Ab Initio Interaction Energies Research Articles

Thermodynamics of NaCl in dense water vapor via cross virial coefficients

Sodium chloride in the fluid phase is important for the chemistry of natural hydrothermal processes in the Earth’s crust and derived industrial utilizations, where thermodynamics is an essential part that can also to some extent fill in missing experimental data. The solubility of sodium chloride in crystalline form (halite) in water vapor is modeled using a novel combination of an accurate equation of state for pure water and a truncated virial equation for water mixed with sodium chloride. In the resulting Helmholtz energy expression, interactions between H2O and NaCl are incorporated through the second (B12), third (C112), and fourth (D1112) cross virial coefficients. The temperature dependence of the coefficients has been determined by regression to experimental data. Specifically, the temperature dependence of B12 is assumed to follow that of a square-well gas, whereas C112 and D1112 are calculated using purely exponential functions of inverse temperature. The temperature dependence of B12 is supported by independent calculations of ab initio interaction energies between H2O and NaCl. For water itself, all terms in the virial equation are collectively modeled by the IAPWS-95 equation of state. For sodium chloride, interactions between two or more NaCl molecules are disregarded. The model shows quantitative agreement with available solubility data in the vapor–halite coexistence region, which implies that the water vapor density is approximately less than 130kgm−3. Its theoretical basis ensures that predictions are reliable in regions where experimental data are missing. The direct calculation of cross virial coefficients is overall useful for modeling geochemical fluids with low solute concentrations, including systems with multiple solvents.

Evaluating the active site-substrate interplay between x-ray crystal structure and molecular dynamics in chorismate mutase.

Designing realistic quantum mechanical (QM) models of enzymes is dependent on reliably discerning and modeling residues, solvents, and cofactors important in crafting the active site microenvironment. Interatomic van der Waals contacts have previously demonstrated usefulness toward designing QM-models, but their measured values (and subsequent residue importance rankings) are expected to be influenceable by subtle changes in protein structure. Using chorismate mutase as a case study, this work examines the differences in ligand-residue interatomic contacts between an x-ray crystal structure and structures from a molecular dynamics simulation. Select structures are further analyzed using symmetry adapted perturbation theory to compute ab initio ligand-residue interaction energies. The findings of this study show that ligand-residue interatomic contacts measured for an x-ray crystal structure are not predictive of active site contacts from a sampling of molecular dynamics frames. In addition, the variability in interatomic contacts among structures is not correlated with variability in interaction energies. However, the results spotlight using interaction energies to characterize and rank residue importance in future computational enzymology workflows.

Kinetic Isotope Effect in Low-Energy Collisions between Hydrogen Isotopologues and Metastable Helium Atoms: Theoretical Calculations Including the Vibrational Excitation of the Molecule.

We present very accurate theoretical results of Penning ionization rate coefficients of the excited metastable helium atoms (4He(23S) and 3He(23S)) colliding with the hydrogen isotopologues (H2, HD, D2) in the ground and first excited rotational and vibrational states at subkelvin regime. The calculations are performed using the current best ab initio interaction energy surface, which takes into account the nonrigidity effects of the molecule. The results confirm a recently observed substantial quantum kinetic isotope effect (Nat. Chem. 2014, 6, 332–335) and reveal that the change of the rotational or vibrational state of the molecule can strongly enhance or suppress the reaction. Moreover, we demonstrate the mechanism of the appearance and disappearance of resonances in Penning ionization. The additional model computations, with the morphed interaction energy surface and mass, give better insight into the behavior of the resonances and thereby the reaction dynamics under study. Our theoretical findings are compared with all available measurements, and comprehensive data for prospective experiments are provided.

Ab Initio Intermolecular Potential Energy Surfaces and Cross Second Virial Coefficients for the Dimer N2-NO.

