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1.
J. Andrés M. Oliva V. S. Safont V. Moliner O. Tapia 《Theoretical chemistry accounts》1999,101(1-3):234-240
The carboxylation and oxygenation processes of a model substrate, 3,4-dihydroxy-2-pentanone, have been theoreticaly characterized
as a set of steps, mimicking the corresponding reactions of D-ribulose-1,5-bisphosphate catalyzed by rubisco. A theoretical characterization is carried out of transition-state structures
and possible molecular intermediates represented as saddle points of index 1 and minimum energy structures, respectively.
The quantum chemical characterization, at the HF/3-21G calculation level, of these stationary points is used to rationalize
and to discuss both catalyzed sequences. The reported set of these stationary points maps out most experimental aspects of
the reaction pathways for the real system.
Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 10 December 1998 相似文献
2.
Polycyclic aromatic hydrocarbons (PAHs) are widely distributed in the environment and are often implicated as potential carcinogens.
It is generally believed that the carcinogenic potential of polycyclic aromatic hydrocarbons is linked to the formation of
ultimate carcinogens generated by metabolic biotransformations. In this paper we propose a methodology that consists of using
both quantum chemical properties and structural features of the reaction sites to predict PAH metabolism. Two essential questions
have been answered: at which sites will the reaction take place and does the transformation consist of epoxidation or hydroxylation?
This methodology has been successfully implemented into an expert system, META, for the evaluation of metabolic transformations
of new chemicals.
Received: 3 April 1998 / Accepted: 6 July 1998 / Published online: 7 October 1998 相似文献
3.
Xavier Prat-Resina Mireia Garcia-Viloca Gerald Monard Angels González-Lafont José M. Lluch Josep Maria Bofill Josep Maria Anglada 《Theoretical chemistry accounts》2002,107(3):147-153
We propose a methodology to locate stationary points on a quantum mechanical/molecular mechanical potential-energy surface.
This algorithm is based on a suitable approximation of an initial full Hessian matrix, either a modified Broyden–Fletcher–Goldfarg–Shanno
or a Powell update formula for the location of, respectively, a minimum or a transition state, and the so-called rational
function optimization. The latter avoids the Hessian matrix inversion required by a quasi-Newton–Raphson method. Some examples
are presented and analyzed.
Received: 16 July 2001 / Accepted: 9 October 2001 / Published online: 9 January 2002 相似文献
4.
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
5.
The dimerization reactions of ketene imine and bis(trifluoromethyl)ketene imine were studied theoretically. All the dimerization
processes take place in a concerted but asynchronous manner, each proceeding through a four-membered ring transition state.
For the ketene imine dimerization reactions, three different processes have almost equal activation barriers, while for the
three bis(trifluoromethyl)ketene imine dimerization processes the reaction giving symmetrical a four-membered heterocyclic
product has the lowest activation barrier.
Received: 15 July 1998 / Accepted 3 September 1998 / Published online: 17 December 1998 相似文献
6.
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
7.
Carlos Alemán 《Theoretical chemistry accounts》1998,99(5):312-319
A quantum mechanical study of the conformational preferences of Hoechst 33258, a synthetic minor groove-binding drug, has
been performed in both gas-phase and aqueous solution. Gas-phase calculations were performed at the HF/6-31G(d) and MP2/6-31G(d) levels of theory, whereas calculations in the aqueous solution phase were performed using the PCM model with the 6-31G(d) basis set. The molecule was divided into three fragments, which were submitted to a systematic and detailed conformational
study. The results clearly indicate that Hoechst 33258 does not adopt a planar conformation in either the gas-phase or aqueous
solution. Thus, a folded conformation is not induced by binding of the molecule to DNA, but is an intrinsic property of the
compound.
Received: 3 March 1998 / Accepted: 29 May 1998 / Published online 19 August 1998 相似文献
8.
Stavros C. Farantos Christian Beck Reinhard Schinke 《Theoretical chemistry accounts》1998,100(1-4):147-153
We investigate, by means of classical and quantum mechanics, how isotopic substitution (H/D) affects the vibrational dynamics
of HCP. The analysis of periodic orbits, including the location of the principal families as well as saddle node bifurcations,
reveals a totally different picture for the phase-space resonance structure for HCP and DCP. While HCP is characterized by
a 1:2 resonance between the CP stretch and the bending mode, DCP shows a 1:2 resonance between the two stretching degrees
of freedom. Saddle node bifurcations, which are associated with large-amplitude motion of H/D moving from the C- to the P-end,
appear at considerably higher energies in DCP than in HCP. These results are in accord with exact quantum mechanical calculations
of the vibrational levels.
Received: 24 June 1998 / Accepted: 10 August 1998 / Published online: 9 October 1998 相似文献
9.
The conductor-like screening model (COSMO) of solvation has been implemented in the Amsterdam density functional program
with maximum flexibility in mind. Four cavity definitions have been incorporated. Several iterative schemes have been tested
for solving the COSMO equations. The biconjugate gradient method proves to be both robust and memory-conserving. The interaction
between the surface charges and the electron density may be calculated by integrating over either the fitted or exact density,
or by calculating the molecular potential. A disk-smearing algorithm is applied in the former case to avoid singularities.
