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51.
Nicolas?Ferré Alessandro?Cembran Marco?Garavelli Massimo?OlivucciEmail author 《Theoretical chemistry accounts》2004,112(4):335-341
A special hybrid quantum mechanics/molecular mechanics forcefield is defined, parameterized and validated for studying the photoisomerization path of the retinal chromophore in the rhodopsin protein. It couples a multireference ab initio Hamiltonian (CASSCF and second-order multireference many-body perturbation theory using a CASSCF reference) to describe the chromophore while the rest of the protein is approximated with the Amber forcefield. The frontier has been carefully parameterized in order to reproduce full quantum mechanics torsional energy profiles, for both the ground state and the first excited state. It is also shown that replacing the chromophore counterion with point charges is a valid approximation. This result is interpreted in terms of a cancellation effect for which a possible explanation is given. 相似文献
52.
Summary Intercalators are molecules capable of sliding between DNA base pairs without breaking up the hydrogen bonds between the DNA bases. On the basis of molecular mechanics calculations structural, models of B-DNA tetranucleotide intercalation complexes of some cytostatic active 9-aminoacridines and of a [d, e]-anellated isoquinoline derivative are presented. The drug complexes are stabilized by energetically favouredvan der Waals interactions and by selective hydrogen bonds between the side chains of the drugs and the DNA bases. Semiempirical quantum chemistry calculations revealed that the chromophoric system of the intercalators is able to form ,-charge-transfer interactions with the purine bases of the base paired deoxytetranucleotides. The theoretical findings are of interest for a more specific drug design of cytostatically active agents.
Molecular Modeling von Interkalationskomplexen antitumoraktiver 9-Aminoacridine sowie eines [d, e]-anellierten Isochinolinderivates mit basengepaarten Desoxytetranukleotiden
Zusammenfassung Interkalatoren sind Moleküle, die in der Lage sind, sich zwischen DNA-Basenpaare einzulagern, ohne die Wasserstoffbrücken zwischen den DNA-Basen aufzubrechen. Auf der Basis von molekülmechanischen Rechnungen werden Tetranukleotid-Interkalationskomplexe von verschiedenen zytostatisch aktiven 9-Aminoacridinen und von einem [d, e]-anellierten Isochinolinderivat präsentiert. Die Komplexe werden durch energetisch günstigevan der Waals-Interaktionen sowie durch selektive Wasserstoffbrückenbindungen zwischen den Seitenketten der Wirkstoffe und den DNA-Basen stabilisiert. Semiempirische quantenchemische Rechnungen ergaben, daß der Chromophor der Interkalatoren in der Lage ist, ,-charge-transfer Wechselwirkungen mit den Purinbasen der basengepaarten Desoxytetranukleotide auszubilden. Die theoretischen Ergebnisse sind für ein spezifischeres Wirkstoffdesign zytostatisch aktiver Verbindungen von Interesse.相似文献
53.
A novel methodology for 'reverse-docking' a cationic peptide-based organocatalyst to a rigid anionic transition state (TS) model for the conjugate addition of azide to alpha,beta-unsaturated carbonyl substrates is described. The resulting docking poses serve as simplified TS models for enantioselective catalysis. Molecular mechanics-based scoring and ranking of the docking poses, followed by clustering and structural analysis, reveal a clear energetic preference for docking to the S-enantiomeric azidation TS model, in agreement with experiment. Clear energetic trends emerged from docking the catalyst to both enantiomers of all six azidation TS models of this study. Structural analysis of the most favorable pose suggests a mechanism for enantioselective catalysis that is consistent with principles of molecular recognition, catalysis, and experimental data. 相似文献
54.
Tingmin Wang Jerald S. Bradshaw Janet C. Curtis Peter Huszthy Reed M. Izatt 《Journal of inclusion phenomena and macrocyclic chemistry》1993,16(2):113-122
Significant - interaction is found in the complexes of (S, S)-dimethylpyridino-18-crown-6 with (R)- and (S)-[-(1-naphthyl)ethyl]ammonium perchlorate. This finding is supported by the1H NOESY NMR spectral technique, greater chemical shift changes of aromatic protons in both host and guest molecules upon complexation, and by molecular mechanics calculations. Because of the flexibility of the ligand, the tripod hydrogen bonding causes13C relaxation times of all periphery carbons to decrease without significant selectivity. Rotational energy barrier calculations of the methyl groups of the complexed ligand also show that the (S, S)-host-(R)-guest is the more stable complex. 相似文献
55.