Ab initio intermolecular potential energy surfaces (PES) of N2-NO have been constructed at the level of theory CCSD(T) with the augmented correlation-consistent basis sets aug-cc-pVmZ (with m = 2, 3, 4). The nitrogen in the closed-shell electronic configuration X1Σ+ and nitric oxide in the open-shell electronic configuration A2Σ+ were employed to calculate ab initio intermolecular interaction energies. The two new ab initio 5-site intermolecular pair potentials at the theoretical level CCSD(T)/aug-cc-pVmZ (with m = 4, 24) were developed appropriately and are suitable for N2-NO dimer by using the nonlinear least-squares fitting method combining MIO and Levenberg–Marquardt algorithms. The correlation quality of these two potentials was found to be very good with R2 values in the range of 0.98372 to 0.99775. The cross second virial coefficients B12(T) of the N2-NO dimer were calculated in the temperature range of 100 to 470 K using the two ab initio 5-site potentials. The discrepancies between the calculated results and the experimental data can be acceptable.

Diagram of vapor‐liquid equilibria for n‐pentane using hybrid Gibbs ensemble Monte Carlo simulation

AbstractIn this paper we report the simulation results using the 5‐site Lennard‐Jones potential function obtained from ab initio interaction energy for n‐pentane at level of theory CCSD(T)/aug‐cc‐pVTZ. The hybrid Gibbs ensemble Monte Carlo (HGEMC) simulation was performed under the same initial conditions for boxes 1 and 2 with 60 molecules and a density of 0.130 g /cm3. The HGEMC simulation was implemented with 106 epochs and value of Cutoff_Radius 10Å. The simulation temperature was varied from 100 to 450 K. The thermodynamic results of the vapor‐liquid equilibria derived from HGEMC‐NVT simulation are consistent with experimental data and other calculation methods.

Quantifying Inter-Residue Contacts through Interaction Energies.

The validity and accuracy of protein modeling is dependent on constructing models that account for the inter-residue interactions crucial for protein structure and function. Residue interaction networks derived from interatomic van der Waals contacts have previously demonstrated usefulness toward designing protein models, but there has not yet been evidence of a connection between network-predicted interaction strength and quantitative interaction energies. This work evaluates the intraprotein contact networks of five proteins against ab initio interaction energies computed using symmetry-adapted perturbation theory. To more appropriately capture the local chemistry of the protein, we deviate from traditional protein network analysis to redefine the interacting nodes in terms of main chain and side chain functional groups rather than complete amino acids. While there is no simple correspondence between the features of the contact network and actual interaction strength, random forest models constructed from minimal structural, network, and chemical descriptors are capable of accurately predicting interaction energy. The results of this work serve as a foundation for the development and improvement of functional group-based contact networks.

A novel intermolecular potential to describe the interaction between the azide anion and carbon nanotubes

In this contribution we propose a novel and accurate intermolecular potential that can be used for the simulation of the azide anion confined inside carbon nanotubes of arbitrary size. The peculiarity of our approach is to include an explicit term, modeling the induction attractive contributions from the negatively charged azide ion, that can be generalized to other ions confined in carbon nanotubes of different size and length. Through a series of accurate DLPNO-CCSD(T) calculations, we show that this potential reproduces the ab initio interaction energy to within a few kcal/mol. The potential is implemented in a molecular dynamics program, with which we carried out illustrative simulations to demonstrate the effectiveness of our approach. At last, the guidelines provided by this investigation can be applied to build up force fields for many neutral/ionic molecular species confined within carbon nanotubes; a crucial requirement to carry out molecular dynamics simulations under a variety of conditions.

