656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | - Markus Reiher
- Laboratorium für Physikalische Chemie ETH Zürich Zürich Switzerland
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5
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Kříž K, Schmidt L, Andersson AT, Walz MM, van der Spoel D. An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation. J Chem Inf Model 2023; 63:412-431. [PMID: 36630710 PMCID: PMC9875315 DOI: 10.1021/acs.jcim.2c01127] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Indexed: 01/12/2023]
Abstract
Force fields (FFs) for molecular simulation have been under development for more than half a century. As with any predictive model, rigorous testing and comparisons of models critically depends on the availability of standardized data sets and benchmarks. While such benchmarks are rather common in the fields of quantum chemistry, this is not the case for empirical FFs. That is, few benchmarks are reused to evaluate FFs, and development teams rather use their own training and test sets. Here we present an overview of currently available tests and benchmarks for computational chemistry, focusing on organic compounds, including halogens and common ions, as FFs for these are the most common ones. We argue that many of the benchmark data sets from quantum chemistry can in fact be reused for evaluating FFs, but new gas phase data is still needed for compounds containing phosphorus and sulfur in different valence states. In addition, more nonequilibrium interaction energies and forces, as well as molecular properties such as electrostatic potentials around compounds, would be beneficial. For the condensed phases there is a large body of experimental data available, and tools to utilize these data in an automated fashion are under development. If FF developers, as well as researchers in artificial intelligence, would adopt a number of these data sets, it would become easier to compare the relative strengths and weaknesses of different models and to, eventually, restore the balance in the force.
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Affiliation(s)
- Kristian Kříž
- Department
of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124Uppsala, Sweden
| | - Lisa Schmidt
- Faculty
of Biosciences, University of Heidelberg, Heidelberg69117, Germany
| | - Alfred T. Andersson
- Department
of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124Uppsala, Sweden
| | - Marie-Madeleine Walz
- Department
of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124Uppsala, Sweden
| | - David van der Spoel
- Department
of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124Uppsala, Sweden
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6
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Madin OC, Shirts MR. Using physical property surrogate models to perform accelerated multi-fidelity optimization of force field parameters †. DIGITAL DISCOVERY 2023; 2:828-847. [PMCID: PMC10259372 DOI: 10.1039/d2dd00138a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 04/28/2023] [Indexed: 06/14/2023]
Abstract
Accurate representations of van der Waals dispersion–repulsion interactions play an important role in high-quality molecular dynamics simulations. Training the force field parameters used in the Lennard Jones (LJ) potential typically used to represent these interactions is challenging, generally requiring adjustment based on simulations of macroscopic physical properties. The large computational expense of these simulations, especially when many parameters must be trained simultaneously, limits the size of training data set and number of optimization steps that can be taken, often requiring modelers to perform optimizations within a local parameter region. To allow for more global LJ parameter optimization against large training sets, we introduce a multi-fidelity optimization technique which uses Gaussian process surrogate modeling to build inexpensive models of physical properties as a function of LJ parameters. This approach allows for fast evaluation of approximate objective functions, greatly accelerating searches over parameter space and enabling the use of optimization algorithms capable of searching more globally. In this study, we use an iterative framework which performs global optimization with differential evolution at the surrogate level, followed by validation at the simulation level and surrogate refinement. Using this technique on two previously studied training sets, containing up to 195 physical property targets, we refit a subset of the LJ parameters for the OpenFF 1.0.0 (Parsley) force field. We demonstrate that this multi-fidelity technique can find improved parameter sets compared to a purely simulation-based optimization by searching more broadly and escaping local minima. Additionally, this technique often finds significantly different parameter minima that have comparably accurate performance. In most cases, these parameter sets are transferable to other similar molecules in a test set. Our multi-fidelity technique provides a platform for rapid, more global optimization of molecular models against physical properties, as well as a number of opportunities for further refinement of the technique. We present a multi-fidelity method for optimizing nonbonded force field parameters against physical property data. Leveraging fast surrogate models, we accelerate the parameter search and find novel solutions that improve force field performance.![]()
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Affiliation(s)
- Owen C. Madin
- Department of Chemical & Biological Engineering, University of Colorado BoulderBoulderCOUSA80309
| | - Michael R. Shirts
- Department of Chemical & Biological Engineering, University of Colorado BoulderBoulderCOUSA80309
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7
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Oliveira MP, Gonçalves YMH, Ol Gheta SK, Rieder SR, Horta BAC, Hünenberger PH. Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set. J Chem Theory Comput 2022; 18:6757-6778. [PMID: 36190354 DOI: 10.1021/acs.jctc.2c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The level of accuracy that can be achieved by a force field is influenced by choices made in the interaction-function representation and in the relevant simulation parameters. These choices, referred to here as functional-form variants (FFVs), include for example the model resolution, the charge-derivation procedure, the van der Waals combination rules, the cutoff distance, and the treatment of the long-range interactions. Ideally, assessing the effect of a given FFV on the intrinsic accuracy of the force-field representation requires that only the specific FFV is changed and that this change is performed at an optimal level of parametrization, a requirement that may prove extremely challenging to achieve in practice. Here, we present a first attempt at such a comparison for one specific FFV, namely the choice of a united-atom (UA) versus an all-atom (AA) resolution in a force field for saturated acyclic (halo)alkanes. Two force-field versions (UA vs AA) are optimized in an automated way using the CombiFF approach against 961 experimental values for the pure-liquid densities ρliq and vaporization enthalpies ΔHvap of 591 compounds. For the AA force field, the torsional and third-neighbor Lennard-Jones parameters are also refined based on quantum-mechanical rotational-energy profiles. The comparison between the UA and AA resolutions is also extended to properties that have not been included as parameterization targets, namely the surface-tension coefficient γ, the isothermal compressibility κT, the isobaric thermal-expansion coefficient αP, the isobaric heat capacity cP, the static relative dielectric permittivity ϵ, the self-diffusion coefficient D, the shear viscosity η, the hydration free energy ΔGwat, and the free energy of solvation ΔGche in cyclohexane. For the target properties ρliq and ΔHvap, the UA and AA resolutions reach very similar levels of accuracy after optimization. For the nine other properties, the AA representation leads to more accurate results in terms of η; comparably accurate results in terms of γ, κT, αP, ϵ, D, and ΔGche; and less accurate results in terms of cP and ΔGwat. This work also represents a first step toward the calibration of a GROMOS-compatible force field at the AA resolution.
