Conformational analysis of [Met5]-enkephalin: Solvation and ionization considerations

[Met5]-Enkephalin has the sequence Tyr-Gly-Gly-Phe-Met. Only the extended conformation of the peptide has been observed by X-ray crystallography. Nuclear magnetic resonance spectroscopy supports the presence of a turn at Gly 3 and Phe 4 in dimethyl sulfoxide. In this study, the peptide conformational states and thermodynamic properties are understood in terms of ionization state and solvent environment. In the calculation, final conformations obtained from multiple independent Monte Carlo simulated annealing conformational searches are starting points for molecular dynamics simulations. In an aqueous environment given by the use of solvation free energy and the zwitterionic state, dominant structural motifs computed are G-P Type II bend, G-G Type II bend, and G-G Type I bend motifs, in order of increasing free energy. In the calculation of the peptide with neutral N- and C-termini and solvation free energy, the extended conformer dominates (by at least a factor of 2.5), and the conformation of another low free energy conformer superimposes well on the pharmacophoric groups of morphine. Neutralization of charge and solvation induce and stabilize the extended conformation, respectively. A mechanism of inter-conversion between the extended conformer and three bent conformers is supported by /-scatter plots, and by the conformer relative free energies. An estimate of the entropy change of receptor unbinding is 8.3 cal K-1 mol-1, which gives rise to a -2.5 kcal/mol entropy contribution to the free energy of unbinding at 25 °C. The conformational analysis methodology described here should be useful in studies on short peptides and flexible protein surface loops that have important biological implications.     

IR spectroscopic study of the conformational lability of 4′-ethyl-4-cyanobiphenyl

The conformational lability of 4-ethyl-4-cyanobiphenyl molecules in solid crystal (SC) and isotropic liquid (IL) states was investigated by IR spectroscopic techniques (experiment and theory). IR absorption spectra were measured at 28°C–95°C in the frequency range 400 cm^–1–4000 cm^–1. Spectrum simulation was performed using the fragment method with allowance for the conformational fluctuations of molecules. The experimental and calculated spectra were compared and analyzed, and it was shown that in the IL, the samples are mixtures of conformers. The temperature changes in the spectra in the stated range are caused by the conformational lability of molecules.Original Russian Text Copyright © 2004 by L. M. Babkov, I. I. Gnatyuk, G. A. Puchkovskaya, and S. V. TrukhachevTranslated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 3, pp. 398–405, May–June, 2004.     

氨基酸分子构象稳定性与光电离解离动力学的氢键效应*

本文综述了氨基酸分子内氢键种类和数目对分子构象稳定性和光电离解离动力学的各种效应：得出分子内含有N···H–O和C=O···H–O氢键的构象具有较高的热力学稳定性; N···H–O氢键导致分子第一电离能数值的增加,同时可以导致电离过程中的质子转移以及后续二氧化碳释放的解离过程。氨基酸分子正离子的稳定性或碳碳化学键断裂解离动力学也不尽相同,丝氨酸分子在电离阈值附近解离过程中表现出奇特的立体效应。     

IR spectra,conformational lability,and intermolecular interactions in long-chain aliphatic compounds

Investigations of the conformational lability and intermolecular interactions in long-chain aliphatic compounds (LACs), namely, in carboxylic acid derivatives (alkyl- and alkoxybenzoic acids; alkylcyclohexanecarboxylic acids and their completely or partially fluoroalkyl-substituted derivatives), 4-cyano-4-p-alkoxybiphenyls, 4-cyano-4-p-alkylbiphenyls, and cholesterol p-n-butyloxybenzoate are reviewed. Major attention is paid to experimental and theoretical IR spectroscopy data. Differential thermal analysis, polarization microscopy, and X-ray diffraction data are also taken into account. A more detailed treatment is presented on IR spectrum simulation based on data about the conformational lability of molecules and their specific (H-bonding) intermolecular interactions. The first mechanism is responsible for the conformational type of polymorphism in LACs and for the structure of the latter in solid crystal (SC) and liquid crystal (LC) states and in isotropic liquids (ILs). The second mechanism complements the structure-forming aspect of polymorphism in carboxylates, which is due to a rearrangement of hydrogen bond systems in H-complexes during polymorphic transitions to the LC and IL states. Both mechanisms are reflected in IR absorption spectra. A more adequate interpretation is possible in order to explain the many spectral features associated with the structure of LAC polymorphs and their H-complexes if these mechanisms are taken into account.Original Russian Text Copyright © 2004 by L.M. BabkovTranslated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 3, pp. 389–397, May–June, 2004.     

