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1.
Frank Jensen 《Theoretical chemistry accounts》1998,99(5):295-300
A total of 36 stationary points have been located on the H2CO potential energy surface by means of gradient extremal following. These 36 points are believed to represent all the important
stationary points on this surface. There is no indication that the structure of the surface becomes less complicated as the
size of the basis set is enlarged at the Hartree-Fock level of theory, but many of the second- and third-order saddle points
disappear when electron correlation is introduced. Of the ten first-order saddle points (transition structures) located, the
majority have reaction paths entering the associated minima in a side-on approach, i.e. these cannot be located by uphill
walking from the minimum.
Received: 5 February 1998 / Accepted: 21 May 1998 / Published online: 29 July 1998 相似文献
2.
Wolfgang Quapp Michael Hirsch Dietmar Heidrich 《Theoretical chemistry accounts》1998,100(5-6):285-299
This paper serves for the better understanding of the branching phenomenon of reaction paths of potential energy hypersurfaces
in more than two dimensions. We apply the recently proposed reduced gradient following (RGF) method for the analysis of potential
energy hypersurfaces having valley-ridge inflection (VRI) points. VRI points indicate the region of possible reaction path
bifurcation. The relation between RGF and the so-called global Newton search for stationary points (Branin method) is shown.
Using a 3D polynomial test surface, a whole 1D manifold of VRI points is obtained. Its relation to RGF curves, steepest descent
and gradient extremals is discussed as well as the relation of the VRI manifold to bifurcation points of these curves.
Received: 8 July 1998 / Accepted: 24 August 1998 / Published online: 23 November 1998 相似文献
3.
A homotopy method is presented that locates both minimizers and saddle points of energy functions in an efficient manner.
In contrast to other methods, it makes possible the exploration of large parts of potential energy surfaces. Along a homotopy
path stationary points of odd and even order occur alternately. A path tracing procedure requiring only gradients and at most
one evaluation of the Hessian matrix is given. Test results on a model potential and three MINDO/3 potentials are reported.
Received: 6 May 1996 / Accepted: 2 April 1998 / Published online: 23 June 1998 相似文献
4.
Jean-Pierre Duneau Serge Crouzy Yves Chapron Monique Genest 《Theoretical chemistry accounts》1999,101(1-3):87-91
The structure and dynamics of the ErbB-2 transmembrane domain have been examined using molecular dynamics techniques both
in vacuum and within an explicit hydrated L-α-dilauroyl-phosphatidyl-ethanolamine environment. In-vacuum simulations show that a highly cooperative structural transition
occurs frequently within the α-helical transmembrane domain which converts to local π-helices. We show that the α-helix alteration
does not depend upon the force field or initial side-chain conformations but is intimately related to the sequence. The membrane-like
environment does not prevent the structural transition in the helix but slows down the peptide dynamics indicating that the
appearance of a π-bulge is not an artifact of the vacuum approximation. The consequences of π-helix formation could be very
huge for the ErbB-2 receptor which is involved in numerous human cancers and also for other membrane proteins wherein similar
local structures are also observed experimentally.
Received: 9 May 1998 / Accepted: 3 September 1998 / Published online: 17 December 1998 相似文献
5.
Kazunari Naka Hirofumi Sato Akihiro Morita Fumio Hirata Shigeki Kato 《Theoretical chemistry accounts》1999,102(1-6):165-169
The free-energy profile for the Menshutkin-type reaction NH3 + CH3Cl → NH3CH3
+ + Cl− in aqueous solution is studied using the RISM-SCF method. The effect of electron correlation on the free-energy profile is
estimated by the RISM-MP2 method at the HF optimized geometries along the reaction coordinate. Solvation was found to have
a large influence on the vibrational frequencies at the reactant, transition state and product; these vibrational frequencies
are utilized to calculate the zero-point energy correction of the free-energy profile. The computed barrier height and reaction
exothermicity are in reasonable agreement with those of experiment and previous calculations. The change of solvation structure
along the reaction path is represented by radial distribution functions between solute-solvent atomic sites. The mechanisms
of the reaction are discussed from the view points of solute electronic and solvation structures.
Received: 26 June 1998/Accepted: 28 August 1998 / Published online: 2 November 1998 相似文献
6.
