共查询到20条相似文献,搜索用时 46 毫秒
1.
Pere M. Deyà Antonio Frontera Guillem A. Suñer David Quiñonero Carolina Garau Antoni Costa Pau Ballester 《Theoretical chemistry accounts》2002,108(3):157-167
The structural and energetic changes associated with C–N bond rotation in a squaric acid derivative as well as in formamide,
3-aminoacrolein and vinylamine have been studied theoretically using ab initio molecular orbital methods. Geometry optimizations
at the MP2(full)/6-31+G* level confirmed an increase in the C–N bond length and a smaller decrease in the C=O length on going
from the equilibrium geometry to the twisted transition state. Other geometrical changes are also discussed. Energies calculated
at the QCISD(T)/6-311+G** level, including zero-point-energy correction, show barrier heights decreasing in the order formamide,
squaric acid derivative, 3-aminoacrolein and vinylamine. The origin of the barriers were examined using the atoms-in-molecules
approach of Bader and the natural bond orbital population analysis. The calculations agree with Pauling's resonance model,
and the main contributing factor of the barrier is assigned to the loss of conjugation on rotating the C–N bond. Finally,
molecular interaction potential calculations were used to study the changes in the nucleophilicity of N and O (carbonyl) atoms
upon C–N rotation, and to obtain a picture of the abilities of the molecules to act in nonbonded interactions, in particular
hydrogen bonds. The molecular interaction potential results confirm the suitability of squaramide units for acting as binding
units in host–guest chemistry.
Received: 13 March 2002 / Accepted: 23 June 2002 / Published online: 21 August 2002 相似文献
2.
R. Q. Topper K. Chung C. M. Boelke D. Louie J. S. Kang R. Hannan T. Kiang L. H. Chan 《Theoretical chemistry accounts》2003,109(4):233-238
2-(Acetylamino)fluorene (AAF), a potent mutagen and a prototypical example of the mutagenic aromatic amines, forms covalent
adducts to DNA after metabolic activation in the liver. A benchmark study of AAF is presented using a number of the most widely
used molecular mechanics and semiempirical computational methods and models. The results are compared to higher-level quantum
calculations and to experimentally obtained crystal structures. Hydrogen bonding between AAF molecules in the crystal phase
complicates the direct comparison of gas-phase theoretical calculations with experiment, so Hartree–Fock (HF) and Becke–Perdew
(BP) density functional theory (DFT) calculations are used as benchmarks for the semiempirical and molecular mechanics results.
Systematic conformer searches and dihedral energy landscapes were carried out for AAF using the SYBYL and MMFF94 molecular
mechanics force fields; the AM1, PM3 and MNDO semiempirical quantum mechanics methods; HF using the 3-21G*and 6-31G* basis
sets; and DFT using the nonlocal BP functional and double numerical polarization basis sets. MMFF94, AM1, HF and DFT calculations
all predict the same planar structures, whereas SYBYL, MNDO and PM3 all predict various nonplanar geometries. The AM1 energy
landscape is in substantial agreement with HF and DFT predictions; MMFF94 is qualitatively similar to HF and DFT; and the
MNDO, PM3 and SYBYL results are qualitatively different from the HF and DFT results and from each other. These results are
attributed to deficiencies in MNDO, PM3 and SYBYL. The MNDO, PM3 and SYBYL models may be unreliable for compounds in which
an amide group is immediately adjacent to an aromatic ring.
Received: 26 May 2002 / Accepted: 12 December 2002 /
Published online: 14 February 2003 相似文献
3.
E. J. Baerends 《Theoretical chemistry accounts》2000,103(3-4):265-269
The paper by Kohn and Sham (KS) is important for at least two reasons. First, it is the basis for practical methods for density
functional calculations. Second, it has endowed chemistry and physics with an independent particle model with very appealing
features. As expressed in the title of the KS paper, correlation effects are included at the level of one-electron equations,
the practical advantages of which have often been stressed. An implication that has been less widely recognized is that the
KS molecular orbital model is physically well-founded and has certain advantages over the Hartree–Fock model. It provides
an excellent basis for molecular orbital theoretical interpretation and prediction in chemistry.