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Affiliation(s)
- Marina P Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Yan M H Gonçalves
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - S Kashef Ol Gheta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A C Horta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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8
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González D, Macaya L, Castillo-Orellana C, Verstraelen T, Vogt-Geisse S, Vöhringer-Martinez E. Nonbonded Force Field Parameters from Minimal Basis Iterative Stockholder Partitioning of the Molecular Electron Density Improve CB7 Host-Guest Affinity Predictions. J Chem Inf Model 2022; 62:4162-4174. [PMID: 35959540 DOI: 10.1021/acs.jcim.2c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Binding affinity prediction by means of computer simulation has been increasingly incorporated in drug discovery projects. Its wide application, however, is limited by the prediction accuracy of the free energy calculations. The main error sources are force fields used to describe molecular interactions and incomplete sampling of the configurational space. Organic host-guest systems have been used to address force field quality because they share similar interactions found in ligands and receptors, and their rigidity facilitates configurational sampling. Here, we test the binding free energy prediction accuracy for 14 guests with an aromatic or adamantane core and the CB7 host using molecular electron density derived nonbonded force field parameters. We developed a computational workflow written in Python to derive atomic charges and Lennard-Jones parameters with the Minimal Basis Iterative Stockholder method using the polarized electron density of several configurations of each guest in the bound and unbound states. The resulting nonbonded force field parameters improve binding affinity prediction, especially for guests with an adamantane core in which repulsive exchange and dispersion interactions to the host dominate.
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Affiliation(s)
- Duván González
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070386 Concepción, Chile
| | - Luis Macaya
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070386 Concepción, Chile
| | - Carlos Castillo-Orellana
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070386 Concepción, Chile
| | - Toon Verstraelen
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark-Zwijnnarde 46, B-9052 Ghent, Belgium
| | - Stefan Vogt-Geisse
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070386 Concepción, Chile
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070386 Concepción, Chile
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9
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Ringrose C, Horton JT, Wang LP, Cole DJ. Exploration and validation of force field design protocols through QM-to-MM mapping. Phys Chem Chem Phys 2022; 24:17014-17027. [PMID: 35792069 DOI: 10.1039/d2cp02864f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The scale of the parameter optimisation problem in traditional molecular mechanics force field construction means that design of a new force field is a long process, and sub-optimal choices made in the early stages can persist for many generations. We hypothesise that careful use of quantum mechanics to inform molecular mechanics parameter derivation (QM-to-MM mapping) should be used to significantly reduce the number of parameters that require fitting to experiment and increase the pace of force field development. Here, we design and train a collection of 15 new protocols for small, organic molecule force field derivation, and test their accuracy against experimental liquid properties. Our best performing model has only seven fitting parameters, yet achieves mean unsigned errors of just 0.031 g cm-3 and 0.69 kcal mol-1 in liquid densities and heats of vaporisation, compared to experiment. The software required to derive the designed force fields is freely available at https://github.com/qubekit/QUBEKit.
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Affiliation(s)
- Chris Ringrose
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
| | - Joshua T Horton
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
| | - Lee-Ping Wang
- Department of Chemistry, The University of California at Davis, Davis, California 95616, USA
| | - Daniel J Cole
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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10
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Boothroyd S, Madin OC, Mobley DL, Wang LP, Chodera JD, Shirts MR. Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties. J Chem Theory Comput 2022; 18:3577-3592. [PMID: 35533269 PMCID: PMC9254460 DOI: 10.1021/acs.jctc.1c01268] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Developing a sufficiently accurate classical force field representation of molecules is key to realizing the full potential of molecular simulations as a route to gaining a fundamental insight into a broad spectrum of chemical and biological phenomena. This is only possible, however, if the many complex interactions between molecules of different species in the system are accurately captured by the model. Historically, the intermolecular van der Waals (vdW) interactions have primarily been trained against densities and enthalpies of vaporization of pure (single-component) systems, with occasional usage of hydration free energies. In this study, we demonstrate how including physical property data of binary mixtures can better inform these parameters, encoding more information about the underlying physics of the system in complex chemical mixtures. To demonstrate this, we retrain a select number of Lennard-Jones parameters describing the vdW interactions of the OpenFF 1.0.0 (Parsley) fixed charge force field against training sets composed of densities and enthalpies of mixing for binary liquid mixtures as well as densities and enthalpies of vaporization of pure liquid systems and assess the performance of each of these combinations. We show that retraining against the mixture data improves the force field's ability to reproduce mixture properties, including solvation free energies, correcting some systematic errors that exist when training vdW interactions against properties of pure systems only.
