Elucidating the crystal structure of the antimalarial drug (+/-)-mefloquine hydrochloride: a tetragonal hydrated species

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Host-guest interactions between xanthones and water: the role of O-H center dot center dot center dot O, C-H center dot center dot center dot O, and pi center dot center dot center dot pi contacts in the channel- and cage-type frameworks

In this article were studied two xanthone derivatives known as 1,5-dihydroxy-8-methoxyxanthone (I) and 1,3,7-trihydroxy-8-methoxyxanthone (II), which show one water molecule into their crystal structures. In xanthone I, there are water wires contributing to build up channel-like cavities along the c axis, whereas in xanthone II the water is surrounded by three xanthone molecules forming a cage-type structure. The geometries of I and II were optimized using the density functional theory method with B3LYP functional, and the results were compared with crystal structure. Both theoretical and experimental investigations reveal a concordance between structural parameters, with the xanthone core presenting an almost flat conformation and substituents adopting the more stable orientations. In the two compounds, the hydroxyl group linked at position 1 is involved in a resonance-assisted hydrogen bond with the carbonyl group. Besides, the supramolecular arrangement of the host/guest systems are stabilized mainly by classical intermolecular hydrogen bonds (O-H center dot center dot center dot O) involving xanthone-to-water and xanthone-to-xanthone. In addition, C-H center dot center dot center dot O weak hydrogen bonds, as well as pi-pi interactions play an important role to stabilize the crystal self-assembly of xanthones I and II. The results reported here underline the role of inclusion of water molecules and their different arrangement into the crystal structure of two xanthone host/guest systems.

Probing the relationships between molecular conformation and intermolecular contacts in N,N-dibenzyl-N '-(furan-2-carbonyl)thiourea

In the crystal structure of the title compound, C20H18N2O2S, molecules are linked by bifurcated C-H center dot center dot center dot O hydrogen-bond interactions, giving rise to chains whose links are composed of alternating centrosymmetrically disposed pairs of molecules and characterized by R-2(2)(10) and R-2(2)(20) hydrogen-bonding motifs. Also, N-H center dot center dot center dot S hydrogen bonds form infinite zigzag chains along the [010] direction, which exhibit the C(4) motif. Hirshfeld surface and fingerprint plots were used to explore the intermolecular interactions in the crystal structure. This analysis confirms the important role of C-H center dot center dot center dot O hydrogen bonds in the molecular conformation and in the crystal structure, providing a potentially useful tool for a full understanding of the intermolecular interactions in acylthiourea derivatives.

Structure, organization and dynamics of functional supramolecular materials studied by solid-state NMR

Functional materials have great importance due to their many important applications. The characterization of supramolecular architectures which are held together by non-covalent interactions is of most importance to understand their properties. Solid-state NMR methods have recently been proven to be able to unravel such structure-property relations with the help of fast magic-angle spinning and advanced pulse sequences. The aim of the current work is to understand the structure and dynamics of functional supramolecular materials which are potentially important for fuel-cell (proton conducting membrane materials) and solar-cell or plastic-electronic applications (photo-reactive aromatic materials). In particular, hydrogen-bonding networks, local proton mobility, molecular packing arrangements, and local dynamics will be studied by the use of advanced solid-state NMR methods. The first class of materials studied in this work is proton conducting polymers which also form hydrogen-bonding network. Different materials, which are prepared for high 1H conduction by different approaches are studied: PAA-P4VP, PVPA-ABPBI, Tz5Si, and Triazole-functional systems. The materials are examples of the following major groups; - Homopolymers with specific functional groups (Triazole functional polysiloxanes). - Acid-base polymer blends approach (PAA-P4VP, PVPA-ABPBI). - Acid-base copolymer approach (Triazole-PVPA). - Acid doped polymers (Triazole functional polymer doped with H3PO4). Perylenebisimide (PBI) derivatives, a second type of important functional supramolecular materials with potent applications in plastic electronics, were also investigated by means of solid-state NMR. The preparation of conducting nanoscopic fibers based on the self-assembling functional units is an appealing aim as they may be incorporated in molecular electronic devices. In this category, perylene derivatives have attracted great attention due to their high charge carrier mobility. A detailed knowledge about their supramolecular structure and molecular dynamics is crucial for the understanding of their electronic properties. The aim is to understand the structure, dynamics and packing arrangements which lead to high electron conductivity in PBI derivatives.

