某些环肽及其相应线型肽在不同溶剂中构象的CD谱研究

We used CD spectroscopy to study the conformations of three cyclic peptides (CP10E: cyclo[Glu(OBz1)-Pro-Gly-Glu(OBzl)-Gly]2, CP10K: cyclo[Lys(Z)-Pro-Gly-Lys(Z)-Gly]2, CP12K: cyclo[Phe-Lys(Z)-Pro-Gly-Lys(Z)-Gly]2 and their correspondent linear peptides (LP10E: Boc-[Glu(OBzl)-Pro-Gly-Glu(OBzl)-Gly]2-OPac, LP10K: Boc-[Lys(Z)-Pro-Lys(Z)-Pro]2-OMe, LP 12K: Bao- [-Lys(Z)-Pro-Gly-Lys(Z)-Gly]2- OMe) in three solvents of different polarity (chloroform, acetonitrile, 2,2,2-triliuroethanol), and it was found that all of linear and cyclicpeptides exists asγ-turn conformation in chloroform, however, in TFE＆ CH3CN solutions, the three linear peptides are inβ Ⅱ-turn conformations. CP10E isβI-turn conformation, CP10K ＆CP12K exists in more than one types of turn conformations. On the basis of our experiments, it was concluded: 1) In the presence of conformational constrained amino acids short linear peptides form obvious secondary structure; 2)The solvent polarity has influence on the peptide conformation and this influence on linear peptides is greater than that on cyclic peptides; 3)The backbone of cyclic peptide has constraint effect on its conformation and makes the secondary structure of cyclic peptide different from that of its relative linear peptide. This information might give some cules in the design of bioactive peptides with different receptor selectivity.     

Enhancement of electrostatic charge dissipation properties of polymers by a sustained‐release effect of mesoporous silica nanoparticles

Small molecular surfactant (SMS), used as antistatic agent of polymers, is prone to the wash‐out effects thus reducing its lifetime. To address this issue, the sustained‐release antistatic agent is prepared by encapsulating SMS (HDC‐102 or HDC‐193) into mesoporous silica nanoparticles such as MCM‐41 and is used to modify the antistatic properties of polystyrene (PS). The water‐resistant test is used to evaluate the sustained‐release effect, and the results showed that the HDC‐102/MCM‐41/PS composite retains favorable antistatic properties with the R_s of 6.2 × 10¹¹ after five times washing, while the HDC‐102/PS loses antistatic properties after twice washing. The contact angle measurement demonstrates that the sustained‐release effect is affected by the characteristics of SMS. Moreover, the coefficient of thermal expansion of SMS/PS composites is decreased, and the thermal decomposition temperature is increased with incorporation of MCM‐41. This approach may be used in polymer systems with the other small molecular additives to prolong their lifetime. Copyright © 2015 John Wiley & Sons, Ltd.     

温控分子动力学研究微管蛋白活性肽链的折叠机制

运用温控和常温分子动力学方法, 研究了微管蛋白活性部位Pep1-28肽链的折叠机制, 总模拟时间为380.0 ns. 对于温控分子动力学, 逐渐降温可以清晰显示Pep1-28肽链的折叠途径, 发生明显折叠的温度约为550 K, 其折叠和去折叠可逆机制为U(>1200 K)←→I1(1200-1000 K)←→I2(800 K)←→I3(600 K)←→I4(450 K)←→F1(400 K)←→F2(300 K), 其中U为去折叠态构象, I1、I2、I3和I4是折叠过程中的四个重要的中间态构象, F1和F2是两个结构相近的折叠态构象. 对于常温(300 K)分子动力学, 其构象转变和折叠过程相当迅速, 很难观察到有效、稳定的中间态构象. 尤其引人注意的是, 其折叠态结构陷入了能量局域极小点, 与温控(300 K)的有较大差异, 两者能量差高达297.53 kJ·mol-1. 可见, 温控分子动力学方法不仅清晰地显示多肽和蛋白质折叠过程的重要中间态构象, 为折叠和去折叠机制提供直接、可靠的依据, 而且还有助于跨越较高的构象能垒, 促使多肽和蛋白质折叠以形成全局能量最低的稳定结构.     