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Affiliation(s)
- Simon Boothroyd
- Boothroyd Scientific Consulting Ltd., 71-75 Shelton Street, London WC2H 9JQ, Greater London, U.K
| | - Owen C Madin
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - David L Mobley
- Department of Chemistry, University of California, Irvine, California 92617, United States
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92617, United States
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - John D Chodera
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
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11
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Rupakheti CR, MacKerell AD, Roux B. Global Optimization of the Lennard-Jones Parameters for the Drude Polarizable Force Field. J Chem Theory Comput 2021; 17:7085-7095. [PMID: 34609863 DOI: 10.1021/acs.jctc.1c00664] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Molecular dynamics (MD) simulations based on atomic models play an important role in the drug-discovery process to screen molecules, estimate binding free energies, and optimize lead compounds in chemical space. Accurate computations of thermodynamic and kinetic properties using MD simulations are highly dependent on the accuracy of the underlying atomic force field. In this context, going beyond the nonpolarizable fixed-charge model by accounting explicitly for induced polarization is highly desirable. The CHARMM polarizable force field based on classical Drude oscillators, in which an auxiliary charged particle is attached via a harmonic spring to its parent nucleus, offers both a computationally convenient and rigorous framework to model explicitly induced electronic polarization in MD simulations. For any molecule of interest, electrostatic partial charges, atomic polarizabilities, and Thole shielding factors, as well as bonded parameters can either be determined from ab initio calculations or ascribed from the knowledge-based library of the CHARMM Generalized force field. While this approach is fairly reliable in general, it is well understood that the overall accuracy of the models with respect to thermodynamic properties such as bulk density, enthalpies, and solvation free energies is particularly sensitive to the nonbonded Lennard-Jones (LJ) parameters. In the present study, we systematically refined the set of LJ parameters for the atom types available in the Drude force field to best match the experimental thermodynamic properties for 416 small druglike organic molecules. To further test the transferability of the optimized parameters, the hydration free energy of 372 molecules was computed. The calculations resulted in a small average error of 0.46 kcal/mol and a Pearson R of 0.9, representing a significant improvement over the additive GAFF force field in our previous study, where an average error of ∼2 kcal/mol was obtained. Such an improvement is consistent with the ability of the polarizable Drude model to more accurately model interactions in different environments. The effort provides a roadmap for the global optimization of force field parameters using experimental data. It is hoped that the present effort will further the application of the Drude polarizable force field in molecular simulations including drug design and discovery.
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Affiliation(s)
- Chetan R Rupakheti
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, Illinois 60637, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, Illinois 60637, United States
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12
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P. Oliveira M, Hünenberger PH. Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: application to oxygen and nitrogen compounds. Phys Chem Chem Phys 2021; 23:17774-17793. [PMID: 34350931 PMCID: PMC8386690 DOI: 10.1039/d1cp02001c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/30/2021] [Indexed: 12/04/2022]
Abstract
The CombiFF approach is a workflow for the automated refinement of force-field parameters against experimental condensed-phase data, considering entire classes of organic molecules constructed using a fragment library via combinatorial isomer enumeration. One peculiarity of this approach is that it relies on an electronegativity-equalization scheme to account for induction effects within molecules, with values of the atomic hardness and electronegativity as electrostatic parameters, rather than the partial charges themselves. In a previous article [M. P. Oliveira, M. Andrey, S. R. Rieder, L. Kern, D. F. Hahn, S. Riniker, B. A. C. Horta and P. H. Hünenberger, J. Chem. Theory. Comput. 2020, 16, 7525], CombiFF was introduced and applied to calibrate a GROMOS-compatible united-atom force field for the saturated acyclic (halo-)alkane family. Here, this scheme is employed for the construction of a corresponding force field for saturated acyclic compounds encompassing eight common chemical functional groups involving oxygen and/or nitrogen atoms, namely: ether, aldehyde, ketone, ester, alcohol, carboxylic acid, amine, and amide. Monofunctional as well as homo-polyfunctional compounds are considered. A total of 1712 experimental liquid densities ρliq and vaporization enthalpies ΔHvap concerning 1175 molecules are used for the calibration (339 molecules) and validation (836 molecules) of the 102 non-bonded interaction parameters of the force field. Using initial parameter values based on the GROMOS 2016H66 parameter set, convergence is reached after five iterations. Given access to one processor per simulated system, this operation only requires a few days of wall-clock computing time. After optimization, the root-mean-square deviations from experiment are 29.9 (22.4) kg m-3 for ρliq and 4.1 (5.5) kJ mol-1 for ΔHvap for the calibration (validation) set. Thus, a very good level of agreement with experiment is achieved in terms of these two properties, although the errors are inhomogeneously distributed across the different chemical functional groups.
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Affiliation(s)
- Marina P. Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCICH-8093 ZürichSwitzerland+41 44 632 5503
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCICH-8093 ZürichSwitzerland+41 44 632 5503
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13
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Qiu Y, Shan W, Zhang H. Force Field Benchmark of Amino Acids. 3. Hydration with Scaled Lennard-Jones Interactions. J Chem Inf Model 2021; 61:3571-3582. [PMID: 34185520 DOI: 10.1021/acs.jcim.1c00339] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Classical protein force fields were reported with too weak protein-water interactions relative to protein-protein interactions, leading to more compact structures and artificial protein aggregation. Here we investigated the impacts of scaled Lennard-Jones (LJ) interactions on the hydration of amino acids and the simulation of folded and intrinsically disordered proteins (IDPs). The obtained optimal scaling parameters reproduce accurately hydration free energies of neutral amino acid side chain analogues and do not affect the compactness and structural stability of folded proteins significantly. The scaling leads to less compact IDPs and varies from case to case. Strengthening the interactions between protein and water oxygen or hydrogen atoms by increasing the interacting LJ well depth (ε) appears more effective than weakening protein-protein interactions by reducing the interacting dispersion coefficients (C6). We demonstrate that weakening water-water interactions is a solution as well to obtaining more favorable protein-water interactions in an indirect way, although modern force fields like Amber ff19SB and a99SB-disp tend to use water models with strong water-water interactions. This is likely a compromise between strong protein-protein interactions and strong water-water interactions. Independent optimization of protein force fields and water models is therefore needed to make both interactions more close to reality, leading to good accuracy without bias or scaling.
