Accurate Intermolecular Potentials Research Articles

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.

Decoding Oxyanion Aqueous Solvation Structure: A Potassium Nitrate Example at Saturation

The ability to probe the structure of a salt solution at the atomic scale is fundamentally important for our understanding of many chemical reactions and their mechanisms. The capability of neutron diffraction to "see" hydrogen (or deuterium) and other light isotopes is exceptional for resolving the structural complexity around the dissolved solutes in aqueous electrolytes. We have made measurements using oxygen isotopes on aqueous nitrate to reveal a small hydrogen-bonded water coordination number (3.9 ± 1.2) around a nitrate oxyanion. This is compared to estimates made using the existing method of nitrogen isotope substitution and those of computational simulations (>5-6 water molecules). The low water coordination number, combined with a comparison to classical molecular dynamics simulations, suggests that ion-pair formation is significant. This insight demonstrates the utility of experimental diffraction data for benchmarking atomistic computer simulations, enabling the development of more accurate intermolecular potentials.

Molecular dynamic simulations of N2-broadened methane line shapes and comparison with experiments

Absorption spectra of methane transitions broadened by nitrogen have been calculated for the first time using classical molecular dynamic simulations. For that, the time evolution of the auto-correlation function of the dipole moment vector, assumed along a C–H axis, was computed using an accurate site-site intermolecular potential for CH4–N2. Quaternion coordinates were used to treat the rotation of the molecules. A requantization procedure was applied to the classical rotation and spectra were then derived as the Fourier-Laplace transform of the auto-correlation function. These computed spectra were compared with experimental ones recorded with a tunable diode laser and a difference-frequency laser spectrometer. Specifically, nine isolated methane lines broadened by nitrogen, belonging to various vibrational bands and having rotational quantum numbers J from 0 to 9, were measured at room temperature and at several pressures from 20 to 945 mbar. Comparisons between measured and calculated spectra were made through their fits using the Voigt profile. The results show that ab initio calculated spectra reproduce with very high fidelity non-Voigt effects on the measurements and that classical molecular dynamic simulations can be used to predict spectral shapes of isolated lines of methane perturbed by nitrogen.

Accurate analytic intermolecular potential for the simulation of Na+ and K+ ion hydration in liquid water

Structural and dynamical properties of the hydration of K+ and Na+ ions have been investigated at atomistic level of detail by molecular dynamics simulations of the ion and 253 water molecules with periodic boundary conditions at the temperatures of 300 and 450K. The intermolecular interactions involved have been modelled by a recently developed approach targeted to accuracy and low computational cost. Radial distribution functions and coordination numbers have been obtained to assess overall reliability of the model. Two different types of water models, rigid and flexible, have been used in simulations, evaluating the effect of adding flexibility to water.

Small and efficient basis sets for the evaluation of accurate interaction energies: aromatic molecule-argon ground-state intermolecular potentials and rovibrational states.

By evaluating a representative set of CCSD(T) ground state interaction energies for van der Waals dimers formed by aromatic molecules and the argon atom, we test the performance of the polarized basis sets of Sadlej et al. (J. Comput. Chem. 2005, 26, 145; Collect. Czech. Chem. Commun. 1988, 53, 1995) and the augmented polarization-consistent bases of Jensen (J. Chem. Phys. 2002, 117, 9234) in providing accurate intermolecular potentials for the benzene-, naphthalene-, and anthracene-argon complexes. The basis sets are extended by addition of midbond functions. As reference we consider CCSD(T) results obtained with Dunning's bases. For the benzene complex a systematic basis set study resulted in the selection of the (Z)Pol-33211 and the aug-pc-1-33321 bases to obtain the intermolecular potential energy surface. The interaction energy values and the shape of the CCSD(T)/(Z)Pol-33211 calculated potential are very close to the best available CCSD(T)/aug-cc-pVTZ-33211 potential with the former basis set being considerably smaller. The corresponding differences for the CCSD(T)/aug-pc-1-33321 potential are larger. In the case of the naphthalene-argon complex, following a similar study, we selected the (Z)Pol-3322 and aug-pc-1-333221 bases. The potentials show four symmetric absolute minima with energies of -483.2 cm(-1) for the (Z)Pol-3322 and -486.7 cm(-1) for the aug-pc-1-333221 basis set. To further check the performance of the selected basis sets, we evaluate intermolecular bound states of the complexes. The differences between calculated vibrational levels using the CCSD(T)/(Z)Pol-33211 and CCSD(T)/aug-cc-pVTZ-33211 benzene-argon potentials are small and for the lowest energy levels do not exceed 0.70 cm(-1). Such differences are substantially larger for the CCSD(T)/aug-pc-1-33321 calculated potential. For naphthalene-argon, bound state calculations demonstrate that the (Z)Pol-3322 and aug-pc-1-333221 potentials are of similar quality. The results show that these surfaces differ substantially from the available MP2/aug-cc-pVDZ potential. For the anthracene-argon complex it proved advantageous to calculate interaction energies by using the (Z)Pol and the aug-pc-1 basis sets, and we expect it to be increasingly so for complexes containing larger aromatic molecules.

