Hydrogen-bonding Patterns (hydrogen-bonding + pattern)

Distribution by Scientific Domains

Selected Abstracts

Hydrogen-bonding patterns in three substituted N -benzyl- N -(3- tert -butyl-1-phenyl-1H -pyrazol-5-yl)acetamides

Gerson López
The molecules of N -(3- tert -butyl-1-phenyl-1H -pyrazol-5-yl)-2-chloro- N -(4-methoxybenzyl)acetamide, C23H26ClN3O2, are linked into a chain of edge-fused centrosymmetric rings by a combination of one C,H...O hydrogen bond and one C,H...,(arene) hydrogen bond. In N -(3- tert -butyl-1-phenyl-1H -pyrazol-5-yl)-2-chloro- N -(4-chlorobenzyl)acetamide, C22H23Cl2N3O, a combination of one C,H...O hydrogen bond and two C,H...,(arene) hydrogen bonds, which utilize different aryl rings as the acceptors, link the molecules into sheets. The molecules of S -[N -(3- tert -butyl-1-phenyl-1H -pyrazol-5-yl)- N -(4-methylbenzyl)carbamoyl]methyl O -ethyl carbonodithioate, C26H31N3O2S2, are also linked into sheets, now by a combination of two C,H...O hydrogen bonds, both of which utilize the amide O atom as the acceptor, and two C,H...,(arene) hydrogen bonds, which utilize different aryl groups as the acceptors. [source]

Hydrogen-bonding patterns in two aroylthiocarbamates and two aroylimidothiocarbonates

Henry Insuasty
In O -ethyl N -benzoylthiocarbamate, C10H11NO2S, the molecules are linked into sheets by a combination of two-centre N,H...O and C,H...S hydrogen bonds and a three-centre C,H...(O,S) hydrogen bond. A combination of two-centre N,H...O and C,H...O hydrogen bonds links the molecules of O -ethyl N -(4-methylbenzoyl)thiocarbamate, C11H13NO2S, into chains of rings, which are linked into sheets by an aromatic ,,, stacking interaction. In O,S -diethyl N -(4-methylbenzoyl)imidothiocarbonate, C13H17NO2S, pairs of molecules are linked into centrosymmetric dimers by pairs of symmetry-related C,H...,(arene) hydrogen bonds, while the molecules of O,S -diethyl N -(4-chlorobenzoyl)imidothiocarbonate, C12H14ClNO2S, are linked by a single C,H...O hydrogen bond into simple chains, pairs of which are linked by an aromatic ,,, stacking interaction to form a ladder-type structure. [source]

Hydrogen-bonding patterns in 3-alkyl-3-hydroxyindolin-2-ones

Diana Becerra
The molecules of racemic 3-benzoylmethyl-3-hydroxyindolin-2-one, C16H13NO3, (I), are linked by a combination of N,H...O and O,H...O hydrogen bonds into a chain of centrosymmetric edge-fused R22(10) and R44(12) rings. Five monosubstituted analogues of (I), namely racemic 3-hydroxy-3-[(4-methylbenzoyl)methyl]indolin-2-one, C17H15NO3, (II), racemic 3-[(4-fluorobenzoyl)methyl]-3-hydroxyindolin-2-one, C16H12FNO3, (III), racemic 3-[(4-chlorobenzoyl)methyl]-3-hydroxyindolin-2-one, C16H12ClNO3, (IV), racemic 3-[(4-bromobenzoyl)methyl]-3-hydroxyindolin-2-one, C16H12BrNO3, (V), and racemic 3-hydroxy-3-[(4-nitrobenzoyl)methyl]indolin-2-one, C16H12N2O5, (VI), are isomorphous in space group P. In each of compounds (II),(VI), a combination of N,H...O and O,H...O hydrogen bonds generates a chain of centrosymmetric edge-fused R22(8) and R22(10) rings, and these chains are linked into sheets by an aromatic ,,, stacking interaction. No two of the structures of (II),(VI) exhibit the same combination of weak hydrogen bonds of C,H...O and C,H...,(arene) types. The molecules of racemic 3-hydroxy-3-(2-thienylcarbonylmethyl)indolin-2-one, C14H11NO3S, (VII), form hydrogen-bonded chains very similar to those in (II),(VI), but here the sheet formation depends upon a weak ,,, stacking interaction between thienyl rings. Comparisons are drawn between the crystal structures of compounds (I),(VII) and those of some recently reported analogues having no aromatic group in the side chain. [source]

QSAR of Human Steroid 5,-Reductase Inhibitors: Where are the differences between isoenzyme type 1 and 2?

