Crystal Conformation Research Articles

Experimental and theoretical second harmonic generation and photoluminescence from the pseudo-centrosymmetric dihydrochloride salt dihydrate of trans-1,2-bis(4-pyridyl)ethene

Here we have prepared a dihydrochloride salt dihydrate of the well-known trans-1,2-bis(4-pyridyl)ethene (BPE) featuring both photoluminescent and nonlinear optical properties. In its triclinic lattice (space group P1), BPE cations are stacked face-to-tail through π⋯π interactions between the spacer double-bonded carbons and the protonated pyridyl ring, with a slippage of 3.45 A always towards the same direction, which is common in other NLO crystals. The existence of inversion symmetry was suggested in its crystal structure, which was ruled out by the SHG emission centred at 487 nm upon excitation at 974 nm. While the fully optimized single molecule of the divalent BPE cation in the gas phase had almost null μ, βtot, βCT and βvec values calculated at the CAM-B3LYP/NLO-V//B3LYP/6-31G* level of theory, these values differed from zero in the crystal conformation. More interestingly, a ca. 4-fold increase in βtot, α and μ was observed for the π⋯π stacked four-molecules as found in its crystal structure. Lastly, this BPE material presents high photoluminescence emission centred at 425 nm under excitation at 366 nm, being therefore a multifunctional optical crystal form.

Helices with additional H-bonds: crystallographic conformations of α,γ-hybrid peptides helices composed of β-hydroxy γ-amino acids (statines).

β-Hydroxy-γ-amino acids (Statines) are a class of naturally occurring non-ribosomal amino acids frequently found in many peptide natural products. Peptidomimetics constituted with statines have been used as inhibitors for various aspartic acid proteases. In contrast to the synthetic γ-amino acids, very little is known about the folding behavior of these naturally occurring β-hydroxy γ-amino acids. To understand the folding behavior of statines, three α,γ-hybrid peptides P1 (Ac-Aib-γPhe-Aib-(R, S)Phesta-Aib-γPhe-Aib-CONH2 ), P2 (Ac-Aib-γPhe-Aib-(S, S)Phesta-Aib-γPhe-Aib-CONH2 ), and P3 (Ac-Aib-γPhe-Aib-(S, S)Phesta-Aib-(S, S)Phesta-Aib-CONH2 ) were synthesized on solid phase and their helical conformations in single crystals were studied. Results suggest that both syn and anti diastereoisomers of statines can be accommodated into the helix without deviating overall helical conformation of α,γ-hybrid peptides. In comparison with syn diastereoisomer, the anti diastereoisomer was found to be directly involved in the intramolecular H-bonding with the backbone carbonyl groups (i to i + 3) similar to the backbone amide NHs in the helix.

The expression and regulation of glucose transporters in tumor cells

<p>Glucose transporter proteins are involved in many physiological and biochemical processes. In particular, the high expressions of sodium-glucose cotransporter and glucose transporter proteins in tumor cells show that these two transporters play a key role in tumor cell metabolism. Studying the crystal structure and conformation of human glucose transporter proteins has enabled the development of drugs based on specific binding sites, opening up a new path towards more effective cancer treatments. This mini review serves to summarize our existing understanding of the metabolic pathways of tumor cells, focusing on the roles of glucose transporter proteins.</p>

Fragment-based discovery of novel pentacyclic triterpenoid derivatives as cholesteryl ester transfer protein inhibitors

Cholesteryl Ester Transfer Protein (CETP) is an important therapeutic target for the treatment of atherosclerotic cardiovascular disease. Our molecular modeling study revealed that pentacyclic triterpenoid compounds could mimic the protein-ligand interactions of the endogenous ligand cholesteryl ester (CE) by occupying its binding site. Alignment of the docking conformations of oleanolic acid (OA), ursolic acid (UA) and the crystal conformations of known CETP inhibitor Torcetrapib in the active site proposed the applicability of fragment-based drug design (FBDD) approaches in this study. Accordingly, a series of pentacyclic triterpenoid derivatives have been designed and synthesized as novel CETP inhibitors. The most potent compound 12e (IC50:0.28 μM) validated our strategy for molecular design. Molecular dynamics simulations illustrated that the more stable hydrogen bond interaction of the UA derivative 12e with Ser191 and stronger hydrophobic interactions with Val198, Phe463 than those of OA derivative 12b mainly led to their significantly different CETP inhibitory activity. These novel potent CETP inhibitors based on ursane-type scaffold should deserve further investigation.

Crystallographic characterization of the α,γ C12 helix in hybrid peptide sequences.

