Polarizable Model Research Articles

Scalable Indirect Free Energy Method Applied to Divalent Cation-Metalloprotein Binding.

Many biological processes are based on molecular recognition between highly charged molecules such as nucleic acids, inorganic ions, charged amino acids, etc. For such cases, it has been demonstrated that molecular simulations with fixed partial charges often fail to achieve experimental accuracy. Although incorporation of more advanced electrostatic models (such as multipoles, mutual polarization, etc.) can significantly improve simulation accuracy, it increases computational expense by a factor of 5-20×. Indirect free energy (IFE) methods can mitigate this cost by modeling intermediate states at fixed-charge resolution. For example, an efficient "reference" model such as a pairwise Amber, CHARMM, or OPLS-AA force field can be used to derive an initial estimate, followed by thermodynamic corrections to a more advanced "target" potential such as the polarizable AMOEBA model. Unfortunately, all currently described IFE methods encounter difficulties reweighting more than ∼50 atoms between resolutions due to extensive scaling of both the magnitude of the thermodynamic corrections and their statistical uncertainty. We present an approach called "simultaneous bookending" (SB) that is fundamentally different from existing IFE methods based on a tunable sampling approximation, which permits scaling to thousands of atoms. SB is demonstrated on the relative binding affinity of Mg2+/Ca2+ to a set of metalloproteins with up to 2972 atoms, finding no statistically significant difference between direct AMOEBA results and those from correcting Amber to AMOEBA. The ability to change the resolution of thousands of atoms during reweighting suggests the approach may be applicable in the future to protein-protein binding affinities or nucleic acid thermodynamics.

Bond-Dependent Thole Model for Polarizability and Spectroscopy.

We present a new model for the calculation of molecular polarizabilities from effective atomic polarizabilities. This model is based on the Thole modified dipole interaction model for molecular polarizabilities, where the total polarizability is computed as a sum of effective atomic polarizabilities modified by dipole-dipole interactions. We extend this model by making the atomic polarizabilities explicit functions of the interatomic distances, scaling them by the radius of the volume an atom occupies in a molecule. We use the SCAN functional to show that this model, denoted TholeL, yields accurate molecular polarizabilities with little dependence on the training set. We also demonstrate that the TholeL model yields accurate polarizabilities for configurations far from the ground state structure for a wide range of molecules. Finally, we show that the TholeL model can be used to generate accurate Raman spectra for water, crystalline urea, and urea in water from ab initio molecular dynamics simulations.

Cross-dimensional electron-phonon coupling in van der Waals heterostructures

The electron-phonon coupling (EPC) in a material is at the frontier of the fundamental research, underlying many quantum behaviors. van der Waals heterostructures (vdWHs) provide an ideal platform to reveal the intrinsic interaction between their electrons and phonons. In particular, the flexible van der Waals stacking of different atomic crystals leads to multiple opportunities to engineer the interlayer phonon modes for EPC. Here, in hBN/WS2 vdWH, we report the strong cross-dimensional coupling between the layer-breathing phonons well extended over tens to hundreds of layer thick vdWH and the electrons localized within the few-layer WS2 constituent. The strength of such cross-dimensional EPC can be well reproduced by a microscopic picture through the mediation by the interfacial coupling and also the interlayer bond polarizability model in vdWHs. The study on cross-dimensional EPC paves the way to manipulate the interaction between electrons and phonons in various vdWHs by interfacial engineering for possible interesting physical phenomena.

Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields.

Many applications in chemistry, biology, and energy storage/conversion research rely on molecular simulations to provide fundamental insight into structural and transport properties of materials with high ionic concentrations. Whether the system is comprised entirely of ions, like ionic liquids, or is a mixture of a polar solvent with a salt, e.g., liquid electrolytes for battery applications, the presence of ions in these materials results in strong local electric fields polarizing solvent molecules and large ions. To predict properties of such systems from molecular simulations often requires either explicit or mean-field inclusion of the influence of polarization on electrostatic interactions. In this manuscript, we review the pros and cons of different treatments of polarization ranging from the mean-field approaches to the most popular explicit polarization models in molecular dynamics simulations of ionic materials. For each method, we discuss their advantages and disadvantages and emphasize key assumptions as well as their adjustable parameters. Strategies for the development of polarizable models are presented with a specific focus on extracting atomic polarizabilities. Finally, we compare simulations using polarizable and nonpolarizable models for several classes of ionic systems, discussing the underlying physics that each approach includes or ignores, implications for implementation and computational efficiency, and the accuracy of properties predicted by these methods compared to experiments.

