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Trans Conformation (trans + conformation)
Selected AbstractsInfluence of substituents on the infrared stretching frequencies of carbonyl group in esters of benzoic acidJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 10 2006Vilve Nummert Abstract Infrared spectra of 25 substituted phenyl esters of benzoic acid C6H5CO2C6H4 -X (XH, 3-Cl, 3-F, 3-CN, 3-NO2, 3-CH3, 3-OH, 3-NH2, 4-Cl, 4-F, 4-NO2, 4-CN, 4-OCH3, 4-CH3, 4-NH2, 2-Cl, 2-F, 2-I, 2-NO2, 2-CF3, 2-CN, 2-CH3, 2-OCH3, 2-N(CH3)2, 2-C(CH3)3), 8 alkyl benzoates C6H5CO2R (XCH3, CH2CH3, CH2Cl, CH2CN, CH2CCH, CH2CH2Cl, CH2CH2OCH3, CH2C6H5), and 22 phenyl esters of substituted benzoic acids X-C6H4CO2C6H5 (X3-Cl, 3-NO2, 3-CH3, 3-N(CH3)2, 4-F, 4-Cl, 4-Br, 4-NO2, 4-CH3, 4-C(CH3)3, 4-OCH3, 4-NH2, 2-Cl, 2-F, 2-Br, 2-I, 2-NO2, 2-CN, 2-CF3, 2-CH3, 2-OCH3, 2-NH2) were recorded in tetrachloromethane in the region of 400,4000,cm,1. Carbonyl stretching frequencies ,CO for meta - and para -substituted phenyl esters of benzoic acid and phenyl esters of meta -substituted benzoic acids were shown to correlate with the substituent constants ,o. The influence of the through resonance effect on ,CO was found to be important in the case of +Rpara substituents in the benzoyl part of phenyl benzoates as well. The carbonyl stretching frequencies of ortho derivatives in phenoxy part were shown to correlate with the inductive substituent constant ,I only. In the benzoyl part of the esters the carbonyl stretching frequencies of cis and trans conformers (relative to the carbonyl group) of ortho derivatives were nicely described by dual parameter equations: (,CO)cis,=,(,CO)o,+,c1,I,+,c3,and (,CO)trans,=,(,CO)o,+,c1,p+,+,c3, (R,=,0.99). The trans isomers of phenyl esters of ortho -substituted benzoic acids showed direct resonance similar to that for para derivatives. The positive steric term found for both the cis and trans conformers could be considered as measure of the steric inhibition of resonance between the phenyl ring and the carboxy-group caused by bulky ortho substituents. The existence of cis/trans conformations was supported by frequency calculations with Density Functional Theory (DFT) method at B3LYP/6-311+G** level for the ortho -substituted benzoates. In the case of alkyl benzoates good correlations of ,CO values were obtained when both the Taft ,* and the steric constants were used. For meta - and para -substituted phenyl benzoates s - trans conformation where the plane of the benzene ring in the benzoyl part of the ester is coplanar with the carbonyl bond plane and the plane of the benzene ring in the phenoxy part is twisted nearly perpendicular relative to the carbonyl bond plane was supported. Copyright © 2006 John Wiley & Sons, Ltd. [source] Crystal structure of a polar nematogen 4-(trans- 4-undecylcyclohexyl) isothiocyanatobenzeneCRYSTAL RESEARCH AND TECHNOLOGY, Issue 10 2007S. Biswas Abstract Crystal and molecular structures of a nematogenic compound 4-(trans- 4-undecylcyclohexyl) isothiocyanatobenzene (11CHBT) have been determined by direct methods using single crystal X-ray diffraction data. The compound (C24H37N1S1) crystallizes in the monoclinic system with the space group P21/c and Z = 4. The unit cell parameters are a = 5.5539(11) Å, b = 8.1341(10) Å, c = 51.494(5) Å, and (= 91.127(14)0. The structure was refined to Rw = 0.051. The molecule is found to be slightly bow-shaped though the alkyl chain is in all- trans conformation. The phenyl ring and the alkyl chain are planar and the cyclohexyl group is in chair conformation. The isothiocyanato groups are almost linear. Parallel imbricated mode of packing of the molecules is found in the crystalline state which is precursor to the nematic phase structure. There are many van der Waals' interactions particularly in the isothiocyanato benzene part of the molecule. Of the various associated pairs of molecules the one having anti-parallel configuration with overlaps in the isothiocyanato phenyl group probably exists in both the crystalline and the nematic phases. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Raman and Rayleigh scattering study of crystalline polyoxyethyleneglycolsCRYSTAL RESEARCH AND TECHNOLOGY, Issue 4-5 2005M. Kozielski Abstract Results of the study of Raman and Rayleigh scattering in crystalline polyoxyethyleneglycols (PEG) and PEG 1500 aqueous solution are reported. The conformational changes of the polymer chain have been studied as a function of PEG water solution concentration and molecular weight. Intensity ratios of the gauche and trans conformation around C,C and C,O bonds have been estimated from the Raman spectra. Moreover, from the Raman band parameters the values of the order parameters versus aqueous solution concentration have been determined. The influence of an external electric field on these parameters has been analysed. Mutual orientation of polyoxyethyleneglycol chains in the crystalline and liquid state has been studied on the basis of the angular correlation parameters obtained from the Rayleigh band intensity as a function of aqueous solution concentration and molecular weight. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Cooperation of two carotene desaturases in the production of lycopene in Myxococcus xanthusFEBS JOURNAL, Issue 16 2007Antonio A. Iniesta In Myxococcus xanthus, all known carotenogenic genes are grouped together in the gene cluster carB,carA, except for one, crtIb (previously named carC). We show here that the first three genes of the carB operon, crtE, crtIa, and crtB, encode a geranygeranyl synthase, a phytoene desaturase, and a phytoene synthase, respectively. We demonstrate also that CrtIa possesses cis -to- trans isomerase activity, and is able to dehydrogenate phytoene, producing phytofluene and ,-carotene. Unlike the majority of CrtI-type phytoene desaturases, CrtIa is unable to perform the four dehydrogenation events involved in converting phytoene to lycopene. CrtIb, on the other hand, is incapable of dehydrogenating phytoene and lacks cis -to- trans isomerase activity. However, the presence of both CrtIa and CrtIb allows the completion of the four desaturation steps that convert phytoene to lycopene. Therefore, we report a unique mechanism where two distinct CrtI-type desaturases cooperate to carry out the four desaturation steps required for lycopene formation. In addition, we show that there is a difference in substrate recognition between the two desaturases; CrtIa dehydrogenates carotenes in the cis conformation, whereas CrtIb dehydrogenates carotenes in the trans conformation. [source] Bridging the gap , structure determination of the red polymorph of tetrahexylsexithiophene by Monte Carlo simulated annealing, first-principles DFT calculations and Rietveld refinementJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3 2002Marcus A. Neumann The crystal structure of the red polymorph of tetrahexylsexithiophene (THST) is solved from X-ray powder diffraction data by a direct-space Monte Carlo simulated-annealing approach. First-principles density functional theory (DFT) calculations are used to distinguish between three nearly identical solutions in the space groups C2/m, C2 and P and to improve the overall accuracy of the crystal structure. The correct space group is found to be C2/m. In all space groups, the thiophene backbone is planar and the hexyl side chains assume an all- trans conformation except for two terminal methyl residues, which adopt a gauche orientation. The ability of first-principles DFT calculations to provide atomic coordinates of single-crystal quality is demonstrated by lattice-energy minimization of the known crystal structure of the yellow polymorph of THST. The combination of Monte Carlo simulated annealing, first-principles DFT calculations and Rietveld refinement presented in this paper is generally applicable. It provides a powerful alternative to standard approaches in cases where the information content of the powder diffraction pattern alone is insufficient to distinguish between different structure solutions. DFT calculations can also provide invaluable guidance in Rietveld refinement. [source] Influence of substituents on the infrared stretching frequencies of carbonyl group in esters of benzoic acidJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 10 2006Vilve Nummert Abstract Infrared spectra of 25 substituted phenyl esters of benzoic acid C6H5CO2C6H4 -X (XH, 3-Cl, 3-F, 3-CN, 3-NO2, 3-CH3, 3-OH, 3-NH2, 4-Cl, 4-F, 4-NO2, 4-CN, 4-OCH3, 4-CH3, 4-NH2, 2-Cl, 2-F, 2-I, 2-NO2, 2-CF3, 2-CN, 2-CH3, 2-OCH3, 2-N(CH3)2, 2-C(CH3)3), 8 alkyl benzoates C6H5CO2R (XCH3, CH2CH3, CH2Cl, CH2CN, CH2CCH, CH2CH2Cl, CH2CH2OCH3, CH2C6H5), and 22 phenyl esters of substituted benzoic acids X-C6H4CO2C6H5 (X3-Cl, 3-NO2, 3-CH3, 3-N(CH3)2, 4-F, 4-Cl, 4-Br, 4-NO2, 4-CH3, 4-C(CH3)3, 4-OCH3, 4-NH2, 2-Cl, 