Density-functional theory-symmetry-adapted intermolecular perturbation theory with density fitting: A new efficient method to study intermolecular interaction energies

A First Principles Development of a General Anisotropic Potential for Polycyclic Aromatic Hydrocarbons

Standard empirical atom-atom potentials are shown to be unable to describe the binding of polycyclic aromatic hydrocarbon (PAH) molecules in the variety of configurations seen in clusters. The main reason for this inadequacy is the lack of anisotropy in these potentials. We have constructed an anisotropic atom-atom intermolecular potential for the benzene molecule from first principles using a symmetry-adapted perturbation theory based on density functional theory (SAPT(DFT)), interaction energy calculations and the Williams-Stone-Misquitta method for obtaining molecular properties in distributed form. Using this potential as a starting point, we have constructed a transferable anisotropic potential to model intermolecular interactions between PAHs. This new potential has been shown to accurately model interaction energies for a variety of dimer configurations for four different PAH molecules, including certain configurations which are poorly modeled with current isotropic potentials. It is intended that this potential will form the basis for further work on the aggregation of PAHs.

Development of additive isotropic site potential for exchange-repulsion energy, based on intermolecular perturbation theory

We have developed an additive spherical site potential for exchange-repulsion energy by applying the local density approximation in Hilbert space, the local-site approximation, and the s-type auxiliary basis set to the equation derived from intermolecular perturbation theory. The method efficiently addresses the decomposition of molecular interactions derived from quantum chemistry into additive spherical site potentials, required as force field input in a statistical-mechanical, reference interaction site model (RISM and 3D-RISM), molecular theory of solvation. The present method reproduces the exchange-repulsion energy between simple molecules obtained from quantum chemical calculations.

Nature of bonding in nine planar hydrogen-bonded adenine...thymine base pairs

In this work, we investigate the mode of binding of all nine hydrogen-bonded structures of the adenine...thymine base pair. The planar H-bonded structures were optimized at the MP2/cc-pVTZ level, and the respective interaction energies, corrected for the basis set superposition error, were determined with the aug-cc-pVDZ basis set. The energy components were obtained from the DFT-SAPT procedure using the aug-cc-pVDZ basis set. The charge-transfer character of the single structures was estimated using NBO characteristics. It was established that dipole-dipole interaction itself cannot explain the preferred structure of the pair. Of the various energy components, first-order electrostatic energy plays the most important role. Second-order energy (the sum of induction and dispersion energies) amounts to about 56% of the electrostatic energy. The delta(HF) term covering among others the charge-transfer energy is rather large. The importance of delta(HF) is reflected by the NBO characteristics and especially by the NBO charge-transfer energy. The sum of the second-order energy and the delta(HF) term is only slightly smaller than the electrostatic energy (75-77%), which reflects the importance of the nonelectrostatic terms even in the case of strong H-bonded complexes. The WC structure, which exists in DNA, represents the seventh local minimum, while the three most stable structures utilize the N9-H proton donor group of the five-membered ring.

On the Nature of Bonding in Lone Pair···π-Electron Complexes: CCSD(T)/Complete Basis Set Limit Calculations

The nature of the stabilization in lone pair···π-electron complexes was investigated using the highly accurate CCSD(T) method based on the complete basis set limit, as well as the DFT-SAPT perturabative method. Specifically, we studied various structures of benzene···water, benzene···dimethylether, and 1,2,4,5-tetracyanobenzene···water complexes. The lone pair···π-electron interactions between an unsubstituted aromatic ring and a water molecule are repulsive in the whole range of vertical distances. Partial stabilization results by rotating the water molecule by 90° (with the water and aromatic ring being localized in parallel planes) or by decreasing the negative charge at oxygen and simultaneously increasing the polarizability of the system, which provides stabilization even for genuine lone pair···π-electron interactions. In these cases, a substantial part of the stabilization stems from dispersion energy. Substituting an aromatic ring by electron-withdrawing cyano groups represents the most powerful way to achieve a substantial stabilization of genuine lone pair···π-electron interactions. This stabilization is comparable to quite strong H-bonding, originating in electrostatic and, to a slightly lesser degree, dispersion energies.

Symmetry-adapted perturbation theory utilizing density functional description of monomers for high-spin open-shell complexes

We present an implementation of symmetry-adapted perturbation theory (SAPT) to interactions of high-spin open-shell monomers forming high-spin dimers. The monomer spin-orbitals used in the expressions for the electrostatic and exchange contributions to the interaction energy are obtained from density functional theory using a spin-restricted formulation of the open-shell Kohn-Sham (ROKS) method. The dispersion and induction energies are expressed through the density-density response functions predicted by the time-dependent ROKS theory. The method was applied to several systems: NH...He, CN...Ne, H2O...HO2, and NH...NH. It provides accuracy comparable to that of the best previously available methods such as the open-shell coupled-cluster method with single, double, and noniterative triple excitations, RCCSD(T), with a significantly reduced computational cost.

