Ewald summation and multiple time step methods for molecular dynamics simulation of biological molecules

Methods by which to determine conditions for a molecular dynamics (MD) simulation of biological molecules were investigated. Derivation of the optimal parameters of the Ewald summation was described so as to give same precision to the real space, the reciprocal space summations and the van der Waals interaction. Later, the procedure by which to determine the condition of the multiple time step method by RESPA (REference System Propagator Algorithm; Tuckerman et al., 1992, J. Chem. Phys., 97, 1990) was described as exemplified by MD simulations of a solvated β-sheet peptide. The conservation of the total energy in a microcanonical ensemble was measured to investigate the stability of the simulation conditions. The most feasible respective combinations of the time steps were: 0.25 fs for bond, angle and torsion interactions; 2 fs for van der Waals interaction and Ewald real-space summation; and 4 fs for Ewald reciprocal-space summation. Though it retained an acceptable accuracy, this condition accelerated the simulation ten-fold compared to that in which a simple velocity-Verlet method with a time step of 0.25 fs was used. The update of the correction term due to excluded neighbors was then investigated. Better results were obtained when the correction was updated with the real-space than when it was updated with the reciprocal-space summation. Finally, an MD simulation as long as 50 ps performed under the optimal Ewald and RESPA parameters was thus determined. The trajectory showed a good stability, indicating the feasibility of the parameters.     

环己烯电化学环氧化的研究

The electrochemical epoxidation of cyclohexene on smooth platinum was investigated by means of convolution potential sweep voltammetry and potential step in H₂O-NaBr-MeCN-(这里有图片19891223-1260-1.gif) system.It is further proved that the electrochemical oxidation of Br^- is irreversible in the system, and the electrochemical epoxidation of cyclohexene shows a characteristic of ECcatatytic mechanism.Based on the analysis of data, some kinetic parameters were determined.     

Synthetic,spectroscopic, and structural Studies on Lanthanide Complexes of Diphosphazane Dioxide Ligands

Lanthanide nitrate complexes of diphosphazane dioxides Ph₂P(O)N(Prⁱ)P(O)Ph₂ ( 1 ) and (PhO)₂P(O)N(Me)P(O)(OPh)₂ ( 2 ) have been synthesised and studied by conductometry, IR, multinuclear NMR spectroscopic methods and X-ray diffraction. Ligand 2 is accessible by two different methods, viz., by direct oxidation of the phosp(III)azane ligand or by starting from phosph(V)azane chloro precursor. The structure of 2 is confirmed by X-ray diffraction. Crystallographic data for 2 : Triclinic, Space group P1 , a = 10.078(1), b = 10.575(3), c = 12.364(4) Å, α = 75.70(2)°, α = 75.56(1)°, γ = 77.68(1)°, Z = 2, V = 1 220 ų; structure refined to R_F = 0.0459 on 3 495 data with F > 3σ(F). The diphosphazane dioxide ligand exhibits trans geometry in the solid state. The structure of a lanthanide complex, [Pr(NO₃)₃( 2 )₂] ( 14 ) is also determined by X-ray diffraction. Crystallographic data for 14 : Trigonal, Space group P3₂, a = b = 15.710(2), c = 40.067(2) Å, Z = 6, V = 8 564 ų; structure refined to R_F = 0.0430 on 8 077 data with F > 5σ(F). The two diphosphazane dioxide ligands and the nitrate groups are coordinated to praseodymium in a bidentate chelate fashion. The geometry around the ten coordinated metal is distorted bicapped square antiprism.     

On the automatic restricted-step rational-function-optimization method

The rational function optimization algorithm is one of the widely used methods to search stationary points on surfaces. However, one of the drawbacks of this method is the step reduction procedure to deal with the overstepping problem. We present and comment on a method such that the step obtained from the solution of the rational function equations possesses the desired correct length. The analysis and discussion of the method is mainly centered on the location and optimization of transition states. Received: 18 June 1998 / Accepted: 17 September 1998 / Published online: 23 November 1998     

D8X射线衍射仪简易变温加热台的研制

成功研制的简易变温加热台,在不更换D8X射线衍射仪的附件情况下,能快速方便的安装在衍射仪上,进行X射线衍射原位变温测试,满足了从室温至600℃的原位变温X射线衍射测试需求.更换附件时间从2~3天缩短至30 min即可进行变温X射线衍射测试,提高了测试效率.同时,节省了购买同类变温加热台近20万元的资金.     

Synthesis and Stereochemistry of New Bis(1,3-Oxathian-2-yl) Derivatives: Epimerisation and Chair–Twist Equilibria

The synthesis and stereochemistry of some new bis(1,3-oxathian-2-yl) derivatives are reported. The conformational behavior of these compounds and the orientation of their substituents are deduced from the NMR spectra, from the X-ray crystal structures of two compounds and from the ab-initio level calculations. The epimerization of diastereoisomers and the chair ⇌ 22,5-twist equilibria were studied by variable temperature NMR.     

