Pair Of Intermolecular Hydrogen Bonds Research Articles

Comparative analysis of the crystal structures of hydrates and sodium salts of monensin and its new C-26 succinate ester

Monensin succinate ester hydrate (2-H2O) has been synthesized by the succinylation of C-26 hydroxyl group of monensin (1) using a simple reaction with succinic anhydride. Additionally, the sodium salt (2-Na) of monensin succinate ester has been obtained. Molecular structures of both compounds (2-H2O and 2-Na) were studied using X-ray diffraction of single crystals and spectroscopic methods. According the crystallographic studies of 2-H2O and 2-Na, the molecules are held together as dimers linked by the centrosymmetric pairs of intermolecular hydrogen bonds between the carboxylic groups. The crystal structures of compounds 2-H2O and 2-Na are compared to those of the known monensin acid hydrate (1-H2O) and 1:1 inclusion complex of monensin A sodium salt with acetonitrile (1-Na-CH3CN) and that of newly obtained monensin sodium salt monohydrate (1-Na-H2O). Comparison of these structures showed a significant impact of C-26 succinate ester moiety on the coordination of the Na+ cation and hydrogen bond.

Synthesis, crystal structure, molecular docking, lattice energy and Hirshfeld surface analysis of an antituberculosis drug of (E)-2-methoxy-5-(((6-methoxypyridin-3yl)imino)methyl)phenol

Synthesis, X-ray structure, molecular docking, lattice energy and Hirshfeld surface analysis of (E)-2-methoxy-5-(((6-methoxypyridin-3yl)imino)methyl)phenol (MMPIMP) is presented in this paper. The compound crystallizes in the monoclinic space group P21/c with unit cell parameters: a = 5.6149 (2), b = 14.5520 (5), c = 29.9813 (8) Å, β = 94.795 (3) and Z = 8. The asymmetric unit contains two crystallographically independent molecules (A and B) and the structure was solved by direct methods using single-crystal X-ray diffraction data and refined by full-matrix least-squares procedure to a final value of R = 0.050 and wR2 = 0.1231 for 3536 observed reflections. The molecular packing in the unit cell is stabilized via O – H… N and C – H… O intermolecular hydrogen bonds. In the crystal packing, pairs of intermolecular hydrogen bonds of the type O–H…N links the molecules into dimers, forming (20) ring motif. To understand the nature and strength of intermolecular interaction in terms of its energy and their quantitative contributions toward the molecular packing, lattice energy analysis was carried out by using PIXEL software. Molecular docking studies were executed to realize the inhibitory activity of the compound MMPIMP against DprE1 (PDB code: 4KW5). The analysis of the Hirshfeld surface and its associated two dimension fingerprint plots has been carried out to examine the intermolecular contacts in the crystal structure.

Syntheses, Characterizations and Crystal Structures of Two New Racemic Amidophosphoesters: rac-(C6H5O)(cyclo-C6H11NH)P(O)N(C4H8)NP(O)(NH-cyclo-C6H11)(OC6H5) and rac-(p-CH3-C6H4NH)P(O)(OC6H4-p-CH3)(OC6H5)

The new racemic compounds, rac-diphenyl bis(cyclo-hexylamido)(piperazine)-1,4-diyldiphosphinate, C28H42N4O4P2 (I), and rac-phenyl(p-methylphenyl)(p-tolylamido)-phosphonate, C20H20NO3P (II), were synthesized and characterized by elemental analysis, 31P, 13C, 1H nuclear magnetic resonance, infrared spectroscopy and single-crystal X-ray diffraction analysis. The phosphorus atoms exhibit distorted tetrahedral environment [O]P=O[N][N] in I and [N]P=O[O][O] in II. In compound I, two (C6H5O)P(O)(NH-cyclo-C6H11) fragments are bridged via a NC4H8N linker that accepts chair conformation. In structure II, the environment of the P atom is a result of the linking of one amido and two different phenoxy groups bonded to the P atom. In crystal structure I, adjacent molecules are linked to each other through hydrogen bonds N–H⋅⋅⋅OP in a two-dimensional network along the ab plane, including $$R_{4}^{4}$$ (26) ring motifs, while in structure II, pairs of intermolecular hydrogen bonds N–H⋅⋅⋅OP lead to the formation of centrosymmetric dimers with the $$R_{2}^{2}$$ (8) graph-set motif.

