Abstract: The so-called D4 model is presented for the accurate computation of London dispersion interactions in density functional theory approximations (DFT-D4) and generally for atomistic modeling methods. In this successor to the DFT-D3 model, the atomic coordination-dependent dipole polarizabilities are scaled based on atomic partial charges which can be taken from various sources. For this purpose, a new charge-dependent parameter-economic scaling function is designed. Classical charges are obtained from an atomic electronegativity equilibration procedure for which efficient analytical derivatives with respect to nuclear positions are developed. A numerical Casimir-Polder integration of the atom-in-molecule dynamic polarizabilities then yields charge- and geometry-dependent dipole-dipole dispersion coefficients. Similar to the D3 model, the dynamic polarizabilities are precomputed by time-dependent DFT and all elements up to radon (Z = 86) are covered. The two-body dispersion energy expression has the usual sum-over-atom-pairs form and includes dipole-dipole as well as dipole-quadrupole interactions. For a benchmark set of 1225 molecular dipole-dipole dispersion coefficients, the D4 model achieves an unprecedented accuracy with a mean relative deviation of 3.8% compared to 4.7% for D3. In addition to the two-body part, three-body effects are described by an Axilrod-Teller-Muto term. A common many-body dispersion expansion was extensively tested, and an energy correction based on D4 polarizabilities is found to be advantageous for larger systems. Becke-Johnson-type damping parameters for DFT-D4 are determined for more than 60 common density functionals. For various standard energy benchmark sets, DFT-D4 slightly but consistently outperforms DFT-D3. Especially for metal containing systems, the introduced charge dependence of the dispersion coefficients improves thermochemical properties. We suggest (DFT-)D4 as a physically improved and more sophisticated dispersion model in place of DFT-D3 for DFT calculations as well as other low-cost approaches like semi-empirical models.

Abstract: The ability to tune the surface partial charge of noble metal catalysts at the nanoscale size dimension is essential for harnessing the activity of nanocatalysts in many important environmental cat...

Abstract: The solubilities of polyethers are surprisingly counter-intuitive. The best-known example is the difference between polyethylene glycol ([–CH2–CH2–O–]n) which is infinitely soluble, and polyoxymethylene ([–CH2–O–]n) which is completely insoluble in water, exactly the opposite of what one expects from the C/O ratios of these molecules. Similar anomalies exist for oligomeric and cyclic polyethers. To solve this apparent mystery, we use femtosecond vibrational and GHz dielectric spectroscopy with complementary ab initio calculations and molecular dynamics simulations. We find that the dynamics of water molecules solvating polyethers is fundamentally different depending on their C/O composition. The ab initio calculations and simulations show that this is not because of steric effects (as is commonly believed), but because the partial charge on the O atoms depends on the number of C atoms by which they are separated. Our results thus show that inductive effects can have a major impact on aqueous solubilities. Polyethers are ubiquitous in our daily lives, and display counterintuitive solubilities in water. Here the authors show, by ultrafast spectroscopies and computations, that solubility does not depend on steric factors but on the interaction of water molecules with the polymer’s charge distribution

Abstract: We propose a semiempirical quantum chemical method, designed for the fast calculation of molecular Geometries, vibrational Frequencies and Non-covalent interaction energies (GFN) of systems with up to a few thousand atoms. Like its predecessors GFN-xTB and GFN2-xTB, the new method termed GFN0-xTB is parameterized for all elements up to radon (Z = 86) and mostly shares well-known density functional tight-binding approximations as well as basis set and integral approximations. The main new feature is the avoidance of the self-consistent charge iterations leading to speed-ups of a factor of 2-20 depending on the size and electronic complexity of the system. This is achieved by including only quantum mechanical contributions up to first-order which are incorporated similar to the previous versions without any pair-specific parameterization. The essential electrostatic electronic interaction is treated by a classical electronegativity equilibration charge model yielding atomic partial charges that enter the electronic Hamiltonian indirectly. Furthermore, the atomic charge-dependent D4 dispersion correction is included to account for long range London correlation effects. Formulas for analytical total energy gradients with respect to nuclear displacements are derived and implemented in the xtb code allowing numerically very precise structure optimizations. The neglect of self-consistent energy terms not only leads to a large gain in computational speed but also can increase robustness in electronically difficult situations because ill-convergence or artificial charge-transfer (CT) is avoided. The comparison of GFN0-xTB and GFN/GFN2-xTB allows dissection of quantum electronic polarization and CT effects thereby improving our understanding of chemical bonding. Compared to the most sophisticated multipole-based GFN2-xTB model (which approaches DFT accuracy for the target properties closely), GFN0-xTB performs slightly worse for non-covalent interactions and molecular structures, while very good results are observed for conformational energies. Vibrational frequencies are obtained less accurately than with GFN/GFN2-xTB but they may still be useful for various purposes like estimating relative thermostatistical reaction energies. Most exceptional is the fact that even relatively complicated transition metal complex structures can be accurately optimized with a non-self-consistent quantum approach. The new method bridges the gap between force-fields and traditional semiempirical methods with its excellent computational cost to accuracy ratio and is intended to explore the chemical space of large molecular systems and solids.

