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Molecular Conformation (molecular + conformation)
Kinds of Molecular Conformation Selected AbstractsA Concerted Approach for the Determination of Molecular Conformation in Ordered and Disordered MaterialsCHEMISTRY - A EUROPEAN JOURNAL, Issue 22 2007Jan Sehnert Abstract We present the successful application of a concerted approach for the investigation of the local environment in ordered and disordered phases in the solid state. In this approach we combined isotope labeling with computational methods and different solid-state NMR techniques. We chose triphenylphosphite (TPP) as an interesting example of our investigations because TPP exhibits two crystalline modifications and two different amorphous phases one of which is highly correlated. In particular we analyzed the conformational distribution in three of these phases. A sample of triply labeled 1-[13C]TPP was prepared and 1D MAS as well as wide-line 13C NMR spectra were measured. Furthermore we acquired 2D 13C wide-line exchange spectra and used this method to derive highly detailed information about the phenyl orientation in the investigated TPP phases. For linkage with a structure model a DFT analysis of the TPP molecule and its immediate environment was carried out. The ab initio calculations of the 13C chemical shift tensor in three- and six-spin systems served as a base for the calculation of 1D and 2D spectra. By comparing these simulations to the experiment an explicit picture of all phases could be drawn on a molecular level. Our results therefore reveal the high potential of the presented approach for detailed studies of the mesoscopic environment even in the challenging case of amorphous materials. [source] Molecular Conformation and Packing of Peptide , Hairpins in the Solid State: Structures of Two Synthetic Octapeptides Containing 1-Aminocycloalkane-1-Carboxylic Acid Residues at the i+2 Position of the , TurnCHEMISTRY - A EUROPEAN JOURNAL, Issue 12 2005Veldore Vidya Harini Abstract Peptide ,-hairpin formation is facilitated by centrally positioned D -Pro-Xxx segments. The synthetic peptides Boc-Leu-Phe-Val- D -Pro-Ac6c-Leu-Phe-Val-OMe (1) and Boc-Leu-Phe-Val- D -Pro-Ac8c-Leu-Phe-Val-OMe (2) were synthesized in order to explore the role of bulky 1-aminocycloalkane-1-carboxylic acid residues (Acnc, where n is the number of carbon atoms in the ring), at the i+2 position of the nucleating , turn in peptide , hairpins. Peptides 1 and 2 crystallize in the monoclinic space group P21 with two molecules in the asymmetric unit. The crystal structures of 1 and 2 provide conformational parameters for four peptide hairpin molecules. In all cases, the central segments adopts a type II, ,-turn conformation, and three of the four possible cross-strand hydrogen bonds are observed. Fraying of the hairpins at the termini is accompanied by the observation of NH,,,, interaction between the Leu(1)NH group and Phe(7) aromatic group. Cross strand stabilizing interactions between the facing residues Phe(2) and Phe(7) are suggested by the observed orientation of aromatic rings. Anomalous far-UV CD spectra observed in solution suggest that close proximity of the Phe rings is maintained even in isolated molecules. In both peptides 1 and 2, the asymmetric unit consists of approximately orthogonal hairpins, precluding the formation of a planar ,-sheet arrangement in the solid state. Solvent molecules, one dioxane and one water in 1, three water molecules in 2, mediate peptide association. A comparison of molecular conformation and packing motifs in available ,-hairpin structures permits delineation of common features. The crystal structures of ,-hairpin peptides provide a means of visualizing different modes of ,-sheet packing, which may be relevant in developing models for aggregates of polypeptides implicated in disease situations. [source] Quantitative Structure,Activity Relationship Models for Predicting Biological Properties, Developed by Combining Structure- and Ligand-Based Approaches: An Application to the Human Ether-a-go-go-Related Gene Potassium Channel InhibitionCHEMICAL BIOLOGY & DRUG DESIGN, Issue 4 2009Alessio Coi A strategy for developing accurate quantitative structure,activity relationship models enabling predictions of biological properties, when suitable knowledge concerning both ligands and biological target is available, was tested on a data set where molecules are characterized by high structural diversity. Such a strategy was applied to human ether-a-go-go-related gene K+ channel inhibition and consists of a combination of ligand- and structure-based approaches, which can be carried out whenever the three-dimensional structure of the target macromolecule is known or may be modeled with good accuracy. Molecular conformations of ligands were obtained by means of molecular