Magnitude and orientation dependence of intermolecular interaction of perfluoropropane dimer studied by high-level ab initio calculations: comparison with propane dimer

Intermolecular interaction energies of 12 orientations of C(3)F(8) dimers were calculated with electron correlation correction by the second-order M?ller-Plesset perturbation method. The antiparallel C(2h) dimer has the largest interaction energy (-1.45 kcal/mol). Electron correlation correction increases the attraction considerably. Electrostatic energy is not large. Dispersion is mainly responsible for the attraction. Orientation dependence of the interaction energy of the C(3)F(8) dimer is substantially smaller than that of the C(3)H(8) dimer. The calculated interaction energy of the C(3)F(8) dimer at the potential minimum is 78% of that of the C(3)H(8) dimer (-1.85 kcal/mol), whereas the interaction energies of the CF(4) and C(2)F(6) dimers are larger than those of the CH(4) and C(2)H(6) dimers. The intermolecular separation in the C(3)F(8) dimer at the potential minimum is substantially larger than that in the C(3)H(8) dimer. The larger intermolecular separation due to the steric repulsion between fluorine atoms is the cause of the smaller interaction energy of the C(3)F(8) dimer at the potential minimum. The calculated intermolecular interaction energy potentials of the C(3)F(8) dimers using an all atom model OPLS-AA (OPLS all atom model) force field and a united atom model force field were compared with the ab initio calculations. Although the two force fields well reproduces the experimental vapor and liquid properties of perfluoroalkenes, the comparison shows that the united atom model underestimates the potential depth and orientation dependence of the interaction energy. The potentials obtained by the OPLS-AA force field are close to those obtained by the ab initio calculations.     

Intermolecular electrostatic energies using density fitting

A method is presented to calculate the electron-electron and nuclear-electron intermolecular Coulomb interaction energy between two molecules by separately fitting the unperturbed molecular electron density of each monomer. This method is based on the variational Coulomb fitting method which relies on the expansion of the ab initio molecular electron density in site-centered auxiliary basis sets. By expanding the electron density of each monomer in this way the integral expressions for the intermolecular electrostatic calculations are simplified, lowering the operation count as well as the memory usage. Furthermore, this method allows the calculation of intermolecular Coulomb interactions with any level of theory from which a one-electron density matrix can be obtained. Our implementation is initially tested by calculating molecular properties with the density fitting method using three different auxiliary basis sets and comparing them to results obtained from ab initio calculations. These properties include dipoles for a series of molecules, as well as the molecular electrostatic potential and electric field for water. Subsequently, the intermolecular electrostatic energy is tested by calculating ten stationary points on the water dimer potential-energy surface. Results are presented for electron densities obtained at four different levels of theory using two different basis sets, fitted with three auxiliary basis sets. Additionally, a one-dimensional electrostatic energy surface scan is performed for four different systems (H2O dimer, Mg2+-H2O, Cu+-H2O, and n-methyl-formamide dimer). Our results show a very good agreement with ab initio calculations for all properties as well as interaction energies.     

Binding Energies of Proton-Bound Dimers of Imidazole and n-Acetylalanine Methyl Ester Obtained by Blackbody Infrared Radiative Dissociation

The dissociation kinetics of protonated n-acetyl-L-alanine methyl ester dimer (AcAlaME(d)), imidazole dimer, and their cross dimer were measured using blackbody infrared radiative dissociation (BIRD). Master equation modeling of these data was used to extract threshold dissociation energies (E(o)) for the dimers. Values of 1.18 +/- 0.06, 1.11 +/- 0.04, and 1.12 +/- 0.08 eV were obtained for AcAlaME(d), imidazole dimer, and the cross dimer, respectively. Assuming that the reverse activation barrier for dissociation of the ion-molecule complex is negligible, the value of E(o) can be compared to the dissociation enthalpy (DeltaH(d) degrees ) from HPMS data. The E(o) values obtained for the imidazole dimer and the cross dimer are in agreement with HPMS values; the value for AcAlaME(d) is somewhat lower. Radiative rate constants used in the master equation modeling were determined using transition dipole moments calculated at the semiempirical (AM1) level for all dimers and compared to ab initio (RHF/3-21G*) calculations where possible. To reproduce the experimentally measured dissociation rates using master equation modeling, it was necessary to multiply semiempirical transition dipole moments by a factor between 2 and 3. Values for transition dipole moments from the ab initio calculations could be used for two of the dimers but appear to be too low for AcAlaME(d). These results demonstrate that BIRD, in combination with master equation modeling, can be used to determine threshold dissociation energies for intermediate size ions that are in neither the truncated Boltzmann nor the rapid energy exchange limit.     