Abstract: For quasi-freestanding 2H-TaS2 in monolayer thickness grown by in situ molecular beam epitaxy on graphene on Ir(111), we find unambiguous evidence for a charge density wave close to a 3 × 3 periodicity. Using scanning tunneling spectroscopy, we determine the magnitude of the partial charge density wave gap. Angle-resolved photoemission spectroscopy, complemented by scanning tunneling spectroscopy for the unoccupied states, makes a tight-binding fit for the band structure of the TaS2 monolayer possible. As hybridization with substrate bands is absent, the fit yields a precise value for the doping of the TaS2 layer. Additional Li doping shifts the charge density wave to a 2 × 2 periodicity. Unexpectedly, the bilayer of TaS2 also displays a disordered 2 × 2 charge density wave. Calculations of the phonon dispersions based on a combination of density-functional theory, density-functional perturbation theory, and many-body perturbation theory enable us to provide phase diagrams for the TaS2 charge density wave as functions of doping, hybridization, and interlayer potentials, and offer insight into how they affect lattice dynamics and stability. Our theoretical considerations are consistent with the experimental work presented and shed light on previous experimental and theoretical investigations of related systems.

Abstract: We conduct molecular dynamics simulations of electrical double-layer capacitors (EDLCs) using a library of ordered, porous carbon electrode materials called zeolite templated carbons (ZTCs). The well-defined pore shapes of the ZTCs enable us to determine the influence of pore geometry on both charging dynamics and charge storage mechanisms in EDLCs, also referred to as supercapacitors. We show that charging dynamics are negatively correlated with the pore-limiting diameter of the electrode material and display signatures of both progressive charging and ion trapping. However, the equilibrium capacitance, unlike charging dynamics, is not strongly correlated to commonly used, purely geometric descriptors such as pore size. Instead, we find a strong correlation of capacitance to the charge compensation per carbon (CCpC), a descriptor we define in this work as the average charge of the electrode atoms within the coordination shell of a counterion. A high CCpC indicates efficient charge storage, as the strong partial charges of the electrode are able to screen counterion charge, enabling higher ion loading and thus more charge storage within the electrode at a fixed applied voltage. We determine that adsorption sites with a high CCpC tend to be found within pockets with a smaller radius of curvature, where the counterions are able to minimize their distance with multiple points on the electrode surface, and therefore induce stronger local partial charges.

Abstract: Molecular dynamics simulations are used to study adsorption of cations on the (010) kaolinite edge surface at and above the pH of zero charge. The cation solutions are highly concentrated and inclu...

Abstract: The conventional definition of asphaltenes is based on their solubility in toluene and their insolubility in heptane. We have utilized this definition to study the influence of partial charge parametrization on the aggregation behavior of asphaltenes using classical atomistic molecular dynamics simulations performed on the microsecond time scale. Under consideration here are toluene- and heptane-based systems with different partial charges parametrized using the general AMBER force field (GAFF). Systems with standard GAFF partial charges calculated by the AM1-BCC and HF/6-31G*(RESP) methods were simulated alongside systems without partial charges. The partial charges implemented differ in terms of the resulting electrical negativity of the asphaltene polyaromatic core, with the AM1-BCC method giving the greatest magnitude of the total core charge. Based on our analysis of the molecular relaxation and orientation, and on the aggregation behavior of asphaltenes in toluene and heptane, we proposed to use the partial charges obtained by the AM1-BCC method for the study of asphaltene aggregates. A good agreement with available experimental data was observed on the sizes of the aggregates, their fractal dimensions, and the solvent entrainment for the model asphaltenes in toluene and heptane. From the results obtained, we conclude that for a better predictive ability, simulation parameters must be carefully chosen, with particular attention paid to the partial charges owing to their influence on the electrical negativity of the asphaltene core and on the asphaltenes aggregation.

