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1.
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
2.
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
3.
Tommi H. Nyrönen Reijo Suontamo Ilkka Pitkänen 《Theoretical chemistry accounts》1999,101(1-3):209-214
A theoretical study of the structure, charge distribution, rotational barrier and fundamental vibrations of anhydrous betaine
(CH3)3NCH2COO (trimethylglycine) was carried out and compared with available experimental data. Calculations were carried out at HF,
MP2 and B3LYP levels using a 6-31+G(d,p) basis set. The calculated rotational barrier of the betaine carboxylic group is 40.5 kJ/mol at the MP4(SDQ)/6-311G(d,p)//HF/6-31+G(d,p) level of theory. The rotation of the carboxylic group changes the molecule from a highly symmetric (C
s
) conformation into a twisted conformation resulting in shortening of the molecule by about 50 pm. Natural population analysis
(NPA) indicates intramolecular interaction between the carboxylic oxygen and the nearest methyl hydrogens resulting in internal
hydrogen bonding. MP4(SDQ)/6-311G(d,p) single-point NPA calculations on a betaine monohydrate model taken from the X-ray geometry show an expected weakening in
the internal hydrogen bond. Calculations explain why betaine preferentially crystallizes in high local C
s
symmetry.
Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 7 December 1998 相似文献
4.
The repulsive ground electronic state X2Σ+ of HeH is strongly coupled to the Rydberg states at small interatomic distances. Such large couplings also occur between
some of the Rydberg states. HeH+ ions that capture an electron in a Rydberg state end up in separated He and H atoms by indirect predissociation. This paper
presents a study of potential functions and pertinent matrix elements involving the lowest electronic states: the 2Σ+ states, X, A, C, and D, and the 2Π states B and E. Individual transition rates as well as total radiative and non-radiative lifetimes have been computed for
the lowest vibrational and rotational levels.
Received: 22 June 1998 / Accepted: 21 August 1998 / Published online: 12 October 1998 相似文献
5.
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
6.
Shinsaku Fujita 《Theoretical chemistry accounts》1998,99(6):404-410
Characteristic monomials for a finite group are obtained by direct subductions of Q-conjugate representations. They are shown to give a generating function that is capable of solving enumeration problems.
Received: 1 May 1998 / Accepted: 16 July 1998 / Published online: 18 September 1998 相似文献
7.
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
8.
H. O. Bertrand A. Pullman K. Zakrzewska B. Hartmann S. Fermandjian 《Theoretical chemistry accounts》1999,101(4):269-273
Phosphorothioate DNAs, have emerged as a new class of potent drugs. They are obtained by the replacement of the anionic oxygens
of the phophodiester backbone by sulphur. A set of parameters has been developed for the FLEX force field implemented in JUMNA
10.0 to take into account the influence of sulphur on the structure of the DNA double helix. The consistency of our parameters
was tested by modelling a phosphorothioate oligomer namely d(GC)8. d(GC)8. Results, obtained on both R-pS and S-pS diastereoisomers, were compared to the phosphodiester counterpart and are in agreement with available experimental data.
Thus, our set of parameters seems suitable for further molecular modelling of other phosphorothioate oligomers.
Received: 15 July 1998 / Accepted: 8 September 1998 / Published online: 10 December 1998 相似文献
9.
Maja Nendel Bernd Goldfuss K. N. Houk Klaus Hafner Udo Grieser 《Theoretical chemistry accounts》1999,102(1-6):397-400
B3LYP/6-31G* calculations on bis-periazulene (cyclohepta[def]-fluorene) predict a triplet ground state for this molecule. The singlet has an aromatic 14π-electron periphery but is 2 kcal/mol
higher in energy. The results agree with earlier predictions by Heilbronner.
Received: 19 August 1998 / Accepted: 6 October 1998 / Published online: 23 February 1999 相似文献
10.
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
11.
12.
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
13.