Received: 16 February 1999 / Accepted: 22 June 1999 / Published online: 9 September 1999 相似文献
4.
Bernhard Metz Marcus Schweizer Hermann Stoll Michael Dolg Wenjian Liu 《Theoretical chemistry accounts》2000,104(1):22-28
A relativistic pseudopotential of the energy-consistent variety simulating the Tl21+ (1s– 4f) core has been generated by adjustment to multiconfiguration Dirac–Hartree–Fock data based on the Dirac–Coulomb–Breit Hamiltonian.
Valence ab initio calculations using this pseudopotential have been performed for atomic excitation energies and for spectroscopic
constants of the X0+ and A0+ states of TlX (X = F, Cl, Br, I). Comparison is made to experiment and to four-component density functional results.
Received: 22 June 1999 / Accepted: 5 August 1999 / Published online: 15 December 1999 相似文献
5.
Abhik Ghosh 《Theoretical chemistry accounts》2000,104(2):157-159
The concept of local symmetry has been applied to faces of planar sites such as carbon–carbon double bonds and aromatic rings
with the principal results being as follows. The two faces of a planar site must have the same local symmetry group. This
local symmetry group is limited to the polar point groups. For cyclic compounds, directed cycles must have chirotopic faces
although the reverse is not necessarily true: chirotopic faces are possible for both directed and undirected cycles. A number
of examples are provided to illustrate these results.
Received: 30 June 1999 / Accepted: 4 October 1999 / Published online: 19 April 2000 相似文献
6.
Hélio F. Dos Santos Mauro V. De Almeida Wagner B. De Almeida 《Theoretical chemistry accounts》2002,107(4):229-240
The reaction between a mesylated compound and sodium azide was previously studied experimentally at a temperature of 140
°C using dimethylformamide as a solvent. The product was assigned on the basis of the analysis of the NMR spectra. In this
work semiempirical (AM1 and PM3), ab initio (Hartree–Fock and MP2) and density functional theory (BLYP functional) quantum
mechanical calculations, using continuum models for describing the solvent effect, were carried out for this process to better
understand the reaction mechanism. Three distinct mechanisms involving a carbocation and epoxide intermediates, and a transition-state
structure for direct attack of the N3
− species to the reactant were investigated. The theoretically calculated preferred reaction pathway passing through an epoxide
intermediate agrees nicely with the experimental proposal, providing a good example of where theoretical calculations can
be of great help to definitively elucidate the reaction mechanism.
Received: 10 July 2001 / Accepted: 20 December 2001 / Published online: 8 April 2002 相似文献
7.
The 5′-GCGTGGGCGT-3′ (T4) oligomer found in the zinc finger 268–DNA complex was mutated into the sequence 5′-GCGGGGGCGT-3′
(G4). A 3D model was constructed from the T4 sequence using an X-ray structure as a template. Molecular dynamics simulations
were used to test the thermal stability of the model. A 500-ps trajectory was obtained for the fully charged complex in water
using GROMOS87. The complex and the G4 sequence are found to have dynamically stationary behavior. Comparisons made with a
previous T4 sequence molecular dynamics simulation show both systems have similar thermal stability. The structure of DNA
appears to be maintained by its global interactions with the protein although the mutated site does not contribute with its
full potential for binding. The protein structure shows some small differences compared to the T4 simulation. The simulation
provided evidence for the role of a chloride ion interacting with the protein and helping in the recognition process.
Received: 21 June 1999 / Accepted: 19 October 1999 / Published online: 14 March 2000 相似文献
8.