手性SalenZn配合物的合成及对咪唑类、吡啶类客体的分子识别研究

合成并表征了手性Salen配体1及其Zn配合物2。详细讨论了配体及配合物的电 子光谱和圆二色光谱性质。用紫外—可见光谱滴定法测定了主体2与4种咪唑、5种 吡啶客体轴向配位反应的平衡常数，研究了主体分子2的分子识别行为。实验结果 表明：各种客体的缔合常数，咪吡类按K(Im)＞K(2—MeIm)＞K(SMIm)＞K(EMIm)顺 序递减;吡啶类按K(Py)＞K(3-Py)＞K(3，5-Py)＞K(2，4—Py)＞K(2，4，6—Py)顺 序递减。测定了识别过程的△rGm^-,△rHm^-,△rSm^-，发现该反应是放热、熵减 小的过程。采用分子力学的方法考察了主客体的最低能量构象，并对该构象进行量 子化学计算，从理论上对实验事实给予较好的解释。     

Conformational preferences of proline oligopeptides

A conformational study on the terminally blocked proline oligopeptides, Ac-(Pro)(n)()-NMe(2) (n = 2-5), is carried out using the ab initio Hartree-Fock level of theory with the self-consistent reaction field method in the gas phase and in solutions (chloroform, 1-propanol, and water) to explore the preference and transition between polyproline II (PPII) and polyproline I (PPI) conformations depending on the chain length, the puckering, and the solvent. The mean differences in the free energy per proline of the up-puckered conformations relative to the down-puckered conformations for both diproline and triproline increases for the PPII-like conformations and decreases for the PPI-like conformations as the solvent polarity increases. These calculated results indicate that the PPII-like structures have preferentially all-down puckerings in solutions, whereas the PPI-like structures have partially mixed puckerings. The free energy difference per proline residue between the PPII- and PPI-like structures decreases as the proline chain becomes longer in the gas phase but increases as the proline chain becomes longer in solutions and the solvent polarity increases. In particular, our calculated results indicate that each of the proline oligopeptides can exist as an ensemble of conformations with the trans and cis peptide bonds in solutions, although the PPII-like structure with all-trans peptide bonds is dominantly preferred, which is reasonably consistent with the previously observed results. In diproline Ac-(Pro)(2)-NMe(2), the rotational barrier to the cis-to-trans isomerization for the first prolyl peptide bond increases as the solvent polarity increases, whereas the rotational barrier for the second prolyl peptide bond does not show the monotonic increase as the solvent polarity increases. When the rotational barriers for these two prolyl peptide bonds were compared, it could be deduced that the conformational transition from PPI with the cis peptide bond to PPII with the trans peptide bond is initiated at the C-terminus and proceeds to the N-terminus in water. This is consistent with the results from NMR experiments on polyproline in D(2)O but opposite to the results from enzymatic hydrolysis kinetics experiments on polyproline.     

Polar Organofluorine Substituents: Multivicinal Fluorines on Alkyl Chains and Alicyclic Rings

This Review outlines the progression, primarily of our own work, but with important contributions from other labs, on the synthesis and properties of multiple vicinally fluorinated alkyl chains and rings. Chain conformations of individual diastereoisomers with -CHF- at adjacent carbons are influenced by stereoelectronic factors associated with the polar C−F bond and the polarised geminal hydrogens. Generally, the chain will prefer a conformation which acts to minimise overall molecular polarity, and where the C−F bonds orient away from each other. However, when vicinal fluorine atoms are positioned on a ring then conformations are more constrained. The ring will adopt optimal conformations such as a chair in cyclohexane and then C−F bonds can be introduced with a stereochemistry that forces parallel (axial) orientations. In the case of cyclohexane, 1,3-diaxial arrangements of C−F bonds impart considerable polarity to the ring, resulting in an electronegative ‘fluorine face’ and an electropositive ‘hydrogen face’. For all-syn 1,2,3,4,5,6-hexafluorocyclohexane, this arrangement generates an unusually polar aliphatic ring system. Most recently the concept has been extended to the preparation of all-syn 1,2,3-trifluorocyclopropanes, a rigid ring system with fluorine atoms on one face and hydrogens on the other. Lipophilicity Log P values of such compounds indicate that they are significantly more polar than their parent alicyclic hydrocarbons and give some positive indication for a future role of such substituents in medicinal chemistry. Expanding to such a role will require access to improved synthesis methods to these motifs and consequently access to a broader a range of building blocks, however some exciting new methods have emerged recently and these are briefly reviewed.     

