Molecular conformation of the racemic indan derivative (+/-)-1-trans-3-(3,4-dichlorophenyl)-2,3-dihydro-1H-indene-1-carboxamide

This paper presents the structural characterization of the indan derivative (+/-)-1-trans-3-(3,4-dichlorophenyl)-2,3-dihydro-1H-indene-1-carboxamide, which was unambiguously determined by X-ray diffraction (XRD) to be a racemate (R/S: 50/50) crystallizing in an achiral crystal structure (P2(1)/c, a = 9.3180(1) , b = 7.9070(2) , c = 19.7550(4) , beta = 103.250(1)A degrees, V = 1416.75(5) (3) and Z = 4). The diastereomers are related by the inversion symmetry and linked by H bond forming a dimer. The crystal packing is stabilized by hydrogen bonds, including the classical one responsible for the formation of centrosymmetric dimers, and non-classical ones involving C-H center dot center dot center dot O and C-H center dot center dot center dot pi-aryl interactions. The intra and intermolecular geometry of the title compound is compared to the (+/-)-1-trans-3-(3,4-dichlorophenyl)-2,3-dihydro-1H-indene-1-carboxylic acid one, which also present an achiral crystal structure from racemates (R/S: 50/50). The two indan derivatives crystallize in a very similar unit cell.

Experimental and theoretical investigation of molecular structure and conformation of the 4-isopropylthioxanthone

In this study, the molecular structure and conformational analyses of the 4-isopropylthioxanthone (4-ITX) are reported according to experimental and theoretical results. The compound crystallizes in the centrosymmetric P (1) over bar space group with only one molecule in the asymmetric unit, presenting the most stable conformation, in which the three fused-rings adopt a planar geometry, and the isopropyl group assumes a torsional angle with less sterical hindrance. The structural and conformational analyses were performed using theoretical calculations such as Hartree-Fock (HF), DFT method in combination with 6-311G(d,p) and 6-31++G(d,p) and the results were compared with infrared spectroscopy (FT-IR) and X-ray diffraction (XRD). The supramolecular assembly of 4-ITX is kept by non-classical C-H center dot center dot center dot O hydrogen bonds and weak interactions such as pi-pi stacking. 4-ITX was also studied by (1)H and (13)C NMR spectroscopy. UV-Vis absorption spectroscopic properties of the 4-ITX showed the long-wavelength maximum shifts towards high energy when the solvent polarity increases. (C) 2011 Elsevier B.V. All rights reserved.

On the relationships between molecular conformations and intermolecular contacts toward crystal self-assembly of mono-, di-, tri-, and tetra-oxygenated xanthone derivatives

Oxygenated xanthones have been extensively investigated over the years, but there are few reports concerning their crystal structure. Our chemical investigations of Brazilian plants resulted in the isolation of four natural products named 1-hydroxyxanthone (I), 1-hydroxy-7-methoxyxanthone (II), 1,5-dihydroxy-3-methoxyxanthone (III), and 1,7-dihydroxy-3,8-dimethoxyxanthone (IV). The structures of these compounds were established on the basis of single crystal X-ray diffraction. The xanthone nucleus conformation is essentially planar with the substituents adopting the orientations less sterically hindered. In addition, classical intermolecular hydrogen bonds (O-H center dot center dot center dot O) present in III and IV give rise to infinite ribbons. However, the xanthone I does not present any intermolecular hydrogen bonds, meanwhile the xanthone II presents only a non-classical one (C-H center dot center dot center dot O). The crystal packing of all xanthone structures is also stabilized by pi-pi interactions. The fingerprint plots, derived from the Hirshfeld surfaces, exhibited significant features of each crystal structures.

Conformational behavior of different possible ways of oligoglycine formation in a solvent-free environment

The possible ways for glycine oligopeptide formation in gas phase, both in the extended P-strand like conformation and folded 2(7)-ribbon like conformations are analyzed using quantum chemical calculations. We focus on the sequential formation of peptide bond through upgradation of the immediate lower order molecule and observe the consequences in other related processes like oligoglycine formation through simultaneous peptide linkage of n glycine monomers and interchange of molecular conformation through peptide linkage. A comparison is made between the structures and binding energies obtained for both conformers. All binding energies are increased by the zero-point energy contribution. The role of electron correlation effects is briefly analyzed. The folded 2(7)-ribbon-like conformations in vacuo are found to be more stable in comparison to the extended structure. (c) 2007 Elsevier B.V. All rights reserved.