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Affiliation(s)
- Yejie Qiu
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Wenjie Shan
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
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14
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Spoel D, Zhang J, Zhang H. Quantitative predictions from molecular simulations using explicit or implicit interactions. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1560] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- David Spoel
- Uppsala Center for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology Uppsala University Uppsala Sweden
| | - Jin Zhang
- Department of Chemistry Southern University of Science and Technology Shenzhen China
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering University of Science and Technology Beijing Beijing China
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15
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Price AJA, Bryenton KR, Johnson ER. Requirements for an accurate dispersion-corrected density functional. J Chem Phys 2021; 154:230902. [PMID: 34241263 DOI: 10.1063/5.0050993] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Post-self-consistent dispersion corrections are now the norm when applying density-functional theory to systems where non-covalent interactions play an important role. However, there is a wide range of base functionals and dispersion corrections available from which to choose. In this work, we opine on the most desirable requirements to ensure that both the base functional and dispersion correction, individually, are as accurate as possible for non-bonded repulsion and dispersion attraction. The base functional should be dispersionless, numerically stable, and involve minimal delocalization error. Simultaneously, the dispersion correction should include finite damping, higher-order pairwise dispersion terms, and electronic many-body effects. These criteria are essential for avoiding reliance on error cancellation and obtaining correct results from correct physics.
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Affiliation(s)
- Alastair J A Price
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd., Halifax, Nova Scotia B3H 4R2, Canada
| | - Kyle R Bryenton
- Department of Physics and Atmospheric Science, Dalhousie University, 6310 Coburg Rd., Halifax, Nova Scotia B3H 4R2, Canada
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd., Halifax, Nova Scotia B3H 4R2, Canada
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16
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Jedwabny W, Dyguda-Kazimierowicz E, Pernal K, Szalewicz K, Patkowski K. Extension of an Atom-Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts. J Phys Chem A 2021; 125:1787-1799. [PMID: 33620223 PMCID: PMC8028329 DOI: 10.1021/acs.jpca.0c11347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/10/2021] [Indexed: 12/17/2022]
Abstract
A dispersion function Das in the form of a damped atom-atom asymptotic expansion fitted to ab initio dispersion energies from symmetry-adapted perturbation theory was improved and extended to systems containing heavier halogen atoms. To illustrate its performance, the revised Das function was implemented in the multipole first-order electrostatic and second-order dispersion (MED) scoring model. The extension has allowed applications to a much larger set of biocomplexes than it was possible with the original Das. A reasonable correlation between MED and experimentally determined inhibitory activities was achieved in a number of test cases, including structures featuring nonphysically shortened intermonomer distances, which constitute a particular challenge for binding strength predictions. Since the MED model is also computationally efficient, it can be used for reliable and rapid assessment of the ligand affinity or multidimensional scanning of amino acid side-chain conformations in the process of rational design of novel drugs or biocatalysts.
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Affiliation(s)
- Wiktoria Jedwabny
- Department
of Chemistry, Wrocław University of
Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Edyta Dyguda-Kazimierowicz
- Department
of Chemistry, Wrocław University of
Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Katarzyna Pernal
- Institute
of Physics, Łódź University
of Technology, Wólczańska
219, 90-924 Łódź, Poland
| | - Krzysztof Szalewicz
- Department
of Physics and Astronomy, University of
Delaware, Newark, Delaware 19716, United
States
| | - Konrad Patkowski
- Department
of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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17
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Oliveira MP, Andrey M, Rieder SR, Kern L, Hahn DF, Riniker S, Horta BAC, Hünenberger PH. Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes. J Chem Theory Comput 2020; 16:7525-7555. [DOI: 10.1021/acs.jctc.0c00683] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Marina P. Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Maurice Andrey
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R. Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Leyla Kern
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - David F. Hahn
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A. C. Horta
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
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18
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Kashefolgheta S, Oliveira MP, Rieder SR, Horta BAC, Acree WE, Hünenberger PH. Evaluating Classical Force Fields against Experimental Cross-Solvation Free Energies. J Chem Theory Comput 2020; 16:7556-7580. [DOI: 10.1021/acs.jctc.0c00688] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Sadra Kashefolgheta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Marina P. Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R. Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A. C. Horta
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - William E. Acree
- Department of Chemistry, University of North Texas, 1155 Union Circle Drive #305070, Denton, Texas 76203, United States
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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19
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Mohebifar M, Rowley CN. An efficient and accurate model for water with an improved non-bonded potential. J Chem Phys 2020; 153:134105. [PMID: 33032419 DOI: 10.1063/5.0014469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A molecular mechanical model for liquid water is developed that uses a physically motivated potential to represent Pauli repulsion and dispersion instead of the standard Lennard-Jones potential. The model has three atomic sites and a virtual site located on the ∠HOH bisector (i.e., a TIP4P-type model). Pauli-repulsive interactions are represented using a Buckingham-type exponential decay potential. Dispersion interactions are represented by both C6/r6 and C8/r8 terms. This higher order C8 dispersion term has been neglected by most force fields. The ForceBalance code was used to define parameters that optimally reproduce the experimental physical properties of liquid water. The resulting model is in good agreement with the experimental density, dielectric constant, enthalpy of vaporization, isothermal compressibility, thermal expansion coefficient, diffusion coefficient, and radial distribution function. A graphical processing unit-accelerated implementation of this improved non-bonded potential can be employed in OpenMM without modification by using the CustomNonBondedForce feature. The efficient and automated parameterization of these non-bonded potentials provides a rational strategy to define a new molecular mechanical force field that treats repulsion and dispersion interactions more rigorously without major modifications to the existing simulation codes or a substantially larger computational cost.