Carbon Dioxide Hydrate Phase Equilibrium and Cage Occupancy Calculations Using Ab Initio Intermolecular Potentials

Gas hydrate deposits are receiving increased attention as potential locations for CO2 sequestration, with CO2 replacing the methane that is recovered as an energy source. In this scenario, it is very important to correctly characterize the cage occupancies of CO2 to correctly assess the sequestration potential as well as the methane recoverability. In order to predict accurate cage occupancies, the guest–host interaction potential must be represented properly. Earlier, these potential parameters were obtained by fitting to experimental equilibrium data and these fitted parameters do not match with those obtained by second virial coefficient or gas viscosity data. Ab initio quantum mechanical calculations provide an independent means to directly obtain accurate intermolecular potentials. A potential energy surface (PES) between H2O and CO2 was computed at the MP2/aug-cc-pVTZ level and corrected for basis set superposition error (BSSE), an error caused due to the lower basis set, by using the half counterpoise method. Intermolecular potentials were obtained by fitting Exponential-6 and Lennard-Jones 6-12 models to the ab initio PES, correcting for many-body interactions. We denoted this model as the “VAS” model. Reference parameters for structure I carbon dioxide hydrate were calculated using the VAS model (site–site ab initio intermolecular potentials) as Δμ(w)(0) = 1206 ± 2 J/mol and ΔH(w)(0) = 1260 ± 12 J/mol. With these reference parameters and the VAS model, pure CO2 hydrate equilibrium pressure was predicted with an average absolute deviation of less than 3.2% from the experimental data. Predictions of the small cage occupancy ranged from 32 to 51%, and the large cage is more than 98% occupied. The intermolecular potentials were also tested by calculating the pure CO2 density and diffusion of CO2 in water using molecular dynamics simulations.

Lennard–Jones parameters for combustion and chemical kinetics modeling from full-dimensional intermolecular potentials

Lennard–Jones parameters for use in combustion modeling, as transport parameters and in pressure-dependent rate-coefficient calculations as collision rate parameters, are calculated from accurate full-dimensional intermolecular potentials. Several first-principles theoretical methods are considered. In the simplest approach, the intermolecular potential is spherically averaged and used to determine Lennard–Jones parameters. This method works well for small species, but it is not suitable for larger species due to unphysical averaging over the repulsive wall. Another method considered is based on full-dimensional trajectory calculations of binary collisions. This method is found to be very accurate, predicting Lennard–Jones collision rates within ∼10% of those obtained via tabulated (experimentally-based) Lennard–Jones parameters. Finally, a computationally efficient method is presented based on one-dimensional minimizations averaged over the colliding partners’ relative orientations. This method is shown to be both accurate and efficient. The good accuracy of the latter two approaches is shown to be a result of their explicit treatment of anisotropy. The effects of finite temperature vibrations and multiple conformers are quantified and are shown to be small. The choice of potential energy surface has a somewhat larger effect, and strategies based both on efficient semiempirical methods and on first-principles direct dynamics are considered. Overall, 75 systems are considered, including seven baths, targets as large as heptane, both molecules and radicals, and both hydrocarbons and oxygenates.