Abstract Quantitative Structure Activity Relationships have been established for inhibitors of human steroid 5,-reductase including 6-azasteroids and non-steroidal compounds. From the applied descriptors, those related to the molecular geometry, electronic properties, and the electrostatic surface were derived from semi-empirical AM1 calculations. A chemical reaction as part of the inhibitory action is indicated by the presence of the ionization potential in the descriptor space. Strong similarities between the variables for the prediction of the binding affinity to the type 1 and IC50 values for the type 2 isoform of the 5,-reductase were observed. The most pronounced differences in the linear regression QSAR equations were found for the descriptors accounting for the hydrogen-bonding interaction, suggesting a different hydrogen-bonding pattern in the binding pocket of both isoforms. Furthermore, the topological indices together with the surface related descriptors point towards a lower content of aromatic amino acids in the binding site of the type 2 isoenzyme. Consequences for the design of new inhibitors are discussed. [source]

Dynamics of molecules in crystals from multi-temperature anisotropic displacement parameters.


The temperature evolution of atomic anisotropic displacement parameters (ADP's) of perdeuterobenzene and of urea in the temperature range between 12 and 123,K is investigated in terms of the model presented in paper I. For the benzene molecule, the temperature-dependent contributions to the ADP's are well described by three molecular librations and three molecular translations. For the urea molecule, the analysis revealed a low-frequency high-amplitude normal mode (~64,cm,1), which combines out-of-plane deformations of the NH2 groups with molecular libration. The pyramidalization motion allows the hydrogen-bonding pattern to be retained quite well, whereas this pattern is heavily distorted in the higher-frequency molecular librations. The results presented for urea go a step beyond those obtainable in a conventional rigid-body or segmented-rigid-body analysis because they show how correlations of atomic displacements in molecular crystals can be determined from the temperature evolution of ADP's. For both molecules, the analysis reveals temperature-independent contributions to the ADP's accounting for the high-frequency internal vibrations. It is the first time that such contributions have been extracted directly from single-crystal diffraction data for light atoms like hydrogen and deuterium as well as for heavier atoms like carbon, nitrogen and oxygen. These contributions agree well with those calculated from independent spectroscopic information. [source]

More examples of the 15-crown-5...H2O,M,OH2...15-crown-5 motif, M = Al3+, Cr3+ and Pd2+

Maxime A. Siegler
Five structures of co-crystals grown from aqueous solutions equimolar in 15-crown-5 (or 15C5) and [M(H2O)6](NO3)n, M = Al3+, Cr3+ and Pd2+, are reported. The hydrogen-bonding patterns in all are similar: metal complexes including the fragment trans -H2O,M,OH2 alternate with 15C5 molecules, to which they are hydrogen bonded, to form stacks. A literature survey shows that this hydrogen-bonding pattern is very common. In each of the two polymorphs of the compound [Al(H2O)6](NO3)3·15C5·4H2O there are two independent cations; one forms hydrogen bonds directly to the 15C5 molecules adjacent in the stack, while the other cation is hydrogen-bonded to two water molecules that act as spacers in the stack. These stacks are then crosslinked by hydrogen bonds formed by the three nitrate counterions and the three lattice water molecules. The hydrogen-bonded stacks in [Cr(H2O)5(NO3)](NO3)2·1.5(15C5)·H2O are discrete rather than infinite; each unit contains two Cr3+ complex cations and three 15C5 molecules. These units are again crosslinked by the uncoordinated nitrate ions and a lattice water molecule. In [Pd(H2O)2(NO3)2]·15C5 the infinite stacks are electrically neutral and are not crosslinked. In [Pd(H2O)2(NO3)2]·2(15C5)·2H2O·2HNO3 a discrete, uncharged unit containing one Pd complex and two 15C5 molecules is `capped off' at either end by a lattice water molecule and an included nitric acid molecule. In all five structures the infinite stacks or discrete units form an array that is at least approximately hexagonal. [source]

Structures of six industrial benzimidazolone pigments from laboratory powder diffraction data

