Functionally relevant protein motions: extracting basin-specific collective coordinates from molecular dynamics trajectories

Functionally relevant motion of proteins has been associated with a number of atoms moving in a concerted fashion along so-called "collective coordinates." We present an approach to extract collective coordinates from conformations obtained from molecular dynamics simulations. The power of this technique for differentiating local structural fluctuations between classes of conformers obtained by clustering is illustrated by analyzing nanosecond-long trajectories for the response regulator protein Spo0F of Bacillus subtilis, generated both in vacuo and using an implicit-solvent representation. Conformational clustering is performed using automated histogram filtering of the inter-C(alpha) distances. Orthogonal (varimax) rotation of the vectors obtained by principal component analysis of these interresidue distances for the members of individual clusters is key to the interpretation of collective coordinates dominating each conformational class. The rotated loadings plots isolate significant variation in interresidue distances, and these are associated with entire mobile secondary structure elements. From this we infer concerted motions of these structural elements. For the Spo0F simulations employing an implicit-solvent representation, collective coordinates obtained in this fashion are consistent with the location of the protein's known active sites and experimentally determined mobile regions.     

Chiral Lewis acid-catalyzed asymmetric Baylis-Hillman reactions

An effective chiral Lewis acid-catalyzed asymmetric Baylis-Hillman reaction is described. Good to high enantioselectivities were obtained using 3 mol % chiral catalyst. Novel camphor-derived dimerized ligands were prepared from the condensation of (+)-ketopinic acid with the corresponding diamines and hydrazine under acidic conditions. When alpha-naphthyl acrylate was used as a Michael acceptor, the reaction is complete within 20 min with high stereoselectivity and in reasonable chemical yields.     

Operator splitting algorithm for isokinetic SLLOD molecular dynamics

We apply an operator splitting method to develop a simulation algorithm that has complete analytical solutions for the Gaussian thermostated SLLOD equations of motion [D. J. Evans and G. P. Morriss, Phys. Rev. A 30, 1528 (1984)] for a system under shear. This leads to a homogeneous algorithm for performing both equilibrium and nonequilibrium isokinetic molecular dynamics simulation. The resulting algorithm is computationally efficient. In particular, larger integration time steps can be used compared to simulations with regular Gaussian thermostated SLLOD equations of motion. The utility and accuracy of the algorithm are demonstrated through application to the Weeks-Chandler-Anderson fluid. Although strict conservation of the kinetic energy suppresses thermal fluctuations in the system, this algorithm does not allow simulations at lower shear rates than those normally afforded by older nonequilibrium molecular dynamics simulations.     

8—氮鸟嘌呤的极谱伏安行为

用循环伏安法（ＣＶ）、电流采样极诸法（ＳＣＰ，即ＴＡＳＴ）、常规脉冲极谱法（ＮＰＰ）、微分脉冲极谱法（ＤＰＰ）、线性扫描伏安法（ＬＳＶ）、Ｏｓｔｅｒｙｏｕｎｇ方波伏安法（ＯＳＷＶ）和计时库仑法（ＣＣ）等电化学技术研究了抗癌药物８－氮鸟嘌呤（８－ａｚａｇｕａｎｉｎｅ，ｇｕａｎａｚｏｌｏ，简称８－ＡＧ）的极谱伏安行为．在 ０． １ｍｏｌ／Ｌ Ｈ２ＳＯ４底液中，８－ＡＧ有一良好的还原峰，峰电位（Ｅｐ）在－０． ９５Ｖ（ｖｓ．Ａｇ／ＡｇＣｌ，下同）附近，８－ＡＧ浓度在４×１０－６～８×１０－４ｍｏｌ／Ｌ范围内．峰高与浓度有良好的线性关系，线性相关系数ｒ＝０．９９９９～０．９９１０，检出限为１× １０－６ｍｏｌ／Ｌ．实验证明了该峰具有吸附性．本文提出了电极反应机理，它包括：酸性介质中８－ＡＧ的质子化、质子化的８－ＡＧ在汞电极上吸附以及完全不可逆的两电子还原过程．同时用量子化学计算方法（全略微分重叠法即ＣＮＤＯ／２）对８－ＡＧ和鸟嘌呤的各原子的净电荷以及Ｗｉｂｅｒｇ键级进行了计算，从理论上解释了８－ＡＧ的电化学还原机理。     

X-ray spectrometry using polycapillary X-ray optics and position sensitive detector