Molecular Dynamics Simulations of Cellulose Oligomers: Conformational Analysis

Summary: The results of classical molecular simulations of cellulose oligomers are presented here. The conformations of the chains in the high temperature melt, room temperature quenched melt and gas phase are compared with respect to various geometrical parameters including square end‐to‐end distances, glycosidic link torsion correlations, ring puckering and hydrogen bonding. The cellulose oligomer melts were relaxed at 800 K with molecular dynamics, and then cooled down in three different ways to obtain dense amorphous systems at 500 K and at room temperature. The sample resulting from the quench (step) shows too much similarity with the melt at 800 K. The two other cooling schemes (ramp, 2ramps) give very similar results for all quantities investigated. The relevance of previous single molecule calculations with respect to the dense amorphous systems is called into question. Comparisons between the chains in the dense systems and those in the gas phase reveal that, even for these relatively short stiff chains, differences exist in the preferred conformations. At high temperatures, where both systems are in equilibrium, the distribution of square end‐to‐end distances are both fairly smooth, but the gas phase clearly prefers more compact conformations. At 300 K, the differences are exacerbated as the equilibrium distribution for the gas phase shows a high proportion of folded conformers, whereas the nonequilibrium quenched systems necessarily retain the extended envelope of the higher temperature. Differences are also evident in the puckering, the rotation of the hydroxymethyl groups and the pattern of hydrogen bonds.

The probability density distribution for the square end‐to‐end distance for octaose in the gas phase (light line) and in the dense phase (dark line) at 300 K.     

Fluxional additives: a second generation control in enantioselective catalysis

The concept of "fluxional additives", additives that can adopt enantiomeric conformations depending on the chiral information in the ligand, is demonstrated in enantioselective Diels-Alder and nitrone cycloaddition reactions. The additive design is modular, and diverse structures are accessible in three steps. Chiral Lewis acids from main group and transition metals show enhancements in enantioselectivity in the presence of these additives.     

Ab initio studies on the vibrational spectra and conformational isomerism of 2,4-dimethyl-1,3-pentadiene

Ab initio was used to study the structure of various conformational isomers and their vibrational spectra of 2,4-dimethyl-1,3-pentadiene (2,4-PD) in detail. Two stable conformations, s-trans and s-cis, were found in which s-trans is more stable. The geometry of stable conformations and charge distributions were studied, and the effect of different basis sets on geometry optimization is discussed. The results of complete optimization indicate that molecular skeleton is nearly in a plane, its largest deviation is only 0.3 degrees. Therefore, it is reasonable and available to hypothesis that the molecule has Cs symmetry. The thermal dynamics conformations were calculated and compared with experimental values. DeltaH(o) between two conformations of 2,4-PD measured from experiment is 4.36 kJ/mol, deltaS(o) is 2.56 J/mol K., calculated results are slightly different from experimental ones. Vibrational frequencies of 2,4-PD conformers have been studied by ab initio molecular orbital calculations using different basis set. The calculated vibrational frequencies are analyzed and compared with the experimental spectra.     

Application of liquid chromatography in polymer non-ionic antistatic additives analysis

This article investigates the applicability of HPLC-UV, ultra performance LC-evaporative light-scattering detection (UPLC-ELSD), HPLC-ESI(+)-MS and HPLC-hybrid linear ion trap (LTQ) Orbitrap MS for the analysis of different non-ionic antistatic additives, Span 20, Span 60, Span 65, Span 80, Span 85 (sorbitan fatty acid esters), Atmer 129 (glycerol fatty acid ester) and Atmer 163 (ethoxylated alkylamine). Several alkyl chain length or different degrees of esterification of polyol derivatives can be present in commercial mixtures of these polymer additives. Therefore, their identification and quantification is complicated. Qualitative composition of the studied compounds was analysed by MS. HPLC-UV, UPLC-ELSD and HPLC-LTQ Orbitrap MS methods were applied to the quantitative determination of the different Spans, Atmer 129 and Atmer 163, respectively. Quality parameters of these methods were established and no derivatization was necessary.     