Jacco Van De Streek
The crystal structures of six industrially produced benzimidazolone pigments [Pigment Orange 36 (, phase), Pigment Orange 62, Pigment Yellow 151, Pigment Yellow 154 (, phase), Pigment Yellow 181 (, phase) and Pigment Yellow 194] were determined from laboratory X-ray powder diffraction data by means of real-space methods using the programs DASH and MRIA, respectively. Subsequent Rietveld refinements were carried out with TOPAS. The crystal phases correspond to those produced industrially. Additionally, the crystal structures of the non-commercial compound `BIRZIL' (a chloro derivative of Pigment Yellow 194) and of a dimethylsulfoxide solvate of Pigment Yellow 154 were determined by single-crystal structure analyses. All eight crystal structures are different; the six industrial pigments even exhibit five different hydrogen-bond topologies. Apparently, the good application properties of the benzimidazolone pigments are not the result of one specific hydrogen-bonding pattern, but are the result of a combination of efficient molecular packing and strong intermolecular hydrogen bonds. [source]

Methyl ,- d -fructopyranoside

Thorsten Allscher
In methyl ,- d -fructopyranoside, C7H14O6, the thermodynamically most stable methyl glycoside of the ketose d -fructose, the pyranose ring is close to being an ideal 2C5 chair. The compound forms bilayers involving a complex hydrogen-bonding pattern of five independent hydrogen bonds. Graph-set analysis was applied to distinguish the hydrogen-bond patterns at unary and higher level graph sets. [source]

l -Isoleucyl- l -asparagine 1.094-hydrate: a hybrid hydrogen-bonding pattern

Carl Henrik Görbitz
The title compound, C10H20N3O4·1.094H2O, crystallizes with two dipeptide molecules in the asymmetric unit, each participating in two head-to-tail chains with hydrogen bonds between the terminal amino and carboxylate groups. As with many other dipeptides, the resulting structure is divided into distinct layers, but as the amide groups of the two peptide molecules participate in different types of interaction, the observed hydrogen bonds within a peptide main-chain layer (as distinct from the side-chain/solvent regions) cannot adapt to any of the four basic patterns observed previously for dipeptides. Instead, a rare hybrid pattern is formed. [source]

2-Amino-8-(2-deoxy-2-fluoro-,- d -arabinofuranosyl)imidazo[1,2- a][1,3,5]triazin-4(8H)-one monohydrate, a 2,-deoxyguanosine analogue with an altered Watson,Crick recognition site

Dawei Jiang
The title compound, C10H12FN5O4·H2O, shows an anti glycosyl orientation [, = ,123.1,(2)°]. The 2-deoxy-2-fluoroarabinofuranosyl moiety exhibits a major C2,- endo sugar puckering (S -type, C2,- endo,C1,- exo, 2T1), with P = 156.9,(2)° and ,m = 36.8,(1)°, while in solution a predominantly N conformation of the sugar moiety is observed. The conformation around the exocyclic C4,,C5, bond is ,sc (trans, gauche), with , = ,78.3,(2)°. Both nucleoside and solvent molecules participate in the formation of a three-dimensional hydrogen-bonding pattern via intermolecular N,H...O and O,H...O hydrogen bonds; the N atoms of the heterocyclic moiety and the F substituent do not take part in hydrogen bonding. [source]

Molecular aggregation in selected crystalline 1:1 complexes of hydrophobic d - and l -amino acids.


The amino acid l -phenylalanine has been cocrystallized with d -2-aminobutyric acid, C9H11NO2·C4H9NO2, d -norvaline, C9H11NO2·C5H11NO2, and d -methionine, C9H11NO2·C5H11NO2S, with linear side chains, as well as with d -leucine, C9H11NO2·C6H13NO2, d -isoleucine, C9H11NO2·C6H13NO2, and d - allo -isoleucine, C9H11NO2·C6H13NO2, with branched side chains. The structures of these 1:1 complexes fall into two classes based on the observed hydrogen-bonding pattern. From a comparison with other l:d complexes involving hydrophobic amino acids and regular racemates, it is shown that the structure-directing properties of phenylalanine closely parallel those of valine and isoleucine but not those of leucine, which shares side-chain branching at C, with phenylalanine and is normally considered to be the most closely related non-aromatic amino acid. [source]