A large succinic acid (HOOC(CH2)2COOH) matrix containing 7 × 7 × 7 unit cells with guest oligonucleotide AGCAGCT was modeled with molecular dynamics simulation
for infrared matrix-assisted laser desorption ionization. We simulated the laser heating of the succinic acid (this data is
still missing from the literature) with λ=2.94 μm infrared laser pulses and compared it to ultraviolet excitation. We did
this in order to elucidate the cluster formation of succinic acid in the gas phase in itself and around the analyte. At this
wavelength, the laser energy is coupled into the matrix through the OH vibrations of the carboxyl groups. The most pronounced
difference we observed at 1,500 K simulation is that infrared heating generates about 10–15 more succinic acid molecules bound
to the analyte in noncovalent complex form than the ultraviolet mode, which generates about 2 molecules thus bound. We report
energy redistribution within the matrix between the host and guest species as well as other dynamical properties. The parameter
and topology data for succinic acid that we used are reported and ready for use in CHARMM computer code environment for simulation.
Revised: 12 October 2001 / Accepted: 27 February 2002 / Published online: 13 June 2002 相似文献
9.
N. Chekirou A. Krallafa A. Bormann 《Journal of inclusion phenomena and macrocyclic chemistry》2005,53(1-2):89-95
Quantum mechanical calculations on the bi(3-sulfonatophenyl) (4-tert-butylphenyl) phosphine/β-cyclodextrin inclusion complex
(TPP/CD) are carried out using semiempirical quantum calculations. Inclusion process pathways described in the present work
lead straight to the most probable structures of the 1:1 association. These investigations suggest that the most stable structure
obtained is that where the aromatic ring bearing the tert-butyl (tBu) group is included into the hydrophobic cavity of the
β-cyclodextrin from the side of the primary hydroxyl groups. Theoretical investigations of the Hartree-Fock level of the inter-proton
proximity between the host and guest molecules in the inclusion complex and their corresponding electronic properties suggest
a deep insertion of the tBu group into the cavity. The host-guest interaction energy of the complex at different levels of
the insertion pathway is reported with the corresponding basis set superposition error (base). The host–guest association
is thermodynamically stable when compared to the separated states and the calculated binding energy is 40.6 kcal mol−1. 相似文献
10.
Steven M. Bachrach Joseph M. Hayes Trang Dao Justin L. Mynar 《Theoretical chemistry accounts》2002,107(5):266-271
Density functional calculations indicate that nucleophilic substitution in the thiolate–disulfide and thiolate–trisulfide
exchange reactions proceeds by an addition–elimination pathway. Solution calculations were performed using B3LYP/6-31+G* and
the polarized continuum method. These solution-phase calculations indicate that for the reactions where the sulfur under attack
bears a hydrogen atom, the substitution proceeds via an addition–elimination mechanism; however, when a methyl group is attached
to the sulfur under attack, the SN2 mechanism is predicted.
Received: 12 October 2001 / Accepted: 28 November 2001 / Published online: 8 April 2002 相似文献
11.
Victor M. Anisimov Nikolay Anikin Vladislav Bugaenko Vladimir Bobrikov Alexey Andreyev 《Theoretical chemistry accounts》2003,109(4):213-219
Accurate electrostatic maps of proteins are of great importance in research of protein interaction with ligands, solvent
media, drugs, and other biomolecules. The large size of real-life proteins imposes severe limitations on computational methods
one can use for obtaining the electrostatic map. Well-known accurate second-order M?ller–Plesset and density functional theory
methods are not routinely applicable to systems larger than several hundred atoms. Conventional semiempirical tools, as less
resource demanding ones, could be an attractive solution but they do not yield sufficiently accurate calculation results with
reference to protein systems, as our analysis demonstrates. The present work performs a thorough analysis of the accuracy
issues of the modified neglect of differential overlap type semiempirical Hamiltonians AM1 and PM3 on example of the calculation
of the molecular electrostatic potential and the dipole moment of natural amino acids. Real capabilities and limitations of
these methods with application to protein modeling are discussed.
Received: 26 April 2002 / Accepted: 19 September 2002 /
Published online: 14 February 2003 相似文献
12.