Molecular simulations for the conformational assessment of a porphyrin-fullerene dyad in different environments

Conformational space of a porphyrin-fullerene dyad with the donor and acceptor connected by a relatively flexible linker is studied by molecular dynamics simulations in both non-polar and polar solvents, as well as in vacuum. The most probable conformations obtained from the vacuum MD simulations were optimized with semi-empirical (SE) and density functional theory (DFT) methods and the extent of the structural changes is assessed. The computational results indicate the co-existence of different conformers in both polar and nonpolar solvents showing agreement with experimental results. The most probable vacuum conformations at 300 K are similar to the ones at 0 K, while the structures most often observed in the solvents show less compact conformations. Optimization with SE and DFT calculations leads to structures, which represent relatively well the folded conformations in solvent, which validates the electronic structure calculations relevant to describing photoinduced electron-transfer in H2P-O34-C60.     

新型手性酪氨酸修饰的锌卟啉对氨基酸酯的分子识别研究

合成并表征了一种L型Boc酪氨酸修饰的自由卟啉(L-BocTyrTAPP)及其锌卟啉配合物Zn(L-BocTyr)TAPP.通过紫外-可见光谱滴定法,研究了手性锌卟啉配合物与四对对映异构的手性氨基酸酯客体在CHCl₃中的分子识别行为.实验结果表明,在分子识别的过程中,缔合常数顺序均为D型略大于L型,且按K(PheOMe)>K(AIaOMe)>K(ValOMe)>K(LeuOMe)的顺序依次减小.同时,利用园二色光谱进一步阐述手性分子识别过程.此外,采用分子力学方法搜索了主客体体系的最低能量构象,从理论上对实验本质进行较深入的探讨.     

有机硅耐磨透明涂料

详细总结了构成有机硅耐磨涂料的主要原料，无机溶胶添加剂、溶剂及其他助剂，对兼有防雾性、可染色性、抗静电性、紫外吸收性的耐磨涂料进行了介绍，给出了ＪＤ涂覆液的制备及涂层的性能。     

Computational protocols for prediction of solute NMR relative chemical shifts. a case study of L-tryptophan in aqueous solution

In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L-tryptophan in aqueous solution, namely a molecular dynamics simulation and a molecular mechanics conformational search with subsequent geometry re-optimization of the stable conformers using a quantum mechanically based method. These spanning protocols represent standard ways of obtaining a set of conformations on which NMR calculations may be performed. The results stemming from the solute-solvent configurations extracted from the MD simulation at 300 K are found to be inferior to the results stemming from the conformations extracted from the MM conformational search in terms of replicating an experimental reference as well as in achieving the correct sequence of the NMR relative chemical shifts of L-tryptophan in aqueous solution. We find this to be due to missing conformations visited during the molecular dynamics run as well as inaccuracies in geometrical parameters generated from the classical molecular dynamics simulations.     

分子动力学模拟极端嗜热核糖结合蛋白的热力学稳定性

采用分子动力学模拟方法研究极端嗜热性核糖结合蛋白(tteRBP)的嗜热机理.在常温(300 K)和最佳活性温度(375 K)时,分别对tteRBP分子进行动力学模拟,结果表明,整体分子均保持结构稳定,但分子内部的协调运动不同.在375 K时蛋白整体柔性显著提高,使分子能够局部调整构象以适应极端高温.蛋白结构变化的分析也确认了高温时构象局部微调对蛋白极端高温稳定性的关键作用.     