(±)-(2,3,4,4a,5,6,7,8-Octa­hydro-2-oxo­naphthalen-1-yl)acetic acid: hydrogen-bonding pattern of the mono­hydrate of an unsaturated bicyclic ,-keto acid

Roger A. Lalancette
In the title compound, C12H16O3·H2O, the water of hydration accepts a hydrogen bond from the carboxyl group and donates hydrogen bonds to the carboxyl carbonyl and the ketone groups of two different neighbors, yielding a complex three-dimensional hydrogen-bonding array. There are two independent hydrated mol­ecules in the asymmetric unit (Z, = 2) related by a pseudo-translation. [source]

Synthesis, Characterization, and Folding Behavior of ,-Amino Acid Derived Polyisocyanides

Sander J. Wezenberg
Abstract Helical polymers of isocyanopeptides derived from ,-amino acids have been synthesized and their architectures have been studied in detail. Similar to their ,-amino acid analogues, the helical conformation in these macromolecules is stabilized by internal hydrogen-bonding arrays along the polymeric backbone. Unexpectedly, the flexibility of the ,-peptide side arms results in a rearrangement of the initial macromolecular architecture, leading to a more stable helical structure possessing a better defined hydrogen-bonding pattern, as was concluded from IR and temperature-dependent circular dichroism studies. Based on these results we propose a dynamic helical model for the ,-amino acid derived polyisocyanopeptides; this model is in contrast to the kinetically stable helical macromolecules that are formed upon polymerization of ,-amino acid based isocyanopeptides. [source]

One-Dimensional CdII Coordination Polymers: Solid Solutions with NiII, Thermal Stabilities and Structures

Dejana Vujovic
Abstract Reactions of Cd(NCS)2 with 2-, 3- and 4-aminobenzonitrile ligands (2ABN, 3ABN and 4ABN respectively) have produced one-dimensional chain polymers of the general formula [M(NCS)2(ABN)2]n with the metal centres linked by double NCS, bridges. The three cadmium polymers [Cd(NCS)2(3ABN)2]n (1), [Cd(NCS)2(2ABN)2]n (2) and [Cd(NCS)2(4ABN)2]n (3) all differ in their hydrogen-bonding patterns. In terms of ABN coordination, both 1 and 2 exhibit terminal amine coordination while in 3 the ABNs are coordinated through the cyano groups. Crystalline solid solutions of 1 of general formula [Cd1,xNix(NCS)2(3ABN)2]n, containing nickel and cadmium in varying proportions, have also been prepared in order to establish the influence of the metal ratio on the thermal stability and bonding parameters of the polymers. The coordination polymers are not good candidates for forming clathrates while their thermal stability (ranging between 147 and 244 °C) depends on the position of functional groups on the ABN ligands and on the Cd:Ni ratio in the solid solutions. The new polymers have been characterised by single crystal X-ray diffraction, X-ray powder diffraction, electron microscopy, infrared spectroscopy, thermogravimetry and differential scanning calorimetry. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source]

Synthesis and Modulation of Bis(triazine) Hydrogen-Bonding Receptors

Pamela V. Mason
Abstract The synthesis of bis(triazine) molecules capable of acting as synthetic receptors for barbiturate guest molecules is described. The binding properties are also reported illustrating the modulation of the binding properties of these species by the modification of the hydrogen-bonding patterns of the receptor molecule, namely 1,3- N,N, -bis[4-(dibenzylamino)-6-(butylamino)-1,3,5-triazin-2-yl]xylylenediamine (1). Thus 1,3- O,O, -bis[4-(dibenzylamino)-6-(butylamino)-1,3,5-triazin-2-yl]benzenedimethanol (3) and 1,3- O,O, -bis[4-(dibenzylamino)-6-(diethylamino)-1,3,5-triazin-2-yl]benzenedimethanol (5) have been prepared, and their binding constants compared to those observed for 1. In the case of compounds 3 and 5 the hydrogen-bonding secondary amines at the apex of the receptor 1 are substituted by non-hydrogen-bonding ether links. The hydrogen-bonding ability is further modified in the case of 5 by the removal of all hydrogen-bond donors from the receptor site, replacing secondary amines by tertiary amines. NMR binding studies illustrate how these simple modifications of the hydrogen-bonding patterns of these receptors influences the overall strength of binding demonstrating a simple mechanism for controlling host-guest complex formation. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source]

