Screened Electrostatic Interactions in Molecular Mechanics

Radial Behavior of Electrostatic Potentials of Atoms and Ions Revisited: Isotropy and Anisotropy

In this paper we revisit earlier work relating to monoatomic atoms and ions published by pioneers in the area of electrostatic potentials. We include plots of the radial distributions of the electrostatic potentials for spherically symmetric atoms and cations, and for singly, doubly and triply negative anions. For atoms with anisotropy in their densities and electrostatic potentials, such as the halonium cations, it is shown how the molecular surface approach for plotting electrostatic potentials complements that achieved by directional radial distributions.

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

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 ρ_liq and vaporization enthalpies ΔH_vap 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 κ_T, the isobaric thermal-expansion coefficient α_P, the isobaric heat capacity c_P, the static relative dielectric permittivity ϵ, the self-diffusion coefficient D, the shear viscosity η, the hydration free energy ΔG_wat, and the free energy of solvation ΔG_che in cyclohexane. For the target properties ρ_liq and ΔH_vap, 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, κ_T, α_P, ϵ, D, and ΔG_che; and less accurate results in terms of c_P and ΔG_wat. This work also represents a first step toward the calibration of a GROMOS-compatible force field at the AA resolution.

Polarizable Water Potential Derived from a Model Electron Density

A new empirical potential for efficient, large scale molecular dynamics simulation of water is presented. The HIPPO (Hydrogen-like Intermolecular Polarizable POtential) force field is based upon the model electron density of a hydrogen-like atom. This framework is used to derive and parametrize individual terms describing charge penetration damped permanent electrostatics, damped polarization, charge transfer, anisotropic Pauli repulsion, and damped dispersion interactions. Initial parameter values were fit to Symmetry Adapted Perturbation Theory (SAPT) energy components for ten water dimer configurations, as well as the radial and angular dependence of the canonical dimer. The SAPT-based parameters were then systematically refined to extend the treatment to water bulk phases. The final HIPPO water model provides a balanced representation of a wide variety of properties of gas phase clusters, liquid water, and ice polymorphs, across a range of temperatures and pressures. This water potential yields a rationalization of water structure, dynamics, and thermodynamics explicitly correlated with an ab initio energy decomposition, while providing a level of accuracy comparable or superior to previous polarizable atomic multipole force fields. The HIPPO water model serves as a cornerstone around which similarly detailed physics-based models can be developed for additional molecular species.

A Quantum Chemical Topology Picture of Intermolecular Electrostatic Interactions and Charge Penetration Energy

Based on the Interacting Quantum Atoms approach, we present herein a conceptual and theoretical framework of short-range electrostatic interactions, whose accurate description is still a challenging problem in molecular modeling. For all the noncovalent complexes in the S66 database, the fragment-based and atomic decomposition of the electrostatic binding energies is performed using both the charge density of the dimers and the unrelaxed densities of the monomers. This energy decomposition together with dispersion corrections gives rise to a pairwise approximation to the total binding energy. It also provides energetic descriptors at varying distance that directly address the atomic and molecular electrostatic interactions as described by point-charge or multipole-based potentials. Additionally, we propose a consistent definition of the charge penetration energy within quantum chemical topology, which is mainly characterized in terms of the intramolecular electrostatic energy. Finally, we discuss some practical implications of our results for the design and validation of electrostatic potentials.

Combining Molecular Dynamic Information and an Aspherical-Atom Data Bank in the Evaluation of the Electrostatic Interaction Energy in Multimeric Protein-Ligand Complex: A Case Study for HIV-1 Protease

Computational analysis of protein–ligand interactions is of crucial importance for drug discovery. Assessment of ligand binding energy allows us to have a glimpse of the potential of a small organic molecule to be a ligand to the binding site of a protein target. Available scoring functions, such as in docking programs, all rely on equations that sum each type of protein–ligand interactions in order to predict the binding affinity. Most of the scoring functions consider electrostatic interactions involving the protein and the ligand. Electrostatic interactions constitute one of the most important part of total interactions between macromolecules. Unlike dispersion forces, they are highly directional and therefore dominate the nature of molecular packing in crystals and in biological complexes and contribute significantly to differences in inhibition strength among related enzyme inhibitors. In this study, complexes of HIV-1 protease with inhibitor molecules (JE-2147 and darunavir) were analyzed by using charge densities from the transferable aspherical-atom University at Buffalo Databank (UBDB). Moreover, we analyzed the electrostatic interaction energy for an ensemble of structures, using molecular dynamic simulations to highlight the main features of electrostatic interactions important for binding affinity.

