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1.
The structure and vibrational frequencies of an aromatic lithium sulfonyl imide, i.e., lithium bis(4-nitrophenylsulfonyl)imide
(LiNPSI) has been studied using self-consistent ab initio Hartree–Fock and hybrid density functional methods. These calculations
engender two linkage isomers, which correspond to the local minima on the potential-energy surface. In the lowest-energy isomer,
the ligand binds to the metal ion through two oxygens, one from each of the different SO2 groups on the central nitrogen and forms a six-membered ring. Another LiNPSI isomer, wherein the anion coordinates through
oxygen and nitrogen atoms and which is 55.9 kJmol−1 higher in energy, has also been obtained. The S–N–S bond angle in the free anion as well as in the LiNPSI complex turns out
to be nearly 121°. A comparison of the vibrational spectra of the free NPSI anion and that of the LiNPSI complex reveals that
the SO2 stretching vibrations at 1,239 and 1,205 cm−1 can be used to differentiate between the two linkage isomers of the complex. The stronger complexation ability of the NPSI
anion, compared to that for (CF3SO2)2N− has been explained in terms of the charge density within the molecular electrostatic potential isosurface encompassing both
SO2 groups of the anion.
Received: 20 February 2002 / Accepted: 25 March 2002 / Published online: 3 June 2002 相似文献
2.
Fully relativistic, four-component Dirac–Fock calculations and quasirelativistic pseudopotential calculations at different
ab initio levels are used to study the bonding trends among the naked, triatomic [OAnO]
q+
groups or the oxyfluorides [AnO
n
F
m
]
q
with f
0 configurations. The triatomic f
0 series is suggested to range from the bent ThO2 via the linear OPaO+ to at least NpO2
3+, a possible new gas-phase species. The neutral oxyfluoride molecules include the experimentally unknown NpO2F3 and PuO2F4. The latter is a candidate for the so far unknown oxidation state Pu(VIII), which is found to lie considerably above Pu(VI),
but to be locally stable. Their all-oxygen isoelectronic analogues are NpO5
3−, known in the solid state, and the unknown PuO6
4−. Further possible candidates for Pu(VIII) are PuO4(D
4h
) and the cube-shaped PuF8(O
h
). Isoelectronic UF8
2− is calculated to be D
4d
, in agreement with experiment.
Received: 18 May 2001 / Accepted: 21 June 2001 / Published online: 11 October 2001 相似文献
3.
Martin Albrecht 《Theoretical chemistry accounts》2002,107(2):71-79
A local-orbital-based ab initio approach to calculate correlation effects on quasi-particle energies in insulating solids
is presented. The use of localized Wannier-type Hartree–Fock orbitals allows correlation effects to be efficiently assessed.
First a Green's function approach based on exact diagonalization is introduced and this is combined with an incremental scheme,
while subsequently different levels of perturbative approximations are derived from the general procedure. With these methods
the band structure of LiF is calculated and good agreement with experiment is found. By comparing the different approximations
proposed, including the exact diagonalization procedure, their relative quality is established.
Received: 25 June 2001 / Accepted: 31 August 2001 / Published online: 19 December 2001 相似文献
4.
An ab initio method has been developed to predict helix formation for polypeptides. The approach relies on the systematic analysis of overlapping oligopeptides to determine the helical propensity for individual residues. Detailed atomistic level modeling, including entropic contributions, and solvation/ionization energies calculated through the solution of the Poisson-Boltzmann equation, is utilized. The calculation of probabilities for helix formation is based on the generation of ensembles of low energy conformers. The approach, which is easily amenable to parallelization, is shown to perform very well for several benchmark polypeptide systems, including the bovine pancreatic trypsin inhibitor, the immunoglobulin binding domain of protein G, the chymotrypsin inhibitor 2, the R69 N-terminal domain of phage 434 repressor, and the wheat germ agglutinin. 相似文献
5.
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
6.
A method applying ab initio direct dynamics has been utilized in studying the hydrogen abstraction reaction HCN + OH → CN + H2O. The geometries of the reactants, products, and the transition state have been optimized at the QCISD/6-311G(d, p) level.