Oleg V. Surov Nugzar Zh. Mamardashvili Gennadiy P. Shaposhnikov Oskar I. Koifman 《Journal of inclusion phenomena and macrocyclic chemistry》2007,58(3-4):329-335
The inclusion of small neutral organic guests (C6H14, CH2Cl2, CH3OH) by calix[4]arene receptors was found by 1H NMR spectroscopy and microanalysis. The studied calix[4]arenes can form stable intramolecular complexes with solvent molecules
which keep the stoichiometric composition without changing under conditions of the sublimation experiment. The saturated vapour
pressures of calix[4]arenes and complexes of calix[4]arenes with solvent molecules were determinated for the first time by
the Knudsen’s effusion method in the wide temperature range. The changing of standard thermodynamic parameters of complexation
by transfer process from condensed state to vapour phase was estimated. It was shown that the large flexibility of the calixarene
ligand structure corresponds to a strongly negative entropic contribution as well as negative enthalpy term to the Gibbs energy
of formation of host–guest complexes in the gas phase. 相似文献
13.
P. Reinhardt 《Theoretical chemistry accounts》2000,104(6):426-438
The techniques of matrix dressing for configuration-interaction (CI)-type or coupled-electron-pair-approximation (CEPA)-type
correlation treatments are reviewed with respect to the application to periodic systems. All methods ranging from canonical
second-order M?ller–Plesset perturbation theory over CI of single and double excitation, CEPA-0 or the averaged-coupled-pair-functional
to self-consistent size-consistent CI can be formulated completely equivalently as an eigenvalue problem or as a solution
to a system of linear equations. The size consistency of each method is obtained in a natural way, and invariance under orbital
rotations is clearly assessible. A remark on the size consistency of the Davidson correction is presented. Additionally, the
direct generation of localized Hartree–Fock orbitals as basic ingredients for the correlation calculations are addressed,
as well as selected results on ring molecules, polymers, and 3D cubic beryllium as a model crystal.
Received: 28 August 1999 / Accepted: 5 March 2000 / Published online: 21 June 2000 相似文献
14.
Gary Tresadern Paul F. Faulder M. Paul Gleeson Zubeir Tai Grant MacKenzie Neil A. Burton Ian H. Hillier 《Theoretical chemistry accounts》2003,109(3):108-117
Hybrid quantum mechanical (QM)/molecular mechanical (MM) calculations are used to study two aspects of enzyme catalysis,
Kinetic isotope effects associated with the hydride ion transfer step in the reduction of benzyl alcohol by liver alcohol
dehydrogenase are studied by employing variational transition-state theory and optimised multidimensional tunnelling. With
the smaller QM region, described at the Hartree–Fock ab initio level, together with a parameterised zinc atom charge, good
agreement with experiment is obtained. A comparison is made with the proton transfer in methylamine dehydrogenase. The origin
of the large range in pharmacological activity shown by a series of α-ketoheterocycle inhibitors of the serine protease, elastase,
is investigated by both force field and QM/MM calculations. Both models point to two different inhibition mechanisms being
operative. Initial QM/MM calculations suggest that these are binding, and reaction to form a tetrahedral intermediate, the
latter process occurring for only the more potent set of inhibitors.
Recieved 3 October 2001 / Accepted: 6 September 2002 / Published online: 31 January 2003
Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American
Chemical Society, 2001
Correspondence to: I. H. Hillier
Acknowledgements. We thank EPSRC and BBSRC for support of the research and D.G. Truhlar for the use of the POLYRATE code. 相似文献
15.
Verónica Jiménez Joel B. Alderete Eduardo J. Delgado Julio Belmar José Gavín 《Structural chemistry》2006,17(2):217-223
NMR diffusion coefficient measurements and PM3 theoretical calculations were employed in the study of the inclusion complexation of allopurinol with β-cyclodextrin (β-CD) at pH 6.5 and 10.0. Experimental findings revealed an increase in the association constant from 16 to 30 M−1 as a consequence of guest deprotonation. PM3 quantum-mechanical calculations were performed to investigate the complexation process between β-CD and allopurinol, considering the most stable neutral and anionic tautomers of the guest. The binding energies obtained from the computational study were in agreement with the experimental observations, indicating that the anionic complex was more stable than the neutral one. Such unusual behavior was related to hydrogen bonding interactions between β-CD and the anionic guest, leading to the increase of the association constant as a consequence of guest deprotonation. 相似文献
16.