Abstract: Flavin containing molecules form a group of important cofactors that assist a wide range of enzymatic reactions. Flavins use the redox-active isoalloxazine system, which is capable of one- and two-electron transfer reactions and can exist in several protonation states. In this work, molecular mechanics force field parameters compatible with the CHARMM36 all-atom additive force field were derived for biologically important flavins, including riboflavin, flavin mononucleotide, and flavin adenine dinucleotide. The model was developed for important protonation and redox states of the isoalloxazine group. The partial charges were derived using the CHARMM force field parametrization strategy, where quantum mechanics water-solute interactions are used to target optimization. In addition to monohydrate energies and geometries, electrostatic potential around the compound was used to provide additional restraints during the charge optimization. Taking into account the importance of flavin-containing molecules special attention was given to the quality of bonded terms. All bonded terms, including stiff terms and torsion angle parameters, were parametrized using exhaustive potential energy surface scans. In particular, the model reproduces well the butterfly motion of isoalloxazine in the oxidized and reduced forms as predicted by quantum mechanics in gas phase. The model quality is illustrated by simulations of four flavoproteins. Overall, the presented molecular mechanics model will be of utility to model flavin cofactors in different redox states. © 2019 Wiley Periodicals, Inc.

Abstract: Atomic partial charges are crucial parameters for Molecular Dynamics (MD) simulations, molecular mechanics calculations, and virtual screening, as they determine the electrostatic contributions to interaction energies. Current methods for calculating partial charges, however, are either slow and scale poorly with molecular size (quantum chemical methods) or unreliable (empirical methods). Here, we present a new charge derivation method based on Graph Nets---a set of update and aggregate functions that operate on molecular topologies and propagate information thereon---that could approximate charges derived from Density Functional Theory (DFT) calculations with high accuracy and an over 500-fold speed up.

Abstract: Structurally modified hydroxyl functionalized pyridinium ionic liquids (ILs), liquid at room temperature, were synthesized and characterized. Alkylated N-(2-hydroxyethyl)-pyridinium ILs were prepared from alkylpyridines via corresponding bromide salts by N-alkylation (65-93 %) and final anion exchange (75-96%). Pyridinium-alkylation strongly influenced the IL physicochemical and electrochemical properties. Experimental values for the ILs physicochemical properties (density, viscosity, conductivity and thermal decomposition temperature), were in good agreement with corresponding predicted values obtained by theoretical calculations. The pyridinium ILs have electrochemical window of 3.0 -5.4 V and were thermally stable up to 405 oC. The IL viscosity and density were measured over a wide temperature range (25-80 oC). Pyridine alkyl-substitution strongly affected the partial positive charge on the nitrogen atom of the pyridinium cations, as shown by charge distribution calculations. On-going studies on Mg complexes of the new ILs demonstrate promising properties for high current density electrodeposition of magnesium.

Abstract: In this work a newly parametrised Coulomb plus Buckingham potential formulation for cubic ZrO2, Y2O3 and yttrium-stabilised zirconia (YSZ) is presented. The density and pair distributions obtained for neat ZrO2 and Y2O3 under ambient conditions are in excellent agreement with experimental data, while the vibrational power spectra are highly similar compared to those obtained via ab initio molecular dynamics simulations at the PBEsol level. In addition, it is shown that the use of effective partial charges has several advantages compared to interaction potentials employing the oxidation states in the evaluation of the coulombic interactions: (i) the diffusion coefficient and the associated activation energy of oxygen ions evaluated for YSZn (n = 4 to 12) display the best agreement with experimental data; (ii) no unphysical reorganisation of the interface and the bulk are observed in simulations of the (110) and (111) surfaces of cubic ZrO2 and Y2O3, while due to the strong coulombic contributions in the case of the tested full-charge models a pronounced restructuring of the interface and the bulk is observed in the ZrO2 case, and (iii) the use of effective partial charges ensures compatibility with existing solvent models and force-fields for the treatment of molecular compounds.

