Tobramycin与16S rRNA A位点复合物的分子动力学模拟

采用分子动力学方法(Molecular dynamics,MD)对托普霉素(Tobramycin)与16S rRNA的A位点复合物的特异性识别机制进行了理论模拟研究,模拟时间为3.6ns.结果表明,A位点中波动最大的部位是两个环外碱基A1492和A1493;tobramycin的环Ⅰ和环Ⅱ是其最保守的结构单元,可能参与了Tobramycin与16S rRNA的A位点之间的特异性识别.另外,发现一个残存时间为3.6ns的'结构化'水分子,它桥接了Tobra-mycin环Ⅱ的N3与环Ⅰ的N6′之间的氢键,稳定了Tobramycin的结构;Tobramycin周围水合密度较高的位点出现在环Ⅰ和环Ⅱ附近,这也正是晶体结构中形成较多水媒介氢键及动力学模拟中结构化水分子出现的位置.动力学模拟证实Tobramycin与16S rRNA间的结合是大量氢键及水分子相互作用的结果,这有助于设计和开发以Tobramycin为基础,具有高亲和力及特异性的16S rRNA抑制剂.

Rock-physics models of hydrate-bearing sediments in permafrost,Qilian Mountains,China

Rock-physics models are constructed for hydrate-bearing sediments in the Qilian Mountains permafrost region using the K–T equation model, and modes I and II of the effective medium model. The K–T equation models the seismic wave propagation in a two-phase medium to determine the elastic moduli of the composite medium. In the effective medium model, mode I, the hydrate is a component of the pore inclusions in mode I and in mode II it is a component of the matrix. First, the P-wave velocity, S-wave velocity, density, bulk modulus, and shear modulus of the sediment matrix are extracted from logging data.. Second, based on the physical properties of the main components of the sediments, rock-physics model is established using the K–T equation, and two additional rock-physics models are established assuming different hydrate-filling modes for the effective medium. The model and actual velocity data for the hydrate-bearing sediments are compared and it is found that the rock-physics model for the hydrate-filling mode II well reproduces the actual data.

Hydrolysis Mechanism of the NAMI-A-type Antitumor Complex （HL）[trans-RuCl4L（dmso-S）] （L=1-methyl-l,2,4-triazole）

The hydrolysis process of Ru（III） complex （HL）[trans-RuC14L（dmso-S）] （L=l-methyl-l,2,4- triazole and dmso-S=S-dimethyl sulfoxide） （1）, a potential antitumor complex similar to the well-known antitumor agent （Him）[trans-RuC14 （dmso-S）（im）] （NAMI-A, im=imidazole）, was investigated using density functional theory combined with the conductor-like polarizable continuum model approach. Tile structural characteristics and the detailed energy profiles for the hydrolysis processes of this complex were obtained. For the first hydrolysis step, complex 1 has slightly higher barrier energies than the reported anticancer drug NAMI-A, and the result is in accordance with the experimental evidence indicating larger half-life for complex 1. For the second hydrolysis step, the formation of cis-diaqua species is thermodynamic preferred to that of trans isomers. In addition, on the basis of the analysis of electronic characteristics of species in the hydrolysis process, the trend in nucleophilic attack abilities of hydrolysis products by pertinent biomolecules is revealed and predicted.

DFT Study of Geometrical and Vibrational Features of Sulfur Containing Amino Acids in Hydrated Media： L-Cysteine and L-Methionine

Geometry optimization at the B3LYP/6-31＋＋G＊ level of theory has been undertaken on clusters containing L-Met （L-methionine） or L-Cys （L-cysteine） surrounded by eight water molecules. The comparison of the structural parameters of L-Met and L-Cys with X-ray experimental values is in good agreement within 4.8%. This result shows that the privileged positions of water molecules and the possible hydrogen bonding network formed around the backbone of both AAs （amino acids） are adequate. Subsequent calculations of the harmonic vibrational modes followed by a post-processing treatment enable us to assign the vibrational modes of L-Met and L-Cys surrounded explicitly by eight water molecules. The frequencies of the assigned modes are in good agreement with available IR （infra red） and Raman values within 5%.

Generalized Energy-Based Fragmentation Approach for Accurate Binding Energies and Raman Spectra of Methane Hydrate Clusters

Methane hydrates(MHs)play important roles in the fields of chemistry,energy,environmental sciences,etc.In this work,we employ the generalized energy-based fragmentation(GEBF)approach to compute the binding energies and Raman spectra of various MH clusters.For the GEBF binding energies of various MH clusters,we first evaluated the various functionals of density functional theory(DFT),and compared them with the results of explicitly correlated combined coupled-cluster singles and doubles with noniterative triples corrections[CCSD(T)(F12^(*))]method.Our results show that the two best functionals are B3PW91-D3 and B97D,with mean absolute errors of only 0.27 and 0.47 kcal/mol,respectively.Then we employed GEBF-B3PW91-D3 to obtain the structures and Raman spectra of MH clusters with mono-and double-cages.Our results show that the B3PW91-D3 functional can well reproduce the experimental C-H stretching Raman spectra of methane in MH crystals,with errors less than 3 cm^(-1).As the size of the water cages increased,the C-H stretching Raman spectra exhibited a redshift,which is also in agreement with the experimental“loose cage-tight cage”model.In addition,the Raman spectra are only slightly affected by the neighboring environment(cages)of methane.The blueshifts of C-H stretching frequencies are no larger than 3 cm^(-1) for CH_(4) from monocages to doublecages.The Raman spectra of the MH clusters could be combined with the experimental Raman spectra to investigate the structures of methane hydrates in the ocean bottom or in the interior of interstellar icy bodies.Based on the B3PW91-D3 or B97D functional and machine learning models,molecular dynamics simulations could be applied to the nucleation and growth mechanisms,and the phase transitions of methane hydrates.

Measurement and modeling of the effective thermal conductivity for porous methane hydrate samples

The effective thermal conductivities of gas-saturated porous methane hydrates were measured by a single-sided transient plane source (TPS) technique and simulated by a generalized fractal model of porous media that based on self-similarity.The density of porous hydrate,measured by the volume of the sample in the experimental system,was used to evaluate the porosity of methane hydrate samples.The fractal model was based on Sierpinski carpet,a thermal-electrical analogy technique and one-dimensional heat flow assumption.Both the experimental and computational results show the effective thermal conductivity of methane hydrate decreases with the porosity increase.The porosity of 0.3 can reduce the thermal conductivity of the methane hydrate by 25%.By analysis of the experimental data and the simulative result,the optimized thermal conductivity of the zero-porosity methane hydrate is about 0.7 W m-1K-1.

Effects of Horizontal Density Distribution on Internal Bond Strength of Flakeboard

Horizontal density variation is a structural phenomenon of non-veneer wood composites. The variation and distribution characteristics of horizontal density have impacts on the products properties. In this study, veneer strip simulated flake boards with 4 kinds of density distribution were made using a mat model. The density variation of the modeled mats was discussed, as well as the relationship between sample size and density variation. The effects of density and density distribution of non-veneer composites on the internal bond strength were analyzed. Result shows that the horizontal density of random formed particleboard follows normal distribution. Density has remarkable influence on internal bond strength (IB). Increasing density helps to improve IB at lower density stage, but has negative impacts on IB at higher density stage. Density variation between testing specimens depends on their sizes. Properly increasing specimen size can decrease the variation of the IBs.