Ab-initio study of hydrogen technology materials for hydrogen storage and proton conduction

This dissertation deals with two specific aspects of a potential hydrogen-based energy economy, namely the problems of energy storage and energy conversion. In order to contribute to the solution of these problems, the structural and dynamical properties of two promising materials for hydrogen storage (lithium imide/amide) and proton conduction (poly[vinyl phosphonic acid]) are modeled on an atomistic scale by means of first principles molecular dynamics simulation methods.rnrnrnIn the case of the hydrogen storage system lithium amide/imide (LiNH_2/Li_2NH), the focus was on the interplay of structural features and nuclear quantum effects. For these calculations, Path-Integral Molecular Dynamics (PIMD) simulations were used. The structures of these materials at room temperature were elucidated; in collaboration with an experimental group, a very good agreement between calculated and experimental solid-state 1H-NMR chemical shifts was observed. Specifically, the structure of Li_2NH features a disordered arrangement of the Li lattice, which was not reported in previous studies. In addition, a persistent precession of the NH bonds was observed in our simulations. We provide evidence that this precession is the consequence of a toroid-shaped effective potential, in which the protons in the material are immersed. This potential is essentially flat along the torus azimuthal angle, which might lead to important quantum delocalization effects of the protons over the torus.rnrnOn the energy conversion side, the dynamics of protons in a proton conducting polymer (poly[vinyl phosphonic acid], PVPA) was studied by means of a steered ab-initio Molecular Dynamics approach applied on a simplified polymer model. The focus was put on understanding the microscopic proton transport mechanism in polymer membranes, and on characterizing the relevance of the local environment. This covers particularly the effect of water molecules, which participate in the hydrogen bonding network in the material. The results indicate that these water molecules are essential for the effectiveness of proton conduction. A water-mediated Grotthuss mechanism is identified as the main contributor to proton conduction, which agrees with the experimentally observed decay on conductivity for the same material in the absence of water molecules.rnrnThe gain in understanding the microscopic processes and structures present in this materials can help the development of new materials with improved properties, thus contributing to the solution of problems in the implementation of fuel cells.

Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees

The 3 angstrom resolution crystal structure of the Escherichia coli catabolite gene activator protein (CAP) complexed with a 30-base pair DNA sequence shows that the DNA is bent by 900. This bend results almost entirely from two 400 kinks that occur between TG/CA base pairs at positions 5 and 6 on each side of the dyad axis of the complex. DNA sequence discrimination by CAP derives both from sequence-dependent distortion of the DNA helix and from direct hydrogen-bonding interactions between three protein side chains and the exposed edges of three base pairs in the major groove of the DNA. The structure of this transcription factor-DNA complex provides insights into possible mechanisms of transcription activation

Crystal structures of isotypic poly[bis(benzimidazolium) [tetra-μ-iodido-stannate(II)]] and poly[bis(5,6-difluorobenzimidazolium) [tetra-μ-iodido-stannate(II)]]

The isostructural title compounds, {(C7H7N2)2[SnI4]}n, (1), and {(C7H5F2N2)2[SnI4]}n, (2), show a layered perovskite-type structure composed of anionic {[SnI4]2-}n sheets parallel to (100), which are decorated on both sides with templating benzimidazolium or 5,6-di­fluoro­benzimidazolium cations, respectively. These planar organic heterocycles mainly form N-H...I hydrogen bonds to the terminal I atoms of the corner-sharing [SnI6] octa­hedra (point group symmetry 2) from the inorganic layer, but not to the bridging ones. This is in contrast to most of the reported structures of related compounds where ammonium cations are involved. Here hydrogen bonding to both types of iodine atoms and thereby a distortion of the inorganic layers to various extents is observed. For (1) and (2), all Sn-I-Sn angles are linear and no out-of-plane distortions of the inorganic layers occur, a fact of relevance in view of the material properties. The arrangement of the aromatic cations is mainly determined through the direction of the N-H...I hydrogen bonds. The coherence between organic bilayers along [100] is mainly achieved through van der Waals inter­actions.

Structure of the histone mRNA hairpin required for cell cycle regulation of histone gene expression.

Expression of replication-dependent histone genes requires a conserved hairpin RNA element in the 3' untranslated regions of poly(A)-less histone mRNAs. The 3' hairpin element is recognized by the hairpin-binding protein or stem-loop-binding protein (HBP/SLBP). This protein-RNA interaction is important for the endonucleolytic cleavage generating the mature mRNA 3' end. The 3' hairpin and presumably HBP/SLBP are also required for nucleocytoplasmic transport, translation, and stability of histone mRNAs. RNA 3' processing and mRNA stability are both regulated during the cell cycle. Here, we have determined the three-dimensional structure of a 24-mer RNA comprising a mammalian histone RNA hairpin using heteronuclear multidimensional NMR spectroscopy. The hairpin adopts a novel UUUC tetraloop conformation that is stabilized by base stacking involving the first and third loop uridines and a closing U-A base pair, and by hydrogen bonding between the first and third uridines in the tetraloop. The HBP interaction of hairpin RNA variants was analyzed in band shift experiments. Particularly important interactions for HBP recognition are mediated by the closing U-A base pair and the first and third loop uridines, whose Watson-Crick functional groups are exposed towards the major groove of the RNA hairpin. The results obtained provide novel structural insight into the interaction of the histone 3' hairpin with HBP, and thus the regulation of histone mRNA metabolism.

