Compound I in heme thiolate enzymes: a comparative QM/MM study

This study directly compares the active species of heme enzymes, so-called Compound I (Cpd I), across the heme-thiolate enzyme family. Thus, sixty-four different Cpd I structures are calculated by hybrid quantum mechanical/molecular mechanical (QM/MM) methods using four different cysteine-ligated heme enzymes (P450(cam), the mutant P450(cam)-L358P, CPO and NOS) with varying QM region sizes in two multiplicities each. The overall result is that these Cpd I species are similar to each other with regard to many characteristic features. Hence, using the more stable CPO Cpd I as a model for P450 Cpd I in experiments should be a reasonable approach. However, systematic differences were also observed, and it is shown that NOS stands out in most comparisons. By analyzing the electrical field generated by the enzyme on the QM region, one can see that (a) the protein exerts a large influence and modifies all the Cpd I species compared with the gas-phase situation and (b) in NOS this field is approximately planar to the heme plane, whereas it is approximately perpendicular in the other enzymes, explaining the deviating results on NOS. The calculations on the P450(cam) mutant L358P show that the effects of removing the hydrogen bond between the heme sulfur and L358 are small at the Cpd I stage. Finally, Mossbauer parameters are calculated for the different Cpd I species, enabling future comparisons with experiments. These results are discussed in the broader context of recent findings of Cpd I species that exhibit large variations in the electronic structure due to the presence of the substrate.     

Electron transfer activation of chromopyrrolic acid by cytochrome p450 en route to the formation of an antitumor indolocarbazole derivative: theory supports experiment

QM/MM calculations support experiment and show that StaP is a P450 that functions like a peroxidase: its active species is the one-electron-reduced Cpd II species with a radical on CPA, by analogy to cytochrome c peroxidase (CcP), and its reaction with the substrate proceeds by overall proton-coupled electron transfer (PCET), in analogy to the corresponding mechanism in horseradish peroxidase (HRP). The electron transfer is enabled by His250, the presence of carboxylate groups in CPA, and by the H-bonding network that tunes the energetic of the process. Theory supports experiment but reveals some novel aspects of this unusual P450.     

An efficient unnatural base pair for PCR amplification

Expansion of the genetic alphabet by an unnatural base pair system provides a powerful tool for modern biotechnology. As an alternative to previous unnatural base pairs, we have developed a new pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and 2-nitropyrrole (Pn), which functions in DNA amplification. Pn more selectively pairs with Ds in replication than another previously reported pairing partner, pyrrole-2-carbaldehyde (Pa). The nitro group of Pn efficiently prevented the mispairing with A. High efficiency and selectivity of the Ds-Pn pair in PCR amplification were achieved by using a substrate mixture of the gamma-amidotriphosphate of Ds and the usual triphosphates of Pn and the natural bases, with Vent DNA polymerase as a 3' to 5' exonuclease-proficient polymerase. After 20 cycles of PCR, the total mutation rate of the Ds-Pn site in an amplified DNA fragment was approximately 1%. PCR amplification of DNA fragments containing the unnatural Ds-Pn pair would be useful for expanded genetic systems in DNA-based biotechnology.     

Efficient configuration selection scheme for vibrational second-order perturbation theory

A fast algorithm of vibrational second-order Moller-Plesset perturbation theory is proposed, enabling a substantial reduction in the number of vibrational self-consistent-field (VSCF) configurations that need to be summed in the calculations. Important configurations are identified a priori by assuming that a reference VSCF wave function is approximated well by harmonic oscillator wave functions and that fifth- and higher-order anharmonicities are negligible. The proposed scheme has reduced the number of VSCF configurations by more than 100 times for formaldehyde, ethylene, and furazan with an error in computed frequencies being not more than a few cm(-1).     