Experimental and theoretical studies on cis-dioxomolybdenum(VI) complexes of ONN-donor thiosemicarbazone

Cis-dioxomolybdenum(VI) chelate complexes with 5-chloro-2-hydroxybenzophenone S-methyl-4-phenylthiose- micarbazone (L) were synthesized in the general formula (MoO$_{2}$(L)D), where D is an odd- or even-numbered alcohol (methanol (1), ethanol (2), n-propanol (3), n-butanol (4), and allyl alcohol (5)). The structures of 1-5 were verified by elemental analysis, Fourier transform infrared (FT-IR), and $^{1}$H NMR spectra. Complex 5 crystallizes in the monoclinic space group P21/n, and its crystalline data showed a dimeric structure formed by a pair of intermolecular hydrogen bonds with 1.92 Å. These dimers are stacked in a similar crystalline structure as a single molecule. The experimental data were compared with the theoretical results obtained by the quantum chemical calculations of the DFT/B3LYP method with LANL2DZ basis set. A detailed interpretation of the FT-IR spectra of the studied compounds was performed based on the total energy distribution. In order to investigate the electronic structures and the UV-Vis spectrum of complex 5, time-dependent density functional theory calculation was taken into account. The interaction energies between the odd- and even-numbered alcohols and remaining parts of complexes 1-4 were evaluated with the help of natural bonding orbital analysis. In addition, the basis set superposition error correction energies were calculated. The results were evaluated by considering the coordinated alcohols with an even number of carbon atoms to have much higher interaction energy than the next lower homologous alcohols with an odd number of carbon atoms.

Structure Characterization of [N-Phenylamino(2-boronphenyl)-R-methyl]phosphonic Acid by Vibrational Spectroscopy and Density Functional Theory Calculations

We present the first Fourier-transform infrared absorption (FT-IR) and Fourier-transform Raman (FT-Raman) analysis of vibrational structure of [N-phenylamino(2-boronphenyl)-R-methyl]phosphonic acid ([PhN-(2-PhB(OH)2)-R-Me]PO3H2). Assignments of experimental wavenumbers are based on performed theoretical calculations using density functional theory (DFT). Theoretical calculations show that the most stable structure of the investigated molecule is dimer incis-transconformation created by a pair of intermolecular hydrogen bonds between the boron hydroxyl groups of two monomers.

7-Methylguanine: protonation, formation of linkage isomers with trans-(NH3)2PtII, and base pairing properties

Three protonated forms of 7-methylguanine (7-MeGH, 1) with different counter ions, [7-MeGH(2)]X (X = NO(3), 1a; ClO(4), 1b; BF(4), 1c) and two Pt(II) complexes, trans-[Pt(NH(3))(2)(7-MeGH-N9)(2)](ClO(4))(2) (4) and trans-[Pt(NH(3))(2)(7-MeGH-N9)(7-MeGH-N3)](ClO(4))(2)·3H(2)O (5) are described and their X-ray crystal structures are reported. 1a-1c form infinite ribbons via pairs of intermolecular hydrogen bonds between N1H···O6 and N3···N2H(2) sites, with anions connecting individual ribbons, thereby generating extended sheets. 4 and 5 do not display unusual features, except that 5 represents a rare case of a bis(nucleobase) complex of Pt(II) in which linkage isomers occur. Unlike in a previously reported compound, [Pt(dien)(7-MeGH-N9)](NO(3))(ClO(4)), the Pt coordination planes and the 7-MeGH planes are not coplanar in 4 and 5. The hydrogen bonding behaviour of 7-MeGH, free and when platinated at N9 (complex 4), was studied in Me(2)SO-d(6). It revealed the following: (i) there is no detectable self-association of 1 in Me(2)SO solution. (ii) 1 and 1-methylcytosine (1-MeC) form Watson-Crick pairs. (iii) 4 does not self-associate. (iv) 4 associates with 1-MeC in the Watson-Crick fashion. (v) 4 and 1 interact in solution, but no model can be proposed at present. (vi) Remarkable interaction shifts between 4 and 1 occur when NH(3) is liberated from trans-(NH(3))(2)Pt(II) to give NH(4)(+) in Me(2)SO-d(6). Feasible models, which imply the presence of deprotonated 7-MeG(-) species are proposed. Finally, DFT calculations were carried out to qualitatively estimate the effect of 7-MeGH acidity in [Pt(dien)(7-MeGH-N9)](2+) in dependence of the dihedral angle between the Pt coordination plane and the nucleobase.

