Estimates of the ab initio limit for sulfur-pi interactions: the H2S-benzene dimer

The interaction between aromatic rings and sulfur atoms in the side chains of amino acids is a factor in the formation and stabilization of alpha-helices in proteins. We studied the H(2)S-benzene dimer as the simplest possible prototype of sulfur-pi interactions. High-quality potential energy curves were obtained using coupled-cluster theory with single, double, and perturbative triple substitutions (CCSD(T)) and a large, augmented quadruple-zeta basis set (aug-cc-pVQZ). The equilibrium intermonomer distance for the hydrogens-down C(2)(v) configuration is 3.8 A with an interaction energy of -2.74 kcal mol(-1). Extrapolating the binding energy to the complete basis set limit gives -2.81 kcal mol(-1). This binding energy is comparable to that of H(2)O-benzene or of the benzene dimer, and the equilibrium distance is in close agreement with experiment. Other orientations of the dimer were also considered at less complete levels of theory. A considerable reduction in binding for the sulfur-down configuration, together with an energy decomposition analysis, indicates that the attraction in H(2)S-benzene is best thought of as arising from a favorable electrostatic interaction between partially positive hydrogens in H(2)S with the negatively charged pi-cloud of the benzene.     

Accurate ab initio binding energies of the benzene dimer

Accurate binding energies of the benzene dimer at the T and parallel displaced (PD) configurations were determined using the single- and double-coupled cluster method with perturbative triple correction (CCSD(T)) with correlation-consistent basis sets and an effective basis set extrapolation scheme recently devised. The difference between the estimated CCSD(T) basis set limit electronic binding energies for the T and PD shapes appears to amount to more than 0.3 kcal/mol, indicating the PD shape is a more stable configuration than the T shape for this dimer in the gas phase. This conclusion is further strengthened when a vibrational zero-point correction to the electronic binding energies of this dimer is made, which increases the difference between the two configurations to 0.4-0.5 kcal/mol. The binding energies of 2.4 and 2.8 kcal/mol for the T and PD configurations are in good accord with the previous experimental result from ionization potential measurement.     

Beyond the benzene dimer: an investigation of the additivity of pi-pi interactions

The benzene dimer is the simplest prototype of pi-pi interactions and has been used to understand the fundamental physics of these interactions as they are observed in more complex systems. In biological systems, however, aromatic rings are rarely found in isolated pairs; thus, it is important to understand whether aromatic pairs remain a good model of pi-pi interactions in clusters. In this study, ab initio methods are used to compute the binding energies of several benzene trimers and tetramers, most of them in 1D stacked configurations. The two-body terms change only slightly relative to the dimer, and except for the cyclic trimer, the three- and four-body terms are negligible. This indicates that aromatic clusters do not feature any large nonadditive effects in their binding energies, and polarization effects in benzene clusters do not greatly change the binding that would be anticipated from unperturbed benzene-benzene interactions, at least for the 1D stacked systems considered. Three-body effects are larger for the cyclic trimer, but for all systems considered, the computed binding energies are within 10% of what would be estimated from benzene dimer energies at the same geometries.     

Modeling pi-pi interactions with the effective fragment potential method: the benzene dimer and substituents

This study compares the results of the general effective fragment potential (EFP2) method to the results of a previous combined coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] and symmetry-adapted perturbation theory (SAPT) study [Sinnokrot and Sherrill, J. Am. Chem. Soc., 2004, 126, 7690] on substituent effects in pi-pi interactions. EFP2 is found to accurately model the binding energies of the benzene-benzene, benzene-phenol, benzene-toluene, benzene-fluorobenzene, and benzene-benzonitrile dimers, as compared with high-level methods [Sinnokrot and Sherrill, J. Am. Chem. Soc., 2004, 126, 7690], but at a fraction of the computational cost of CCSD(T). In addition, an EFP-based Monte Carlo/simulated annealing study was undertaken to examine the potential energy surface of the substituted dimers.     

An ab initio study of intermolecular interactions of nitromethane dimer and nitromethane trimer

Different geometries of nitromethane dimer and nitromethane trimer have been fully optimized employing the density functional theory B3LYP method and the 6-31++G** basis set. Three-body interaction energy has been obtained with the ab initio supermolecular approach at the levels of MP2/6-31++G**//B3LYP/6-31++G** and MP2/aug-cc-pVDZ//B3LYP/6-31++G**. The internal rotation of methyl group induced by intermolecular interaction has been observed theoretically. For the optimized structures of nitromethane dimer, the strength of C--H...O--N H-bond ranges from -9.0 to -12.4 kJ mol(-1) at the MP2/aug-cc-pVDZ//B3LYP/6-31++G** level, and the B3LYP method underestimates the interaction strength compared with the MP2 method, while MP2/6-31++G**//B3LYP/6-31++G** calculated DeltaE(C) is within 2.5 kJ mol(-1) of the corresponding value at the MP4(SDTQ)/6-31G**//B3LYP/6-31++G** level. The analytic atom-atom intermolecular potential has been successfully regressed by using the MP2/6-31++G**//B3LYP/6-31++G** calculated interaction energies of nitromethane dimer. For the optimized structures of nitromethane trimer the three-body interaction energies occupy small percentage of corresponding total binding energies, but become important for the compressed nitromethane explosive. In addition, it has been discovered that the three-body interaction energy in the cyclic nitromethane trimer is more and more negative as intermolecular distances decrease from 2.2 to 1.7 A.     

