Electronic Journal of Theoretical Chemistry

Electronic Journal of Theoretical ChemistryVolume 2, Issue 1 p. 215-217 Software ReviewFree Access CS Chem3D Pro 3.5 and CS MOPAC Pro (Mac and Windows) UK A. Hinchliffe, A. Hinchliffe Department of Chemistry, UMIST, Sackville Street, Manchester, M60 1QD, UKSearch for more papers by this author A. Hinchliffe, A. Hinchliffe Department of Chemistry, UMIST, Sackville Street, Manchester, M60 1QD, UKSearch for more papers by this author First published: 15 March 2001 https://doi.org/10.1002/ejtc.54Citations: 4AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Citing Literature Volume2, Issue11997Pages 215-217 RelatedInformation

Electronegativity is one of the most enduring concepts in chemistry, which, on occasion, has been referred to as the third dimension of the periodic table. All this without a secure theoretical basis for this concept. It has now been found that the ground-state energy of the valence electron of an atom in its promotion state provides this theoretical basis. It can be calculated from first principles by simulated compression of the atom to the point where the valence electron decouples from the core and behaves like a free particle in an impenetrable sphere. This calculated energy represents the atomic Fermi level, which is the electronic chemical potential of a single atom in its valence state. All empirical statements about electronegativity are readily reconciled with this theoretical concept which, in addition, closely reflects the expected periodicity. (C) 1997 by John Wiley & Sons, Ltd.

The molecular geometries of various 3-substituted malondialdehyde and acetylacetone derivatives, in their chelate, open and H-centred conformations, were optimized and the hydrogen bond energies evaluated, in order to estimate the effect of 3-substitution steric hindrance on the hydrogen bond strength. Calculations were performed at the ab initio 3-21G and 6-31G** level, with and without correlation energy inclusion, using the Moller-Plesset approach (where possible) and the B3LYP functional. The frequencies of the O-H stretching mode were evaluated, too. The obtained results indicate that the C-s chelate conformations are the most stable structures. The O ... O distances are rather longer than the values typical of the H-centred conformers, at least in gas phase. The strengthening of the hydrogen bridge, on passing from the parent to the 3-substituted derivatives, is not so relevant as expected on the ground of literature data, the maximum increase being about 21 kJ mol(-1) (in 3-t-butyl-acetylacetone). An increase of the steric effect to stress the O ... O distance caused the breaking of the hydrogen bridge instead of strengthening, so indicating that the literature X-ray geometries (in particular the O ... O distances) are governed, at least partially, by crystalline forces. (C) 1997 by John Wiley & Sons, Ltd.

A. The refined structure was found to be non-planar. The plane of the pyridinium ring is rotated relative to the ylide carbanion plane by 39.47. A comparative study with the AM1 semi-empirical method shows a good agreement with X-ray diffraction data. Indeed the standard deviations between the calculated and experimental values are 0.038 ˚ A and 0.056 for bond lengths and bond angles, respectively. ©1997 by John Wiley & Sons, Ltd.

We present an ab initio SCF-MO study of the static dipole polarizability of some neutral and charged species of naphthalene (C10H8)(q), (q = -2, -1, 0, +1, +2). The charged species involve additions and removals of electrons to and from the HOMO and LUMO pi-electron orbitals. The polarizability calculations were performed using the Coupled Perturbed Hartree-Fock method, and in addition, we used direct analytical differentiation of the energy expression. We used a series of split valence basis sets augmented with sp diffuse and polarized functions STO/6 31+G(md,np, (m = n = 1,2,3), and all geometries were fully optimized. Molecular structure optimizations were generally started from the geometry predicted for neutral naphthalene with D-2h symmetry at the HF/6-31G** level of theory.The Hartree-Fock results indicate that the anisotropies of the components of the dipole polarizability tensor of neutral naphthalene (q = 0) are in agreement with our own previous theoretical calculations and with the experimental values corresponding to laser Stark spectroscopy in a naphthalene molecular beam, This agreement with experimental results can be further improved with extension of the number of polarized functions in the basis set,We also analyse the effect of the negative and positive charges on the naphthalene molecule on the polarizability tensor components. The variation of molecular geometry also plays a part in these changes.

A set of explicit formulae for the familiar energy integrals arising from s and p GTFs are given, which are corrected versions of some formulae which have been in the literature for three decades.