Computational Insights into Endo/Exo Selectivity of the Diels-Alder Reaction in Explicit Solvent at Ab Initio Quantum Mechanical/Molecular Mechanical Level.

The microscopic insight into the endo/exo stereoselectivity of the Diels-Alder (DA) reaction between cyclopentadiene and methyl vinyl ketone (MVK) has posed a challenge to the computational chemists, which requires an accurate free-energy (FE) landscape. Although ab initio (ai) quantum mechanical/molecular mechanical (QM/MM) calculations are capable of providing accurate conformation energies, they are far too expensive for free-energy calculations, in which large-scale sampling in the phase space is always indispensable. Recently, on the basis of the idea of reference-potential methods, a new approach termed MBAR+wTP method was proposed by us ( Li ; J. Chem. Theory Comput. 2018 , 14 , 5583 ) for the calculations of ai QM/MM FE profiles with a much less computational expense. In this work, we applied this method to investigate the endo/exo stereoselectivity of the Diels-Alder (DA) reaction at B3LYP/MM level and the results indicate that this method can yield more accurate activation free energies than the semiempirical Hamiltonian PM6 and the "sampling-free" quantum mechanical methods at B3LYP and MP2 levels using a polarizable continuous solvent model (PCM). The stereoselectivity mainly comes from the solvation effect. At the transition state, the first peak of the solvent distribution near the oxygen atom in MVK is slightly closer for the endo pathway than that for the exo pathway, whereas the difference at PM6 level is negligible. Nonetheless, in terms of the stereoselectivity, we obtained an endo/exo ratio of 2 with this method, which is still 1 order of magnitude smaller than the experimental measurement. Although the endo/exo ratio from the MP2/PCM calculation agrees well with the experiment, the absolute reaction barriers deviate by about 5 kcal mol-1. This work issues a warning to the use of the computational methods that are routinely employed for the study of organic reactions in the condensed phase, and it also brings a new method that is affordable and more reliable.

Hydration and Dispersion Forces in Hydroxypropylcellulose Phase Behavior.

Many-body polarization and hydration forces can strongly affect the equilibrium structure and energetics of mixed phases. Accurately reproducing both forces presents a challenge to force field models because it requires balancing hydrogen bonding at short range with many-body orientational order and dispersive attraction at long range. This work reports the first comparison of experimental measurements of the pressure-area isotherm for hydroxypropylcellulose (HPC) against molecular dynamics results with four different force field models-united-atom, all-atom (OPLS and CHARMM), and Drude oscillator models. All force fields exhibit the experimentally determined, exponentially shaped repulsive force at short range. Above a critical temperature of about 40 °C and a lattice spacing of around 14 Å, HPC experiments show a reversible, heat-induced polymer aggregation into an ordered phase driven by loss of water. The nonpolarizable force fields do not display the critical point and instead show biphasic behavior at all temperatures tested. This indicates net attractive forces at intermediate lattice spacings. In contrast, the Drude polarizable force field shows positive osmotic pressure and a single, homogeneous phase over all temperatures and spacings tested. Analysis of structural data from our simulations provides several clues to help interpret these findings. Although all force fields show similar water-water hydrogen bond numbers in the mixed phase, the polarizable model predicts that water-HPC hydrogen bonds are much more favorable than HPC-HPC hydrogen bonds when polymers are dispersed. At high density, water is driven out and replaced by HPC-HPC hydrogen bonds. The polarizable force field shows that both effects have a stronger dependence on polymer density than any of the nonpolarizable models. Our observations support the conclusion that hydration forces are coupled to the polymer coordination number by local, structural waters and that long-range dispersive attraction is overestimated by pairwise additive models.

Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems.