A three-dimensional supramolecular network structure through hydrogen bonding and π–π interaction: synthesis, structure, and the fluorescence detection of balsalazide disodium

Three co-crystal compounds with different dimensions were synthesized. The fluorescence properties of co-crystal 1 were studied, especially detecting balsalazide disodium.

Fast Evaluation of Two-Center Integrals over Gaussian Charge Distributions and Gaussian Orbitals with General Interaction Kernels

We present efficient algorithms for computing two-center integrals and integral derivatives, with general interaction kernels K(r₁₂), over Gaussian charge distributions of general angular momenta l. While formulated in terms of traditional ab initio integration techniques, full derivations and required secondary information, as well as a reference implementation, are provided to make the content accessible to other fields. Concretely, the presented algorithms are based on an adaption of the McMurchie-Davidson Recurrence Relation (MDRR) combined with analytical properties of the solid harmonic transformation; this obviates all intermediate recurrences except the adapted MDRR itself, and allows it to be applied to fully contracted auxiliary kernel integrals. The technique is particularly well-suited for semiempirical molecular orbital methods, where it can serve as a more general and efficient replacement of Slater-Koster tables, and for first-principles quantum chemistry methods employing density fitting. But the formalism's high efficiency and ability of handling general interaction kernels K(r₁₂) and multipolar Gaussian charge distributions may also be of interest for modeling electrostatic interactions and short-range exchange and charge penetration effects in classical force fields and model potentials. With the presented technique, a 4894 × 4894 univ-JKFIT Coulomb matrix J_AB = (A|1/r₁₂|B) (183 MiB) can be computed in 50 ms on a Q2'2018 notebook CPU, without any screening or approximations.

Universal Method for Electrostatic Interaction Energies Estimation with Charge Penetration and Easily Attainable Point Charges

Our new model of electron density augmented by point charges (aug-PROmol) provides an estimation of electrostatic interaction energies including penetration effects ( ChemPhysChem 2016, 17, 2455-2460). In this paper we prove that it can be applied using sources of point charges other than those from direct restrained fitting to electrostatic potential (RESP). We used a newly established databank of tabulated invariom point charges and a widely known semiempirical method. Both sources perform equivalently to the basic aug-PROmol method as well as to reference energies at the DFT-SAPT/aug-cc-pVTZ level of theory. This is possible due to the universal character of the penetration model included in the aug-PROmol. Aug-PROmol may become a basis for development of new nonbonded terms in force fields or a high success rate scoring function.

Polarizable Drude Model with s-Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields

Gas-phase electric properties of molecules can be computed routinely using wave function methods or density functional theory (DFT). However, these methods remain computationally expensive for high-throughput screening of the vast chemical space of virtual compounds. Therefore, empirical force fields are a more practical choice in many cases, particularly since force field methods allow one to routinely predict the physicochemical properties in the condensed phases. This work presents Drude polarizable models, to increase the physical realism in empirical force fields, where the core particle is treated as a point charge and the Drude particle is treated either as a 1 s-Gaussian or a ns-Slater ( n = 1, 2, 3) charge density. Systematic parametrization to large high-quality quantum chemistry data obtained from the open access Alexandria Library ( https://doi.org/10.5281/zenodo.1004711 ) ensures the transferability of these parameters. The dipole moments and isotropic polarizabilities of the isolated molecules predicted by the proposed Drude models are in agreement with experiment with accuracy similar to DFT calculations at the B3LYP/aug-cc-pVTZ level of theory. The results show that the inclusion of explicit polarization into the models reduces the root-mean-square deviation with respect to DFT calculations of the predicted dipole moments of 152 dimers and clusters by more than 50%. Finally, we show that the accuracy of the electrostatic interaction energy of the water dimers can be improved systematically by the introduction of polarizable smeared charges as a model for charge penetration.

Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges

Computer simulations of biomolecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in biomolecular systems and are therein described by atomic point charges. In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute's electron density computed with an implicit solvent model, and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the AM1-BCC and the MBIS atomic charge methods. The latter includes the solvent polarization and presents a root-mean-square error of 2.0 kcal mol-1 for the 613 organic molecules studied. The largest deviation was observed for phosphorus-containing molecules and the molecules with amide, ester and amine functional groups.

Steric "attraction": not by dispersion alone

Non-covalent interactions between neutral, sterically hindered organic molecules generally involve a strong stabilizing contribution from dispersion forces that in many systems turns the 'steric repulsion' into a 'steric attraction'. In addition to London dispersion, such systems benefit from electrostatic stabilization, which arises from a short-range effect of charge penetration and gets bigger with increasing steric bulk. In the present work, we quantify this contribution for a diverse set of molecular cores, ranging from unsubstituted benzene and cyclohexane to their derivatives carrying tert-butyl, phenyl, cyclohexyl and adamantyl substituents. While the importance of electrostatic interactions in the dimers of sp2-rich (e.g., π-conjugated) cores is well appreciated, less polarizable assemblies of sp3-rich systems with multiple short-range CH···HC contacts between the bulky cyclohexyl and adamantyl moieties are also significantly influenced by electrostatics. Charge penetration is drastically larger in absolute terms for the sp2-rich cores, but still has a non-negligible effect on the sp3-rich dimers, investigated herein, both in terms of their energetics and equilibrium interaction distances. These results emphasize the importance of this electrostatic effect, which has so far been less recognized in aliphatic systems compared to London dispersion, and are therefore likely to have implications for the development of force fields and methods for crystal structure prediction.

Mode specific THz spectra of solvated amino acids using the AMOEBA polarizable force field

We have used the AMOEBA model to simulate the THz spectra of two zwitterionic amino acids in aqueous solution, which is compared to the results on these same systems using ab initio molecular dynamics (AIMD) simulations. Overall we find that the polarizable force field shows promising agreement with AIMD data for both glycine and valine in water. This includes the THz spectral assignments and the mode-specific spectral decomposition into intramolecular solute motions as well as distinct solute-water cross-correlation modes some of which cannot be captured by non-polarizable force fields that rely on fixed partial charges. This bodes well for future studies for simulating and decomposing the THz spectra for larger solutes such as proteins or polymers for which AIMD studies are presently intractable. Furthermore, we believe that the current study on rather simple aqueous solutions offers a way to systematically investigate the importance of charge transfer, nuclear quantum effects, and the validity of computationally practical density functionals, all of which are needed to fully quantitatively capture complex dynamical motions in the condensed phase.

An optimized charge penetration model for use with the AMOEBA force field

The principal challenge of using classical physics to model biomolecular interactions is capturing the nature of short-range interactions that drive biological processes from nucleic acid base stacking to protein-ligand binding. In particular most classical force fields suffer from an error in their electrostatic models that arises from an ability to account for the overlap between charge distributions occurring when molecules get close to each other, known as charge penetration. In this work we present a simple, physically motivated model for including charge penetration in the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) force field. With a function derived from the charge distribution of a hydrogen-like atom and a limited number of parameters, our charge penetration model dramatically improves the description of electrostatics at short range. On a database of 101 biomolecular dimers, the charge penetration model brings the error in the electrostatic interaction energy relative to the ab initio SAPT electrostatic interaction energy from 13.4 kcal mol^-1 to 1.3 kcal mol^-1. The model is shown not only to be robust and transferable for the AMOEBA model, but also physically meaningful as it universally improves the description of the electrostatic potential around a given molecule.