Analyses of the partition coefficient, log P, using ab initio MO parameter and accessible surface area of solute molecules

Hiroshi Chuman
Abstract To analyze the log Psol/w values (sol: n -octanol or chloroform, w: water) in the framework of the molecular orbital (MO) procedure, we selected solute descriptors such as the solvation energy difference between aqueous and organic solvent phases and the "surface" area of solute molecules to which water molecules are accessible. The solvation energy of solute molecules in their minimum free-energy conformation was calculated using the ab initio self-consistent reaction field-MO method with the conductor-like screening model. The experimentally measured log Psol/w value of various solutes except for those of amphiprotics was shown to be analyzable reasonably well by the MO model with additional descriptors for the hydrogen-bonding patterns in the solute,solvent interactions. © 2004 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 93:2681,2697, 2004 [source]

Graph-set and packing analysis of hydrogen-bonded networks in polyamide structures in the Cambridge Structural Database

W. D. Samuel Motherwell
The hydrogen-bond networks and crystal packing of 81 unique secondary di- and polyamides in the Cambridge Structural Database are investigated. Graph-set analysis, as implemented in the RPluto program, is used to classify network motifs. These have been rationalized in terms of the relative dispositions of the amide groups. Peptide and retropeptides exhibit significant conformational flexibility, which permits alternative hydrogen-bonding patterns. In peptides, dihedral angles of ,,,,, 105° allow an antiparallel ladder arrangement, containing rings of either the same or alternating sizes. For retropeptides, and diamides with an odd number of CH2 spacers, this conformation leads to a parallel ladder with rings of equal size. If , approaches ,60° and , 180°, ladders adopt a helical twist, and if the conformation is distorted further, a three-dimensional network is usually adopted. Diamides with aromatic or an even number of CH2 spacers generally form either antiparallel ladders or sheets, although some exhibit both polymorphs. Symmetry relationships within and between hydrogen-bonded chains, ladders and sheets in the crystal packing have also been analysed. Polyamides form considerably more complex networks, although many of the structural motifs present in the diamides occur as components of these networks. [source]

Different hydrogen-bonding modes in two closely related oximes

Grzegorz Dutkiewicz
Two closely related oximes, namely 1-chloroacetyl-3-ethyl-2,6-diphenylpiperidin-4-one oxime, C21H23ClN2O2, (I), and 1-chloroacetyl-2,6-diphenyl-3-(propan-2-yl)piperidin-4-one oxime, C22H25ClN2O2, (II), despite their identical sets of hydrogen-bond donors and acceptors, display basically different hydrogen-bonding patterns in their crystal structures. While the molecules of (I) are organized into typical centrosymmetric dimers, created by oxime,oxime O,H...N hydrogen bonds, in the structure of (II) there are infinite chains of molecules connected by O,H...O hydrogen bonds, in which the carbonyl O atom from the chloroacetyl group acts as the hydrogen-bond acceptor. Despite the differences in the hydrogen-bond schemes, the ,OH groups are always in typical anti positions (C,N,O,H torsion angles of ca 180°). The oxime group in (I) is disordered, with the hydroxy groups occupying two distinct positions and C,C,N,O torsion angles of approximately 0 and 180° for the two alternatives. This disorder, even though the site-occupancy factor of the less occupied position is as low as ca 0.06, is also observed at lower temperatures, which seems to favour the statistical and not the dynamic nature of this phenomenon. [source]

Benzene-1,4-diboronic acid,4,4,-bipyridine,water (1/2/2)

Araceli Vega
In the presence of water, benzene-1,4-diboronic acid (1,4-bdba) and 4,4,-bipyridine (4,4,-bpy) form a cocrystal of composition (1,4-bdba)(4,4,-bpy)2(H2O)2, in which the molecular components are organized in two, so far unknown, cyclophane-type hydrogen-bonding patterns. The asymmetric unit of the title compound, C6H8B2O4·2C10H8N2·2H2O, contains two 4,4,-bpy, two water molecules and two halves of 1,4-bdba molecules arranged around crystallographic inversion centers. The occurrence of O,H...O and O,H...N hydrogen bonds involving the water molecules and all O atoms of boronic acid gives rise to a two-dimensional hydrogen-bonded layer structure that develops parallel to the (01) plane. This supramolecular organization is reinforced by ,,, interactions between symmetry-related 4,4,-bpy molecules. [source]