Cation−π Interactions: Accurate Intermolecular Potential from Symmetry-Adapted Perturbation Theory

Symmetry-adapted perturbation theory (SAPT) is used to decompose the total intermolecular interaction energy between the ammonium cation and a benzene molecule into four physically motivated individual contributions: electrostatics, exchange, dispersion, and induction. Based on this rigorous decomposition, it is shown unambiguously that both the electrostatic and the induction energy components contribute almost equally to the attractive forces stabilizing the dimer with a nonnegligible contribution coming from the dispersion term. A polarizable potential model for the interaction of ammonium cation with benzene is parametrized by fitting these four energy components separately using the functional forms of the AMOEBA force field augmented with the missing charge penetration energy term calculated as a sum over pairwise electrostatic energies between spherical atoms. It is shown that the proposed model is able to produce accurate intermolecular interaction energies as compared to ab initio results, thus avoiding error compensation to a large extent.

Abinitiocalculations of the spectral shapes of CO2isolated lines including non-Voigt effects and comparisons with experiments

Wepresentafully ab initiomodelandcalculationsofthespectralshapesofabsorptionlinesinapuremolecular gas under conditions where the influences of collisions and of the Doppler effect are significant. Predictions of the time dependence of dipole autocorrelation functions (DACFs) are made for pure CO2 at room temperature using requantized classical molecular dynamics simulations. These are carried, free of any adjusted parameter, on the basis of an accurate anisotropic intermolecular potential. The Fourier-Laplace transforms of these DACFs then yield calculated spectra which are analyzed, as some measured ones, through fits using Voigt line profiles. Comparisonsbetweentheoryandvariousexperimentsnotonlyshowthatthemainline-shapeparameters(Lorentz pressure-broadening coefficients) are accurately predicted, but that subtle observed non-Voigt features are also quantitatively reproduced by the model. These successes open renewed perspectives for the understanding of the mechanisms involved (translational-velocity and rotational-state changes and their dependences on the molecular speed) and the quantification of their respective contributions. The proposed model should also be of great help for the test of widely used empirical line-shape models and, if needed, the construction of more physically based ones.

A molecular H2 potential for heterogeneous simulations including polarization and many-body van der Waals interactions

A highly accurate aniostropic intermolecular potential for diatomic hydrogen has been developed that is transferable for molecular modeling in heterogeneous systems. The potential surface is designed to be efficacious in modeling mixed sorbates in metal-organic materials that include sorption interactions with charged interfaces and open metal sites. The potential parameters are compatible for mixed simulations but still maintain high accuracy while deriving dispersion parameters from a proven polarizability model. The potential includes essential physical interactions including: short-range repulsions, dispersion, and permanent and induced electrostatics. Many-body polarization is introduced via a point-atomic polarizability model that is also extended to account for many-body van der Waals interactions in a consistent fashion. Permanent electrostatics are incorporated using point partial charges on atomic sites. However, contrary to expectation, the best potentials are obtained by permitting the charges to take on values that do not reproduce the first non-vanishing moment of the electrostatic potential surface, i.e., the quadrupole moment. Potential parameters are fit to match ab initio energies for a representative range of dimer geometries. The resulting potential is shown to be highly effective by comparing to electronic structure calculations for a thermal distribution of trimer geometries, and by reproducing experimental bulk pressure-density isotherms. The surface is shown to be superior to other similarly portable potential choices even in tests on homogeneous systems without strong polarizing fields. The present streamlined approach to developing such potentials allows for a simple adaptation to other molecules amenable to investigation by high-level electronic structure methods.

A quantitative study of the clustering of polycyclic aromatic hydrocarbons at high temperatures

The clustering of polycyclic aromatic hydrocarbon (PAH) molecules is investigated in the context of soot particle inception and growth using an isotropic potential developed from the benchmark PAHAP potential. This potential is used to estimate equilibrium constants of dimerisation for five representative PAH molecules based on a statistical mechanics model. Molecular dynamics simulations are also performed to study the clustering of homomolecular systems at a range of temperatures. The results from both sets of calculations demonstrate that at flame temperatures pyrene (C(16)H(10)) dimerisation cannot be a key step in soot particle formation and that much larger molecules (e.g. circumcoronene, C(54)H(18)) are required to form small clusters at flame temperatures. The importance of using accurate descriptions of the intermolecular interactions is demonstrated by comparing results to those calculated with a popular literature potential with an order of magnitude variation in the level of clustering observed. By using an accurate intermolecular potential we are able to show that physical binding of PAH molecules based on van der Waals interactions alone can only be a viable soot inception mechanism if concentrations of large PAH molecules are significantly higher than currently thought.

