scholarly journals The molecular and crystal structures of 4-N-(2-acetamido-2-deoxy-β-d-glucopyranosyl)-l-asparagine trihydrate and 4-N-(β-d-glucopyranosyl)-l-asparagine monohydrate. The X-ray analysis of a carbohydrate–peptide linkage

1974 ◽  
Vol 143 (1) ◽  
pp. 197-205 ◽  
Author(s):  
L. T. J. Delbaere
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Torsion Angle ◽  
Chair Conformation ◽  
Amide Group ◽  
British Library ◽  
X Ray ◽  
Peptide Linkage ◽  
Lending Library ◽  
The Mean

X-ray analyses have shown that the glucopyranose rings of GlcNAc-Asn [4-N-(2-acetamido-2-deoxy-β-d-glucopyranosyl)-l-asparagine] and Glc-Asn [4-N-(β-d-glucopyranosyl)-l-asparagine] both have the C-1 chair conformation and also that the glucose–asparagine linkage of each molecule is present in the β-anomeric configuration. The dimensions (the estimated standard deviations of the last digit are in parentheses) of the glycosidic bond in GlcNAc-Asn and Glc-Asn are, respectively, C(1)-N(1) 0.1441(6)nm, 0.146(2)nm; angle O(5)-C(1)-N(1) 106.8(3)°, 105.7(8)° angle C(2)-C(1)-N(1) 111.1(4)°, 110.4(9)° angle C(1)-N(1)-C(9) 121.4(4)°, 120.5(9)°. The glycosidic torsion angle C(9)-N(1)-C(1)-C(2) is 141.0° and 157.6° in GlcNAc-Asn and Glc-Asn respectively. Hydrogen-bonding is extensive in these two crystal structures and does affect one torsion angle in particular. Two very different values of χ1(N-Cα-Cβ-Cγ) occur for the asparagine residue of the two different molecules; the values of χ1, −69.0° in GlcNAc-Asn and 61.9° in Glc-Asn, correspond to two different staggered conformations about the Cα-Cβbond as the NH3+group is adjusted to different hydrogen-bonding patterns. The two trans-peptide groups in GlcNAc-Asn show small distortions in planarity whereas that in Glc-Asn is more non-planar. The mean plane through the atoms of the amide group at C(2) in GlcNAc-Asn is approximately perpendicular (69°) to the mean plane through the C(2), C(3), C(5) and O(5) atoms of the glucose ring and that at C(1) is less perpendicular (65°). The mean plane through the atoms of the amide group in Glc-Asn makes an angle of only 55° with the mean plane through these same four atoms of the glucose ring. The N(1)-H bond of the amide at C(1) is trans to the C(1)-H bond in these two compounds; the N(2)-H bond of the amide at C(2) is trans to the C(2)-H bond in GlcNAc-Asn. The values of the observed and final calculated structure amplitudes have been deposited as Supplementary Publication SUP 50035 (26 pages) at the British Library (Lending Division), (formerly the National Lending Library for Science and Technology), Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies may be obtained on the terms given in Biochem. J. (1973) 131, 5.

scholarly journals Structures of furanosides: geometrical analysis of low-temperature X-ray and neutron crystal structures of five crystalline methyl pentofuranosides

2001 ◽  
Vol 57 (2) ◽  
pp. 213-220 ◽  
Author(s):  
Artem Evdokimov ◽  
A. Joseph Gilboa ◽  
Thomas F. Koetzle ◽  
Wim T. Klooster ◽  
Arthur J. Schultz ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Critical Role ◽  
Chair Conformation ◽  
Geometrical Analysis ◽  
X Ray ◽  
Wide Range ◽  
First Time ◽  
Ring Conformations

Crystal structures of all five crystalline methyl D-pentofuranosides, methyl α-D-arabinofuranoside (1), methyl β-D-arabinofuranoside (2), methyl α-D-lyxofuranoside (3), methyl β-D-ribofuranoside (4) and methyl α-D-xylofuranoside (5) have been determined by means of cryogenic X-ray and neutron crystallography. The neutron diffraction experiments provide accurate, unbiased H-atom positions which are especially important because of the critical role of hydrogen bonding in these systems. This paper summarizes the geometrical and conformational parameters of the structures of all five crystalline methyl pentofuranosides, several of them reported here for the first time. The methyl pentofuranoside structures are compared with the structures of the five crystalline methyl hexopyranosides for which accurate X-ray and neutron structures have been determined. Unlike the methyl hexopyranosides, which crystallize exclusively in the C 1 chair conformation, the five crystalline methyl pentofuranosides represent a very wide range of ring conformations.

scholarly journals The crystal structures and mechanical properties of the uranyl carbonate minerals roubaultite, fontanite, sharpite, widenmannite, grimselite and čejkaite

2020 ◽  
Vol 7 (21) ◽  
pp. 4197-4221 ◽  
Author(s):  
Francisco Colmenero ◽  
Jakub Plášil ◽  
Jiří Sejkora
Keyword(s):  
Mechanical Properties ◽  
Hydrogen Bonding ◽  
Diffraction Pattern ◽  
Crystal Structures ◽  
First Principles ◽  
X Ray Diffraction ◽  
Carbonate Minerals ◽  
X Ray ◽  
Uranyl Carbonate

The structure, hydrogen bonding, X-ray diffraction pattern and mechanical properties of six important uranyl carbonate minerals, roubaultite, fontanite, sharpite, widenmannite, grimselite and čejkaite, are determined using first principles methods.