Interplay of point multipole moments and charge penetration for intermolecular electrostatic interaction energies from the University at Buffalo pseudoatom databank model of electron density

The strength of the University at Buffalo DataBank (UBDB) in E_es estimation is mainly due to charge overlap effects because the UBDB offers continuous representation of charge density which allows for a direct account of charge penetration in the derivation of electrostatic energies. In the UBDB model, these effects begin to play an important role at distances below twice the equilibrium distance and significantly increase as distances decrease. At equilibrium distances they are responsible for 30-50% of E_es for polar molecules and around 90% of E_es for nonpolar molecules. When the energy estimation from the UBDB is reduced to point multipoles, the results are comparable to point charges fitted to electrostatic potentials. On the other hand, particular components of energy from point multipole moments from the UBDB model are sensitive to the type of interaction and might be helpful in the characterization of interactions.

Performance of the AMOEBA Water Model in the Vicinity of QM Solutes: A Diagnosis Using Energy Decomposition Analysis

The importance of incorporating solvent polarization effects into the modeling of solvation processes has been well-recognized, and therefore a new generation of hybrid quantum mechanics/molecular mechanics (QM/MM) approaches that accounts for this effect is desirable. We present a fully self-consistent, mutually polarizable QM/MM scheme using the AMOEBA force field, in which the total energy of the system is variationally minimized with respect to both the QM electronic density and the MM induced dipoles. This QM/AMOEBA model is implemented through the Q-Chem/LibEFP code interface and then applied to the evaluation of solute-solvent interaction energies for various systems ranging from the water dimer to neutral and ionic solutes (NH₃, NH₄⁺, CN^-) surrounded by increasing numbers of water molecules (up to 100). In order to analyze the resulting interaction energies, we also utilize an energy decomposition analysis (EDA) scheme which identifies contributions from permanent electrostatics, polarization, and van der Waals (vdW) interaction for the interaction between the QM solute and the solvent molecules described by AMOEBA. This facilitates a component-wise comparison against full QM calculations where the corresponding energy components are obtained via a modified version of the absolutely localized molecular orbitals (ALMO)-EDA. The results show that the present QM/AMOEBA model can yield reasonable solute-solvent interaction energies for neutral and cationic species, while further scrutiny reveals that this accuracy highly relies on the delicate balance between insufficiently favorable permanent electrostatics and softened vdW interaction. For anionic solutes where the charge penetration effect becomes more pronounced, the QM/MM interface turns out to be unbalanced. These results are consistent with and further elucidate our findings in a previous study using a slightly different QM/AMOEBA model ( Dziedzic et al. J. Chem. Phys. 2016 , 145 , 124106 ). The implications of these results for further refinement of this model are also discussed.

Materials Genome in Action: Identifying the Performance Limits of Physical Hydrogen Storage

The Materials Genome is in action: the molecular codes for millions of materials have been sequenced, predictive models have been developed, and now the challenge of hydrogen storage is targeted. Renewably generated hydrogen is an attractive transportation fuel with zero carbon emissions, but its storage remains a significant challenge. Nanoporous adsorbents have shown promising physical adsorption of hydrogen approaching targeted capacities, but the scope of studies has remained limited. Here the Nanoporous Materials Genome, containing over 850 000 materials, is analyzed with a variety of computational tools to explore the limits of hydrogen storage. Optimal features that maximize net capacity at room temperature include pore sizes of around 6 Å and void fractions of 0.1, while at cryogenic temperatures pore sizes of 10 Å and void fractions of 0.5 are optimal. Our top candidates are found to be commercially attractive as "cryo-adsorbents", with promising storage capacities at 77 K and 100 bar with 30% enhancement to 40 g/L, a promising alternative to liquefaction at 20 K and compression at 700 bar.

Physical Molecular Mechanics Method for Damped Dispersion

Damped dispersion can be a significant component of the interaction energy in many physical and chemical processes, for example, physisorption and noncovalent complexation. For physically interpreting and modeling such processes, it is convenient to have an analytic method to calculate damped dispersion that is readily applicable across the entire periodic table. Of the available methods to calculate damped dispersion energy for interacting systems with overlapping charge distributions, we select symmetry-adapted perturbation theory (SAPT) as providing a reasonable definition, and of the possible analytic forms, we choose the D3(BJ) method. However, the available parametrizations of D3(BJ) include not only damped dispersion energy but also corrections for errors in specific exchange-correlation functionals. Here we present a parametrization that provides a physical measure of damped dispersion without such density functional corrections. The method generalizes an earlier method of Pernal and co-workers to all elements from hydrogen to plutonium.

