A series of aromatic polymers and copolymers have been investigated that contain a combination of 2,5-thienylene and 1,4-phenylene linkages. l,4-Bis-(2-thienyl)phenylene monomers have been prepared with a variety of substituents on the 2,5-phenylene positions. Subsequent oxidative polymerization of these monomers, both chemically and electrochemically, yield a family of polymers containing a thiophene-phenylene-thiophene repeat unit. Theoretical modeling, using both PRDDO and ab initio methods, has been used to correlate the thiophene-phenylene torsional angles with band gaps. In addition, polymer band structure has been investigated using the Extended Hiickel method.

The electronic and molecular structures of Ca3P2 and Ca6P4 are investigated using high-level ab initio methods. The lowest energy structure for Ca3P2 is found to be a Jahn-Teller distorted triplet. An excited-state singlet is found with various post HF methods; however, DFT incorrectly predicts a closed shell singlet to be the ground state. For the Ca6P4 system, both DFT and ab initio methods give consistent relative energies. The computational results demonstrate that the energetics are very sensitive to the size of the Ca basis set. Enhancing the Ca basis sets with additional s and p valence functions significantly affects the calculated energies.

The mechanisms of matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) has been investigated by focusing on the interaction between MALDI matrices and several tripeptides. 2,5-dihyroxybenzoic acid, α-cyano-4-hydroxy-cinnamic acid and 3,5-dihyroxybenzoic acid were studied as MALDI matrices interacting with four tripeptide sequences taken from bovine insulin: glutamic acid-arginine-glycine, glutamine-histidine-leucine, serine-histidine-leucine and threonine-proline-lysine. Molecular dynamics/simulated annealing calculations followed by geometrical refinement via density functional theory reveal a variety of matrix/peptide interactions. Most matrix-tripeptide clusters are bound through the side chains of the amino acids. In all clusters, the ionization potential (IP) of the matrix bound to the tripeptide is reduced relative to that of the free matrix. The origin of this IP lowering is discussed. In many cases, ionization of the cluster resulted in spontaneous proton transfer between the matrix and the tripeptide. The exothermicity of the spontaneous proton transfer reaction is considerably greater for the 2,5-DHB and HCCA clusters than for the 3,5-DHB clusters. This is of significance because the former two matrices are known to be very effective matrices for the MALDI process, while 3,5-DHB, although structurally similar to the others, is completely nonfunctional as a MALDI matrix.

Subnanometer size cluster precursors of uncapped CdS quantum dots were produced via the electroporation of synthetic dioleoylphosphatidylcholine (DOPC) unilamellar bilayer vesicles of mean hydrodynamic diameter Dh = 175 nm. During electroporation, Cd2+ ions are ejected from the interior compartments of the vesicles into the bulk solution where they react with S(2-) ions to form CdS monomers. The monomers adsorb on the exterior surface of the vesicles, where their spontaneous self-aggregation to (CdS)n clusters occurs on the hour and day time scale. The stepwise growth of the clusters was monitored through the time evolution of the UV absorption spectrum of the solution. The process is characterized by initial stepwise blue shifts of the absorption maxima: 285 nm --> 269 nm --> 245/275 nm --> 240 nm --> 236 nm, followed by a red shift to 494 nm. Nonlocal density functional theory (DFT) calculations of the optimized geometry and HOMO-LUMO gap of (CdS)n particles with n = 1-6 were carried out. The optimized structures are characterized by strong Cd-Cd bonds, with the S atoms bridging those bonds or capping the faces of the Cd polyhedra. The structure of such clusters bears no resemblance to fragments of the bulk crystal. The trend of the calculated HOMO-LUMO gaps facilitates the attribution of aggregation numbers (n) to particular clusters responsible for the observed absorption bands: n = 1 (285 nm), n = 2 (269 nm), n = 4 (245/275 nm --> 240 nm), n = 5 (236 nm), and larger quantum dots absorbing around 494 nm. The multiple bands assigned to the tetramer reflect the existence of its two distinct structures with similar stability.

The equilibrium nature of a plume of laser desorbed material is explored through the application of a simple equilibrium model to the ion signals observed in 355 nm laser desorption/ionization mass spectra of mixtures of the MALDI matrix α-cyano-4-hydroxycinnamic acid (αCHCA) with the amino acids glycine, alanine, valine, isoleucine, and phenylalanine. In these studies it is found that there are systematic and predictable increases in the relative yield of protonated amino acid with increases in amino acid gas-phase basicity. In addition, the thermodynamic values extracted from the equilibrium plot are shown to be in good agreement with values obtained from computational investigation of plausible αCHCA proton donor species. These results are supportive of a picture wherein the laser-desorbed material is viewed as a dense plume in which facile charge transfer occurs leading, ultimately, to a thermodynamically equilibrated distribution of proton donor and proton acceptor species.

