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Cambridge Structural Database (cambridge + structural_database)
Selected AbstractsThe Role of C,H···H,B Interactions in Establishing Rotamer Configurations in Metallabis(dicarbollide) SystemsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 16 2010Emilio José Juárez-Pérez Abstract The aim of this work is to explore the self-interaction capability of the anion [3,3,-Co(1,2-C2B9H11)2], through Ccluster,H···H,B (Cc,H···H,B) dihydrogen bonds. A set of theoretical and empirical data aiming to establish the main rules that account for the binding mode between the negatively charged borane framework made by [3,3,-Co(1,2-C2B9H11)2], and the [NMe4]+ ions have been compiled. The interaction between cation and anion is mainly electrostatic but the covalent contribution is also proven and quantified. The existing intermolecular H···H short contacts have been studied and are compared with available data from the Cambridge Structural Database. The results show that the electronic configuration of the transition metal atom in the sandwich complex is not enough to define the preferred rotamer due to the influence of the anion environment and the H···H interactions present in the solid state. We present a methodology with widely used theoretical tools to study cation···cobaltabisdicarbollide interactions in the solid state. [source] Bent and Linear Forms of the (,-Oxo)bis[trichloroferrate(III)] Dianion: An Intermolecular Effect , Structural, Electronic and Magnetic PropertiesEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 23 2003Agustí Lledós Abstract We have analyzed the great diversity of Fe,O,Fe angles, 140,180°, found in the X-ray structures of the (,-oxo)bis[trichloroferrate(III)] dianion [Cl3FeOFeCl3]2, from both experimental and theoretical points of view. Theoretical calculations show that only the linear isomer is found as a minimum on the potential energy surface. Detailed analysis of the crystal packing indicates that the angular form is due to attractive intermolecular interactions. Analysis of a selected reduced set of the 45 crystal structures retrieved from the Cambridge Structural Database allowed us to classify the bending of the [Cl3FeOFeCl3]2, dianion in three categories, depending on the balance and strength of the intermolecular O···H,X contacts. A crystal diffraction study on the bis(benzyltrimethylammonium) salt has shown both bent (144.6°) and linear (180°) forms of the (,-oxo)bis[trichloroferrate(III)] dianion. The magnetic susceptibility of this compound has been fitted by assuming two equally weighted contributions (Jang and Jlin) of the two forms, considering Jang , Jlin estimated by theoretical calculations. The obtained Jang and Jlin of ,117 and ,133 cm,1 respectively, agree well with B3LYP results. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Macrocyclic Cyclo[n]malonates , Synthetic Aspects and Observation of Columnar Arrangements by X-ray CrystallographyEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 10 2006Nikos Chronakis Abstract A variety of achiral and chiral macrocyclic oligomalonates were synthesised in a one-step procedure through condensation of malonyl dichloride with ,,,-diols. We have investigated the applicability of this method by varying the length and type of the spacers in the diol. Product distribution analysis revealed that the preferential formation of monomeric, dimeric, or trimeric macrocyclic malonates can be controlled by choosing diols with specific spacers connecting the hydroxy groups. Of special interest are the macrocyclic bismalonates, as they show pronounced crystallisability and arrange into columnar motifs in the solid state. They feature distinctive dihedral angles: all ester moieties adopt anti conformations whereas the planes of the carboxy moieties of each malonate residue arrange in an approximately orthogonal fashion. The latter geometry is enforced by the macrocyclic structures, as revealed by a conformational search in the Cambridge Structural Database. The X-ray diffraction data show that C=O···H,C, and C,O···H,C hydrogen bonds stabilise the columnar arrangement of the dimeric rings with formation of tubular assemblies. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] Copper-Binding Motifs: Structural and Theoretical AspectsHELVETICA CHIMICA ACTA, Issue 5 2003Amy Kaufman, Katz In this paper, we report the results of a study involving the coordination geometries of CuI, CuII, and CuIII crystal structures in the Cambridge Structural Database, and on Cu binding sites in proteins taken from the Protein Data Bank. The motifs used to bind two bridged Cu ions are also described. In addition, we report the results of ab initio molecular-orbital calculations performed on a variety of model CuI/CuII complexes (CuI/CuII,XnYm (X, Y=NH3, SH2); n+m=4; n=0,4) to provide data on the structural and energetic changes that occur in isolated complexes when the oxidation state of the Cu ion is changed from II to I while the coordination number is conserved. The use of such simple ligands in these calculations