docking, performed in a previously built theoretical model of the channel pore, so that descriptors depending upon the three-dimensional molecular structure were properly computed. A modification of the directed sphere-exclusion algorithm was developed and exploited to properly splitting the whole dataset into Training/Test set pairs. Molecular descriptors, computed by means of the codessa program, were used for the search of reliable quantitative structure,activity relationship models that were subsequently identified through a rigorous validation analysis. Finally, pIC50 values of a prediction set, external to the initial dataset, were predicted and the results confirmed the high predictive power of the model within a quite wide chemical space. [source] Optimization of activated carbon-based decontamination of fish oil by response surface methodologyEUROPEAN JOURNAL OF LIPID SCIENCE AND TECHNOLOGY, Issue 7 2007Åge Oterhals Abstract The effect of activated carbon (AC) adsorption on the reduction of persistent organic pollutants (POP) in fish oil was studied based on response surface methodology at a 5-g/kg AC inclusion level. Pretreatment of the oil by alkali refining and bleaching increased the POP levels. The tested process variables (contact time and temperature) affected the AC adsorption rate and significant first- and second-order response models could be established. Polychlorinated dibenzo- p -dioxins and dibenzofurans (PCDD/F) showed a very rapid adsorption behavior and the concentration and toxic equivalent (TEQ) level could be reduced by 99%. Adsorption of dioxin-like polychlorinated biphenyls (DL-PCB) was less effective and depended on ortho substitution, i.e. non- ortho PCB were adsorbed more effectively than mono- ortho PCB with a maximum of 87 and 21% reduction, respectively, corresponding to a DL-PCB-TEQ reduction of 73%. A common optimum for both PCDD/F and DL-PCB adsorption could not be identified. AC treatment had no effect on the level of polybrominated diphenyl ether flame retardants. The differences in adsorption patterns may be explained based on molecular conformation. No change in oil quality could be observed based on oxidation parameters. Compliance with present PCDD/F and DL-PCB legislation levels in fish oil can be achieved based on AC adsorption. [source] Probing the Local Conformation within ,-Conjugated One-dimensional Supramolecular Stacks using Frequency Modulation Atomic Force MicroscopyADVANCED MATERIALS, Issue 41 2009Benjamin Grévin Frequency-modulation atomic force microscopy is used to investigate the local conformation within 1D stacks obtained by the self-assembly of ,-conjugated molecules from solution. The structural parameters extracted from the experimental data can be interpreted in terms of local molecular conformation, by comparison with models obtained by molecular mechanics and dynamics simulations. [source] Effect of Heat Treatment on Bovine Lactoperoxidase Activity in Skim Milk: Kinetic and Thermodynamic AnalysisJOURNAL OF FOOD SCIENCE, Issue 1 2003E. Marín ABSTRACT: The effect of heat on lactoperoxidase activity in bovine milk was studied over a range of 68 to 76 °C. Values of residual enzymatic activity after different treatments were studied by kinetic analysis, obtaining D-values and the Z-value (3.1 °C). Denaturation of lactoperoxidase, measured by loss in activity, can be described as a 1st-order reaction. Rate constants were calculated, as was the energy of activation, which was 737.69 kJ/mol. Thermodynamic parameters were also calculated. The high value obtained for the variation in enthalpy of activation indicates that a high amount of energy is required to initiate denaturation, probably due to the molecular conformation of lactoperoxidase. [source] Maternal and fetal serum transformed alpha-fetoprotein levels in normal pregnancyJOURNAL OF OBSTETRICS AND GYNAECOLOGY RESEARCH (ELECTRONIC), Issue 2 2009Fernando González-Bugatto Abstract Aim:, To evaluate transformed alpha-fetoprotein (t-AFP) (a new molecular conformation of alpha-fetoprotein) levels in maternal serum and fetal serum in normal pregnancy. Methods:, Prospective longitudinal study. Fifty pregnant women were studied in two groups: 25 were evaluated in each trimester of pregnancy and near term (12, 20, 32 and 36 weeks) and the other 25 were evaluated at the time of planned cesarean section at term. In the first group, maternal serum t-AFP was measured and in the second group, maternal and fetal serum t-AFP were analyzed. Results:, Maternal serum t-AFP levels (medians) were 14.73 ng/mL in the first trimester, 28.29 ng/mL in the second trimester, 30.45 ng/mL in the early third trimester and 8.06 ng/mL in late pregnancy. t-AFP levels were significantly higher in maternal than in fetal serum (P < 0.001). There were no significant correlations between AFP and t-AFP levels in maternal