Steered molecular dynamic (SMD) is a powerful technique able to accelerate rare event sampling in Molecular Dynamics (MD) simulations by applying an external force to a set of chosen atoms. Despite generating nonequilibrium simulations, SMD remains capable of reconstructing equilibrium properties such as the Potential of Mean Force (PMF). Of course, one would like to use all types of force fields (FF) ranging from classical ones to more advanced polarizable models using point induced dipoles and distributed multipoles such as AMOEBA. To enable such studies, the SMD methodology has been implemented in the framework of the massively parallel Tinker-HP software allowing for both long polarizable and non-polarizable MD simulations of large proteins. To validate this new implementation, we first compared the Tinker-HP SMD results to the literature. Tests have been performed on three different benchmark systems: the M-A deca-alanine (112 atoms), the ubiquitin (9737 atoms), and the CD2CD58 complex (97594 atoms). Non-polarizable (AMBER99, AMBER99SB, CHARMM22/CMAP, and OPLS-AA/L) and polarizable (AMOEBAPRO13 and AMOEBABIO18) force fields have been used. For each one of them, PMFs have been reconstructed and compared in terms of free energy barrier and hydrogen bonding fluctuations behavior over time. Using a SMD velocity of 0.01 Å/ps applied to a set of 20 trajectories, we show that polarizable and non-polarizable force fields do not always agree. As it could be anticipated, strong discrepancies are noticed between polarizable and non-polarizable models when considered in vacuum, whereas results are more comparable when a water environment is added. However, for the largest system, i.e., the CD2CD58 complex, strong differences related to the modeling of a salt bridge are noticed exhibiting some potential issues with classical FFs. Overall, such simulations highlight the importance of the inclusion of polarization effects as PMF free energy barriers computed with AMOEBA always decrease compared to non-polarizable force fields.

Molecular polarizability in open ensemble simulations of aqueous nanoconfinements under electric field.

Molecular polarization at aqueous interfaces involves fast degrees of freedom that are often averaged-out in atomistic-modeling approaches. The resulting effective interactions depend on a specific environment, making explicit account of molecular polarizability particularly important in solutions with pronounced anisotropic perturbations, including solid/liquid interfaces and external fields. Our work concerns polarizability effects in nanoscale confinements under electric field, open to an unperturbed bulk environment. We model aqueous molecules and ions in hydrophobic pores using the Gaussian-charge-on-spring BK3-AH representation. This involves nontrivial methodology developments in expanded ensemble Monte Carlo simulations for open systems with long-ranged multibody interactions and necessitates further improvements for efficient modeling of polarizable ions. Structural differences between fixed-charge and polarizable models were captured in molecular dynamics simulations for a set of closed systems. Our open ensemble results with the BK3 model in neat-aqueous systems capture the ∼10% reduction of molecular dipoles within the surface layer near the hydrophobic pore walls in analogy to reported quantum mechanical calculations at water/vapor interfaces. The polarizability affects the interfacial dielectric behavior and weakens the electric-field dependence of water absorption at pragmatically relevant porosities. We observe moderate changes in thermodynamic properties and atom and charged-site spatial distributions; the Gaussian distribution of mobile charges on water and ions in the polarizable model shifts the density amplitudes and blurs the charge-layering effects associated with increased ion absorption. The use of polarizable force field indicates an enhanced response of interfacial ion distributions to applied electric field, a feature potentially important for in silico modeling of electric double layer capacitors.

Understanding Water Structure in an Ion-Pair Solvation Shell in the Vicinity of a Water/Membrane Interface.

The anomalous properties of interfacial water at the surface of a lipid membrane and their implications on nearby chemical processes are well recognized. However, we have found that ion pairing thermodynamics may not be significantly affected by interfacial water in a classical, nonpolarizable force field. To trace the root cause of such a counterintuitive finding, we performed atomistic molecular dynamics simulations to explore the impact of polarizable interactions and characterize the hydration structure of a sodium chloride (NaCl) ion pair at the surface of a model lipid membrane and in a bulk phase. Our study reveals that the effect of the aqueous interface on the first solvation shell of the ion pair and thus on the ion pairing thermodynamics becomes more pronounced in the polarizable model, and that the free energy profile along the interionic distance cannot capture the difference in the degree of solvent participation in ion pairing at the water/membrane interface. This study also forms the basis for the future design of a reaction coordinate that takes the behavior of the interfacial water into account.

Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects.

Atomistic biomolecular simulations predominantly utilize additive force fields (FF), where the electrostatic potential is modeled by fixed point charges. Among other consequences, the lack of polarizability in these models undermines the balance of hydrophilic/hydrophobic nonbonded interactions. Simulations of water/alkane systems using the TIP3P water model and CHARMM36 parameters reveal a 1 kcal/mol overestimate of the experimental transfer free energy of water to hexadecane; more recent optimized water models (SPC/E, TIP4P/2005, TIP4P-Ew, TIP3P-FB, TIP4P-FB, OPC, TIP4P-D) overestimate this transfer free energy by approximately 2 kcal/mol. In contrast, the polarizable SWM4-NDP and SWM6 water models reproduce experimental values to within statistical error. As an alternative to explicitly modeling polarizability, this paper develops an efficient automated workflow to optimize pair-specific Lennard-Jones parameters within an additive FF. Water/hexadecane is used as a prototype and the free energy of water transfer to hexadecane as a target. The optimized model yields quantitative agreement with the experimental transfer free energy and improves the water/hexadecane interfacial tension by 6%. Simulations of five different lipid bilayers show a strong increase of water permeabilities compared to the unmodified CHARMM36 lipid FF which consistently improves match with experiment: the order-of-magnitude underestimate for monounsaturated bilayers is rectified and the factor of 2.8-4 underestimate for saturated bilayers is turned into a factor of 1.5-3 overestimate. While agreement with experiment is decreased for the diffusion constant of water in hexadecane, alkane transfer free energies, and the bilayers' area per lipid, the method provides a permeant-specific route to achieve a wide range of heterogeneous observables via rapidly optimized pairwise parameters.

A new insight of structures, bonding and electronic properties for 6-mercaptopurine and Ag8 clusters configurations: a theoretical perspective

BackgroundMany reports have also shown that the silver nanoparticles can effectively increase the anticancer drug activity and intensely enhance the drug curative effect. The adsorption of 6MP on nanomaterials has received a lot of attentions because of the drug coordination to its chemotherapeutic activity. The geometrical structures, chemical bonds, molecular orbital properties as well as density of states for the configurations were analyzed to deeply understand the interactions between the 6MP and Ag8 clusters for high effect anticancer drug production.ResultsIn this work, the density functional theory B3LYP has been used to investigate the structures and properties of the configurations between 6-mercaptopurine (6MP) and Ag8 clusters using 6-311++G** level as well as an effective pseudo potential LANL2DZ. The geometries of ten configurations were optimized with full freedom. The geometrical structures, chemical bonds, molecular orbital properties as well as density of states for partial configurations were analyzed based on the density functional calculations. Polarizable continuum solvent model (PCM) in self-consistent reaction field (SCRF) were used for the aqueous calculations. The influences of temperature and pressure on the stability of the predominant configurations in the gas phase were further considered using standard statistical thermodynamic methods from 50 to 500 K and at 1 bar or 100 bar.ConclusionThe result shows that there are ten stable configurations in the gas phase and there is a strong chemical bond between a Ag and S atom in the most stable configuration. The analysis of density of states also shows that the Ag–S chemical bond in the most stable configuration has been formed. Moreover, the results show that the temperature and the pressure will significantly influence the stability of the configurations in the gas phase. Additionally, when the solvent effect was considered, we found that there are only seven stable configurations and the solvent have different effect on various configurations.