Interaction energy anisotropy of the pyrrole dimer: ab initio theoretical study

The van der Waals pyrrole dimer is studied using supermolecular and perturbation ab initio treatment with inclusion of correlation energy. The influence of selected geometry variations on the interaction energy components is investigated. Our calculations verified the minimum on the potential energy surface deduced from microwave spectra. Its stability is possibly related not to the extremal values of the selected interaction energy contributions but its physical origin is connected with the delicate equilibrium between the repulsive and attractive forces. Any structure variation connected with the extremal attraction energy is more than compensated for by the repulsion energy. Received: 11 June 1998 / Accepted: 6 October 1998 / Published online: 1 February 1999     

High-accuracy quantum mechanical studies of pi-pi interactions in benzene dimers

Although supramolecular chemistry and noncovalent interactions are playing an increasingly important role in modern chemical research, a detailed understanding of prototype noncovalent interactions remains lacking. In particular, pi-pi interactions, which are ubiquitous in biological systems, are not fully understood in terms of their strength, geometrical dependence, substituent effects, or fundamental physical nature. However, state-of-the-art quantum chemical methods are beginning to provide answers to these questions. Coupled-cluster theory through perturbative triple excitations in conjunction with large basis sets and extrapolations to the complete basis set limit have provided definitive results for the binding energy of several configurations of the benzene dimer, and benchmark-quality ab initio potential curves are being used to calibrate new density functional and force-field models for pi-pi interactions. Studies of substituted benzene dimers indicate flaws in the conventional wisdom about substituent effects in pi-pi interactions. Three-body and four-body interactions in benzene clusters have also been examined.     

Towards highly accurate ab initio thermochemistry of larger systems: benzene

The high accuracy extrapolated ab initio thermochemistry (HEAT) protocol is applied to compute the total atomization energy (TAE) and the heat of formation of benzene. Large-scale coupled-cluster calculations with more than 1500 basis functions and 42 correlated electrons as well as zero-point energies based on full cubic and (semi)diagonal quartic force fields obtained with the coupled-cluster singles and doubles with perturbative treatment of the triples method and atomic natural orbital (ANO) triple- and quadruple-zeta basis sets are presented. The performance of modifications to the HEAT scheme and the scaling properties of its contributions with respect to the system size are investigated. A purely quantum-chemical TAE and associated conservative error bar of 5463.0 ± 3.1 kJ mol(-1) are obtained, while the corresponding 95% confidence interval, based on a statistical analysis of HEAT results for other and related molecules, is ± 1.8 kJ mol(-1). The heat of formation of benzene is determined to be 101.5 ± 2.0 kJ mol(-1) and 83.9 ± 2.1 kJ mol(-1) at 0 K and 298.15 K, respectively.     

An ab initio study of tunneling splittings in the water dimer

Tunneling splittings in the water dimer have been determined by the semiclassical WKB method, based on pathways characterized at the computational level of second-order M?ller-Plesset (MP2) theory with basis sets of aug-cc-pVTZ quality. This calculation takes into account all three acceptor tunneling, donor-acceptor interchange, and bifurcation tunneling rearrangements of the water dimer. The tunneling splittings were evaluated as 7.73 cm(-1) (large splitting) and 0.42 cm(-1) (small splitting), which are in good agreement with the corresponding experimental values of 11.18 cm(-1) and 0.70 cm(-1), respectively.     

An ab initio multireference perturbation theory study on the manganese dimer

The potential energy curves of the ground state and of some excited states of the manganese dimer have been calculated over a wide range of internuclear distances using the second order n-electron valence state perturbation theory applied to a complete active space self-consistent field reference wave function. The ground state of Mn(2), for which also the third order NEVPT has been used, is calculated to be a singlet belonging to the Sigma(g) (+) symmetry, characterized by a large equilibrium internuclear distance R(e) of 3.7-3.8 A, by a low dissociation energy D(e) of 0.07-0.08 eV, and by a small harmonic frequency omega(e) of 43 cm(-1). The experimental evidence that Mn(2) is a van der Waals molecule is thus confirmed. Among the excited states, (11)Pi(u), which is usually indicated as the ground state by density functional theory studies, appears as a low-lying state with R(e)=2.50 A, D(e)=1.35 eV, and omega(e)=246 cm(-1).     