Abstract: DFT/D + U and density functional based tight binding (DFTB) molecular modeling was used to investigate the role of the structural, electronic and optical properties of reduced graphene oxide surface (r-GO), hybridized with hydrated TiO2 moieties of various size, ranging from small molecular Ti2O4 clusters into extended Ti43O86 rutile type nanocrystals of ~5 nm diameter. The calculated adhesion energies, varying from -5.048 eV (r-GO|Ti2O4), -12.159 eV (r-GO|Ti5O10), -18.499 eV (r-GO|Ti15O30) to -42.484 eV (r-GO|Ti43O86), indicate high stability of these composites. It was shown that electronic interactions at the r-GO|(1 1 0)TiO2 interface give rise to net charge flow from the r-GO substrate towards the TiO2 moieties, analyzed in terms of the partial charge density 3D plots and an interfacial dipole moment formation. The DOS structure of the composites was calculated by means of the time dependent DFTB approach, and the position and composition of the VB and CB edges, along with the presence of weak mid-gap 2p C states originating from the intact graphene-like patches in the r-GO substrate were discussed in detail in the context of conceivable photocatalytic activity of the composites. The constructed band alignment diagram implies formation of the staggered type II scheme, with the electric field offset that is sensitive to the titania cluster size. In the case of the nano-reticular TiO2, where only a fraction of the Ti atoms is engaged in the Ti-O-C linkers formation, recombination of the photogenerated charges is inhibited owing to favorable spatial separation effect. For small molecular TiO2 clusters with all Ti cations anchored to the r-GO layer fast cross-relaxation quenches the beneficial interfacial charge separation effect, since the strong hybridization of the oxygen and carbon states provides a convenient pathway for the efficient electronic coupling between the CB edge states of r-GO and the VB edge states of the TiO2 moieties. A phenomenological model of the molecular r-GO|Ti2O4 and the reticular r-GO|Ti43O86 composites was constructed in account for different photocatalytic behavior of both junctions.

Abstract: We explore the molecular nature of doping in organic semiconductors (OSCs) by employing a liquid crystalline organic semiconductor based on phenyl naphthalene as a model. The mesophase nature of composites that include a charge transfer complex (CTC) between the OSC (8-PNP-O12) and an electron acceptor (F4TCNQ) has been investigated by means of differential scanning calorimetry, polarized optical microscopy and X-ray scattering. Optical and vibrational spectroscopies allow us to explore the characteristics and the amount of charge transfer in the CTC and expose some properties that appear only in the complexed state. We have found this system to exhibit partial charge transfer, which manifests itself in all the phase states of the host 8-PNP-O12, as well as in solution. Due to the lowering of molecular symmetry as a result of the charge transfer, one of the previously IR-only vibrational bands of the nitrile group is found to be now active in the Raman spectrum. We have also made an attempt to further investigate the influence of dopant introduction on the bulk hole mobility of 8-PNP-O12. It is found that the presence of the CTC promotes the hole transport in the Smectic B mesophase, however it seems to have a somewhat negative influence in the less ordered smectic A mesophase. This work aims to establish the link between the inevitable change of molecular geometry that occurs on charge transfer with the results obtained by spectroscopic techniques and electronic charge carrier mobility measurements.

Abstract: We present molecular beam electric deflection experiments on neutral gold-doped tin clusters. The experimental SnNAu (N = 6–16) cluster beam profiles are interpreted by means of classical trajectory simulations supplied, with cluster structures generated by a genetic algorithm based on density functional theory. The combined experimental and theoretical analysis confirms that at least nine tin atoms are necessary to form a cage that is capable of encapsulating a gold atom, with high symmetry only marginally distorted by the gold atom. Two-component DFT calculations reveal that for some clusters spin–orbit effects are necessary to properly describe these species. Partial charge analysis methods predict the presence of charge transfer effects from the tin host to the dopant, resulting in a negatively charged gold atom.