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Affiliation(s)
- Mohamad Mohebifar
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador A1B 3X7, Canada
| | - Christopher N Rowley
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador A1B 3X7, Canada
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20
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Kelly BD, Smith WR. A Simple Method for Including Polarization Effects in Solvation Free Energy Calculations When Using Fixed-Charge Force Fields: Alchemically Polarized Charges. ACS OMEGA 2020; 5:17170-17181. [PMID: 32715202 PMCID: PMC7376688 DOI: 10.1021/acsomega.0c01148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/11/2020] [Indexed: 06/11/2023]
Abstract
The incorporation of polarizability in classical force-field molecular simulations is an ongoing area of research. We focus here on its application to hydration free energy simulations of organic molecules. In contrast to computationally complex approaches involving the development of explicitly polarizable force fields, we present herein a simple methodology for incorporating polarization into such simulations using standard fixed-charge force fields, which we call the alchemically polarized charges (APolQ) method. APolQ employs a standard classical alchemical free energy change simulation to calculate the free energy difference between a fully polarized solute particle in a condensed phase and its unpolarized state in a vacuum. APolQ can in principle be applied to any microscopically homogeneous system (e.g., pure or mixed solvents). We applied APolQ to hydration free energy data for a test set of 45 neutral solute molecules in the FreeSolv database and compared results obtained using three different water models (SPC/E, TIP3P, and OPC3) and using minimal basis iterative Stockholder (MBIS) and restrained electrostatic potential (RESP) partial charge methodologies. In comparison with AM1-BCC, we found that APolQ outperforms it for the test set. Despite our method using default GAFF parameters, the MBIS partial charges yield absolute average deviations 1.5-1.9 kJ mol-1 lower than using AM1 bond charge correction (AM1-BCC). We conjecture that this method can be further improved by fitting the Lennard-Jones and torsional parameters to partial charges derived using MBIS or RESP methodologies.
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Affiliation(s)
- Braden D. Kelly
- Department
of Mathematics and Statistics, University
of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - William R. Smith
- Department
of Mathematics and Statistics, University
of Guelph, Guelph, Ontario N1G 2W1, Canada
- Department
of Chemical Engineering, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Faculty
of Science, Ontario Tech University, Oshawa, Ontario L1H 7K4, Canada
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21
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Kamiya N, Kayanuma M, Fujitani H, Shinoda K. A New Lipid Force Field (FUJI). J Chem Theory Comput 2020; 16:3664-3676. [PMID: 32384238 DOI: 10.1021/acs.jctc.9b01195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
To explore inhomogeneous and anisotropic systems such as lipid bilayers, the Lennard-Jones particle mesh Ewald (LJ-PME) method has been applied without a conventional isotropic dispersion correction. As the popular AMBER and CHARMM lipid force fields were developed using a cutoff scheme, their lipid bilayers unacceptably shrink when using the LJ-PME method. In this study, a new all-atom lipid force field (FUJI) was developed on the basis of the AMBER force-field scheme including the Lipid14 van der Waals parameters. Point charges were calculated using the restrained electrostatic potentials of many lipid conformers. Further, torsion energy profiles were calculated using high-level ab initio molecular orbitals (LCCSD(T)/Aug-cc-pVTZ//LMP2/Aug-cc-pVTZ), following which the molecular mechanical dihedral parameters were derived through a fast Fourier transform. By incorporation of these parameters into a new lipid force field without fitting experimental data, the desired lipid characteristics such as the area per lipid and lateral diffusion coefficients were obtained through GROMACS molecular dynamics simulations using the LJ-PME method and virtual hydrogen sites. The calculated area per lipid and lateral diffusion coefficients showed satisfactory agreement with experimental data. Furthermore, the electron-density profiles along the membrane normal were calculated for pure lipid bilayers, and the resulting membrane thicknesses agreed well with the experimental values. As the new lipid force field is compatible with FUJI for protein and small molecules, the new FUJI force field will offer accurate modeling for complex systems consisting of various membrane proteins and lipids.
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Affiliation(s)
- Nozomu Kamiya
- Fujitsu Limited Bio-IT R&D Office, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Megumi Kayanuma
- Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Hideaki Fujitani
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Keiko Shinoda
- Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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22
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Visscher KM, Geerke DP. Deriving a Polarizable Force Field for Biomolecular Building Blocks with Minimal Empirical Calibration. J Phys Chem B 2020; 124:1628-1636. [PMID: 32073849 PMCID: PMC7061328 DOI: 10.1021/acs.jpcb.9b10903] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/23/2020] [Indexed: 12/31/2022]
Abstract
Force field parametrization involves a complex set of linked optimization problems, with the goal of describing complex molecular interactions by using simple classical potential-energy functions that model Coulomb interactions, dispersion, and exchange repulsion. These functions comprise a set of atomic (and molecular) parameters and together with the bonded terms they constitute the molecular mechanics force field. Traditionally, many of these parameters have been fitted in a calibration approach in which experimental measures for thermodynamic and other relevant properties of small-molecule compounds are used for fitting and validation. As these approaches are laborious and time-consuming and represent an underdetermined optimization problem, we study methods to fit and derive an increasing number of parameters directly from electronic structure calculations, in order to greatly reduce possible parameter space for the remaining free parameters. In the current work we investigate a polarizable model with a higher order dispersion term for use in biomolecular simulation. Results for 49 biochemically relevant molecules are presented including updated parameters for hydrocarbon side chains. We show that our recently presented set of QM/MM derived atomic polarizabilities can be used in direct conjunction with partial charges and a higher order dispersion model that are quantum-mechanically determined, to freeze nearly all (i.e., 132 out of 138) nonbonded parameters to their quantum determined values.