2-F, 2-Br, 2-I, 2-NO2, 2-CN, 2-CF3, 2-CH3, 2-OCH3, 2-NH2) were recorded in tetrachloromethane in the region of 400,4000,cm,1. Carbonyl stretching frequencies ,CO for meta - and para -substituted phenyl esters of benzoic acid and phenyl esters of meta -substituted benzoic acids were shown to correlate with the substituent constants ,o. The influence of the through resonance effect on ,CO was found to be important in the case of +Rpara substituents in the benzoyl part of phenyl benzoates as well. The carbonyl stretching frequencies of ortho derivatives in phenoxy part were shown to correlate with the inductive substituent constant ,I only. In the benzoyl part of the esters the carbonyl stretching frequencies of cis and trans conformers (relative to the carbonyl group) of ortho derivatives were nicely described by dual parameter equations: (,CO)cis,=,(,CO)o,+,c1,I,+,c3,and (,CO)trans,=,(,CO)o,+,c1,p+,+,c3, (R,=,0.99). The trans isomers of phenyl esters of ortho -substituted benzoic acids showed direct resonance similar to that for para derivatives. The positive steric term found for both the cis and trans conformers could be considered as measure of the steric inhibition of resonance between the phenyl ring and the carboxy-group caused by bulky ortho substituents. The existence of cis/trans conformations was supported by frequency calculations with Density Functional Theory (DFT) method at B3LYP/6-311+G** level for the ortho -substituted benzoates. In the case of alkyl benzoates good correlations of ,CO values were obtained when both the Taft ,* and the steric constants were used. For meta - and para -substituted phenyl benzoates s - trans conformation where the plane of the benzene ring in the benzoyl part of the ester is coplanar with the carbonyl bond plane and the plane of the benzene ring in the phenoxy part is twisted nearly perpendicular relative to the carbonyl bond plane was supported. Copyright © 2006 John Wiley & Sons, Ltd. [source] Monolayers of sulfur-containing molecules at metal surfaces as studied using SERS: 3, 3,-thiodipropionic acid and 3-mercaptopropionic acid adsorbed on silver and copperJOURNAL OF RAMAN SPECTROSCOPY, Issue 6-7 2005Andrzej Kudelski Abstract The modification of metal surfaces with self-assembled thiol monolayers is the subject of intensive studies owing to both its fundamental interest in surface chemistry and its potential technological significance. In this work, the applicability of surface-enhanced Raman scattering (SERS) to determine the conformation and pKa values of ,-terminated thiol molecules was investigated. 3, 3,-Thiodipropionic acid (TDPA) and 3-mercaptopropionic acid (MPA) monolayers were spontaneously formed on silver and copper surfaces by adsorption from TDPA and MPA solutions, respectively. The structure of the monolayers formed was determined from SERS measurements. The SERS investigations showed that molecules forming TDPA monolayers prefer to adopt a gauche conformation of the,S,C,C chains, whereas in MPA monolayers formed from 1 mM MPA aqueous solution a significant part of the adsorbed molecules adopts a trans conformation. Formation on the metal surface of an MPA monolayer with high surface coverage of MPA makes dissociation of the carboxylic groups of MPA significantly more difficult. Analogous changes in the strength of similar adsorbed compounds have been reported by other groups. In contrast to those results, we found that the formation of monolayers from TDPA increases its acidic strength even at high surface coverage when monolayers are formed from relatively concentrated TDPA solutions. Probably the interaction of carboxylic groups with the metal surface is easier for TDPA than for MPA for geometric reasons. We consider that ionization of carboxylic groups increases the strength of this interaction. Copyright © 2005 John Wiley & Sons, Ltd. [source] X-ray crystal structures of diacetates of 6-s- cis and 6-s- trans astaxanthin and of 7,8-didehydroastaxanthin and 7,8,7,,8,-tetradehydroastaxanthin: comparison with free and protein-bound astaxanthinsACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2009Giuditta Bartalucci The crystal structures of the 6-s- cis [s- cis -(1)] and 6-s- trans [s- trans -(1)] conformers of the diacetates of astaxanthin (AXT) and those of (3S,3,S)-7,8-didehydroastaxanthin [(3S,3,S)-3,3,-dihydroxy-7,8-didehydro-,,,-carotene-4,4,-dione (2)] and (3S,3,S)-7,8,7,,8,-tetradehydroastaxanthin [(3S,3,S)-3,3,-dihydroxy-7,8,7,,8,-tetradehydro-,,,-carotene-4, 4,-dione (3)] are reported. The conformations of these four molecules vary in particular with the angle of twist of the end rings out of the plane of the polyene chain; for s- cis -(1), the end rings are twisted out of the plane of the polyene chain by an angle of ,49.0,(5)°, and the conformation is therefore similar to that found for unesterified AXT as well as for the carotenoids, canthaxanthin and ,,,-carotene. For s- trans -(1), the end rings are coplanar with the polyene chain and its conformation is much more similar to that of the protein-bound AXT in the blue protein, crustacyanin, which is found in the shell of lobsters, although s- trans -(1) shows much less bowing of the polyene chain. In (2) and (3) the end rings are also almost coplanar with the polyene chain with the end rings in (2) in the s- cis conformation, and in (3) in the s- trans conformation. Thus, an extensive ensemble of the possible , end-ring conformations has been determined. These structures are compared with one another as well as unbound, unesterified AXT and protein-bound AXT. Also, the effect of the end-ring conformations on the colour and UV,vis spectra of the crystals was established. [source] In-situ high-pressure study of the ordered phase of ethyl propionateACTA CRYSTALLOGRAPHICA SECTION B, Issue 1 2007Roman Gajda Ethyl propionate, C5H10O2 (m.p. 199,K), has been in-situ pressure-frozen and its structure determined at 1.34, 1.98 and 2.45,GPa. The crystal structure of the new high-pressure phase (denoted ,) is different from phase , obtained by lowering the temperature. The freezing pressure of ethyl propionate at 296,K is 1.03,GPa. The molecule assumes an extended chain s-trans,trans,trans conformation, only slightly distorted from planarity. The closest intermolecular contacts in both phases are formed between carbonyl O and methyl H atoms; however, the ethyl-group H atoms in phase , form no contacts shorter than 2.58,Å. A considerable molecular volume difference of 24.2,Å3 between phases , and , can be rationalized in terms of degrees of freedom of molecules arranged into closely packed structures: the three degrees of freedom allowed for rearrangements of molecules confined to planar sheets in phase ,, but are not sufficient for obtaining a densely packed pattern. [source] Structural comparison of three N -(4-halogenophenyl)- N,-[1-(2-pyridyl)ethylidene]hydrazine hydrochloridesACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2010Julia Heilmann-Brohl 2-{1-[(4-Chloroanilino)methylidene]ethyl}pyridinium chloride methanol solvate, C13H13ClN3+·Cl,·CH3OH, (I), crystallizes as discrete cations and anions, with one molecule of methanol as solvent in the asymmetric unit. The N,C,C,N torsion angle in the cation indicates a cis conformation. The cations are located parallel to the (02) plane and are connected through hydrogen bonds by a methanol solvent molecule and a chloride anion, forming zigzag chains in the direction of the b axis. The crystal structure of 2-{1-[(4-fluoroanilino)methylidene]ethyl}pyridinium chloride, C13H13FN3+·Cl,, (II), contains just one anion and one cation in the asymmetric unit but no solvent. In contrast with (I), the N,C,C,N torsion angle in the cation corresponds with a trans conformation. The cations are located parallel to the (100) plane and are connected by hydrogen bonds to the chloride anions, forming zigzag chains in the direction of the b axis. In addition, the crystal packing is stabilized by weak ,,, interactions between the pyridinium and benzene rings. The crystal of (II) is a nonmerohedral monoclinic twin which emulates an orthorhombic diffraction pattern. Twinning occurs via a twofold rotation about the c axis and the fractional contribution of the minor twin component refined to 0.324,(3). 