Raymond A. Poirier

Comparison of geometries and electronic structures of polyacetylene, polyborole, polycyclopentadiene, polypyrrole, polyfuran, polysilole, polyphosphole, polythiophene, polyselenophene and polytellurophene

Abstract 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 π-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 π-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 (CH 2 , SiH 2 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 π-system. The bandgap of polypyrrole is the largest of all polymers studied. This can be attributed to the large π-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 delecalized π-systems.

Cumulative atomic multipole representation of the molecular charge distribution and its basis set dependence

Abstract A simple procedure to decompose the theoretical molecular charge distribution into cumulative atomic multipoles supplementing any population analysis scheme has been described and tested for a number of molecules in extended basis sets. This approach may be applied to describe local charge distributions in neutral as well as charged systems and also leads to a simplified point-charge model conserving the local anisotropy of the atomic charge distribution in molecules. Such an approach may be useful in estimating intermolecular interactions, representing the molecular environment in solvent effect or enzyme catalytic activity studies, evaluation of molecular electrostatic potentials or tracing the quality of basis set functions.

Design of low band gap polymers employing density functional theory—hybrid functionals ameliorate band gap problem

Band gaps in solids and excitation energies in finite systems are underestimated significantly if estimated from differences between eigenvalues obtained within the local spin density approximation (LSDA). In this article we present results on 20 small‐ and medium‐sized π‐systems which show that HOMO–LUMO energy differences obtained with the B3LYP, B3P86, and B3PW91 functionals are in good agreement with vertical excitation energies from UV‐absorption spectra. The improvement is a result of the use of the exact Hartree–Fock exchange with hybrid methods. Negative HOMO energies and negative LUMO energies do not provide good estimates for IPs and EAs. In contrast to Hartree–Fock theory, where IPs are approximated well and EAs are given poorly, DFT hybrid methods underestimate IPs and EAs by about the same amount. LSDA yields reasonable EAs but poor IPs. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1943–1953, 1997

Spectroscopy of the transition state (theory). II. Absorption by H‡3 in H+H2→H‡3→H2+H

Absorption spectra of transition state configurations in the reaction H+H2→H‡3 →H2+H have been computed. The density of H‡3 in configuration space was obtained from a classical trajectory study of collinear reaction on the Siegbahn, Liu, Truhlar, and Horowitz (SLTH) ab initio potential energy surface (PES). Vertical transitions were assumed to an upper PES H*3 modeled on limited ab initio data; four different model PES for H*3 were examined. The effects of varying reagent collision energy, varying reagent vibrational excitation, varying isotopic mass, and varying optical transition moment were explored. Transition state spectra were also computed for thermal distributions of H+H2, at 300 and 1000 K. The transition state spectra obtained constituted a wing extending as far as 40 000 cm−1 to the ‘‘red’’ of the Lyman‐α transition. As illustrated here, the wing exhibited features that reflected the dynamics of reaction on the SLTH PES.

Intermolecular interactions using small basis sets: Perturbation theory calculations avoiding basis set superposition error

Abstract As preliminary numerical examples, we report some calculations on intermolecular interactions using a new method of perturbation theory introduced recently. The He…He, LiH…LiH and water—water interactions are studied with small basis sets. The essential feature of the method is that it eliminates basis set superposition errors without any a posteriori collection. Within the range of applicability of the perturbational treatment, the results may be superior to standard vibrational calculations which suffer from large basis set superposition errors.

Some periodic trends in organic compounds containing O, S, Se, and Te: An ab initio study

Abstract Calculated geometries, ionization energies, dipole moments and net atomic charges are compared for a series of organic compounds: CH 3 XH, H 2 CX, (CH 3 ) 2 CX, (CH 3 ) 2 X, CX, and chalcophenes, containing group-VI elements (XO, S, Se, Te). All calculations are performed using the standard 3-21G basis set. The results indicate that when comparing properties of compounds containing O, S, Se or Te, the standard 3-21G basis set for group-VI elements should include a d polarization function on S.

Mechanisms for the Deamination Reaction of Cytosine with H2O/OH− and 2H2O/OH−: A Computational Study

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)).

Comparisons of Computational and Experimental Thermochemical Properties of α-Amino Acids

This study provides comprehensive benchmark calculations for the thermochemical properties of the common α-amino acids. Calculated properties include the proton affinity, gas-phase basicity, protonation entropy, ΔH°(acid), ΔG°(acid), and enthalpies of formation for the protonated and deprotonated α-amino acids. In order to determine the performance at various levels of theory, including density functional methods and composite methods, the calculated thermochemical properties are compared to experimental results. For all the common α-amino acids investigated, the thermochemical properties computed with the Gaussian-n theories were found to be quite consistent with each other in terms of mean absolute deviation from experiment. While all Gaussian-n theory values can serve as benchmarks, we focus on the G3MP2 values as it is the least resource-intensive of the Gaussian-n theories considered.

Ab initio study of neutral O2, SO, S2, C2H2 and their mono- and dications

For the twelve title species, the bond order according to Mayers definition, the Mulliken overlap population and the force constants are determined using the minimal STO-3G, split-valence 3-21G and 6-31G* (5d) basis sets. In general all these properties increase with increasing formal charge for each diatomic species. In contrast, the internuclear distances decrease with increasing formal charge. These findings indicate that the outer electrons in the three neutral diatomic species reside in antibonding orbitals; removing them results in triple bonds in the dications which are all predicted to be stable in their ground states in spite of the electrostatic repulsion. The best predictions for the unknown internuclear distances in the ionic ground states are: re(O22+) = 1.046; re(SO1+) = 1.411; re(SO2+) = 1.359; re (S21+) = 1.800 and re(S22+) =1.732 A. For acetylene, the behaviour on removal of the electrons is opposite to that observed for the diatomics: the bond order, overlap population and force constants all decrease with increasing formal charge. Both the acetylenic cation and dication are predicted to be stable, linear species in their electronic ground states with re(CC) = 1.247 and re(CH) = 1.076 A for the monocation and re(CC) = 1.326 and re(CH) = 1.116 A for the triplet dication. Using the SCF optimized structures, the total energies for the species were computed at the CISD and CISD-Q levels. These lead to predicted second ionization potentials of about 24.1, 19.1, 16.6 and 19.9 eV for O2, SO, S2 and C2H2, respectively.

AB Initio molecular orbital calculations on the si2h4molecule

Abstract Ab initio molecular orbital calculations using an extended Gaussian basis set have been performed on C 2 H 4 , CH 2 SiH 2 and Si 2 H 4 . The species CH 2 and SiH 2 have also been examined. Geometries were partially optimized and the energy difference between the planar singlet and orthogonal or twist triplet geometries of Si 2 H 4 was studied in order to provide a measure of the strength of the Si-Si bond in this molecule. Mulliken population analyses were carried out on CH 2 CH 2 and SiH 2 SiH 2 , to further study the nature of the Si-Si double bond in comparison with the C—C double bond.