Evaluation of DFT Methods and Implicit Solvation Models for Anion‐Binding Host‐Guest Systems

AbstractAlthough supramolecular chemistry is traditionally an experimental discipline, computations have emerged as important tools for the understanding of supramolecules. We have explored how well commonly used density functional theory quantum mechanics and polarizable continuum solvation models can calculate binding affinities of host‐guest systems. We report the calculation of binding affinities for eight host–guest complexes and compare our results to experimentally measured binding free energies that span the range from −2.3 to −6.1 kcal mol−1. These systems consist of four hosts (biotin[6]uril, triphenoxymethane, cryptand, and bis‐thiourea) with different halide ions (F−, Cl−, Br−) in various media including organic and aqueous. The mean average deviation (MAD) of calculated from measured ΔGa is 2.5 kcal mol−1 when using B3LYP‐D3 with either CPCM or PCM. This MAD value lowers even more by eliminating two outliers: 1.1 kcal mol−1 for CPCM and 1.2 kcal mol−1 for PCM. The best DFT and implicit solvation model combination that we have studied is B3LYP−D3 with either CPCM or PCM.

Ion-Hydroxyl Interactions: From High-Level Quantum Benchmarks to Transferable Polarizable Force Fields.

Ion descriptors in molecular mechanics models are calibrated against reference data on ion-water interactions. It is then typically assumed that these descriptors will also satisfactorily describe interactions of ions with other functional groups, such as those present in biomolecules. However, several studies now demonstrate that this transferability assumption produces, in many different cases, large errors. Here we address this issue in a representative polarizable model and focus on transferability of cationic interactions from water to a series of alcohols. Both water and alcohols use hydroxyls for ion-coordination, and, therefore, this set of molecules constitutes the simplest possible case of transferability. We obtain gas phase reference data systematically from "gold-standard" quantum Monte Carlo and CCSD(T) methods, followed by benchmarked vdW-corrected DFT. We learn that the original polarizable model yields large gas phase water → alcohol transferability errors - the RMS and maximum errors are 2.3 and 5.1 kcal/mol, respectively. These errors are, nevertheless, systematic in that ion-alcohol interactions are overstabilized, and systematic errors typically imply that some essential physics is either missing or misrepresented. A comprehensive analysis shows that when both low- and high-field responses of ligand dipole polarization are described accurately, then transferability improves significantly - the RMS and maximum errors in the gas phase reduce, respectively, to 0.9 and 2.5 kcal/mol. Additionally, predictions of condensed phase transfer free energies also improve. Nevertheless, within the limits of the extrathermodynamic assumptions necessary to separate experimental estimates of salt dissolution into constituent cationic and anionic contributions, we note that the error in the condensed phase is systematic, which we attribute, at least, partially to the parametrization in long-range electrostatics. Overall, this work demonstrates a rational approach to boosting transferability of ionic interactions that will be applicable broadly to improving other polarizable and nonpolarizable models.

Stacking-dependent interlayer phonons in 3R and 2H MoS2

We have investigated the interlayer shear and breathing phonon modes in MoS2 with pure 3R and 2H stacking order by using polarization-dependent ultralow-frequency Raman spectroscopy. We observe up to three shear branches and four breathing branches in MoS2 with thickness from 2 to 13 layers. The breathing modes show the same Raman activity behavior for both polytypes, but the 2H breathing frequencies are consistently several wavenumbers higher than the 3R breathing frequencies, signifying that 2H MoS2 has slightly stronger interlayer lattice coupling than 3R MoS2. In contrast, the shear-mode Raman spectra are strikingly different for 2H and 3R MoS2. While the strongest shear mode corresponds to the highest-frequency branch in the 2H structure, it corresponds to the lowest-frequency branch in the 3R structure. Such distinct and complementary Raman spectra of the 3R and 2H polytypes allow us to survey a broad range of shear modes in MoS2, from the highest to lowest branch. By combining the linear chain model, group theory, effective bond polarizability model and first-principles calculations, we can account for all the major observations in our experiment.

Anisotropic structure and dynamics of water under static electric fields.

We study the structure and dynamics of water subject to a range of static external electric fields, using molecular dynamics simulations. In particular, we monitor the changes in hydrogen bond kinetics, reorientation dynamics, and translational motions of water molecules. We find that water molecules translate and rotate slower in electric fields because the tendency to reinstate the aligned orientation reduces the probability of finding a new hydrogen bond partner and hence increases the probability of reforming already ruptured bonds. Furthermore, dipolar alignment of water molecules with the field results in structural and dynamic anisotropies even though the angularly averaged metrics indicate only minor structural changes. Through comparison of selected nonpolarizable and polarizable water models, we find that the electric field effects are stronger in polarizable water models, where field-enhanced dipole moments and thus more stable hydrogen bonds lead to slower switching of hydrogen bond partners and reduced translational mobility, compared to a nonpolarizable water model.

