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1.
Fuqiang Ban Kathryn N. Rankin James W. Gauld Russell J. Boyd 《Theoretical chemistry accounts》2002,108(1):1-11
The purpose of this overview is to highlight the broad scope and utility of current applications of density functional theory
(DFT) methods for the study of the properties and reactions of biomolecules. This is illustrated using examples selected from
research carried out within our research group and in collaboration with others. The examples include the hyperfine coupling
constants of amino acid radicals, the use of an amino acid as a chiral catalyst for the formation of carbon–carbon bonds in
the aldol reaction, hydrogen-bond mediated catalysis of an aminolysis reaction, radiation-induced protein–DNA cross-links,
and the mechanism by which an antitumor drug cleaves DNA. We demonstrate that DFT-based methods can be applied successfully
to a broad range of problems that remain beyond the scope of conventional electron-correlation methods. Furthermore, we show
that contemporary computational quantum chemistry complements experiment in the study of biological systems.
Received: 19 December 2001 / Accepted: 8 April 2002 / Published online: 4 July 2002 相似文献
2.
Addition–elimination reactions involving a nucleophile and a remote leaving group [SH
N(AE)tele] are well-known under basic conditions, especially amongst electron-poor six-membered heterocycles, but are less commonly
encountered for five-membered heterocycles and are rare under acidic conditions. Concentrated HCl converts 1-hydroxy-1H-pyrazolo[3,4-c] isoquinoline and 1-hydroxy-1H-pyrazolo[3,4-c]quinoline into 3-chloro-1H-pyrazolo[3,4-c]isoquinoline and 3-chloro-1H-pyrazolo[3,4-c]quinoline, respectively. However, apparently neither the isomeric 1-hydroxy-1H-pyrazolo[4,3-c](iso)-quinolines nor the parent 1-hydroxypyrazole undergo this reaction. Additionally, all these systems are refractory under
basic conditions. We present a plausible mechanism for the reaction, involving the 3-addition of Cl- to the diprotonated heterocycle, followed by the elimination of water. Calculations of the initial transition states and
intermediates, using optimisation at B3LYP/6-311+G(d,p), including thermochemistry [HF/6-31+G(d)], and single-point Poisson–Boltzmann
self-consistent reaction field determination of the free energy of solvation (Jaguar Poisson–Boltzmann self-consistent reaction
field), support this mechanism and reproduce the observed order of reactivity, the addition step being 2–4 kcal less favourable
for the isomeric 1-hydroxy-1H-pyrazolo[4,3-c](iso)quinolines and provide a rationalisation for the role of strong acid.
Received: 27 June 2002 / Accepted: 6 September 2002 /
Published online: 14 February 2003 相似文献
3.
4.
5.
The structures and the conformational energies of nonprotonated, monoprotonated and diprotonated 1,2-ethanediamine have been
investigated through density functional theory. The relative performance of local and gradient-corrected functionals is discussed.
The existence of hydrogen-bond formation has been determined with electron localisation function calculations. Proton affinities
for nonprotonated and monoprotonated 1,2-ethanediamine have been calculated and are in agreement with experimental data. The
influence of solvation has been accounted for through the self-consistent isodensity polarisable continuum model. The results
for the nonprotonated conformers show that solvation stabilises those conformers which have the lone pair in an antiperiplanar
conformation. Solvation of the monoprotonated conformer stabilises significantly the “anti” conformation, which is unstable
in the gas phase. For the di-protonated species, solvation stabilises slightly the gauche conformer, which is unstable in
the gas phase.
Received: 28 September 1999 / Accepted: 2 May 2000 / Published online: 27 September 2000 相似文献
6.
Rajeev Prabhakar Margareta R. A. Blomberg Per E. M. Siegbahn 《Theoretical chemistry accounts》2000,104(6):461-470
A concerted mechanism for proton exchange between water and the amino acid side chains of cysteine, serine, arginine and
glutamic acid has been investigated with hybrid density functional theory. The models used include, besides the amino acid
side chain, a number of water molecules ranging from one to five in some cases. The modeling of the amino acids without their
backbones is shown to be an excellent approximation. Long-range polarization effects were incorporated through a dielectric
cavity method allowing a better comparison to existing measurements for free amino acids in water. The barriers converge rather
fast with the number of water molecules for all the present amino acids and the converged values are in reasonable agreement
with experiments with discrepancies in the range 2–6 kcal/mol. The dielectric effects were found to be small for all systems
except cysteine, where there is a lowering of the barrier by 3–5 kcal/mol. The transition states for these concerted pathways
form rings in which the separated charges can be stabilized.