Polycapillary X-ray optics (capillary X-ray lens) are now popular in X-ray fluorescence (XRF) analysis. Such an X-ray lens can collect X-rays emitted from an X-ray source in a large solid angle and form a very intense X-ray microbeam which is very convenient for microbeam X-ray fluorescence (MXRF) analysis giving low minimum detection limits (MDLs) in energy dispersive X-ray fluorescence (EDXRF). A new method called position sensitive X-ray spectrometry (PSXS) which combines an X-ray lens used to form an intense XRF source and a position sensitive detector (PSD) used for wavelength dispersive spectrometry (WDS) measurement was developed recently in the X-ray Optics Laboratory of Institute of Low Energy Nuclear Physics (ILENP) at Beijing Normal University. Such a method can give high energy and spacial resolution and high detection efficiency simultaneously. A short view of development of both the EDXRF using a capillary X-ray lens and the new PSXS is given in this paper.     

Copper-catalysed photoinduced decarboxylative alkynylation: a combined experimental and computational study

Redox-active esters (RAEs) as alkyl radical precursors have demonstrated great advantages for C–C bond formation. A decarboxylative cross-coupling method is described to afford substituted alkynes from various carboxylic acids using copper catalysts CuCl and Cu(acac)₂. The photoexcitation of copper acetylides with electron-rich NEt₃ as a ligand provides a general strategy to generate a range of alkyl radicals from RAEs of carboxylic acids, which can be readily coupled with a variety of aromatic alkynes. The scope of this cross-coupling reaction can be further expanded to aliphatic alkynes and alkynyl silanes using a catalytic amount of preformed copper-phenylacetylide. In addition, DFT calculations revealed the favorable reaction pathway and that the bidentate acetylacetonate ligand of the copper intermediate plays an important role in inhibiting the homo-coupling of the alkyne.

Redox-active esters (RAEs) as alkyl radical precursors have demonstrated great advantages for Cu-catalysed C–C bond formation.     

甲基绿－萃取光度法测定锑

本文用Ｃｅ（ＳＯ＿４）＿２作氧化剂，在６ｍｏｌ／Ｌ　ＨＣｌ溶液中将Ｓｂ（Ⅲ）氧化为Ｓｂ（Ⅴ），过量的氧化剂用盐酸羟胺还原，生成的［ＳｂＣｌ＿６］￣－与甲基绿形成离子缔合物，在２ｍｏｌ／ＬＨＣｌ溶液中被ＣＨＣｌ＿３萃取。Ｔｌ、Ｉｎ、Ｇａ、Ａｕ等２０种离子共存时不干扰测定，用于金属镉及废水中测定微量锑，结果满意。     

Cure behavior of epoxy resin/MMT/DETA nanocomposite

The Flory's gelation theory, non-equilibrium thermodynamic fluctuation theory and Avrami equation have been used to predict the gel time t _g and the cure behavior of epoxy resin/organo-montmorillonite/diethylenetriamine intercalated nanocomposites at various temperatures and organo-montmorillonite loadings. The theoretical prediction is in good agreement with the experimental results obtained by dynamic torsional vibration method, and the results show that the addition of organo-montmorillonite reduces the gelation time t _gand increases the rate of curing reaction, the value of k, and half-time of cure after gelation point t_1/2 decreases with the increasing of cure temperature, and the value of n is ~2 at the lower temperatures (<60°C) and decreases to ~1.5 as the temperature increases, and the addition of organo-montmorillonite decreases the apparent activation energy of the cure reaction before gelation point, but has no apparent effect on the apparent activation energy of the cure reaction after gelation point. There is no special curing process required for the formation of epoxy resin/organo-montmorillonite/diethylenetriamine intercalated nanocomposite. This revised version was published online in July 2006 with corrections to the Cover Date.     

DFT studies on the multi‐channel reaction of CH3S+NO2

The mechanisms for the reaction of CH₃S with NO₂ are investigated at the QCISD(T)/6‐311++G(d,p)//B3LYP/6‐311++G(d,p) on both single and triple potential energy surfaces (PESs). The geometries, vibrational frequencies, and zero‐point energy (ZPE) correction of all stationary points involved in the title reaction are calculated at the B3LYP/6‐311++G(d,p) level. More accurate energies are obtained at the QCISD(T)/6‐311++G(d,p). The results show that 5 intermediates and 14 transition states are found. The reaction is more predominant on the single PES, while it is negligible on the triple PES. Without any barrier height for the whole process, the main channel of the reaction is to form CH₃SONO and then dissociate to CH₃SO+NO. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007