Improper hydrogen-bonded cyclohexane C-Hax?Yax contacts: experimental evidence from H NMR spectroscopy of suitable axial cyclohexane models

B3LYP/6-31+G(d,p) calculations predicted the presence of improper hydrogen-bonded C-H_ax?Y_ax contacts of different strength in cyclohexane derivatives;¹ it was predicted that the addition of an appropriate bridging fragment X_ax between an axial substituent Y₁ and a cyclohexane carbon would strengthen the improper hydrogen-bonded contact C-H_ax?Y₁ when the X_ax-Y₁ bond vector bisects the cyclohexane ring. To support the theoretical predictions with experimental evidence for this effect, several 2-substituted adamantane analogues with suitable improper H-bonded C-H_ax?O contacts of different strength were synthesized, as models of the corresponding cyclohexane derivatives, and their ¹H NMR spectra were recorded at 298 K. The ¹H NMR signal separation within the cyclohexane ring γ-CH₂s is increased when the B3LYP/6-31+G(d,p)-calculated strength of the H-bonded C-H_ax?O=C_ax contact interaction is increased.     

微波波谱方法与应用研究进展

综述了微波波谱法及其应用研究进展,阐述了微波波谱法的基本原理及仪器构造。对微波波谱法在分子结构及构象分析、弱相互作用体系的研究、分析化学、星际物质的探测等方面的应用进行了综述。并展望了微波波谱方法未来的发展趋势。     

Using fractal to solve the multiple minima problem in molecular mechanics calculation

This article presents an approach using fractal to solve the multiple minima problem. We use the Newton–Raphson method of the MM3 molecular mechanics program to scan the conformational spaces of a model molecule and a real molecule. The results show each energy minimum, maximum point, and saddle point has a basin of initial points converging to it in conformational spaces. Points converging to different extrema are mixed, and form fractal structures around basin boundaries. Singular points seem to involve in the formation of fractal. When searching within a small region of fractal basin boundaries, the self‐similarity of fractal makes it possible to find all energy minima, maxima, and saddle points from which global minimum may be extracted. Compared with other methods, this approach is efficient, accurate, conceptually simple, and easy to implement. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1101–1108, 2000     

Ab initio Study on Ionization Energies of 3-Amino-1-propanol

Fourteen conformers of 3-amino-1-propanol as the minima on the potential energy surface are examined at the MP2/6-311++G** level. Their relative energies calculated at B3LYP, MP3 and MP4 levels of theory indicated that two most stable conformers display the in-tramolecular OH…N hydrogen bonds. The vertical ionization energies of these conformers calculated with ab initio electron propagator theory in the P3/aug-cc-pVTZ approximation are in agreement with experimental data from photoelectron spectroscopy. Natural bond orbital analyses were used to explain the differences of IEs of the highest occupied molec-ular ortibal of conformers. Combined with statistical mechanics principles, conformational distributions at various temperatures are obtained and the temperature dependence of pho-toelectron spectra is interpreted.     

Photoluminescence of 2-(2′-hydroxy-5′-methylbenzoyl)-1,5-diphenylpyrrole in aqueous and β-cyclodextrin environments: manifestation of open and closed conformers

Steady-state fluorometric studies have been performed on 2-(2′-hydroxy-5′-methylbenzoyl)-1,5-diphenylpyrrole (HMBDPP) in aqueous and aqueous β-cyclodextrin (β-CD) environments at ambient temperature. The fluorophore mostly shows a single emission in aqueous solution. Addition of β-CD to the aqueous solution of the fluorophore results in the development of another emission band at higher energy. The difference in the fluorometric behaviour is assigned to a remarkable change in the polarity of the microenvironment within the supramolecular structural environment compared to that of the bulk aqueous phase. Semi-empirical calculation (AM1-SCI) rules out the possibility of intramolecular proton transfer reaction in any of the S₀, S₁ and T₁ states of the fluorophore. It is proposed that HMBDPP exists mostly in the intermolecularly hydrogen-bonded form (open conformer) in aqueous solution while within β-CD environment, it is the intramolecularly hydrogen-bonded form (closed conformer) that predominates.     

Covalent fixed multicyclic polystyrene conformers

Covalent fixed multicyclic polystyrene conformers were synthesized from inconvertible polystyrene conformers based on p‐tert‐butylthiacalix[4]arene by azidation and subsequent click coupling. Selective 1D NOESY analyses confirmed that the spatial structures of star polystyrene precursors and multicyclic polystyrenes were preserved during the azidation and click coupling processes. The conformation of star polymers affected degree of decrease in the hydrodynamic volume after cyclization but had little effect on glass transition behavior. The rigid core of star polymer increased the T_g but in the case of multicyclic polymer, this influence of core structure was reduced. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 4020–4026