Development of a Simple Electron Transfer and Polarization Model and Its Application to Biological Systems

Here we present a new method for point charge calculation which we call Q_ET (charges by electron transfer). The intent of this work is to develop a method that can be useful for studying charge transfer in large biological systems. It is based on the intuitive framework of the Q_EQ method with the key difference being that the Q_ET method tracks all pairwise electron transfers by augmenting the Q_EQ pseudoenergy function with a distance dependent cost function for each electron transfer. This approach solves the key limitation of the Q_EQ method which is its handling of formally charged groups. First, we parametrize the Q_ET method by fitting to electrostatic potentials calculated using ab initio quantum mechanics on over 11,000 small molecules. On an external test set of over 2500 small molecules the Q_ET method achieves a mean absolute error of 1.37 kcal/mol/electron when compared to the ab initio electrostatic potentials. Second, we examine the conformational dependence of the charges on over 2700 tripeptides. With the tripeptide data set, we show that the conformational effects account for approximately 0.4 kcal/mol/electron on the electrostatic potentials. Third, we test the Q_ET method for its ability to reproduce the effects of polarization and electron transfer on 1000 water clusters. For the water clusters, we show that the Q_ET method captures about 50% of the polarization and electron transfer effects. Finally, we examine the effects of electron transfer and polarizability on the electrostatic interaction between p38 and 94 small molecule ligands. When used in conjunction with the Generalized-Born continuum solvent model, polarization and electron transfer with the Q_ET model lead to an average change of 17 kcal/mol on the calculated electrostatic component of ΔG.

Calculations of the absolute binding free energies for Ralstonia solanacearum lectins bound with methyl-α-l-fucoside at molecular mechanical and quantum mechanical/molecular mechanical levels

In this work, both a molecular mechanical (MM) method and a hybrid quantum mechanical/molecular mechanical (QM/MM) method have been applied in the study of the binding affinities of methyl-α-l-fucoside to Ralstonia solanacearum lectins.

Assessing Ion-Water Interactions in the AMOEBA Force Field Using Energy Decomposition Analysis of Electronic Structure Calculations

AMOEBA is a molecular mechanics force field that addresses some of the shortcomings of a fixed partial charge model, by including permanent atomic point multipoles through quadrupoles, as well as many-body polarization through the use of point inducible dipoles. In this work, we investigate how well AMOEBA formulates its non-bonded interactions, and how it implicitly incorporates quantum mechanical effects such as charge penetration (CP) and charge transfer (CT), for water-water and water-ion interactions. We find that AMOEBA's total interaction energies, as a function of distance and over angular scans for the water dimer and for a range of water-monovalent cations, agree well with an advanced density functional theory (DFT) model, whereas the water-halides and water-divalent cations show significant disagreement with the DFT result, especially in the compressed region when the two fragments overlap. We use a second-generation energy decomposition analysis (EDA) scheme based on absolutely localized molecular orbitals (ALMOs) to show that in the best cases AMOEBA relies on cancellation of errors by softening of the van der Waals (vdW) wall to balance permanent electrostatics that are too unfavorable, thereby compensating for the missing CP effect. CT, as another important stabilizing effect not explicitly taken into account in AMOEBA, is also found to be incorporated by the softened vdW interaction. For the water-halides and water-divalent cations, this compensatory approach is not as well executed by AMOEBA over all distances and angles, wherein permanent electrostatics remains too unfavorable and polarization is overdamped in the former while overestimated in the latter. We conclude that the DFT-based EDA approach can help refine a next-generation AMOEBA model that either realizes a better cancellation of errors for problematic cases like those illustrated here, or serves to guide the parametrization of explicit functional forms for short-range contributions from CP and/or CT.

