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1.
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
2.
Improper,blue-shifting hydrogen bond 总被引:3,自引:0,他引:3
3.
Pornpun Rattananakin Charles U. PittmanJr. Willard E. Collier Svein Saebø 《Structural chemistry》2007,18(3):399-407
Twelve push–pull ethylene derivatives, NH2CH=CHX, NH2C≡CCH=CHX, and −OCHX=CHX (with X=BH2, C≡N, NO2, and CH2
+) have been studied by ab initio calculations. The rotational barrier around the central double bond was chosen as a probe
for push–pull effects, as push–pull effects would remove electron density from the central double bond. The amount of reduction
of double bond character will increase with the contribution of the zwitterionic resonance hybrid structure. Complete geometry
optimizations and calculations of vibrational frequencies were performed for all minima and transition state structures of
these 12 systems. The calculations were carried out with the B3LYP and MP2 methods using the 6-311+G(d,p) and the 6-311++G(d,p)
basis sets. All the systems investigated exhibited properties consistent with push–pull effects such as elongated C=C double
bonds, dipolar electronic structures, and reduced barriers to internal rotation. 相似文献
4.
A test of the quality of the electrostatic properties and polarizabilities used in the nonempirical molecular orbital (NEMO)
potential is carried out for formamide by calculating the molecular dipole moment and polarizability at the second-order M?ller–Plesset
(MP2) level of theory. The molecular dipole moment is 11% lower at the MP2 level than at the Hartree–Fock (HF) level, whereas
the isotropic part of the polarizability is increased by 36% by adding electron correlation and using a considerably larger
basis set. The atomic charges, dipole moments and polarizabilities obtained at the HF level are rescaled to get the correct
molecular properties at the MP2 level. The potential minimum for the cyclic dimer of formamide is −17.50 kcal/mol with the
MP2-scaled properties and is significantly lower than other potentials give. Two intermolecular potentials are constructed
and used in subsequent molecular dynamics simulations: one with the regular NEMO potential and the other with the rescaled
MP2 properties. A damping of the electrostatic field at short intermolecular distances is included in the present NEMO model.
The average energies for liquid formamide are lower for the MP2-scaled model and are in good agreement with experimental results.
The lowering of the simulation energy for the MP2-scaled potential indicates the strong dispersive interactions in liquid
formamide.
Received: 20 March 2000 / Accepted: 18 April 2000 / Published online: 18 August 2000 相似文献
5.
Concerted as well as stepwise reaction pathways for cyclization of 3-azido-propenal to isoxazole have been investigated by
density functional (B3LYP) and ab initio methods up to CCSD(T)/cc-pVQZ methods. These calculations clearly establish the pathway
with concerted albeit asynchronous nitrogen extrusion and ring closure as the most feasible mechanism. Barriers for cyclization
increase in the order Hartree–Fock<B3LYP<ACPF<CCSD(T). According to the geometrical parameters and the electronic structure
of the TS as evidenced by natural bond order analysis this cyclization can be interpreted as a pseudopericyclic (heteroelectrocyclic)
reaction.
Received: 26 May 2002 / Accepted: 18 June 2002 /
Published online: 14 February 2003 相似文献
6.
Davor Margetić Ronlad N. Warrener Mirjana Eckert-Maksić Ivana Antol Zoran Glasovac 《Theoretical chemistry accounts》2003,109(4):182-189
DFT calculations of 7′–oxasesquinorbornenes and 7,7′-dioxasesquinorbornenes using the B3LYP/6–31G* method are reported.
All the investigated structures (syn- and anti- derivatives) showed significant non-planarity of the central double bond, with the exception of those anti-derivatives possessing symmetrical structures. The influence of the replacement of the methylene groups at position 7- of
the norbornene fragment with oxygen and the introduction of second and third (peripheral) double bonds and benzene rings on
the molecular and electronic structures of these molecules have also been investigated.
Received: 11 November 2002 / Accepted: 6 June 2002 /
Published online: 29 April 2003 相似文献
7.
