An extension of the AM1 semiempirical molecular orbital technique, AM1*, is introduced. AM1* uses AM1 parameters and theory unchanged for the elements H, C, N, O and F. The elements P, S and Cl have been reparameterized using an additional set of d orbitals in the basis set and with two-center core-core parameters, rather than the Gaussian functions used to modify the core-core potential in AM1. Voityuk and Rösch's AM1(d) parameters have been adopted unchanged for AM1* with the exception that new core-core parameters are defined for Mo-P, Mo-S and Mo-Cl interactions. Thus, AM1* gives identical results to AM1 for compounds with only H, C, N, O, and F, AM1(d) for compounds containing Mo, H, C, N, O and F only, but differs for molybdenum compounds containing P, S or Cl. The performance and typical errors of AM1* are discussed.
Density functional and molecular orbital theory calculations on models for cobalamin suggest that NO binds similarly to the Co(II) and Co(III) oxidation states. However, Co(III) can bind water far more strongly than Co(II) as a sixth ligand, so that the competition between water and NO complexation strongly favors water for Co(III) in the gas phase. Although the Co(II) oxidation state is found to bind water slightly more strongly than NO in the gas phase, the inclusion of solvation effects via the polarizeable continuum model makes NO binding more favorable. Thus, the experimentally observed ability of cob(II)alamin to bind NO in aqueous solution is the result of its weak complexation with water and the relatively poor solvation of NO. Calculated vibrational frequencies support the interpretation of the cob(II)alamin-NO complex as being cob(III)alamin-NO-, although the DFT calculations underestimate the degree of charge transfer in comparison to Hartree-Fock calculations.
Dedicated to Professor Wolfgang Kirmse on the occasion of his 75th birthdayThe controversies over concerted versus stepwise diradical mechanisms of potentially pericyclic reactions have subsided with improvements in the understanding of stereoselectivity in thermal rearrangements that involve modestly stabilized diradical intermediates. The thermal rearrangements of vinylcyclopropanes [1] and vinylcyclobutanes, [2] including bicyclo[3.2.0]hept-2-ene, [3] involve diradical intermediates that lack a deep potential energy well, and their outcomes deviate from statistical predictions. The thermal rearrangement of 6-methylenebicyclo[3.2.0]hept-2-ene (1) to 5-methylenenorbornene (3) is more intriguing, as it yields a nonrandom distribution of products despite the stabilizing effect of the 6-methylene substituent on the intermediate 2.Dideuterio labeling has revealed a preference for [1,3] over [3,3] shifts, [4] and the stereochemistry observed with methyl labels has led to the hypothesis that diradical intermediates do not equilibrate rotationally before collapsing to form the bicyclic products.[5] New experimental studies of monodeuterated species currently show modest levels of both regioand stereoselectivity (Table 1), [6] and DFT and ab initio calculations provide a theoretical framework for understanding these results.UB3 LYP and CASSCF calculations indicate that two modes of C1ÀC7 cleavage produce stereoisomeric diallyl intermediates 2 from 1 (Figure 1). The favored transition state, TS-12 n, moves C7 toward C3 and places the 7x substituent in an E configuration. In contrast, TS-12 x moves C7 away from C3 and puts the 7x substituent in the Z position. The preference (1.8 kcal mol À1 ; CASPT2//UB3 LYP) for TS-12 n over TS-12 x is analogous to torquoselectivity in electro- Table 1: Deuterium label distribution in product 3 from the thermolysis of 7x-, 8E-, and 8Z-1, extrapolated to t = 0 min.
Amino acids are constituents of proteins and enzymes which take part almost in all metabolic reactions. Glutamic acid, with an ability to form a negatively charged side chain, plays a major role in intra and intermolecular interactions of proteins, peptides, and enzymes. An exhaustive conformational analysis has been performed for all eight possible forms at B3LYP/cc-pVTZ level. All possible neutral, zwitterionic, protonated, and deprotonated forms of glutamic acid structures have been investigated in solution by using polarizable continuum model mimicking water as the solvent. Nine families based on the dihedral angles have been classified for eight glutamic acid forms. The electrostatic effects included in the solvent model usually stabilize the charged forms more. However, the stability of the zwitterionic form has been underestimated due to the lack of hydrogen bonding between the solute and solvent; therefore, it is observed that compact neutral glutamic acid structures are more stable in solution than they are in vacuum. Our calculations have shown that among all eight possible forms, some are not stable in solution and are immediately converted to other more stable forms. Comparison of isoelectronic glutamic acid forms indicated that one of the structures among possible zwitterionic and anionic forms may dominate over the other possible forms. Additional investigations using explicit solvent models are necessary to determine the stability of charged forms of glutamic acid in solution as our results clearly indicate that hydrogen bonding and its type have a major role in the structure and energy of conformers.
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