Douglas P. Linder

Thermal rate constants for R+N2H2→RH+N2H (R=H, OH, NH2) determined from multireference configuration interaction and variational transition state theory calculations

Ab initio electronic structure calculations were performed to determine features of the potential energy surface for abstraction of a hydrogen atom from N2H2 by H, OH, and NH2. Based on multireference configuration interaction calculations with basis sets up to correlation consistent polarized valence triple zeta, the barrier heights determined for these reactions are 4.3, 3.0, and 4.4 kcal/mol, respectively. Using features of the potential energy surface along minimum energy paths determined at the complete active space self‐consistent‐field level of theory, variational transition state theory calculations were performed to determine the rate coefficients over the temperature range 300–3000 K. The temperature dependent computed rate coefficients for the three reactions are well represented by the following three‐parameter expressions: kH(T) =1.41×10−19T2.63 exp(115.8/T) cm3 molec−1 s−1, kOH(T)=9.84×10−23 T3.40 exp(686.3/T) cm3 molec−1 s−1, and kNH2(T)=1.46×10−25T4.05 exp(810.5/T) cm3 molec−1 s−1. Abstrac...

The diagnostic vibrational signature of pentacoordination in heme carbonyls.

Heme-carbonyl complexes are widely exploited for the insight they provide into the structural basis of function in heme-based proteins, by revealing the nature of their bonded and nonbonded interactions with the protein. This report presents two novel results which clearly establish a FeCO vibrational signature for crystallographically verified pentacoordination. First, anisotropy in the NRVS density of states for νFe–C and δFeCO in oriented single crystals of [Fe(OEP)(CO)] clearly reveals that the Fe–C stretch occurs at higher frequency than the FeCO bend and considerably higher than any previously reported heme carbonyl. Second, DFT calculations on a series of heme carbonyls reveal that the frequency crossover occurs near the weak trans O atom donor, furan. As νFe–C occurs at lower frequencies than δFeCO in all heme protein carbonyls reported to date, the results reported herein suggest that they are all hexacoordinate.

Methanethiol Binding Strengths and Deprotonation Energies in Zn(II)–Imidazole Complexes from M05-2X and MP2 Theories: Coordination Number and Geometry Influences Relevant to Zinc Enzymes

Zn(II) is used in nature as a biocatalyst in hundreds of enzymes, and the structure and dynamics of its catalytic activity are subjects of considerable interest. Many of the Zn(II)-based enzymes are classified as hydrolytic enzymes, in which the Lewis acidic Zn(II) center facilitates proton transfer(s) to a Lewis base, from proton donors such as water or thiol. This report presents the results of a quantum computational study quantifying the dynamic relationship between the zinc coordination number (CN), its coordination geometry, and the thermodynamic driving force behind these proton transfers originating from a charge-neutral methylthiol ligand. Specifically, density functional theory (DFT) and second-order perturbation theory (MP2) calculations have been performed on a series of [(imidazole)nZn-S(H)CH3](2+) and [(imidazole)nZn-SCH3](+) complexes with the CN varied from 1 to 6, n = 0-5. As the number of imidazole ligands coordinated to zinc increases, the S-H proton dissociation energy also increases, (i.e., -S(H)CH3 becomes less acidic), and the Zn-S bond energy decreases. Furthermore, at a constant CN, the S-H proton dissociation energy decreases as the S-Zn-(ImH)n angles increase about their equilibrium position. The zinc-coordinated thiol can become more or less acidic depending upon the position of the coordinated imidazole ligands. The bonding and thermodynamic relationships discussed may apply to larger systems that utilize the [(His)3Zn(II)-L] complex as the catalytic site, including carbonic anhydrase, carboxypeptidase, β-lactamase, the tumor necrosis factor-α-converting enzyme, and the matrix metalloproteinases.

Computational modeling of factors that modulate the unique FeNO bonding in {FeNO}6 heme–thiolate model complexes

A density functional theory account of the changes in FeNO bonding that occur in response to both bonded and nonbonded structural perturbations is reported for a series of {FeNO}6 heme–thiolate model complexes. Using [Fe(porphine)(SCH3)NO] as the reference complex, we constructed models to mimic equatorial (cis), distal, and proximal influences of protein environments. Overall, the results from these calculations reveal that the Fe–NO and N–O bond strengths change in the same direction upon variations in structure and environment. These bonding changes are manifested in unique direct correlations between the Fe–NO and N–O vibrational frequencies and bond lengths, as evidenced by their positive slopes (slopes of the familiar inverse or backbonding correlations are negative). The electronic origin of the direct correlations appears to derive from the electron density distribution in high-energy molecular orbitals. This variability modulates the FeNO antibonding character throughout the triatomic FeNO moiety. The results of this study suggest that the stabilities and reactivities of {FeNO}6 centers in heme–thiolate enzymes can be modulated over a significant range through a variety of bonded and nonbonded means.

Abinitio determination of the energy barriers and rate constants for HOBO+HF→FBO+H2O and OBBO+HF→FBO+HBO

We report ab initio calculations of features of the potential energy surfaces for two reactions of potential importance for the combustion of boron in fluorine‐containing environments; HF+HOBO→H2O+FBO and HF+OBBO→FBO+HBO. Both reactions proceed through four‐center transition states and yield the product FBO, a stable molecule that appears to play a similar role for B/F/O/H combustion as the isoelectronic CO2 does for hydrocarbon combustion. Multireference configuration interaction calculations with valence triple‐zeta, double polarization basis sets yield energy barriers of 27.2 and 46.2 kcal/mol, respectively, for these two reactions. Transition state theory calculations based on the ab initio potential energy surface information yield the following three‐parameter fits for the temperature‐dependent rate coefficients. kHOBO(T)=1.436×102 T2.71 exp(−11 917/T) cm3/mol s and kOBBO(T)=4.819×104 T2.38 exp(−22 028/T) cm3/mol s. Both reactions are predicted to be orders of magnitude slower than the estimated rat...