Received: 25 October 1999 / Accepted: 5 April 2000 / Published online: 21 June 2000 相似文献
7.
The electron affinities of Ti, V, Cr, Fe, Co, Ni, and Cu are computed using the density function theory and CCSD(T) approaches.
Overall the CCSD(T) approach yields the best results. For this property, the B3LYP, BLYP, and BP86 functionals perform better
than the BPW91, PBEPBE, and PBE1PBE ones. The accuracy of all the methods is higher if the number of 3delectrons is the same in the neutral atom and the anion. This is especially true for the density functional theory methods.
Received: 23 January 2002 / Accepted: 1 April 2002 / Published online: 24 June 2002 相似文献
8.
Jing-yao Liu Ze-sheng Li Zhen-wen Dai Xu-ri Huang Chia-chung Sun 《Theoretical chemistry accounts》2002,108(3):179-186
The hydrogen-abstraction reaction C2H5F+O → C2H4F+OH has been studied by a dual-level direct dynamics method. For the reaction, three reaction channels, one for α-abstraction
and two for β-abstraction, have been identified. The potential-energy surface information is obtained at the MP2(full)/6-311G(d,p)
and PMP2(full)/6-311G(3df,3pd) (single-point) levels. By canonical variational transition-state theory, rate constants for
each reaction channel are calculated with a small-curvature tunneling correction. The total rate constant is calculated from
the sum of the individual rate constants and the temperature dependence of the branching ratios is obtained over a wide range
of temperatures from 300 to 5,000 K. The agreement of the rate constants with experiment is good in the experimental temperature
range from 1,000 to 1,250 K. The calculated results indicate that at low temperatures α-abstraction is most likely to be the
major reaction channel, while β-abstraction channels will significantly contribute to the whole reaction rate as the temperature
increases.
Received: 23 January 2002 / Accepted: 23 June 2002 / Published online: 20 September 2002 相似文献
9.
Formate, HCOO−, is a small ion that can be used as a convenient model to represent general carboxylic acids as well as the terminal side
chains of glutamic and aspartic amino acids in biological systems. Several ab initio techniques (Hartree–Fock and density
functional theory methods) were used to study the formate anion in aqueous solution, where the solvent was treated as an electrostatic
influence by means of a self-consistent-reaction-field (SCRF) method. The comparison of calculated frequencies with Raman
experimental data constitutes a good test for the solvation model employed in this work. The results showed that the application
of a SCRF method not only produced smaller errors but also improved the linear correlation between predicted and experimental
values. This latter characteristic enables a more efficient application of a linear scaling factor, λ, which corrects the
calculated frequencies. In fact, the application of λ to the values calculated for the continuum, when compared to those obtained
for a vacuum, resulted in smaller root-mean-square errors of the deviations from the experimental data.
Received: 15 May 2000 / Accepted: 19 June 2000 / Published online: 11 September 2000 相似文献
10.
Jordi Poater Miquel Solà Miquel Duran Xavier Fradera 《Theoretical chemistry accounts》2002,107(6):362-371
Localization, λ(A), and delocalization indices, δ(A,B), as defined in the atoms in molecules theory, are a convenient tool for the analysis of molecular electronic structure from
an electron-pair perspective. These indices can be calculated at any level of theory, provided that first- and second-order
electron densities are available. In particular, calculations at the Hartree–Fock (HF) and configuration interaction (CI)
levels have been previously reported for many molecules. However, λ(A) and δ(A,B) cannot be calculated exactly in the framework of Kohn–Sham (KS) density functional theory (DFT), where the electron-pair
density is not defined. As a practical workaround, one can derive a HF-like electron-pair density from the KS orbitals and
calculate approximate localization and delocalization indices at the DFT level. Recently, several calculations using this
approach have been reported. Here we present HF, CI and approximate DFT calculations of λ(A) and δ(A,B) values for a number of molecules. Furthermore, we also perform approximate CI calculations using the HF formalism to obtain
the electron-pair density. In general, the approximate DFT and CI results are closer to the HF results than to the CI ones.
