Combinatorial Synthesis and Multidimensional NMR Spectroscopy: An Approach to Understanding Protein–Ligand Interactions

Combinatorial chemistry is a laboratory emulation of natural recombination and selection processes. Strategies in this developing discipline involve the generation of diverse, molecular libraries through combinatorial synthesis and the selection of compounds that possess a desired property. Such approaches can facilitate the identification of ligands that bind to biological receptors, promoting our chemical understanding of cellular processes. This article illustrates that the coupling of combinatorial synthesis, multidimensional NMR spectroscopy, and biochemical methods has enhanced our understanding of a protein receptor used commonly in signal transduction, the Src Homology 3 (SH3) domain. This novel approach to studying molecular recognition has revealed a set of rules that govern SH3–ligand interactions, allowing models of receptor–ligand complexes to be constructed with only a knowledge of the polypeptide sequences. Combining combinatorial synthesis with structural methods provides a powerful new approach to understanding how proteins bind their ligands in general.     

Complete-active-space self-consistent-field/Amber parameterization of the Lys296–retinal–Glu113 rhodopsin chromophore-counterion system

A special hybrid quantum mechanics/molecular mechanics forcefield is defined, parameterized and validated for studying the photoisomerization path of the retinal chromophore in the rhodopsin protein. It couples a multireference ab initio Hamiltonian (CASSCF and second-order multireference many-body perturbation theory using a CASSCF reference) to describe the chromophore while the rest of the protein is approximated with the Amber forcefield. The frontier has been carefully parameterized in order to reproduce full quantum mechanics torsional energy profiles, for both the ground state and the first excited state. It is also shown that replacing the chromophore counterion with point charges is a valid approximation. This result is interpreted in terms of a cancellation effect for which a possible explanation is given.     

Molecular modeling of intercalation complexes of antitumor active 9-aminoacridine and a [d,e]-anellated isoquinoline derivative with base paired deoxytetranucleotides

Summary Intercalators are molecules capable of sliding between DNA base pairs without breaking up the hydrogen bonds between the DNA bases. On the basis of molecular mechanics calculations structural, models of B-DNA tetranucleotide intercalation complexes of some cytostatic active 9-aminoacridines and of a [d, e]-anellated isoquinoline derivative are presented. The drug complexes are stabilized by energetically favouredvan der Waals interactions and by selective hydrogen bonds between the side chains of the drugs and the DNA bases. Semiempirical quantum chemistry calculations revealed that the chromophoric system of the intercalators is able to form ,-charge-transfer interactions with the purine bases of the base paired deoxytetranucleotides. The theoretical findings are of interest for a more specific drug design of cytostatically active agents.

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Molecular Modeling von Interkalationskomplexen antitumoraktiver 9-Aminoacridine sowie eines [d, e]-anellierten Isochinolinderivates mit basengepaarten Desoxytetranukleotiden

Zusammenfassung Interkalatoren sind Moleküle, die in der Lage sind, sich zwischen DNA-Basenpaare einzulagern, ohne die Wasserstoffbrücken zwischen den DNA-Basen aufzubrechen. Auf der Basis von molekülmechanischen Rechnungen werden Tetranukleotid-Interkalationskomplexe von verschiedenen zytostatisch aktiven 9-Aminoacridinen und von einem [d, e]-anellierten Isochinolinderivat präsentiert. Die Komplexe werden durch energetisch günstigevan der Waals-Interaktionen sowie durch selektive Wasserstoffbrückenbindungen zwischen den Seitenketten der Wirkstoffe und den DNA-Basen stabilisiert. Semiempirische quantenchemische Rechnungen ergaben, daß der Chromophor der Interkalatoren in der Lage ist, ,-charge-transfer Wechselwirkungen mit den Purinbasen der basengepaarten Desoxytetranukleotide auszubilden. Die theoretischen Ergebnisse sind für ein spezifischeres Wirkstoffdesign zytostatisch aktiver Verbindungen von Interesse.