eliminates constraints on the geometric changes that may be imposed by more-complicated ligands. [source] Crystal structure prediction of organic pigments: quinacridone as an exampleJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 1 2007N. Panina The structures of the ,, , and , polymorphs of quinacridone (Pigment Violet 19) were predicted using Polymorph Predictor software in combination with X-ray powder diffraction patterns of limited quality. After generation and energy minimization of the possible structures, their powder patterns were compared with the experimental ones. On this basis, candidate structures for the polymorphs were chosen from the list of all structures. Rietveld refinement was used to validate the choice of structures. The predicted structure of the , polymorph is in accordance with the experimental structure published previously. Three possible structures for the , polymorph are proposed on the basis of X-ray powder patterns comparison. It is shown that the , structure in the Cambridge Structural Database is likely to be in error, and a new , structure is proposed. The present work demonstrates a method to obtain crystal structures of industrially important pigments when only a low-quality X-ray powder diffraction pattern is available. [source] Conformational analysis of thiopeptides: derivation of sp2 sulfur parameters for the CFF91 force fieldJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2001Tran Trung Tran Abstract When a sulfur atom is used to substitute for the oxygen in peptide bonds, its bulkiness should restrict the conformational space available to an amino acid. This conformational restriction as well as the ability to confer resistance to enzymatic degradation in the body means that thio-substituted amino acids are potentially useful building blocks for drug design. To simulate the effects of thio substitution, force field parameters for sp2 sulfur are required. In this article, parameters for the thioamide group have been derived for the molecular mechanics CFF91 force field (available at http://www.ludwig.edu.au/archive/tran). The bond increment charges were obtained by fitting to ab initio charges and dipoles. The van der Waals parameters were obtained by fitting to high-resolution crystallographic data, and the nonbonded parameters were verified by comparing with experimentally derived lattice energy. The bonded parameters were derived by least-square fits to the ab initio calculated energy surfaces, i.e., conformational energy as well as their first and second derivatives of seven model thioamide molecules. When the sp2 sulfur parameters were tested on a set of seven X-ray crystallographic structures from the Cambridge Structural Database, they satisfactorily reproduced the bond lengths, bond angles, torsional angles, and nonbonded distances of all the crystal structures. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1010,1025, 2001 [source] Occurrence of pharmaceutically acceptable anions and cations in the Cambridge Structural DatabaseJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 10 2005Delia A. Haynes Abstract The occurrence of a number of pharmaceutically acceptable counterions in the Cambridge Structural Database (CSD) has been investigated. The results have been compared to the occurrence of the same counterions in a list of known pharmaceutical salts. Chloride salts are by far the highest occurring in both groups. The occurrence of hydrates in the structures of salts of pharmaceutically acceptable counterions in the CSD has also been investigated. It was found that salts of these counterions show an increased tendency to hydrate when compared to the database average. The CSD was also searched for co-crystals of the list of pharmaceutically acceptable acids and bases corresponding to the list of counterions used for the salt investigation. © 2005 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 94:2111-2120, 2005 [source] Probing the influence of stereoelectronic effects on lithium affinity in 1,3- and 1,4-dioxa systemsJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 7 2001Bishwajit Ganguly Abstract A combined computational and structural study of the lithium affinity (LA) of O,C,O systems exhibiting the anomeric effect and of O, C,C,O systems exhibiting the gauche effect is presented. QM ab initio calculations using the MP2/6,31G* basis set were carried out on the gas-phase lithium affinities of dimethoxymethane (DMOM), dimethoxyethane (DMOE), 1,3-dioxane (DOX) and cis - and trans -tetraoxadecalin (TOD), along with that of dimethyl ether and of its dimer as reference compounds. Structural parameters were retrieved from the Cambridge Structural Database (CSD) for diethyl ether dimer and O,C,C,O lithium complexes and these agreed well with the calculated data. The computed lithium affinities of dimethoxymethane and dimethoxyethane were found to be conformationally dependent. The LAs are conformationally dependent (wherever applicable) and decrease in the order: (Me2O)2 >,DMOE >,DMOM >,DOD >,DOX >,trans -TOD, but cis -TOD restores the high