《Journal of Molecular Structure》1995,343(1-3):125-132
A computer method has been developed which is an alternative to molecular dynamics in the sense that it pictures conformational motion. It simulates propagation in conformational movement based on conformational interconversion phenomena. The method starts with the knowledge of the topology of the conformational potential energy hyper-surface, which is described by the minima and the transition states. The topology is obtained by the recently described software
. The simulation of conformational motion is based on the Boltzmann statistics of movement between the minima and the transition states at a given temperature. The method is illustrated for methyl--glucopyranoside and -
-galNAc(1-3)[-
-Fuc(1-2)]Gal-O-Me molecules. Conformational transitions of hydroxyl groups as well as glycosidic linkages are discussed. 相似文献
56.
The performance of a recently developed method to generate representative atomistic models of amorphous polymers has been investigated. This method, which is denoted SuSi, can be defined as a random generator of energy minima. The effects produced by different parameters used to define the size of the system and the characteristics of the generation algorithm have been examined. Calculations have been performed on poly(L,D-lactic) acid (rho = 1.25 g/cm3) and nylon 6 (rho = 1.084 g/cm(3)), which are important commercial polymers. 相似文献
57.
D. M. Turdybekov K. M. Turdybekov E. V. Burdel'naya A. Zh. Turmukhambetov S. M. Adekenov Yu. V. Gatilov 《Chemistry of Natural Compounds》2003,39(1):19-21
The structure of lappacontine hydrobromide hydrate was solved by an x-ray structure analysis. 相似文献
58.
From the de Broglie matter wave hypothesis and Planck’s energy quantization law, and assuming conservation of energy in the
absorption of a photon and its consequent conversion to kinetic energy of motion by a material particle initially at rest,
one can deduce a simple mathematical relationship between the wavelength λ (or frequency ν), of the photon absorbed by the
particle at rest, and the resulting de Broglie matter wave length, λD, of the particle with kinetic energy of motion of mv2/2. The relationship so deduced, λD∝√λ, suggests that visible wavelengths of light, from about 4000 ?, in the violet, to beyond about 7000 ?, in the red, on
absorption by an electron at rest, lead to material electron wavelengths, λD, of the order of the size of the electron transfer proteins seen in the photosynthetic reaction centers of photosynthesizing
organisms, at about a size of 50–100 ?. In addition to understanding the mechanism of photosynthesis as a material wave mediated
phenomenon, further areas of importance of the relations pointed out in this paper are in the design of experiments to gain
a deeper understanding of the basic tenets of wave mechanics, and in the use of tunable lasers to probe various properties
of material waves, and to precisely control their properties for applications including lithography. 相似文献
59.
Teik-Cheng Lim 《Journal of mathematical chemistry》2003,33(3-4):279-285
The van der Waals forces for non-bonded interaction can be expressed either by the Exponential-6 or by the Lennard-Jones(m-n) potential functions, whereby m > n. Hitherto a relationship exists between the Exponential-6 and the Lennard-Jones(12-6) potential functions, with a scaling factor = 13.772 at or near the equilibrium and = 12.0 for long range interaction. This paper attempts to develop relationships between Exponential-6 and a more generalized Lennard-Jones(m-n). Analysis reveals that the relationship exists only when n = 6 and that two sets of scaling factors (as functions of index m) applies for the relationship between Exponential-6 and the Lennard-Jones(m-6), whereby m > 6. 相似文献
60.
It is proposed that in molecular mechanics calculation points belonging to various stable or meta-sta-ble conformtrs are mixed up and form fractal structures in conformation space.The calculation results show the following two phenomena:(i)Two levels of structure with fractal feature were observed.Around the conformer without mirror symmetry points belonging to the conformer and its enantiomer are mixed up and form the first level of fractal structure; on the boundary of the attractive basin o{ each atlractor,points belonging to different attractors form the second level of fractal structure.(ii) The variation of molecular mechanics parameters will influence the structure and area of each attractive basin significantly The above phenomena may become the basis of a new method for solving the troublesome multi-minimum-point problem in molecular mechanics calculation. 相似文献