     

表面活性剂的基体辅助激光解吸电离/质谱分析表征

利用基体辅助激光解吸电离／质谱（MALDI－MS）技术对表面活性剂的分析表征进行了详细研究。以2，5－二羟基苯甲酸作为基体，考察MALDI样品制备方法如液滴干燥法、快速干燥法及三明治法对测定结果的影响，发现三明治方法更适合表面活性剂的分析。MALDI可以准确测定离子型表面活性剂的分子量，同时对于非离子型表面活性剂，还可以测定其平均聚合度和分子量的分布。     

红外光谱法研究LB膜中的分子取向

The structure information of orientation and packing of molecular chains can be obtained from infrared transmission and reflection-absorbance (RA) spectra. In the present paper, on the basis of Umemura et al., their FORTRAN program of minicomputer was developed and can be run on 486 personal computer. By comparison of infrared transmission and RA intensities, surface enhancement factors and molecular orientation angle were calculated using the above program, and the influence of complex refractive index, angle of incidence, and thickness of LB film were discussed. These results are consistent with that of Umemura et al.     

建立在群对称轨道(SMO)及特征组态(CD)基础上的CI方法与程序发展

ISMO－CDCI方法点群理论，特别是不可约张量方法，在量子化学理论方法发展以及简化概念与计算方面，发挥了重要作用．但在国外的量子化学计算程序（如G94）中，在后自洽场（opt－SCF）计算方面，很少用到对称约化．在文献中，只见有关hbeltah群（DZh与它的子群）对称约化用于组态相关计算的报导．由于多重耦合系数的计算复杂，蜕化不可约表示多体问题的对称约化难于得到解决．我们提出了一个统一与普遍的方法，它能解决所有分子体系多体相关的点群对称约化问题［‘－6］，这个方法的核心是群对称轨道（SMO）概念的提出．SMO的基本特…     

Accurate Gaussian basis sets for the H2O molecule generated with the molecular improved generator coordinate Hartree–Fock method

The molecular improved generator coordinate Hartree–Fock (MIGCHF) method is used to generate accurate basis sets of primitive Gaussian-type functions for the H₂O molecule. Sequences of increasing size atom centered basis sets are employed to explore the accuracy that can be achieved with this method. Using the O(24s14p8d5f2g1h);H(22s9p5d2f1g) basis set, the HF and second-order electron correlation energies of the H₂O ground state at the experimental geometry are computed as −76.0674680 and −0.3491935 hartree, respectively. The HF energy is in error by 20 μhartree and the second-order correlation energy corresponds to 96.5% of an estimate of the limiting value. The relevance of the present calculations is to show the accuracy that can be achieved in studies of small polyatomic molecules with the MIGCHF method.     

Molecular vibrations in a gradient extremal path

Summary The calculation of vibrational states using a gradient extremal path is discussed. Gradient extremal paths are defined by local criteria, which lead to stable solutions. This has certain advantages in comparison with a steepest-descent path, which is often difficult to determine accurately. For cases where a reaction path formalism is applicable, a path based on the gradient extremal concept gives results in close agreement with those obtained using traditional steepest-descent methods. We present algorithms for carrying out such calculations and also give some numerical results.     

An investigation into the construction of molecular models by the template joining method

Summary The results of a wide-ranging investigation into some of the different methods available for performing the joining of templates to build molecular models show that the choice of algorithm can significantly affect the quality of the results obtained, and different algorithms are most suited to particular categories of join.     

硫醇的分子连接性指数与气相色谱保留值

硫醇的分子连接性指数与气相色谱保留值赵邦屯王利亚（洛阳师专化学系洛阳４７１０２２）关键词硫醇分子连接性指数气相色谱保留值中图分类号Ｏ６５７．７１有机化合物的色谱保留行为与其结构之间的定量关系研究一直是物理化学、分析化学和生物化学的研究对象之一。长期以...