1,2,3-propanetriol radicals formed during oxidative stress.

The presented results attempt to approximate the proper structure of the radical formed as a result of the oxidation of 1,2,3-propanetriol. To fulfil the aim unstable radical originated in 1,2,3-propanetriol was trapped by PBN. Resulted spin adduct was measured using EPR spectroscopy and the isotropic hyperfine coupling constants aiso (14 N) and aiso (1 H) were obtained by simulation of the EPR spectrum. The next step consisted of conducting a comparative analysis of EPR parameters, based on the calculations conducted at the DFT and MP2 methods level in open-shell formalism including solvent effects. For comparison, calculations were also carried out at the level of combined methods (UB3LYP/QCISD and UMP2/QCISD) in terms of the ONIOM formalism. Comparison of the experimental EPR data of the isotropic hyperfine coupling constants aiso (14 N) and aiso (1 H) with the calculated parameters indicate that oxidation of 1,2,3-propanetriol leads to a carbon centred radical where unpaired electron is situated on the second (middle) carbon of 1,2,3-propanetriol. What is important, this conclusion could be made regardless of the chosen calculation method. However, it could be stated that for calculation of the isotropic hyperfine coupling constants aiso (14 N) and aiso (1 H) of PBN/gly• adducts, UMP2 polarisable conductor calculation model with two ethanol molecules is explicitly defined.

Ion-Hydroxyl Interactions: From High-Level Quantum Benchmarks to Transferable Polarizable Force Fields

Ion descriptors in molecular mechanics models are calibrated against reference data on ion-water interactions. It is then typically assumed that these descriptors will also satisfactorily describe interactions of ions with other functional groups, such as those present in biomolecules. However, several studies now demonstrate that this transferability assumption produces, in many different cases, large errors. Here we address this issue in a representative polarizable model and focus on transferability of cationic interactions across alcohols that, like water, also use hydroxyls for coordination. We obtain gas phase reference data from vdW-corrected DFT after benchmarking against “gold-standard” diffusion Monte Carlo and CCSD(T) methods. Taken together with experimental condensed phase data, the collected reference energies inform us that the original polarizable model yields large water -> alcohol transferability errors - the RMS and maximum errors are greater than 4.5 and 10 kcal/mol, respectively. These errors are, nevertheless, systematic in that ion-alcohol interactions are over-stabilized, and systematic errors typically imply that some essential physics is either missing or misrepresented. A comprehensive analysis shows that when both low and high-field responses of ligand dipole polarization are described accurately, then transferability improves significantly - the RMS and maximum errors in the gas phase reduce, respectively, to 0.9 and 2.5 kcal/mol. Condensed phase transfer free energies also improve, as the RMS error decreases from 8.9 to 6.6 kcal/mol, however, the error still remains systematic, which we attribute to the parameterization in long range electrostatics. Overall, this work demonstrates a rational approach to boosting transferability of ionic interactions that will be applicable broadly to improving other polarizable and non-polarizable models.

Optimized Parameters for the Drude Polarizable Force Field for Small Organic Molecules

