Geometries of monomers through hexamers of cylopentadiene, pyrrole, furan, silole, phosphole, thiophene, selenophene and tellurophene, and monomers through nonamers of borole were optimized employing density functional theory with a slightly modified B3P86 hybrid functional. Bandgaps and bandwidths were obtained by extrapolating the appropriate energy levels of trimers through hexamers (hexamers through nonamers for borole) to infinity. Bandgaps increase with increasing ~-donor strengths of the heteroatom. In general, second period heteroatoms lead to larger bandgaps than their higher period analogs. Polyborole is predicted to have a very small or no energy gap between the occupied and the unoccupied w-levels. Due to its electron deficient nature polyborole differs significantly from the other polymers. It has a quinoid structure and a large electron affinity. The bandgaps of heterocycles with weak donors (CH2, Sill2 and PH) are close to that of polyacetylene. For polyphosphole this is due to the pyramidal geometry at the phosphorous which prevents interaction of the phosphorus lone pair with the or-system. The bandgap of polypyrrole is the largest of all polymers studied. This can be attributed to the large w-donor strength of nitrogen. Polythiophene has the third largest bandgap. The valence bandwidths differ considerably for the various polymers since the avoided crossing between the flat HOMO-1 band and the wide HOMO band occurs at different positions. The widths of the wide HOMO bands are similar for all systems studied. All of the polymers studied have strongly delocalized or-systems.
DFT calculations on a series of oligomers have been used to estimate band gaps, ionization potentials, electron affinities, and bandwidths for polyacetylene, polythiophene, polypyrrole, polythiazole, and a thiophenethiazole copolymer. Using a slightly modified hybrid functional, we obtain band gaps within 0.1 eV of experimental solid-state values. Calculated bond lengths and bond angles for the central ring of sexithiophene differ by less than 0.026 Å and 0.7 from those of the sexithiophene crystal structure. IPs and EAs are overestimated by up to 0.77 eV compared to experimental bulk values. Extrapolated bandwidths agree reasonably well with bandwidths from band structure calculations.
The reactant and transition-state structures for several s N 2 reactions between different nucleophiles and methyl and ethyl chloride and fluoride have been calculated at the H F / 6 -1 3 + G * level. The secondary a-deuterium kinetic isotope effects for these reactions were calculated with Sim's BEBOVIB-IV program. The results demonstrate that the magnitude of these isotope effects is determined by an inverse stretching vibration contribution and a normal bending vibration contribution to the isotope effect. The stretching vibration contribution to the isotope effect is essentially constant for each substrate while the bending vibration contribution varies with the nucleophile and the looseness of the s N 2 transition state. Thus, the out-of-plane bending vibration model for relating the magnitude of secondary a-deuterium kinetic isotope effects to transition-state structure is correct. The bending vibration contribution to the isotope effect is greater in the ethyl substrate reactions than in the methyl substrate reactions. As a result, larger isotope effects and looser transition states are found for the s N 2 reactions of larger substrates. Looser transition states and larger isotope effects are also observed for the s N 2 reactions with softer nucleophiles.
The mechanism for the deamination reaction of cytosine with H(2)O and OH(-) to produce uracil was investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels and for anions at the B3LYP/6-31+G(d) level. Single-point energies were also determined at B3LYP/6-31+G(d), MP2/GTMP2Large, and G3MP2 levels of theory. Thermodynamic properties (DeltaE, DeltaH, and DeltaG), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway that was investigated. Intrinsic reaction coordinate analysis was performed to characterize the transition states on the potential energy surface. Two pathways for deamination with H(2)O were found, a five-step mechanism (pathway A) and a two-step mechanism (pathway B). The activation energy for the rate-determining steps, the formation of the tetrahedral intermediate for pathway A and the formation of the uracil tautomer for pathway B, are 221.3 and 260.3 kJ/mol, respectively, at the G3MP2 level of theory. The deamination reaction by either pathway is therefore unlikely because of the high barriers that are involved. Two pathways for deamination with OH(-) were also found, and both of them are five-step mechanisms. Pathways C and D produce an initial tetrahedral intermediate by adding H(2)O to deprotonated cytosine which then undergoes three conformational changes. The final intermediate dissociates to product via a 1-3 proton shift. Deamination with OH(-), through pathway C, resulted in the lowest activation energy, 148.0 kJ/mol, at the G3MP2 level of theory.
The structures, frequencies, and interaction energies of small
n = 1−4,
were calculated by ab initio Hartree−Fock theory with small- and
medium-sized basis sets (STO-3G, 3-21G,
6-31G*, 6-31G**, 6-31+G*, 6-31+G*(5d), 6-311G*). The
interaction energies were corrected for basis set
superposition error (BSSE) by Mayer's CHA/CE formalism. The
gives an excellent description of the binding energy. The geometry
and symmetric stretch frequency for
+ of 248
cm-1 (255 cm-1
expt) are well described at the HF/6-31G* level. The choice of
of the supermolecule was demonstrated to be of minor importance (±4
kJ/mol). The binding energies were
rationalized on crowding around the ion and a weakening Li−O
interaction. The first ab initio calculation
(STO-3G, 3-21G, 6-31G*, 6-31+G*) of a full second-solvation sphere of
a metal cation is presented ([Li(H2O)4
n = 4,8). The second solvation sphere of four waters
raises the frequency of the Li−O
vibration by 18 cm-1 (7%).
Mechanisms for the deamination reaction of cytosine with H 2O/OH (-) and 2H 2O/OH (-) to produce uracil were investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at MP2 and B3LYP using the 6-31G(d) basis set and at B3LYP/6-31+G(d) levels of theory. Single point energies were also determined at MP2/G3MP2Large and G3MP2 levels of theory. Thermodynamic properties (Delta E, Delta H, and Delta G), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway investigated. Intrinsic reaction coordinate (IRC) analysis was performed to characterize the transition states on the potential energy surface. Seven pathways for the deamination reaction were found. All pathways produce an initial tetrahedral intermediate followed by several conformational changes. The final intermediate for all pathways dissociates to product via a 1-3 proton shift. The activation energy for the rate-determining step, the formation of the tetrahedral intermediate for pathway D, the only pathway that can lead to uracil, is 115.3 kJ mol (-1) at the G3MP2 level of theory, in excellent agreement with the experimental value (117 +/- 4 kJ mol (-1)).
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