Ab initio studies on the tri- and diphosphate fragments of adenosine triphosphate

Pyrophosphate prototypes such as methyl triphosphate and methyl diphosphate molecules in their different protonation states have been investigated at high levels of quantum chemical calculations. The optimized geometries, the thermochemistry of the hydrolysis and the molecular orbitals contributing to the high energy of these compounds have been analyzed. These investigations provide insights into the "high energy" character of ATP molecule. Further, the dependence of vibrational frequencies on the number of phosphate groups and the charged states has also been presented. These results can aid the interpretation of spectra obtained by experiments on complexes containing pyrophosphate prototypes.

Bond length distortions associated with torsion potentials; ab-initio studies on methanedio

The 4-31G basis set is used to study the bond length variations as functions of dihedral angels in methanediol. This study is compared with O---C---O bond angle optimization studies by Gorenstein and Kar and the possible reason for bond length shorteing in the trans---trans configuration is analysed.

Ab initio studies on the tri- and diphosphate fragments of adenosine triphosphate

Pyrophosphate prototypes such as methyl triphosphate and methyl diphosphate molecules in their different protonation states have been investigated at high levels of quantum chemical calculations. The optimized geometries, the thermochemistry of the hydrolysis and the molecular orbitals contributing to the high energy of these compounds have been analyzed. These investigations provide insights into the ``high energy'' character of ATP molecule. Further, the dependence of vibrational frequencies on the number of phosphate groups and the charged states has also been presented. These results can aid the interpretation of spectra obtained by experiments on complexes containing pyrophosphate prototypes. (c) 2005 Elsevier B.V. All rights reserved.

Ab initio molecular orbital calculations on ion-molecule and ion pair-molecule complexes of the water-lithium cyanide system

Ab initio molecular orbital (MO) calculations with the 3-21G and 6-31G basis sets were performed on a series of ion-molecule and ion pair-molecule complexes for the H2O + LiCN system. Stabilisation energies (with counter-poise corrections), geometrical parameters, internal force constants and harmonic vibrational frequencies were evaluated for 16 structures of interest. Although the interaction energies are smaller, the geometries and relative stabilities of the monohydrated contact ion pair are reminiscent of those computed for the complexes of the individual ions. Thus, interaction of the oxygen lone pair with lithium leads to a highly stabilised C2v structure, while the coordination of water to the cyanide ion involves a slightly non-linear hydrogen bond. Symmetrical bifurcated structures are computed to be saddle points on the potential energy surface, and to have an imaginary frequency for the rocking mode of the water molecule. On optimisation the geometries of the solvent shared ion pair structures (e.g. Li+cdots, three dots, centered OH2cdots, three dots, centered CN−) revealed a proton transfer from the water molecule leading to hydrogen bonded forms such as Li-O-Hcdots, three dots, centered HCN. The variation in the force constants and harmonic frequencies in the various structures considered are discussed in terms of ion-molecular and ion pair-molecule interactions.

Ab initio molecular orbital calculations on ion pair-water complexes of metal halides and oxides

Ab initio MO calculations are performed on a series of ion-molecular and ion pair-molecular complexes of H2O + MX (MX = LiF, LiCl, NaCl, BeO and MgO) systems. BSSE-corrected stabilization energies, optimized geometrical parameters, internal force constants and harmonic vibrational frequencies have been evaluated for all the structures of interest. The trends observed in the geometrical parameters and other properties calculated for the mono-hydrated contact ion pair complexes parallel those computed for the complexes of the individual ions. The bifurcated structures are found to be saddle points with an imaginary frequency corresponding to the rocking mode of water molecules. The solvent-shared ion pair complexes have high interaction energies. Trends in the internal force constant and harmonic frequency values are discussed in terms of ion-molecular and ion-pair molecular interactions.