Grain-boundary segregation of 3d-transition metal solutes in bcc Fe: ab initio local-energy and d-electron behavior analysis

We present ab initio calculations of grain-boundary (GB) segregation of the series of 3d transition-metal (TM) solutes in bcc Fe, taking advantage of the local-energy analysis. For 11(3 3 2) and 3(1 1 1) symmetrical tilt GBs, the segregation behaviors of 3d-TM solutes can be classified into three groups. The early TMs (Sc, Ti and V) are preferentially segregated to the looser sites of GBs antiferromagnetically, the late TMs (Co, Ni and Cu) are preferentially segregated to the tighter sites of GBs ferromagnetically, and the middle TMs (Cr and Mn) are segregated antiferromagnetically without fixed site preference. TMs at both ends of the 3d series show larger segregation-energy gains, while Mn shows a cusp at the center, which is similar to the ab initio interaction energies between the 3d-TM solutes and a screw-dislocation core in bcc Fe. By the local-energy analysis combined with the local densities of states, the segregation of the early TMs is mainly attributed to the stabilization of surrounding Fe atoms by the TM solute at the looser sites of GBs, and that of the late TMs is mainly attributed to the stabilization of the TM solute itself from bulk Fe to GB sites and the destabilization of Fe atoms around the TM solute in bulk Fe. The cusp at Mn is mainly caused by the destabilization of Fe atoms around the Mn solute in bulk Fe, due to nearly-localized high-spin d states of Mn, in contrast to substantial d-d hybridization for Mn in GBs. For each group of 3d-TM solutes, the effects on the magnetic and mechanical properties of Fe GBs are also analyzed by the d-electron behavior in common with the segregation mechanism.

Protein Residue Networks from Energetic and Geometric Data: Are They Identical?

Protein residue networks (PRN) from energetic and geometric data are probably not identical. PRNs constructed from ab initio pair interaction energies are analyzed for the first time and compared to PRN based on center of mass separation. We use modern, previously unused algorithms such as global and local efficiencies to quantitatively confirm that both types of PRNs do exhibit small-world character. The main novelty finding is that interaction energy-based PRNs preserve small-world character even when clustered. A node hierarchy independent of the cutoff energy used for the edge creation is characteristic for them. Efficiency centrality identifies hubs responsible for such behavior. The interaction energy-based PRNs seem to comply with the scale-free network model with respect to efficiency centrality distribution as opposed to distance based PRNs. Community detection is introduced into protein network research as an extension beyond cluster analysis to study tertiary and quaternary structures.

Calculation of cross second virial coefficients using ab initio intermolecular potential energy surfaces for dimer H2-N2

The ab initio intermolecular pair potentials of dimer H2-N2 were calculated from all constructed orientations, using the level of the theory CCSD(T) and basis sets aug-cc-pVmZ (m = 2, 3, 4, 23, 24, 34). The complete basis sets limit aug-cc-pVmZ (m = 23, 24, 34) were extrapolated by ab initio interaction energies at the level of the theory CCSD(T) with correlation-consistent basis sets aug-cc-pVmZ (m = 2, 3, 4). Then the quantum mechanical results were used for developing two new 5-site intermolecular potential functions by fitting ab initio intermolecular energies of dimer H2-N2. The ab initio fitted intermolecular potentials are used in standard thermodynamic relationships to get the cross second virial coefficients B12(T) of the hydrogen-nitrogen mixture. The calculated results are in good agreement with the experimental data.

Polarizable atomic multipole-based force field for DOPC and POPE membrane lipids

ABSTRACTA polarizable atomic multipole-based force field for the membrane bilayer models 1,2-dioleoyl-phosphocholine (DOPC) and 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE) has been developed. The force field adopts the same framework as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) model, in which the charge distribution of each atom is represented by the permanent atomic monopole, dipole and quadrupole moments. Many-body polarization including the inter- and intra-molecular polarization is modelled in a consistent manner with distributed atomic polarizabilities. The van der Waals parameters were first transferred from existing AMOEBA parameters for small organic molecules and then optimised by fitting to ab initio intermolecular interaction energies between models and a water molecule. Molecular dynamics simulations of the two aqueous DOPC and POPE membrane bilayer systems, consisting of 72 model molecules, were then carried out to validate the force field parameters. Membrane width, area per lipid, volume per lipid, deuterium order parameters, electron density profile, etc. were consistent with experimental values.