The solid-state conformations of two αγ hybrid peptides Boc-[Aib-γ(4) (R)Ile]4 -OMe 1 and Boc-[Aib-γ(4) (R)Ile]5 -OMe 2 are described. Peptides 1 and 2 adopt C12 -helical conformations in crystals. The structure of octapeptide 1 is stabilized by six intramolecular 4 → 1 hydrogen bonds, forming 12 atom C12 motifs. The structure of peptide 2 reveals the formation of eight successive C12 hydrogen-bonded turns. Average backbone dihedral angles for αγ C12 helices are peptide 1, Aib; φ (°) = -57.2 ± 0.8, ψ (°) = -44.5 ± 4.7; γ(4) (R)Ile; φ (°) = -127.3 ± 7.3, θ1 (°) = 58.5 ± 12.1, θ2 (°) = 67.6 ± 10.1, ψ (°) = -126.2 ± 16.1; peptide 2, Aib; φ (°) = -58.8 ± 5.1, ψ (°) = -40.3 ± 5.5; ψ(4) (R)Ile; φ (°) = -123.9 ± 2.7, θ1 (°) = 53.3 θ 4.9, θ 2 (°) = 61.2 ± 1.6, ψ (°) = -121.8 ± 5.1. The tendency of γ(4) -substituted residues to adopt gauche-gauche conformations about the C(α) -C(β) and C(β) -C(γ) bonds facilitates helical folding. The αγ C12 helix is a backbone expanded analog of α peptide 310 helix. The hydrogen bond parameters for α peptide 310 and α-helices are compared with those for αγ hybrid C12 helix. Copyright © 2016 European Peptide Society and John Wiley & Sons.

DNA polymorphism in crystals: three stable conformations for the decadeoxynucleotide d(GCATGCATGC).

High-resolution structures of DNA fragments determined using X-ray crystallography or NMR have provided descriptions of a veritable alphabet of conformations. They have also shown that DNA is a flexible molecule, with some sequences capable of adopting two different structures. Here, the first example is presented of a DNA fragment that can assume three different and distinct conformations in crystals. The decanucleotide d(GCATGCATGC) was previously reported to assume a single-stranded double-fold structure. In one of the two crystal structures described here the decamer assumes both the double-fold conformation and, simultaneously, the more conventional B-type double-helical structure. In the other crystal the sequence assumes the A-type double-helical conformation. These results, taken together with CD spectra, which were recorded as the decamer was titrated against four metal ions and spermine, indicate that the molecule may exist as a mixed population of structures in solution. Small differences in the environmental conditions, such as the concentration of metal ion, may decide which of these crystallizes out. The results also support the idea that it may be possible for DNA to change its structure to suit the binding requirements of proteins or drugs.

Beeswax organogels: Influence of gelator concentration and oil type in the gelation process

This work focused on how different types of oil phase, MCT (medium chain triglycerides) and LCT (long chain triglycerides), exert influence on the gelation process of beeswax and thus properties of the organogel produced thereof. Organogels were produced at different temperatures and qualitative phase diagrams were constructed to identify and classify the type of structure formed at various compositions. The microstructure of gelator crystals was studied by polarized light microscopy. Melting and crystallization were characterized by differential scanning calorimetry and rheology (flow and small amplitude oscillatory measurements) to understand organogels' behaviour under different mechanical and thermal conditions. Fourier transform infrared spectroscopy (FTIR) analysis was employed for a further understanding of oil-gelator chemical interactions. Results showed that the increase of beeswax concentration led to higher values of storage and loss moduli (G′, G″) and complex modulus (G*) of organogels, which is associated to the strong network formed between the crystalline gelator structure and the oil phase. Crystallization occurred in two steps (well evidenced for higher concentrations of gelator) during temperature decreasing. Thermal analysis showed the occurrence of hysteresis between melting and crystallization. Small angle X-ray scattering (SAXS) analysis allowed a better understanding in terms of how crystal conformations were disposed for each type of organogel. The structuring process supported by medium or long-chain triglycerides oils was an important exploit to apprehend the impact of different carbon chain-size on the gelation process and on gels' properties.

Helical Nano-crystallite (HNC) Phases: Chirality Synchronization of Achiral Bent-Core Mesogens in a New Type of Dark Conglomerates.