LA (better than DMOE) by virtue of multiple coordination. Copyright © 2001 John Wiley & Sons, Ltd. [source] Molecular crystal global phase diagrams.ACTA CRYSTALLOGRAPHICA SECTION A, Issue 1 2010In previous parts of this series [Mettes et al. (2004). Acta Cryst. A60, 621,636; McClurg & Keith (2010). Acta Cryst. A66, 38,49] a method for constructing global phase diagrams (GPDs) for molecular crystals was developed and the method was applied to single-component ordered crystal structures of tetrahedral molecules. GPDs are useful for visualizing what types of crystal structures a given molecule may assume depending on molecular form/interaction. Their construction uses group-theoretical methods which enumerate all possible symmetry breakings during a statistical mechanical high-to-low temperature search. In this work these results are expanded upon by outlining a method to determine a sufficiently rich parameter space to represent the experimentally observed crystal structures in a data set derived from the Cambridge Structural Database. This is significant because previous work (Mettes et al., 2004) did not specify the number of parameters needed for GPDs. Although there are suggestions in the literature that thousands of parameters are required to adequately describe tetrahedral molecule intermolecular potentials, it is found that 15 parameters are sufficient to represent the structures of the test data. The origin of this difference and its implications for determining GPD parameter values from a more detailed intermolecular potential and for interpreting GPD parameter values are discussed. [source] An investigation into structural changes due to deuterationACTA CRYSTALLOGRAPHICA SECTION A, Issue 3 2008S. J. Fisher Perdeuteration of proteins is becoming more commonplace and the assumption is in general that deuteration does not affect protein structure. In this work, the effect of deuteration on structure is examined by data mining, largely of the Cambridge Structural Database but also of the Inorganic Crystal Structure Database, for deuterated and hydrogenated pairs of small-molecule structures analysed by neutron and X-ray crystallography. Differences between these small-molecule structures have been calculated and the results thus far follow the initial assumption. However, functional changes are known, e.g. D2O is toxic to living systems but H2O is not, kinetics change, small pH to pD changes occur, proteins stiffen in D2O and ferroelectrics alter their properties. [source] Bond lengths in organic and metal-organic compounds revisited: X,H bond lengths from neutron diffraction dataACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2010Frank H. Allen The number of structures in the Cambridge Structural Database (CSD) has increased by an order of magnitude since the preparation of two major compilations of standard bond lengths in mid-1985. It is now of interest to examine whether this huge increase in data availability has implications for the mean bond-length values published in the late 1980s. Those compilations reported mean X,H bond lengths derived from rather sparse information and for rather few chemical environments. During the intervening years, the number of neutron studies has also increased, although only by a factor of around 2.25, permitting a new analysis of X,H bond-length distributions for (a) organic X = C, N, O, B, and (b) a variety of terminal and homometallic bridging transition metal hydrides. New mean values are reported here and are compared with earlier results. These new overall means are also complemented by an analysis of X,H distances at lower temperatures (T, 140,K), which indicates the general level of librational effects in X,H systems. The study also extends the range of chemical environments for which statistically acceptable mean X,H bond lengths can be obtained, although values from individual structures are also collated to further extend the chemical range of this compilation. Updated default `neutron-normalization' distances for use in hydrogen-bond and deformation-density studies are also proposed for C,H, N,H and O,H, and the low-temperature analysis provides specific values for certain chemical environments and hybridization states of X. [source] Universal prediction of intramolecular hydrogen bonds in organic crystalsACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2010Peter T. A. Galek A complete exploration of intramolecular hydrogen bonds (IHBs) has been undertaken using a combination of statistical analyses of the Cambridge Structural Database and computation of ab initio interaction energies for prototypical hydrogen-bonded fragments. Notable correlations have been revealed between computed energies, hydrogen-bond geometries, donor and acceptor chemistry, and frequencies of occurrence. Significantly, we find that 95% of all observed IHBs correspond to the five-, six- or seven-membered rings. Our method to predict a propensity for hydrogen-bond occurrence in a crystal has been adapted for such IHBs, applying topological and chemical descriptors derived from our findings. In