Vibrational corrections to transition properties

The vibrational contributions to second-order transition properties are considered in the framework of the Born—Oppenheimer approximation. It is shown that the usual formula for vibrational second-order transition matrix elements is incomplete and needs to be supplemented by a term of purely vibrational origin. This pure vibrational contribution is calculated for vibrational transition polarizabilities in LiH and BeF and found to be quite significant. Its inclusion in theoretically calculated data for the Raman intensities appears to be necessary

Importance of electron correlation effects and basis set superposition error in calculations of interaction energies and interaction-induced electric properties in hydrogen-bonded complexes: a model study

A detailed study of the interaction energies and interaction-induced electric dipole properties in model linear hydrogen cyanide complexes (HCN) m (m = 2–4) is carried out within the finite field HF SCF, MP2, CCSD and CCSD(T) approximations using the recently developed LPol-n (n = ds, fs, dl, fl) basis sets. The importance of high-order correlation effects and the basis set superposition error is evaluated. To correct for the latter is crucial for obtaining accurate interaction energy values, but the error can safely be neglected in the estimation of induced electric properties when the LPol-n (n = ds, fs, dl, fl) basis sets are used. Correlation effects are important in the evaluation of both the interaction energies and the induced electric properties of the systemsThis work was supported by the Spanish Ministerio de Ciencia e Innovación (CTQ2008-01861/BQU project), the Xunta de Galicia and FEDER (Axuda para Consolidación e Estructuración de Unidades de Investigación Competitivas do Sistema Universitario de Galicia 2007/050, and 2007-2013 and INCITE09 314 252 PR projects), and by the Foundation for Polish Science within the Homing Plus programme (Homing Plus/2010-1/2), cofinanced from European Regional Development Fund within Innovative Economy Operational ProgrammeS

Dynamics of fibers in a wide microchannel

Dynamics of single flexible non-Brownian fibers, tumbling in a Poiseuille flow between two parallel solid plane walls, is studied with the use of the hydromultipole numerical code, based on the multipole expansion of the Stokes equations, corrected for lubrication. It is shown that for a wide range of the system parameters, the migration rate towards the middle plane of the channel increases for fibers, which are closer to a wall, or are more flexible (less stiff), or are longer. The faster motion towards the channel center is accompanied by a slower translation along the flow and a larger fiber deformation.Comment: 9 pages, 16 figure

Time dependent density functional theory calculation of van der Waals coefficient C6_{6} of alkali-metal atoms Li, Na, K, alkali dimers Li2_{2}, Na2_{2}, K2_{2} and sodium clusters Nan_{n}

In this paper we employ all-electron time dependent density functional theory (TDDFT) to calculate the long range dipole-dipole dispersion coefficient (van der Waals coefficient) $C_{6}$ of alkali-metal atoms Li, Na, K, alkali-metal atom dimers Li$_{2}$, Na$_{2}$, K$_{2}$ and sodium clusters containing even number of atoms ranging from 2 to 20 atoms. The dispersion coefficients are obtained via Casimir-Polder expression which relates it to the frequency dependent linear polarizabilty at imaginary frequencies. The frequency dependent polarizabilities are calculated by employing TDDFT--based complete sum-over-states expressions for the atoms, and direct TDDFT linear response theory for the closed shell dimers and clusters.Comment: 14 pages of text and 4 figure

Quantum mechanical studies of lincosamides

Lincosamides are a class of antibiotics used both in clinical and veterinary practice for a wide range of pathogens. This group of drugs inhibits the activity of the bacterial ribosome by binding to the 23S RNA of the large ribosomal subunit and blocking protein synthesis. Currently, three X-ray structures of the ribosome in complex with clindamycin are available in the Protein Data Bank, which reveal that there are two distinct conformations of the pyrrolidinyl propyl group of the bound clindamycin. In this work, we used quantum mechanical methods to investigate the probable conformations of clindamycin in order to explain the two binding modes in the ribosomal 23S RNA. We studied three lincosamide antibiotics: clindamycin, lincomycin, and pirlimycin at the B3LYP level with the 6-31G** basis set. The focus of our work was to connect the conformational landscape and electron densities of the two clindamycin conformers found experimentally with their physicochemical properties. For both functional conformers, we applied natural bond orbital (NBO) analysis and the atoms in molecules (AIM) theory, and calculated the NMR parameters. Based on the results obtained, we were able to show that the structure with the intramolecular hydrogen bond C=O…H–O is the most stable conformer of clindamycin. The charge transfer between the pyrrolidine-derivative ring and the six-atom sugar (methylthiolincosamide), which are linked via an amide bond, was found to be the dominant factor influencing the high stability of this conformer

Intriguing Electrostatic Potential of CO: Negative Bond-ends and Positive Bond-cylindrical-surface

The strong electronegativity of O dictates that the ground state of singlet CO has positively charged C and negatively charged O, in agreement with ab initio charge analysis, but in disagreement with the dipole direction. Though this unusual phenomenon has been fairly studied, the study of electrostatic potential (EP) for noncovalent interactions of CO is essential for better understanding. Here we illustrate that both C and O atom-ends show negative EP (where the C end gives more negative EP), favoring positively charged species, whereas the cylindrical surface of the CO bond shows positive EP, favoring negatively charged ones. This is demonstrated from the interactions of CO with Na+, Cl-, H2O, CO and benzene. It can be explained by the quadrupole driven electrostatic nature of CO (like N2) with very weak dipole moment. The EP is properly described by the tripole model taking into account the electrostatic multipole moments, which has a large negative charge at a certain distance protruded from C, a large positive charge on C, and a small negative charge on O. We also discuss the EP of the first excited triplet COopen0

Ab initio studies of structures and properties of small potassium clusters

We have studied the structure and properties of potassium clusters containing even number of atoms ranging from 2 to 20 at the ab initio level. The geometry optimization calculations are performed using all-electron density functional theory with gradient corrected exchange-correlation functional. Using these optimized geometries we investigate the evolution of binding energy, ionization potential, and static polarizability with the increasing size of the clusters. The polarizabilities are calculated by employing Moller-Plesset perturbation theory and time dependent density functional theory. The polarizabilities of dimer and tetramer are also calculated by employing large basis set coupled cluster theory with single and double excitations and perturbative triple excitations. The time dependent density functional theory calculations of polarizabilities are carried out with two different exchange-correlation potentials: (i) an asymptotically correct model potential and (ii) within the local density approximation. A systematic comparison with the other available theoretical and experimental data for various properties of small potassium clusters mentioned above has been performed. These comparisons reveal that both the binding energy and the ionization potential obtained with gradient corrected potential match quite well with the already published data. Similarly, the polarizabilities obtained with Moller-Plesset perturbation theory and with model potential are quite close to each other and also close to experimental data.Comment: 33 pages including 10 figure