SAFT-γ Force Field for the Simulation of Molecular Fluids. 1. A Single-Site Coarse Grained Model of Carbon Dioxide

An application of the "top-down" concept for the development of accurate coarse-grained intermolecular potentials of complex fluids is presented. With the more common "bottom-up" procedure, coarse-grained models are constructed from a suitable simplification of a detailed atomistic representation, and small adjustments to the intermolecular parameters are made by comparison with limited experimental data where necessary. In contrast, in the top-down approach, a molecular-based equation of state is used to obtain an effective coarse-grained intermolecular potential that reproduces the macroscopic experimental thermophysical properties over a wide range of conditions. These coarse-grained intermolecular potentials can then be used in conventional molecular simulation to obtain properties (such as structure or dynamics) that are not directly accessible from the equation of state or at extreme conditions where the theory is expected to fail. To demonstrate our procedure, a coarse-grained model for carbon dioxide (CO(2)) is obtained from a recent implementation of the statistical associating fluid theory of variable range (SAFT-VR) employing a Mie (generalized Lennard-Jones) potential; the parameters of this single-site Mie model of CO(2) are estimated by optimizing the equation of state's description of the experimental vapor-pressure and saturated liquid density data. This approach is only viable because of the excellent agreement of the SAFT-VR Mie EoS with simulation data. Our single-site SAFT-γ coarse-grained model for CO(2) is used in Monte Carlo molecular simulation to assess the adequacy of the description of the fluid-phase behavior and properties that were not used to develop the potential model such as the enthalpy of vaporization, interfacial tension, density profiles, supercritical densities, and second-derivative thermodynamic properties (thermal expansivity, isothermal compressibility, heat capacity, Joule-Thompson coefficient, and speed of sound). The accuracy of the description with the single-site SAFT-γ model of CO(2) is found to be of similar quality to that of more sophisticated intermolecular potentials such as a six-site (three LJ centers and three charged sites) all-atom model. The SAFT-γ top-down approach to coarse-graining resolves a key challenge with coarse-graining techniques: the provision of a direct robust link between the microscopic and macroscopic scales.

Accurate Intermolecular Potentials with Physically Grounded Electrostatics.

A strategy is proposed to include the missing charge penetration energy term directly into a force field using a sum over pairwise electrostatic energies between spherical atoms as originally suggested by Spackman. This important contribution to the intermolecular potential can be further refined to reproduce the accurate electrostatic energy between monomers in a dimer by allowing for the radial contraction-expansion of atomic charge densities. The other components of a force field (exchange-repulsion and dispersion) are parametrized to reproduce the accurate data calculated by symmetry-adapted perturbation theory (SAPT). As a proof-of-concept, we have derived the force field parameters suitable for modeling intermolecular interactions between polycyclic aromatic hydrocarbons (PAH). It is shown that it is possible to have a balanced force field suitable for molecular simulations of large molecules avoiding error cancellation to a large extent.

Molecular dynamics simulations for CO2 spectra. III. Permanent and collision-induced tensors contributions to light absorption and scattering