contrast to intermolecular hydrogen bonding, it is found that IHBs can be predicted across the complete chemical landscape from a single optimized probability model, which is presented. Predictivity of 85% has been obtained for generic organic structures, which can exceed 90% for discrete classes of IHB. [source] A list of organic kryptoracematesACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2010László Fábián A list of 181 organic kryptoracemates has been compiled. This class of crystallographic oddities is made up of racemic compounds (i.e. pairs of resolvable enantiomers) that happen to crystallize in Sohnke space groups (i.e. groups that include only proper symmetry operations). Most (151) of the 181 structures could have crystallized as ordered structures in non-Sohnke groups. The remaining 30 structures do not fully meet this criterion but would have been classified as kryptoracemates by previous authors. Examples were found and checked with the aid of available software for searching the Cambridge Structural Database, for generating and comparing InChI strings, and for validating crystal structures. The pairs of enantiomers in the true kryptoracemates usually have very similar conformations; often the match is near-perfect. There is a pseudosymmetric relationship of the enantiomers in about 60% of the kryptoracemate structures, but the deviations from inversion or glide symmetry are usually quite easy to spot. Kryptoracemates were found to account for 0.1% of all organic structures containing either a racemic compound, a meso molecule, or some other achiral molecule. The centroid of a pair of enantiomers is more likely (99.9% versus 99% probability) to be located on an inversion center than is the centroid of a potentially centrosymmetric molecule. [source] Cluster analyses of metal-organic fragments using the dSNAP softwareACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2009Anna Collins The dSNAP computer program has been used to classify searches of the Cambridge Structural Database for two ligands: ,O,CH2,CH2,O, and N(CH2CH2O,)3 commonly found in metal-organic systems. The clustering method used is based on total geometries (i.e. all the lengths and angles involving all the atoms in the search fragment, whether bonded or not) and proved capable of distinguishing in a wholly automatic, objective way between different types of metal complex purely on the basis of the geometry of the ligand and the relative positions of the O atoms to the metals. [source] Crystallochemical formula as a tool for describing metal,ligand complexes , a pyridine-2,6-dicarboxylate exampleACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2009Viktor N. Serezhkin Compounds (299) containing 494 symmetrically independent pyridine-2,6-dicarboxylate moieties have been investigated. Among them the structures of Na3[Nd(Pydc)3]·14H2O and Na3[Er(Pydc)3]·11.5H2O, where H2Pydc is pyridine-2,6-dicarboxylic acid, were determined by single-crystal X-ray diffraction, while the others were taken from the Cambridge Structural Database. The characteristics of any complex by means of the `method of crystallochemical analysis' are described, and the coordination types of all the Pydc ions and crystallochemical formulae of all the compounds were determined. Although the ion can act as a mono-, bi-, tri-, tetra- and pentadentate ligand, 96% of Pydc ions are coordinated to the central A atom in the tridentate-chelating mode. The dependence of the denticity and geometry of pyridine-2,6-dicarboxylate, as well as of the composition of Pydc-containing complexes, was studied as a function of the nature of the A atom, the molar ratio Pydc:A and the presence of neutral or acidic ligands in the reaction mixture. [source] Persistent hydrogen bonding in polymorphic crystal structuresACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2009Peter T. A. Galek The significance of hydrogen bonding and its variability in polymorphic crystal structures is explored using new automated structural analysis methods. The concept of a chemically equivalent hydrogen bond is defined, which may be identified in pairs of structures, revealing those types of bonds that may persist, or not, in moving from one polymorphic form to another. Their frequency and nature are investigated in 882 polymorphic structures from the Cambridge Structural Database. A new method to compare conformations of equivalent molecules is introduced and applied to derive distinct subsets of conformational and packing polymorphs. The roles of chemical functionality and hydrogen-bond geometry in persistent interactions are systematically explored. Detailed structural comparisons reveal a large majority of persistent hydrogen bonds that are energetically crucial to structural stability. [source] Using cluster analysis to study transition-metal geometries: four-coordinate complexes with two salicylaldiminato or related ligandsACTA CRYSTALLOGRAPHICA SECTION B, Issue 4 2007Andrew Parkin Cluster analysis is shown to be an effective method to analyse and classify metal coordination geometry in a very