Meaningful efforts in computer-aided drug dsign (CADD) need accurate molecular mechanical force fields to quantitatively characterize protein-ligand interactions. The most widely used strategy to ascribe force field parameters for new compounds apply pre-defined tabulated values following knowledge-based rules. Two widely used approaches following this strategy are the General Amber Force Field (GAFF) and the CHARMM General Force Field (CGenFF). While these approaches are extremely useful, an important limitation of using pre-tabulated parameter values is that they may be inadequate in the context of a specific molecule. To resolve this issue, we previously introduced the General Automated Atomic Model Parameterization (GAAMP) to automatically generate the parameters of atomic models of small molecules using the results from ab initio quantum mechanical (QM) calculations as target data [DOI:10.1021/ct4003477]. The GAAMP protocol uses QM data to optimize the bond, valence angle, and dihedral angle internal parameters, and atomic partial charges. However, the Lennard-Jones (LJ) 6-12 parameters cannot easily be refined from QM data and are unchanged from the initial atom types assignments severely limiting the achievable accuracy by these models. Here, we systematically optimize the LJ parameters of the Drude force field to reproduce experimental neat liquid densities and enthalpies of vaporization for a large set of compounds, covering a wide range of chemical functionalities. The optimization is carried out by constructing an objective function and exploiting the analytical gradient information within an optimization framework. The new set of LJ parameters will help to improve the accuracy of the computed physical properties of diverse small organic molecules. These developments will provide the necessary tools to widely apply drude polarizable force field model for drug discovery endeavors.

Improving the description of solvent pairwise interactions using local solute/solvent three-body functions. The case of halides and carboxylates in aqueous environment.

We propose a general strategy to remediate force-field artifacts in describing pairwise interactions among similar molecules M in the vicinity of another chemical species, C, like water molecules interacting at short distance from a monoatomic ion. This strategy is based on introducing a three-body potential energy term that alters the pairwise interactions among M-type molecules when they lie at short range from the species C. In other words the species C is the center of a space domain where the pairwise interactions among the molecules M is altered. Here, we apply it to improve the description of the water interactions provided by the polarizable water model TCPE/2013 in the vicinity of halides, from F- to At- , and of the prototypical carboxylate anion CH3 COO- . We show the accuracy and the transferability of such an approach to investigate not only the hydration process of single anions but also of a salt solution in aqueous phase. This strategy can be used to remediate the drawbacks of any kind of force fields. © 2019 Wiley Periodicals, Inc.

Development of Polarizable Gaussian Model for Molecular Mechanical Calculations I: Atomic Polarizability Parameterization To Reproduce ab Initio Anisotropy.

A set of atomic polarizability parameters for a new polarizable Gaussian model (pGM) has been developed with the goal to accurately reproduce the polarizability anisotropy, taking advantage of its ability to attenuate all short-range electrostatic interactions, by fitting the ab initio molecular polarizability tensors ( A pq) calculated at the B3LYP/aug-cc-pVTZ level. For comparison, we also rederived the parameters for three Thole models in which the 1-2 (bonded), 1-3 (separated by two bonds), and 1-4 (separated by three bonds) interactions are fully included. The average percent errors (APEs) of molecular polarizability tensors for 4842 molecules or dimers are 2.98, 3.76, 3.28, and 3.82% for the pGM, Thole linear, Thole exponential, and Thole Amoeba models, respectively, with atom-type independent, universal screening factors (USF). The APEs are reduced further to 2.30, 2.69, 2.25, and 2.48% for the four corresponding polarizable models with atom-type dependent, variable screening factors (VSF). It is encouraging that the pGM with variable screening factors achieved APEs of 1.83 for 1155 amino acid analogs, dipeptides, and tetrapeptides, 1.39 for 28 nucleic acid bases, 0.708 for 1464 water clusters, and 1.99 for 85 dimers of water and biological building blocks. Compared to the new set of models, the APEs of the old Thole models that were fitted to isotropic molecular polarizabilities are 8.7% for set A (without the 1-2 and 1-3 interactions) and 6.3% for set D (with the 1-2 and 1-3 interactions) models, respectively. MPAD, a metric of molecular polarization anisotropy difference based on the diagonal terms of molecular polarizability tensors was defined and applied to assess the polarizable models in reproducing the ab initio molecular polarization anisotropy. The MPADs are 3.71, 4.70, 4.11, and 4.77% for the pGM, Thole linear, Thole exponential, and Thole Amoeba USF models, respectively. The APEs are reduced further to 2.85, 3.58, 2.90, and 3.15% for the four corresponding VSF models. Thus, the new pGM and Thole models notably improve molecular polarization anisotropy. Since pGM attenuates all short-range electrostatic interactions, its application is expected to improve stability in charge fitting, energy, and force calculations and the accuracy of multibody polarization.