versus fetal serum. Conclusions:, t-AFP increases during pregnancy until the early third trimester and then falls before delivery. t-AFP levels are higher in maternal than in fetal serum which suggests that native AFP is transformed to t-AFP either in the mother or in the placenta. [source] Crystal polymorphism in a carbamazepine derivative: OxcarbazepineJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 2 2010Katie M. Lutker Abstract Although crystal polymorphism of carbamazepine (CBZ), an anticonvulsant used to treat epilepsy, has been known for decades, the phenomenon has only recently been noted for its keto-derivative oxcarbazepine (OCB). Here it is demonstrated that OCB possesses at least three anhydrous polymorphs. Although all forms are morphologically similar, making differentiation between crystal modifications by optical microscopy difficult, powder X-ray diffraction, Raman spectroscopy, and thermomicroscopy show distinctive differences. These techniques provide an efficient method of distinguishing between the three polymorphs. The crystal structure of form II of OCB is reported for the first time and the structure of form I has been redetermined at low temperature. Remarkably, both the molecular conformation and crystal packing of form II are in excellent agreement with the blind prediction made in 2007. © 2009 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 99:794,803, 2010 [source] Conformational polymorphism in aripiprazole: Preparation, stability and structure of five modificationsJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 6 2009Doris E. Braun Abstract Five phase-pure modifications of the antipsychotic drug aripiprazole were prepared and characterized by thermal analysis, vibrational spectroscopy and X-ray diffractometry. All modifications can be produced from solvents, form I additionally by heating of form X° to ,120°C (solid,solid transformation) and form III by crystallization from the melt. Thermodynamic relationships between the polymorphs were evaluated on the basis of thermochemical data and visualized in a semi-schematic energy/temperature diagram. At least six of the ten polymorphic pairs are enantiotropically and two monotropically related. Form X° is the thermodynamically stable modification at 20°C, form II is stable in a window from about 62,77°C, and form I above 80°C (high-temperature form). Forms III and IV are triclinic (), I and X° are monoclinic (P21) and form II orthorhombic (Pna21). Each polymorph exhibits a distinct molecular conformation, and there are two fundamental N,HO hydrogen bond synthons (catemers and dimers). Hirshfeld surface analysis was employed to display differences in intermolecular short contacts. A high kinetic stability was observed for three metastable polymorphs which can be categorized as suitable candidates for the development of solid dosage forms. © 2008 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 98:2010,2026, 2009 [source] The use of post-mortem Raman spectroscopy in explaining friction and wear behaviour of sintered polyimide at high temperatureLUBRICATION SCIENCE, Issue 3 2006P. Samyn Abstract Due to their thermal stability and high strength, polyimides are an aromatic type of polymer that is used in sliding equipment functioning under high loads and elevated temperature. However, its tribological behaviour under high temperature and atmospheric conditions is not fully understood. It has been reported that a transition from high towards lower friction occurs ,somewhere' in the temperature region between 100°C and 200°C; however, a correlation with changes in the polyimide molecular structure remains difficult to illustrate and it is not certain whether or not this transition is correlated to lower wear. In the present work sliding experiments under controlled bulk temperatures between 100°C and 260°C are performed. A transition is observed in both friction and wear at 180°C which is further explained by microscopic analysis of the transfer film on the steel counterface and Raman spectroscopy of the worn polymer surfaces. A close examination of the spectra reveals transitions in relative intensity of certain absorption bands, pointing to different orientation effects of the molecular conformation at the polymer sliding surface at 180°C. Copyright © 2006 John Wiley & Sons, Ltd. [source] A new approach to automated first-order multiplet analysisMAGNETIC RESONANCE IN CHEMISTRY, Issue 5 2002Sergey Golotvin Abstract The dependence of the values of NMR spin,spin coupling constants on molecular conformation can be a valuable tool in the structure determination process. The continuing increase in the resonance frequency of modern NMR spectrometers allows an increasing number of resonances to be examined using first-order multiplet analysis. While this can easily be done for the simplest patterns (doublets, triplets, quartets), more complex patterns can be extremely difficult to analyze. The task of deducing the coupling constant values from a multiplet is the reverse process of generating a conventional splitting tree from a single line (chemical shift) by sequential branching using a given set of coupling constants. We present a simple, straightforward method of deducing coupling constant values from first-order multiplets based on a general inverted splitting tree algorithm but also including a peak intensity normalization procedure that utilizes multiplet symmetry and generates a set of possible first-order intensity distribution patterns. When combined with an inverted splitting tree algorithm, it is possible to find an intensity pattern that allows the deduction of a proper set of coupling constants. Copyright © 2002 John Wiley & Sons, Ltd. [source] CODES/Neural Network Model: a Useful Tool for in Silico Prediction of Oral Absorption and Blood-Brain Barrier Permeability of Structurally Diverse DrugsMOLECULAR INFORMATICS, Issue 2-3 2004Isabel Dorronsoro Abstract Two different neural network models able to predict both oral absorption (OA) and blood-brain barrier (BBB) permeability of structurally diverse drugs in use clinically are presented here. Using the descriptors generated by CODES, a program which codifies molecules from a topological point of view, we avoid the uncertain choice of molecular conformation and physicochemical parameters. In this work, a method called Reduction of Dimensions, designed for compressing data, is applied for the first time in order to minimize the bias factor added to a QSAR study when the selection of descriptors are performed. [source] Comparison of the effects of pressure on three layered hydrates: a partially successful attempt to predict a high-pressure phase transitionACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2009Russell D. L. Johnstone We report the effect of pressure on the crystal structures of betaine monohydrate (BTM), l -cysteic acid monohydrate (CAM) and S -4-sulfo- l -phenylalanine monohydrate (SPM). All three structures are composed of layers of zwitterionic molecules separated by layers of water molecules. In BTM the water molecules make donor interactions with the same layer of betaine molecules, and the structure remains in a compressed form of its ambient-pressure phase up to 7.8,GPa. CAM contains bi-layers of l -cysteic acid molecules separated by water molecules which form donor interactions to the bi-layers above and below. This phase is stable up to 6.8,GPa. SPM also contains layers of zwitterionic molecules with the waters acting as hydrogen-bond donors to the layers above and below. SPM undergoes a single-crystal to single-crystal phase transition above 1,GPa in which half the water molecules reorient so as to form one donor interaction with another water molecule within the same layer. In addition, half of the S -4-sulfo- l -phenylalanine molecules change their conformation. The high-pressure phase is stable up to 6.9,GPa, although modest rearrangements in hydrogen bonding and molecular conformation occur at 6.4,GPa. The three hydrates had been selected on the basis of their topological similarity (CAM and SPM) or dissimilarity (BTM) with serine hydrate, which undergoes a phase transition at 5,GPa in which the water molecules change orientation. The phase transition in SPM shows some common features with that in serine hydrate. The principal directions of compression in all three structures were found to correlate with directions of hydrogen bonds and distributions of interstitial voids. [source] A conformational polymorphic transition in the high-temperature ,-form of chlorpropamide on cooling: a new ,,-formACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2009Tatiana N. Drebushchak Structural changes in the high-temperature ,-polymorph of chlorpropamide, 4-chloro- N -(propylaminocarbonyl)benzenesulfonamide, C10H13ClN2O3S, on cooling down to 100,K and on reverse heating were followed by single-crystal X-ray diffraction. At temperatures below 200,K the phase transition into a new polymorph (termed the ,,-form) has been observed for the first time. The polymorphic transition preserves the space group Pna21, is reversible and is accompanied by discontinuous changes in the cell volume and parameters, resulting from changes in molecular conformation. As shown by IR spectroscopy and X-ray powder diffraction, the phase transition in a powder sample is inhomogeneous throughout the bulk, and the two phases co-exist in a wide temperature range. The cell parameters and the molecular conformation in the new polymorph are close to those in the previously known ,-polymorph, but the packing of the z-shaped molecular ribbons linked by hydrogen bonds inherits that of the ,-form and is different from the packing in the ,-polymorph. A structural study of the ,-polymorph in the same temperature range has revealed no phase transitions. [source] Structures of mono-unsaturated triacylglycerols.ACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2008The ,-2 crystal structures of a series of saturated and trans -mono-unsaturated triacylglycerols (TAGs) have been solved from high-resolution powder synchrotron diffraction data. The series comprises symmetric as well as asymmetric even-numbered TAGs and the trans -mono-unsaturated ones all have a single elaidoyl chain. The structures have been solved with the direct-space parallel-tempering program FOX and refined with the Rietveld program GSAS. The ,-2 structures all crystallized in the space group with the same molecular conformation. Within the resolution of the data no significant difference in packing or conformation is observed between trans -mono-unsaturated TAGs and saturated (stearoyl or palmitoyl) chain-containing analogues, in spite of the lower melting points of the former. An analysis of the position of the stepped methyl end-plane in the various subgroups of TAGs confirms most but not all suppositions found in the literature. [source] Rietveld refinement of a wrong crystal structureACTA CRYSTALLOGRAPHICA SECTION B, Issue 6 2007Christian Buchsbaum Rietveld refinements are generally used to confirm crystal structures solved from powder diffraction data. If the Rietveld refinement converges with low R values and with a smooth difference curve, and the structure looks chemically sensible, the resulting structure is generally considered to be close to the correct crystal structure. Here we present a counter example: The Rietveld refinement of the X-ray powder pattern of ,-quinacridone with the crystal structure of ,-quinacridone gives quite a smooth difference curve; the resulting crystal structure looks reasonable in terms of molecular conformation, molecular packing and intermolecular hydrogen bonds. However, neither the lattice parameters, the molecular packing nor the conformation of the molecules show any similarity with the actual structure, which was determined from single-crystal data. This example shows that a successful Rietveld refinement is not always final proof of the correctness of a crystal structure; in special cases the resulting crystal structure may still be wrong. [source] Interplay between dipolar, stacking and hydrogen-bond interactions in the crystal structures of unsymmetrically substituted esters, amides and nitriles of (R,R)- O,O,-dibenzoyltartaric acidACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2001Urszula Rychlewska The compounds analysed are the O,O,-dibenzoyl derivatives of (R,R)-tartaric acid, asymmetrically substituted by ester, amide and nitrile groups. Benzoylation does not introduce drastic changes to the molecular conformation. All investigated molecules adopt the planar T conformation of the four-carbon chain with noticeably smaller departures from the ideal conformation than observed in the nonbenzoylated analogs. Primary and secondary amides always orient the C=O bond antiperiplanar (a) with respect to the nearest C*,O bond, while methylester groups adjust their conformation to that adopted by the amide substituent situated at the other end of the molecule. Tertiary amides and carboxyl groups place their carbonyls at the same side as the nearest C*,O bond (the s form), but often deviations from coplanarity of the two bonds are significant and higher than those observed in the nonbenzoylated series. The results presented demonstrate the importance of dipole/dipole interactions between CO and ,C*H groups in stabilizing the molecular conformation, and between carbonyl groups in stabilizing crystal packing of the molecules that lack classical hydrogen-bond donor groups. An illustration is provided as to how a small change in mutual orientation of molecules arranged in a close-packed fashion causes a change in the character of intermolecular interactions from van der Waals to sandwich stacking between the benzoyloxy phenyls, and to dipolar between the benzoyloxy carbonyls. Hydrogen-bonded molecules tend to orient in a head-to-tail mode; the head-to-head arrangement being limited to cases in which terminal carbonyl groups are situated at one side of the molecule. The orientation of the benzoyloxy substituents with respect to the carbon main chain is such that the (O=)C,O,C,H bond system often deviates significantly from planarity. [source] N - n -Alkyl N,N -dimethylammonioacetic acid bromides: the first complete series of crystal and molecular structure determinations of an amphiphilic compound with alkyl chain lengths n = 1,..., 16ACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2000Rainer Rudert The molecular and crystal structures of 16 N - n -alkyl N,N -dimethylammonioacetic acid bromides with chain lengths