The relationship between proton-proton NMR coupling constants and substituent electronegativities—I : An empirical generalization of the karplus equation
TL;DR: In this paper, a new coupling constant-torsion angle relation for the three-bond 1H-1H spin-spin coupling constant is formulated, which includes a correction for the electronegativity of substituents.
About: This article is published in Tetrahedron.The article was published on 1980-01-01. It has received 1909 citations till now. The article focuses on the topics: Karplus equation & Coupling constant.
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TL;DR: An integrated molecular modeling system for designing and studying organic and bioorganic molecules and their molecular complexes using molecular mechanics is described in this article, which allows the construction, display and manipulation of molecules and complexes having as many as 10,000 atoms and provides interactive, state-of-the-art molecular mechanics on any subset of up to 1000 atoms.
Abstract: An integrated molecular modeling system for designing and studying organic and bioorganic molecules and their molecular complexes using molecular mechanics is described. The graphically controlled, atom-based system allows the construction, display and manipulation of molecules and complexes having as many as 10,000 atoms and provides interactive, state-of-the-art molecular mechanics on any subset of up to 1,000 atoms. The system semiautomates the graphical construction and analysis of complex structures ranging from polycyclic organic molecules to biopolymers to mixed molecular complexes. We have placed emphasis on providing effective searches of conformational space by a number of different methods and on highly optimized molecular mechanics energy calculations using widely used force fields which are supplied as external files. Little experience is required to operate the system effectively and even novices can use it to carry out sophisticated modeling operations. The software has been designed to run on Digital Equipment Corporation VAX computers interfaced to a variety of graphics devices ranging from inexpensive monochrome terminals to the sophisticated graphics displays of the Evans & Sutherland PS300 series.
3,507 citations
TL;DR: This chapter presents literature data on the high-resolution, 1H-NMR spectroscopy of carbohydrates derived from glycoconjugates and discusses the results for carbohydrates related to the glycoproteins of N-glycosylic type.
Abstract: Publisher Summary This chapter discusses the application of high-resolution, 1H-nuclear magnetic resonance (NMR) spectroscopy to the structural analysis of carbohydrates related to glycoproteins. Glycoproteins are biopolymers consisting of a polypeptide backbone bearing one or more covalently linked carbohydrate chains. The carbohydrate chains of glycoproteins may be classified according to the type of linkage to the polypeptide backbone. N-Glycosylic chains are attached to the amide group of asparagine (Asn), whereas the O-glycosylic chains are linked to the hydroxyl group of amino acid residues such as serine (Ser), threonine (Thr), and hydroxylysine (Hyl). The high-resolution, 1H-NMR spectroscopy technique, in conjunction with methylation analysis, is extremely suitable for the structural studies of N-, as well as on O-, glycosylic glycans. For the interpretation of the 1H-NMR spectrum of a carbohydrate chain in terms of primary structural assignments, the concept of “structural reporter groups” was developed. This means that the chemical shifts of protons resonating at clearly distinguishable positions in the spectrum, together with their coupling constants and the line widths of their signals, bear the information essential to permit the assigning of the primary structure. This chapter presents literature data on the high-resolution, 1H-NMR spectroscopy of carbohydrates derived from glycoconjugates. It also discusses the results for carbohydrates related to the glycoproteins of N-glycosylic type.
797 citations
462 citations
TL;DR: Insight is provided into the resonance assignment methods that are the first and crucial step of all NMR studies, into the determination of base‐pair geometry, Into the examination of local and global RNA conformation, and into the detection of interaction sites of RNA.
Abstract: NMR spectroscopy is a powerful tool for studying proteins and nucleic acids in solution. This is illustrated by the fact that nearly half of all current RNA structures were determined by using NMR techniques. Information about the structure, dynamics, and interactions with other RNA molecules, proteins, ions, and small ligands can be obtained for RNA molecules up to 100 nucleotides. This review provides insight into the resonance assignment methods that are the first and crucial step of all NMR studies, into the determination of base-pair geometry, into the examination of local and global RNA conformation, and into the detection of interaction sites of RNA. Examples of NMR investigations of RNA are given by using several different RNA molecules to illustrate the information content obtainable by NMR spectroscopy and the applicability of NMR techniques to a wide range of biologically interesting RNA molecules.