Ab initio electronic structure calculations using MP2 wavefunctions have been used to investigate a reaction path for the
hydrosilation reaction catalyzed by divalent titanium [modeled by TiH2, TiCl2, and Ti(C5H5)2]. Optimized structures and energies are presented. All model reactions predict a barrierless reaction path compared to a
barrier of 78 kcal/mol for the uncatalyzed reaction.
Received: 11 August 1998 / Accepted: 3 September 1998 / Published online: 23 February 1999 相似文献
7.
The rational function optimization algorithm is one of the widely used methods to search stationary points on surfaces. However,
one of the drawbacks of this method is the step reduction procedure to deal with the overstepping problem. We present and
comment on a method such that the step obtained from the solution of the rational function equations possesses the desired
correct length. The analysis and discussion of the method is mainly centered on the location and optimization of transition
states.
Received: 18 June 1998 / Accepted: 17 September 1998 / Published online: 23 November 1998 相似文献
8.
Complexes of ammonia with propane and cyclopropane: electrostatic guidelines for ab initio treatment
A model based on the molecular electrostatic potential (MESP) is employed for the investigation of structures and energies
of complexes of ammonia with propane and cyclopropane. The electrostatic model geometries are employed as starting points
for an ab initio investigation at the self-consistent field and second-order M?ller-Plesset (MP2) levels. The most stable
structures of C3H6..NH3 and C3H8..NH3 complexes have the interaction energies of 10.07 kJ/mol and 8.15 kJ/mol, respectively, at the MP2/6-31G(d,p) level. The energy rank order of the structures is not altered with the use of the 6-31++G(d,p) basis set, and the basis␣set superposition error has little effect. The interaction energy decomposition analysis shows
that the electrostatic component is dominant over the other ones. MESP topography thus seems to offer valuable hints for predicting
the structures of weakly bonded complexes.
Received: 8 July 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998 相似文献
9.
Xue CB Luo WC Jiang L Xie XY Xiao T Yan L 《Applied biochemistry and biotechnology》2007,143(2):101-114
Phenoloxidase (PO) is a key enzyme in insect development, responsible for catalyzing the hydroxylation of tyrosine into o-diphenols and the oxidation of o-diphenols into o-quinones. In the present study, the kinetic assay in air-saturated solutions and the kinetic behavior of PO from Pieris rapae (Lepidoptera) larvae in the oxidation of l-tyrosine (a monophenol) and l-DOPA (l-3, 4-dihydroxyphenylalanine) (a diphenol) was studied. The inhibitory effects of 3-hydroxy-4-methoxybenzaldehyde thiosemicarbazone
(3-H-4-MBT) on the monophenolase and diphenolase activities of PO were also studied. The results show that 3-H-4-MBT can inhibit
both the monophenolase and diphenolase activities of PO. The lag period of l-tyrosine oxidation catalyzed by the enzyme was obviously lengthened and the steady-state activities of the enzyme sharply
decreased. The inhibitor was found to be noncompetitively reversible with a K
I (K
I = K
IS) of 0.30 μmol/L and an estimated IC50 of 0.14 ± 0.02 μmol/L for monophenolase and 0.26 ± 0.04 μmol/L for diphenolase. In the time course of the oxidation of l-DOPA catalyzed by the enzyme in the presence of different concentrations of 3-H-4-MBT, the rate decreased with increasing
time until a straight line was approached. The microscopic rate constants for the reaction of 3-H-4-MBT with the enzyme were
determined. 相似文献
10.
M. Compiani P. Fariselli P. L. Martelli R. Casadio 《Theoretical chemistry accounts》1999,101(1-3):21-26
Protein secondary structures result both from short-range and long-range interactions. Here neural networks are used to implement
a procedure to detect regions of the protein backbone where local interactions have an overwhelming effect in determining
the formation of stretches in α-helical conformation. Within the framework of a modular view of protein folding we have argued
that these structures correspond to the initiation sites of folding. The hypothesis to be tested in this paper is that sequence
identity beside ensuring similarity of the three-dimensional conformation also entails similar folding mechanisms. In particular,
we compare the location and sequence variability of the initiation sites extracted from a set of proteins homologous to horse
heart cytochrome c. We present evidence that the initiation sites conserve their position in the aligned sequences and exhibit a more reduced
variability in the residue composition than the rest of the protein.
Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 11 November 1998 相似文献
11.
Kouichi Takeshita 《Theoretical chemistry accounts》1999,101(5):343-351
Ab initio calculations have been performed to study the molecular structures and the vibrational levels of the first ionic
states of vinyl fluoride, vinyl chloride, trifluoroethylene, and trichloroethylene. The equilibrium molecular structures and
vibrational modes of these states are presented. The theoretical ionization intensity curves including the vibrational structures
are also presented and compared with the photoelectron spectra.
Received: 11 September 1998 / Accepted: 13 October 1998 / Published online: 1 February 1999 相似文献
12.
A. C. Camproux P. Tuffery L. Buffat C. André J. F. Boisvieux S. Hazout 《Theoretical chemistry accounts》1999,101(1-3):33-40
Hidden Markov models were used to identify recurrent short 3D structural building blocks (SSBBs) describing protein backbones.
Polypeptide chains were broken down into successive short segments defined by their inter-alpha-carbon distances. Fitting
the model to a database of nonredundant proteins identified 12 distinct SSBBs and described the preferred pathways by which
SSBBs were assembled to form the 3D structure of the proteins. Protein backbones were labelled in terms of these SSBBs. The
observed SSBB preferences for fragments located between regular secondary structures suggested that they depended more on
the following regular structure than on the preceding one. Extraction of repeated series of SSBBs between regular secondary
structures showed some structural specificity within different connection types. These results confirm that SSBBs can be used
as building blocks for analyzing protein structures, and can yield new information on the structures of the coils flanking
secondary structures.
Received: 14 May 1998 / Accepted: 4 August 1998 / Published online: 16 November 1998 相似文献
13.
Vishal P. Oza Pritesh P. Parmar Sushil Kumar R. B. Subramanian 《Applied biochemistry and biotechnology》2010,160(6):1833-1840
Withania somnifera L. has been traditionally used as a sedative and hypnotic. The present study was carried out for the purification, characterization,
and in vitro cytotoxicity of l-asparaginase from W. somnifera L. l-Asparaginase was purified from the fruits of W. somnifera L. up to 95% through chromatography. The purified l-asparaginase was characterized by size exclusion chromatography, polyacrylamide gel electrophoresis (PAGE), and 2D PAGE.
The antitumor and growth inhibition effect of the l-asparaginase was assessed using [3-(4, 5-dimethyl-thiazol-2yl)-2, 5-diphenyl-tetrazolium bromide] (MTT) colorimetric dye
reduction method. The purified enzyme is a homodimer, with a molecular mass of 72 ± 0.5 kDa, and the pI value of the enzyme was around 5.1. This is the first report of the plant containing l-asparaginase with antitumor activity. Data obtained from the MTT assay showed a LD50 value of 1.45 ± 0.05 IU/ml. W. somnifera L. proved to be an effective and a novel source of l-asparaginase. Furthermore, it shows a lot of similarity with bacterial l-asparaginases EC-2. 相似文献
14.
The B3LYP density functional method using the extended basis set 6-311++G(3df) was used to calculate the stationary points
along the reaction coordinate 2NO + O2 → 2NO2. The results of the calculation were compared with the reported physicochemical characteristics of this reaction. The origin
of the barrierless activation of the oxygen molecule and driving force for the spontaneous oxidation of NO were examined. 相似文献
15.
V. Moliner J. Andrés M. Oliva V. S. Safont O. Tapia 《Theoretical chemistry accounts》1999,101(1-3):228-233
The present study elucidates structural features related to the molecular mechanism in the carboxylation step of the reaction
catalyzed by Rubisco. Starting from the initial X-ray Protein Data Bank structure of a Rubisco monomer, the reactive subsystem
in vacuo is subjected to quantum chemical semiempirical and ab initio studies, while the effects of the protein environments
are included by means of a hybrid quantum mechanical/molecular mechanical (QM/MM) approach. The QM/MM is used to characterize
the transition structure for carboxylation inside the protein. The calculations were made with the AM1/CHARMM/GRACE scheme.
Comparisons between the in vacuo and in situ transition structures show remarkable invariance with respect to geometric parameters,
index and transition vector amplitudes. The transition state couples the carbon dioxide attack to the C2 center of the substrate
in its dienol form with a simultaneous intramolecular hydrogen transfer from the C2 atom to the hydroxyl group linked to the
C3 center. This study suggests that carboxylation may be simultaneously coupled to the activation of the C3 center in the
enzyme.
Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 10 December 1998 相似文献
16.
Gerald Löffler 《Theoretical chemistry accounts》1999,101(1-3):163-169
We performed a very long molecular dynamics simulation of a peptide in explicit water molecules and ions and averaged the
electrostatic potential caused by peptide, water and ions at eight points in the vicinity of the peptide. These electrostatic
potential values were directly compared to the potential calculated by solving the non-linear Poisson-Boltzmann equation for
the system, which describes the solvent using continuum electrostatics. We analyze the contribution of dielectric constant,
conformational flexibility and solvation effects on the electrostatic potential at these eight points.
Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 23 November 1998 相似文献
17.
Svetlana G. Kirillova Victor M. Andrianov Rostislav G. Zhbankov 《Theoretical chemistry accounts》1999,101(1-3):215-222
Results of a comparative analysis of conformational possibilities of the hexopyranose ring of six epoxysaccharides differing
from each other by the position of the oxirane ring within the limits of the hexapyranose ring and having different orientations
of substituents and different positions of the oxirane ring with respect to the skeleton plane of the molecules are presented.
Numerical simulations based on the Wiberg and Boyd method made it possible to determine all the stationary forms in which
anhydropyranose rings can exist. The effect of various structural factors on the character of conformational transformations,
heights of transition barriers, and the energy of stationary forms has been investigated. Normal vibrational modes of the
stationary forms of the compounds were calculated using molecular mechanics. Based on results of our simulations, we predict
a strong effect of steric factors on the vibrational spectra of sugar epoxides.
Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 17 December 1998 相似文献
18.
Molecular mechanics calculations were performed with the JUMNA program on d(GCGTGOGTGCG) · d(CGCACTCACGC) where “O” is a
modified abasic site: 3-hydroxy-2-(hydroxymethyl)tetrahydrofuran. From energy minimizations, for intrahelical or extrahelical
positions of the unpaired thymine, various structures with different curvatures were obtained. Dynamical properties of this
abasic sequence were also investigated through the controlled studies of DNA bending. Poisson-Boltzmann calculations were
used to mimic the electrostatic effect of solvent on this sequence. The lowest energy structures show an acceptable agreement
with experimental data.
Received: 1 June 1998 / Accepted: 17 September 1998 / Published online: 10 December 1998 相似文献
19.
Coupled advances in empirical force fields and classical molecular dynamics simulation methodologies, combined with the availability
of faster computers, has lead to significant progress towards accurately representing the structure and dynamics of biomolecular
systems, such as proteins, nucleic acids, and lipids in their native environments. Thanks to these advances, simulation results
are moving beyond merely evaluating force fields, displaying expected structural fluctuations, or demonstrating low root-mean-squared
deviations from experimental structures and now provide believable structural insight into a variety of processes such as
the stabilization of A-DNA in mixed water and ethanol solution or reversible β-peptide folding in methanol. The purpose of this overview is to take stock of these recent advances in biomolecular simulation
and point out some common deficiencies exposed in longer simulations. The most significant methodological advances relate
to the development of fast methods to properly treat long-range electrostatic interactions, and in this regard the fast Ewald
methods are becoming the de facto standard.
Received: 9 April 1998 / Accepted: 21 May 1998 / Published online: 13 August 1998 相似文献
20.
Nobuaki Miura Takeshi Noro Fukashi Sasaki You Osanai 《Theoretical chemistry accounts》1998,99(4):248-254
The electron affinities of the Sc and Ti atoms have been obtained by configuration interaction calculations. Energy convergence
with respect to the systematic expansion of both the one-electron basis set and the configuration space was investigated for
valence electrons, and the inclusion of correlation contributions from core electrons and relativistic effects gave the electron
affinities of 0.181 eV and 0.163 eV for Sc and Ti, respectively. These are in excellent agreement with the observed values
of 0.189 ± 0.020 eV and 0.080 eV. The same approach was applied for the first excited states and positive ions of both atoms.
Excellent agreement with the experimental results was also obtained for these states.
Received: 16 February 1998 / Accepted: 2 April 1998 / Published online: 23 June 1998 相似文献