Classical molecular dynamics simulations have been performed for gaseous CO(2) starting from an accurate anisotropic intermolecular potential. Through calculations of the evolutions of the positions and orientations of a large number of molecules, the time evolutions of the permanent and collision-induced electric dipole vector and polarizability tensor are obtained. These are computed from knowledge of static molecular parameters taking only the leading induction terms into account. The Laplace transforms of the auto-correlation functions of these tensors then directly yield the light absorption and scattering spectra. These predictions are, to our knowledge, the first in which the contributions of permanent and collision-induced tensors are simultaneously taken into account for gaseous CO(2), without any adjusted parameter. Comparisons between computations and measurements are made for absorption in the region of the ν(3) infrared band and for depolarized Rayleigh scattering in the roto-translational band. They demonstrate the quality of the model over spectral ranges from the band center to the far wings where the spectrum varies by several orders of magnitude. The contributions of the permanent and interaction-induced (dipole and polarizability) tensors are analyzed for the first time, through the purely permanent (allowed), purely induced, and cross permanent∕induced components of the spectra. It is shown that, while the purely induced contribution is negligible when compared to the collision-broadened allowed component, the cross term due to interferences between permanent and induced tensors significantly participates to the wings of the bands. This successfully clarifies the long lasting, confusing situation for the mechanisms governing the wings of the CO(2) spectra considered in this work.

Accurate three-dimensional intermolecular potential of the He–MgH complex

An accurate three-dimensional interaction potential energy surface of the He–MgH(2Σ+) van der Waals complex is developed using the partially spin-restricted open-shell single and double excitation coupled cluster method with perturbative triples [RCCSD(T)] level of theory for a large number of geometries. The calculated single point energies at each of five rMgH values are first fitted by an analytic two-dimensional potential model. The five model potentials are then used to construct the three-dimensional potential energy surface by interpolating along (r−re) by a four-order polynomial. Based on the three-dimensional potential energy surface, the vibrational average potential is obtained. Bound state energy levels of He–MgH complex and cross sections for rotational relaxation are calculated within the spin-free approximation.

Toward an Accurate Modeling of the Water−Zeolite Interaction: Calibrating the DFT Approach

The performances of nine selected exchange-correlation functionals for the description of the interaction of water with clusters modeling the silicalite-1 zeolite have been assessed. The chosen structural models cover different classes of interactions between water and a zeolite backbone, ranging from electrostatics to van der Waals types. Almost all of the considered functionals give qualitatively correct results for the considered systems with respect to the reference MP2 data. However, among all of the models, only two (M05-2X and B97-D) provide a quantitative agreement for all of the clusters taken into account. These functionals can thus be envisaged as affordable methods to study weakly interacting systems as well as to provide a database for the development of accurate and transferable intermolecular potentials for classical simulations.

Explicit Hydrogen-Bond Potentials and Their Application to NMR Scalar Couplings in Proteins.

Hydrogen bonds (H bonds) are fundamental for the stability, structure, and dynamics of chemically and biologically relevant systems. One of the direct means to detect H bonds in proteins is NMR spectroscopy. As H bonds are dynamic in nature, atomistic simulations offer a meaningful way to characterize and analyze properties of hydrogen bonds, provided a sufficiently accurate interaction potential is available. Here, we use explicit H-bond potentials to investigate scalar coupling constants (h3)JNC' and characterize the conformational ensemble for increasingly accurate intermolecular potentials. By considering a range of proteins with different overall topology a general procedure to improve the hydrogen-bonding potential ("morphing potentials") based on experimental information is derived. The robustness of this approach is established through explicit simulations in full solvation and comparison with experimental results. The H-bond potentials used here lead to more directional H bonds than conventional electrostatic representations employed in molecular mechanics potentials. It is found that the optimized potentials lead to H-bond geometries in remarkable agreement with previous ab initio and knowledge-based approaches to H bonds in model systems and in proteins. This suggests that, by combining theory, computation, and experimental data, H-bonding potentials can be improved and are potentially useful to better study coupling, energy transfer, and allosteric communication in proteins.

Modelling organic crystal structures using distributed multipole and polarizability-based model intermolecular potentials

