197 research outputs found
Towards physical interpretation of substituent effects : the case of N- and C3-substituted pyrrole derivatives
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 C of alkali-metal atoms Li, Na, K, alkali dimers Li, Na, K and sodium clusters Na
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) of alkali-metal atoms Li, Na, K, alkali-metal
atom dimers Li, Na, K 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
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
Towards physical interpretation of substituent effects: the case of N- and C3-substituted pyrrole derivatives
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
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
Lateral migration of flexible fibers in Poiseuille flow between two parallel planar solid walls
Unimolecular Decomposition of 5-Aminotetrazole and its Tautomer 5-Iminotetrazole: New Insight from Isopotential Searching
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