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Affiliation(s)
- Koen M. Visscher
- AIMMS Division of Molecular
Toxicology, De Boelelaan
1108, 1081 HV Amsterdam, The Netherlands
| | - Daan P. Geerke
- AIMMS Division of Molecular
Toxicology, De Boelelaan
1108, 1081 HV Amsterdam, The Netherlands
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23
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Inakollu VS, Geerke DP, Rowley CN, Yu H. Polarisable force fields: what do they add in biomolecular simulations? Curr Opin Struct Biol 2020; 61:182-190. [PMID: 32044671 DOI: 10.1016/j.sbi.2019.12.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022]
Abstract
The quality of biomolecular simulations critically depends on the accuracy of the force field used to calculate the potential energy of the molecular configurations. Currently, most simulations employ non-polarisable force fields, which describe electrostatic interactions as the sum of Coulombic interactions between fixed atomic charges. Polarisation of these charge distributions is incorporated only in a mean-field manner. In the past decade, extensive efforts have been devoted to developing simple, efficient, and yet generally applicable polarisable force fields for biomolecular simulations. In this review, we summarise the latest developments in accounting for key biomolecular interactions with polarisable force fields and applications to address challenging biological questions. In the end, we provide an outlook for future development in polarisable force fields.
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Affiliation(s)
- Vs Sandeep Inakollu
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong NSW 2522, Australia; Molecular Horizons, University of Wollongong, Wollongong NSW 2522 Australia; Illawarra Health and Medical Research Institute, Wollongong NSW 2522, Australia
| | - Daan P Geerke
- AIMMS Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands.
| | - Christopher N Rowley
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada.
| | - Haibo Yu
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong NSW 2522, Australia; Molecular Horizons, University of Wollongong, Wollongong NSW 2522 Australia; Illawarra Health and Medical Research Institute, Wollongong NSW 2522, Australia.
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24
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Lahey SLJ, Rowley CN. Simulating protein-ligand binding with neural network potentials. Chem Sci 2020; 11:2362-2368. [PMID: 34084397 PMCID: PMC8157423 DOI: 10.1039/c9sc06017k] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 01/22/2020] [Indexed: 01/14/2023] Open
Abstract
Drug molecules adopt a range of conformations both in solution and in their protein-bound state. The strain and reduced flexibility of bound drugs can partially counter the intermolecular interactions that drive protein-ligand binding. To make accurate computational predictions of drug binding affinities, computational chemists have attempted to develop efficient empirical models of these interactions, although these methods are not always reliable. Machine learning has allowed the development of highly-accurate neural-network potentials (NNPs), which are capable of predicting the stability of molecular conformations with accuracy comparable to state-of-the-art quantum chemical calculations but at a billionth of the computational cost. Here, we demonstrate that these methods can be used to represent the intramolecular forces of protein-bound drugs within molecular dynamics simulations. These simulations are shown to be capable of predicting the protein-ligand binding pose and conformational component of the absolute Gibbs energy of binding for a set of drug molecules. Notably, the conformational energy for anti-cancer drug erlotinib binding to its target was found to be considerably overestimated by a molecular mechanical model, while the NNP predicts a more moderate value. Although the ANI-1ccX NNP was not trained to describe ionic molecules, reasonable binding poses are predicted for charged ligands, but this method is not suitable for modeling charged ligands in solution.
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Affiliation(s)
- Shae-Lynn J Lahey
- Memorial University of Newfoundland St. John's Newfoundland and Labrador Canada
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25
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Otero-de-la-Roza A, LeBlanc LM, Johnson ER. What is “many-body” dispersion and should I worry about it? Phys Chem Chem Phys 2020; 22:8266-8276. [DOI: 10.1039/d0cp01213k] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
“Many-body” dispersion can refer to two distinct phenomena, here termed electronic and atomic many-body effects, both of which cause the dispersion energy to be non-additive.
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Affiliation(s)
- A. Otero-de-la-Roza
- Departamento de Química Física y Analítica and MALTA-Consolider Team
- Facultad de Química
- Universidad de Oviedo
- 33006 Oviedo
- Spain
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26
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Bashardanesh Z, Elf J, Zhang H, van der Spoel D. Rotational and Translational Diffusion of Proteins as a Function of Concentration. ACS OMEGA 2019; 4:20654-20664. [PMID: 31858051 PMCID: PMC6906769 DOI: 10.1021/acsomega.9b02835] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/14/2019] [Indexed: 05/21/2023]
Abstract
Atomistic simulations of three different proteins at different concentrations are performed to obtain insight into protein mobility as a function of protein concentration. We report on simulations of proteins from diluted to the physiological water concentration (about 70% of the mass). First, the viscosity was computed and found to increase by a factor of 7-9 going from pure water to the highest protein concentration, in excellent agreement with in vivo nuclear magnetic resonance results. At a physiological concentration of proteins, the translational diffusion is found to be slowed down to about 30% of the in vitro values. The slow-down of diffusion found here using atomistic models is slightly more than that of a hard sphere model that neglects the electrostatic interactions. Interestingly, rotational diffusion of proteins is slowed down somewhat more (by about 80-95% compared to in vitro values) than translational diffusion, in line with experimental findings and consistent with the increased viscosity. The finding that rotation is retarded more than translation is attributed to solvent-separated clustering. No direct interactions between the proteins are found, and the clustering can likely be attributed to dispersion interactions that are stronger between proteins than between protein and water. Based on these simulations, we can also conclude that the internal dynamics of the proteins in our study are affected only marginally under crowding conditions, and the proteins become somewhat more stable at higher concentrations. Simulations were performed using a force field that was tuned for dealing with crowding conditions by strengthening the protein-water interactions. This force field seems to lead to a reproducible partial unfolding of an α-helix in one of the proteins, an effect that was not observed in the unmodified force field.