The crystal structure of the Rev binding element of HIV-1 reveals novel base pairing and conformational variability

The crystal and molecular structure of an RNA duplex corresponding to the high affinity Rev protein binding element (RBE) has been determined at 2.1-Å resolution. Four unique duplexes are present in the crystal, comprising two structural variants. In each duplex, the RNA double helix consists of an annealed 12-mer and 14-mer that form an asymmetric internal loop consisting of G-G and G-A noncanonical base pairs and a flipped-out uridine. The 12-mer strand has an A-form conformation, whereas the 14-mer strand is distorted to accommodate the bulges and noncanonical base pairing. In contrast to the NMR model of the unbound RBE, an asymmetric G-G pair with N2-N7 and N1-O6 hydrogen bonding, is formed in each helix. The G-A base pairing agrees with the NMR structure in one structural variant, but forms a novel water-mediated pair in the other. A backbone flip and reorientation of the G-G base pair is required to assume the RBE conformation present in the NMR model of the complex between the RBE and the Rev peptide.

Covalent intermediate trapped in 2-keto-3-deoxy-6- phosphogluconate (KDPG) aldolase structure at 1.95-Å resolution

2-Keto-3-deoxy-6-phosphogluconate (KDPG) aldolase catalyzes the reversible cleavage of KDPG to pyruvate and glyceraldehyde-3-phosphate. The enzyme is a class I aldolase whose reaction mechanism involves formation of Schiff base intermediates between Lys-133 and a keto substrate. A covalent adduct was trapped by flash freezing KDPG aldolase crystals soaked with 10 mM pyruvate in acidic conditions at pH 4.6. Structure determination to 1.95-Å resolution showed that pyruvate had undergone nucleophilic attack with Lys-133, forming a protonated carbinolamine intermediate, a functional Schiff base precursor, which was stabilized by hydrogen bonding with active site residues. Carbinolamine interaction with Glu-45 indicates general base catalysis of several rate steps. Stereospecific addition is ensured by aromatic interaction of Phe-135 with the pyruvate methyl group. In the native structure, Lys-133 donates all of its hydrogen bonds, indicating the presence of an ɛ-ammonium salt group. Nucleophilic activation is postulated to occur by proton transfer in the monoprotonated zwitterionic pair (Glu-45/Lys-133). Formation of the zwitterionic pair requires prior side chain rearrangement by protonated Lys-133 to displace a water molecule, hydrogen bonded to the zwitterionic residues.

Peptide hybrids containing α- and β-amino acids: Structure of a decapeptide β-hairpin with two facing β-phenylalanine residues

A β-hairpin conformation has been characterized in crystals of the decapeptide t-butoxycarbonyl-Leu-Val-βPhe-Val-DPro-Gly-Leu-βPhe-Val-Val-methyl ester [βPhe; (S)-β3 homophenylalanine] by x-ray diffraction. The polypeptide chain reversal is nucleated by the centrally positioned DPro-Gly segment, which adopts a type-I′ β-turn conformation. Four intramolecular cross-strand hydrogen bonds stabilize the peptide fold. The βPhe(3) and βPhe(8) residues occupy facing positions on the hairpin, with the side chains projecting on opposite faces of the β-sheet. At the site of insertion of β-residues, the polarity of the peptide units along each strand reverses, as compared with the α-peptide segments. In this analog, a small segment of a polar sheet is observed, where adjacent CO and NH groups line up in opposite directions in each strand. In the crystal, an extended β-sheet is formed by hydrogen bonding between strands of antiparallel pairs of β-hairpins. The crystallographic parameters for C65H102N10O13⋅ 3H2O are: space group P212121; a = 19.059(8) Å, b = 19.470(2) Å, c = 21.077(2) Å; Z = 4; agreement factor R1 = 9.12% for 3,984 data observed >4σ(F) and a resolution of 0.90 Å.

Crystal structure of a DNA decamer showing a novel pseudo four-way helix-helix junction.