A new crystal structure and fluorescence property of N-2-flurobenzoyl-N′-4-tolylthiourea

A new crystal of N-2-flurobenzoyl-N′-4-tolylthiourea (FBTT) was obtained from slow evaporation of solvent benzene and the crystal structure of FBTT was determined by X-ray diffraction method. The packing mode of FBTT molecules was affected by crystallization conditions. The new crystal of FBTT crystallizes in the monoclinic with the space group C2/c, and it was stabilized by two pairs of intermolecular interactions. The first pair of intermolecular hydrogen bonds are N(1 #)–H(1 #)⋯S(1) and N(1)–H(1)⋯S(1 #1), the second pair of intermolecular hydrogen bonds, are C(11 #)–H(11 #)⋯O(1) and C(11)–H(11)⋯O(1 #). There also have other unpaired intermolecular hydrogen bonds C(15)–H(15C)⋯O(1 #1) and C(15 #2)–H(15 #2)⋯O(1). Double fluorescence bands are observed in both non-polar and polar solvents. The fluorescence emission at 350–360 nm originates from the transitions of π ∗ → π state and is assigned to S 2 fluorescence for the nature of LE state. The long wavelength fluorescence emission with large Stokes shift is the characteristic of ESIPT state. All experimental results are supported by MP2 and CASSCF calculations.

Trans-Dimethanolbis(1,1,1-trifluoro-5,5-dimethylhexane-2,4-dionato)cobalt(II)

The Co atom of the title compound, [Co(C8H10F3O2)2(CH3OH)2], which is located on a crystallographic inversion center, exhibits a distorted octahedral geometry. The bidentate acetylacetonate-like ligands are in a trans arrangement. The plane through the acetylacetonate unit is tilted with respect to the CoO4 plane by 17.41 (7)°, which is in the same range as observed for similar Co(acac)2OR 2 derivatives. Via the methanol hydroxy groups, each molecule participates in two pairs of intermolecular hydrogen bonds that create a network of hydrogen-bonded chains along the direction of the a axis.

(E)-N-(2-Bromophenyl)-3-(2-chloro-3,3,3-trifluoroprop-1-enyl)-2,2-dimethylcyclopropanecarboxamide

In the title compound, C15H14BrClF3NO, the benzene and cyclopropane rings make a dihedral angle of 76.3 (3)°. The amide and methine H atoms are both linked to the amide O atom in an adjacent molecule by a pair of intermolecular hydrogen bonds, N—H...O...H—C, leading to the formation of chains along the b axis.

Crystal and Molecular Structure of 6,6′-Dimethoxy-gossypol:Acetic acid (1:1)

By crystallization from dilute solutions of acetic acid (2–4%) in diethyl ether, acetone, or methyl ethyl ketone, 6,6′-dimethoxy-gossypol forms a solvate with acetic acid in a one-to-one molar ratio. The compound crystallizes in the triclinic P $$ \overline{1} $$ space group and has unit cell dimensions of a = 7.5793(10) A, b = 14.7211(19) A and c = 14.740(2) A, α = 106.260(3)°, β = 102.310(3)°, γ = 95.975(3)°, Z = 2. The structure was solved by direct methods and refined to an R1 value of 0.0394 on 4252 observed reflections. Enantiomeric pairs of dimethoxy-gossypol molecules form centrosymmetic dimers that are characterized by a pair of intermolecular hydrogen bonds and by hydrophobic stacking between pairs of naphthalene rings. The acetic acid molecule accepts a hydrogen bond from a gossypol hydroxyl group and donates to a hydrogen bond with one of the aldehyde groups of an adjacent gossypol molecule. Although there is less hydrogen bonding in this structure than in the gossypol:acetic acid (1:1) structure, the molecular packing of the two compounds is similar. Crystal and molecular structure of 6,6′-dimethoxy-gossypol:acetic acid (1:1) Michael K. Dowd and Edwin D. Stevens The molecular structure of the acetic acid solvate of 6,6′-dimethoxy-gossypol is presented.