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Affiliation(s)
- Zahedeh Bashardanesh
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-75124 Uppsala, Sweden
| | - Johan Elf
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-75124 Uppsala, Sweden
| | - Haiyang Zhang
- Department
of Biological Science and Engineering, School of Chemistry and Biological
Engineering, University of Science and Technology
Beijing, 100083 Beijing, China
| | - David van der Spoel
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-75124 Uppsala, Sweden
- E-mail: . Phone: +46 18 4714205
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27
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Oliveira Bortot L, Bashardanesh Z, van der Spoel D. Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation. J Chem Inf Model 2019; 60:322-331. [DOI: 10.1021/acs.jcim.9b00971] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Leandro Oliveira Bortot
- Laboratory of Biological Physics, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Avenida do Café s/n, 14040-903 Ribeirão Preto-SP, Brazil
| | - Zahedeh Bashardanesh
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden
| | - David van der Spoel
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden
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28
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Cole DJ, Cabeza de Vaca I, Jorgensen WL. Computation of protein-ligand binding free energies using quantum mechanical bespoke force fields. MEDCHEMCOMM 2019; 10:1116-1120. [PMID: 31391883 PMCID: PMC6644397 DOI: 10.1039/c9md00017h] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/26/2019] [Indexed: 12/17/2022]
Abstract
A quantum mechanical bespoke molecular mechanics force field is derived for the L99A mutant of T4 lysozyme and used to compute absolute binding free energies of six benzene analogs to the protein. Promising agreement between theory and experiment highlights the potential for future use of system-specific force fields in computer-aided drug design.
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Affiliation(s)
- Daniel J Cole
- School of Natural and Environmental Sciences , Newcastle University , Newcastle upon Tyne NE1 7RU , UK .
| | - Israel Cabeza de Vaca
- Department of Chemistry , Yale University , New Haven , Connecticut 06520-8107 , USA
| | - William L Jorgensen
- Department of Chemistry , Yale University , New Haven , Connecticut 06520-8107 , USA
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29
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Tetrel Interactions from an Interacting Quantum Atoms Perspective. Molecules 2019; 24:molecules24122204. [PMID: 31212835 PMCID: PMC6632095 DOI: 10.3390/molecules24122204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/05/2019] [Accepted: 06/07/2019] [Indexed: 02/06/2023] Open
Abstract
Tetrel bonds, the purportedly non-covalent interaction between a molecule that contains an atom of group 14 and an anion or (more generally) an atom or molecule with lone electron pairs, are under intense scrutiny. In this work, we perform an interacting quantum atoms (IQA) analysis of several simple complexes formed between an electrophilic fragment (A) (CH3F, CH4, CO2, CS2, SiO2, SiH3F, SiH4, GeH3F, GeO2, and GeH4) and an electron-pair-rich system (B) (NCH, NCO-, OCN-, F-, Br-, CN-, CO, CS, Kr, NC-, NH3, OC, OH2, SH-, and N3-) at the aug-cc-pvtz coupled cluster singles and doubles (CCSD) level of calculation. The binding energy ( E bind AB ) is separated into intrafragment and inter-fragment components, and the latter in turn split into classical and covalent contributions. It is shown that the three terms are important in determining E bind AB , with absolute values that increase in passing from electrophilic fragments containing C, Ge, and Si. The degree of covalency between A and B is measured through the real space bond order known as the delocalization index ( δ AB ). Finally, a good linear correlation is found between δ AB and E xc AB , the exchange correlation (xc) or covalent contribution to E bind AB .
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30
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Gabrys PA, Zornberg LZ, Macfarlane RJ. Programmable Atom Equivalents: Atomic Crystallization as a Framework for Synthesizing Nanoparticle Superlattices. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805424. [PMID: 30970182 DOI: 10.1002/smll.201805424] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/08/2019] [Indexed: 06/09/2023]
Abstract
Decades of research efforts into atomic crystallization phenomenon have led to a comprehensive understanding of the pathways through which atoms form different crystal structures. With the onset of nanotechnology, methods that use colloidal nanoparticles (NPs) as nanoscale "artificial atoms" to generate hierarchically ordered materials are being developed as an alternative strategy for materials synthesis. However, the assembly mechanisms of NP-based crystals are not always as well-understood as their atomic counterparts. The creation of a tunable nanoscale synthon whose assembly can be explained using the context of extensively examined atomic crystallization will therefore provide significant advancement in nanomaterials synthesis. DNA-grafted NPs have emerged as a strong candidate for such a "programmable atom equivalent" (PAE), because the predictable nature of DNA base-pairing allows for complex yet easily controlled assembly. This Review highlights the characteristics of these PAEs that enable controlled assembly behaviors analogous to atomic phenomena, which allows for rational material design well beyond what can be achieved with other crystallization techniques.