An empirical potential for the O-H·O Hydrogen bond: Part I. Comparison with ab initio molecular orbital results

An empirical potential energy function has been devised for the O-H·O hydrogen bond, for use with the MMI force field. The energy of the hydrogen bond is described as the sum of van der Waals, electrostatic and Morse components. The function has been used to calculate the potential energy hypersurface of the water dimer, and the results are compared with published ab initio molecular orbital studies. Satisfactory agreement is obtained except for orientations involving very short H·H contacts. The geometry and hydrogen bond energy of the equilibrium linear form of (H₂O)₂ are calculated to be r(O·O) = 2.84 Å, θ = 36°, ΔE = ?5.35 kcal mol^?1, which are close to the values obtained by experiment, and from molecular orbital calculations. The relative importance of the electrostatic component of the empirical hydrogen bond energy is consistent with molecular orbital energy decomposition studies. The empirical function has also been used to calculate the energy of the water trimer in orientations which serve as models for the crystallographic bifurcated hydrogen bond. The results indicate that, in these orientations, the trimer is typically 0–3 kcal mol^?1 more stable than the dimer, a result which is consistent with ab initio calculations.     

Ab initio MO study of dipole—dipole interactions in acetonitrile dimers

MO STO-3G ab initio calculations have been carried out for the antiparallel dipole and the head-to-tail dipole model of acetonitrile dimers. The optimized interaction enthalpy is about half of the lowest experimental estimate. The calculated interaction distance for the antiparallel dipole model is very close to the sum of intermolecular radii of N and C; the distance for the head-to-tail model is about 20% higher than the sum of N and H intermolecular radii. The discussion of the interaction in terms of the supermolecule MO's suggests for both models a bonding of mainly electrostatic character. The shortcomings of the STO-3G basis set in dealing with this problem are compared with those reported in the literature. The influence of the basis set on the calculated electron distribution in acetonitrile monomer was examined as a preliminary part of the present study, and is also reported in the paper.     

Role of dipolar interaction in the mesoscopic domains of phospholipid monolayers: dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylethanolamine

The role of dipolar interactions in determining the lipid domain shapes at the air-water interface with a change in the chemical structure of the head groups of lipids is theoretically studied. The phospholipids considered are dipalmitoylphosphatidylcholine (D,L-DPPC) and dipalmitoylphosphatidylethanolamine (DPPE). Despite closely similar chemical structures, the domains of the two lipids are strikingly different. The DPPC domains exhibit elongated arms, while the DPPE domains are nearly round-shaped. To compare the dipolar repulsions in the domains of the two phospholipids, different energy-minimized conformers of DPPC and DPPE are studied using the semiempirical quantum chemical method (PM3). It is found that the dipole moment of DPPC is significantly larger than that of DPPE. The in-plane and out-of-plane components of the dipole moments are calculated using grazing incidence X-ray diffraction data at different surface pressure values, as used in the experiment. The result indicates that the magnitude of the dipolar interaction is significantly larger in DPPC than that in DPPE over the surface pressure range considered. The enhanced dipolar repulsion corroborates well with the difference in the domain shapes in the two phospholipid monolayers. The larger dipolar repulsion in DPPC leads to development of elongated domain arms, while relatively less dipolar repulsion allows a closed shape of the condensed-phase DPPE domains.     

Gradients of the polarization energy in the effective fragment potential method

The effective fragment potential (EFP) method is an ab initio based polarizable classical method in which the intermolecular interaction parameters are obtained from preparative ab initio calculations on isolated molecules. The polarization energy in the EFP method is modeled with asymmetric anisotropic dipole polarizability tensors located at the centroids of localized bond and lone pair orbitals of the molecules. Analytic expressions for the translational and rotational gradients (forces and torques) of the EFP polarization energy have been derived and implemented. Periodic boundary conditions (the minimum image convention) and switching functions have also been implemented for the polarization energy, as well as for other EFP interaction terms. With these improvements, molecular dynamics simulations can be performed with the EFP method for various chemical systems.     