Long-range corrected density functional calculations of chemical reactions: redetermination of parameter

Chemical reaction calculations were carried out using the long-range correction (LC) scheme, which improves long-range exchange effects in density functional theory (DFT) [J. Chem. Phys. 115, 3540 (2001); 120, 8425 (2004)]. A new determination of the LC scheme parameter mu was made by a root mean square fit of the percent error in calculated atomization energies. As a result, the parameter mu was optimized as 0.47, which is higher than the previous one (mu=0.33). Using this new parameter mu, LC-DFT was firstly applied to geometry optimizations of the G2 benchmark set molecules. Consequently, this new LC-DFT gave more accurate bond lengths and bond angles than previous LC-DFT and hybrid B3LYP results. Following this result, the authors calculated reaction barrier height energies of benchmark reaction sets, which have been underestimated in conventional DFT calculations. Calculated results showed that LC-DFT provided much more accurate barrier height energies with errors less than half those of previous LC-DFT and B3LYP studies. To test the general validity of the new LC-DFT, the authors finally calculated reaction enthalpies. As a result, they found that the LC scheme using the new mu clearly improved the accuracy of calculated enthalpies. The authors therefore conclude that the insufficient inclusion of long-range exchange effects is responsible for the underestimation of reaction barriers in DFT calculations and that LC-DFT using the new parameter is a powerful tool for theoretically investigating chemical reactions.     

New implementation of molecular double point‐group symmetry in four‐component relativistic Gaussian‐type spinors

A new, practical implementation of double‐group symmetry to relativistic Gaussian spinors is presented for four‐component relativistic molecular calculations. We show that the systematic adaptability to irreducible representations under arbitrary point‐group symmetry, as well as Kramers (time‐reversal) symmetry, is inherent in the present basis spinors, which possess the analytic structure of Dirac atomic spinors. The implementation of double‐group symmetry entails significant computational efficiencies in the relativistic second‐order Møller–Plesset perturbation calculation on Au₂ and the density functional theory (DFT) calculation with the B3LYP functional on octahedral UF₆, in which the highest symmetries used are, respectively, C and D. The four‐component B3LYP equilibrium geometry of UF₆ is reported. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Anionic Polymerization of New Dual-Functionalized Styrene and α-Methylstyrene Derivatives Having Styrene or α-Methylstyrene Moieties

Anionic polymerizations of four new dual-functionalized styrene and α-methylstyrene derivatives, 3-(4-(4-isopropenylphenoxy)butyl)styrene ( 4 ), 3-(4-(2-isopropenylphenoxy)butyl)-α-methylstyrene ( 5 ), 4-(4-(4-isopropenylphenoxy)butyl)-α-methylstyrene ( 6 ), and 4-(4-(2-vinylphenoxy)butyl)styrene ( 7 ), were carried out in THF at -78 °C with sec-BuLi as an initiator. Both 4 and 5 underwent anionic polymerization in a living manner to quantitatively afford functionalized polystyrenes and poly(α-methylstyrene)s having α-methylstyrene moiety in each monomer unit and precisely controlled chain lengths. On the other hand, insoluble polymers were obtained by the anionic polymerization of 6 and 7 under the same conditions. The positional effect of substituent on anionic polymerization was discussed.     

Binding energies and electronic structures of Cu(OH2)n and Cu(NH3)n (n=1–4): anomaly of the two ligand Cu complexes

Ab initio calculations up to MP4(SDTQ) level and density functional theory have been used to estimate binding energies and electronic structures of Cu⁺(L)_n (L=OH₂, NH₃, n=1–4) complexes using TZP basis set types. The computed binding energies agree well with experimental values. General trends in structures and energetics are recorded for both Cu⁺(OH₂)_n and Cu⁺(NH₃)_n systems. The first two ligands are more strongly bound to Cu⁺ than the third and fourth molecules. The 4s–3dσ hybridization and electrostatic interactions are the main factors behind the higher binding energies for the first two ligands. Analysis of HOMO mixed orbitals in the copper ion as well as in complexes indicates shrinking of the orbital lobes directed to the ligand with shrinking more effective in the two ligand system. The lower binding energies for the third and fourth ligands were attributed to the attenuation of sdσ hybridization and decreasing of Cu–L attraction at long separation which is necessary to relieve Cu–L and L–L exchange repulsions. NBO analysis and charge-model calculations support the presence of sdσ hybridization and electron transfer to the copper ion in case of the first two ligands.