Soluble polymers have been prepared that are designed to undergo enhanced rates of hydrolysis at pH values less than that
observed in blood circulation. The degradable element in the polymer mainchain is derived from cis-aconityl acid and is defined by a carboxylic acid pendent functionality (C-4) that is cis across a double bond to an amide
at C-1 in the polymer mainchain. While degradation studies in vitro have confirmed these polymers do undergo enhanced rates
of degradation at acidic pH values, there is also increasing evidence that during the degradation process the double bond
isomerises to the trans configuration and thus prevents the full degradation of a polymer. From a molecular modelling perspective
we are seeking to understand the propensity for this cis–trans isomerisation and the mechanism of this cis–trans isomerisation
is discussed.
Received: 29 April 2002 / Accepted: 6 September 2002 /
Published online: 14 February 2003 相似文献
8.
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
9.
David Quiñonero Antonio Frontera Salvador Tomàs Guillem A. Suñer Jeroni Morey Antoni Costa Pau Ballester Pere M. Deyà 《Theoretical chemistry accounts》2000,104(1):50-66
A computational study of the mechanism of host–guest complexation between quaternary ammonium compounds and squaramido-based
tripodal receptors has been carried out. Semiempirical molecular orbital calculations, which are in qualitative agreement
with experimental results have been performed using the PM3 Hamiltonian. Molecular interaction potential (MIP) maps were used
to analyze the suitability of both host and guest binding units for a high-affinity recognition process. MIP calculations
were computed from PM3 wavefunctions of the corresponding ammonium cations and dimethyl squaramide as a model compound for
the hydrogen-bond-acceptor unit of the receptors. MIP analyses are helpful for understanding the host–guest process from the
point of view of the double-complementarity principle.
Received: 23 June 1999 / Accepted: 22 September 1999 / Published online: 17 January 2000 相似文献
10.
Michael P. Barnett 《Theoretical chemistry accounts》2002,107(4):241-245
In the course of checking our work on the symbolic calculation of molecular integrals over Slater orbitals, we obtained some
results in substantial disagreement with two recent articles that describe numerical schemes. We believe that these schemes
suffer from digital erosion, possibly because recurrence formulas were used outside their regions of stability. Our results
were obtained using the ζ-function method, which expands the orbital on one atom onto the other, and integrates in polar coordinates.
They were checked using elliptic coordinates. Both sets of calculations were performed symbolically. We summarize these calculations
and discuss the impact of symbolic calculation on the accuracy of molecular computations.
Received: 31 August 2001 / Accepted: 29 October 2001 / Published online: 8 April 2002 相似文献
11.
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
12.
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
13.
The structures, properties and the bonding character for sub-carbonyl Si, SiCO and Si(CO)2, in singlet and triplet states have been investigated using complete-active-space self-consistent field (CASSCF), density
functional theory and second-order M?ller–Plesset methods with a 6-311+G* basis set. The results indicate that the SiCO species
possesses a 3∑− ground state, and the singlet 1Δ excited state is higher in energy than the 3∑− state by 17.3 kcalmol−1 at the CASSCF–MP2/6-311+G* level and by 16.4 kcalmol−1 at the CCSD(T)/6-311+G* level. The SiCO ground state may be classified as silene (carbonylsilene), and its COδ− moiety possesses CO− property. The formation of SiCO causes the weakening of CO bonds. The Si–C bond consists of a weak σ bond and two weak π
bonds. Although the Si–C bond length is similar to that of typical Si–C bonds, the bond strength is weaker than the Si–C bonds
in Si-containing alkanes; the calculated dissociation energy is 26.2 kcalmol−1 at the CCSD(T)/6-311+G* level. The corresponding bending potential-energy surface is flat; therefore, the SiCO molecule is
facile. For the bicarbonyl Si systems, Si(CO)2, there exist two V-type structures for both states. The stablest state is the singlet state (1A1), and may be referred to the ground state. The triplet state (3B1) is energetically higher in energy than the 1A1 state by about 40 kcalmol−1 at the CCSD(T)/6-311 + G* level. The bond lengths in the 1A1 state are very close to those of the SiCO species, but the SiCO moieties are bent by about 10°, and the CSiC angles are only
about 78°. The corresponding 3B1 state has a CSiC angle of about 54° and a SiCO angle of about 165°, but its Si–C and C–O bonds are longer than those in the
1A1 state by about 0.07 and 0.03 ?, respectively. This Si(CO)2 (1A1) has essentially silene character and should be referred to as a bicarbonyl silene. Comparison of the CO dissociation energies
of SiCO and Si(CO)2 in their ground states indicates that the first CO dissociation energy of Si(CO)2 is smaller by about 7 kcalmol−1 than that of SiCO; the average one over both CO groups is also smaller than that of SiCO. A detailed bonding analysis shows
that the possibility is small for the existence of polycarbonyl Si with more than three CO. This prediction may also be true
for similar carbonyl complexes containing other nonmetal and non-transition-metal atoms or clusters.