Dynamical dimer method for the determination of transition states with ab initio molecular dynamics

A dynamical formulation of the dimer method for the determination of transition states is presented. The method is suited for ab initio molecular dynamics using the fictitious Lagrangian formulation. The method has been applied to the conrotatory ring opening of chlorocyclobutadiene, an example, where the application of the drag method is problematic.     

An ab initio intermolecular potential energy surface for the F(2) dimer

Two analytical representations for the potential energy surface of the F(2) dimer were constructed on the basis of ab initio calculations up to the fourth-order of M?ller-Plesset (MP) perturbation theory. The best estimate of the complete basis set limit of interaction energy was derived for analysis of basis set incompleteness errors. At the MP4/aug-cc-pVTZ level of theory, the most stable structure of the dimer was obtained at R = 6.82 au, theta(a) = 12.9 degrees , theta(b) = 76.0 degrees , and phi = 180 degrees , with a well depth of 716 microE(h). Two other minima were found for canted and X-shaped configurations with potential energies around -596 and -629 microE(h), respectively. Hexadecapole moments of monomers play an important role in the anisotropy of interaction energy that is highly R-dependent at intermediate intermolecular distances. The quality of potentials was tested by computing values of the second virial coefficient. The fitted MP4 potential has a more reasonable agreement with experimental values.     

An ab initio calculation on proton transfer in the benzoic acid dimer

We have made an ab initio calculation of the barriers for proton transfer in the hydrogen-bonded dimers of benzoic acid and acetic acid. Geometrical optimization values which are closer to the experiment one.     

F2 dimer: Improved intermolecular potential energy surface using ab initio calculations

A computational study on the intermolecular potential energy of 44 different orientations of F₂ dimers is presented. Basis set superposition error (BSSE) corrected potential energy surface is calculated using the supermolecular approach at CCSD(T) and QCISD(T) levels of theory. The interaction energies obtained using the aug‐cc‐pVDZ and aug‐cc‐pVTZ basis sets are extrapolated to the complete basis set limit using the latest extrapolation scheme. The basis set effect is checked and it is found that the extrapolated intermolecular energies provide the best compromise between the accuracy and computational cost. Among 1320 energy points of F₂–F₂ system covering more relative orientations, the most stable structure of the dimers was obtained with a well depth of ?146.62 cm^?1 that related to cross configuration, and the most unstable structure is related to linear orientation with a well depth of ?52.63 cm^?1. The calculated second virial coefficients are in good agreement with experimental data. The latest extrapolation scheme of the complete basis set limit at the CCSD(T) level of theory is used to determine the intermolecular potential energy surface of the F₂ dimer. Comparing the results obtained by the latest scheme with those by older schemes show that the new approach provides the best compromise between accuracy and computational cost.     

The ab initio limit quartic force field of BH3

The complete quartic force field of BH(3) has been converged to the ab initio limit by extrapolation of core-valence correlation-consistent basis set series (cc-pCVXZ, X = T, Q, 5) of all-electron CCSD(T) (coupled-cluster singles and doubles with perturbative triples) energy points. Additional computations including full coupled-cluster treatments through quadruple excitations (CCSDTQ), scalar relativistic effects, and diagonal Born-Oppenheimer corrections (DBOC) were concurrently executed. Within second-order vibrational perturbation theory (VPT2) our quartic force field yields the fundamental frequencies nu(1) = 2502.3 cm(-1), nu(2) = 1147.2 cm(-1), nu(3) = 2602.1 cm(-1), and nu(4) = 1196.5 cm(-1), in excellent agreement with observed gas-phase fundamentals, displaying a mean absolute error of only 0.3 cm(-1). Our converged prediction for the equilibrium bond length of BH(3) is r(e) = 1.1867 A.     

Modeling intercalation through the sandwich‐type interactions between benzene and 14 polyaromatic molecules: DFT and ab initio results

We use second order Moller Plesset perturbation theory and several density functional theory methods to calculate the counterpoise corrected electronic interaction energies between benzene and a series of polyaromatic molecules. These systems serve as a simple model for DNA intercalation. We show that addition of nitrogen atoms to the polyaromatic molecules always increases sandwich‐type interactions, and that, of the density functional theory methods studied, only SVWN can mimic the interaction energies and optimal separations obtained with perturbation theory. SVWN reproduces the optimal molecular distances obtained with perturbation theory very well, and often comes within less than 10% of the interaction energy. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Guanine and adenine-amino acids interactions: An ab initio study

Ab initio calculations using an STO-3G Gaussian basis set are performed in order to obtain the binding energy to the 06 and N7 of guanine of such amino acid models as the guanidinium ion for arginine, the ammonium ion for lysine, the methanol for serine, and the formamide for glutamic acid. The binding of formamide to adenine is also investigated. The charged ions exhibit a much higher binding energy to the bases, as expected, than the uncharged molecules. The order of binding strength is NH > guanidinium+ > formamide > methanol, and for formamide, guanine > adenine.