large number of four-coordinate bis -salicylaldimato (or bis- ,-iminoketonate) transition-metal complexes available in the Cambridge Structural Database. The methods described require no prior knowledge of chemistry to be input; retrieved structures are automatically clustered into groups based purely on the geometric similarity of the fragments and these groupings can then be interpreted by the structural chemist. [source] Crystal packing in vicinal diols CnHm(OH)2ACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2002Carolyn Pratt Brock The O,H,O bonds in vic -diols CnHm(OH)2 have been studied using data retrieved from the Cambridge Structural Database. About half of these diols form complete, or almost complete, sets of intermolecular O,H,O bonds (i.e. two satisfied donors per molecule). For this half of the structures the frequencies of high-symmetry space groups and of structures with Z,,>,1 (more than one molecule in the asymmetric unit) are substantially elevated. The most common motif among fully bonded structures is an dimer, which can be linked in a variety of ways to form one-, two- or even three-dimensional patterns. Most of the other half of the vic -diols form simple O,H,O chains in which each OH group participates in only one intermolecular hydrogen bond. The space-group frequencies for this second group of structures are unexceptional. The most important factor determining the extent of O,H,O bond formation is the degree of substitution of the vic -diol. The spatial segregation of OH groups that is necessary for the formation of O,H,O bonds is found to make the dense filling of space more difficult because the intermolecular spacings that are appropriate for the O,H,O bonds may be inappropriate for the rest of the molecule. [source] Amino and cyano N atoms in competitive situations: which is the best hydrogen-bond acceptor?ACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2001A crystallographic database investigation The relative hydrogen-bond acceptor abilities of amino and cyano N atoms have been investigated using data retrieved from the Cambridge Structural Database and via ab initio molecular orbital calculations. Surveys of the CSD for hydrogen bonds between HX (X = N, O) donors, N,T,C,N (push,pull nitriles) and N,(Csp3)n,C,N molecular fragments show that the hydrogen bonds are more abundant on the nitrile than on the amino nitrogen. In the push,pull family, in which T is a transmitter of resonance effects, the hydrogen-bonding ability of the cyano nitrogen is increased by conjugative interactions between the lone pair of the amino substituent and the C,N group: a clear example of resonance-assisted hydrogen bonding. The strength of the hydrogen-bonds on the cyano nitrogen in this family follows the experimental order of hydrogen-bond basicity, as observed in solution through the pKHB scale. The number of hydrogen bonds established on the amino nitrogen is greater for aliphatic aminonitriles N,(Csp3)n,C,N, but remains low. This behaviour reflects the greater sensitivity of the amino nitrogen to steric hindrance and the electron-withdrawing inductive effect compared with the cyano nitrogen. Ab initio molecular orbital calculations (B3LYP/6-31+G** level) of electrostatic potentials on the molecular surface around each nitrogen confirm the experimental observations. [source] Space-group changes: a revision to a revisionACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2001Richard E. Marsh The space group for the entry under the reference codes FEBMUU and FEBMUU01 in the Cambridge Structural Database (1992) should be further corrected to space group rather than (FEBMUU) or (FEBMUU01). [source] Graph-set and packing analysis of hydrogen-bonded networks in polyamide structures in the Cambridge Structural DatabaseACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2000W. D. Samuel Motherwell The hydrogen-bond networks and crystal packing of 81 unique secondary di- and polyamides in the Cambridge Structural Database are investigated. Graph-set analysis, as implemented in the RPluto program, is used to classify network motifs. These have been rationalized in terms of the relative dispositions of the amide groups. Peptide and retropeptides exhibit significant conformational flexibility, which permits alternative hydrogen-bonding patterns. In peptides, dihedral angles of ,,,,, 105° allow an antiparallel ladder arrangement, containing rings of either the same or alternating sizes. For retropeptides, and diamides with an odd number of CH2 spacers, this conformation leads to a parallel ladder with rings of equal size. If , approaches ,60° and , 180°, ladders adopt a helical twist, and if the conformation is distorted further, a three-dimensional network is usually adopted. Diamides with aromatic or an even number of CH2 spacers generally form either antiparallel ladders or sheets, although some exhibit both polymorphs. Symmetry relationships within and between hydrogen-bonded chains, ladders and sheets in the crystal packing have also been analysed. Polyamides form considerably more complex