Molecular recognition X. A novel procedure for the detection of the intermolecular hydrogen bonds present in a protein•oligosaccharide complex

1992 ◽  
Vol 70 (1) ◽  
pp. 241-253 ◽  
Author(s):  
P. V. Nikrad ◽  
H. Beierbeck ◽  
R. U. Lemieux
Keyword(s):  
Crystal Structure ◽  
Molecular Recognition ◽  
Hydrogen Bonds ◽  
Aqueous Phase ◽  
Hard Sphere ◽  
Hydroxyl Groups ◽  
Intermolecular Hydrogen Bonds ◽  
Methyl Derivatives ◽  
Derivatives Of ◽  
Hydrogen Bonded

The relative potencies of both the monodeoxy and mono-O-methyl derivatives of the Leb-OMe tetrasaccharide (α-L-Fuc-(1 → 2)-β-D-Gal-(1 → 3)-[α-L-Fuc-(1 → 4)]-β-D-GlcNAc-OMe) as inhibitors of the complexation of a Leb artificial antigen by the lectin IV of Griffoniasimplicifolia are interpreted in terms of the X-ray crystal structure at 2.5 Å resolution of the GS-IV • Leb-OMe complex. Both kinds of derivatives maintain high potencies when the hydroxyl groups involved appear, in the crystal structure, to be in contact with the aqueous phase. Hydroxyl groups situated at the periphery of the combining site and hydrogen bonded to the protein can also be deoxygenated without important loss in potency. However, their methylation leads to a strong decrease in the stability of the complex, because the steric bulk of the introduced methyl group causes loss of complementarity. In contrast, the hydroxyl groups that form hydrogen bonds with the protein along the base of the shallow amphiphilic cleft of the combining site can neither be deoxygenated nor methylated without virtually complete loss of binding activity. Thus, the procedure can provide an appreciation of the various kinds of hydrogen bonds that are present in a protein • oligosaccharide complex. Hard-sphere calculations supported these contentions since an energetically favorable orientation was indicated for a methoxy group at any one of the five positions that were expected to remain in contact with the aqueous phase. However, the calculations, as expected, showed the introduction of strong destabilizing nonbonded interactions when the methylation involved hydroxyl groups that are hydrogen bonded to the protein in the complex. The results are in accord with the previously made rationalization of the near linear enthalpy–entropy compensation found for the active deoxy congeners. Keywords: molecular recognition, lectin IV of Griffoniasimplicifolia, O-methyl derivatives of the Lewis b-OMe tetrasaccharide, detection of intermolecular hydrogen bonds, hard-sphere calculations.

scholarly journals Effect of pressure on the crystal structure of L-serine-I and the crystal structure of L-serine-II at 5.4 GPa

2005 ◽  
Vol 61 (1) ◽  
pp. 58-68 ◽  
Author(s):  
Stephen A. Moggach ◽  
David R. Allan ◽  
Carole A. Morrison ◽  
Simon Parsons ◽  
Lindsay Sawyer
Keyword(s):  
Crystal Structure ◽  
Phase Transition ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Ambient Pressure ◽  
Crystal Form ◽  
Hydroxyl Groups ◽  
Orthorhombic Space Group ◽  
Crystal Forms ◽  
Hydrogen Bonded

