General definition of ring puckering coordinates

Cremer, Dieter; Pople, J. A.

doi:10.1021/ja00839a011

Cited by 7,721 publications

(6,175 citation statements)

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“…The octahedral coordination sphere around the central atom is composed of three carbonyl ligands in fac con guration, one chlorido ligand as well as one molecule of bis(2-pyridylmethanone), the latter coordinating via its two nitrogen atoms to the central atom. A puckering analysis of the six-membered chelate ring according to Cremer & Pople [4] shows the latter to adopt a B4,1 conformation on carbon and rhenium (B C1,Re1 ) [5]. Re-C bond lengths cover a narrow range of 1.904 (7) [6], the values found in the present study are among the most comon ones reported so far.…”

Section: Atom Sitesupporting

confidence: 67%

Crystal structure of chlorido-tricarbonyl-bis(2-pyridylmethanone-N,N′)-rhenium(I), C14H8ClN2O4Re

Mukiza

Gerber

Hosten

2015

Zeitschrift Für Kristallographie - New Crystal Structures

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C14H 8 ClN 2 O4Re, triclinic, P¯ (no. 2), a = 7.5566(3) Å, b = 8.3079(3) Å, c = 12.0017(6) Å, α = 83.583(1)°, β = 88.746(2)°, CCDC no.: 1267/4339 Source of materialThe compound was obtained upon reacting the Schi base derived from 2,6-diazaaniline and bis(2-pyridylmethanone) with Re(CO)5Cl in toluene. Crystals suitable for the di raction study were obtained upon free evaporation of the solvent at ambient conditions.

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Section: Atom Sitesupporting

confidence: 67%

Crystal structure of chlorido-tricarbonyl-bis(2-pyridylmethanone-N,N′)-rhenium(I), C14H8ClN2O4Re

Mukiza

Gerber

Hosten

2015

Zeitschrift Für Kristallographie - New Crystal Structures

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“…For the purposes of this system, an individual ribose with d between 55°and 110°is treated as C39-endo, and one with d between 120°and 175°as C29-endo. It is possible for other sugar puckers (as described by the pseudorotation phase/amplitude system) (Altona and Sundaralingam 1972;Cremer and Pople 1975) to occur within those d values, but there are so few well-authenticated examples at high resolution (Altona and Sundaralingam 1972;Olson 1982;Gelbin et al 1996) that they could not be analyzed separately here. C39-endo or C29-endo sugar puckers, as diagnosed by their d values, are referred to here in abbreviated form as C39 or C29.…”

Section: Definition Of a Consensus Modular Nomenclaturementioning

confidence: 99%

RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

Richardson

Schneider²,

Murray³

et al. 2008

RNA

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A consensus classification and nomenclature are defined for RNA backbone structure using all of the backbone torsion angles. By a consensus of several independent analysis methods, 46 discrete conformers are identified as suitably clustered in a qualityfiltered, multidimensional dihedral angle distribution. Most of these conformers represent identifiable features or roles within RNA structures. The conformers are given two-character names that reflect the seven-angle dezabgd combinations empirically found favorable for the sugar-to-sugar ''suite'' unit within which the angle correlations are strongest (e.g., 1a for A-form, 5z for the start of S-motifs). Since the half-nucleotides are specified by a number for dez and a lowercase letter for abgd, this modular system can also be parsed to describe traditional nucleotide units (e.g., a1) or the dinucleotides (e.g., a1a1) that are especially useful at the level of crystallographic map fitting. This nomenclature can also be written as a string with two-character suite names between the uppercase letters of the base sequence (N1aG1gN1aR1aA1cN1a for a GNRA tetraloop), facilitating bioinformatic comparisons. Cluster means, standard deviations, coordinates, and examples are made available, as well as the Suitename software that assigns suite conformer names and conformer match quality (suiteness) from atomic coordinates. The RNA Ontology Consortium will combine this new backbone system with others that define base pairs, base-stacking, and hydrogen-bond relationships to provide a full description of RNA structural motifs.