Methyl 4- O -,- d -galactopyranosyl ,- d -mannopyranoside methanol 0.375-solvate

Xiaosong Hu
Methyl ,- d -galactopyranosyl-(1,4)-,- d -mannopyranoside methanol 0.375-solvate, C13H24O11·0.375CH3OH, (I), was crystallized from a methanol,ethanol solvent system in a glycosidic linkage conformation, with ,, (O5Gal,C1Gal,O1Gal,C4Man) = ,68.2,(3)° and ,, (C1Gal,O1Gal,C4Man,C5Man) = ,123.9,(2)°, where the ring is defined by atoms O5/C1,C5 (monosaccharide numbering); C1 denotes the anomeric C atom and C6 the exocyclic hydroxymethyl C atom in the ,Galp and ,Manp residues, respectively. The linkage conformation in (I) differs from that in crystalline methyl ,-lactoside [methyl ,- d -galactopyranosyl-(1,4)-,- d -glucopyranoside], (II) [Pan, Noll & Serianni (2005). Acta Cryst. C61, o674,o677], where ,, is ,93.6° and ,, is ,144.8°. An intermolecular hydrogen bond exists between O3Man and O5Gal in (I), similar to that between O3Glc and O5Gal in (II). The structures of (I) and (II) are also compared with those of their constituent residues, viz. methyl ,- d -mannopyranoside, methyl ,- d -glucopyranoside and methyl ,- d -galactopyranoside, revealing significant differences in the Cremer,Pople puckering parameters, exocyclic hydroxymethyl group conformations and intermolecular hydrogen-bonding patterns. [source]

Influence of anion substitution on hydrogen-bonding patterns of salt compounds: cytosinium hydrogen sulfate and cytosinium perchlorate

Med Abdellatif Bensegueni
In the two title compounds, cytosinium hydrogen sulfate, C4H6N3O+·HSO4,, (I), and cytosinium perchlorate, C4H6N3O+·ClO4,, (II), the asymmetric units comprise a cytosinium cation with hydrogen sulfate and perchlorate anions, respectively. The crystal structures of (I) and (II) are similar; that of (I) is characterized by a three-dimensional N,H...O, O,H...O and C,H...O hydrogen-bonded network. In (I) and (II), two-dimensional layers are formed by N,H...O and C,H...O hydrogen bonds and, in the case of (I), they are linked by O,H...O hydrogen bonds where the anion acts as a donor and the cation as an acceptor. The hydrogen-bonded sheets in (II) form an angle of 87.1°. [source]

Hydrogen-bonded supramolecular motifs in 2-amino-4,6-dimethoxypyrimidinium picrate and pyrimethaminium picrate dimethyl sulfoxide solvate

Kaliyaperumal Thanigaimani
In the crystal structures of 2-amino-4,6-dimethoxypyrimidinium 2,4,6-trinitrophenolate (picrate), C6H10N3O2+·C6H2N3O7,, (I), and 2,4-diamino-5-(4-chlorophenyl)-6-ethylpyrimidin-1-ium (pyrimethaminium or PMN) picrate dimethyl sulfoxide solvate, C12H14ClN4+·C6H2N3O7,·C2H6OS, (II), the 2-amino-4,6-dimethoxypyrimidine and PMN cations are protonated at one of the pyrimidine N atoms. The picrate anion interacts with the protonated cations through bifurcated N,H...O hydrogen bonds, forming R21(6) and R12(6) ring motifs. In (I), Z, = 2. In (II), two inversion-related PMN cations are connected through a pair of N,H...N hydrogen bonds involving the 4-amino group and the uncharged N atom of the pyrimidine ring, forming a cyclic hydrogen-bonded R22(8) motif. In addition to the pairing, the O atom of the dimethyl sulfoxide solvent molecule bridges the 2-amino and 4-amino groups on both sides of the paired bases, resulting in a self-complementary ,DADA, array of quadruple hydrogen-bonding patterns. [source]

The influence of sulfur substituents on the molecular geometry and packing of thio derivatives of N -methylphenobarbital