Intermolecular Contacts Influencing the Conformational and Geometric Features of the Pharmaceutically Preferred Mebendazole Polymorph C

Mebendazole (MBZ) is a common benzimidazole anthelmintic that exists in three different polymorphic forms, A, B, and C. Polymorph C is the pharmaceutically preferred form due to its adequated aqueous solubility. No single crystal structure determinations depicting the nature of the crystal packing and molecular conformation and geometry have been performed on this compound. The crystal structure of mebendazole form C is resolved for the first time. Mebendazole form C crystallizes in the triclinic centrosymmetric space group and this drug is practically planar, since the least-squares methyl benzimidazolylcarbamate plane is much fitted on the forming atoms. However, the benzoyl group is twisted by 31(1)degrees from the benzimidazole ring, likewise the torsional angle between the benzene and carbonyl moieties is 27(1)degrees. The formerly described bends and other interesting intramolecular geometry features were viewed as consequence of the intermolecular contacts occurring within mebendazole C structure. Among these features, a conjugation decreasing through the imine nitrogen atom of the benzimidazole core and a further resonance path crossing the carbamate one were described. At last, the X-ray powder diffractogram of a form C rich mebendazole mixture was overlaid to the calculated one with the mebendazole crystal structure. (C) 2008 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 98:2336-2344, 2009

Molecular Ordering of Layer-by-Layer Polyelectrolyte Films Studied by Sum-Frequency Vibrational Spectroscopy

The molecular arrangement in organic thin films is crucial for their increasing technological applications. Here, we use vibrational spectroscopy by sum-frequency generation (SFG) to study the ordering of polyelectrolyte layers adsorbed on silica for all steps of layer-by-layer (LbL) self-assembly. In situ measurements during adsorption and rinsing showed that the adsorbed polymer has a disordered conformation and confirmed surface charge overcompensation upon polyelectrolyte adsorption by probing the interfacial electric field. In dry films, the polymer chains acquired a net orientational ordering, which was affected, however, by the adsorption of subsequent layers. Such a detailed characterization may allow the control of LbL film structure and functionality with unprecedented power.

Molecular Ordering in Layer-by-Layer Polyelectrolyte Films Studied by Sum-Frequency Vibrational Spectroscopy: The Effects of Drying Procedures

Sum-Frequency Vibrational Spectroscopy (SFVS) has been used to investigate the effect of nitrogen-flow drying on the molecular ordering of Layer-by-Layer (LbL) films of poly(allylamine hydrochloride) (PAH) alternated with poly(styrene sulfonate) (PSS). We find that films dried by spontaneous water evaporation are more ordered and homogeneous than films dried by nitrogen flow. The latter are quite inhomogeneous and may have regions with highly disordered polymer conformation. We propose that drying by spontaneous water evaporation reduces the effect of drag by the drying front, while during nitrogen-flow drying the fast evaporation of water ""freezes"" the disordered conformation of adsorbed polyelectrolyte molecules. These findings are important for many applications of LbL films, since device performance usually depends on film morphology and its molecular structure.

Analysis of Agonist and Antagonist Effects on Thyroid Hormone Receptor Conformation by Hydrogen/Deuterium Exchange

Thyroid hormone receptors (TRs) are ligand-gated transcription factors with critical roles in development and metabolism. Although x-ray structures of TR ligand-binding domains (LBDs) with agonists are available, comparable structures without ligand (apo-TR) or with antagonists are not. It remains important to understand apo-LBD conformation and the way that it rearranges with ligands to develop better TR pharmaceuticals. In this study, we conducted hydrogen/deuterium exchange on TR LBDs with or without agonist (T(3)) or antagonist (NH(3)). Both ligands reduce deuterium incorporation into LBD amide hydrogens, implying tighter overall folding of the domain. As predicted, mass spectroscopic analysis of individual proteolytic peptides after hydrogen/deuterium exchange reveals that ligand increases the degree of solvent protection of regions close to the buried ligand-binding pocket. However, there is also extensive ligand protection of other regions, including the dimer surface at H10-H11, providing evidence for allosteric communication between the ligand-binding pocket and distant interaction surfaces. Surprisingly, C-terminal activation helix H12, which is known to alter position with ligand, remains relatively protected from solvent in all conditions suggesting that it is packed against the LBD irrespective of the presence or type of ligand. T(3), but not NH(3), increases accessibility of the upper part of H3-H5 to solvent, and we propose that TR H12 interacts with this region in apo-TR and that this interaction is blocked by T(3) but not NH(3.) We present data from site-directed mutagenesis experiments and molecular dynamics simulations that lend support to this structural model of apo-TR and its ligand-dependent conformational changes. (Molecular Endocrinology 25: 15-31, 2011)

