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51.
52.
The accuracy of biological simulations depends, in large part, on the treatment of electrostatics. Due to the availability of accurate experimental values, calculation of pKa provides stringent evaluation of computational methods. The generalized solvent boundary potential (GSBP) and Ewald summation electrostatic treatments were recently implemented for combined quantum mechanical and molecular mechanics (QM/MM) simulations by our group. These approaches were tested by calculating pKa shifts due to differences in electronic structure and electrostatic environment; the shifts were determined for a series of small molecules in solution, using various electrostatic treatments, and two residues (His 31, Lys 102) in the M102K T4-lysozyme mutant with large pKa shifts, using the GSBP approach. The calculations utilized a free energy perturbation scheme with the QM/MM potential function involving the self-consistent charge density functional tight binding (SCC-DFTB) and CHARMM as the QM and MM methods, respectively. The study of small molecules demonstrated that inconsistent electrostatic models produced results that were difficult to correct in a robust manner; by contrast, extended electrostatics, GSBP, and Ewald simulations produced consistent results once a bulk solvation contribution was carefully chosen. In addition to the electrostatic treatment, the pKa shifts were also sensitive to the level of the QM method and the scheme of treating QM/MM Coulombic interactions; however, simple perturbative corrections based on SCC-DFTB/CHARMM trajectories and higher level single point energy calculations were found to give satisfactory results. Combining all factors gave a root-mean-square difference of 0.7 pKa units for the relative pKa values of the small molecules compared to experiment. For the residues in the lysozyme, an accurate pKa shift was obtained for His 31 with multiple nanosecond simulations. For Lys 102, however, the pKa shift was estimated to be too large, even after more than 10 nanosecond simulations for each lambda window; the difficulty was due to the significant, but slow, reorganization of the protein and water structure when Lys 102 was protonated. The simulations support that Lys 102 is deprotonated in the X-ray structure and the protein is highly destabilized when this residue is protonated. 相似文献
53.
Qiang Xu Prof. Dr. Nobuko Tsumori Prof. Dr. Ling Jiang Masanobu Kondo Ryuichi Arakawa Prof. Dr. 《化学:亚洲杂志》2007,2(5):599-608
Carbonyldinitrosyltris(fluorosulfato)tungstate(II) and ‐molybdate‐(II) anions, [fac‐M(CO)(NO)2(SO3F)3]? (M=W, Mo), which are novel weakly coordinating anions that contain a metal carbonyl/nitrosyl moiety, have been generated in fluorosulfonic acid and completely characterized by multinuclear NMR, IR, and Raman spectroscopy as well as ESI mass spectrometry. ESI MS measurements performed for the first time on a superacidic solution system unambiguously reveal the formation of the monoanionic, mononuclear W and Mo complexes formulated as [M(CO)(NO)2(SO3F)3]? (M=W, Mo). Multinuclear NMR spectroscopic studies at natural abundance and 13C and 15N enrichment clearly indicate the presence of one CO ligand, two equivalent NO ligands, and two types of nonequivalent SO3F? groups in a 2:1 ratio. The IR and Raman spectra reveal that the two equivalent NO ligands have a cis conformation, thus indicating a fac structure. Density functional calculations at the B3LYP level of theory predict that these anions have a singlet ground state (1A′) with a Cs symmetry along with C–O and N–O vibrational frequencies that are in agreement with the experimental observations. Mulliken population analysis shows that the monovalent negative charge is dispersed on the bulky sphere, the surface of which is covered by all the negatively charged O and F atoms with charge densities much lower than SO3F?, suggesting that [fac‐M(CO)(NO)2(SO3F)3]? (M=W, Mo) are weakly nucleophilic and poorly coordinating anions. 相似文献
54.
Mutation of the active-site residue Cys38 of N-Ada converts it from a sacrificial DNA repair protein to an enzyme that uses methanethiol as an external sacrificial reagent to repair DNA methyl phosphotriesters catalytically. 相似文献
55.
YanXiaCAO MiaoDU QiangZHENG 《中国化学快报》2004,15(5):567-570
The study on rheological properties of a series of mica-filled polypropylene (PP) composites was carried out. The influence of surface-treatment of mica particles on dynamic rheological behavior of the composites were dealt with. The viscosity (η) and dynamic modulus ( G‘ ) of the composite melts were higher than those of PP matrix, especially those for systems treated with silane, which was attributed to the interfacial adhesion enhancement. However, surface-treatment of mica by titanate resulted in lower η and G‘, as compared with the treatment by silane. The reason for this is believed to be the formation of the mono-molecular layer on the mica surface. 相似文献
56.
57.
Wu X Ding S Ding Q Gray NS Schultz PG 《Journal of the American Chemical Society》2002,124(49):14520-14521
Purmorphamine, which is a 2,6,9-trisubstituted purine compound, was discovered through cell-based high-throughput screening from a heterocycle combinatorial library. It differentiates multipotent mesenchymal progenitor cells into an osteoblast lineage. It will serve as a unique chemical tool to study the molecular mechanisms of osteogenesis of stem cells and bone development. 相似文献
58.
[Chemical reaction: See text] We have developed a general, efficient, and inexpensive catalyst system for arylation of amines by using 10 mol % of CuI as the copper source, 20 mol % of diphenyl pyrrolidine-2-phosphonate (DPP) as the ligand, K3PO4 as the base, and DMF containing 2% water (v/v) as the solvent. 相似文献
59.
A two-tiered organizing scheme with multiple-length scales for construction of dandelion-like hollow CuO microspheres has been elucidated: (1) mesoscale formation of rhombic building units from smaller nanoribbons via oriented aggregation and (2) macroscopic organization of these units into the CuO microspheres. This self-assembly concept may also be applicable to other metal oxides by creating geometric constraints for constructional units. 相似文献
60.