between n = 1 and n = 16 have been determined. All compounds from n = 5 to n = 16 form bilayers with interdigitated chains. The even-numbered chains display the chain packing type M2II. The chain packing of the odd-numbered chain compounds is less regular. The head groups of all compounds are connected via electrostatic N+,Br, interactions, and by OH,Br, hydrogen bonds. The compounds with short chains are packed in different ways. Their molecular conformation depends on the crystal packing. [source] N4 -Methyl- N4 -(2-methylphenyl)-1H -pyrazolo[3,4- d]pyrimidine-4,6-diamine,ethanol,hydrazine (1/0.865/0.135): hydrogen-bonded ribbons containing four independent ring typesACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2009Jorge Trilleras N4 -Methyl- N4 -(2-methylphenyl)-1H -pyrazolo[3,4- d]pyrimidine-4,6-diamine crystallizes from ethanol as a mixed solvate, C13H14N6·0.865C2H6O·0.135N2H4, (I), where the hydrazine has been carried through from the initial preparation. Within the heterocyclic component, the 2-methylphenyl substituent is disordered over two sets of sites. There is an intramolecular C,H...,(arene) hydrogen bond, which may control the molecular conformation of the heterocycle. The heterocyclic molecules are linked by two independent N,H...N hydrogen bonds in a chain containing two types of R22(8) ring. The ethanol component is linked to this chain by a combination of O,H...N and N,H...O hydrogen bonds and the hydrazine component by two N,H...N hydrogen bonds, so generating two R33(9) rings and thus forming a ribbon containing four distinct ring types. [source] 3-Oxoandrosta-4,6-dien-17,-yl 2-methyl-1H -imidazole-1-carboxylate and 3-oxo-5,-androst-17,-yl 2-methyl-1H -imidazole-1-carboxylate: C,H..., and ,,, intermolecular interactionsACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2009Manuela Ramos Silva The title compounds, C24H30N2O3, (I), and C24H34N2O3, (II), both contain an androstane backbone and a 2-methylimidazole-1-carboxylate moiety at the 17-position. Compound (I) contains two symmetry-independent molecules (denoted 1 and 2), while compound (II) contains just one molecule in the asymmetric unit. The C,C,O,C torsion angle that reflects the twisting of the 2-methylimidazole-1-carboxylate moiety from the mean steroid plane is 143.1,(2)° for molecule 1 of (I), 73.1,(3)° for molecule 2 of (I) and 86.63,(17)° for (II). The significance of this study lies in its observation of significant differences in both molecular conformation and supramolecular aggregation between the molecules of the title compounds. The solid-state conformations compared with those obtained theoretically from ab initio methods for the isolated molecules show large differences, especially in the orientation of the methylimidazole substituent. [source] Partial ordering of tripivaloylmethane at 110,KACTA CRYSTALLOGRAPHICA SECTION C, Issue 8 2008Vladimir Stilinovi Tripivaloylmethane [systematic name: 4-(2,2-dimethylpropanoyl)-2,2,6,6-tetramethylheptane-3,5-dione], C16H28O3, is known to crystallize at room temperature in the space group R3m with three molecules in the unit cell. The molecules are conformationally chiral and pack so that each molecular site is occupied with equal probability by the two enantiomers. Upon cooling to 110,K, the structure partially orders; two molecules in the unit cell order into two different conformations of opposite chirality, while the third remains disordered. The symmetry of the resulting crystal is P3, with each of the molecules lying about a different threefold rotation axis. This paper describes an unusual case of order,disorder phase transition in which the structure partially orders by changes of molecular conformation in the single crystals. Such behaviour is of interest in the study of phase transitions and molecular motion in the solid state. [source] 2-[(E)-(4-Chlorophenyl)methyleneamino]- N -(X -methylphenyl)-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide, where X = 2 and 3ACTA CRYSTALLOGRAPHICA SECTION C, Issue 11 2004The title compounds, both C23H21ClN2OS, are isomeric, with (I) and (II) being the N -3-methylphenyl and N -2-methylphenyl derivatives, respectively. The dihedral angle between the 4-chlorophenyl group and the thiophene ring in (II) [38.1,(1)°] is larger than that in (I) [7.1,(1)°], indicating steric repulsion between the chlorophenyl and o -toluidine groups in (II). In both compounds, an intramolecular N,H,N hydrogen bond forms a pseudo-six-membered ring, thus locking the molecular conformation. In the crystal structures, molecules are connected via N,H,O hydrogen bonds, forming chains along the b axis in (I) and along the c axis in (II). Intermolecular C,H,O/S and ,,, interactions are also observed in (II), but not in (I). [source] Red, orange and yellow crystals of 4,5-bis(4-methoxyphenyl)-2-(3-nitrophenyl)-1H -imidazoleACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2000Yoshinobu Inouye Red non-solvate crystals of the title compound from ethanol, C23H19N3O4, orange solvate crystals from tert -butanol, C23H19N3O4·C4H10O, yellow solvate crystals from dioxane,water, C23H19N3O4·0.5C4H8O2, and intense yellow solvate crystals from benzene,N,N,-dimethylformamide, C23H19N3O4·C6H6, differ from each other in their molecular conformation and hydrogen-bonding scheme. The bathochromic shifts of the crystal color are explained by the molecular planarity and charge-transfer effect among the imidazole molecules. [source] Using a conformation-dependent stereochemical library improves crystallographic refinement of proteinsACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2010Dale E. Tronrud The major macromolecular crystallographic refinement packages restrain models to ideal geometry targets defined as single values that are independent of molecular conformation. However, ultrahigh-resolution X-ray models of proteins are not consistent with this concept of ideality and have been used to develop a library of ideal main-chain bond lengths and angles that are parameterized by the ,/, angle of the residue [Berkholz et al. (2009), Structure, 17, 1316,1325]. Here, it is first shown that the new conformation-dependent library does not suffer from poor agreement with ultrahigh-resolution structures, whereas current libraries have this problem. Using the TNT refinement package, it is then shown that protein structure refinement using this conformation-dependent library results in models that have much better agreement with library values of bond angles with little change in the R values. These tests support the value of revising refinement software to account for this new paradigm. [source] Weak Attractive Interactions between Methylthio Groups and Electron-Deficient Alkenes in peri -Naphthalenes: A Competition with Conjugative EffectsCHEMISTRY - A EUROPEAN JOURNAL, Issue 29 2006Jane O'Leary Dr. Abstract The solid-state conformations of five peri -disubstituted naphthalenes bearing a methylthio group and an electron-deficient alkene indicate a weak attractive interaction between the functional groups in four cases in which out-of-plane displacements lead to a common orientation of the MeS,,,sp2 -C vector to the alkene bond. In some cases the interaction is not strong enough to outweigh the tendency of the alkene to conjugate with the aromatic ring, and in one case this optimisation of conjugation alone controls the molecular conformation. The methylthio group lies close to the aromatic plane in all but one example for which the plane of the sulfide group is presented to the alkene. [source] Molecular Conformation and Packing of Peptide , Hairpins in the Solid State: Structures of Two Synthetic Octapeptides Containing 1-Aminocycloalkane-1-Carboxylic Acid Residues at the i+2 Position of the , TurnCHEMISTRY - A EUROPEAN JOURNAL, Issue 12 2005Veldore Vidya Harini Abstract Peptide ,-hairpin formation is facilitated by centrally positioned D -Pro-Xxx segments. The synthetic peptides Boc-Leu-Phe-Val- D -Pro-Ac6c-Leu-Phe-Val-OMe (1) and Boc-Leu-Phe-Val- D -Pro-Ac8c-Leu-Phe-Val-OMe (2) were synthesized in order to explore the role of bulky 1-aminocycloalkane-1-carboxylic acid residues (Acnc, where n is the number of carbon atoms in the ring), at the i+2 position of the nucleating , turn in peptide , hairpins. Peptides 1 and 2 crystallize in the monoclinic space group P21 with two molecules in the asymmetric unit. The crystal structures of 1 and 2 provide conformational parameters for four peptide hairpin molecules. In all cases, the central segments adopts a type II, ,-turn conformation, and three of the four possible cross-strand hydrogen bonds are observed. Fraying of the hairpins at the termini is accompanied by the observation of NH,,,, interaction between the Leu(1)NH group and Phe(7) aromatic group. Cross strand stabilizing interactions between the facing residues Phe(2) and Phe(7) are suggested by the observed orientation of aromatic rings. Anomalous far-UV CD spectra observed in solution suggest that close proximity of the Phe rings is maintained even in isolated molecules. In both peptides 1 and 2, the asymmetric unit consists of approximately orthogonal hairpins, precluding the formation of a planar ,-sheet arrangement in the solid state. Solvent molecules, one dioxane and one water in 1, three water molecules in 2, mediate peptide association. A comparison of molecular conformation and packing motifs in available ,-hairpin structures permits delineation of common features. The crystal structures of ,-hairpin peptides provide a means of visualizing different modes of ,-sheet packing, which may be relevant in developing models for aggregates of polypeptides implicated in disease situations. [source] Guest-dependent conformation