Indeed, the approximate calculations take into account Coulomb electron correlation effects on the first-order electron density
but not on the electron-pair density. In summary, approximate DFT and CI localization and delocalization indices are easy
to calculate and can be useful in the analysis of molecular electronic structure; however, one should take into account that
this approximation increases systematically the delocalization between covalently bonded atoms, with respect to the exact
CI results.
Received: 13 February 2002 / Accepted: 24 April 2002 / Published online: 18 June 2002 相似文献
11.
This work deals with theoretical investigations on the oxygen–transition metal bond in systems containing linear chains of
Ti–O units. From an experimental point of view, in the recent past a number of systems containing linearly arranged Ti–O units
were synthesized, in which the Ti atom is complexed with Schiff bases such as acacen and salen. The theoretical study presented
here has been carried out applying the density functional theory to model compounds of these systems, in order to shed light
on the interactions between the transition metal and oxygen. Calculations have been performed on Ti–O oligomers (dimers, trimers
and tetramers) by means of density functional theory at the gradient-corrected level of theory, optimizing the molecular geometries.
Calculations have also been performed on linear polymers of the same systems, applying periodic boundary conditions, in order
to compare the results with those of oligomeric analogues.
Received: 12 January 2002 / Accepted: 16 April 2002 / Published online: 5 July 2002 相似文献
12.
N. Sundaraganesan H. Umamaheswari B. Dominic Joshua C. Meganathan M. Ramalingam 《Journal of Molecular Structure》2008,850(1-3):84-93
The molecular geometry and vibrational frequencies of indole and 5-aminoindole in the ground state have been calculated by using the Hartree–Fock and density functional method with 6-311++G(d,p) basis set. The optimized geometrical parameters obtained by DFT calculations are in good agreement with the experimental values. Comparison of the observed fundamental vibrational frequencies of indole and 5-aminoindole with the calculated results by density functional and Hartree–Fock methods indicates that B3LYP is superior to the scaled Hartree–Fock approach for molecular vibrational problems. The theoretical spectrograms for FT-IR spectrum of 5-aminoindole have been constructed. 相似文献
13.
Yusuf Erdogdu M. Tahir Güllüolu 《Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy》2009,74(1):162-167
The experimental and theoretical vibrational spectra of 2 and 3-methylpiperidine (abbreviated as 2-MP and 3-MP) were studied. The FT-Infrared spectra of 2-MP and 3-MP molecules were recorded in the liquid phase. The structural and spectroscopic analysis of the title molecules were made by using density functional harmonic calculations. For the title molecules, only one form was found most stable structure by using B3LYP level with the 6-311G (d,p) basis set. Selected experimental bands were assigned and characterized based on the scaled theoretical wave numbers by their total energy distribution (TED). 相似文献
14.
The self-consistent reaction field (SCRF) method based on Onsager's reaction field theory is applied to investigate the effect of polar media on molecular structures of complexes of trimethylamime (TMA) with SOx (x=2,3). The calculated SCRF N–S bond lengths at the MPW1PW91/6-311+G(3df) level are in satisfactory agreement with the experimental N–S bond lengths for the TMA–SOx upon crystallization. The results are enough to demonstrate the usefulness of the reaction field theory in providing qualitative understanding of the medium effect on the partially bonded system such as TMA–SOx. 相似文献
15.
Ab initio calculations with inclusion of correlation effects at the MP2/6-31G* level have been used to predict the interaction
energy of stacked cytosine dimer (C/C) as a function of twisting and sliding in the gas phase. Systematic calculations have
also been carried out on the solvation free energies of various rotated and translated C/C dimers using a polarized continuum
model approach at the HF/6-31G* level with a view to probe the role of various degrees of freedom on the free energy of solvation
of the C/C dimer. The interaction energy of the C/C dimer decreases upon changing from a parallel to an antiparallel conformation
in the gas phase. The 180°-rotated conformation has been found to be the most stable arrangement when compared to other rotated
positions. The rotated and translated dimers exhibit lower solvation free energy than the parallel conformation. The decrease
in the dipole moment upon rotation from the parallel to the antiparallel conformation indicates the cancellation of charge
distribution upon rotation in the z direction of one cytosine base with respect to the other. The calculation reveals that the present approach could not yield
association energy, ΔΔG
Asso, in a solvent medium. This may be due to the fact that in the case of floppy molecules the contribution from translational,
rotational and vibrational free energies plays a significant role in the calculation of ΔΔG
Asso.
