An alignment‐free methodology for modelling field‐based 3D‐structure activity relationships using inductive logic programming

Traditional 3D‐quantitative structure–activity relationship (QSAR)/structure–activity relationship (SAR) methodologies are sensitive to the quality of an alignment step which is required to make molecular structures comparable. Even though many methods have been proposed to solve this problem, they often result in a loss of model interpretability. The requirement of alignment is a restriction imposed by traditional regression methods due to their failure to represent relations between data objects directly. Inductive logic programming (ILP) is a class of machine‐learning methods able to describe relational data directly. We propose a new methodology which is aimed at using the richness in molecular interaction fields (MIFs) without being restricted by any alignment procedure. A set of MIFs is computed and further compressed by finding their minima corresponding to the sites of strongest interaction between a molecule and the applied test probe. ILP uses these minima to build easily interpretable rules about activity expressed as pharmacophore rules in the powerful language of first‐order logic. We use a set of previously published inhibitors of factor Xa of the benzamidine family to discuss the problems, requirements and advantages of the new methodology. Copyright © 2007 John Wiley & Sons, Ltd.     

丁烷衍生物类木脂素13C NMR化学位移预测

借助原子电性作用矢量(AEIV)和原子杂化状态指数(AHSI),对39种丁烷衍生物类木脂素共计854个等价C原子进行表征,并建立用于模拟该类分子13C NMR化学位移的多元线性回归方程.所得定量结构波谱关系(QSSR)模型及留一法交互检验相关系数分别为r=0.981和q=0.962.进一步用从马尾松松针中分离所得新木脂素中20个13C NMR化学位移对模型进行外部验证,预测结果与实验值较接近.表明所建模型有良好稳定性和泛化力,可对丁烷衍生物类木脂素13C NMR谱学数据准确模拟.     

13C isotope effects on 1H chemical shifts: NMR spectral analysis of 13C‐labelled D‐glucose and some 13C‐labelled amino acids

The one‐ and two‐bond ¹³C isotope shifts, typically ?1.5 to ?2.5 ppb and ?0.7 ppb respectively, in non‐cyclic aliphatic systems and up to ?4.4 ppb and ?1.0 ppb in glucose cause effects that need to be taken into account in the adaptive NMR spectral library‐based quantification of the isotopomer mixtures. In this work, NMR spectral analyses of some ¹³C‐labelled amino acids, D ‐glucose and other small compounds were performed in order to obtain rules for prediction of the ¹³C isotope effects on ¹H chemical shifts. It is proposed that using the additivity rules, the isotope effects can be predicted with a sufficient accuracy for amino acid isotopomer applications. For glucose the effects were found strongly non‐additive. The complete spectral analysis of fully ¹³C‐labelled D ‐glucose made it also possible to assign the exocyclic proton signals of the glucose. Copyright © 2009 John Wiley & Sons, Ltd.     

Complete 1H and 13C NMR chemical shift assignment of N1‐ and N3‐alkylnitrohistidines and of 1,4,6,7‐tetrahydroimidazo[4,5‐b]pyridines

¹H and ¹³C NMR data for 13 nitrohistidine derivatives are reported, providing a diagnostic method for the elucidation of the N¹‐( 2 ) and the N³‐substituted ( 3 ) regioisomers. Spectral assignments of constrained surrogates of His ( 4 ) and of the His–Gly dipeptide ( 5 and 6 ) are also described. The structure of the compounds was confirmed by NOESY and heteronuclear (¹³C, ¹H) short‐ and long‐range correlation experiments. Copyright © 2003 John Wiley & Sons, Ltd.     

Investigation of the relationship of the glass‐transition temperature and the polymer structure by fuzzy set theory

Fuzzy set theory can be used to study the relationship between the glass‐transition temperature (T_g) and structure of polymers. We used the method to map this relationship and obtained T_g's for 241 polymers with a standard deviation of 20 K (the confidence bound was 90%). We also used the method to predict T_g's for 15 polymers with a standard deviation of 67 K (the confidence bound was 90%). This study demonstrates that fuzzy set theory can be effectively used for determining the quantitative structure–property relationship of polymers. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 454–459, 2002; DOI 10.1002/polb.10105     

1H, 13C NMR studies of new 3‐aminophenol isomers linked to pyridinium salts

¹H and ¹³C NMR spectroscopic data of 20 new non‐symmetrical compounds were assigned by a combination of 1D and 2D NMR experiments (DEPT, HSQC, and HMBC). These compounds contain a 4‐(N,N‐dimethylamino)‐ or 4‐(pyrrolidin‐1‐yl)pyridinium moiety and a 3‐nitro‐, 3‐amino‐, or 3‐hydroxyphenyl ring, linked by p‐xylene, 4,4′‐dimethylbiphenyl, 1,2‐bis(p‐tolyl)ethane, or 1,4‐bis(p‐tolyl)butane. Copyright © 2013 John Wiley & Sons, Ltd.     