The gas-phase basicities and gas-phase proton affinities of sinapic acid and ferulic acid, which are common matrices used in matrix assisted laser desorption/ionization mass spectroscopy, have been calculated using density functional theory at the B3LYP/6-311+G(2df,p)//B3LYP/6-31G** level. Respectively, the GBs of the two acids are 869.0 and 862.4kJ/mol while the gas-phase PAs of the same systems are 903.4 and 896.0kJ/mol. Our results indicate that the protonation in these systems takes place on the carboxylic sites. In addition, the GAs of the radical cations of these acids has also been calculated. The calculated GAs of SA and FA radical cations are 899.8 and 889.6kJ/mol, respectively. Our results indicate that deprotonation in the two radical cations takes place on the phenol sites. We also provide the first estimates of the vertical ionization potentials (IPs) of the same systems at the B3LYP/6-311++G(2df,p)//B3LYP/6-31+G** level using the lowest energy structure found for each acid. The calculated IPs of SA and FA are 7.54 and 7.82eV, respectively.

The alkyl group migration reaction CH3Co(CO)(4) --> CH3(CO)Co(CO)(3) and the carbonyl association reaction CH3(CO)Co(CO)(3) + CO --> CH3(CO)Co(CO)(4) have been thoroughly investigated via density functional theory techniques. In the migratory insertion reaction, two stable 16-electron acyl intermediates have been located on the B3LYP potential energy surface. Both species have the carbons of the acyl groups in the axial position. One of the intermediates is stabilized by the formation of an agostic interaction to the formally vacant site of the trigonal bipyramid, and the other is stabilized by the acyl oxygen adopting an eta(2) coordination geometry. The transition states between all the intermediates, as well as several internal rotation processes, have been located. An interesting feature of this reaction is that alkyl group migration is accompanied by a simultaneous twist of the alkyl group into the equatorial plane of the original trigonal bipyramid, and therefore the reaction does not take place on a C-s symmetry potential energy surface. The transition states for CO association with each intermediate have also been characterized. Our calculations indicate that the formation of the acyl intermediates proceeds via methyl migration and that thermal carbonylation of the agostically stabilized and the eta(2) stabilized intermediates is probably competitive.

An attempt is made to assign several of the peaks observed in the anion photodetachment photoelectron spectra of Al3P- and Al3P3- reported by Gdmez, Taylor and Neumark [J. Phys. Chem. A 2001, 105, 6886]. For the Al3P/Al3P- system, equilibrium geometries and harmonic vibrational frequencies are computed for several low-lying electronic states of the neutral molecule and the anion at the B3LYP, MP2, and CCSD(T) levels of theory using the 6-311+G(2df) one-particle basis set. Al3P- has a B-2(2) (C-2nu) ground state, whereas a near degeneracy is found between the (1)A(1) (C-3nu) and (1)A(1) (C-2nu) states of the Al3P molecule. The assignment of the Al3P- electron detachment spectrum is based on transitions from the B-2(2) (C-2nu) ground state of the anion to neutral states with the same C-2nu geometry. On the other hand, the adiabatic electron affinity (AEA) of Al3P is computed as the difference in the total energies of the 2132 (C-2nu) ground state of the anion and the (1)A(1) (C-3nu) ground state of the neutral. Its value is 1.76 eV at the CCSD(T) level. A value of 2.051 +/- 0.020 eV reported as the AEA of Al3P in the photoelectron study is assigned to the energy difference between the zero point vibrational levels of the 2132 (C-2nu) state of the anion and (1)A(1) (C(2)nu) state of the neutral. In the case of the Al3P3-/Al3P3 system, the smallest basis set used is 6-311+G(d) and the largest is 6-311+G(3df). The anion has a (2)A'(1) (D-3h) ground state that is well separated from other states, whereas, the (1)A'(1) (D-3h) and the (1)A' (C-s) states of the neutral have almost the same energy. Vertical electron detachment energies (VEDE) computed for transitions originating from the (2)A'(1) ground state of the anion to neutral states with the D-3h geometry are in very good agreement with the experimental photoelectron data. Assuming a (1)A'(1) (D-3h) ground state, the AEA of Al3P3 is computed to be 2.39 eV at the CCSD(T) level. For a (1)A' (C-s) ground state, a value of 2.46 eV is obtained at the same level of theory. The experimental AEA of Al3P3 obtained from the photoelectron study is 2.450 +/- 0.020 eV.