Structural Studies on N-(2,4,6-Trimethylphenyl)-methyl/ chloro-acetamides, 2,4,6-(CH3)3C6H2NH-CO-CH3–yXy (X = CH3 or Cl and y = 0, 1, 2)

2006 ◽  
Vol 61 (10-11) ◽  
pp. 588-594 ◽  
Author(s):  
Basavalinganadoddy Thimme Gowda ◽  
Jozef Kožíšek ◽  
Hartmut Fuess
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structural Data ◽  
The Other ◽  
Side Chain ◽  
Structural Studies ◽  
Asymmetric Unit ◽  
Lattice Constants ◽  
Peptide Linkage ◽  
The Mean

TMPAThe effect of substitutions in the ring and in the side chain on the crystal structure of N- (2,4,6-trimethylphenyl)-methyl/chloro-acetamides of the configuration 2,4,6-(CH3)3C6H2NH-COCH3− yXy (X = CH3 or Cl and y = 0,1, 2) has been studied by determining the crystal structures of N-(2,4,6-trimethylphenyl)-acetamide, 2,4,6-(CH3)3C6H2NH-CO-CH3 (); N-(2,4,6- trimethylphenyl)-2-methylacetamide, 2,4,6-(CH3)3C6H2NH-CO-CH2-CH3 (TMPMA); N-(2,4,6- trimethylphenyl)-2,2-dimethylacetamide, 2,4,6-(CH3)3C6H2NH-CO-CH(CH3)2 (TMPDMA) and N-(2,4,6-trimethylphenyl)-2,2-dichloroacetamide, 2,4,6-(CH3)3C6H2NH-CO-CHCl2 (TMPDCA). The crystallographic system, space group, formula units and lattice constants in Å are: TMPA: monoclinic, Pn, Z = 2, a = 8.142(3), b = 8.469(3), c = 8.223(3), β = 113.61(2)◦; TMPMA: monoclinic, P21/n, Z = 8, a = 9.103(1), b = 15.812(2), c = 16.4787(19), α = 89.974(10)◦, β = 96.951(10)◦, γ =89.967(10)◦; TMPDMA: monoclinic, P21/c, Z = 4, a =4.757(1), b= 24.644(4), c =10.785(2), β = 99.647(17)◦; TMPDCA: triclinic, P¯1, Z = 2, a = 4.652(1), b = 11.006(1), c = 12.369(1), α = 82.521(7)◦, β = 83.09(1)◦, γ = 79.84(1)◦. The results are analyzed along with the structural data of N-phenylacetamide, C6H5NH-CO-CH3; N-(2,4,6-trimethylphenyl)-2-chloroacetamide, 2,4,6-(CH3)3C6H2NH-CO-CH2Cl; N-(2,4,6-trichlorophenyl)-acetamide, 2,4,6-Cl3C6H2NH-COCH3; N-(2,4,6-trichlorophenyl)-2-chloroacetamide, 2,4,6-Cl3C6H2NH-CO-CH2Cl; N-(2,4,6-trichlorophenyl)- 2,2-dichloroacetamide, 2,4,6-Cl3C6H2NH-CO-CHCl2 and N-(2,4,6-trichlorophenyl)- 2,2,2-trichloroacetamide, 2,4,6-Cl3C6H2NH-CO-CCl3. TMPA, TMPMA and TMPDCA have one molecule each in their asymmetric units, while TMPDMA has two molecules in its asymmetric unit. Changes in the mean ring distances are smaller on substitution as the effect has to be transmitted through the peptide linkage. The comparison of the other bond parameters reveal that there are significant changes in them on substitution.

The structures of marialite (Me6) and meionite (Me93) in space groups P42/n and I4/m, and the absence of phase transitions in the scapolite series

2011 ◽  
Vol 26 (2) ◽  
pp. 119-125 ◽  
Author(s):  
Sytle M. Antao ◽  
Ishmael Hassan
Keyword(s):  
Phase Transitions ◽  
High Resolution ◽  
Crystal Structures ◽  
Unit Cell ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Space Groups ◽  
Cell Parameters ◽  
The Mean

