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991.
992.
993.
Recent experimental work carried out in this laboratory on the ultrafast dynamics of myoglobin (Mb) is summarized with a stress on structural and vibrational energy relaxation. Studies on the structural relaxation of Mb following CO photolysis revealed that the structural change of heme itself, caused by CO photodissociation, is completed within the instrumental response time of the time-resolved resonance Raman apparatus used (approximately 2 ps). In contrast, changes in the intensity and frequency of the iron-histidine (Fe-His) stretching mode upon dissociation of the trans ligand were found to occur in the picosecond regime. The Fe-His band is absent for the CO-bound form, and its appearance upon photodissociation was not instantaneous, in contrast with that observed in the vibrational modes of heme, suggesting appreciable time evolution of the Fe displacement from the heme plane. The band position of the Fe-His stretching mode changed with a time constant of about 100 ps, indicating that tertiary structural changes of the protein occurred in a 100-ps range. Temporal changes of the anti-Stokes Raman intensity of the v4 and v7 bands demonstrated immediate generation of vibrationally excited heme upon the photodissociation and decay of the excited populations, whose time constants were 1.1 +/- 0.6 and 1.9 +/- 0.6 ps, respectively. In addition, the development of the time-resolved resonance Raman apparatus and prospects in this research field are described. 相似文献
994.
Joanna Trylska Pawe Grochowski Maciej Geller 《International journal of quantum chemistry》2001,82(2):86-103
The approximate valence bond (AVB) method was parameterized to obtain the potential energy surface for ongoing classical and further quantum classical molecular dynamics simulations describing the enzymatic reaction of the human immunodeficiency virus type 1 protease (HIV‐1 PR). The parameterized AVB method allows to describe the complete enzymatic reaction, including a proton transfer between a water molecule and an aspartic acid, nucleophilic attack of a hydroxy anion on the substrate peptide bond, conformational changes of an intermediate, two proton transfers between the intermediate and aspartic acids, and cleavage of the intermediate into reaction products. The AVB method was parameterized based on density functional theory (DFT) calculations performed for small molecular systems. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 82: 86–103, 2001 相似文献
995.
采用分子动力学模拟(MD)方法对甲醇和乙醇在超临界二氧化碳中的无限稀释扩散系数进行了模拟计算, 并应用泰勒分散理论, 采用超临界色谱仪对模拟结果进行了实验验证. 模拟计算值与实验值较吻合, 且变化规律基本一致, 表明采用这种新方法可以准确有效地预测超临界体系的扩散性质, 能够方便地应用于工程设计. 相似文献
996.
G. A. Abakumov V. I. Nevodchikov N. O. Druzhkov L. N. Zakharov L. G. Abakumova Yu. A. Kurskii V. K. Cherkasov 《Russian Chemical Bulletin》1997,46(4):771-776
New di-o-quinones of the biphenyl series, namely, 2,2′-dialkyl-5,5′-di-tert-butylbiphenyl-3,4,3′,4′-diquinones, were synthesized. Their structures were established by IR and NMR spectroscopy. The molecular
structure of 2,2′-dimethyl-5,5′-di-tert-butylbiphenyl-3,4,3′,4′-diquinone was established by X-ray structural analysis. The structure is characterized by orthogonal
(the torsion angle is 82.9°) mutual arrangement ofo-benzoquinone fragments. ESR studies demonstrated that chemical reduction of diquinone proceeds in four oneelectron stages
to form paramagnetic mono- and trianions as intermediates. Quinopyrocatechols, which are intermediates in the synthesis of
di-o-quinones, were isolated and characterized.
Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 4, pp. 804–809, April, 1997. 相似文献
997.