The spatial conformations of two diastereoisomers of the tripeptide N alpha-Z-N epsilon-Bz-Lys-Ala-Sar-OBzl have been investigated by vibrational spectroscopies. It has been shown that the conformers contain a permanent hydrogen-bonded C7-like structure and that another hydrogen-bonded ring can exist as a C10 or a C11-like structure. (C) 1997 by John Wiley & Sons, Ltd.

The tripeptide N alpha-Z-N epsilon-Bz-Lys-Ala-Sar-OBzl is an antagonist of substance P at the human NK1 receptor, with a low affinity constant (< 1 mu m). In this paper, we have carried out a theoretical conformational study of its diastereoisomers (S, S) and (S, R) by molecular dynamics performed with AMBER and SPASIBA force fields. The obtained conformational spaces have been analyzed in terms of conformational energy distributions and classified into families according to the letter-code convention to partition the phi-psi map. Some of these predicted theoretical conformations are characterized by the presence of gamma-turn. (C) 1997 by John Wiley & Sons, Ltd.

The geometrical structure and vibrational modes of the complex formed between the copper atom and NO molecule for the ground state have been studied by means of an ab initio MO method. The ground and low-lying electronic states were determined by using the singly excited configuration interaction (CI) calculations. The bent structure with a Cu-N-O angle of 117 degrees is obtained as the most stable form of the complex at the MP2/6-311G* level. Harmonic vibrational frequencies calculated for the bent form (1494 and 592 cm(-1)) are in reasonable agreement with the experimental values observed for the CuNO complex in argon matrix at 17 K by a Fourier transform infrared (FTIR) spectroscopy (1611 and 609 cm(-1)). The charge on each atom is calculated to be +0.28 for Cu and -0.28 for the NO molecule at the ground state, suggesting that the bonding nature of the complex has an almost covalent character. The absorption bands of the complex are assigned to be a pi*(in-plane) --> pi* (out-of-plane) local excitation within the NO molecule ((1)A' --> (1)A '') for the first electronic excitation, and a pi*(in-plane) --> 4s back-donation like transition from NO to Cu for the second excitation band appearing in the visible region. A third absorption band is assigned to be a pi*(in-plane) --> 4p back-donation like transition from NO to the copper atom. (C) 1997 by John Wiley & Sons, Ltd.

The results of hybrid density functional calculations are reported at the B3-LYP level using all-electron basis sets for Y-X-Y-X-Y (X = B, Al, Ga, In; Y = O, S, Se) species in their linear and bent structures. While Al2O3 is linear, In2O3 has both linear and bent ground-state structures. All other species have only bent structures as a minima. In2Se3 tends to be a shallow U-shaped structure. A(l)2O(3), with the maximum X-Y electronegativity difference, has maximum ionic bonding. At the other extreme, B2Se3 has the least electronegativity difference and maximum X-Y covalent bonding. The natural charge analysis distinctively illustrates this by the polarization of charges between X and Y in the X2Y3 systems. The results of NBO analysis are also discussed.

The energy surface of the urea molecule was studied at the Moller-Plesset, B-LYP and B3-LYP density functional levels. The scanning of the energy surface indicates the presence of two energy minima corresponding to nonplanar C-2 and C-s symmetry structures. The C-2 symmetry structure is the most stable one, while the C-s symmetry isomer lies 6 kJ mol(-1) above the lowest energy minimum. The infrared spectra of the C-2 symmetry stable isomer were computed at the MP2/DZ(d,p), B-LYP/DZ(d,p), B-LYP/6-311+G(d,p) and B3-LYP/6-311++G(2d,p) levels and the assignment of the harmonic vibrational frequencies was accomplished through the calculated potential energy distribution of urea and urea-d(4). The comparison between the MP2/DZ(d,p) and B-LYP/DZ(d,p) infrared spectra of the C-2 and C-s symmetry isomers is presented and discussed. (C) 1997 by John Wiley & Sons, Ltd.

Hartree-Fock calculations using the PM3 Hamiltonian have been carried out on neutral and charged states of helicenes to assess how the force constants of these `nanosprings' are influenced by increasing or decreasing electron density. We find that one can modulate the nanospring stiffness electronically but this effect is small; a better approach is to vary the length of the nanospring, if possible, or otherwise modify the underlying composition of the spring. (C) 1997 by John Wiley & Sons, Ltd.