New insights into the transitional behaviour of methyl-6-O-(n-dodecanoyl)-α-D-glucopyranoside using variable temperature FTIR spectroscopy and X-ray diffraction

The liquid crystalline behaviour of methyl-6-O-(n-dodecanoyl)-α-D-glucopyranoside, 1, has been characterised using X-ray diffraction and variable temperature Fourier transform infrared (FTIR spectroscopy). 1 exhibits a monotropic interdigitated smectic A phase consisting of bilayers in which the alkyl chains are overlapped. The crystal–isotropic transition is accompanied by a pronounced decrease in the strength of the hydrogen bonding network involving the sugar groups resulting in a marked change in the environment of the alkyl chains. The isotropic phase consists of disordered smectic-like domains stabilised via hydrogen bonding between the sugar groups. At the transition to the smectic A phase, a subtle change in hydrogen bonding is observed which is manifested by a change in the temperature dependence of the OH stretching peak position in the FTIR spectrum. On crystallisation, the strong hydrogen bonding network is re-established accompanied by a change in the conformational distribution of the alkyl chains. A model is proposed in which a combination of hydrogen bonding (enthalpic effects) and conformational arrangements (entropic effects) promotes initially the formation of smectic-like domains in the isotropic phase and subsequently stabilises the smectic A phase by inhibiting the microphase separation leading to the crystal phase.     

Measurement of microchannel fluidic resistance with a standard voltage meter

A simplified method for measuring the fluidic resistance (R_fluidic) of microfluidic channels is presented, in which the electrical resistance (R_elec) of a channel filled with a conductivity standard solution can be measured and directly correlated to R_fluidic using a simple equation. Although a slight correction factor could be applied in this system to improve accuracy, results showed that a standard voltage meter could be used without calibration to determine R_fluidic to within 12% error. Results accurate to within 2% were obtained when a geometric correction factor was applied using these particular channels. When compared to standard flow rate measurements, such as meniscus tracking in outlet tubing, this approach provided a more straightforward alternative and resulted in lower measurement error. The method was validated using 9 different fluidic resistance values (from ∼40 to 600 kPa s mm⁻³) and over 30 separately fabricated microfluidic devices. Furthermore, since the method is analogous to resistance measurements with a voltage meter in electrical circuits, dynamic R_fluidic measurements were possible in more complex microfluidic designs. Microchannel R_elec was shown to dynamically mimic pressure waveforms applied to a membrane in a variable microfluidic resistor. The variable resistor was then used to dynamically control aqueous-in-oil droplet sizes and spacing, providing a unique and convenient control system for droplet-generating devices. This conductivity-based method for fluidic resistance measurement is thus a useful tool for static or real-time characterization of microfluidic systems.     

Acetate anion-selective encapsulation in the ellipsoidal cavity of symmetrical α,α′,δ,δ′-tetramethyl-cucurbit[6]uril

Four symmetrical α,α′,δ,δ′-tetramethyl-cucurbit[6]uril-based compounds have been prepared and characterised by X-ray crystallography. Their crystal structures displayed the acetate anion-selective encapsulating capability of symmetrical α,α′,δ,δ′-tetramethyl-cucurbit[6]uril. The host–guest interaction between the symmetrical α,α′,δ,δ′-tetramethyl-cucurbit[6]uril and the acetate anion in aqueous solution has also been observed by variable temperature ¹H NMR spectroscopy.     

Free‐energy differences between states with different conformational ensembles

Multiple conformations separated by high‐energy barriers represent a challenging problem in free‐energy calculations due to the difficulties in achieving adequate sampling. We present an application of thermodynamic integration (TI) in conjunction with the local elevation umbrella sampling (LE/US) method to improve convergence in alchemical free‐energy calculations. TI‐LE/US was applied to the guanosine triphosphate (GTP) to 8‐Br‐GTP perturbation, molecules that present high‐energy barriers between the anti and syn states and that have inverted preferences for those states. The convergence and reliability of TI‐LE/US was assessed by comparing with previous results using the enhanced‐sampling one‐step perturbation (OSP) method. A linear interpolation of the end‐state biasing potentials was sufficient to dramatically improve sampling along the chosen reaction coordinate. Conformational free‐energy differences were also computed for the syn and anti states and compared to experimental and theoretical results. Additionally, a coupled OSP with LE/US was carried out, allowing the calculation of conformational and alchemical free energies of GTP and 8‐substituted GTP analogs. © 2013 Wiley Periodicals, Inc.