The crystal structures of marialite (Me6) from Badakhshan, Afghanistan and meionite (Me93) from Mt. Vesuvius, Italy were obtained using synchrotron high-resolution powder X-ray diffraction (HRPXRD) data and Rietveld structure refinements. Their structures were refined in space groups I4/m and P42/n, and similar results were obtained. The Me6 sample has a formula Ca0.24Na3.37K0.24[Al3.16Si8.84O24]Cl0.84(CO3)0.15, and its unit-cell parameters are a=12.047555(7), c=7.563210(6) Å, and V=1097.751(1) Å3. The average ⟨T1-O⟩ distances are 1.599(1) Å in I4/m and 1.600(2) Å in P42/n, indicating that the T1 site contains only Si atoms. In P42/n, the average distances of ⟨T2-O⟩=1.655(2) and ⟨T3-O⟩=1.664(2) Å are distinct and are not equal to each other. However, the mean ⟨T2,3-O⟩=1.659(2) Å in P42/n and is identical to the ⟨T2′-O⟩=1.659(1) Å in I4/m. The ⟨M-O⟩ [7]=2.754(1) Å (M site is coordinated to seven framework O atoms) and M-A=2.914(1) Å; these distances are identical in both space groups. The Me93 sample has a formula of Na0.29Ca3.76[Al5.54Si6.46O24]Cl0.05(SO4)0.02(CO3)0.93, and its unit-cell parameters are a=12.19882(1), c=7.576954(8) Å, and V=1127.535(2) Å3. A similar examination of the Me93 sample also shows that both space groups give similar results; however, the C–O distance is more reasonable in P42/n than in I4/m. Refining the scapolite structure near Me0 or Me100 in I4/m forces the T2 and T3 sites (both with multiplicity 8 in P42/n) to be equivalent and form the T2′ site (with multiplicity 16 in I4/m), but ⟨T2-O⟩ is not equal to ⟨T3-O⟩ in P42/n. Using different space groups for different regions across the series implies phase transitions, which do not occur in the scapolite series.

scholarly journals Corymbolone

2014 ◽  
Vol 70 (7) ◽  
pp. o758-o758 ◽  
Author(s):  
Stacey Burrett ◽  
Dennis K. Taylor ◽  
Edward R. T. Tiekink
Keyword(s):  
Hydrogen Bonding ◽  
Title Compound ◽  
Crystal Packing ◽  
Chair Conformation ◽  
Compound C ◽  
The Mean

The title compound, C15H24O2[systematic name: (4S,4aR,6R,8aR)-4a-hydroxy-4,8a-dimethyl-6-(prop-1-en-2-yl)octahydronaphthalen-1(2H)-one], features two edge-shared six-membered rings with the hydroxyl and methyl substituents at this bridge beingtrans. One adopts a flattened chair conformation with the C atoms bearing the carbonyl and methyl substituents lying 0.5227 (16) and 0.6621 (15) Å, respectively, above and below the mean plane through the remaining four C atoms (r.m.s. deviation = 0.0145 Å). The second ring, bearing the prop-1-en-2-yl group, has a chair conformation. Supramolecular helical chains along thebaxis are found in the crystal packing, which are sustained by hydroxy–carbonyl O—H...O hydrogen bonding.

X-ray studies on crystalline complexes involving amino acids and peptides. XL. Conformational variability, recurring and new features of aggregation, and effect of chirality in the malonic acid complexes of DL- and L-arginine

2002 ◽  
Vol 58 (6) ◽  
pp. 1051-1056 ◽  
Author(s):  
N. T. Saraswathi ◽  
M. Vijayan
Keyword(s):  
Amino Acids ◽  
Hydrogen Bonding ◽  
Amino Acid ◽  
Crystal Structures ◽  
Malonic Acid ◽  
Conformational Flexibility ◽  
X Ray ◽  
Conformational Variability ◽  
Aggregation Pattern ◽  
Positively Charged

The crystal structures of the complexes of malonic acid with DL- and L-arginine, which contain positively charged argininium ions and negatively charged semimalonate ions, further demonstrate the conformational flexibility of amino acids. A larger proportion of folded conformations than would be expected on the basis of steric consideration appears to occur in arginine, presumably because of the requirements of hydrogen bonding. The aggregation pattern in the DL-arginine complex bears varying degrees of resemblance to patterns observed in other similar structures. An antiparallel hydrogen-bonded dimeric arrangement of arginine, and to a lesser extent lysine, is a recurring motif. Similarities also exist among the structures in the interactions with this motif and its assembly into larger features of aggregation. However, the aggregation pattern observed in the L-arginine complex differs from any observed so far, which demonstrates that all the general patterns of amino-acid aggregation have not yet been elucidated. The two complexes represent cases where the reversal of the chirality of half the amino-acid molecules leads to a fundamentally different aggregation pattern.

scholarly journals Structures of (S)-(−)-4-oxo-2-azetidinecarboxylic acid and 3-azetidinecarboxylic acid from powder synchrotron diffraction data

2006 ◽  
Vol 62 (4) ◽  
pp. 606-611 ◽  
Author(s):  
Asiloé J. Mora ◽  
Michela Brunelli ◽  
Andrew N. Fitch ◽  
Jonathan Wright ◽  
Maria E. Báez ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Diffraction Data ◽  
Direct Methods ◽  
X Ray Diffraction ◽  
Synchrotron Diffraction ◽  
X Ray ◽  
The Asymmetry

The crystal structures of the four-membered heterocycles (S)-(−)-4-oxo-2-azetidinecarboxylic acid (I) and 3-azetidinecarboxylic acid (II) were solved by direct methods using powder synchrotron X-ray diffraction data. The asymmetry of the oxoazetidine and azetidine rings is discussed, along with the hydrogen bonding.

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