2-{1-[(4-Fluoroanilino)methylidene]ethyl}pyridinium chloride methanol disolvate, C13H13FN3+·Cl,·2CH3OH, (III), is a pseudopolymorph of (II). It crystallizes with two anions, two cations and four molecules of methanol in the asymmetric unit. Two symmetry-equivalent cations are connected by hydrogen bonds to a chloride anion and a methanol solvent molecule, forming a centrosymmetric dimer. A further methanol molecule is hydrogen bonded to each chloride anion. These aggregates are connected by C,H...O contacts to form infinite chains. It is remarkable that the geometric structures of two compounds having two different formula units in their asymmetric units are essentially the same. [source] An ice-like water hexamer with symmetry in the hydrogen-bonded structure of 2,3,5,6-tetrafluoro-1,4-bis(imidazol-1-ylmethyl)benzene dihydrateACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2010Huan Xu An ice-like hexameric water cluster, stabilized by the flexible bis-imidazolyl compound 2,3,5,6-tetrafluoro-1,4-bis(imidazol-1-ylmethyl)benzene (Fbix), is found in the trigonal R crystal structure of the title compound, C14H10F4N4·2H2O or Fbix·2H2O. The Fbix molecule lies about an inversion centre with one water molecule in the asymmetric unit in a general position. A cyclic chair-like hexameric water cluster with symmetry is generated with a hydrogen-bonded O...O distance within the hexamer of 2.786,(3),Å. The Fbix molecule adopts a trans conformation, where the imidazole ring makes a dihedral angle of 70.24,(11)° with the central tetrafluorinated aromatic ring. Each water hexamer is connected by six Fbix molecules through intermolecular O,H...N hydrogen bonds [N...O = 2.868,(3),Å] to yield a three-dimensional supramolecular network with primitive cubic (pcu) topology. Large voids in each single pcu network lead to fourfold interpenetrated aggregates of Fbix·2H2O. [source] Two polymorphs of N -(2,6-difluorophenyl)formamideACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2009Bernard Omondi The structures of two distinct polymorphic forms of N -(2,6-difluorophenyl)formamide, C7H5F2NO, have been studied using single crystals obtained under different crystallizing conditions. The two forms crystallize in different space groups, viz. form (Ia) in the orthorhombic Pbca and form (Ib) in the monoclinic P21 space group. Each polymorph crystallizes with one complete molecule in the asymmetric unit and they have a similar molecular geometry, showing a trans conformation with the formamide group being out of the plane of the aromatic ring. The packing arrangements of the two polymorphs are quite different, with form (Ia) having molecules that are stacked in an alternating arrangement, linked into chains of N,H...O hydrogen bonds along the crystallographic a direction, while form (Ib) has its N,H...O hydrogen-bonded molecules stacked in a linear fashion. A theoretical study of the two structures allows information to be gained regarding other contributing interactions, such as ,,, and weak C,H...F, in their crystal structures. [source] Quinolin-6-ol at 100,KACTA CRYSTALLOGRAPHICA SECTION C, Issue 2 2009Anna Michta The title compound, C9H7NO, has two symmetry-independent molecules in the asymmetric unit, which have different conformations of the hydroxy group with respect to the quinoline ring. One of the molecules adopts a cis conformation, while the other shows a trans conformation. Each type of independent molecule links into a separate infinite O,H...N hydrogen-bonded chain with the graph-set notation C(7). These chains are perpendicular in the unit cell, one extended in the a -axis direction and the other in the b -axis direction. There is also a weak C,H...O hydrogen bond with graph-set notation D(2), which runs in the c -axis direction and joins the two separate O,H...N chains. The significance of this study lies in the comparison drawn between the experimental and calculated data of the crystal structure of the title compound and the data of several other derivatives possessing the hydroxy group or the quinoline ring. The correlation between the IR spectrum of this compound and the hydrogen-bond energy is also discussed. [source] Butane-1,4-diyl bis(chloroacetate)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 12 2004Lourdes Urpí The title compound, C8H12Cl2O4, lies about an inversion centre. The molecular conformation is characterized by a conformation for the butanedioxy moiety and a trans conformation for the ClCH2,C(=O)O bond. The molecular packing is stabilized by a network of weak CH2,O=C intermolecular hydrogen bonds, where each molecule interacts with its four closest neighbours. [source] 3-Methoxy-5-(4-methylphenyldiazenyl)salicylaldehyde and 3-methoxy-5-(2-methylphenyldiazenyl)salicylaldehydeACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2004Cem Cüneyt Ersanl The two title molecules, both C15H14N2O3, are roughly planar and display a trans conformation with respect to the ,N=N, double bond, as found for other diazene derivatives. In both