AB-initio study of alpha-silyl and beta-silyl substituent effects on vinyl radicals

The geometries of alpha- and beta-silyl substituted vinyl radicals and of alpha,beta-disilylvinyl radical have been optimised with the STO-3G and the STO-3G* basis sets. The relative stabilities of various conformers have been determined at the UMP2/6-31G* level. The stabilisation of vinyl radicals through alpha-silyl substitution is larger than that due to corresponding alkyl groups. The presence of an alpha-silyl group also leads to a tendency towards linearisation of the vinyl radical centre and a corresponding reduction in the inversion barrier. In marked contrast, the beta-silyl effect is negligible. The geometric, conformational and energetic consequences are insignificant. Overall, the silyl substituent effect at vinyl radicals is very different from that computed earlier for the vinyl cations, but qualitatively similar to that found in carbanions.

An examination of the BEBO model with the results of ab initio calculations of a reaction series

The BEBO (bond energy-bond order) model of Johnston and Parr is examined with the results of ab initio MO calculations on a series of metathetic reactions which involve hydrogen transfer. Energies are calculated at the 6-31G**/PMP2 = full//6-31G** level while the bond orders are estimated using the 6-31G** basis set with the geometry optimisation at the single configuration unrestricted Hartree-Fock frame. Our analysis reveals that the bond-order exponent in the BEBO theory is greater than unity for the reaction series and the entropy term becomes implicitly present in the BEBO model.

Use of L matrix to obtain reliable ab initio force constants of polyatomic molecules: ethylene as a test system

Direct use of experimental eigenvalues of the vibrational secular equation on to the ab initio predicted eigenvector space is suggested as a means of obtaining a reliable set of intramolecular force constants. This method which we have termed RECOVES (recovery in the eigenvector space) is computationally simple and free from arbitrariness. The RECOVES force constants, by definition, reproduce the experimental vibrational frequencies of the parent molecule exactly. The ab initio calculations were carried out for ethylene as a test molecule and the force constants obtained by the present procedure also correctly predict the vibrational frequencies of the deuterated species. The RECOVES force constants for ethylene are compared with those obtained by using the SQM procedure.

Electron donor-acceptor complexes of I-2 with diethyl ether and diethyl sulphide. An ab initio MO study

The charge-transfer complexes of I-2 with the n-donors diethyl ether and diethyl sulfide were studied at the Hartree-Fock and MP2 levels. The structures were fully optimized using the 3-21G((*)) basis set as well as with effective core potentials. The calculations consistently yield a C-2v structure for the ether-I-2 complex, but an unsymmetrical form for the sulfide-I-2 complex. A natural bond orbital analysis and the BSSE-corrected complexation energies reveal stronger interactions in the sulfide complex. The computed orbital energies of the monomers and complexes reproduce the trends in experimentally observed vertical ionization potentials.

Electron donor-acceptor complex of ICl with diethyl ether - He I photoelectron spectroscopy and ab initio molecular orbital study

The He I photoelectron spectrum of the diethyl ether-ICl complex has been obtained. The oxygen orbitals are shifted to higher binding energies and that of ICl to lower binding energies owing to complex formation. Ab initio molecular orbital (MO) calculations of the complex molecule showed that the bonding is between the sigma-type lone pair of oxygen and the I atom and that the complex has C-2v symmetry. The binding energy of the complex is computed to be 8.06 kcal mol(-1) at the MP2/3-21G* level. The orbital energies obtained from the photoelectron spectra of the complex are compared and assigned with orbital energies obtained by MO calculations. Natural bond orbital analysis (NBO) shows that charge transfer is from the sigma-type oxygen lone pair to the iodine atom and the magnitude of charge transfer is 0.0744 e.