Parameterization of peptide 13C carbonyl chemical shielding anisotropy in molecular dynamics simulations. 总被引:1,自引:0,他引:1
Daniel M Jordan K Maria Mills Ioan Andricioaei Akash Bhattacharya Kim Palmo Erik R P Zuiderweg 《Chemphyschem》2007,8(9):1375-1385
NMR chemical shielding anisotropy (CSA) relaxation is an important tool in the study of dynamical processes in proteins and nucleic acids in solution. Herein, we investigate how dynamical variations in local geometry affect the chemical shielding anisotropy relaxation of the carbonyl carbon nucleus, using the following protocol: 1) Using density functional theory, the carbonyl (13)C' CSA is computed for 103 conformations of the model peptide group N-methylacetamide (NMA). 2) The variations in computed (13)C' CSA parameters are fitted against quadratic hypersurfaces containing cross terms between the variables. 3) The predictive quality of the CSA hypersurfaces is validated by comparing the predicted and de novo calculated (13)C' CSAs for 20 molecular dynamics snapshots. 4) The CSA fluctuations and their autocorrelation and cross correlation functions due to bond-length and bond-angle distortions are predicted for a chemistry Harvard molecular mechanics (CHARMM) molecular dynamics trajectory of Ca(2+)-saturated calmodulin and GB3 from the hypersurfaces, as well as for a molecular dynamics (MD) simulation of an NMA trimer using a quantum mechanically correct forcefield. We find that the fluctuations can be represented by a 0.93 scaling factor of the CSA tensor for both R(1) and R(2) relaxations for residues in helix, coil, and sheet alike. This result is important, as it establishes that (13)C' relaxation is a valid tool for measurement of interesting dynamical events in proteins. 相似文献
998.
Ritch JS Chivers T Eisler DJ Tuononen HM 《Chemistry (Weinheim an der Bergstrasse, Germany)》2007,13(16):4643-4653
A synthetic protocol for the tert-butyl-substituted dichalcogenoimidodiphosphinates [Na(tmeda){(EPtBu(2))(2)N}] (3 a, E=S; 3 b, E=Se; 3 c, E=Te) has been developed. The one-electron oxidation of the sodium complexes [Na(tmeda){(EPR(2))(2)N}] with iodine produces a series of neutral dimers (EPR(2)NPR(2)E--)(2) (4 b, E=Se, R=iPr; 4 c, E=Te, R=iPr; 5 a, E=S, R=tBu; 5 b, E=Se, R=tBu; 5 c, E=Te, R=tBu). Attempts to prepare 4 a (E=S, R=iPr) in a similar manner produced a mixture including HN(SPiPr(2)). Compounds 4 b, 4 c and 5 a-c were characterised by multinuclear NMR spectra and by X-ray crystallography, which revealed two alternative structures for these dimeric molecules. The derivatives 4 b, 4 c, 5 a and 5 b exhibit acyclic structures with a central chalcogen-chalcogen linkage that is elongated by approximately 2 % (E=S), 6 % (E=Se) and 8 % (E=Te) compared to typical single-bond values. By contrast, 5 c adopts an unique spirocyclic contact ion-pair structure in which a [(TePtBu(2))(2)N](-) ion is Te,Te' chelated to an incipient [(TePtBu(2))(2)N](+) cyclic ion. DFT calculations of the relative energies of the two structural isomers indicate a trend towards increasing stability for the contact ion pair relative to the corresponding dichalcogenide on going from S to Se to Te for both the isopropyl and tert-butyl series. The two-electron oxidation of [Na(tmeda){(EPtBu(2))(2)N}] (E=S, Se, Te) with iodine produced the salts [(EPtBu(2))(2)N](+)X(-) (7 a, E=S, X=I(3); 7 b, E=Se, X=I; 7 c, E=Te, X=I), which were characterised by X-ray crystallography. Compound 7 a exists as a monomeric, ion-separated complex with [d(S--S)=2.084(2) A]; 7 b and 7 c are dimeric [d(Se--Se)=2.502(1) A; d(Te--Te)=2.884(1) A]. 相似文献
999.
1000.
Emanuela Emanuele Dimitra Markovitsi Philippe Millié Krystyna Zakrzewska 《Chemphyschem》2005,6(7):1387-1392
The singlet excited states of the model DNA duplex (dA)10.(dT)10 are studied. Calculations are performed in the exciton theory framework. Molecular dynamics calculations provide the duplex geometry. The dipolar coupling is determined using atomic transition charges. The monomer transition energies are simulated by Gaussian functions resembling the absorption bands of nucleosides in aqueous solutions. Most of the excited states are found to be delocalized over at least two bases and result from the mixing of different monomer states. Their properties are only weakly affected by conformational changes of the double helix. On average, the highest oscillator strength is carried by the upper eigenstates. The duplex absorption spectra are shifted a few nanometers to higher energies with respect to the spectra of noninteracting monomers. The states with larger spatial extent are located close to the maximum of the absorption spectrum. 相似文献