Modeling of serine protease prototype reactions with the flexible effective fragment potential quantum mechanical/molecular mechanical method

A complete cycle of chemical transformations for the serine protease prototype reaction is modeled following calculations with the flexible effective fragment quantum mechanical/molecular mechanical (QM/MM) method. The initial molecular model is based on the crystal structure of the trypsin–bovine pancreatic trypsin inhibitor complex including all atoms of the enzyme within approximately 15–18 Å of the oxygen center O of the catalytic serine residue. Several selections of the QM/MM partitioning are considered. Fractions of the side chains of the residues from the catalytic triad (serine, histidine and aspartic acid) and a central part of a model substrate around the C–N bond to be cleaved are included into the QM subsystem. The remaining part, or the MM subsystem, is represented by flexible chains of small effective fragments, whose potentials explicitly contribute to the Hamiltonian of the QM part, but the corresponding fragment–fragment interactions are described by the MM force fields. The QM/MM boundaries are extended over the C–C bonds of the peptides assigned to the QM subsystem in the enzyme, C–C and C–N bonds in model substrates. Multiple geometry optimizations have been performed by using the RHF/6-31G method in the QM part and OPLSAA or AMBER sets of MM parameters, resulting in a series of stationary points on the complex potential-energy surfaces. All structures generally accepted for the serine protease catalytic cycle have been located. Energies at the stationary points found have been recomputed at the MP2/6-31+G^* level for the QM part in the protein environment. Structural changes along the reaction path are analyzed with special attention to hydrogen-bonding networks. In the case of a model substrate selected as a short peptide CH₃(NHCO-CH₂)₂ – HN–CO–(CH₂–NHCO)CH₃ the computed energy profile for the acylation step shows too high activation energy barriers. The energetics of this rate-limiting step is considerably improved, if more realistic model for the substrate is considered, following the motifs of the ThrI11–GlyI12–ProI13-–CysI14–LysI15–AlaI16–ArgI17–IleI18–IleI19 sequence of the bovine pancreatic trypsin inhibitor.     

Chiral molecular glass: synthesis and characterization of enantiomerically pure thiophene-based [7]helicene

Synthesis of thiophene-based [7]helicenes, which are functionalized for both design of organic chiral glasses with strong chiroptical properties and for further homologation to higher [n]helicenes, is reported. The key synthetic transformations are kinetic resolution of the intermediate diketone and the annelation step forming the center benzene ring by means of an intramolecular McMurry reaction. Based upon X-ray crystallographic determinations of the absolute configurations for (+)-enantiomers of the diketone and the [7]helicene, stereochemical correlation between the (R) axial chirality of the diketone and the (M) helical chirality of the [7]helicene is established. One such enantiopure trimethylsilyl-substituted [7]helicene possesses enchanced chiroptical properties and forms a chiral molecular glass.     

气相分子吸收光谱法测定地下水中亚硝酸盐氮、氨氮、硝酸盐氮

采用气相分子吸收光谱法测定地下水中的亚硝酸盐氮(NO2^-)、氨氮(NH4^+)、硝酸盐氮(NO3^-)。考察NO2^-,NH4^+和NO3^-测定时的相互干扰,并给出了相应的消除方法。研究结果表明,测定NO2^-时,NH4^+和NO3^-无干扰;NO2^-对测定NH4^+和NO3^-产生干扰,可分别采用分段法和加入2滴10%氨基磺酸溶液的方法消除干扰;对于不含NO2^-或NO2-含量不高的地下水样品,可简化操作步骤直接测定NO3^-。该方法测定结果的相对标准偏差为0.73%~2.74%(n=12),样品加标回收率为97.67%~100.28%。所用检测仪器具有流动注射、自动进样及在线绘制标准曲线的功能,简化了标准方法中的样品前处理过程,减少了样品的损失,实现了自动化分析,大幅提高了检测结果的准确度和工作效率。     

Incorporating the effect of ionic strength in free energy calculations using explicit ions

The incorporation of explicit ions to mimic the effect of ionic strength or to neutralize the overall charge on a system in free energy calculations using molecular dynamics simulations is investigated. The difference in the free energy of hydration between two triosephosphate isomerase inhibitors calculated at five different ion concentrations is used as an example. We show that the free energy difference can be highly sensitive to the presence of explicit ions even in cases where the mutation itself does not involve a change in the overall charge. The effect is most significant if the molecule carries a net charge close to the site mutated. Furthermore, it is shown that the introduction of a small number of ions can lead to very severe sampling problems suggesting that in practical calculations convergence can best be achieved by incorporating either no counterions or by simulating at high ionic strength to ensure sufficient sampling of the ion distribution.     

Synthesis and Structure of Some N-[3-(Het)aryl-2-propenylidene]trifluoromethylanilines

The reactions of 4-nitrocinnamaldehyde with trifluoromethylanilines in the presence of molecular sieves were studied, and a series of new aromatic and heterocyclic aldimines were synthesized. The molecular and crystal structure of some of them were determined by X-ray crystallographic analysis.     