Analysis of the intermolecular interactions between CH3OCH3, CF3OCH3, CF3OCF3, and CH2F2, CHF3

The intermolecular interaction energy curves of CH(3)OCH(3)-CH(2)F(2), CF(3)OCH(3)-CH(2)F(2), CF(3)OCF(3)-CH(2)F(2), CH(3)OCH(3)-CHF(3), CF(3)OCH(3)-CHF(3), and CF(3)OCF(3)-CHF(3) complexes were calculated by the MP2 level ab initio molecular orbital method using the 6-311G** basis set augmented with diffuse polarization functions. We investigate the fluorine substitution effects of both methane and dimethyl ether on intermolecular interactions. In addition, orientation dependence of intermolecular interaction energies is also studied with utilizing eight types of orientations. Our analyses demonstrate that partial fluorinations of methane make electrostatic interaction dominant, and consequently enhance attractive interaction at several specific orientations. On the contrary, fluorine substitutions of dimethyl ether substantially decrease the electrostatic interaction between ether and CH(2)F(2) or CHF(3); thus, there is no such characteristic interaction between the C-H of fluorinated methane and ether oxygen of CF(3)OCF(3) as conventional hydrogen bonding, due to reduced polarity of fluorinated ether. The combination of different pairs of the electrostatic interaction is therefore responsible for the intermolecular interaction differences among the complexes investigated herein and also their orientations.     

Super-molecule calculations of intermolecular forces between long-chain molecules

Intermolecular interactions between paraffin chains (C₃C₉) in four different mutual orientations have been studied by PCILO and INDO methods. The PCILO method is found to be superior. It is observed that polarity optimization is not required for these interaction studies although it most certainly would be for molecules with more polar bonds. The calculated interaction energies per carbon atom extrapolated to long-chain length are (0.09–0.22) kcal mol^?1 depending upon the orientation and geometry. The effect of a polar head group on the intermolecular interactions of long-chain molecules is also studied using the propionic acid dimer as model. Lone-pair interactions cause one of the dimer orientations to be totally repulsive.     

Interaction potentials and free energies for ferroelectric liquid crystals in the model of polar non-uniaxial molecules

Abstract

The possible forms of the model interaction potentials are proposed for rigid polar non-uniaxial molecules with the molecular dipole moment making an arbitrary angle with the molecule's long axis. The molecule orientation is described by the direction of two molecular axes: its dipole moment and the long axis. The intermolecular potentials dependent on both molecular axes orientations are considered. The simple model interaction potentials between chiral molecules are used. It is shown that the form of the interaction potential determines the set of the relevant order parameters of the system. The free energy is calculated in the Landau expansion form in terms of the relevant order parameters.     

Ab initio quantum chemical studies of the electronic properties of the hydrogen bonded N2HF,N2HCl, (HCN)2 and NH3HCN complexes

The results of ab initio self-consistent field (SCF) and configuration interaction (CI) calculations on the hydrogen bonded N₂HF, N₂HCl, (HCN)₂ and NH₃HCN complexes, using basis sets that range from double-zeta plus polarization to triple-zeta plus double polarization, are reported. The primary objective of this work has been to calculate the changes in the dipole moments and the electric field gradients (EFGs) at the quadrupolar ¹⁴N, ²H and ³⁵Cl nuclei that are induced by H-bonding. Since the interpretation of the H-bond induced shifts requires a knowledge of the molecular dynamics in weakly H-bonded molecular complexes such as those studied in the present work, we have taken into account the effects of vibrational averaging on both the EFGs and dipole moments utilizing harmonic intermolecular force fields that were generated using ab initio SCF methods. The results of these calculations are compared with the corresponding experimental quantities that are obtained from the microwave spectra of these complexes.     

Computer simulation of solid and liquid benzene with an atomistic interaction potential derived from ab initio calculations

Molecular dynamics atomistic simulations of solid and liquid benzene have been performed, employing a model intermolecular potential derived from quantum mechanical calculations. The ab initio database includes approximately 200 geometries of the benzene dimer with interaction energies computed at the MP2 level of theory. The accuracy of the modeled force field results is satisfactory. The thermodynamic and structural properties, calculated in the condensed phases, are compared with experimental data and previous simulation results. Single particle and collective dynamical properties are also investigated through the calculation of translational and rotational diffusion coefficients, reorientational dynamics, and viscosities. The agreement of these data with experimental measurements confirms the reliability of the proposed force field.     