A Universal and Straightforward Approach to Include Penetration Effects in Electrostatic Interaction Energy Estimation

To compensate for the lack of the explicit treatment of charge penetration in classical force fields, we propose a new charge-distribution model based on a promolecule augmented with point charges (aug-PROmol). It relies on a superposition of spherical atomic electron densities obtained for each chemical element from SCF energy optimized atomic orbitals. Atomic densities are further rescaled by partial point charges computed from fits to the molecular electrostatic potential. Aug-PROmol was tested on the S66 benchmark dataset extended to nonequilibrium geometries (J. Chem. Theory Comput., 2011, 7, 3466). The model does not need any additional parametrization other than point charges. Despite its simplicity, aug-PROmol approximates the electrostatic energy with good agreement (RMSE=0.76 kcal mol(-1) to DFT-SAPT with B3LYP/aug-cc-pVTZ).

Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles

We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions.

Energetics of proton release on the first oxidation step in the water-oxidizing enzyme

In photosystem II (PSII), the Mn₄CaO₅ cluster catalyses the water splitting reaction. The crystal structure of PSII shows the presence of a hydrogen-bonded water molecule directly linked to O4. Here we show the detailed properties of the H-bonds associated with the Mn₄CaO₅ cluster using a quantum mechanical/molecular mechanical approach. When O4 is taken as a μ-hydroxo bridge acting as a hydrogen-bond donor to water539 (W539), the S₀ redox state best describes the unusually short O4–O_W539 distance (2.5 Å) seen in the crystal structure. We find that in S₁, O4 easily releases the proton into a chain of eight strongly hydrogen-bonded water molecules. The corresponding hydrogen-bond network is absent for O5 in S₁. The present study suggests that the O4-water chain could facilitate the initial deprotonation event in PSII. This unexpected insight is likely to be of real relevance to mechanistic models for water oxidation.

The availability of crystal structures of photosystem II opens up the possibility of gaining insights into its mechanism. Here, the authors use a computational approach and propose a deprotonation event at O4 followed by long-range proton-transfer along a chain of strongly bonded water molecules.

General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field

Classical molecular mechanics force fields typically model interatomic electrostatic interactions with point charges or multipole expansions, which can fail for atoms in close contact due to the lack of a description of penetration effects between their electron clouds. These short-range penetration effects can be significant and are essential for accurate modeling of intermolecular interactions. In this work we report parametrization of an empirical charge-charge function previously reported (Piquemal J.-P.; J. Phys. Chem. A2003, 107, 10353) to correct for the missing penetration term in standard molecular mechanics force fields. For this purpose, we have developed a database (S101×7) of 101 unique molecular dimers, each at 7 different intermolecular distances. Electrostatic, induction/polarization, repulsion, and dispersion energies, as well as the total interaction energy for each complex in the database are calculated using the SAPT2+ method (Parker T. M.; J. Chem. Phys.2014, 140, 094106). This empirical penetration model significantly improves agreement between point multipole and quantum mechanical electrostatic energies across the set of dimers and distances, while using only a limited set of parameters for each chemical element. Given the simplicity and effectiveness of the model, we expect the electrostatic penetration correction will become a standard component of future molecular mechanics force fields.

Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model

A set of improved parameters for the AMOEBA polarizable atomic multipole water model is developed. An automated procedure, ForceBalance, is used to adjust model parameters to enforce agreement with ab initio-derived results for water clusters and experimental data for a variety of liquid phase properties across a broad temperature range. The values reported here for the new AMOEBA14 water model represent a substantial improvement over the previous AMOEBA03 model. The AMOEBA14 model accurately predicts the temperature of maximum density and qualitatively matches the experimental density curve across temperatures from 249 to 373 K. Excellent agreement is observed for the AMOEBA14 model in comparison to experimental properties as a function of temperature, including the second virial coefficient, enthalpy of vaporization, isothermal compressibility, thermal expansion coefficient, and dielectric constant. The viscosity, self-diffusion constant, and surface tension are also well reproduced. In comparison to high-level ab initio results for clusters of 2-20 water molecules, the AMOEBA14 model yields results similar to AMOEBA03 and the direct polarization iAMOEBA models. With advances in computing power, calibration data, and optimization techniques, we recommend the use of the AMOEBA14 water model for future studies employing a polarizable water model.