networks, although many of the structural motifs present in the diamides occur as components of these networks. [source] Structure correlation study of four-coordinate copper(I) and (II) complexesACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2000Paul R. Raithby The geometries of four-coordinate CuI and CuII complexes in the Cambridge Structural Database (CSD) have been analysed systematically and compared using symmetry-deformation coordinates and principal component analysis. The observed stereochemistries have been rationalized in terms of the d -electron configurations, interligand repulsion and ,-bonding effects. The results confirm that the majority of four-coordinate copper(I) complexes in the CSD adopt tetrahedral geometries and deviations from tetrahedral symmetry are caused by the presence of chelating ligands or by the incorporation of copper centres into dimeric or polymeric structures. Four-coordinate copper(II) complexes generally adopt geometries close to square planar; this is particularly evident for bis(chelate) complexes where ,-bonding is important. Distortions towards tetrahedral geometries are attributable to steric interactions of bulky substituents in the bidentate ligands. [source] The assignment and validation of metal oxidation states in the Cambridge Structural DatabaseACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2000Gregory P. Shields A methodology has been developed for the semi-automatic assignment and checking of formal oxidation states for metal atoms in the majority of metallo-organic complexes stored in the Cambridge Structural Database (CSD). The method uses both chemical connectivity and bond-length data, via ligand donor group templates and bond-valence sums, respectively. In order to use bond-length data, the CSD program QUEST has been modified to allow the coordination sphere of metal atoms to be recalculated using user-defined criteria at search time. The new methodology has been used successfully to validate the +1, +2 and +3 oxidation states in 743 four-coordinate copper complexes in the CSD for which atomic coordinates are available in ca 99% of structures using one or other method, and both succeed for >86% of structures. [source] A new polymorph of cis,transoid,cis -dicyclohexano-18-crown-6.ACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2003Erratum In the Comment of the paper by Kravtsov et al. [Acta Cryst. (2002), C58, o683o684], there in an error in a cited Cambridge Structural Database (Allen, 2002) refcode. The correct text is `Only recently, the atomic coordinates for the known monoclinic polymorph of the cis,transoid,cis isomer became available from a private communication (Nazarenko, 2002; CCDC refcode DCHXCS01).' The updated reference is given below. [source] PURY: a database of geometric restraints of hetero compounds for refinement in complexes with macromolecular structuresACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2008Miha Andreja The number and variety of macromolecular structures in complex with `hetero' ligands is growing. The need for rapid delivery of correct geometric parameters for their refinement, which is often crucial for understanding the biological relevance of the structure, is growing correspondingly. The current standard for describing protein structures is the Engh,Huber parameter set. It is an expert data set resulting from selection and analysis of the crystal structures gathered in the Cambridge Structural Database (CSD). Clearly, such a manual approach cannot be applied to the vast and ever-growing number of chemical compounds. Therefore, a database, named PURY, of geometric parameters of chemical compounds has been developed, together with a server that accesses it. PURY is a compilation of the whole CSD. It contains lists of atom classes and bonds connecting them, as well as angle, chirality, planarity and conformation parameters. The current compilation is based on CSD 5.28 and contains 1978 atom classes and 32,702 bonding, 237,068 angle, 201,860 dihedral and 64,193 improper geometric restraints. Analysis has confirmed that the restraints from the PURY database are suitable for use in macromolecular crystal structure refinement and should be of value to the crystallographic community. The database can be accessed through the web server http://pury.ijs.si/, which creates topology and parameter files from deposited coordinates in suitable forms for the refinement programs MAIN, CNS and REFMAC. In the near future, the server will move to the CSD website http://pury.ccdc.cam.ac.uk/. [source] Small revisions to predicted distances around metal sites in proteinsACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2006Marjorie M. Harding A new analysis has been made of distances around metal sites in protein structures in the Protein Data Bank determined with resolution ,1.25,Ĺ and equivalent distances have been extracted from the Cambridge Structural Database. They are for the metals Na, Mg, K, Ca, Mn, Fe, Co, Cu, Zn and the donor atoms O of water, O of Asp and Glu, O of the main-chain carbonyl group, N of His and S