1H, 13C, 17O NMR and quantum‐chemical study of the stereochemistry of the sulfoxide and sulfone derivatives of 3‐arylidene‐1‐thioflavan‐4‐one epoxides

The oxidation of the trans,cis‐( 2 ) and trans,trans‐epoxides ( 3 ) of differently substituted (Z)‐3‐arylidene‐1‐thioflavan‐4‐ones ( 1 ) with dimethyldioxirane (DMD) yielded the appropriate sulfoxides ( 4, 5 ) and sulfones ( 6, 7 ). The structures were elucidated by the extensive application of one‐ and two‐dimensional ¹H, ¹³C and ¹⁷O NMR spectroscopy. The conformational analysis was achieved by the application of ³J(C,H) coupling constants, NOESY responses and ab initio calculations. The preferred ground‐state conformers (twisted envelope‐A, twisted envelope‐B for 6 and twisted envelope‐A, envelope‐B for 7 ) were obtained as global minima of the theoretical ab initio MO study and also the examination of the ¹⁷O and ¹³C chemical shifts, calculated for the global minima structures of the sulfone isomers by the GIAO method. Analogous results, obtained for the sulfoxide isomers ( 4, 5 ), not only led to the preferred conformers but also gave evidence for the trans arrangement of the 2‐Ph group and the oxygen atom of the S?O group. Chemical shift differences between the isomers, sulfoxides and sulfones were corroborated by ab initio calculations of the anisotropic effects of the oxirane ring and the S?O and SO₂ groups. Copyright © 2003 John Wiley & Sons, Ltd.     

Experimental and theoretical study of the intramolecular C–H···N and C–H···S hydrogen bonding effects in the 1H and 13C NMR spectra of the 2‐(alkylsulfanyl)‐5‐amino‐1‐vinylpyrroles: a particular state of amine nitrogen

In the ¹H NMR spectra of the 1‐vinylpyrroles with amino‐ and alkylsulfanyl groups in 5 and 2 positions, an extraordinarily large difference between resonance positions of the H_A and H_B terminal methylene protons of the vinyl group is discovered. Also, the one‐bond ¹J(C_β,H_B) coupling constant is surprisingly greater than the ¹J(C_β,H_A) coupling constant in pyrroles under investigation, while in all known cases, there was a reverse relationship between these coupling constants. These spectral anomalies are substantiated by quantum chemical calculations. The calculations show that the amine nitrogen lone pair is removed from the conjugation with the π‐system of the pyrrole ring so that it is directed toward the H_B hydrogen. These factors are favorable to the emergence of the intramolecular C–H_B???N hydrogen bonding in the s‐cis(N) conformation. On the other hand, the spatial proximity of the sulfur to the H_B hydrogen provides an opportunity of the intramolecular C–H_B???S hydrogen bonding in the s‐cis(S) conformation. Presence of the hydrogen bond critical points as well as ring critical point for corresponding chelate ring revealed by a quantum theory of atoms in molecules (QTAIM) approach confirms the existence of the weak intramolecular C–H???N and C–H???S hydrogen bonding. Therefore, an unusual high‐frequency shift of the H_B signal and the increase in the ¹J(C_β,H_B) coupling constant can be explained by the effects of hydrogen bonding. Copyright © 2013 John Wiley & Sons, Ltd.     

Tautomeric behaviour and isotopic multiplets in the 13C NMR spectra of partially deuterated 5‐arylazo‐pyrimidine (1H,3H,5H)‐2,4,6‐triones and 5‐arylazo‐2‐thioxo‐pyrimidine (1H,3H,5H)‐4,6‐diones—evidence for elucidation of tautomeric forms

NMR spectra of the synthesized azo dyes, 5‐arylazo‐pyrimidine (1H,3H,5H)‐2,4,6‐triones (5a–g), 1,3‐dimethyl‐5‐arylazo‐pyrimidine (1H,3H,5H)‐2,4,6‐triones (6a–g), and 5‐arylazo‐2‐thioxo‐pyrimidine (1H,3H,5H)‐4,6‐diones (7a–g) were studied in (CD₃)₂SO (three drops of CD₃OD were added into solutions of the dyes in two different concentrations). All dyes showed intramolecular hydrogen bonding. Dyes 5a–7a showed bifurcated intramolecular hydrogen bonds. Tautomeric behaviours of some of N‐methylated azo dyes (6a‐g) were studied in two different concentrations. The solvent–substrate proton exchange of dyes 5a–d, 6a and 7a–e was examined in presence of three drops of CD₃OD. The dyes which were soluble in (CD₃)₂SO containing CD₃OD showed isotopic splitting (β‐isotope effect) in the ¹³C NMR spectra. Copyright © 2009 John Wiley & Sons, Ltd.     

Chiral recognition by enantioselective liquid chromatography: Mechanisms and modern chiral stationary phases

An overview of the state-of-the-art in LC enantiomer separation is presented. This tutorial review is mainly focused on mechanisms of chiral recognition and enantiomer distinction of popular chiral selectors and corresponding chiral stationary phases including discussions of thermodynamics, additivity principle of binding increments, site-selective thermodynamics, extrathermodynamic approaches, methods employed for the investigation of dominating intermolecular interactions and complex structures such as spectroscopic methods (IR, NMR), X-ray diffraction and computational methods. Modern chiral stationary phases are discussed with particular focus on those that are commercially available and broadly used. It is attempted to provide the reader with vivid images of molecular recognition mechanisms of selected chiral selector–selectand pairs on basis of solid-state X-ray crystal structures and simulated computer models, respectively. Such snapshot images illustrated in this communication unfortunately cannot account for the molecular dynamics of the real world, but are supposed to be helpful for the understanding. The exploding number of papers about applications of various chiral stationary phases in numerous fields of enantiomer separations is not covered systematically.