Diphtheria toxoid conformation in the context of its nanoencapsulation within liposomal particles sandwiched by chitosan

Chitosan (alpha alpha-(1-4)-amino-2-deoxy-beta beta-D-glucan) is a deacetylated form of chitin, a polysaccharide from crustacean shells. Its unique characteristics, such as positive charge, biodegradability, biocompatibility, nontoxicity, and rigid structure, make this macromolecule ideal for an oral vaccine delivery system. We prepared reverse-phase evaporation vesicles (REVs) sandwiched by chitosan (Chi) and polyvinylic alcohol (PVA). However, in this method, there are still some problems to be circumvented related to protein stabilization. During the inverted micelle phase of protein nanoencapsulation, hydrophobic interfaces are expanded, leading to interfacial adsorption, followed by protein unfolding and aggregation. Here, spectroscopic and immunological techniques were used to ascertain the effects of the Hoffmeister series ions on diphtheria toxoid (Dtxd) stability during the inverted micelle phase. A correlation was established between the salts used in aqueous solutions and the changes in Dtxd solubility and conformation. Dtxd alpha alpha-helical content was quite stable, which led us to conclude that encapsulation occurred without protein aggregation or without exposition of hydrophobic residues. Dtxd aggregation was 98% avoided by the kosmotropic, PO

Crystal and molecular structures of three 2-sulphur-substituted cyclohexanones studied by X-ray crystallography and by ab initio molecular orbital calculations

The conformational features of three 2-sulphur-substituted cyclohexanone derivatives, which differ in the number of sulphur-bound oxygen atoms, i.e. zero (I), one (II) and two (III), were investigated by single crystal X-ray crystallography and geometry optimized structures determined using Hartree-Fock method. In each of (I)-(III) an intramolecular S center dot center dot center dot O(carbonyl) interaction is found with the magnitude correlated with the oxidation state of the sulphur atom, i.e. 2.838(3) angstrom in (I) to 2.924(2) angstrom in (II) to 3.0973(18) angstrom in (III). There is an inverse relationship between the strength of this interaction and the magnitude of the carbonyl bond. The supramolecular aggregation patterns are primarily determined by C-H center dot center dot center dot O contacts and are similarly influenced by the number of oxygen atoms in the molecular structures. Thus, a supramolecular chain is found in the crystal structure of (I). With an additional oxygen atom available to participate in C-H center dot center dot center dot O interactions, as in (II), a two-dimensional array is found. Finally, a three-dimensional network is found for (III). Despite there being differences in conformations between the experimental structures and those calculated in the gas-phase, the S center dot center dot center dot O interactions persist. The presence of intermolecular C-H center dot center dot center dot O interactions involving the cyclohexanone-carbonyl group in the solid-state, disrupts the stabilising intramolecular C-H center dot center dot center dot O interaction in the energetically-favoured conformation. (I): C(12)H(13)NO(3)S, triclinic space group P (1) over bar with a = 5.392(3) angstrom b = 10.731(6) angstrom, c = 11.075(6) angstrom, alpha = 113.424(4)degrees, beta = 94.167(9)degrees, gamma = 98.444(6)degrees, V = 575.5(6) angstrom(3), Z = 2, R(1) = 0.052; (II): C(12)H(13)NO(4)S, monoclinic P2(1)/n, a = 7.3506(15) angstrom, b = 6.7814(14) angstrom, c = 23.479(5) angstrom, beta = 92.94(3)degrees, V = 1168.8(4) angstrom(3), Z = 4, R(1) = 0.046; (III): C(12)H(13)NO(5)S, monoclinic P2(1)/c, a = 5.5491(11) angstrom, b = 24.146(3) angstrom, c = 11.124(3) angstrom, beta = 114.590(10)degrees, V = 1355.3(5) angstrom(3), Z = 4, R(1) = 0.051.