Methane Adsorption in Zr-Based MOFs: Comparison and Critical Evaluation of Force Fields.

The search for nanoporous materials that are highly performing for gas storage and separation is one of the contemporary challenges in material design. The computational tools to aid these experimental efforts are widely available, and adsorption isotherms are routinely computed for huge sets of (hypothetical) frameworks. Clearly the computational results depend on the interactions between the adsorbed species and the adsorbent, which are commonly described using force fields. In this paper, an extensive comparison and in-depth investigation of several force fields from literature is reported for the case of methane adsorption in the Zr-based Metal–Organic Frameworks UiO-66, UiO-67, DUT-52, NU-1000, and MOF-808. Significant quantitative differences in the computed uptake are observed when comparing different force fields, but most qualitative features are common which suggests some predictive power of the simulations when it comes to these properties. More insight into the host–guest interactions is obtained by benchmarking the force fields with an extensive number of ab initio computed single molecule interaction energies. This analysis at the molecular level reveals that especially ab initio derived force fields perform well in reproducing the ab initio interaction energies. Finally, the high sensitivity of uptake predictions on the underlying potential energy surface is explored.

Application of a simple quantum chemical approach to ligand fragment scoring for Trypanosoma brucei pteridine reductase\xa01 inhibition

There is a need for improved and generally applicable scoring functions for fragment-based approaches to ligand design. Here, we evaluate the performance of a computationally efficient model for inhibitory activity estimation, which is composed only of multipole electrostatic energy and dispersion energy terms that approximate long-range ab initio quantum mechanical interaction energies. We find that computed energies correlate well with inhibitory activity for a compound series with varying substituents targeting two subpockets of the binding site of Trypanosoma brucei pteridine reductase 1. For one subpocket, we find that the model is more predictive for inhibitory activity than the ab initio interaction energy calculated at the MP2 level. Furthermore, the model is found to outperform a commonly used empirical scoring method. Finally, we show that the results for the two subpockets can be combined, which suggests that this simple nonempirical scoring function could be applied in fragment–based drug design.

Molecular Dynamics Simulation Study of ClF in Water: Halogen Bonding Interaction in Liquid

Does the halogen bonding interaction co-exist in liquid when it competes with the hydrogen bonding interaction? The classical molecular dynamics simulations for the solvation properties of ClF molecule in water are performed with the Lennard-Jones plus Coulomb electrostatic potential parameters that are optimized with ab initio interaction energy calculations for the pre-reactive H2O⋯ClF complex. We find that the halogen bonding interactions occur between O and Cl atoms and have the comparable strength and population with respect to the hydrogen bonding interactions of Cl⋯H.

Calculation of second virial coefficients using ab initio intermolecular pair potentials for F2-F2 and H2-F2 dimers

The ab initio intermolecular pair potentials of dimers F2-F2 and H2-F2 were calculated from all constructed orientations, using the level of theory CCSD(T) and basis sets aug-cc-pVmZ (m=2, 3, 23). The complete basis set limit aug-cc-pV23Z was extrapolated by ab initio interaction energies at the level of theory CCSD(T) with two basis sets aug-cc-pVmZ (m=2, 3). Then the quantum mechanical results were used for constructing two new 5-site potential functions by fitting ab initio energies of dimers F2-F2 and H2-F2. The correlation between ab initio and the fitted ab initio energies of 5-site pair potentials for dimers F2-F2 and H2-F2 is appeared by fitness values R2 in range 0.99749–0.99997. The fitted potentials were used in standard thermodynamic relations to obtain the second virial coefficients and the results were compared to experimental data.