Solution- and bound-state conformational study of N,N',N"-triacetyl chitotriose and other analogous potential inhibitors of hevamine: application of trNOESY and STD NMR spectroscopy

The solution-state conformations of N,N',N"-triacetyl chitotriose (1) and other potential chitinase inhibitors 2-4 were studied using a combination of NMR spectroscopy (NOESY) and molecular mechanics calculations. Determination solely of the global energy minimum conformation was found to be insufficient for an agreement with the NMR results. An appropriate consistency between the NMR experimental data and theoretical calculations was only reached by assessing the structures as population-weighted average conformers based on Boltzmann distributions derived from the calculated relative energies. Analogies, but also particular differences, between the synthetic compounds 2-4 and the naturally-occurring N,N',N"-triacetyl chitotriose were found. Furthermore, the conformation of compounds 1 and 2 when bound to hevamine was also studied using transferred NOESY experiments and the binding process was found to impart a level of conformational restriction on the ligands. The preferred conformation as determined for 1 in the bound state to hevamine belonged to one of the conformational families found for the compound when free in solution, although full characterisation of the bound-state conformations was impeded due to severe signal overlap. Saturation transfer difference NMR experiments were also employed to analyse the binding epitopes of the bound compounds. We thus determined that it is mainly the acetyl amido groups of the trisaccharide and the heterocyclic moiety which are in close contact with hevamine.     

Co‐Conformational Distribution of Nanosized [2]Catenanes Determined by Pulse EPR Measurements

The co‐conformational ensembles of three differently sized [2]catenanes were studied by measuring pair correlation functions corresponding to the separation of nitroxide spin labels—one attached to each of the two macrocycles—with the double electron–electron resonance (DEER) experiment. A geometric model for the [2]catenanes was derived that approximates the macrocycles by circles and takes into account the topological constraint. Comparison of the experimental to the theoretically predicted pair correlation functions gives insight into the co‐conformational distribution and the size of the macrocycles. It was found that the macrocycles of the medium‐ and large‐sized catenanes in chloroform are close to fully expanded, while they are partially collapsed in glassy o‐terphenyl. For the small‐sized catenane, moderate interaction between the unsaturated sections of the macrocycles in chloroform is indicated by a slight overrepresentation of short label‐to‐label separations in the pair correlation function.     

Binding Ensembles of p53-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

Designing peptide inhibitors of the p53-MDM2 interaction against cancer is of wide interest. Computational modeling and virtual screening are a well established step in the rational design of small molecules. But they face challenges for binding flexible peptide molecules that fold upon binding. We look at the ability of five different peptides, three of which are intrinsically disordered, to bind to MDM2 with a new Bayesian inference approach (MELD × MD). The method is able to capture the folding upon binding mechanism and differentiate binding preferences between the five peptides. Processing the ensembles with statistical mechanics tools depicts the most likely bound conformations and hints at differences in the binding mechanism. Finally, the study shows the importance of capturing two driving forces to binding in this system: the ability of peptides to adopt bound conformations (ΔGconformation) and the interaction between interface residues (ΔGinteraction).     

Molecular caps for full quantum mechanical computation of peptide-water interaction energy

We present a systematic study of numerical accuracy of various forms of molecular caps that are employed in a recently developed molecular fractionation scheme for full quantum mechanical computation of protein-molecule interaction energy. A previously studied pentapeptide (Gly-Ser-Ala-Asp-Val) or P5 interacting with a water molecule is used as a benchmark system for numerical testing. One-dimensional potential energy curves are generated for a number of peptide-water interaction pathways. Our study shows that various forms of caps all give consistently accurate energies compared to the corresponding full system calculation with only small deviations. We also tested the accuracy of cutting peptide backbone at different positions and comparisons of results are presented.     

Electronically-coupled MM quadruply-bonded complexes of molybdenum and tungsten

The reaction of M2(O2CBu(t))4 (M = Mo, W) with a dicarboxylic acid in toluene yields compounds of general formula [M2]-O2C-X-CO2-[M2] ([M2] = M2(O2CBu(t))3; X = conjugated spacer). The M2 units are electronically coupled via interactions between the M2 delta and dicarboxylate pi* orbitals, and the magnitude of this coupling is revealed by electronic structure calculations and spectroscopic data. These compounds show intense metal to ligand charge transfer (MLCT) absorptions in the visible region of the electronic spectrum that are temperature and solvent dependent. Evidence of electronic coupling is seen in their cyclic voltammograms, which show two successive one-electron oxidations. The extent of electronic coupling in the mixed valence radical cations [M2]-O2C-X-CO2-[M2]+, generated by oxidation with one equivalent of AgPF6 or FeCp2PF6, is evaluated by EPR and UV-vis-NIR spectroscopic data, and delocalized behavior is observed in compounds with W2 units separated by up to 13.6 angstroms. The simplicity of the frontier M2 orbital interactions with the bridge pi orbitals provides a convenient system with which to study electron transfer in mixed valence systems, as compared to the extensively studied, but more complicated, dinuclear t(2g)6/t(2g)5 mixed valence compounds. Oligomeric and polymeric compounds incorporating M2 units have also been synthesized, having general formula [M2(O2CR)2(O2C-Thio-CO2)]n (Thio = n-hexyl substituted ter- and quinque-thiophenes). They can be deposited as thin films by spin coating, and show photoluminescence and electroluminescence. These metallo-polythiophenes show potential for application in electronic materials. (