compounds, there are intramolecular O,H,O hydrogen bonds and the crystal packing is governed by weak intermolecular C,H,O hydrogen bonds and ,,, stacking. [source] 3,6-Bis(dimethylamino)-10-propylacridinium iodideACTA CRYSTALLOGRAPHICA SECTION C, Issue 11 2001Raffaella Puliti In the title compound, C20H26N3+·I,, the acridinium moiety shows mirror symmetry about the central C,N vector. The fused tricyclic system is only approximately planar and the geometry is affected by the presence of both dimethylamino groups and the propyl substitution at the central N atom. The propyl chain adopts an extended trans conformation and the plane through the chain C atoms is perpendicular to the mean plane through the rings. The I, ion is involved in short-range hydrogen-bonding interactions with two centrosymmetrically related cations via three activated acridinium C atoms. Stacks of acridinium cations propagate through the crystal along the c direction. The ring overlap is partial, but the dimethylamino groups also participate in the stacking. [source] Acetone-4-methylthiosemicarbazone at 220,KACTA CRYSTALLOGRAPHICA SECTION C, Issue 2 2000Simon Parsons In the title compound, C5H11N3S, the trans conformation is stabilized by a weak intramolecular N,H,N hydrogen bond. Unusually, one N,H bond is not involved in any hydrogen-bond interactions and instead the molecules form a one-dimensional polymer via N,H,S intermolecular hydrogen bonds. [source] The structure of the genomic Bacillus subtilis dUTPase: novel features in the Phe-lidACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2010Javier García-Nafría dUTPases are a ubiquitous family of enzymes that are essential for all organisms and catalyse the breakdown of 2-deoxyuridine triphosphate (dUTP). In Bacillus subtilis there are two homotrimeric dUTPases: a genomic and a prophage form. Here, the structures of the genomic dUTPase and of its complex with the substrate analogue dUpNHpp and calcium are described, both at 1.85,Å resolution. The overall fold resembles that of previously solved trimeric dUTPases. The C-terminus, which contains one of the conserved sequence motifs, is disordered in both structures. The crystal of the complex contains six independent protomers which accommodate six dUpNHpp molecules, with three triphosphates in the trans conformation and the other three in the active gauche conformation. The structure of the complex confirms the role of several key residues that are involved in ligand binding and the position of the catalytic water. Asp82, which has previously been proposed to act as a general base, points away from the active site. In the complex Ser64 reorients in order to hydrogen bond the phosphate chain of the substrate. A novel feature has been identified: the position in the sequence of the `Phe-lid', which packs against the uracil moiety, is adjacent to motif III, whereas in all other dUTPase structures the lid is in a conserved position in motif V of the flexible C-terminal arm. This requires a reconsideration of some aspects of the accepted mechanism. [source] Analysis of quinazoline and pyrido[2,3- d]pyrimidine N9,C10 reversed-bridge antifolates in complex with NADP+ and Pneumocystis carinii dihydrofolate reductaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2002Vivian Cody Structural studies of two ternary complexes of Pneumocystis carinii dihydrofolate reductase (pcDHFR) with the cofactor NADP+ and potent antifolates, the N9,C10 reversed-bridge inhibitor 2,4-diamino-6-[N -(2,,5,-dimethoxybenzyl)- N -methylamino]quinazoline (1) and its 3,,5,-dimethoxypyrido[2,3- d]pyrimidine analog (2), were carried out. Data for the monoclinic crystals were refined to 1.90,Å resolution for the complex with (1) (R = 0.178) and to 2.1,Å resolution for the complex with (2) (R = 0.193). The effect of the N9,C10 reversed-bridge geometry is to distort the bridge from coplanarity with the pyrido[2,3- d]pyrimidine or quinazoline ring system and to twist the C10 methylene conformation toward a gauche conformation. This change also influences the conformation of the methoxybenzyl ring, moving it away from a trans position. This change places the 5,-methoxy group deeper within the hydrophobic pocket made by Ile65, Pro66 and Phe69 of the pcDHFR active site. These results also revealed the first observation of an unusual conformation for the reversed-bridge geometry (C5,C6,N9,C10 torsion angle) in antifolate (2). The electron