Crystal structure prediction for organic molecules requires both the fast assessment of thousands to millions of crystal structures and the greatest possible accuracy in their relative energies. We describe a crystal lattice simulation program, DMACRYS, emphasizing the features that make it suitable for use in crystal structure prediction for pharmaceutical molecules using accurate anisotropic atom-atom model intermolecular potentials based on the theory of intermolecular forces. DMACRYS can optimize the lattice energy of a crystal, calculate the second derivative properties, and reduce the symmetry of the spacegroup to move away from a transition state. The calculated terahertz frequency k = 0 rigid-body lattice modes and elastic tensor can be used to estimate free energies. The program uses a distributed multipole electrostatic model (Q, t = 00,...,44s) for the electrostatic fields, and can use anisotropic atom-atom repulsion models, damped isotropic dispersion up to R(-10), as well as a range of empirically fitted isotropic exp-6 atom-atom models with different definitions of atomic types. A new feature is that an accurate model for the induction energy contribution to the lattice energy has been implemented that uses atomic anisotropic dipole polarizability models (alpha, t = (10,10)...(11c,11s)) to evaluate the changes in the molecular charge density induced by the electrostatic field within the crystal. It is demonstrated, using the four polymorphs of the pharmaceutical carbamazepine C(15)H(12)N(2)O, that whilst reproducing crystal structures is relatively easy, calculating the polymorphic energy differences to the accuracy of a few kJ mol(-1) required for applications is very demanding of assumptions made in the modelling. Thus DMACRYS enables the comparison of both known and hypothetical crystal structures as an aid to the development of pharmaceuticals and other speciality organic materials, and provides a tool to develop the modelling of the intermolecular forces involved in molecular recognition processes.

An Accurate and Transferable Intermolecular Diatomic Hydrogen Potential for Condensed Phase Simulation.

An anisotropic many-body H2 potential energy function has been developed for use in heterogeneous systems. The intermolecular potential has been derived from first principles and expressed in a form that is readily transferred to exogenous systems, e.g. in modeling H2 sorption in solid-state materials. Explicit many-body polarization effects, known to be important in simulating hydrogen at high density, are incorporated. The analytic form of the potential energy function is suitable for methods of statistical physics, such as Monte Carlo or Molecular Dynamics simulation. The model has been validated on dense supercritical hydrogen and demonstrated to reproduce the experimental data with high accuracy.

An analytical potential energy function to model protonated peptide soft-landing experiments. The CH3NH3+/CH4 interactions

To model soft-landing of peptide ions on surfaces, it is important to have accurate intermolecular potentials between these ions and surfaces. As part of this goal, ab initio calculations at the MP2/aug-cc-pVTZ level of theory, with basis set superposition error (BSSE) corrections, were performed to determine both the long-range attractive and short-range repulsive potentials for CH(4) interacting with the -NH(3)(+) group of CH(3)NH(3)(+). Potential energy curves for four different orientations between CH(4) and CH(3)NH(3)(+) were determined from the calculations to obtain accurate descriptions of the interactions between the atoms of CH(4) and those of -NH(3)(+). A universal analytic function was not found that could accurately represent both the long-range and short-range potentials for collision energies as high as those obtained in surface-induced-dissociation (SID) experiments. Instead, long-range and short-range analytic potentials were developed separately, by simultaneously fitting the four ab initio potential energy curves with a sum of two-body interactions between the atoms of CH(4) and -NH(3)(+), and then connecting these long-range and short-range two-body potentials with switching functions. Following a previous work [J. Am. Chem. Soc., 2002, 124, 1524], these two-body potentials may be used to describe the interactions of the N and H atoms of the -NH(3)(+) group of a protonated peptide ion with the H and C atoms of alkane-type surfaces such as alkyl thiol self-assembled monolayers and H-terminated diamond. Accurate short-range and long-range potentials are imperative to model protonated peptide ion soft-landing experiments. The former controls the collision energy transfer, whereas the latter describes the binding of the ion to the surface. A comparison of the ab initio potential energy curves for CH(3)NH(3)(+)/CH(4) with those for NH(4)(+)/CH(4) shows that they give nearly identical two-body interactions between the atoms of -NH(3)(+) and those of CH(4), showing that the smaller NH(4)(+)/CH(4) system may be used to obtain the two-body potentials. A comparison of the four ab initio potential energy curves reported here for CH(3)NH(3)(+)/CH(4), with those given by the AMBER and CHARMM molecular mechanical potentials, show that these latter potentials "roughly" approximate the long-range attractions, but are grossly in error for the short-range repulsions. The work reported here illustrates that high-level ab initio calculations of intermolecular potentials between small model molecules may be used to develop accurate analytical intermolecular potentials between peptide ions and surfaces.