Search results for "Calculation"
showing 10 items of 594 documents
Five-to-Six Membered Ring-rearrangements in the Reaction of 5-Perfluoroalkyl-1,2,4-oxadiazoles with Hydrazine and Methylhydrazine
2006
The hydrazinolysis reaction of 5-perfluoroalkyl-1,2,4-oxadiazoles with hydrazine or methylhydrazine as bidentate nucleophiles has been investigated. The reaction occurred through the addition of the bidentate nucleophile to the C(5)-N(4) double bond of the 1,2,4-oxadiazole followed by ring-opening and ring-closure (ANRORC) involving the second nucleophilic site of the reagent. This ring-closure step could involve either the original C(3) of the 1,2,4-oxadiazole (giving a five-to-five membered ring rearrangement) or an additional electrophilic center linked to it (exploiting a five-to-six membered ring rearrangement). An alternative initial nucleophilic attack may involve the additional elec…
A DFT study of the molecular mechanisms of the nucleophilic addition of ester-derived lithium enolates and silyl ketene acetals to nitrones: Effects …
2006
9 pages, 6 schemes, 3 figures, 2 tables.
B-DNA Structure and Stability as Function of Nucleic Acid Composition. Dispersion-Corrected DFT Study of Dinucleoside-Monophosphate Single and Double…
2013
actions of the sugar-phosphate skeleton with water; (6) hydrophobic interactions of the DNA cylindrical core, made up by the hydrogen-bonded and stacked nitrogen bases, with the water solvent. Recently, there has been increasing effort in developing and applying quantum chemical methods able to reproduce the structure of native B-DNA and to correctly describe the energy involved in the intrastrand and interstrand noncovalent interactions between the nucleotide monomers. This topic has been approached by both wave function methods and density functional theory. [2] Water solvent and sodium counterions also play an important role in the formation and relative stabilization of the double-helic…
Advanced descriptors for long-range noncovalent interactions between SARS-CoV-2 spikes and polymer surfaces.
2021
The recent pandemic triggered numerous societal efforts aimed to control and limit the spread of SARS-CoV-2. One of these aspects is related on how the virion interacts with inanimate surfaces, which might be the source of secondary infection. Although recent works address the adsorption of the spike protein on surfaces, there is no information concerning the long-range interactions between spike and surfaces, experimented by the virion when is dispersed in the droplet before its possible adsorption. Some descriptors, namely the interaction potentials per single protein and global potentials, were calculated in this work. These descriptors, evaluated for the closed and open states of the sp…
Why Are Some Enzymes Dimers? Flexibility and Catalysis in Thermotoga maritima Dihydrofolate Reductase
2019
[Image: see text] Dihydrofolate reductase from Thermotoga maritima (TmDFHFR) is a dimeric thermophilic enzyme that catalyzes the hydride transfer from the cofactor NADPH to dihydrofolate less efficiently than other DHFR enzymes, such as the mesophilic analogue Escherichia coli DHFR (EcDHFR). Using QM/MM potentials, we show that the reduced catalytic efficiency of TmDHFR is most likely due to differences in the amino acid sequence that stabilize the M20 loop in an open conformation, which prevents the formation of some interactions in the transition state and increases the number of water molecules in the active site. However, dimerization provides two advantages to the thermophilic enzyme: …
Magneto-structural correlations and DFT calculations in two rare tetranuclear copper(II)-clusters with doubly phenoxo and end-on azido bridges: Synth…
2010
International audience; By slightly changing the synthetic conditions, we have prepared two closely related linear tetranuclear CuII complexes with the symmetrical ONNO donor tetradentate Schiff-base ligand [H2L = (OH)C6H4(CH3)Cdouble bond; length as m-dashN(CH2)3Ndouble bond; length as m-dashC(CH3)C6H4(OH)] and with azide ions. These two distinctly coloured crystalline products were characterized by elemental analysis, IR and UV–Vis spectroscopy, CV, EPR spectra and variable temperature magnetic measurements. Single crystal X-ray diffraction studies of the green [Cu4(μ-L)2(μ1,1-N3)2(N3)2] (1) and the red [Cu4(μ-L)2(μ1,1-N3)2(N3)2(H2O)2] (2) crystals show that the coordination environment o…
Conformational investigation of α,β‐dehydropeptides. XV: N‐acetyl‐α,β‐dehydroamino acid N ′N ′‐dimethylamides: conformational properties from infrare…
2005
The FTIR spectra were analysed in the region of the nu(s)(N-H), AI(C=O) and nu(s)(Calpha=Cbeta) bands for a series of Ac-DeltaXaa-NMe2, where DeltaXaa = DeltaAla, (Z)-DeltaAbu, (Z)-DeltaLeu, (Z)-DeltaPhe and DeltaVal, to determine a predominant solution conformation of these alpha,beta-dehydropeptide-related molecules. Measurements were taken in CCl4, DCM and MeCN solutions. In the same way, spectra of saturated analogues Ac-Xaa-NMe2, where Xaa = Ala, Abu, Leu, Phe and Val, were investigated. To help interpret the spectroscopic results, conformational maps were calculated by the B3LYP/6-31+G** method. Also, the relative energies of all conformers of the dehydro compounds in vacuo as well as…
Double-CO32− Centered [CoII5] Wheel and Modeling of Its Magnetic Properties
2010
A high-spin Co(II) cluster with a rare pentagonal molecular structure and formula [Co(5)(CO(3))(2)(bpp)(5)]ClO(4) (1; Hbpp is 2,6-bis(phenyliminomethyl)-4-methylphenolate) has been synthesized and characterized by single-crystal X-ray diffraction. This topology arises from fusing five [Co(2)(bpp)] moieties in a cyclic manner around two CO(3)(2-) central ligands, resulting in propeller-like configuration. The irregular coordination of the carbonate ions to the metal centers results in a combination of coordination numbers (CNs) of the Co(II) ions of five and six. The bulk magnetization of this complicated magnetically exchanged system has been modeled successfully by employing a matrix diago…
Crystal structure, Hirshfeld surface analysis and HOMO–LUMO analysis of (E)-4-bromo-N′-(4-methoxybenzylidene)benzohydrazide
2018
The title Schiff base compound, C15H13BrN2O2, displays an E configuration with respect to the C=N double bond, which forms a dihedral angle of 58.06 (9)° with the benzene ring. In the crystal, the molecules are linked into chains parallel to the b axis by N—H...O and C—H...O hydrogen bonds, giving rise to rings with an R 2 1(6) graph-set motif. The chains are further linked into a three-dimensional network by C—H...π interactions. A Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from C...H (33.2%), H...H (27.7%), Br...H/H...Br (14.2%) and O...H/H...O (13.6%) interactions. The title compound has also been characterized by frontier molecu…
Geometrical and conformational preferences of the 9‐fluorenylmethoxycarbonyl‐amino moiety
2004
Structural parameters, originating from x-ray crystallographic data, have been compiled for 13 derivatives of amino acids, peptides and related compounds, which contain a total of 14 Fmoc-NH- moieties. For these moieties, molecular geometries and conformations--described by the omegao, theta1, theta2 and theta3' torsion angles--were analysed and compared with the corresponding parameters for the Z-NH- and Boc-NH-moieties (290 and 553, respectively). To gain a deeper insight into the conformational features of the Fmoc-NH- moiety, ab initio free molecule calculations were performed for fully relaxed minima. Also the potential energy surface as a function of the torsion angles (theta3', theta…