Hydrogen bonding of modified bases involving Watson-Crick sites: Crystal structure and conformation of Benzyl 6-aminopurine-7-carboxylate

Crystals of benzyl 6-aminopurine-7-carboxylate (C13H11N5O2) are monoclinic, space group C2/c, Z = 8, with a = 25.448 (9), b = 6.052 (1), c = 16.975 (6)A, β = 112.05 (5)°, M = 269.27, Dm= 1.49, Dx= 1.48 g/cm3. The structure was determined from three-dimensional diffractometric data by the multisolution technique and refined to a final reliability factor of 0.068. The molecule is planar with an intramolecular hydrogen bond from one of the amino hydrogens, Ha(N6) to the keto oxygen O(10) of the acyl group. The molecules are hydrogen bonded across the center of inversion by a pair of intermolecular hydrogen bonds using the Watson-Crick sites. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Crystal structure of human SH3BGRL protein: The first structure of the human SH3BGR family representing a novel class of thioredoxin fold proteins

Introduction. The humanSH3BGRL (h-SH3BGRL) gene is a member of the human SH3BGR family. The human SH3BGR (SH3 binding glutamic acid-rich) gene was cloned and characterized in 1997 in an effort to identify new genes located to chromosome 21. After the characterization of SH3BGR, three novel human genes, h-SH3BGRL, h-SH3BGRL2, and h-SH3BGRL3, were identified, showing a high homology to the N-terminal region of the h-SH3BGR protein. They are therefore believed to be a new family of human gene, the h-SH3BGR gene family. The h-SH3BGRL gene located to chromosome Xq13.3 encodes for a small protein of 114 amino acids, which is apparently widely expressed in many tissues including liver and blood. The h-SH3BGRLprotein features a prolinerich sequence (PLPPQIF), which contains both the SH3 binding (PXXP) and the Homer EVH1 binding (PPXXF) motif. This proline-rich region is highly conserved in h-SH3BGR family and was expected to be functionally important. Although it is known that the SH3BGRL gene is missing in a mentally retarded male patient, the exact functional role of h-SH3BGRL is still needed to be defined. Here we report the crystal structure of h-SH3BGRL protein determined by the SIRAS method. The structure indicates that SH3BGRL can not bind to the SH3 or Homer EVH1 domain as previously expected due to our finding that the binding motif (PLPPQIF) is buried in the tertiary structure. As the first structure of the human SH3BGR protein family, the tertiary structure of h-SH3BGRL shows a typical thioredoxin fold at the Nterminal part and a helix-loop-helix motif at the Cterminal lobe. Sequence and structure comparisons show that h-SH3BGRL belongs to the thioredoxin fold protein family but it is distinct from all five classes of the thioredoxin fold proteins identified thus far. According to the unique structural and functional characterizations, h-SH3BGRL represents a novel class of the thioredoxin fold proteins.