Spontaneous generation of macroscopic homochirality in soft matter systems by self-assembly of exclusively achiral molecules under achiral conditions is a challenging task with relevance for fundamental scientific research and technological applications. Dark conglomerate phases (DC phases), being optically isotropic mesophases composed of conglomerates of macroscopic chiral domains and formed by some non-chiral bent-core mesogens, represent such a case. Here we report two new series of non-symmetric bent-core molecules capable of forming a new type of mirror symmetry broken DC phases. In the synthesized molecules, a bent 4-bromoresorcinol core is connected to a phenyl benzoate wing and an azobenzene wing with or without additional peripheral fluorine substitution. The self-assembly was investigated by DSC, polarizing microscopy, electro-optical studies and XRD. Chiral and apparently achiral DC phases were observed besides distinct types of lamellar liquid crystalline phases with different degree of polar order, allowing the investigation of the transition from smectic to DC phases. This indicates a process in which increased packing density at first gives rise to restricted rotation and thus to growing polar order, which then leads to chirality synchronization, layer frustration and nano-scale crystallization. Topological constraints arising from the twisted packing of helical conformers in lamellar crystals is proposed to lead to amorphous solids composed of helical nano-crystallites with short coherence length (HNC phases). This is considered as a third major type of DC phases, distinct from the previously known liquid crystalline sponge phases and the helical nano-filament phases (HNF phases). Guidelines for the molecular design of new materials capable of self-assembly into these three types of DC phases are proposed.

Crystal structure, conformation and vibrational characteristics of diethyl 4,4′-disulfanediylbis(6-methyl-2-phenylpyrimidine-5-carboxylate) – A new pharmaceutical cure

The crystal and molecular structures of diethyl 4,4′-disulfanediylbis(6-methyl-2-phenylpyrimidine-5-carboxylate) have been determined by X-ray diffraction and quantum chemical DFT analysis. The title compound crystallizes in orthorhombic Pbca (D2h15) space group, with one molecule in the asymmetric unit. The molecular structure of the studied compound has been determined using the DFT B3LYP/6-311G(2d,2p) approach and compared to that derived from X-ray studies. The IR and Raman spectra have been measured and their wavenumbers have been compared to those calculated for the optimized geometry of the studied compound. The characteristic vibrations of the 4,4′-dithiobispyrimidine N2C4SSC4N2 skeleton have been identified and on this basis the correlation between the disulfide bridge conformation and vibrational data have been discussed.

Crystal Structure and Asymmetric Conformation of a K+ Channel RCK Domain

Regulator of conductance of K+ (RCK) domains govern K+ channel and transporter activity through binding of cytosolic nucleotides or ions, although the locations and ligand-selectivities of activation sites within these domains can vary. To gain further insight toward structures of activation sites and ligand-dependent conformational changes in RCK domains, we solved the crystal structure of the cytosolic RCK domain from a Ca2+-gated K+ channel cloned from Thermoplasma volcanium. Crystals were grown in the presence of Mg2+, an activator of the Thermoplasma K+ channel, and the structure was solved to 2.95 A resolution. The structure was found to contain two RCK domains per asymmetric unit, forming a homodimer. Interestingly, this homodimer was captured in an asymmetric state, and structural alignment of the chains with one another revealed a “hinge” that immediately followed the domain's N-terminal Rossmann fold region. This asymmetry suggested that the RCK dimer might either be in an intermediate, partially-liganded state, or (alternatively) that the asymmetric conformation represents the fully-liganded state. To determine the locations of divalent cation binding sites, the domain was co-crystallized with Ba2+. The Ba2+-bound structure yielded the same asymmetric conformation observed in the Mg2+ co-crystal, and the anomalous difference Fourier map revealed only one Ba2+ binding site, located at the RCK domain dimer interface and thus forming a metal bridge between adjacent subunits. Crystallization of the domain in a four-fold symmetrical “gating ring” form and small-angle X-ray scattering profiles obtained over a range of [Ca2+] are consistent with the idea that formation of the intersubunit metal bridge may drive a conformational change in the gating ring, which in turn may modulate channel gating.

Study of the Incorporation Behavior of L-Leu and D-Leu in L-Val Crystallization

Branched-Chain Amino Acids (BCAAs) are essential amino acids mainly produced through fermentation. With respect to BCAA crystallization, the incorporation behavior of L-form BCAAs as a guest amino acid in the crystallization of L-form BCAAs is well known. However, the incorporation behavior of D-form BCAAs as a guest amino acid in the crystallization of L-form BCAAs is not clear. In this study, we focused on the crystal conformation and incorporation behavior of D-Leucine (D-Leu) and L-leucine (L-Leu) in the crystallization of L-valine (L-Val). Moreover, the difference in the incorporation behavior was investigated on the basis of the distribution ratio of crystals to mother liquor, and the crystal structure and interaction energy were calculated using a molecular dynamics method. The crystal composed of L-Leu in L-Val formed as a solid solution and L-Leu was substituted into the crystal lattice of L-Val. In the case where D-Leu was added as a guest amino acid during L-Val crystallization, D-Leu was not incorporated into the L-Vallattice because the interaction energy between a D-Leu molecule and the L-Val crystal lattice was substantially greater than that between an L-Leu molecule and the L-Val crystal lattice.