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“…17 The most popular definition was introduced by Cremer and Pople (CP) who expressed the ring conformation as a function of the Cartesian atomic coordinates. 19 Alternatively, spherical polar coordinates can be derived by Fourier transform from the ring torsion angles. 20,21 In the preceding paper, 17 we have derived quantitative expressions for the characterization of the pyranose and other six-membered ring conformations which rely heavily on the definitions of the natural internal coordinates introduced by Pulay et al 22,23 If τ 1 , τ 2 , τ 3 , τ 4 , τ 5 , and τ 6 torsion angles are defined by the C 1 C 2 C 3 C 4 ,C 2 C 3 C 4 C 5 ,C 3 C 4 C 5 O, C 4 C 5 OC 1 ,C 5 -OC 1 C 2 , and OC 1 C 2 C 3 atom sets, respectively, displacement into the 1 C 4 chair conformation is described by the internal coordinate.…”

Section: Conformational Constraintsmentioning

confidence: 99%

Conformational Pathways of Saturated Six-Membered Rings. A Static and Dynamical Density Functional Study

et al. 2005

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Vous avez des questions? Nous pouvons vous aider. Pour communiquer directement avec un auteur, consultez la première page de la revue dans laquelle son article a été publié afin de trouver ses coordonnées. Si vous n'arrivez pas à les repérer, communiquez avec nous à PublicationsArchive-ArchivesPublications@nrc-cnrc.gc.ca. Questions? Contact the NRC Publications Archive team atPublicationsArchive-ArchivesPublications@nrc-cnrc.gc.ca. If you wish to email the authors directly, please see the first page of the publication for their contact information. NRC Publications Archive Archives des publications du CNRCThis publication could be one of several versions: author's original, accepted manuscript or the publisher's version. / La version de cette publication peut être l'une des suivantes : la version prépublication de l'auteur, la version acceptée du manuscrit ou la version de l'éditeur. NRC Publications Record / Notice d'Archives des publications de CNRC:http://nparc.cisti-icist.nrc-cnrc.gc.ca/eng/view/object/?id=357c916e-19e7-4437-b461-25622e976464 http://nparc.cisti-icist.nrc-cnrc.gc.ca/fra/voir/objet/?id=357c916e-19e7-4437-b461-25622e976464 Wako-shi, Saitama 351, Japan ReceiVed: April 27, 2005; In Final Form: July 12, 2005 The conformation of the six-membered ring of pyranosyl sugars has pronounced effects on the physical and chemical properties of carbohydrates. We present a method to determine key features of the potential energy surfaces, such as transition states associated with the inversion pathways of the model compounds cyclohexane, tetrahydropyran, p-dioxane, m-dioxane, s-trioxane, and 2-oxanol. Finally, we make the first determination of the pathways for inversion of penta-O-methyl-R-D-glucopyranose and penta-O-methyl--D-glucopyranose. For both anomers, a transition state with five coplanar atoms with appreciable O E character was found. The method is based on constrained Car-Parrinello ab initio molecular dynamics, as implemented in the projector augmented-wave (PAW) method. The constraints are derived from the normal modes of six-membered rings and are described in terms of the canonical conformations 1 C 4 chair, 1,4 B boat, and O S 2 skew-boat. The PAW derived trajectories are in agreement with previous suggestions in the literature that pseudorotation is an important feature of such conformational interconversions. The dynamic nature as well as the internal coordinate-based constraints provide a method which can reliably accommodate pseudorotation. To determine semiquantitative energies, we recalculate key conformations using standard quantum mechanical calculations while keeping the ring dihedral angles frozen at their values found in the dynamics. In all cases where experimental barriers are known, our results are in excellent agreement.

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General definition of ring puckering coordinates

Cited by 7,721 publications

References 9 publications

Crystal structure of chlorido-tricarbonyl-bis(2-pyridylmethanone-N,N′)-rhenium(I), C14H8ClN2O4Re

Crystal structure of chlorido-tricarbonyl-bis(2-pyridylmethanone-N,N′)-rhenium(I), C14H8ClN2O4Re

RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

Conformational Pathways of Saturated Six-Membered Rings. A Static and Dynamical Density Functional Study

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