Literature values for the gas-phase basicity (GB) and proton affinity (PA) of glutamic acid range from 216 to 224 kcal/mol (GB) and 218 to 241 kcal/mol (PA). In this paper, a high-level theoretical study aimed at resolving the apparent disagreement among the experimental values is presented. Hartree-Fock, MP2, and DFT calculations with lar ge basis sets were carried out on the neutral and protonated forms of glutamic acid. Nine protonated and 21 neutral conformers were located at the HF/3-21G and B3LYP/6-31+G** levels with full geometry optimization and characterization of stationary points. The energetics were subsequently reevaluated at the MP2(full)/6-311 + G(2d,p)//B3LYP/6-31 + G** level. Thermodynamic data in the harmonic approximation were obtained at the B3LYP/6-31+G**: level. This data was used to estimate the gas-phase distribution of conformers at 298 K, The lowest energy structures of protonated and neutral glutamic acid both exhibit cyclic structures due to the formation of intramolecular hydrogen bonds. The calculated PA and GB are 224.4 and 214.4 kcal/mol, respectively. It is shown that, when certain empirical corrections for the entropy of cyclization are omitted and appropriate adjustments are made to thermodynamic scales, the GB and gas-phase PA values reported here are in excellent agreement with a variety of previous experimental measurements.

We present a theoretical study of the geometric structure of Co(corrin)(L)(R)+ (R = CH3, i-C3H7 and adenosyl and L = NH3, pyridine and 5,6-dimethylbenzimidazole) as model systems for the vitamin B12 coenzyme. We have optimized the geometries of nine corrin derivatives with axial ligands of varying degrees of steric bulkiness. In addition, we have included reoptimized geometries for nine dimethylglyoxime derivatives. Our goal was to compare and contrast calculated geometries for corrin models to those found for the corresponding dimethylglyoxime derivatives, which are often used as a model of the corrin group in experimental systems. We found that the dimethylglyoxime model is appropriate for axial CoC distances, but not for axial CoN distances.

A variation of the frozen-core potential (FCP) method is developed and implemented within the modified version of the method of partial retention of diatomic differential overlap (PRDDO/M). The explicit treatment of core electrons is replaced with a potential based on the actual core-valence integrals rather than upon an arbitrary model potential. The core-valence orthogonality requirement is replaced by an energy shift operator. PRDDO/M/FCP calculations exhibit good agreement with ab initio calculations with the same basis set, while reducing the computational cost significantly. (C) 1997 John Wiley & Sons, Inc.

In part I of this series, the PESP (parameterized electrostatic potential) method was described and applied to the calculation of electrostatic-potential-derived charges for a wide variety of organic and inorganic systems. Based on PRDDO/M wave functions and parameterized against ab initio MP2/6-31G** calculations, PESP is an order of magnitude faster than nb initio STO-3G calculations, while achieving a level of accuracy that rivals that of far more sophisticated ab initio methods. In this study, the application of the PESP method to the high potential regions of molecules containing I-I, C, N, O, F, P, S, Cl, and Br is described. For a collection of 48 molecules and 55 distinct lone pair minima, PESP yields the location and depth Rf lone pair minima to an average accuracy (relative to MP2/6-31G**) of 0.03 Angstrom and 2.5 kcal/mol, respectively. Similarly, the location and well depths of minima in the ir regions of organic molecules are calculated to an accuracy of 0.08 Angstrom and 1.5 kcal/mol. PESP electrostatic potential maps are, in some cases, virtually indistinguishable from those obtained at the MP2/6-31G** level. (C) 1997 John Wiley & Sons, Inc.

A new approach for the calculation of electrostatic potential derived atomic charges is presented. Based on molecular orbital calculations in the PRDDO/M approximation, the new parametrized electrostatic potential (PESP) method is parametrized against ab initio MP2/6-31G** calculations. For a data set of 820 atoms in 145 molecules containing H, C, N, O, F, P, S, Cl, and Br (including hypervalent species), the PESP method achieves a mean absolute error of 0.037 e(-) with a correlation coefficient of 0.990. Unlike other approximate approaches, no scaling factor is required to improve the agreement between PESP charges and the underlying ab initio results. PESP calculations are an order of magnitude faster than the simplest ab initio calculation (STO-3G) on large molecules while achieving a level of accuracy that rivals much more elaborate nb initio methods. (C) 1997 by John Wiley & Sons, Inc.

: Here are significant findings of the project for period September 92-96. Theoretical studies indicate that extended chains consisting of isomeric TTF structures have electronic properties and stabilities comparable to TTF extended structures and are therefore of considerable interest as possible polymeric organic superconductive compositions. Synthetic strategies were developed to prepare polymeric TTF and isomeric TTF structures. Dramatically simplified synthetic procedures were developed to prepare TTF and ET-TTF donors in high yield and large quantities from inexpensive starting materials. Developed new techniques to purify, characterize and grow large single crystals of TTF and ET-TTF. Synthesized new organic conductive polymers with good electrical conductivities and processibility. Developed new processing and doping techniques for polyalkylthiophenes to provide consistently high conductivity materials.