density is consistent with the presence of two models (conformers 2-1 and 2-2) that result from inversion of the geometry at N9. The four examples of N9,C10 reversed-bridge antifolates cluster in two conformations, with the structure of quinazoline (1) similar to that previously reported for its 2,,5,-dimethoxypyrido[2,3- d]pyrimidine analog (3). The two conformers of (2) differ from these and each other by a twisted-bridge geometry that results in the dimethoxybenzyl ring occupying the same conformational space. Conformer 2-2 also has the N9,C10 reversed bridge perpendicular to the pyrido[2,3- d]pyrimidine plane, in contrast to the gauche,trans conformation normally observed. As a result of these changes, the N9 methyl probes conformational space in the active site not normally occupied by antifolate structures. The N9 methyl of conformer 2-2 makes close contacts to the conserved Leu25 as well as the hydroxyl O atoms of the nicotinamide ribose and Ser64, whereas the other three reversed-bridge conformers make weak hydrophobic contacts with Ile123, Thr61 and Ile65. These antifolates are ten times more selective for pcDHFR than the C9,N10 bridge parent trimetrexate. However, pyrido[2,3- d]pyrimidines (2) and (3) are three times more selective for pcDHFR than quinazoline (1) is for rat liver DHFR. These data suggest that the loss of hydrogen-bonding interactions with N8 is more important to potency than the interactions of the methoxybenzyl substituents. [source] A C-terminal disulfide bond in the copper-containing amine oxidase from pea seedlings violates the twofold symmetry of the molecular dimerACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2006Anthony P. Duff The structure of a newly crystallized form of the copper-dependent amine oxidase from pea seedlings has been refined at a resolution of 2.2,Å to a final R factor of 0.181. The structure (form II) was originally discovered during a study of xenon binding to copper-dependent amine oxidases as a probe for dioxygen-binding sites [Duff et al. (2004), J. Mol. Biol.344, 599,607]. The form II crystals belong to space group P21, with two dimers in the asymmetric unit. The overall structure is very similar to the crystals of form I in space group P212121 with a dimer in the asymmetric unit [Kumar et al. (1996), Structure, 4, 943,955]. In form I the last three residues (644,647) observable in the two subunits were apparently splayed apart. It was noted that the absence of a disulfide bond between the Cys647 residues of the two subunits was inconsistent with chemical evidence for the absence of free sulfhydryl groups. In both of the crystallographically independent dimers of form II the two subunits are clearly joined by a disulfide bridge between the C-terminal cysteine residues. This is only possible if the two polypeptide chains in the dimer adopt different conformations near the C-terminus so that the twofold symmetry is lost. A proline residue (645) two residues before the cysteine has a cis conformation in one chain and a trans conformation in the other. As a result, the disulfide bond lies more than 5,Å from the twofold axis. The loss of local twofold symmetry in form II can be explained by intermolecular contacts, which provide an asymmetric environment. [source] New Metal-Organic Frameworks with Large Cavities: Selective Sorption and Desorption of Solvent MoleculesCHEMISTRY - A EUROPEAN JOURNAL, Issue 26 2007Yan Wang Abstract Five novel transition metal complexes [CdII3(tpba-2)2(SCN)6],6,THF,3,H2O (1), [CuII3(tpba-2)2(SCN)6],6,THF,3,H2O (2), [NiII3(tpba-2)2(SCN)6],6,THF,3,H2O (3), [CdII2(tpba-2)(SCN)3]ClO4 (4), [CuI3(SCN)6(H3tpba-2)] (5) [TPBA-2 = N,,N,,,N,,, -tris(pyrid-2-ylmethyl)-1,3,5-benzenetricarboxamide, THF=tetrahydrofuran] were obtained by reactions of the corresponding transition metal salts with TPBA-2 ligand in the presence of NH4SCN using layering or solvothermal method, respectively. The results of X-ray crystallographic analysis showed that complexes 1, 2 and 3 are isostructural and have the same 2D honeycomb network structure with Kagomé lattice, in which all the MII (M = Cd, Cu, Ni) atoms are six-coordinated, and the TPBA-2 ligands adopt cis,cis,cis conformation while the thiocyanate anions act as terminal ligands. Capsule-like motifs are found in 1, 2 and 3, in which six THF molecules are hosted, and the results of XPRD and solid-state 13C,NMR spectral measurements showed that the compound 1 can