Alicja Janik
The room-temperature crystal structures of four new thio derivatives of N -methylphenobarbital [systematic name: 5-ethyl-1-methyl-5-phenylpyrimidine-2,4,6(1H,3H,5H)-trione], C13H14N2O3, are compared with the structure of the parent compound. The sulfur substituents in N -methyl-2-thiophenobarbital [5-ethyl-1-methyl-5-phenyl-2-thioxo-1,2-dihydropyrimidine-4,6(3H,5H)-dione], C13H14N2O2S, N -methyl-4-thiophenobarbital [5-ethyl-1-methyl-5-phenyl-4-thioxo-3,4-dihydropyrimidine-2,6(1H,5H)-dione], C13H14N2O2S, and N -methyl-2,4,6-trithiophenobarbital [5-ethyl-1-methyl-5-phenylpyrimidine-2,4,6(1H,3H,5H)-trithione], C13H14N2S3, preserve the heterocyclic ring puckering observed for N -methylphenobarbital (a half-chair conformation), whereas in N -methyl-2,4-dithiophenobarbital [5-ethyl-1-methyl-5-phenyl-2,4-dithioxo-1,2,3,4-tetrahydropyrimidine-6(5H)-one], C13H14N2OS2, significant flattening of the ring was detected. The number and positions of the sulfur substituents influence the packing and hydrogen-bonding patterns of the derivatives. In the cases of the 2-thio, 4-thio and 2,4,6-trithio derivatives, there is a preference for the formation of a ring motif of the R22(8) type, which is also a characteristic of N -methylphenobarbital, whereas a C(6) chain forms in the 2,4-dithio derivative. The preferences for hydrogen-bond formation, which follow the sequence of acceptor position 4 > 2 > 6, confirm the differences in the nucleophilic properties of the C atoms of the heterocyclic ring and are consistent with the course of N -methylphenobarbital thionation reactions. [source]

Structure of grouper iridovirus purine nucleoside phosphorylase

You-Na Kang
Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of purine ribonucleosides to the corresponding free bases and ribose 1-phosphate. The crystal structure of grouper iridovirus PNP (givPNP), corresponding to the first PNP gene to be found in a virus, was determined at 2.4,Å resolution. The crystals belonged to space group R3, with unit-cell parameters a = 193.0, c = 105.6,Å, and contained four protomers per asymmetric unit. The overall structure of givPNP shows high similarity to mammalian PNPs, having an ,/, structure with a nine-stranded mixed ,-barrel flanked by a total of nine ,-helices. The predicted phosphate-binding and ribose-binding sites are occupied by a phosphate ion and a Tris molecule, respectively. The geometrical arrangement and hydrogen-bonding patterns of the phosphate-binding site are similar to those found in the human and bovine PNP structures. The enzymatic activity assay of givPNP on various substrates revealed that givPNP can only accept 6-oxopurine nucleosides as substrates, which is also suggested by its amino-acid composition and active-site architecture. All these results suggest that givPNP is a homologue of mammalian PNPs in terms of amino-acid sequence, molecular mass, substrate specificity and overall structure, as well as in the composition of the active site. [source]

Conformational Flexibility of Tetralactam Macrocycles and Their Intermolecular Hydrogen-Bonding Patterns in the Solid State

Abstract Flexible rigidity: Tetralactam macrocycles of the Hunter type bear a rigid scaffold (see space-filling representation), but can still widely adapt to the properties of a guest molecule inside their cavities. X-ray crystal structures of a series of differently substituted macrocycles reveal a remarkably broad variety of intermolecular hydrogen-bonding patterns organizing the macrocycles in the crystals in intriguingly different ways. Despite their rigid scaffold, tetralactam macrocycles (TLMs) display a remarkable degree of conformational flexibility, as revealed by analysis of the corresponding X-ray crystal structures. This flexibility is not limited to the rotatability of the TLM amide groups but also applies to the m -xylene rings, and it thus has a great impact on the overall shape of the macrocycle cavity. The conformational properties of the TLMs give rise to a broad variety of intermolecular hydrogen-bonding patterns, including infinite ladders, an interesting catemer motif, and short CH,,,OC hydrogen bonds. These results are in accord with previous theoretical calculations, support a structural model proposed earlier for an interpretation of scanning tunneling microscopy images, and substantially contribute to the understanding of the adaptability of macrocyclic scaffolds, which is crucial for guest binding or templated syntheses with TLMs. [source]