Here are significant findings of the project for period September 92-96. Theoretical studies indicate that extended chains consisting of isomeric TTF structures have electronic properties and stabilities comparable to TTF extended structures and are therefore of considerable interest as possible polymeric organic superconductive compositions. Synthetic strategies were developed to prepare polymeric TTF and isomeric TTF structures. Dramatically simplified synthetic procedures were developed to prepare TTF and ET-TTF donors in high yield and large quantities from inexpensive starting materials. Developed new techniques to purify, characterize and grow large single crystals of TTF and ET-TTF. Synthesized new organic conductive polymers with good electrical conductivities and processibility. Developed new processing and doping techniques for polyalkylthiophenes to provide consistently high conductivity materials.

The conformations and electronic structures of several five-membered-ring polymers were investigated with the partial retention of diatomic differential overlap (PRDDO) method. Band structures of the polymers were calculated using the modified extended Huckel (MEH) method. The polymers considered in this study are analogous to heterocyclic polymers such as polythiophene, polyfuran, and polypyrrole; however, they have bridging groups of XY(2) (XY(2) = CH2, CF2, SiH2, and SiF2) instead of heteroatoms. The relative stability of the aromatic and quinoid forms of these polymers was examined through an oligomer approach. The evolution of the band gaps of these systems was analyzed in terms of bond-length alternations, changes in the C1-C4 distances, and the effects of pure electronic interactions between the polymeric backbone and the bridging groups. It was found that insertion of the bridging group into the polymeric backbone affects the band gap in two distinct ways. The decrease of the C1-C4 distance relative to that found in cis-polyacetylenes narrows the band gap of the aromatic form and widens the band gap of the quinoid form. On the other hand, electronic interactions tend to increase the band gap of the aromatic form and decrease the band gap of the quinoid form. The electronic effect of a CH2 group on the band gap is small but not negligible (ca. 0.7 eV), and the resultant band gaps of both the aromatic and quinoid forms are comparable to those of polyacetylenes. The electronic interactions of the other bridging groups are so small that the quinoid forms became more stable in the ground state.

The electronic structure of tetrathiafulvalene (TTF) and its three conformational isomers, 2,5-dimethylene-1,3-dithiolo[4,5-d] -1.3-dithiol (DDD), 1,4,5,8-tetrathianaphthalene (TTN), and bis(4-methylene-1,3-dithietan-2-ylidene) (BMDY), are studied using ab initio and PRDDO molecular orbital calculations and extended Huckel band calculations. The one-dimensional expansion of DDD is identical to that of TTF. TTN has two conformations, corresponding to a boat and chair form. Our calculations show that TTF is the most stable structure among the monomers studied. The stability of the polymers arising from these monomers is estimated by oligomer calculations extrapolated to infinite chain length. The bandwidths of their highest occupied band are rather narrow (0.54-1.03 eV); however, the three highest valence bands of each isomer are separated from each other by 0.1-0.4 eV. The calculated band gaps (2.7-2.9 eV) of all the isomers are larger than that of polythiophene (1.75 eV), whereas the ionization potentials (9.7-10.1 eV) are smaller than that of polythiophene (11.0 eV). Thus, it should be easier to make a p-type conductor by doping the systems with an electron-accepting molecule.

The highly fluorinated chiral ${C}_{3h}$ molecule ${\mathrm{C}}_{60}$${\mathrm{F}}_{48}$ was observed to sequentially attach two electrons in the gas phase to produce ${\mathrm{C}}_{60}$${\mathrm{F}}_{48}^{2\ensuremath{-}}$ and ${\mathrm{C}}_{60}$${\mathrm{F}}_{46}^{2\ensuremath{-}}$ + ${\mathrm{F}}_{2}$. The first electron affinity (EA) of ${\mathrm{C}}_{60}$${\mathrm{F}}_{48}$ was measured to be 4.06 \ifmmode\pm\else\textpm\fi{} 0.3 eV. The first and second EA were calculated to be E${\mathrm{A}}_{1}$ = 5.07 eV and E${\mathrm{A}}_{2}$ = 2.27 eV for the more symmetric ${D}_{3d}$ isomer. The dianion was found to be more stable with respect to electron detachment than the singly charged anion. This remarkable stability of the dianion is attributed to a potential barrier resulting from the long range Coulomb repulsion and short range electron-molecule binding.