Biomedical subjects

Rafał Podeszwa

Publications and source records attributed to Rafał Podeszwa.

3 recordsLinked to original sources

PubMed2006

Potential energy surface for the benzene dimer and perturbational analysis of pi-pi interactions.

We present a complete 6-dimensional potential energy surface for the benzene dimer obtained using symmetry-adapted perturbation theory (SAPT) of intermolecular interactions based on Kohn-Sham's description of monomers. Ab initio calculations were performed for 491 dimer geometries in a triple-zeta-quality basis set supplemented by bond functions. An accurate analytic fit to the ab initio results has been developed and low-energy stationary points on the potential energy surface have been found. We have determined that there are three minima on the surface. Two of them, the tilted T-shape and the parallel-displaced, are nearly isoenergetic with interaction energies of -2.77 and -2.74 kcal/mol, respectively. The third minimum, a twisted edge-to-edge conformation, is significantly less attractive, with the interaction energy equal to -1.82 kcal/mol. Both the T-shape and sandwich geometries, sometimes assumed to be minima, are shown to be only saddle points. The potential energy surface is extremely flat between the two lowest minima, the barrier being only 0.10 kcal/mol above the global minimum. The second-virial coefficient obtained with the new potential agrees well with experimental results over a wide range of temperatures. The SAPT approach rigorously decomposes the interaction energy into physical components. The relative importance of these components has been analyzed.

Benzene↗

PubMed2005

Intermolecular potentials based on symmetry-adapted perturbation theory with dispersion energies from time-dependent density-functional calculations.

Recently, three of us have proposed a method [Phys. Rev. Lett. 91, 33201 (2003)] for an accurate calculation of the dispersion energy utilizing frequency-dependent density susceptibilities of monomers obtained from time-dependent density-functional theory (DFT). In the present paper, we report numerical calculations for the helium, neon, water, and carbon dioxide dimers and show that for a wide range of intermonomer separations, including the van der Waals and short-range repulsion regions, the method provides dispersion energies with accuracies comparable to those that can be achieved using the current most sophisticated wave-function methods. If the dispersion energy is combined with (i) the electrostatic and first-order exchange interaction energies as defined in symmetry-adapted perturbation theory (SAPT) but computed using monomer Kohn-Sham (KS) determinants, and (ii) the induction energy computed using the coupled KS static response theory, (iii) the exchange-induction and exchange-dispersion energies computed using KS orbitals and orbital energies, the resulting method, denoted by SAPT(DFT), produces very accurate total interaction potentials. For the helium dimer, the only system with nearly exact benchmark values, SAPT(DFT) reproduces the interaction energy to within about 2% at the minimum and to a similar accuracy for all other distances ranging from the strongly repulsive to the asymptotic region. For the remaining systems investigated by us, the quality of the SAPT(DFT) interaction energies is so high that these energies may actually be more accurate than the best available results obtained with wave-function techniques. At the same time, SAPT(DFT) is much more computationally efficient than any method previously used for calculating the dispersion and other interaction energy components at this level of accuracy.

Journal Article↗

PubMed2004

Coupled-cluster singles and doubles for extended systems.

Coupled-cluster theory with connected single and double excitation operators (CCSD) and related approximations, such as linearized CCSD, quadratic configuration interaction with single and double excitation operators, coupled-cluster with connected double excitation operator (CCD), linearized CCD, approximate CCD, and second- and third-order many-body perturbation theories, are formulated and implemented for infinitely extended one-dimensional systems (polymers), on the basis of the periodic boundary conditions and distance-based screening of integrals, density matrix elements, and excitation amplitudes. The variation of correlation energies with the truncation radii of short- and long-range lattice sums and with the number of wave vector sampling points in the first Brillouin zone is examined for polyethylene, polyacetylene, and polyyne, and is shown to be a function of the degree of pi-electron conjugation or the fundamental band gaps. The t2 and t1 amplitudes in the atomic orbital (AO) basis are obtained by first computing the t amplitudes in the Bloch-orbital basis and subsequently back-transforming them into the AO basis. The plot of these AO-based t amplitudes as a function of unit cells also indicates that the t2 amplitudes of polyacetylene and polyyne exhibit appreciably slower decay than those of polyethylene, although the asymptotic decay behavior is invariably 1/r3. The AO-based t1 amplitudes appear to correlate strongly with the electronic structure, and they decay seemingly exponentially for polyethylene whereas they stay at a constant magnitude across the seventh nearest neighbors of polyacetylene and polyyne, which attests to far reaching effects of nondynamical electron correlation mediated by orbital rotation. Nonetheless, the unit cell contributions to the correlation energies taper below 10(-6) hartree after 15 A for all three polymers. The basis set dependence of the decay behavior of t2 amplitudes is also examined for linear hydrogen fluoride polymer (HF)infinity and linear beryllium polymer (Be)infinity employing the STO-3G, 6-31G, and 6-31G* basis sets, and proves to be rather small.

Journal Article↗