257 research outputs found
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
KinFams: De-Novo Classification of Protein Kinases Using CATH Functional Units
Protein kinases are important targets for treating human disorders, and they are the second most targeted families after G-protein coupled receptors. Several resources provide classification of kinases into evolutionary families (based on sequence homology); however, very few systematically classify functional families (FunFams) comprising evolutionary relatives that share similar functional properties. We have developed the FunFam-MARC (Multidomain ARchitecture-based Clustering) protocol, which uses multi-domain architectures of protein kinases and specificity-determining residues for functional family classification. FunFam-MARC predicts 2210 kinase functional families (KinFams), which have increased functional coherence, in terms of EC annotations, compared to the widely used KinBase classification. Our protocol provides a comprehensive classification for kinase sequences from >10,000 organisms. We associate human KinFams with diseases and drugs and identify 28 druggable human KinFams, i.e., enriched in clinically approved drugs. Since relatives in the same druggable KinFam tend to be structurally conserved, including the drug-binding site, these KinFams may be valuable for shortlisting therapeutic targets. Information on the human KinFams and associated 3D structures from AlphaFold2 are provided via our CATH FTP website and Zenodo. This gives the domain structure representative of each KinFam together with information on any drug compounds available. For 32% of the KinFams, we provide information on highly conserved residue sites that may be associated with specificity.Adeyelu T, Bordin N, Waman VP, Sadlej M, Sillitoe I, Moya-Garcia AA, Orengo CA. KinFams: De-Novo Classification of Protein Kinases Using CATH Functional Units. Biomolecules. 2023; 13(2):277. https://doi.org/10.3390/biom1302027
Towards physical interpretation of substituent effects : the case of N- and C3-substituted pyrrole derivatives
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
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
Phenylisoserine in the gas-phase and water: Ab initio studies on neutral and zwitterion conformers
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