Abstract: We present an explicit solvent alchemical free-energy method for optimizing the partial charges of a ligand to maximize the binding affinity with a receptor. This methodology can be applied to known ligand-protein complexes to determine an optimized set of ligand partial atomic changes. Three protein-ligand complexes have been optimized in this work: FXa, P38, and the androgen receptor. The sets of optimized charges can be used to identify design principles for chemical changes to the ligands which improve the binding affinity for all three systems. In this work, beneficial chemical mutations are generated from these principles and the resulting molecules tested using free-energy perturbation calculations. We show that three quarters of our chemical changes are predicted to improve the binding affinity, with an average improvement for the beneficial mutations of approximately 1 kcal/mol. In the cases where experimental data are available, the agreement between prediction and experiment is also good. The results demonstrate that charge optimization in explicit solvent is a useful tool for predicting beneficial chemical changes such as pyridinations, fluorinations, and oxygen to sulfur mutations.

Abstract: The electronic structural origin of the THz and IR spectral changes occurring upon halogen-bond formation is examined by employing the technique of electron density analysis. Theoretical calculations and analyses are conducted for the complexes of pentafluoroiodobenzene (C6F5I) and nitryl chloride (O2NCl) formed with other (halogen-bond accepting) molecules taken as typical examples. It is shown that, in the case of the C-I stretching mode of C6F5I appearing in the THz spectral region, the intensity enhancement occurring upon halogen-bond formation arises from the intermolecular charge flux and (together with the vibrational frequency) is correlated to the partial charge-transfer and covalent nature of the halogen bond. For the N-Cl stretching vibration of O2NCl, it is shown that the high-frequency shift occurring upon complex formation with NH3 arises mainly from the electrostatic effect, while the reduction of its IR intensity arises from the polarization effect and, to a larger extent, from the intermolecular charge flux. These results indicate, therefore, that there are some observable spectroscopic properties in the THz and IR region that are mainly controlled by (and, hence, shed light on) the partial charge-transfer and covalent nature of halogen bonding.

Abstract: Knowing the charge-transport properties of molten oxides is essential for industrial applications, particularly when attempting to control the energy required to separate a metal from its ore conce...

Abstract: A key factor in computational drug design is the consistency and reliability with which intermolecular interactions between a wide variety of molecules can be described. Here we present a procedure to efficiently, reliably and automatically assign partial atomic charges to atoms based on known distributions. We formally introduce the molecular charge assignment problem, where the task is to select a charge from a set of candidate charges for every atom of a given query molecule. Charges are accompanied by a score that depends on their observed frequency in similar neighbourhoods (chemical environments) in a database of previously parameterised molecules. The aim is to assign the charges such that the total charge equals a known target charge within a margin of error while maximizing the sum of the charge scores. We show that the problem is a variant of the well-studied multiple-choice knapsack problem and thus weakly \mathcal {NP} NP -complete. We propose solutions based on Integer Linear Programming and a pseudo-polynomial time Dynamic Programming algorithm. We demonstrate that the results obtained for novel molecules not included in the database are comparable to the ones obtained performing explicit charge calculations while decreasing the time to determine partial charges for a molecule from hours or even days to below a second. Our software is openly available.

Abstract: The stability of complex compounds formed from the ligand di- n -butyldithiophosphate (DBDTP) and its derivatives, with ions of rare-earth elements (REEs), such as gadolinium ion (Gd 3+ ), is an important factor in the separation and purification processes of the elements using solvent extraction method. The complex stability is dependent, one of which, on the partial charge of the donor atom (S atom in this case) in the molecule of DBDTP or its derivatives. The more negative the partial charge of the donor atom, the more stable is the complex compound formed. The purpose of this study is to explore the effect of electron donating, and of electron withdrawing groups, as well as the effect of the structure of the butyl group in the molecules of DBDTP and or its derivatives on the partial charge of the donor atom. The method used was the semi empirical quantum mechanical calculations, i.e. the Austin Model 1 (AM1). The results of the study showed that the electron withdrawing group of -CN had resulted in the most positive charge on the donor atom, if it is on the second carbon atom of the butyl group in the DBDTP and or its derivatives. Conversely, in the same carbon atom position, the donating electron group of -CH=CH 2 had generated the most negative partial charge on the donor atom. Furthermore, the results of this study also revealed that the sec -butyl isomer produced the most negative partial charge on the donor atom, among other isomers.