Several self-consistent field/COSMO coupling schemes were examined in an attempt to reduce computational effort. A gradient-preserving
algorithm for removing outlying charge has been implemented. Preliminary optimized radii are given. Applications to the benzene
oxide-oxepin valence tautomerization and to glycine conformation are presented.
Received: 13 November 1998 / Accepted: 16 December 1998 / Published online: 16 March 1999 相似文献
10.
Patricia Amara Martin J. Field Cristobal Alhambra Jiali Gao 《Theoretical chemistry accounts》2000,104(5):336-343
Hybrid quantum mechanical (QM) and molecular mechanical (MM) potentials are becoming increasingly important for studying
condensed-phase systems but one of the outstanding problems in the field has been how to treat covalent bonds between atoms
of the QM and MM regions. Recently, we presented a generalized hybrid orbital (GHO) method that was designed to tackle this
problem for hybrid potentials using semiempirical QM methods [Gao et al. (1998) J Phys Chem A 102: 4714–4721]. We tested the method on some small molecules and showed that it performed well when compared to the purely
QM or MM potentials. In this article, we describe the formalism for the determination of the GHO energy derivatives and then
present the results of more tests aimed at validating the model. These tests, involving the calculation of the proton affinities
of some model compounds and a molecular dynamics simulation of a protein, indicate that the GHO method will prove useful for
the application of hybrid potentials to solution-phase macromolecular systems.
Received: 4 October 1999 / Accepted: 18 December 1999 / Published online: 5 June 2000 相似文献
11.
Jianwei Che Tahir Çağın William A. Goddard III 《Theoretical chemistry accounts》1999,102(1-6):346-354
We present a general approach for describing chemical processes (bond breaking and bond formation) in materials using force
fields (FF) that properly describe multiple bonds at small distances while describing nonbond (Coulomb and van der Waals)
interactions at long distances. This approach is referred to as the generalized extended empirical bond-order dependent FF.
In this paper we use the Brenner empirical bond-order dependent FF for the short-range interactions and report applications
on the energetics and structures of graphite crystal, dynamics of molecular crystals, and distortions of bucky tubes.
Received: 7 August 1998 / Accepted: 26 October 1998 / Published online: 16 March 1999 相似文献
12.
Adam Liwo Jarosław Pillardy Rajmund Kaźmierkiewicz Ryszard J. Wawak Małgorzata Groth Cezary Czaplewski Stanisaw Ołdziej Harold A. Scheraga 《Theoretical chemistry accounts》1999,101(1-3):16-20
A united-residue model of polypeptide chains developed in our laboratories with united side-chains and united peptide groups
as interaction sites is presented. The model is designed to work in continuous space; hence efficient global-optimization
methods can be applied. In this work, we adopted the distance-scaling method that is based on continuous deformation of the original
rugged energy hypersurface to obtain a smoothed surface. The method has been applied successfully to predict the structures
of simple motifs, such as the three-helix bundle structure of the 10-58 fragment of staphylococcal protein A in de novo folding
simulations and more complicated motifs in inverse-folding simulations.
Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998 相似文献
13.
Bernd Hartke 《Theoretical chemistry accounts》1998,99(4):241-247
By an application to small silicon clusters Si
N
(with N = 4,5,7,10) it is shown that truly global geometry optimization on an ab initio or density functional theory level can be achieved, at a computational cost of approximately
1–5 traditional local optimization runs (depending on cluster size). This extends global optimization from the limited area
of empirical potentials into the realm of ab initio quantum chemistry.
Received: 24 February 1998 / Accepted: 6 March 1998 / Published online: 17 June 1998 相似文献
14.
A large-scale one-centre expansion with a radial B-spline basis set is implemented for bound and continuum states. A Kohn-Sham
hamiltonian is employed with Hartree and exchange-correlation potentials calculated from the SCF electron density taken from
a previous LCAO calculation. An inverse iteration method is used to obtain the continuum wavefunction, from which the cross
section and asymmetry parameter are calculated. The convergence with respect to angular momentum and cut-off radius is analysed
for N2. The relevance of multipolar contributions even at large distances is shown and suggestions for further improvements are
given. In order to show that the present method is suitable to treat systems of moderate size, the (CH3)3N molecule has also been calculated and the results are compared with experiment.
Received: 19 May 1998 / Accepted: 20 August 1998 / Published online: 7 December 1998 相似文献
15.
J.-M. Moulis 《Theoretical chemistry accounts》1999,101(1-3):223-227
Rubredoxins are small electron transfer proteins containing one iron atom at their active site. The rubredoxin from the anaerobic
bacterium Clostridium pasteurianum has been subjected to molecular dynamics studies starting from the minimized solvated structure. The results of the simulations
have been compared with identical ones carried out with selected mutated forms of the protein obtained by molecular modeling.