Novel synthesis, reactivity, and stereochemistry of substituted 3-trifluoromethyl- and 3-perfluoroalkyl-3-phenoxyprop-2-enal

Substituted 3-phenoxy-3-perfluoroalkylprop-2-enals 3a-s are synthesized in high yields starting from a gem-iodoacetoxy derivative 1 and phenoxides 2. Then efficient syntheses of push-pull derivatives 4, 5,8a,b, and nonconjugated analogues 6 and 7 illustrate the synthetic potentialities of 3. Stereochemical studies of these perfluoroalkyl-containing trisubstituted olefinic derivatives 3-8b revealed that the (4)J(CF) coupling constant observed in the (13)C NMR spectra was crucial in the determination of their configurations and conformations in solution. The solvent polarity effect on the stereochemistry of push-pull compounds 3-5 and 8a,b was studied. Unusual significant medium polarity effect on the stereochemistry of imino enol ether derivative 4 was observed.     

Relationships of Surfactant Head Group Weight Fraction and Some Polarity Terms by Gas Chromatography

 Polarity, partition coefficient (K), methanol carbon number of surfactant ((CMeOH)S), and methanol carbon number of surfactant head group ((CMeOH)HG) are measured on six alkanolamides and five polyoxyethylenated long chain amines as stationary phases. From the measured methanol carbon numbers, polarity indices, (IP)S and (IP)HG, are calculated. The determined polarity terms are plotted against the head group weight fraction ( fHG ) of the investigated surfactants and several equations have been developed. The study reveals that the molecular structural gap between alkanolamides and polyoxyethylenated long chain amines diminished when HLB numbers of these surfactant classes are plotted against fHG values. Consequently, a general equation relating HLB and fHG is obtained.     

Shape persistence and bistability of planar three-fold core polyphenylene dendrimers: a molecular dynamics study

We present an atomistic molecular dynamics investigation of the structural time evolution of isolated polyphenylene dendrimers, carbon based dendrimers with a planar core formed by a 1,3,5 trisubstituted benzene ring. Simulations are carried out at low (80 K) and room temperature. A general classification of the conformations (core conformations) assumed by the three dendrimer branches with respect to the planar core is presented. It is found that out of the six possible core conformations only four are stable, the remaining two being unstable for steric reasons. For second generation dendrimers, two of the four accessible core conformations are associated with an open arrangement of the three branches attached to the planar 3-fold core of the dendrimer, whereas the remaining two are associated with a collapsed arrangement of two branches. At low temperature the initial conformation is generally conserved whereas at room temperature jumps among the four possible core conformations are observed in the nanosecond time range. For second generation dendrimers the core conformation jumps are associated with an oscillation between two global shape states: open and collapsed. The computed bistability of the global shape suggests additional possible functional uses for some of these carbon based dendrimers.     

Solvent effects on isomerization and spectral properties of photochromic-switching diarythene derivatives in polar and apolar solutions

The photocyclization behavior and dynamic conformational transition of photochromic switches of diarythene derivatives in solutions are investigated by using the density functional theory (DFT) and molecular dynamics (MD) simulations. Three possible conformations, antiparallel (anti), parallel (para), and twist, for the open-ring isomers of 1,2-bis(2-methylbenzothiophene-3-yl)maleic anhydride are located. Both PCM-B3LYP/6-31G* calculations and MD simulations demonstrate that anti and twist open-ring isomers can interconvert freely in n-hexane and acetonitrile solutions at room temperature. The statistical ratio of twist to anti isomers from MD simulations is 2.09 in n-hexane and 1.07 in CH(3)CN, in qualitative agreement with those (1.18 in n-hexane and 1.05 in CH(3)CN) estimated from Arrhenius analysis of DFT activation energies. The solvent polarity has little influence on the isomerization of open-ring isomers in the ground state. Due to the evident charge transfer upon excitations, the solvent effects on the electronic structures and absorption spectra of low-lying excited states (S(1) and S(2)) are more significant. For such charge-transfer excited states, the long-range corrected functional CAM-B3LYP gives better agreement with the experimental spectra than B3LYP. The solvent polarity and polarization of the charge-transfer excited states are crucial for fabricating the novel functionalized photochromic molecular switches.