Estimating stacking interaction energy using atom in molecules properties: Homodimers of benzene and pyridine (original) (raw)
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The Journal of chemical physics, 2005
The potential energy surface for the benzene dimer in stacked conformations (84 points calculated) was computed at the MP2(FC)6-31+G(2d,2p) level of theory. Electron density (ED) distribution computed using the MP2(FC), B3LYP, and Hartree-Fock methods with the same basis set is studied in the frame of topological analysis. It is found that ED topology does not depend on the method of calculation. The values of the ED and its Laplacian in the cage critical point calculated using different methods are determined to be linearly dependent with the slope depending on basis set. Correlation equations based on these properties allow the interaction energy between benzene rings to be predicted with 8% mean relative error in the energy for the given region of the potential energy surface. This provides a new method for the estimation of stacking interaction energy using ED properties calculated with low level quantum-chemical methods.
Journal of Biophysical Chemistry, 2011
The use of appropriate level of theories for studying weak interactions such as stacking of aromatic molecules has been an important aspect, since the high level methods have limitations for application to large molecules. The differences in the stacking energies of various structures are found significant for identifying the most favored stacked benzene rings and the pyridine rings. The most favored structure of benzene rings obtained from various methods are similar, and also comparable with that of reported accurate CCSD(T) method. The effect of basis set in the stacking energies of MP2 calculations is small. Thus the moderately accurate methods may be feasible for studying the stacking interactions as demonstrated for benzene and pyridine molecules.
Journal of Physical Chemistry A, 2004
State-of-the-art electronic structure theory has been applied to generate potential energy curves for the sandwich, T-shaped, and parallel-displaced configurations of the simplest prototype of aromatic π-π interactions, the benzene dimer. Results were obtained using second-order Møller-Plesset perturbation theory (MP2) and coupled-cluster with singles, doubles, and perturbative triples [CCSD(T)] with different augmented, correlationconsistent basis sets. At the MP2 level, the smallest basis set used (a modified aug-cc-pVDZ basis) underestimates the binding by ∼0.5 kcal mol -1 at equilibrium and by ∼1 kcal mol -1 at smaller intermonomer distances compared to results with a modified aug-cc-pVQZ basis (denoted aug-cc-pVQZ*). The best MP2 binding energies differ from the more accurate CCSD(T) values by up to 2.0 kcal mol -1 at equilibrium and by more than 2.5 kcal mol -1 at smaller intermonomer distances, highlighting the importance of going beyond MP2 to achieve higher accuracy in binding energies. Symmetry adapted perturbation theory is used to analyze interaction energies in terms of electrostatic, dispersion, induction, and exchange-repulsion contributions.
Atom–bond pairwise additive representation for intermolecular potential energy surfaces
Chemical Physics Letters, 2004
A method has been developed to describe the force field of atomic species interacting with hydrocarbon molecules, either aliphatic or aromatic, of use for molecular dynamics simulations. The potential energy surfaces are represented by a simple analytical form written as a sum of atom-bond interaction contributions, for which a new potential model, [n(x),m], is proposed. The prototypical systems, methane and benzene, interacting with rare gases He, Ne, Ar, Kr and Xe, are analyzed as test cases. The method appears suitable for extensions to more complex systems, including modifications for treating ion-ion and ion-molecule interactions.
The Journal of Physical Chemistry A, 2009
A method has been developed to describe the force field of atomic species interacting with hydrocarbon molecules, either aliphatic or aromatic, of use for molecular dynamics simulations. The potential energy surfaces are represented by a simple analytical form written as a sum of atom-bond interaction contributions, for which a new potential model, [n(x),m], is proposed. The prototypical systems, methane and benzene, interacting with rare gases He, Ne, Ar, Kr and Xe, are analyzed as test cases. The method appears suitable for extensions to more complex systems, including modifications for treating ion-ion and ion-molecule interactions.
The Journal of Physical Chemistry A, 2004
The present work focuses on the influence of aromatic stacking on the ability of an aromatic nitrogen base to accept a hydrogen bond. Substituent effects were studied at the MP2 level for 10 complexes of a substituted benzene stacked with pyridine in a parallel offset conformation. The interaction energies between each substituted benzene and pyridine were analyzed in terms of Hartree-Fock, correlation, and electrostatic contributions. It appears that the basicity of pyridine is directly related to the electrostatic interaction between the cycles. It increases with increasing electron donating character of the benzene substituents. Also, density functional theory based descriptors such as global and local hardnesses and the benzene ring polarizability are found to adequately predict the interaction energy. These findings may be important in the study of DNA/ RNA chains.
Physical Chemistry Chemical Physics, 2006
Potential energy surfaces for the parallel-displaced, T-shaped and sandwich structures of the benzene dimer are computed with density fitted local second-order Møller-Plesset perturbation theory (DF-LMP2) as well as with the spin-component scaled (SCS) variant of DF-LMP2. While DF-LMP2 strongly overestimates the dispersion interaction, in common with canonical MP2, the DF-SCS-LMP2 interaction energies are in excellent agreement with the best available literature values along the entire potential energy curves. The DF-SCS-LMP2 dissociation energies for the three structures are also compared with new complete basis set estimates of the interaction energies obtained from accurate coupled cluster (CCSD(T)) and DF-SCS-MP2 calculations. Since LMP2 is essentially free of basis set superposition errors, counterpoise corrections are not required. As a result, DF-SCS-LMP2 is computationally inexpensive and represents an attractive method for the study of larger π-stacked systems such as truncated sections of DNA. *
Journal of Physical Chemistry A, 2002
Intermolecular interaction of the propane dimer was calculated with the MP2 level electron correlation correction using several basis sets up to the cc-pVQZ. The calculated interaction energy greatly depends on the basis set. Small basis sets underestimate the attraction considerably. The effects of electron correlation beyond MP2 are not large. Intermolecular interaction energies of 23 orientations of propane dimers were calculated at the MP2 level with a large basis set including multiple polarization functions. In all dimers, the inclusion of electron correlation considerably increases the attraction. The dispersion interaction is found to be the major source of attraction, whereas the electrostatic interaction is very small. The C 2h dimer in which the two C 2 axes of propane monomers have antiparallel orientation has the largest binding energy. The separation between the two methylene carbon atoms at the potential minimum in this dimer is the shortest among the 23 dimers. The short separation, which increases the dispersion energy, is the cause of the large binding energy of the C 2h dimer. The estimated MP2 and CCSD(T) interaction energies of the propane dimer at the basis set limit are -1.99 and -1.94 kcal/mol, respectively.
Parallel interactions of aromatic and heteroaromatic molecules
Hemijska industrija, 2016
Parallel interactions of aromatic and heteroaromatic molecules are very important in chemistry and biology. In this review, recent findings on preferred geometries and interaction energies of these molecules are presented. Benzene and pyridine were used as model systems for studying aromatic and heteroaromatic molecules, respectively. Searches of Cambridge Structural Database show that both aromatic and heteroaromatic molecules prefer interacting at large horizontal displacements, even though previous calculations showed that stacking interactions (with offsets of about 1.5 ?) are the strongest. Calculations of interaction energies at large horizontal displacements revealed that the large portion of interaction energy is preserved even when two molecules do not overlap. These substantial energies, as well as the possibility of forming larger supramolecular structures, make parallel interactions at large horizontal displacements more frequent in crystal structures than stacking inter...