Surface residues, which are highly conserved among rubredoxins and close to the cysteine ligands, can be replaced by glutamates,
i.e. long chain carboxylates. The main structural consequence is a shift of the protein backbone bearing conserved aromatic
residues. Reciprocally, substitution of the aromatic residue closest to the iron atom shifts the cysteine-containing peptide
fragments. These observations have been related to the changes in electron transfer and redox properties previously measured
for this set of rubredoxin molecular variants.
Received: 16 May 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998 相似文献
16.
High-resolution energy spectra of electrons released in Penning ionization collisions of metastable rare gas atoms Rg*(ns) (Rg = He, Ne, Ar, Kr, Xe) with several open-shell and closed-shell atoms are analyzed to determine the well depth of the
potential energy curve which describes the respective autoionizing collision complex. We thereby elucidate trends in the chemical
interaction of Rg* with closed-shell target atoms A(ns
2) and establish a basis for detailed comparison with the respective interactions involving open-shell, ground state alkali
atoms A(ns). From electron energy spectra due to␣associative ionization (RgH+ formation) in Rg* + H(1s) collisions, we determine binding energies for the RgH+(1Σ) ground state potential (Rg = Ne, Ar, Kr, Xe) with uncertainties around 0.03 eV.
Received: 30 June 1998 / Accepted: 5 August 1998 / Published online: 28 October 1998 相似文献
17.
High-level ab initio electronic structure theories have been applied to investigate the detailed reaction mechanism of the
spin-forbidden reaction CH(2∏) + N2 → HCN + N(4S). The G2M(RCC) calculations provide accurate energies for the intermediates and transition states involved in the reaction,
whereas the B3LYP/6-311G(d,p) method overestimates the stability of some intermediates by as much as about 10 kcal/mol. A few new structures have been
found for both the doublet and quartet electronic states, which are mainly involved in the dative pathways. However, due to
the higher energies of these structures, the dominant mechanism remains the one involving the C
2 intersystem-crossing step. The C
2 minima on the seam of crossing (MSX) structures and the spin-orbit coupling between the doublet and quartet electronic states
are rather close to those found in previous studies. Vibrational frequencies orthogonal to the normal of the seam which have
been applied in a separate publication to calculate the rate of the CH(2∏) + N2 → HCN + N(4S) reaction with a newly proposed nonadiabatic transition-state theory for spin-forbidden reactions have been calculated at
the MSX from first principles.
Received: 23 June 1998 / Accepted: 21 September 1998 / Published online: 8 February 1999 相似文献
18.
Jun-ichi Aihara 《Theoretical chemistry accounts》1999,102(1-6):134-138
A very simple but general index of kinetic stability, T, is proposed for π-electron systems, which is defined as a highest occupied molecular orbital (HOMO)- lowest unoccupied molecular orbital (LUMO)
energy separation multiplied by the number of conjugated atoms. This new index can be justified by relating it to the approximate
form of the superdelocalizability, an index of chemical reactivity defined by Fukui et al. It is best suited for predicting
the kinetic stability of fullerenes. All isolable fullerene isomers have T values larger than 13.
Received: 24 June 1998 / Accepted: 3 September 1998 / Published online: 17 December 1998 相似文献
19.
Visual valence bond rules for chemical reactions 总被引:1,自引:0,他引:1
A symmetry-adaptation rule of the valence bond structure for concerted reactions was developed within the bonded tableau
valence bond formalism. According to a symmetry analysis of the valence bond structure segments accounting for the reaction,
one can predict whether a chemical process is favored or unfavored. This method is based on conceptual resonance theory and
the visual valence bond approach, without carrying out any explicitly theoretical calculations to know orbital details. Furthermore,
by imposing a phase factor on each bonding pair, namely, the phase alternation postulate, the mechanisms of the concerted
reactions can be easily outlined. These rules have been applied to organic and inorganic reactions including the participation
of biradicals and species with multi-reference character.
Received: 7 September 1998 / Accepted: 9 November 1998 / Published online: 1 February 1999 相似文献
20.
Alain Cartier David Brown Bernard Maigret Sandrine Boschi-Muller Sophie Rahuel-Clermont Guy Branlant 《Theoretical chemistry accounts》1999,101(1-3):241-245
In the framework of a theoretical approach to the relationship between structure and reactivity of the catalytic centers
of enzymes, glyceraldehyde-3 phosphate dehydrogenase (GAPDH) has been chosen as a model enzyme. In GAPDH, the proximity of
His176 increases the reactivity of Cys149 at neutral pH; however, its presence alone is not sufficient to explain the reactivity of the catalytic Cys. In order to
determine which other interactions play an important role, a study of the geometric and electronic structure of the catalytic
site has been made using a hybrid quantum mechanics/molecular mechanics local self-consistent field method. This allows the
computation of the electronic properties of amino acid residues in subsystems influenced by other parts of the macromolecule.
The quantum subsystem was centered on the Cys149 residue of GAPDH. The structures of GAPDH taken from the crystallographic database did not include hydrogen atoms and these
had to be added taking into account the fact that, in the active site, His176 has three tautomeric forms: δ-His protonated, ε-His protonated and His+. The results presented here suggest that the most stable His…Cys system in GAPDH is a strongly hydrogen-bonded Cys149
−/His176
+ ion pair.
Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 23 November 1998 相似文献