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Empirical Calculations (empirical + calculation)

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Chemistry100%

Selected Abstracts

Interaction Energies for the Purine Inhibitor Roscovitine with Cyclin-Dependent Kinase 2: Correlated Ab Initio Quantum-Chemical, DFT and Empirical Calculations

CHEMISTRY - A EUROPEAN JOURNAL, Issue 16 2006
Petr Dobe
Abstract The interaction between roscovitine and cyclin-dependent kinase 2 (cdk2) was investigated by performing correlated ab initio quantum-chemical calculations. The whole protein was fragmented into smaller systems consisting of one or a few amino acids, and the interaction energies of these fragments with roscovitine were determined by using the MP2 method with the extended aug-cc-pVDZ basis set. For selected complexes, the complete basis set limit MP2 interaction energies, as well as the coupled-cluster corrections with inclusion of single, double and noninteractive triples contributions [CCSD(T)], were also evaluated. The energies of interaction between roscovitine and small fragments and between roscovitine and substantial sections of protein (722 atoms) were also computed by using density-functional tight-binding methods covering dispersion energy (DFTB-D) and the Cornell empirical potential. Total stabilisation energy originates predominantly from dispersion energy and methods that do not account for the dispersion energy cannot, therefore, be recommended for the study of protein,inhibitor interactions. The Cornell empirical potential describes reasonably well the interaction between roscovitine and protein; therefore, this method can be applied in future thermodynamic calculations. A limited number of amino acid residues contribute significantly to the binding of roscovitine and cdk2, whereas a rather large number of amino acids make a negligible contribution. [source]

Structural motifs in the maturation process of peptide hormones.

JOURNAL OF PEPTIDE SCIENCE, Issue 2 2002
The somatostatin precursor.
Abstract Synthetic peptides reproducing both the native domain around the dibasic cleavage site of pro-somatostatin, and mutated sequences thereof, previously assayed in site-directed mutagenesis experiments, have been studied by CD in different solvent systems, such as water, TFE/H2O, MeCN/H2O and aqueous SDS, in order to ascertain the ability of each solvent to stabilize secondary structural motifs. A combination of deconvolution methods and empirical calculations, that allow subtraction of the contributions due to unordered structures from the spectra, suggests that mainly two distinct families of ordered conformers containing ,-helix and/or structurally different ,-turns are present in solution, the relative stability of the different conformers depending on the nature of the solvent. The presence of ,-turns is in line with a previous NMR study in DMSO and DMSO/H2O. Comparison of the CD spectra in aqueous SDS of peptides undergoing processing with a sequence not processed in vivo shows that only the latter possesses a stable and detectable ,-helix population. This observation suggests that the structuration involving ,-turns but no ,-helix, which was observed by CD both in SDS and organic solvent/H2O mixtures at high water contents, might be of biological significance. The similarity of this structuration to molecular models obtained from NMR data in DMSO and DMSO/H2O is discussed. Copyright © 2002 European Peptide Society and John Wiley & Sons, Ltd. [source]

Theoretical study on 19F magnetic shielding constants of some metal fluorides

MAGNETIC RESONANCE IN CHEMISTRY, Issue 11 2003
Shu-Hui Cai
Abstract A study is presented of 19F NMR magnetic shielding constants of MF2 (M = Zn, Cd), ,-PbF2, MF3 (M = Al, Ga, In), AMF3 (A = K, Rb, Cs, Ba; M = Mg, Ca, Li, Zn, Cd), BaMgF4, BaZnF4 and Ba2ZnF6 using the DFT/GIAO method. The aug-cc-pVTZ basis set was used for the fluorine atom under investigation and LanL2DZ for the remaining fluorine atoms. The 3,21G(2d) basis set was used for the aluminum atom and CRENBL for the other metal atoms. When appropriate cluster models were employed, the theoretical results obtained from the B3LYP/GIAO calculations are in good agreement with experimental measurements and may be better than those obtained from empirical calculations. The correlation coefficient and the slope of the fitting line between our theoretical predictions and the experimental observations are close to unity. Copyright © 2003 John Wiley & Sons, Ltd. [source]

Energetic N,N,N,,N, -Tetraaminopiperazinium Salts

CHEMSUSCHEM CHEMISTRY AND SUSTAINABILITY, ENERGY & MATERIALS, Issue 3 2008
Haixiang Gao Prof.
Abstract The formation of tetraaminopiperazinium salts using water as solvent provides a green, straightforward approach to highly energetic salts that exhibit good thermal stabilities and moderate densities. The N,N,N,,N, -tetraaminopiperazinium cation was selected for this study because of its high nitrogen,nitrogen bond content and its high positive heat of formation. Theoretical and empirical calculations on energetic salts based on this nitrogen-rich cation reveal them to have high positive molar enthalpies of formation, as high as 1034.0,kJ,mol,1, supporting the application of these new salts as potential energetic materials. [source]