Single-point energies were further evaluated at the QCISD(T)/6-311+G(2df, 2p)//QCISD/6-311G(d, p) level. The barrier heights
for the forward and reverse reactions were predicted to be 15.95 and 7.51 kcal mol−1 at the QCISD(T)/6-311 + G(2df, 2p)//QCISD/6-311G(d, p) level, respectively. The reaction rate constants were calculated in
the temperature range from 298 to 4,000 K using the canonical variational transition-state theory with a small-curvature tunneling
correction. The results of the calculation show that the theoretical rate constants are in good agreement with experimental
data over the measured temperature range of 400–2,600 K.
Received: 18 August 2002 / Accepted: 30 August 2002 / Published online: 20 November 2002
Acknowledgements. Our thanks are due to D.G. Truhlar for providing the POLYRATE 8.2 program. This work was supported by the National Science
Foundation of China. We also thank D.C. Fang and Y. M. Xie for their valuable help, and P.R. Yan for reading our paper.
Correspondence to: Q. S. Li e-mail: qsli@mh.bit.edu.cn 相似文献
7.
Geometry optimization was performed for the ground states of FeCO, Fe(CO)2, and Fe(CO)3 at various levels of ab initio calculations, and the bond lengths and dissociation energies obtained were in reasonable agreement
with experimental results. The nature of bonding was studied for these molecules using a complete-active-space self-consistent-field
method. From the Mulliken population analysis, it was found that the traditional donation and back donation mechanism is valid
for these molecules, including Fe(CO)3, which has a pyramidal structure.
Received: 27 September 1999 / Accepted: 13 January 2000 / Published online: 19 April 2000 相似文献
8.
A new methodology for the prediction of molecular crystal structures using only the atomic connectivity of the molecule under consideration is presented. The approach is based on the global minimization of the lattice enthalpy of the crystal. The modeling of the electrostatic interactions is accomplished through a set of distributed charges that are optimally and automatically selected and positioned based on results of quantum mechanical calculations. A four-step global optimization algorithm is used for the identification of the local minima of the lattice enthalpy surface. A parallelized implementation of the algorithm permits a much more extensive search of the solution space than has hitherto been possible, allowing the identification of crystal structures in less frequently occurring space groups and with more than one molecule in the asymmetric unit. The algorithm has been applied successfully to the prediction of the crystal structures of 3-aza-bicyclo(3.3.1)nonane-2,4-dione (P2(1)/a, Z' = 1), allopurinol (P2(1)/c, Z' = 1), 1,3,4,6,7,9-hexa-azacycl(3.3.3)azine (Pbca, Z' = 2), and triethylenediamine (P6(3)/m, Z' = 1). In all cases, the experimentally known structure is among the most stable predicted structures, but not necessarily the global minimum. 相似文献
9.
The relationship between band structure and the topology of the orbital interactions between neighboring chemical units comprising
several model one-dimensional polymers with helical (screw-axis) symmetry is analyzed. A perturbative model of orbital interactions
based on a tight binding implementation of the extended Hückel method is developed. The model accounts for both the band topologies
and the seemingly anomalous band extrema within the Brillouin zone constructed using the chemical repeat unit of the polymer.
Received: 5 November 2001 / Accepted: 14 January 2002 / Published online: 3 May 2002 相似文献
10.
Chris Roberts Roy L. Johnston Nicholas T. Wilson 《Theoretical chemistry accounts》2000,104(2):123-130
This article describes the application of a genetic algorithm for the structural optimization of 19–50-atom clusters bound
by medium-range and short-range Morse pair potentials. The GA is found to be efficient and reliable for finding the geometries
corresponding to the previously published global minima [Doye JPK, Wales DJ (1997) J Chem Soc Faraday Trans 93: 4233]. Using the genetic algorithm, only a relatively small number of energy evaluations and minimizations are required
to find the global minima. By contrast, a simple random search algorithm often cannot find the global minima of the larger
clusters, even after many thousands of searches.
Received: 27 October 1999 / Accepted: 7 December 1999 / Published online: 19 April 2000 相似文献
11.
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
12.