The crystal structure of L-serine has been determined at room temperature at pressures between 0.3 and 4.8 GPa. The structure of this phase (hereafter termed L-serine-I), which consists of the molecules in their zwitterionic tautomer, is orthorhombic, space group P212121. The least compressible cell dimension (c), corresponds to chains of head-to-tail NH...carboxylate hydrogen bonds. The most compressible direction is along b, and the pressure-induced distortion in this direction takes the form of closing up voids in the middle of R-type hydrogen-bonded ring motifs. This occurs by a change in the geometry of hydrogen-bonded chains connecting the hydroxyl groups of the —CH2OH side chains. These hydrogen bonds are the longest conventional hydrogen bonds in the system at ambient pressure, having an O...O separation of 2.918 (4) Å and an O...O...O angle of 148.5 (2)°; at 4.8 GPa these parameters are 2.781 (11) and 158.5 (7)°. Elsewhere in the structure one NH...O interaction reaches an N...O separation of 2.691 (13) Å at 4.8 GPa. This is amongst the shortest of this type of interaction to have been observed in an amino acid crystal structure. Above 4.8 GPa the structure undergoes a single-crystal-to-single-crystal phase transition to a hitherto uncharacterized polymorph, which we designate L-serine-II. The OH...OH hydrogen-bonded chains of L-serine-I are replaced in L-serine-II by shorter OH...carboxyl interactions, which have an O...O separation of 2.62 (2) Å. This phase transition occurs via a change from a gauche to an anti conformation of the OH group, and a change in the NCαCO torsion angle from −178.1 (2)° at 4.8 GPa to −156.3 (10)° at 5.4 GPa. Thus, the same topology appears in both crystal forms, which explains why it occurs from one single-crystal form to another. The transition to L-serine-II is also characterized by the closing-up of voids which occur in the centres of other R-type motifs elsewhere in the structure. There is a marked increase in CH...O hydrogen bonding in both phases relative to L-serine-I at ambient pressure.

1-(4-Chlorophenyl)-4-(2-furoyl)-3-(2-furyl)-1H-pyrazol-5-ol

2007 ◽  
Vol 63 (3) ◽  
pp. o1289-o1290 ◽  
Author(s):  
Jin-Zhou Li ◽  
Heng-Qiang Zhang ◽  
Hong-Xin Li ◽  
Pi-Zhi Che ◽  
Tian-Chi Wang
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Intermolecular Hydrogen Bond ◽  
Hydroxyl Groups ◽  
Intermolecular Hydrogen Bonds ◽  
Compound C ◽  
Graph Set

The crystal structure of the title compound, C18H11ClN2O4, contains intra- and intermolecular hydrogen bonds that link the ketone and hydroxyl groups. The intermolecular hydrogen bond results in the formation of a dimer with an R 2 2(12) graph-set motif.

Molecular recognition XI. The synthesis of extensively deoxygenated derivatives of the H-type 2 human blood group determinant and their binding by an anti-H-type 2 monoclonal antibody and the lectin 1 of Ulexeuropaeus

1992 ◽  
Vol 70 (1) ◽  
pp. 254-271 ◽  
Author(s):  
Ulrike Spohr ◽  
Eugenia Paszkiewicz-Hnatiw ◽  
Naohiko Morishima ◽  
Raymond U. Lemieux
Keyword(s):  
Monoclonal Antibody ◽  
Molecular Recognition ◽  
Blood Group ◽  
Human Blood ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Human Blood Group ◽  
Derivatives Of ◽  
Hydrogen Bonded

The relative potencies of a wide variety of deoxygenated derivatives of the methyl glycoside of α-L-Fuc-(1 → 2)-β-D-Gal-(1 → 4)- β-D-GlcNAc (the H-type 2 human blood group related trisaccharide) for the inhibition of the binding of an artificial H-type 2 antigen by the lectin I of Ulexeuropaeus confirmed the previous evidence that the key and productive interaction involves only the three hydroxyl groups of the α-L-fucose unit, the hydroxyl at the 3-position of the β-D-galactose residue, and the nonpolar groups in their immediate environment. Except for the acetamido group and the hydroxymethyl of the β-D-Gal unit, which stay in the aqueous phase, on complex formation the remaining three hydroxyl groups appear to come to reside at or near the periphery of the combining site since their replacement by hydrogen causes relatively small changes (< ± 1 kcal/mol) in the stability of the complex (ΔG0). Relatively much larger but compensating changes occur for the enthalpy and entropy terms, and these may arise primarily from the differences in the water structure about the periphery of the combining site and the oligosaccharide both prior to and after complexation. It is proposed that steric constraints lead to an ordered state of the water molecules hydrogen-bonded to the polar groups within the cleft formed by the key region of the amphiphilic combining site. Their release to form less ordered clusters of more strongly hydrogen-bonded water molecules in bulk solution would contribute importantly to the driving force for complexation. It is demonstrated that the surface used for the binding of H-type 2-OMe by a monoclonal anti-H antibody is virtually identical to that used by the Ulex lectin. Keywords: molecular recognition, H-type 2 blood group determinant and deoxygenated derivatives, lectin I of Ulexeuropaeus, anti-H-type 2 monoclonal antibody, enthalpy–entropy compensation.