Received: 17 April 2002 / Accepted: 11 August 2002 / Published online: 4 November 2002
Acknowledgements. This work was supported by the National Natural Science Foundation of China (29973022) and the Foundation for Key Teachers
in University of the State Ministry of Education of China.
Correspondence to: Y. Bu e-mail: byx@sdu.edu.ch 相似文献
14.
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
15.
Summary. A crystal structure determination of a bilirubin analog with a sulfur instead of a C(10)–CH2 linking the two dipyrrinones is reported. Conformation-determining torsion angles and key hydrogen bond distances and angles
are compared to those obtained from molecular dynamics calculations as well as to the corresponding data from X-ray determinations
and molecular dynamics calculations of bilirubin. Like other bilirubins, the component dipyrrinones of the analog are present
in the bis-lactam form with (Z)-configurated double bonds at C(4) and C(15). Despite the large differences in bond lengths and angles at –S–vs.–CH2–, the crystal structure shows considerable similarity to bilirubin: both pigments adopt a folded, intramolecularly hydrogen-bonded
ridge-tile conformation stabilized by six hydrogen bonds – although the interplanar angle of the ridge-tile conformation of
the title compound is smaller (∼ 86°) than that of bilirubin (∼ 98°). The collective data indicate that even with long C–S
bond lengths and a smaller C–S–C bond angle at the pivot point on the ridge-tile seam, intramolecular hydrogen bonding persists.
Received August 16, 2001. Accepted September 12, 2001 相似文献
16.
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
17.
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
18.
The most stable structures of V
x
O
y
+/V
x
O
y
(x=1, 2, y=1–5) clusters and their interaction with O2 are determined by density functional calculations, the B3LYP functional with the 6-31G* basis set. The nature of the bonding
of these clusters and the interaction with O2 have been studied by topological analysis in the framework of both the atoms-in-molecules theory of Bader and the Becke–Edgecombe
electron localization function. Bond critical points are localized by means of the analysis of the electron density gradient
field, ∇ρ(r), and the electron localization function gradient field, ∇η(r). The values of the electron density properties, i.e., electron density, ρ(r), Laplacian of the electron density, ∇2ρ(r), and electron localization function, η(r), allow the nature of the bonds to be characterized, and linear correlation is found for the results obtained in both gradient
fields. Vanadium-oxygen interactions are characterized as unshared-electron interactions, and linear correlation is observed
between the electron density properties and the V–O bond length. In contrast, O2 units involve typical shared-electron interactions, as for the dioxygen molecule. Four different vanadium–oxygen interactions
are found and characterized: a molecular O2 interaction, a peroxo O2
2− interaction, a superoxo O2
− interaction and a side-on O2
− interaction.
Received: 15 October 2001 / Accepted: 30 January 2002 / Published online: 24 June 2002 相似文献
19.
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
20.
Sequential Monte Carlo/quantum mechanical calculations are performed to study the solvent effects on the electronic absorption
spectrum of formamide (FMA) in aqueous solution, varying from hydrogen bonds to the outer solvation shells. Full quantum-mechanical
intermediate neglect of differential overlap/singly excited configuration interaction calculations are performed in the supermolecular
structures generated by the Monte Carlo simulation. The largest calculation involves the ensemble average of 75 statistically
uncorrelated quantum mechanical results obtained with the FMA solute surrounded by 150 water solvent molecules. We find that
the n → π* transition suffers a blueshift of 1,600 cm−1 upon solvation and the π → π* transition undergoes a redshift of 800 cm−1. On average, 1.5 hydrogen bonds are formed between FMA and water and these contribute with about 20% and about 30% of the
total solvation shifts of the n → π* and π → π* transitions, respectively. The autocorrelation function of the energy is used
to sample configurations from the Monte Carlo simulation, and the solvation shifts are shown to be converged values.
Received: 14 March 2002 / Accepted: 3 April 2002 / Published online: 24 June 2002 相似文献