The crystal structure of the decanucleotide d(CGCAATTGCG)2 has been solved by a combination of molecular replacement and heavy-atom procedures and has been refined to an R factor of 20.2% at 2.7 A. It is not a fully base-paired duplex but has a central core of eight Watson-Crick base pairs flanked by unpaired terminal guanosines and cytosines. These participate in hydrogen-bonding arrangements with adjacent decamer duplexes in the crystal lattice. The unpaired guanosines are bound in the G+C regions of duplex minor grooves. The cytosines have relatively high mobility, even though they are constrained to be in one region where they are involved in base-paired triplets with G.C base pairs. The 5'-AATT sequence in the duplex region has a narrow minor groove, providing further confirmation of the sequence-dependent nature of groove width.

Crystal and molecular structure of paclitaxel (taxol).

Paclitaxel (formerly called taxol), an important anticancer drug, inhibits cell replication by binding to and stabilizing microtubule polymers. As drug-receptor interactions are governed by the three-dimensional stereochemistries of both participants, we have determined the crystal structure of paclitaxel to identify its conformational preferences that may be related to biological activity. The monoclinic crystals contain two independent paclitaxel molecules in the asymmetric unit plus several water and dioxane solvent molecules. Taxane ring conformation is very similar in both paclitaxel molecules and is similar to the taxane ring conformation found in the crystal structure of the paclitaxel analogue docetaxel (formerly called taxotere). The two paclitaxel molecules have carbon-13 side-chain conformations that differ from each other and from that of the corresponding side chain in the docetaxel crystal structure. The carbon-13 side-chain conformation of one paclitaxel molecule is similar to what was proposed from NMR studies done in polar solvents, while that of the other paclitaxel molecule is different and hitherto unobserved. The paclitaxel molecules interact with each other and with solvent atoms through an extensive network of hydrogen bonds. Analysis of the hydrogen-bonding network together with structure-activity studies may suggest which atoms of paclitaxel are important for binding to microtubule receptors.

Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove.

Sequence analysis of peptides naturally presented by major histocompatibility complex (MHC) class I molecules has revealed allele-specific motifs in which the peptide length and the residues observed at certain positions are restricted. Nevertheless, peptides containing the standard motif often fail to bind with high affinity or form physiologically stable complexes. Here we present the crystal structure of a well-characterized antigenic peptide from ovalbumin [OVA-8, ovalbumin-(257-264), SIINFEKL] in complex with the murine MHC class I H-2Kb molecule at 2.5-A resolution. Hydrophobic peptide residues Ile-P2 and Phe-P5 are packed closely together into binding pockets B and C, suggesting that the interplay of peptide anchor (P5) and secondary anchor (P2) residues can couple the preferred sequences at these positions. Comparison with the crystal structures of H-2Kb in complex with peptides VSV-8 (RGYVYQGL) and SEV-9 (FAPGNYPAL), where a Tyr residue is used as the C pocket anchor, reveals that the conserved water molecule that binds into the B pocket and mediates hydrogen bonding from the buried anchor hydroxyl group could not be likewise positioned if the P2 side chain were of significant size. Based on this structural evidence, H-2Kb has at least two submotifs: one with Tyr at P5 (or P6 for nonamer peptides) and a small residue at P2 (i.e., Ala or Gly) and another with Phe at P5 and a medium-sized hydrophobic residue at P2 (i.e., Ile). Deciphering of these secondary submotifs from both crystallographic and immunological studies of MHC peptide binding should increase the accuracy of T-cell epitope prediction.

Disulfide bond mutagenesis and the structure and function of the head-to-tail macrocyclic trypsin inhibitor SFTI-1

SFTI-1 is a novel 14 amino acid peptide comprised of a circular backbone constrained by three proline residues, a hydrogen-bond network, and a single disulfide bond. It is the smallest and most potent known Bowman-Birk trypsin inhibitor and the only one with a cyclic peptidic backbone. The solution structure of [ABA(3,11)]SFTI-1, a disulfide-deficient analogue of SFTI-1, has been determined by H-1 NMR spectroscopy. The lowest energy structures of native SFTI-1 and [ABA(3,11)]SFTI-1 are similar and superimpose with a root-mean-square deviation over the backbone and heavy atoms of 0.26 +/- 0.09 and 1.10 +/- 0.22 Angstrom, respectively. The disulfide bridge in SFTI-1 was found to be a minor determinant for the overall structure, but its removal resulted in a slightly weakened hydrogen-bonding network. To further investigate the role of the disulfide bridge, NMR chemical shifts for the backbone H-alpha protons of two disulfide-deficient linear analogues of SFTI-1, [ABA(3,11)]SFTI-1[6,5] and [ABA(3,11)]SFTI-1[1,14] were measured. These correspond to analogues of the cleavage product of SFTI-1 and a putative biosynthetic precursor, respectively. In contrast with the cyclic peptide, it was found that the disulfide bridge is essential for maintaining the structure of these open-chain analogues. Overall, the hydrogen-bond network appears to be a crucial determinant of the structure of SFTI-1 analogues.