scholarly journals allo-Inositol

2006 ◽  
Vol 62 (7) ◽  
pp. o2578-o2579
Author(s):  
Arnaud Bonnet ◽  
William Jones ◽  
W. D. Samuel Motherwell
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Chair Conformation ◽  
Hydroxyl Groups ◽  
Intermolecular Hydrogen Bonds ◽  
Compound C ◽  
Hydrogen Bond Donors

In the crystal structure of the title compound, C6H12O6, molecules adopt a chair conformation. The H atoms were located and their positions refined satisfactorily. The molecules form one intramolecular and 12 intermolecular hydrogen bonds; all hydroxyl groups act as hydrogen-bond donors and acceptors.

Molecular recognition XII. The binding of the H human blood group determinants and congeners by a lectin of Galactiatenuiflora

1992 ◽  
Vol 70 (5) ◽  
pp. 1511-1530 ◽  
Author(s):  
Rémy Cromer ◽  
Ulrike Spohr ◽  
Deveshwari P. Khare ◽  
Jacques LePendu ◽  
Raymond U. Lemieux
Keyword(s):  
Molecular Recognition ◽  
Complex Formation ◽  
Blood Group ◽  
Aqueous Phase ◽  
Human Blood ◽  
Hydroxyl Groups ◽  
Human Blood Group ◽  
Hydrogen Bonded

The H-type 2 human blood group-related trisaccharide (α-L-Fuc-(1c → 2b)-β-D-Gal-(1b → 4a)-β-D-GlcNAc-OMe (52)) is bound by the anti-H lectin of Galactiatenuiflora very differently than by the lectin I of Ulexeuropaeus. The reason why the Galactia lectin binds the H-type 1 related trisaccharide (α-L-Fuc-(1c → 2b)-β-D-Gal-(1b → 3a)-β-D-GlcNAc-OMe (5)) more strongly and methyl α-L-fucopyranoside much more weakly than does the Ulex lectin is that, for the Galactia lectin, the hydroxyl groups at positions 3a, 3b, 4b, and 4c are indispensable to complex formation whereas it is the hydroxyl groups at positions 3b, 2c, 3c, and 4c which provide the key polar intractions in the case of the Ulex lectin. The H-type 2 (52)•Galactia lectin complex appears to have the hydroxyl groups at positions 6b, 2c, and 3c at or near the periphery of the combining site and the three key hydroxyl groups hydrogen bonded to the protein deep within the combining site and sheltered from water. The CH3O-1a, NHAc-2a, and CH2OH-6a groups likely remain in the aqueous phase remote from the surface of the protein.

Crystal structure of i -erythritol and its relationship to some derived d and l and racemic substances

1959 ◽  
Vol 250 (1262) ◽  
pp. 301-315 ◽  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Tetragonal Structure ◽  
Hydroxyl Group ◽  
Hydroxyl Groups ◽  
Main Structure ◽  
Hydrogen Bonded

Meso erythritol forms a tetragonal structure in which the molecules are centro-symmetric. Each α -hydroxyl group forms part of a tetragonal spiral of hydrogen bonds. These spirals alone are sufficient to link all the molecules of the crystal into a three-dimensional hydrogen-bonded complex. The β -hydroxyl groups of neighbouring molecules form closed circuits of four hydrogen bonds in a tetrahedron so flattened as to be almost a square. These closed circuits are also by themselves sufficient to link all molecules in the crystal into a three-dimensional complex. When some of the hydroxyl groups are replaced by fluorine atoms of approximately the same size, the main structure should be retained if sufficient hydrogen bonding is left. It is possible, therefore, to predict structures for meso , d , l and racemic forms of some of the fluoro-substituted derivatives. 2-deoxy-2-fluoro (±) erythritol has been examined and found to have the expected racemic structure. The possibility of forms transitional between dextro , racemic, and laevo , is discussed.