First principles potential for the acetylene dimer and refinement by fitting to experiments

We report the definition and refinement of a new first principles potential for the acetylene dimer. The ab initio calculations were performed with the DFT-SAPT combination of symmetry-adapted intermolecular perturbation method and density functional theory, and fitted to a model site-site functional form. Comparison of the calculated microwave spectrum with experimental data revealed that the barriers to isomerization were too low. This potential was refined by fitting the model parameters in order to reproduce the observed transitions, an excellent agreement within ~1 MHz being achieved.     

The intermolecular vibrations of the bifurcated water dimer: An Ab initio study

The intermolecular modes of the bifurcated water dimer are determined at the HF level using an extended basis set. In these computations, the donor libration frequency is found to be real and the bifurcated structure does not collapse toward the linear dimer. This result is contrary to all previous ab initio computations, which have predicted a Hessian with one negative eigenvalue. A good representation of other intermolecular modes, such as the libration of the acceptor, also requires an extended basis set. An interesting infrared active transition is predicted around 444 cm^?1. This transition, which corresponds to the donor wag, is found in the low-temperature spectrum of water in a N₂ matrix.     

Faint features of the rotationalS 0(0) andS 0(1) transitions of H2

The complete collision induced absorption spectrum of H₂ - H₂ pairs at a temperature of 77 K, including the faint features due to bound and quasi-bound (H₂)₂ dimers, has been calculated from first principles and compared in detail with recently published laboratory measurements. An empirical anisotropic intermolecular potential energy surface (“F84”), and an ab initio induced dipole moment function due to Meyer were used in the calculations. The close coupled formalism was applied to determine the multiple-component scattering and bound-state wave functions. Comparisons between experiment and theory show very good general agreement: all the faint hydrogen dimer features that are observed are reproduced theoretically. The observed pressure broadening of sharper dimer features could also be partially accounted for in the calculations. The remaining disagreements between theory and experiment in the intensities and positions of the features are very useful for deriving the small modifications required to further improve the F 84 surface, especially in the region of the attractive potential well.     

Intermolecular potential energy surface of the N2-CO dimer: ab initio investigation and analytical representation

In this work, for the first time, an analytical four-dimensional representation for the intermolecular potential of the N(2)-CO dimer is constructed from ab initio calculations. The most stable structure of dimer is found to be a distorted T-shape conformation with CO forming the top and N(2) the leg of T. Important structures of the dimer are characterized, and surprisingly, it is found that in contrast with general assumptions, the potential energy surface of the N(2)-CO dimer has a single symmetry unique minimum. The energy profile of a minimum energy path that connects two T-shaped saddle points to the minimum structure is derived. Important structures are characterized along this path to represent the concerted internal rotation of monomers within the complex. The second virial coefficient is calculated from the fitted PES, and reasonable agreement is found with recent experimental results.     

Chiral self-recognition: direct spectroscopic detection of the homochiral and heterochiral dimers of propylene oxide in the gas phase

In this report, we describe rotational spectroscopic and high-level ab initio studies of the 1:1 chiral molecular adduct of propylene oxide dimer. The complexes are bound by weak secondary hydrogen bonds, that is, the O(epoxy)...H-C noncovalent interactions. Six homochiral and six heterochiral conformers were predicted to be the most stable configurations where each monomer acts as a proton acceptor and a donor simultaneously, forming two six- or five-membered intermolecular hydrogen-bonded rings. Rotational spectra of six, that is, three homochiral and heterochiral conformer pairs, out of the eight conformers that were predicted to have sufficiently large permanent electric dipole moments were measured and analyzed. The relative conformational stability order and the signs of the chiral recognition energies of the six conformers were determined experimentally and were compared to the ab initio computational results. The experimental observations and the ab initio calculations suggest that the concerted effort of these weak secondary hydrogen bonds can successfully lock the subunits in a particular orientation and that the overall binding strength is comparable to a classic hydrogen bond.     

Theoretical studies on hydroquinone-benzene clusters

High-level ab initio calculations were carried out to evaluate the interaction between the hydroquinone and benzene molecules. The intermolecular interaction energy was calculated using the M?ller-Plesset second-order perturbation theory at the complete basis set limit and also at the coupled cluster theory with single, double, and perturbatively triple excitations. The calculated binding energy is larger than the benzene dimer interaction energy. The T-shaped cluster (T-a) and the parallel conformation (P-a) are calculated to be nearly isoenergetic. Owing to the large energy gain in the attraction by electron correlation, the dispersion interaction is important for the attraction.