Roman G. Efremov Dmitry E. Nolde Gérard Vergoten Alexander S. Arseniev 《Theoretical chemistry accounts》1999,101(1-3):170-174
A recently developed implicit solvation model is applied to Monte Carlo simulations of peptides in bilayer-mimetic and polar
environments. The model employs the formalism of atomic solvation parameters and reproduces experimental data. Solvent effects
on the␣structure of the following peptides were studied: 20-residue poly-Leu and poly-Val, transmembrane helix A of bacteriorhodopsin,
magainin2. It was shown that a␣membrane-like environment considerably promotes α-helix formation (all the peptides were found
to be α-helical), while simulations in water reveal helix distortion. Consistency of the results with experimental data and
further implications of the model are discussed.
Received: 24 April 1998 / Accepted: 3 September 1998 / Published online: 10 December 1998 相似文献
14.
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
15.
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
16.
Sachiko Nakai Fumio Yoneda Tokio Yamabe Kenichi Fukui 《Theoretical chemistry accounts》1999,102(1-6):147-160
Possible inhibition mechanisms of flavin (isoalloxazine) with (−)-deprenyl as an acetylenic irreversible inhibitor have been
investigated in detail by ab initio methods with the 6-31G* basis set through the simplified model compounds 3-formyl-2-imino-1-hydropyrazine
and propargylamine. The resulting compounds have been verified by calculations with the 3-21G basis set using flavin itself
and the model of (−)-deprenyl for confirmation of the reactions through the simplified models. Two cyclic O4,N5- and C4a,N5-covalent
adducts have been found. The latter was the most stable and was considered to be the final irreversible product. The intermediates
in the reaction, the acyclic C4a- or N5-allenic compounds and their hydrogen-transferred cyanine-type compounds, are in agreement
with the results of experimental photochemical reactions. In most of the reaction processes, hydrogen migration played an
important role.
Received: 26 June 1998 / Accepted: 28 August 1998 / Published online: 11 November 1998 相似文献
17.
An effective approach for evaluating folding free-energy surfaces of explicit all-atom models is developed and examined.
This approach is based on using the potential of a simplified protein model as a reference potential for calculating the free
energy of the corresponding explicit model. Preliminary results are presented for the folding free energy of a 12-residue
helix. The potential of the method for studies of protein-folding processes is discussed, emphasizing the ability to determine
the difference between the results of simplified and explicit models. This can help in establishing the validity of simplified
folding models.
Received: 30 December 1998 / Accepted: 27 January 1999 / Published online: 5 May 1999 相似文献
18.
William T. G. Johnson David A. Hrovat Anne Skancke Weston Thatcher Borden 《Theoretical chemistry accounts》1999,102(1-6):207-225
Ab initio calculations on the lowest singlet and triplet states of 2,2-disilylcyclopentane-1,3-diyl find that the singlet
lies well below the triplet. The C
2 singlet diradical is calculated to be a minimum on the potential energy surface with an enthalpic barrier to ring closure
of ΔH
‡
298 = 13.5 kcal/mol at the CASPT2/6-31G* level of theory. The energy of the 1,3-divinyl-substituted singlet diradical is calculated
to be only 0.8 kcal/mol higher than that of 5,5-disilyl-1,3-divinylbicyclo[2.1.0]pentane at this level of theory, but the
transition state for their equilibration is computed to be 12.8 kcal/mol above the diradical in energy.
Received: 2 July 1998 / Accepted: 4 August 1998 / Published online: 16 November 1998 相似文献
19.
Substituent effects on the structure of radicals and parent hydrocarbons formed by isolated or condensed three-membered rings
have been investigated by Hartree-Fock, post-Hartree-Fock and density functional methods. The trends of structural parameters
computed for the hydrocarbon systems are in agreement with available experimental data. Substituent effects can be rationalized
in terms of interactions between localized orbitals obtained by natural bond analysis. The effects are even larger in free
radicals and can be analyzed using the same model.
Received: 13 March 1998 / Accepted: 13 July 1998 / Published online: 9 October 1998 相似文献
20.
Subduction of Q-conjugacy representations and characteristic monomials for combinatorial enumeration
Shinsaku Fujita 《Theoretical chemistry accounts》1998,99(4):224-230
A new method of combinatorial enumeration is presented. The subduction of Q-conjugacy representations gives a characteristic subduction table and a characteristic monomial table. A cycle index is defined
on the basis of such monomials and used for combinatorial enumeration of isomers.
Received: 10 October 1997 / Accepted: 13 February 1998 / Published online: 17 June 1998 相似文献