Computational study of the binding orientation and affinity of PPARγ agonists: inclusion of ligand-induced fit by cross-docking

A cross-docking study for describing differential binding energies of PPARγ and agonists was successful after the inclusion of protein flexibility through the use of several crystal receptor conformations.

Crystal structures and conformers of CyMe4-BTBP

Abstract The crystal structure of new conformation of the CyMe4-BTBP ligand (ttc) has been presented. The ttt conformer of this compound in a form of THF solvate has been also crystallized. The geometries of six possible conformations (ttt, ttc, tct, tcc, ctc and ccc) of the CyMe4-BTBP ligand have been modeled in the gas phase and in solutions (MeOH and H2O) by DFT calculations using B3LYP/6-31G(d,p) method. According to the calculations, in the three different media the conformers with trans orientation of the N atoms in the bipyridyl moiety are the most stable.

Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation.

Small organic molecules are often flexible, i.e., they can adopt a variety of low-energy conformations in solution that exist in equilibrium with each other. Two main search strategies are used to generate representative conformational ensembles for molecules: systematic and stochastic. In the first approach, each rotatable bond is sampled systematically in discrete intervals, limiting its use to molecules with a small number of rotatable bonds. Stochastic methods, on the other hand, sample the conformational space of a molecule randomly and can thus be applied to more flexible molecules. Different methods employ different degrees of experimental data for conformer generation. So-called knowledge-based methods use predefined libraries of torsional angles and ring conformations. In the distance geometry approach, on the other hand, a smaller amount of empirical information is used, i.e., ideal bond lengths, ideal bond angles, and a few ideal torsional angles. Distance geometry is a computationally fast method to generate conformers, but it has the downside that purely distance-based constraints tend to lead to distorted aromatic rings and sp(2) centers. To correct this, the resulting conformations are often minimized with a force field, adding computational complexity and run time. Here we present an alternative strategy that combines the distance geometry approach with experimental torsion-angle preferences obtained from small-molecule crystallographic data. The torsional angles are described by a previously developed set of hierarchically structured SMARTS patterns. The new approach is implemented in the open-source cheminformatics library RDKit, and its performance is assessed by comparing the diversity of the generated ensemble and the ability to reproduce crystal conformations taken from the crystal structures of small molecules and protein-ligand complexes.

RNA approaches the B-form in stacked single strand dinucleotide contexts.

Duplex RNA adopts an A-form structure, while duplex DNA interconverts between the A- and B-forms depending on the environment. The C2'-endo sugar pucker seen in B-form DNA can occur infrequently in ribose sugars as well, but RNA is not understood to assume B-form conformations. Through analysis of over 45,000 stacked single strand dinucleotide (SSD) crystal structure conformations, this study demonstrates that RNA is capable of adopting a wide conformational range between the canonical A- and B-forms at the localized SSD level, including many B-form-like conformations. It does so through C2'-endo ribose conformations in one or both nucleotides, and B-form-like neighboring base stacking patterns. As chemical reactions on nucleic acids involve localized changes in chemical bonds, the understanding of how enzymes distinguish between DNA and RNA nucleotides is altered by the energetic accessibility of these rare B-form-like RNA SSD conformations. The existence of these conformations also has direct implications in parametrization of molecular mechanics energy functions used extensively to model nucleic acid behavior., 2016. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 65-82, 2016.

Spectroscopic Studies of Dual Fluorescence in 2-((4-Fluorophenyl)amino)-5-(2,4-dihydroxybenzeno)-1,3,4-thiadiazole.

The paper presents results of fluorescence analysis of ionic and nonionic 2-((4-fluorophenyl)amino)-5-(2,4-dihydroxybenzeno)-1,3,4-thiadiazole (FABT) in monocrystals and solutions. We found a single fluorescence band in the case of FABT crystals grown in methanol and dual fluorescence for FABT crystals grown in an aqueous environment. The effect of dual fluorescence was preserved for FABT dissolved in aqueous solutions with pH ranging from 7.5 to 1. In contrast, FABT dissolved in methanol exhibited a single fluorescence band. The dual fluorescence effect is associated with conformational changes in the FABT molecule, which can be induced by aggregation effects. On the basis of crystallographic data, two types of FABT crystal molecule conformations were distinguished. In methanol, FABT molecules are in conformation "S" (the -OH group from the resorcyl ring oriented toward the sulfur atom from the 1,3,4-thiadiazole ring), which a gives single fluorescence band. In water, FABT in conformation "N" (the -OH group from the resorcyl ring oriented toward the nitrogen atom from the 1,3,4-thiadiazole ring due to 180° rotation) has two fluorescence bands. This significant finding implies the possibility of performing a rapid analysis of conformational changes in FABT molecules using fluorescence spectroscopy both in solutions and in biological samples.