Received: 13 December 2001 / Accepted: 25 March 2002 / Published online: 13 June 2002 相似文献
16.
Branko S. Jursic 《Theoretical chemistry accounts》1998,100(5-6):329-332
Selective bond dissociation energies for CH3SH and CH3CH2SH radical cations were evaluated with G1, G2, G2MP2, B3LYP, BLYP, and SVWN computational methods. It was determined that
both G2 and CBSQ evaluate very accurate bond dissociation energies for thiol radical cations, while gradient-corrected BLYP
computes the best energies of three employed DFT methods. For the CH3CH2SH radical cation, new, higher than previously estimated selective bond dissociation energies were suggested.
Received: 10 September 1997 / Accepted: 9 September 1998 / Published online: 11 November 1998 相似文献
17.
18.
The physical properties of chemicals are strongly influenced by their protonation state, affecting, for example, solubility
or hydrogen-bonding characteristics. The ability to accurately calculate protonation states in the form of pK
as is, therefore, desirable. Calculations of pK
a changes in a series of substituted pyridines are presented. Computations were performed using both ab initio and semiempirical
approaches, including free energies of solvation via reaction-field models. The selected methods are readily accessible with
respect to both software and computational feasibility. Comparison of calculated and experimental pK
as shows the experimental trends to be reasonably reproduced by the computations with root-mean-square differences ranging
from 1.22 to 4.14 pK
a units. Of the theoretical methods applied the best agreement occurred using the second-order M?ller–Plesset/6-31G(d)/isodensity
surface polarized continuum solvation model, while the more computationally accessible Austin model 1/Solvent model 2 (SM2)
approach yielded results similar to the ab initio methods. Analysis of component contributions to the calculated pK
as indicates the largest source of error to be associated with the free energies of solvation of the protonated species followed
by the gas-phase protonation energies; while the latter may be improved via the use of higher levels of theory, enhancements
in the former require improvements in the solvation models. The inclusion of alternate minimum in the computation of pK
as is also indicated to contribute to differences between experimental and calculated pK
a values.
Received: 27 April 1999 / Accepted: 27 July 1999 / Published online: 2 November 1999 相似文献
19.
José A. Rodriguez 《Theoretical chemistry accounts》2002,107(3):117-129
The surface chemistry of oxides is relevant for many technological applications: catalysis, photoelectrolysis, electronic-device
fabrication, prevention of corrosion, sensor development, etc. This article reviews recent theoretical works that deal with
the surface chemistry of oxides. The account begins with a discussion of results for the adsorption of CO and NO on oxides,
systems which have been extensively studied in the literature and constitute an ideal benchmark for testing the quality of
different levels of theory. Then, systematic studies concerned with the behavior of adsorbied alkali metals and sulfur-containing
molecules are presented. Finally, a correlation between the electronic and chemical properties of mixed-metal oxides is analyzed
and basic principles for designing chemically active oxides are introduced. Advances in theoretical methods and computer capabilities
have made possible a fundamental understanding of many phenomena associated with the chemistry of molecules on oxide surfaces.
Still many problems in this area remain as a challenge, and the approximate nature of most theoretical methods makes necessary
a close coupling between theory and experiment. Following this multidisciplinary approach, the importance of band-orbital
interactions for the reactivity of oxide surfaces has become clear. Simple models based on band-orbital mixing can explain
trends found for the interaction of many adsorbates with oxide surfaces. These simple models provide a conceptual framework
for modifying or controlling the chemical activity of pure oxides and for engineering mixed-metal oxides. In this respect,
theoretical calculations can be very useful for predicting the best ways for enhancing the reactivity of oxide systems and
reducing the waste of time, energy and materials characteristic of an empirical design.
Received: 21 June 2001 / Accepted: 8 October 2001 / Published online: 1 February 2002 相似文献