of Cys. Some revisions are recommended to the tables of `target distances' previously given [Harding (2001), Acta Cryst. D57, 401,411; Harding (2002), Acta Cryst. D58, 872,874]. As well as small changes in many distances and a large improvement for Mg,Ocarboxylate, the table includes an indication of how reliable each prediction may be. Special attention was given to carboxylate interactions. When the carboxylate group is monodentate, the M,Ocarboxylate distance is well defined, but for bidentate carboxylate groups a wide range of distances is allowable; when the metal is Co, Cu or Zn the M,O1 and M,O2 distances are clearly inversely correlated; for the more purely electrostatic interactions involving Na, K and Ca there is a wider scatter of distances and little correlation. [source] Recurring main-chain anion-binding motifs in short polypeptides: nestsACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2004E. James Milner-White A novel tripeptide motif called a nest has recently been described in proteins with the function of binding anionic, or partially anionic, atoms such as carbonyl O atoms. In the present work, a search for nests in small polypeptides stored in the Cambridge Structural Database is reported. 37 unique examples were found: over half form part of hydrogen-bond arrangements resembling those in proteins, such as Schellman/paperclip loop motifs, various types of ,-turn and Asx-turns or Ser/Thr-turns, while a third are in novel situations, some involving binding to anionic groups from other molecules within the crystal complex. An example is the antibiotic vancomycin, which incorporates a prominent nest forming part of a peptide-binding site. This nest binds the carboxylate of the C-terminal d -alanine of the bacterial cell-wall precursor peptide, thereby inhibiting the final step of bacterial cell-wall synthesis. As in proteins, a number of nests occur in short peptides with an alternating glycine/l -amino-acid sequence but, uniquely to non-ribosomally synthesized short peptides, several nests within them are constructed from alternating d - and l -amino acids, and such sequences seem to specially favour nests. [source] PRODRG: a tool for high-throughput crystallography of protein,ligand complexesACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2004Alexander W. Schüttelkopf The small-molecule topology generator PRODRG is described, which takes input from existing coordinates or various two-dimensional formats and automatically generates coordinates and molecular topologies suitable for X-ray refinement of protein,ligand complexes. Test results are described for automatic generation of topologies followed by energy minimization for a subset of compounds from the Cambridge Structural Database, which shows that, within the limits of the empirical GROMOS87 force field used, structures with good geometries are generated. X-ray refinement in X-PLOR/CNS, REFMAC and SHELX using PRODRG -generated topologies produces results comparable to refinement with topologies from the standard libraries. However, tests with distorted starting coordinates show that PRODRG topologies perform better, both in terms of ligand geometry and of crystallographic R factors. [source] Life-science applications of the Cambridge Structural DatabaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 6-1 2002Robin Taylor Several studies show that the molecular geometries and intermolecular interactions observed in small-molecule crystal structures are relevant to the modelling of in vivo situations, although the influence of crystal packing is sometimes important and should always be borne in mind. Torsional distributions derived from the Cambridge Structural Database (CSD) can be used to map out potential-energy surfaces and thereby help identify experimentally validated conformational minima of molecules with several rotatable bonds. The use of crystallographic data in this way is complementary to in vacuo theoretical calculations since it gives insights into conformational preferences in condensed-phase situations. Crystallographic data also underpin many molecular-fragment libraries and programs for generating three-dimensional models from two-dimensional chemical structures. The modelling of ligand binding to metalloenzymes is assisted by information in the CSD on preferred coordination numbers and geometries. CSD data on intermolecular interactions are useful in structure-based inhibitor design both in indicating how probable a protein,ligand interaction is and what its geometry is likely to be. They can also be used to guide searches for bioisosteric replacements. Crystallographically derived information has contributed to many life-science software applications, including programs for locating binding `hot spots' on proteins, docking ligands into enzyme active sites, de novo ligand design, molecular superposition and three-dimensional QSAR. Overall, crystallographic data in general, and the CSD in particular, are very significant tools for the rational design of biologically active molecules. [source] | |||||||||||||||||||||||||