Geert Brocks 《Theoretical chemistry accounts》2000,104(2):116-122
Density functional calculations using pseudopotentials and a plane-wave basis set are applied to study the geometry and the
electronic structure of conjugated polymers consisting of heterocyclic aromatic rings. This article focuses on the computational
methods. The influence of the pseudopotentials on the structural and electronic properties is studied. The rates of convergence
of these properties with respect to the basis set size and the density of sampling points for the Brillouin zone integration
are considered. The effects of using different exchange–correlation potentials (local density or generalized gradient approximations)
are examined. It is shown that smooth norm-conserving pseudopotentials used for calculations on conjugated polymers lead to
converged results with a moderately sized basis set.
Received: 20 August 1999 / Accepted: 23 November 1999 / Published online: 19 April 2000 相似文献
17.
Transport cross sections and collision integrals are tabulated for a wide range of energies and temperatures for the interactions
B–B and Al–Al. For aluminum, a semiclassical approximation was used to determine the scattering phase shifts from which the
transport cross sections were calculated. For boron, the smaller reduced mass and the deep potential wells required the phase
shifts at lower energies to be determined from a numerical solution of the time-independent Schroedinger equation; the semiclassical
approximation was used at higher energies where the two methods agree. The variations of the collision integrals for viscosity
and diffusion are presented graphically as a function of temperature. The results are applied to estimate the transport properties
of gallium.
Received: 9 July 1999 / Accepted: 18 August 1999 / Published online: 2 November 1999 相似文献
18.
Olga Dmitrenko Robert D. Bach Rafal R. Sicinski Wolfgang Reischl 《Theoretical chemistry accounts》2003,109(4):170-175
B3LYP calculations in conjunction with natural bond orbital population analysis have been performed for a previtamin D model
and corresponding transition structures for the [1,7]-hydrogen migration. In addition the 19,19-difluoro, 19-methoxy and 19-fluoro
substituted analogs were investigated. The calculated activation barriers decrease in the following order: CHF2>CH3>CH2OCH3 (24.8, 23.5 and 20.1 kcal/mol). This is in qualitative agreement with experiments. It has been suggested that a decrease
of the barrier by a 19-methoxy substituent and its increase by a 19,19-difluoro substituent are phenomena of different origin.
In the case of 19-methoxy substitution, the effect is due to the charge redistribution in the triene system and the decrease
of the C(19)–H bond energy. The effect of two fluorine substituents at C-19 on the activation barrier is suggested to originate
from the combination and balance of several factors: electrostatic repulsion between the negative fluorine atom and the π-electron
cloud over the conjugated system, an increase of the HOMO–LUMO gap, and geminal difluoro substitution affecting C–F and C–C
bond energies.
Received: 17 May 2002 / Accepted: 11 September 2002 /
Published online: 14 February 2003 相似文献
19.
The complexation of p-tert-butylphenyl p-tert-butylbenzoate and N-(p-tert-butylphenyl)-p-tert-butylbenzamide with a β-cyclodextrin derivative formed by two cyclodextrin units linked by a disulfide bridge on one of the
C6 atoms has been studied by computational methods. The better amide solubility and the better internal interactions of the
ester complex explain the experimentally observed better association constant for the ester. The free-energy perturbation
methodology and molecular mechanics/Poisson–Boltzmann surface area analysis have been used to explain the problem and to compare
the results.
Received: 14 April 2002 / Accepted: 11 August 2002 / Published online: 4 November 2002
Acknowledgements. The Kollman group at the University of California San Francisco is gratefully acknowledged for support and encouragement
throughout all this study. The authors thank UAB for inland and outland fellowships to I.B.. Financial support was obtained
from grant no. PPQ2000-0369 from the “Ministerio de Ciencia y Tecnologia” (Spain). Intensive computations were performed either
with the computers of the Kollman group or with those of CESCA-C4 (Catalonia, Spain).
Correspondence to: C. Jaime e-mail: carlos.jaime@uab.es 相似文献
20.
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