Three-Dimensional Conformation of Folded Polymers in Single Crystals.

The chain-folding mechanism and structure of semicrystalline polymers have long been controversial. Solid-state NMR was applied to determine the chain trajectory of (13)C CH3-labeled isotactic poly(1-butene) (iPB1) in form III chiral single crystals blended with nonlabeled iPB1 crystallized in dilute solutions under low supercooling. An advanced (13)C-(13)C double-quantum NMR technique probing the spatial proximity pattern of labeled (13)C nuclei revealed that the chains adopt a three-dimensional (3D) conformation in single crystals. The determined results indicate a two-step crystallization process of (i) cluster formation via self-folding in the precrystallization stage and (ii) deposition of the nanoclusters as a building block at the growth front in single crystals.

γ- and β-Peptide Foldamers from Common Multifaceted Building Blocks: Synthesis and Structural Characterization.

Structural characterization of 3,4-disubstituted γ-peptide and 2,3-disubstituted β-peptide foldamers derived from common multifaceted β-nitromethyl γ-amino acids and the chemical transformation of the β-nitromethyl group in γ-peptides into various functional derivatives are reported. The γ(3,4)-oligomers and α,γ-hybrid peptides showed characteristic C14-and C12-helical conformations in single crystals. Further, the new 2,3-disubstituted acyclic β-peptide showed the C6-helical conformation despite the poor geometry of H-bonds.

Chalcogenated (S)-(−)-nicotine derivatives as chiral linkers for 1D coordination polymers

Reactions of zinc(II) chloride with (S)-(−)-nicotine (Nic), cotinine, thionicotine and selenonicotine in 1:1molar ratio yielded new metal complexes, which were characterized by elemental analysis, infrared, 13C and 1H NMR spectral methods. Single crystal X-ray diffraction studies of ZnCl2 complexes with thionicotine and selenonicotine revealed that the two complexes form isostructural crystals build of 1D coordination polymers (CP) and that coordination to metal centers alters the conformation of the parent organic ligand from syn to anti. Quantum chemical calculations indicate that in the isolated state the anti conformation of the uncoordinated chalcogen nicotine lactams is slightly more preferred energetically and it does not undergo substantial changes upon coordination to the metal center. The preference for the syn conformation in crystals of thio- and selenolactams of nicotine might be ascribed to their involvement in columnar stacking interactions, which do not operate in the isolated state and are also absent in crystals of their adducts with ZnCl2. This study has provided useful information regarding functionalization of (S)-(−)-nicotine molecule as a mixed-donor-atom ligand to enforce formation of 1D coordination polymers.

Sulfonic Acid Salts of Donepezil and Stabilization of Amorphous Donepezil via Formation of Amorphous Salts

Three crystal structures of donepezil salts formed with sulfonic acids were obtained. Interestingly, donepezil-besylate and donepezil-tosylate share similar crystal molecular conformations and crystal packing. On the basis of PXRD patterns, donepezil-mesylate and donepezil-esylate are likely to share similar crystal structures. The sulfonyl hydroxides of all three sulfonic acids form an intermolecular hydrogen bond with the piperidyl amine of donepezil. Solid state characterization showed that the Tg’s of all four amorphous donepezil salts are similar to each other and increase significantly compared to Tg of donepezil. Stability analysis found that the amorphous salts of donepezil formed with mesylate and esylate led to significantly improved physical stability under accelerated stability conditions, but the other donepezil-sulfonic acid salts did not. Solubility data showed that mesylate/esylate salts of donepezil significantly increase the solubility of donepezil that is not shown by other salt forms. Solubility analysis indicated that the solubility of donepezil-mesylate and donepezil-esylate is extremely high compared to that of donepezil-besylate and donepezil-tosylate. We concluded that the extremely high solubility is responsible for delaying the rate of nucleation and thus improving the physical stability of amorphous donepezil. This study highlights that the aqueous solubility of amorphous material is an important factor when considering the physical stability of amorphous material under high relative humidity.