UVPES and ab initio molecular orbital studies on the electron donor-acceptor complexes of bromine with methylamines

The He I photoelectron spectra of bromine, methylamine, and their complex have been obtained, and the spectra show that lone-pair orbital energy of nitrogen in methylamine is stabilized by 1.8 eV and the bromine orbital energies are destabilized by about 0.5 eV due to complexation. Ab initio calculations have been performed on the charge-transfer complexes of Br-2 with ammonia and methyl-, dimethyl-, and trimethylamines at the 3-21G*, 6-311G, and 6-311G* levels and also with effective core potentials. Calculations predict donor and acceptor orbital energy shifts upon complexation, and there is a reasonable agreement between the calculated and experimental results. Complexation energies have been corrected for BSSE. Frequency analysis has confirmed that ammonia and trimethylamine form complexes with C-3v symmetry and methylamine and dimethylamine with C-s symmetry. Calculations reveal that the lone-pair orbital of nitrogen in amine and the sigma* orbital of Br-2 are involved in the charge-transfer interaction. LANL1DZ basis seems to be consistent and give a reliable estimate of the complexation energy. The computed complexation energies, orbital energy shifts, and natural bond orbital analysis show that the strength of the complex gradually increases from ammonia to trimethylamine.

An ab-initio study of the role of lone pairs in the structure and insulator-metal transition in SnO and PbO

We have performed density functional calculations on tetragonal SnO and PbO (litharge) in the space group P4/nmm with the specific intention of examining the role played by Sn 5s and Pb 6s lone pairs in stabilizing the structure, and in giving rise to semi-metallic behavior (of SnO at ambient pressure and of PbO in the gamma phase). Use of the electron localization function has permitted real-space visualization of the lone pair in these structures. We also discuss the electronic structure of the orthorhombic PbO (massicot, space group Pbma) which again has localized lone pairs, contrary to some earlier expectation. (C) 2002 Editions scientifiques et medicales Elsevier SAS. All rights reserved.

Unimolecular HCl elimination from 1,2-dichloroethane: A single pulse shock tube and ab initio study

Thermal decomposition of 1,2-dichloroethane (1,2-DCE) has been studied in the temperature range of 10501175 K behind reflected shock waves in a single pulse shock tube. The unimolecular elimination of HCl is found to be the major channel through which 1,2-DCE decomposes under these conditions. The rate constant for the unimolecular elimination of HCl from 1,2-dichloroethane is found to be 10(13.98+/-0.80) exp(-57.8+/-2.0/RT) s(-1), where the activation energy is given in kcal mol(-1) and is very close to that value for CH3CH2Cl (EC). Ab initio (HF and MP2) and DFT calculations have been carried out to find the activation barrier and the structure of the transition state for this reaction channel from both EC and 1,2-DCE. The preexponential factors calculated at various levels of theory (BF/6-311++G**, MP2/6-311++G**, and B3LYP/6-311++G**) are (approximate to10(15) s(-1)) significantly larger than the experimental results. If the torsional mode in the ground state is treated as free internal rotation the preexponential factors reduce significantly, giving excellent agreement with experimental values. The DFT results are in excellent (fortuitous?) agreement with the experimental value for activation energy for 1,2-DCE while the MP2 and HF results seem to overestimate the barrier. However, DFT results for EC is 4.5 kcal mol(-1) less than the previously reported experimental values. At all levels, theory predicts an increase in HCI elimination barrier on beta-Cl substitution on EC.

Thermal decomposition of haloethanols: single pulse shock tube and ab initio studies

This paper reports single pulse shock tube and ab initio studies on thermal decomposition of 2-fluoro and 2-chloroethanol at T=1000–1200 K. Both molecules have HX (X = F/Cl) and H2O molecular elimination channels. The CH3CHO formed by HX elimination is chemically active and undergoes secondary decomposition resulting in the formation of CH4, C2H6, and C2H4. A detailed kinetic simulation indicates that the formation of C2H4 could not be quantitatively explained as arising exclusively from secondary CH3CHO decomposition. Contributions from primary radical processes need to be considered to explain C2H4 quantitatively. Ab initio calculations on HX and H2O elimination reactions from the haloethanols at HF, MP2, and DFT levels with various basis sets up to 6/311++G**are reported. It is pointed out that due to strong correlations between A and Eα, comparison of these two parameters between experimental and theoretical results could be misleading.