Search results for "Fragment molecular orbital"
showing 6 items of 6 documents
G2(MP2) Investigation of Alane-[X(CH3)3]- (X = C, Si, and Ge) and Alane-Y(CH3)3 (Y = N, P, and As) Interactions
2001
Alane-[X(CH3)3]- (X = C, Si, and Ge) and alane-Y(CH3)3 (Y = N, P, and As) have been investigated as donor−acceptor complex types at the G2(MP2) level of theory. The results show that the anionic complexes are more stable than the neutral ones. They show also that this stability decreases when going from carbon to germanium for [H3AlX(CH3)3]- complexes and from nitrogen to arsenic for H3AlY(CH3)3 complexes. The interaction diagrams prove that the evolution of complexation energy depends on the coordination mode. In fact, it is a result of two interaction types: interaction between “a1” symmetry fragment molecular orbital (stabilizing) and interactions between “e” symmetry fragment molecular…
Comparative G2(MP2) molecular orbital study of [H 3 AlX(CH 3 ) 2 ] − (X=N, P, and As) and H 3 AlY(CH 3 ) 2 (Y=O, S, and Se) donor–acceptor complexes
2001
Abstract [H3AlX(CH3)2]− (X=N, P, and As) and H3AlY(CH3)2 (Y=O, S, and Se) donor–acceptor complexes have been studied using G2(MP2) level of theory. The coordination mode, the structural and the methyl substitution effects upon complexation are analyzed. The interaction of the alane with the donor ligand is stronger in the anionic complexes than in the neutral ones and the methylated complexes are more stable than the hydrogenated ones. The coordination is ensured by tow interactions having a reverse character: interaction between a′ symmetry fragment molecular orbital (stabilizing) and interaction between a″ symmetry occupied molecular orbital (destabilizing) of the two fragments. A linear …
Simulations of the substitutional sites of Cr3+in LiNbO3from molecular orbital models
1992
Abstract The location of Cr3+ center in LiNbO3 crystals, is analysed from two types of molecular orbital (MO) calculations using MS-LSD and DFT-LCGTO methods. The optimization of the geometries according to the total energies of Cr3+ center at the two sites are presented.
Density functional theory fragment descriptors to quantify the reactivity of a molecular family: Application to amino acids
2007
By using the exact density functional theory, one demonstrates that the value of the local electronic softness of a molecular fragment is directly related to the polarization charge (Coulomb hole) induced by a test electron removed (or added) from (at) the fragment. Our finding generalizes to a chemical group a formal relation between these molecular descriptors recently obtained for an atom in a molecule using an approximate atomistic model [P. Senet and M. Yang, J. Chem. Sci. 117, 411 (2005)]. In addition, a practical ab initio computational scheme of the Coulomb hole and related local descriptors of reactivity of a molecular family having in common a similar fragment is presented. As a b…
The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer
2021
Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering…
Structure‐ and Interaction‐Based Design of Anti‐SARS‐CoV‐2 Aptamers
2022
Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with …