of 18-crown-6 tetracarboxylic acid: Relation to chiral separation of racemic amino acidsCHIRALITY, Issue 7 2008Hiroomi Nagata Abstract (+)-18-Crown-6 tetracarboxylic acid (18C6H4) has been used as a chiral selector for various amines and amino acids. To further clarify the structural scaffold of 18C6H4 for chiral separation, single crystal X-ray analysis of its glycine+ (1), H3O+ (2), H5O (3), NH (4), and 2CH3NH (5) complexes was performed and the guest-dependent conformation of 18C6H4 was investigated. The crown ether ring of 18C6H4 in 3, 4, and 5 took a symmetrical C2 or C2 -like conformation, whereas that in 1 and 2 took an asymmetric C1 conformation, which is commonly observed in complexes with various optically active amino acids. The overall survey of the present and related complexes suggests that the molecular conformation of 18C6H4 is freely changeable within an allowable range, depending on the molecular shape and interaction mode with the cationic guest. On the basis of the present results, we propose the allowable conformational variation of 18C6H4 and a possible transition pathway from its primary conformation to the conformation suitable for chiral separation of racemic amines and amino acids. Chirality, 2008. © 2008 Wiley-Liss, Inc. [source] String Fit: a new structurally oriented X-ray and neutron reflectivity evaluation techniqueJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3 2001Erich Politsch A novel method for the analysis of neutron and X-ray reflectivity measurements is presented. In contrast to existing methods, the new data fitting approach is structurally oriented and therefore only requires information about the chemical structure of studied molecules and no other ad hoc assumptions. Apart from the inversion of reflectivity into scattering length density profile, the inversion of scattering length density profile into molecular arrangement is addressed systematically for non-trivial molecular conformations for the first time. This includes the calculation of structural characteristics, such as radius of gyration or chain order parameters, based on measured reflectograms. Another important option is the possibility to evaluate simultaneously neutron and X-ray reflectograms of a given sample. For better convergence, especially for complex simultaneous evaluations, an effective extension of the normally used least-squares deviation function is introduced. Different simulated molecular ensembles are used to illustrate the features of the new approach; typically, excellent agreement between the simulated starting and final deduced data sets is achieved. [source] Processing of a Strong Biodegradable Poly[(R)-3-hydroxybutyrate] Fiber and a New Fiber Structure Revealed by Micro-Beam X-Ray Diffraction with Synchrotron RadiationMACROMOLECULAR RAPID COMMUNICATIONS, Issue 11 2004Tadahisa Iwata Abstract Summary: Biodegradable poly[(R)-3-hydroxybutyrate] (P(3HB)) fibers with high tensile strength of 1.32 GPa were processed from ultra-high-molecular-weight P(3HB) by a method combining cold-drawing and two-step-drawing procedures at room temperature. The distribution of molecular structures in a mono-filament was analyzed by micro-beam X-ray diffraction with synchrotron radiation. It was revealed that the P(3HB) fiber has a new core-sheath structure consistent with two types of molecular conformations: a 21 helix conformation in the sheath region and a planar zigzag conformation in the core region. P(3HB) fiber processed by cold-drawing in ice water and two-step drawing at room temperature, and subsequently annealing at 50,°C. [source] Solid-state NMR studies of the molecular structure of TaxolMAGNETIC RESONANCE IN CHEMISTRY, Issue 6 2006Yu Ho Abstract Solid-state 13C{1H} cross-polarization/magic angle spinning spectroscopy (CP/MAS) has been utilized to extract the molecular structure information of Taxol, which is an anti-tumor therapeutic medicine extracted from the yew bark. The 13C signals have chemical shift values quite consistent with those measured in solution phase, and the overall chemical shift range is over 200 ppm. Notably, most of the 13C resonances of the taxane ring have two clearly resolved spectral components except the resonance peaks of C-15, C-16 and C-17, which are located at the central part of the taxane ring. On the basis of our NMR data, we propose that these doublets originate from two slightly different molecular conformations of the taxane ring and still the central part of the ring remains structurally similar. Furthermore, it is demonstrated that the 13C chemical shift difference deduced from the doublet splittings can serve as a direct measure of the structural difference between the two conformations, which could possibly correlate with the anti-tumor activity of Taxol. Copyright © 2006 John Wiley & Sons, Ltd. [source] | |||||||||||||||||||