Modeling the noncovalent interactions at the metabolite binding site in purine riboswitches

We present gas phase quantum chemical studies on the metabolite binding interactions in two important purine riboswitches, the adenine and guanine riboswitches, at the B3LYP/6-31G(d,p) level of theory. In order to gain insights into the strucutral basis of their discriminative abilities of regulating gene expression, the structural properties and binding energies for the gas phase optimized geometries of the metabolite bound binding pocket are analyzed and compared with their respective crystal geometries. Kitaura-Morokuma analysis has been carried out to calculate and decompose the interaction energy into various components. NBO and AIM analysis has been carried out to understand the strength and nature of binding of the individual aptamer bases with their respective purine metabolites. The Y74 base, U in case of adenine riboswitch and C in case of guanine riboswitch constitutes the only differentiating element between the two binding pockets. As expected, with W:W cis G:C74 interaction contributing more than 50% of the total binding energy, the interaction energy for metabolite binding as calculated for guanine (-46.43 Kcal/mol) is nearly double compared to the corresponding value for that of adenine (-24.73 Kcal/mol) in the crystal context. Variations in the optimized geometries for different models and comparison of relative contribution to metabolite binding involving four conserved bases reveal the possible role of U47:U51 W:H trans pair in the conformational transition of the riboswitch from the metabolite free to metabolite bound state. Our results are also indicative of significant contributions from stacking and magnesium ion interactions toward cooperativity effects in metabolite recognition.

Predicting structure of molecular crystals from first principles

A recently developed method, symmetry-adapted perturbation theory based on the density-functional description of monomers [SAPT(DFT)], is shown to be sufficiently accurate and numerically efficient to facilitate predictions of the structure of molecular crystals from first principles. In one application, a SAPT(DFT) potential was used to generate and order polymorphs of the cyclotrimethylene trinitramine crystal, resulting in the lowest-energy structure in excellent agreement with the experimental crystal. In a different application, a SAPT(DFT)-based calculation reproduced the lattice energy of the benzene crystal to within a few percent.

Another role of proline: stabilization interactions in proteins and protein complexes concerning proline and tryptophane

Proline-tryptophan complexes derived from experimental structures are investigated by quantum chemical procedures known to properly describe the London dispersion energy. We study two geometrical arrangements: the "L-shaped", stabilized by an H-bond, and the "stacked-like", where the two residues are in parallel orientation without any H-bond. Interestingly, the interaction energies in both cases are comparable and very large ( approximately 7 kcal mol(-1)). The strength of stabilization in the stacked arrangement is rather surprising considering the fact that only one partner has an aromatic character. The interaction energy decomposition using the SAPT method further demonstrates the very important role of dispersion energy in such arrangement. To elucidate the structural features responsible for this unexpectedly large stabilization we examined the role of the nitrogen heteroatom and the importance of the cyclicity of the proline residue. We show that the electrostatic interaction due to the presence of the dipole, caused by the nitrogen heteroatom, contributes largely to the strength of the interaction. Nevertheless, the cyclic arrangement of proline, which allows for the largest amount of dispersive contact with the aromatic partner, also has a notable-effect. Geometry optimizations carried out for the "stacked-like" complexes show that the arrangements derived from protein structure are close to their gas phase optimum geometry, suggesting that the environment has only a minor effect on the geometry of the interaction. We conclude that the strength of proline non-covalent interactions, combined with this residue's rigidity, might be the explanation for its prominent role in protein stabilization and recognition processes.

Improved supermolecular second order Møller-Plesset intermolecular interaction energies using time-dependent density functional response theory

The supermolecular second order Moller-Plesset (MP2) intermolecular interaction energy is corrected by employing time-dependent density functional (TDDFT) response theory. This is done by replacing the uncoupled second order dispersion contribution contained in the supermolecular MP2 energy with the coupled dispersion energy obtained from the TDDFT approach. Preliminary results for the rare gas dimers He2, Ne2, and Ar2 and a few structures of the (HF)2 and (H2O)2 dimers show that the conventional MP2 interaction energies are considerably improved by this procedure if compared to coupled cluster singles doubles with perturbative triples [CCSD(T)] interaction energies. However, the quality of the interaction energies obtained in this way strongly depends on the exchange-correlation potential employed in the monomer calculations: It is shown that an exact exchange-only potential surprisingly often performs better than an asymptotically corrected hybrid exchange-correlation potential. Therefore the method proposed in this work is similar to the method by Cybulski and Lytle [J. Chem. Phys., 127, 141102 (2007)] which corrects the supermolecular MP2 energies with a scaled dispersion energy from time-dependent Hartree-Fock. The results in this work are also compared to the combination of density functional theory and intermolecular perturbation theory.

Theoretical study on the complexes of benzene with isoelectronic nitrogen-containing heterocycles

The pi-pi interactions between benzene and the aromatic nitrogen heterocycles pyridine, pyrimidine, 1,3,5-triazine, 1,2,3-triazine, 1,2,4,5-tetrazine, and 1,2,3,4,5-pentazine are systematically investigated. The T-shaped structures of all complexes studied exhibit a contraction of the C--H bond accompanied by a rather large blue shift (40-52 cm(-1)) of its stretching frequency, and they are almost isoenergetic with the corresponding displaced-parallel structures at reliable levels of theory. With increasing number of nitrogen atoms in the heterocycle, the geometries, frequencies, energies, percentage of s character at C, and the electron density in the C--H sigma antibonding orbital of the complexes all increase or decrease systematically. Decomposition analysis of the total binding energy showed that for all the complexes, the dispersion energy is the dominant attractive contribution, and a rather large attraction originating from electrostatic contribution is compensated by its exchange counterpart.