Abstract: The adsorption of triblock copolymer’s moieties such as DME, 1,2-DME, and 1,2-DMP on a Rutile surface has been studied by DFT. The insights into their adsorption mechanism have been investigated by analyzing various physical and chemical properties such as the adsorption energies, the structural properties, difference of charge density, density of state, bond overlap population, and the atomic partial charge. Dispersion interaction plays a major role on the absorption energy in 1,2-DME, and the upward bridging oxygen configurations of DME and 1,2-DMP; whilst electrostatic and polarization energies are insignificant. A new Ob-Ti bond has been formed from the overlap of lone-pair electrons between orbital O 2p and Ti 3d in downward bridging oxygen configurations of DME and 1,2-DMP, which results in a significantly larger adsorption energies compared with other configurations. The molecular torsion is considered as a barrier that prevent Ob-down of 1,2-DME to create the bond with Ti.

Abstract: In most cases, calculations of properties of metal-organic frameworks (MOFs) based on classical force fields (FFs) are the most suitable in terms of the ratio between accuracy and computational cost, especially in efforts to screen a large number of structures. Such calculations require an initial partial charge assignment to describe the Coulomb contribution. In this study, we would like to present a machine-learning algorithm for MOF partial charge prediction and its verification on experimental data using the FF approach. Proposed ML method offers the accuracy of reference DFT calculations at a fraction of the computational cost with linear scalability.

Abstract: Although the charge flux effect or the geometric dependence of the atomic partial charges have been known for a long time, how it can be effectively handled is not yet established. Here, we present a charge interpolation scheme as a new general tool for representing the charge flux in an analytically well-defined manner. By applying it to the anionic GFP chromophore with the diabatically represented atomic charges, we show that the charge interpolation provides a substantial improvement on the accuracy of the geometry-dependent changes in the molecular dipole moments in the gas phase. We also test the scheme toward describing the electrostatic term in the solvation energy in the aqueous environment and observe that it is also improved but that the extent of the improvement is somewhat limited. We show that the remaining errors can be largely corrected by introducing atomic polarizabilities. Overall, our results show that charge interpolation is an amenable approach for describing the charge flux effect and that its description in the condensed phase should be accompanied by proper treatments of polarization effects.

Abstract: Many molecular simulation force fields represent the charge distributions of molecules with atom-centered partial charges, so simulations with these force fields require that partial charges be assigned to the molecules of interest. The restrained electrostatic potential (RESP) approach is a highly regarded and widely used method of assigning partial charges to varied organic compounds. RESP uses gas-phase HF/6-31G* as the underlying quantum chemical method, intending the resulting overpolarization of molecules to approximate the self-polarization that occurs in the condensed phase setting. However, it is far from clear that this fortuitous overpolarization is optimal or consistent across all compounds. In order to reach a higher level of accuracy, we propose a next generation of this approach, termed RESP2. In RESP2, the charges are derived from higher-level quantum chemical calculations carried out for both gas and aqueous phase, the latter using a continuum solvent model. The polarity of the final charges is tuned by a mixing parameter, δ, which scales the relative contributions of the gas- and aqueous-phase charges. We find that simply substituting RESP2 charges for RESP charges in the context of regular LJ parameters does not lead to clear improvement in liquid-state densities and heats of vaporization but does improve the accuracy of observables expected to depend most strongly on the accuracy of the charge model, i.e., dielectric constants and molecular dipole moments. However, when Lennard-Jones (LJ) parameters are optimized in the context of RESP charges, based on liquid properties, significant improvement in accuracy can be achieved, even with a sharply reduced set of LJ types. We argue that RESP2 with δ≈0.6 (60% aqueous and 40% gas-phase charges) is an accurate and robust method of generating atom-centered partial charges. The present study also highlights the value of optimizing LJ parameters along with the electrostatic model and suggests that a small set of LJ types can be a good starting point for a systematic re-optimization of this important nonbonded term.