Molecular dynamics (MD) simulations are extensively used in the study of the structures and functions of proteins. Ab initio protein structure prediction is one of the most important subjects in computational biology, and many trials have been performed using MD simulation so far. Since the results of MD simulations largely depend on the force field, reliable force field parameters are indispensable for the success of MD simulation. In this work, we have modified atom charges in a standard force field on the basis of water-phase quantum chemical calculations. The modified force field turned out appropriate for ab initio protein structure prediction by the MD simulation with the generalized Born method. Detailed analysis was performed in terms of the conformational stability of amino acid residues, the stability of secondary structure of proteins, and the accuracy for prediction of protein tertiary structure, comparing the modified force field with a standard one. The energy balance between alpha-helix and beta-sheet structures was significantly improved by the modification of charge parameters. 相似文献
13.
14.
José R. Mohallem 《Theoretical chemistry accounts》2002,107(6):372-374
It is shown that a supposed catastrophe of Bader's theory of atoms in molecules, suggested by Cassam-chena? and Jayatilaka
[Theor Chem Acc (2001) 105: 213] is merely a consequence of the approximate character of the adiabatic Born–Oppenheimer theory of molecular
structure, and that nonadiabatic approaches could be in accordance with Bader's ideas.
Received: 4 April 2001 / Accepted: 5 September 2001 / Published online: 3 June 2002 相似文献
15.
16.
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
17.
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
18.
A simple and variationally stable quasi-relativistic method based on a modified low-order (LO) approximation to the normalized
elimination of the small component (NESC) method is presented. The modification of the original LO-NESC scheme implies the
use of an energy-independent factor in the relativistic correction to the potential energy. This factor cuts off the potential
energy at short distances from the nucleus and in this way restores the variational stability of LO-NESC. The new method,
dubbed LO-NESC-effective potential (EP) was tested in calculations on one-, two- and many-electron atoms. The LO-NESC-EP can
be easily implemented into the existing nonrelativistic quantum-chemical program codes because its Hamiltonian matrix can
be expressed entirely in terms of the integrals appearing in a nonrelativistic calculation.
Received: 1 April 2002 / Accepted: 23 June 2002 / Published online: 30 August 2002 相似文献
19.
Jacek Koput 《Journal of computational chemistry》2019,40(21):1911-1918
Accurate structure and potential energy surface of germylene, GeH2, in its ground electronic state 1A1 were determined from ab initio calculations using the coupled-cluster approach in conjunction with the correlation-consistent basis sets up to sextuple-zeta quality. The Born-Oppenheimer equilibrium structural parameters for the 1A1 state are estimated to be re(GeH) = 1.5793 Å and ∠e(HGeH) = 91.19∘. The term value Te for the lowest excited electronic state ã3B1 of GeH2 is predicted to be 9140 cm–1. The vibration-rotation energy levels for the 1A1 state of the 74GeH2, 74GeD2, 72GeH2, and 70GeH2 isotopologues were determined using a variational approach and compared with the experimental data. The role of the core-electron correlation, higher-order valence-electron correlation, scalar relativistic, spin-orbit, and adiabatic effects for prediction of the structure and vibration-rotation dynamics of the GeH2 molecule is discussed. © 2019 Wiley Periodicals, Inc. 相似文献
20.
The radial electron-pair intracule (relative motion) H(u) and extracule (center-of-mass motion) D(R) densities in position space were known to reveal four types of maxima which are related to the four inner electron shells,
K, L, M, and N, of atoms. The corresponding radial electron-pair intracule Hˉ(v) and extracule Dˉ(P) densities in momentum space are studied for the 102 atoms from He (atomic number Z=2) to Lr (Z=103). The densities Hˉ(v) and Dˉ(P) are found to have either one maximum or two maxima, and the numbers of maxima in Hˉ(v) and Dˉ(P) are the same for 98 atoms. For these atoms, the locations υ
max and P
max and the heights Hˉ
max
and Dˉ
max
of the corresponding maxima satisfy the approximate relations υ
max ≅ 2P
max and Hˉ
max
≅Dˉ
max
/2. On the basis of their Z-dependence, the maxima in Hˉ(v) and Dˉ(P) of the 102 atoms are classified into five types. Shell-pair decompositions of the radial densities show that these maxima
reflect five outer electron shells of atoms.
Received: 24 January 2001 / Accepted: 12 March 2001 / Published online: 13 June 2001 相似文献