selectively desorb and adsorb THF molecules occurring along with the re-establishment of its crystallinity. In contrast to 1, 2 and 3, complex 4 has different 2D network structure, resulting from TPBA-2 ligands with cis,trans,trans conformation, thiocyanate anions serving as end-to-end bridging ligands, and the incomplete replacement of perchlorate anions, which further link the 2D layers into 3D framework by the hydrogen bonds. In complex 5, the CuII atoms are reduced to CuI during the process of solvothermal reaction, and the CuI atoms are connected by thiocyanate anions to form a 3D porous framework, in which the protonated TPBA-2 ligands are hosted in the cavities as templates. [source] Mechanistic Study of the Reaction of Thiol-Containing Enzymes with ,,,-Unsaturated Carbonyl Substrates by Computation and ChemoassaysCHEMMEDCHEM, Issue 6 2010Alexander Paasche Abstract We investigated the reactions between substituted ,,,-unsaturated carbonyl compounds (Michael systems) and thiols by computations as well as chemoassays. The results give insight into variations in the underlying mechanisms as a function of the substitution pattern. This is of interest for the mechanisms of inhibition of the SARS coronavirus main protease (SARS-CoV Mpro) by etacrynic acid derivatives as well as for the excess toxicity of substituted ,,,-unsaturated carbonyl compounds. This study compares possible reaction courses including 1,4-addition followed by a ketonization step, and underscores the importance of a base-catalyzed step for the reactivity of thiol groups in enzymes. Phenyl and methyl substituents at the Michael system decrease the reactivity of the electrophilic compound, but chlorophenyl substituents partly recover the reactivity. Computations also indicate that electron-pushing substituents lead to a change in the reaction mechanism. The conformation of the Michael system is also found to significantly influence reactivity: the s - cis conformation leads to higher reactivity than the s - trans conformation. The computed data explain the trends in measured inhibition potencies of substituted ,,,-unsaturated carbonyl compounds and of reaction rates in chemical assays. They also indicate that the reversibility of inhibition does not stand in contrast to the formation of a new covalent bond between inhibitor and protease. [source] 1,2,3-Trimethoxy-4-[(E)-2-phenylvinyl]benzene and (E,E)-1,4-bis(2,3,4-trimethoxyphenyl)buta-1,3-dieneACTA CRYSTALLOGRAPHICA SECTION C, Issue 7 2009Jana Sopková-de Oliveira Santos The stilbene derivative 1,2,3-trimethoxy-4-[(E)-2-phenylvinyl]benzene, C17H18O3, (I), and its homocoupling co-product (E,E)-1,4-bis(2,3,4-trimethoxyphenyl)buta-1,3-diene, C22H26O6, (II), both have double bonds in trans conformations in their conjugated linkages. In the structure of stilbene (I), the aromatic rings deviate significantly from coplanarity, in contrast with coproduct (II), the core of which is rigorously planar. The deviation in stilbene (I) seems to be driven by intermolecular electrostatic interactions. Diene (II) sits on a crystallographic inversion centre, which bisects the conjugated linkage. [source] Near-atomic resolution crystal structure of an A-DNA decamer d(CCCGATCGGG): cobalt hexammine interaction with A-DNAACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2003Boopathy Ramakrishnan The structure of the DNA decamer d(CCCGATCGGG) has been determined at 1.25,Å resolution. The decamer crystallized in the tetragonal space group P43212, with unit-cell parameters a = b = 44.3, c = 24.8,Å and one strand in the asymmetric unit. The structure was solved by the molecular-replacement method and refined to Rwork and Rfree values of 16.3 and 18.5%, respectively, for 5969 reflections. The decamer forms the A-form DNA duplex, with the abutting crystal packing typical of A-DNA. The crystal packing interactions seem to distort the local conformation: A5 adopts the trans/trans conformation for the torsion angles , and , instead of the usual gauche,/gauche+ conformations, yielding G*(G·C) base triplets. The highly hydrated [Co(NH3)6]3+ ion adopts a novel binding mode to the DNA duplex, binding directly to phosphate groups and connecting to N7 and O6 atoms of guanines by water bridges. Analysis of thermal parameters (B factors) shows that the nucleotides involved in abutting crystal packing are thermally more stable than other nucleotides in the duplex. [source] | ||||||||||