Dimers of N‐Heterocyclic Carbene Copper, Silver, and Gold Halides: Probing Metallophilic Interactions through Electron Density Based Concepts

Homobimetallic metallophilic interactions between copper, silver, and gold-based [(NHC)MX]-type complexes (NHC=N-heterocyclic carbene, i.e, 1,3,4-trimethyl-4,5-dihydro-1H-1,2,4-triazol-5-ylidene; X=F, Cl, Br, I) were investigated by means of ab initio interaction energies, Ziegler-Rauk-type energy-decomposition analysis, the natural orbital for chemical valence (NOCV) framework, and the noncovalent interaction (NCI) index. It was found that the dimers of these complexes predominantly adopt a head-to-tail arrangement with typical M⋅⋅⋅M distance of 3.04-3.64 Å, in good agreement with the experimental X-ray structure determined for [{(NHC)AuCl}2 ], which has an Au⋅⋅⋅Au distance of 3.33 Å. The interaction energies between silver- and gold-based monomers are calculated to be about -25 kcal mol(-1) , whereas that for the Cu congener is significantly lower (-19.7 kcal mol(-1) ). With the inclusion of thermal and solvent contributions, both of which are destabilizing, by about 15 and 8 kcal mol(-1) , respectively, an equilibrium process is predicted for the formation of dimer complexes. Energy-decomposition analysis revealed a dominant electrostatic contribution to the interaction energy, besides significantly stabilizing dispersion and orbital interactions. This electrostatic contribution is rationalized by NHC(δ(+) )⋅⋅⋅halogen(δ(-) ) interactions between monomers, as demonstrated by electrostatic potentials and derived charges. The dominant NOCV orbital indicates weakening of the π backdonation in the monomers on dimer formation, whereas the second most dominant NOCV represents an electron-density deformation according to the formation of a very weak M⋅⋅⋅M bond. One of the characteristic signals found in the reduced density gradient versus electron density diagram corresponds to the noncovalent interactions between the metal centers of the monomers in the NCI plots, which is the manifestation of metallophilic interaction.

Hydration of Cisplatin Studied by an Effective Ab Initio Pair Potential Including Solute-Solvent Polarization.

The hydration of cis-[PtCl2(NH3)2] (cisplatin) has been studied by means of classical molecular dynamics simulations using a new interaction potential obtained by fitting about 4000 ab initio interaction energies calculated at the MP2 level. The functional form included several r(-n) terms (n = 4, 6, 8, 12) to achieve an accurate description of the interactions in the different regions around the cisplatin. Bulk solvent effects on the cisplatin-water molecule interactions have been included by means of a continuum model. Radial Distribution Function (RDF) analysis does not provide a clear enough description of the hydration pattern due to the intricate solvent arrangement around the solute. Angle-solved RDFs and spatial distribution functions have been used to provide more detailed pictures of the local hydration structure around the two ligands, chloride and ammine groups, and the axial region. Based on this information, it is shown a more convenient way to compute the running coordination number for the first hydration shell by simultaneously considering angle-solved RDFs centered on the ligand representative atoms of the complex: ammino N, Cl, and Pt atoms. This way, the hydration number is obtained by integrating over an interlocking-sphere volume built by the spheres centered on the cation and the main atoms of each ligand. Compared to previous works dealing with cisplatin hydration, the global hydration number for the first coordination shell is now higher and involves about 27 water molecules. The importance of the structural sampling, the computational level, as well as the functional form adopted for the interaction potential are thoroughly discussed with respect to the previous proposed intermolecular potential.

Multipole-Based Force Fields from ab Initio Interaction Energies and the Need for Jointly Refitting All Intermolecular Parameters.