Conformational and electronic interaction studies of some p-substituted α-bromo-α-ethylsulfonylacetophenones

The preferred conformations of p-substituted α-bromo-α-ethylsulfonylacetophenones Y–PhC(O)CH(Br)SO 2Et (Y=OMe 1, Me 2, H 3, Cl 4, Br 5, CN 6 and NO 2 7) are determined by ν CO IR analysis; HF/6-31G** ab initio computations and X-ray diffraction (for 3). In the gas phase, compound 3 shows the existence of two stable conformers. The more stable and more polar c 1 conformer presents the α-ethylsulfonyl and the α-bromo substituents in syn-periplanar ( quasi-cis) and syn-clinal ( gauche) geometries, respectively, with respect to the carbonyl group. For the second, less stable and less polar, c 2 conformer, both the α substituents assume a syn-clinal ( gauche) geometry. The larger stabilisation of the c 1 conformer relative to c 2, in the gas phase, is attributed to the summing up of the n Br/π ∗ CO and σ C–Br/π ∗ CO hyperconjugative interactions and O CO δ− ⋯S SO 2 δ+, H CH 2[SO 2 Et] ⋯O CO δ− and O SO 2 δ− ⋯C CO δ+ orbital and electrostatic interactions, which are stronger for the c 1 conformer relative to c 2. In solution, only the more polar c 1 conformer has been detected, due to its stronger solvation energy relative to that of the c 2 conformer. The mean carbonyl frequency shifts (Δ ν) close to zero, in CCl 4, for the single ν CO band of the title compounds 1–7 gives further support for its assignment to the c 1 conformer as both the quasi-cis conformer of the α-ethylsulfonylacetophenones and the gauche conformer of the α-bromocetophenones present (Δ ν) values close to zero. X-ray diffraction analysis for 3 indicates that it exists in the solid state in the c′ 1 conformation, which is reasonably close to the c 1 one, and it is stabilised intramolecularly by the same interactions responsible for the stabilisation of conformer c 1 in the gas phase. Furthermore, these molecules form centro-symmetric dimers in the crystal, which are stabilised through two pairs of intermolecular hydrogen bonds, i.e. H [o-Ph] δ+ ⋯O SO 2 δ− and H [α-CH] δ+ ⋯O SO 2 δ− .

Supramolecular Ribbons. Crystal Structure and Spectroscopic Properties of 2,2′-Bipyrroyl

A crystal structure determination of 2,2′-bipyrroyl (1; 2,2′-dipyrryl-diketone, bis (2-pyrrolyl)ethanedione) and its spectroscopic properties in solution are reported. In the crystal, 1 self-assembles via hydrogen bonding into supramolecular ribbons that extend indefinitely through the crystal lattice. The observed molecular conformation is one where each pyrrole ring and adjacent carbonyl group are co-planar (torsion angle ∼ 0.9°), with the N-H pointing in the same direction as the C=O. The two carbonyls have a transoid but not co-planar geometry with a torsion angle of ∼128°. Adjacent molecules in the crystal are linked by pairs of intermolecular hydrogen bonds, pyrrole NH to carbonyl oxygen, to form a matrix of polymeric chains that lie like neatly stacked, parallel streams of ribbons. Molecular mechanics calculations on the monomer indicate an intra-molecularly hydrogen bonded planar conformation (sp, ap, sp) at the global energy minimum. In CHCl3, 1 is monomeric according to vapor pressure osmometry (MWobs=179±10 vsċMWcalc=188). In THF, the measured molecular weight is 340±15, which corresponds best to one molecule of 1 solvated by two THF molecules (MW=322 for C10H8N2O4ċ2 C4H8O) rather than to a dimer.

1H-Indole-3-propionic Acid

The title compound, C11H11NO2, has a fully extended propionic acid side chain. The molecules are held together as dimers by centrosymmetric pairs of intermolecular hydrogen bonds between the carboxyl groups. The O⋯O distance is 2.649 (2) Å.

(±)-2-[Hydroxy(4-methoxyphenyl)methyl]-2H-1,4-benzothiazin-3(4H)-one Hydrate

The title compound, C16H15NO3S.H2O, is a derivative of benzothiazine. The molecular packing is stabilized by a three-dimensional hydrogen-bonding network. The benzothiazine ring is distorted showing a half-chair conformation. The benzene ring is planar but the methoxy group deviates significantly from planarity. A pair of intermolecular hydrogen bonds forms a centrosymmetric dimer in the crystal. There are intermolecular hydrogen bonds with a water molecule. The hydroxy(4-methoxyphenyl)methyl group and carbonyl O(20) atom are pseudo-equatorial with respect to the benzothiazine ring.