A Crystallographic Study of Bis[S-benzyl-5-bromo-2-oxoindolin-3-ylidenemethanehydrazonthioate] Disulfide Solvated with Dimethylsulfoxide

2012 ◽  
Vol 9 (2) ◽  
pp. 87
Author(s):  
Mohd Abdul Fatah Abdul Manan ◽  
M. Ibrahim M. Tahir ◽  
Karen A. Crouse ◽  
Fiona N.-F. How ◽  
David J. Watkin
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Solvent Molecule ◽  
Site Occupancy ◽  
Unit Cell Parameters ◽  
Intermolecular Hydrogen Bonds ◽  
Triclinic Space Group ◽  
Cell Parameters ◽  
Crystallographic Study ◽  
Thiol Form

The crystal structure of the title compound has been determined. The compound crystallized in the triclinic space group P -1, Z = 2, V = 1839 .42( 18) A3 and unit cell parameters a= 11. 0460( 6) A, b = 13 .3180(7) A, c=13. 7321 (8) A, a = 80.659(3 )0, b = 69 .800(3 )0 and g = 77 .007 (2)0 with one disordered dimethylsulfoxide solvent molecule with the sulfur and oxygen atoms are distributed over two sites; S101/S102 [site occupancy factors: 0.6035/0.3965] and 0130/0131 [site occupancy factor 0.3965/0.6035]. The C22-S2 l and C 19-S20 bond distances of 1. 779(7) A and 1. 788(8) A indicate that both of the molecules are connected by the disulfide bond [S20-S21 2.055(2) A] in its thiol form. The crystal structure reveals that both of the 5-bromoisatin moieties are trans with respect to the [S21-S20 and CI 9-Nl 8] and [S20-S21 and C22-N23] bonds whereas the benzyl group from the dithiocarbazate are in the cis configuration with respect to [S21-S20 and C19-S44] and [S20-S21 and C22-S36] bonds. The crystal structure is further stabilized by intermolecular hydrogen bonds of N9-H35···O16 formed between the two molecules and N28-H281 ···O130, N28-H281 ···O131 and C4 l-H4 l l ···O 131 with the solvent molecule.

scholarly journals Organotin(IV) selenate derivatives – Crystal structure of [{(Ph3Sn)2SeO4} ⋅ CH3OH] n

2021 ◽  
Vol 44 (1) ◽  
pp. 213-217
Author(s):  
Waly Diallo ◽  
Hélène Cattey ◽  
Laurent Plasseraud
Keyword(s):  
Crystal Structure ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Point Of View ◽  
Intermolecular Hydrogen Bonds

Abstract Crystallization of [(Ph3Sn)2SeO4] ⋅ 1.5H2O in methanol leads to the formation of [{(Ph3Sn)2SeO4} ⋅ CH3OH] n (1) which constitutes a new specimen of organotin(IV) selenate derivatives. In the solid state, complex 1 is arranged in polymeric zig-zag chains, composed of alternating Ph3Sn and SeO4 groups. In addition, pendant Ph3Sn ⋅ CH3OH moieties are branched along chains according to a syndiotactic organization and via Sn-O-Se connections. From a supramolecular point of view, intermolecular hydrogen bonds established between the selenate groups (uncoordinated oxygen) and the hydroxyl functions (CH3OH) of the pendant groups link the chains together.

scholarly journals 2,6-Bis(4-methoxybenzylidene)cyclohexanone

2006 ◽  
Vol 62 (5) ◽  
pp. o1910-o1912 ◽  
Author(s):  
Ray J. Butcher ◽  
H. S. Yathirajan ◽  
B. K. Sarojini ◽  
B. Narayana ◽  
J. Indira
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Photon Absorption ◽  
Intermolecular Hydrogen Bonds ◽  
Two Photon Absorption ◽  
Two Photon ◽  
Compound C ◽  
Centrosymmetric Dimers

The title compound, C22H22O3, demonstrates a two-photon absorption. Its metrical parameters are similar to those of related cyclohexanone derivatives. In the crystal structure, two sets of centrosymmetric dimers formed by weak C—H...O intermolecular hydrogen bonds combine to form molecular tapes along [101].

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