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Affiliation(s)
- Paul A Gabrys
- Department of Materials Science and Engineering, Massachusetts Institute of Technology (MIT), 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Leonardo Z Zornberg
- Department of Materials Science and Engineering, Massachusetts Institute of Technology (MIT), 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Robert J Macfarlane
- Department of Materials Science and Engineering, Massachusetts Institute of Technology (MIT), 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
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Yokogawa D. Isotropic Site-Site Dispersion Potential Constructed Using Quantum Chemical Calculations and a Geminal Auxiliary Basis Set. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20180341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Daisuke Yokogawa
- Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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32
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Visscher KM, Geerke DP. Deriving Force-Field Parameters from First Principles Using a Polarizable and Higher Order Dispersion Model. J Chem Theory Comput 2019; 15:1875-1883. [PMID: 30763086 PMCID: PMC6581419 DOI: 10.1021/acs.jctc.8b01105] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Indexed: 11/30/2022]
Abstract
In this work we propose a strategy based on quantum mechanical (QM) calculations to parametrize a polarizable force field for use in molecular dynamics (MD) simulations. We investigate the use of multiple atoms-in-molecules (AIM) strategies to partition QM determined molecular electron densities into atomic subregions. The partitioned atomic densities are subsequently used to compute atomic dispersion coefficients from effective exchange-hole-dipole moment (XDM) calculations. In order to derive values for the repulsive van der Waals parameters from first principles, we use a simple volume relation to scale effective atomic radii. Explicit inclusion of higher order dispersion coefficients was tested for a series of alkanes, and we show that combining C6 and C8 attractive terms together with a C11 repulsive potential yields satisfying models when used in combination with our van der Waals parameters and electrostatic and bonded parameters as directly obtained from quantum calculations as well. This result highlights that explicit inclusion of higher order dispersion terms could be viable in simulation, and it suggests that currently available QM analysis methods allow for first-principles parametrization of molecular mechanics models.
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Affiliation(s)
- Koen M. Visscher
- AIMMS Division of Molecular Toxicology,
Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
| | - Daan P. Geerke
- AIMMS Division of Molecular Toxicology,
Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, the Netherlands
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Visscher KM, Swope WC, Geerke DP. A QM/MM Derived Polarizable Water Model for Molecular Simulation. Molecules 2018; 23:E3131. [PMID: 30501058 PMCID: PMC6321318 DOI: 10.3390/molecules23123131] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 11/26/2022] Open
Abstract
In this work, we propose an improved QM/MM-based strategy to determine condensed-phase polarizabilities and we use this approach to optimize a new and simple polarizable four-site water model for classical molecular simulation. For the determination of the model value for the polarizability from QM/MM, we show that our proposed consensus-fitting strategy significantly reduces the uncertainty in calculated polarizabilities in cases where the size of the local external electric field is small. By fitting electrostatic, polarization and dispersion properties of our water model based on quantum and/or combined QM/MM calculations, only a single model parameter (describing exchange repulsion) is left for empirical calibration. The resulting model performs well in describing relevant pure-liquid thermodynamic and transport properties, which illustrates the merit of our approach to minimize the number of free variables in our model.
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Affiliation(s)
- Koen M Visscher
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, De Boelelaan 1108, 1081 HV Amsterdam, The Netherlands.
| | - William C Swope
- IBM Almaden Research Center, 650 Harry Road, San Jose, CA 95120, USA.
| | - Daan P Geerke
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, De Boelelaan 1108, 1081 HV Amsterdam, The Netherlands.
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Bashardanesh Z, van der Spoel D. Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids. J Phys Chem B 2018; 122:8018-8027. [DOI: 10.1021/acs.jpcb.8b05770] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Zahedeh Bashardanesh
- Uppsala Center for Computational Chemistry, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, P.O. Box 596, SE-75124 Uppsala, Sweden
| | - David van der Spoel
- Uppsala Center for Computational Chemistry, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, P.O. Box 596, SE-75124 Uppsala, Sweden
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35
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Feng X, Otero-de-la-Roza A, Johnson ER. The effect of electronic excitation on London dispersion. CAN J CHEM 2018. [DOI: 10.1139/cjc-2017-0726] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Atomic and molecular dispersion coefficients can now be calculated routinely using density-functional theory. In this work, we present the first determination of how electronic excitation affects molecular C6 London dispersion coefficients from the exchange-hole dipole moment (XDM) dispersion model. Excited states are typically found to have larger dispersion coefficients than the corresponding ground states, due to their more diffuse electron densities. A particular focus is both intramolecular and intermolecular charge-transfer excitations, which have high absorbance intensities and are important in organic dyes, light-emitting diodes, and photovoltaics. In these classes of molecules, the increase in C6 for the electron-accepting moiety is largely offset by a decrease in C6 for the electron-donating moiety. As a result, the change in dispersion energy for a chromophore interacting with neighbouring molecules in the condensed phase is minimal.
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Affiliation(s)
- Xibo Feng
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd, P.O. Box 15000, Halifax, NS B3H 4R2, Canada
| | - Alberto Otero-de-la-Roza
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, BC V1V 1V7, Canada
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd, P.O. Box 15000, Halifax, NS B3H 4R2, Canada
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Walters ET, Mohebifar M, Johnson ER, Rowley CN. Evaluating the London Dispersion Coefficients of Protein Force Fields Using the Exchange-Hole Dipole Moment Model. J Phys Chem B 2018; 122:6690-6701. [DOI: 10.1021/acs.jpcb.8b02814] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Evan T. Walters
- Department of Chemistry, Memorial University of Newfoundland, St. John’s A1C 5S7, Newfoundland and Labrador, Canada
| | - Mohamad Mohebifar
- Department of Chemistry, Memorial University of Newfoundland, St. John’s A1C 5S7, Newfoundland and Labrador, Canada
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie University, Halifax B3H 4R2, Nova Scotia, Canada
| | - Christopher N. Rowley
- Department of Chemistry, Memorial University of Newfoundland, St. John’s A1C 5S7, Newfoundland and Labrador, Canada
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37
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Riniker S. Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview. J Chem Inf Model 2018; 58:565-578. [DOI: 10.1021/acs.jcim.8b00042] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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