Crystal and molecular structure of methyl 2-bis(pentyloxy)phosphoryl-2-phenylsulfonamido-3,3,3-trifluoropropionate

Crystal and molecular structure of methyl 2-bis(pentyloxy)phosphoryl-2-phenylsulfonamido-3,3,3-trifluoropropionate (I) was determined by XRD analysis: space group\(P\bar 1\), a=9.406(3), b=12.068(6), c=14.150(8) A, α=66.88(5), β=68.61(5), γ=71.33(5)°, Z=2, R=0.090 (CAD-4 automatic diffractometer, λCuKα, 1950 independent reflections with I≥2σ). The S and P atoms of molecule I have a distorted tetrahedral coordination. The S−N−C−P torsion angle is 159.4°. The two pentyl substituents in structure I have different conformations, and their atoms make rather intense thermal vibrations. In crystal structure I, the molecules are linked into centrosymmetric H-dimers by pairs of intermolecular hydrogen bonds N−H...O=P.

Heterocyclic tautomerism. XI. Structures of 5,5′-bitetrazole and 1-methyl-5-(2′-pyridyl)tetrazole at 130 K

The X-ray crystal structures of 5,5′-bitetrazole and 1-methyl-5-(2′-pyridyl)tetrazole at 130 K are described. 5,5′-Bitetrazole exists as the 1 H, 1'H-tautomer and packs in chains held together by pairs of intermolecular hydrogen bonds. It crystallizes in the monoclinic space group P21/n witha=4.945(1),b=6.367(1),c=8.491(1) A and β=99.233(7)o. In 1-methyl-5-(2′-pyridyl)tetrazole the two heterocyclic rings are nearly coplanar and the molecular packing is controlled by intermolecular π−π interactions. It crystallizes in the triclinic space group P1 witha=6.667(1),b=7.135(1),c=9.202(1)A, α=89.59(1), β=69.08(1), and γ=66.62(1)o.

Non-steroidal anti-inflammatory drugs. III. Structure of indoprofen: 2-[4-(1-oxo-2-isoindolinyl)phenyl]propionic acid.

Indoprofen, 4-(1,3-dihydro-1-oxo-2H-isoindol-2-yl)-alpha-methylbenzeneaceti c acid, C17H15NO3, a non-steroidal anti-inflammatory agent, falls into the class of phenylpropionic acids that includes ibuprofen, ketoprofen and flubirprofen. It adopts a planar conformation apart from the carboxylic acid group. There is a small twist of 8.8 (2) degrees between the mean planes of the isoindolinyl and phenyl rings. The rotation of the carboxyl group out of the plane of the adjacent phenyl ring seems to be connected with anti-inflammatory activity and is similar to that found in other 2-phenylpropionic acids. A pair of intermolecular hydrogen bonds connects two carboxylic acid groups across a centre of symmetry with an O...O distance of 2.61 (1) A.

Molecular and crystal structure of the regenerated form of (1 → 3)-α- d-mannan

The crystal structure of the hydrated form of (1 → 3)-α- d-mannan, obtained by solid-state deacetylation of the partially O-acetylated mannan, was analyzed by combined X-ray diffraction and stereochemical-model refinement techniques. The structure crystallizes in a four-chain, monoclinic unit cell with parameters a = 11.33 Å, b = 18.36 Å, c (fiber repeat) = 8.25 Å, and γ = 101.75°, and the most probable space group is P2 1. In the most probable structure the chain-backbone conformation is a two-fold helix, but with all four O-6 rotational positions nonequivalent. The chains pack with antiparallel polarity and are connected by pairs of intermolecular hydrogen bonds that form an infinite, zig-zag sheet. There are 16 water molecules in the unit cell, generally embedded between the sheets in crystallographic positions, providing additional hydrogen bonding and establishing a three-dimensional hydrogen-bond network in the crystal structure. The reliability of the structure analysis is indicated by the X-ray residual R″ = 0.281, based on 98 hkl reflection intensities.