439 citations
TL;DR: The recommendations presented here are designed to support easier communication of NMR data and NMR structures of proteins and nucleic acids through unified nomenclature and reporting standards.
Abstract: The recommendations presented here are designed to support easier communication of NMR data and NMR structures of proteins and nucleic acids through unified nomenclature and reporting standards. Much of this document pertains to the reporting of data in journal articles; however, in the interest of the future development of structural biology, it is desirable that the bulk of the reported information be stored in computer-accessible form and be freely accessible to the scientific community in standardized formats for data exchange. These recommendations stem from an IUPAC-IUBMB-IUPAB inter-union venture with the direct involvement of ICSU and CODATA. The Task Group has reviewed previous formal recommendations and has extended them in the light of more recent developments in the field of biomolecular NMR spectroscopy. Drafts of the recommendations presented here have been examined critically by more than 50 specialists in the field and have gone through two rounds of extensive modification to incorporate suggestions and criticisms.
401 citations
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TL;DR: In this article, the valence-bond theory for the contact electron-spin coupling of nuclear magnetic moments is used to calculate the proton−proton, proton-fluorine, and fluorine-florine coupling constants in ethanic and ethylenic molecules.
Abstract: The valence‐bond theory for the contact electron‐spin coupling of nuclear magnetic moments is used to calculate the proton‐proton, proton‐fluorine, and fluorine‐fluorine coupling constants in ethanic and ethylenic molecules. A considerable simplification is introduced into the theory by approximations which reduce the problem to one involving only a small number of electrons and canonical structures. The agreement between calculated and experimental values is such as to demonstrate that the mechanism considered is the one of primary importance for the nuclear coupling in the compounds studied. Of particular interest is the theoretical confirmation of the observation that in ethylenic compounds the trans coupling between nuclei (HH, HF, FF) is considerably larger than cis coupling.
2,754 citations
2,207 citations
TL;DR: In this article, the authors derived approximate formulae involving the LCAO coefficients for the three contributions due to the electron orbital effect, dipolar interaction between nuclear and electron spins and the Fermi contact effect.
Abstract: Molecular orbital theory in the LCAO form is used in a study of the indirect coupling between nuclear spins through the electronic environment. By retaining only the largest one-centre integrals, approximate formulae involving the LCAO coefficients are derived for the three contributions due to (1) the electron orbital effect, (2) the dipolar interaction between nuclear and electron spins and (3) the Fermi contact effect. The theory is then applied in detail to the coupling between directly bonded atoms, when the contact term is usually dominant. Approximate calculations indicate that the reduced coupling constant K AB (defined as (2πtħγAγB)J AB, where γ A and γB are the nuclear magnetogyric ratios and J AB is the usual constant in cycles/second) is negative if one of the atoms is fluorine. Broad agreement is obtained with the available experimental data for atoms up to fluorine connected by single bonds and a tentative pattern for signs and magnitudes is suggested.
514 citations
TL;DR: In this paper, the authors discuss the calculation approaches to determine molecular structure and energy by force-field methods, including the ab initio method, the force field method, mechanical model, and energy minimization schemes.
Abstract: Publisher Summary This chapter discusses the calculation approaches to determine molecular structure and energy by force-field methods. These include the ab initio method, the force-field method, mechanical model, and energy minimization schemes. Methods for determining the internal energy of an organic molecule traditionally depend on heats of combustion. Because calculations of the force-field variety have become so accurate and efficient, many studies using such calculations to attack problems in molecular structure have been and are currently being carried out. These studies give, as a minimum, the bond lengths, bond angles, and torsional angles of the molecules examined, in addition to information concerning energy. The force-field method offers a rapid, convenient and reliable method for the determination of molecular structures and energies. While there are limitations to the method, as there are with each of the experimental methods, the usefulness of this technique is generally appreciated.
441 citations