Distributed atomic multipole (MTP) moments promise significant improvements over point charges (PCs) in molecular force fields, as they (a) more realistically reproduce the ab initio electrostatic potential (ESP) and (b) allow to capture anisotropic atomic properties such as lone pairs, conjugated systems, and σ holes. The present work focuses on the question of whether multipolar electrostatics instead of PCs in standard force fields leads to quantitative improvements over point charges in reproducing intermolecular interactions. To this end, the interaction energies of two model systems, benzonitrile (BZN) and formamide (FAM) homodimers, are characterized over a wide range of dimer conformations. It is found that although with MTPs the monomer ab initio ESP can be captured better by about an order of magnitude compared to point charges (PCs), this does not directly translate into better describing ab initio interaction energies compared to PCs. Neither ESP-fitted MTPs nor refitted Lennard-Jones (LJ) parameters alone demonstrate a clear superiority of atomic MTPs. We show that only if both electrostatic and LJ parameters are jointly optimized in standard, nonpolarizable force fields, atomic are MTPs clearly beneficial for reproducing ab initio dimerization energies. After an exhaustive exponent scan, we find that for both BZN and FAM, atomic MTPs and a 9-6 LJ potential can reproduce ab initio interaction energies with ∼30% (RMSD 0.13 vs 0.18 kcal/mol) less error than point charges (PCs) and a 12-6 LJ potential. We also find that the improvement due to using MTPs with a 9-6 LJ potential is considerably more pronounced than with a 12-6 LJ potential (≈ 10%; RMSD 0.19 versus 0.21 kcal/mol).

Ab initio ground state phenylacetylene–argon intermolecular potential energy surface and rovibrational spectrum

We evaluate the phenylacetylene-argon intermolecular potential energy surface by fitting a representative number of ab initio interaction energies to an analytic function. These energies are calculated at a grid of intermolecular geometries, using the CCSD(T) method and the aug-cc-pVDZ basis set extended with a series of 3s3p2d1f1g midbond functions. The potential is characterized by two equivalent global minima where the Ar atom is located above and below the phenylacetylene plane at a distance of 3.5781 Å from the molecular center of mass and at an angle of 9.08° with respect to the axis perpendicular to the phenylacetylene plane and containing the center of mass. The calculated interaction energy is -418.9 cm(-1). To check further the potential, we obtain the rovibrational spectrum of the complex and the results are compared to the available experimental data.

Development of Polarizable Models for Molecular Mechanical Calculations. 4. van der Waals Parametrization

In the previous publications of this series, we presented a set of Thole induced dipole interaction models using four types of screening functions. In this work, we document our effort to refine the van der Waals parameters for the Thole polarizable models. Following the philosophy of AMBER force field development, the van der Waals (vdW) parameters were tuned for the Thole model with linear screening function to reproduce both the ab initio interaction energies and the experimental densities of pure liquids. An in-house genetic algorithm was applied to maximize the fitness of "chromosomes" which is a function of the root-mean-square errors (RMSE) of interaction energy and liquid density. To efficiently explore the vdW parameter space, a novel approach was developed to estimate the liquid densities for a given vdW parameter set using the mean residue-residue interaction energies through interpolation/extrapolation. This approach allowed the costly molecular dynamics simulations be performed at the end of each optimization cycle only and eliminated the simulations during the cycle. Test results show notable improvements over the original AMBER FF99 vdW parameter set, as indicated by the reduction in errors of the calculated pure liquid densities (d), heats of vaporization (H(vap)), and hydration energies. The average percent error (APE) of the densities of 59 pure liquids was reduced from 5.33 to 2.97%; the RMSE of H(vap) was reduced from 1.98 to 1.38 kcal/mol; the RMSE of solvation free energies of 15 compounds was reduced from 1.56 to 1.38 kcal/mol. For the interaction energies of 1639 dimers, the overall performance of the optimized vdW set is slightly better than the original FF99 vdW set (RMSE of 1.56 versus 1.63 kcal/mol). The optimized vdW parameter set was also evaluated for the exponential screening function used in the Amoeba force field to assess its applicability for different types of screening functions. Encouragingly, comparable performance was observed when the optimized vdW set was combined with the Thole Amoeba-like polarizable model, particularly for the interaction energy and liquid density calculations. Thus, the optimized vdW set is applicable to both types of Thole models with either linear or Amoeba-like screening functions.