We report accurate ab initio studies of the dipole polarizabilities of the title molecules at the Hartree-Fock and density functional levels of theory. The molecular geometry was optimized in each case at the HF/6-311G(3d,2p) level of theory, and polarizabilities were then calculated with and without the addition of additional diffuse functions. In the case of ethene, 18 different DFT formulations were used, as follows; all combinations of the GAUSSIAN94 three inbuilt exchange functionals (Slater; X alpha and Becke88) with the six inbuilt correlation functionals (Vosko Wilk and Nusair = VWN; Modified VWN, Lee Yang and Parr; Perdew Local; Perdew 86 and Perdew/Wang 91). The remaining molecules were treated using the BLYP density functional formulation. We also give semi-empirical (AM1) polarizability calculations for comparison.We also report a successful attempt to correlate the mean molecular polarizability [alpha] with the molecular volume as calculated by molecular mechanics. (C) 1997 by John Wiley & Sons, Ltd.

The geometry of 2-(2-methyl-3-chloroanilino) nicotinic acid was studied in the gas phase and in the solid state using ab initio Hartree-Fock methods. Three different conformers were found in the gas phase. The structures of two polymorphic forms were optimized in a crystalline environment modeled by point charges. The calculations were carried out using the 6-31G basis set for the H, C, N and O atoms and the 6-6-31G basis set for the Cl atom. The MIA method was used in the SCF procedure of all calculations. (C) 1997 by John Wiley & Sons, Ltd.

We report accurate ab initio studies of the geometries, electric dipole moments and dipole polarizabilities of the title molecules at the Hartree-Fock and density functional (BLYP) levels of theory. The molecular geometry was optimized in each case at the HF/6-311G(3d,2p) level of theory, and polarizabilities were then calculated at the same geometry but with the addition of two standard sets of diffuse Gaussian primitives.The density functional procedure gives a significant improvement in all three principal values of the dipole polarizability tensor.We also report semi-empirical dipole polarizability calculations for comparison; in each case the geometry was optimized before the properties were calculated. Semi-empirical methods give a poor representation of the dipole polarizability for these molecules. (C) 1997 by John Wiley & Sons, Ltd.

All the possible keto and enol conformations of 3-formylmalondialdehyde I and 3-formylacetylacetone II were fully optimized at the ab initio MP2/6-31G** level. The most stable forms, which are the chelate ones, were further studied also with the density functional theory, using the Becke's three parameters hybrid method and the LYP (Lee, Yang and Parr) functional in order to test the effect of correlation energy, coming from different approaches, on the stability order. Although the stability difference (Delta E) is remarkably affected by the approach adopted for its evaluation, all results indicate that both compounds, in gas phase, exist as a mixture of their two chelate tautomers, E-1 (having the formyl C=O group and the C=C double bond of the chelate ring in cis position) and E-3 (formyl C=O and C=C in trans position). The hydrogen bond energy is slightly higher than in the parent compounds malondialdehyde and acetylacetone, in line with the calculated frequencies of the O-H stretching mode and with the shortening of the (OO)-O-... distance. (C) 1997 by John Wiley & Sons, Ltd.

An ab initio force field for the amidocyano-pyridinium methylide has been deduced from calculations based on density functional theory. The force constants derived from these ab initio calculations are used in order to establish an empirical force field for cycloimmonium ylides, where the transferability of the derived force constants was tested. In this way, we proposed a new atom-type for the ylidic carbon atom and for the cyclic nitrogen atom. The goal of this force field is to provide good quality geometries for cycloimmonium ylide molecules by energy minimization. The predicted structures for dicyano-pyridinium methylide, amidocyano-pyridinium methylide and the pyridinium cation using the Tripos force field with parameters established by density functional ab initio calculations were in good agreement with those of the experimental X-ray diffraction data. A general harmonic parameterization for the cycloimmonium ylides consistent with the available molecular mechanics models has been proposed. This report points out the importance of the ab initio force field availability to predict the structures of the cycloimmonium ylides. This study also includes a full conformational analysis. (C) 1997 by John Wiley & Sons, Ltd.

SUMMARY A Fourier transform Raman spectra of solid dicyano-pyridinium methylide is reported. Observed frequencies for normal modes are compared with those calculated from normal coordinate analysis carried on the basis of an ab initio force field for dicyano-pyridinium methylide. This force field has been deduced fromab initio calculations based on the density functional theory approach. A careful scaling of the internal force constants using correct vibrational assignments is shown to predict quite accurately our experimental vibrational frequencies and the potential energy distribution for dicyano-pyridinium methylide. Thus, a general valence force field for cycloimmonium ylides is constructed on the basis of structure and vibrational spectra of dicyano-pyridinium methylide. ©1997 by John Wiley & Sons, Ltd.