Synthesis,spectroscopic and structural elucidation of sympathomimetic amine,tyraminium dihydrogenphosphate

The synthesis, isolation, spectroscopic and structural elucidation of sympathomimetic amine, tyramine dihydrogenphosphate are of interest due to its biological activity and the establishing correlation between spectroscopic properties and structure. The complex approach for investigation included single crystal X-ray diffraction, new technique in linear-polarized IR-spectroscopy in solid state and quantum chemical calculations with a view to predict the electronic structure and vibrational data of interacting species in entitled compound, the correlation structure–spectroscopic properties as well as the influence of intermolecular interaction on IR-characteristic bands are carried out.     

Solution and solid state conformational preferences of a family of cyclic disulphide bridged tetrapeptides

A set of cyclic tetrapeptides of the general form cyclo (Boc‐Cys‐Pro‐ X ‐Cys‐OMe) with X being L‐ / D‐Ala , L‐ / D‐Val , and L‐ / D‐Trp was synthesized. These peptides serve as model systems for structure elucidation in solution and feature a variety of structural motifs — namely a β‐turn with intramolecular hydrogen bonding interactions, cis/trans isomerism, and a disulphide bond. In this work, we performed a comprehensive structural analysis focussing on their β‐turn conformational preferences using NMR, VCD, and Raman spectroscopy. Our results provide evidence for a strong influence of a single stereocenter on the structures of the peptides whereas solvent polarity does not significantly affect them. Additionally, the solid state conformational preferences were studied by crystal structure analysis. Overall, a general trend for the conformational preferences of this set of peptides can be concluded from the results of the complementary investigations.     

Afc can adopt either the fully extended or a turn conformation

Summary We have synthesized by solution methods and fully characterized two sets of terminally protected peptides based on the tricyclic C^α,α-disubstituted glycine Afc. The conformational preferences of the Afc/Gly peptides were examined by FT-IR absorption and¹H NMR techniques, while those of the Afc/TOAC peptides were primarily investigated by using fluorescence spectroscopy. The X-ray diffraction structure of an Afc derivative was also analyzed. The body of solution and crystal-state experimental data conclusively confirms previous findings that the Afc residue may either adopt the fully extended (C₅) or a turn conformation.     

Extensive de novo solid-state NMR assignments of the 33 kDa C-terminal domain of the Ure2 prion

We present the de novo resonance assignments for the crystalline 33 kDa C-terminal domain of the Ure2 prion using an optimized set of five 3D solid-state NMR spectra. We obtained, using a single uniformly ¹³C, ¹⁵N labeled protein sample, sequential chemical-shift information for 74% of the N, Cα, Cβ triples, and for 80% of further side-chain resonances for these spin systems. We describe the procedures and protocols devised, and discuss possibilities and limitations of the assignment of this largest protein assigned today by solid-state NMR, and for which no solution-state NMR shifts were available. A comparison of the NMR chemical shifts with crystallographic data reveals that regions with high crystallographic B-factors are particularly difficult to assign. While the secondary structure elements derived from the chemical shift data correspond mainly to those present in the X-ray crystal structure, we detect an additional helical element and structural variability in the protein crystal, most probably originating from the different molecules in the asymmetric unit, with the observation of doubled resonances in several parts, including entire stretches, of the protein. Our results provide the point of departure towards an atomic-resolution structural analysis of the C-terminal Ure2p domain in the context of the full-length prion fibrils.     

Crystal structure determination of the β-cyclodextrin-p-aminobenzoic acid inclusion complex from powder X-ray diffraction data

The 1:1 inclusion complex of β-cyclodextrin and p-aminobenzoic acid was prepared and characterized by TG-DTA. The crystal structure of the complex was solved directly from powder X-ray diffraction data using the direct space approach and refined using Rietveld refinement techniques. The complex crystallizes in monoclinic P2₁ space group, with unit cell parameters a = 20.7890 ?, b = 10.2084 ?, c = 15.1091 ?, β = 110.825°, V = 2997 ?³. The amino group is located at the wide side of the β-cyclodextrin cavity, forming hydrogen bonds with β-cyclodextrin, and the carboxyl group is located at the narrow side. The crystallographic data obtained from powder diffraction data were compared with the single crystallographic data, and the result shows that solving crystal structure of cyclodextrins inclusion complexes of such complexity is accessible to powder diffractionists to some extent.     

VCD Robustness of the Amide‐I and Amide‐II Vibrational Modes of Small Peptide Models

The rotational strengths and the robustness values of amide‐I and amide‐II vibrational modes of For(AA)_nNHMe (where AA is Val, Asn, Asp, or Cys, n = 1–5 for Val and Asn; n = 1 for Asp and Cys) model peptides with α‐helix and β‐sheet backbone conformations were computed by density functional methods. The robustness results verify empirical rules drawn from experiments and from computed rotational strengths linking amide‐I and amide‐II patterns in the vibrational circular dichroism (VCD) spectra of peptides with their backbone structures. For peptides with at least three residues (n ≥ 3) these characteristic patterns from coupled amide vibrational modes have robust signatures. For shorter peptide models many vibrational modes are nonrobust, and the robust modes can be dependent on the residues or on their side chain conformations in addition to backbone conformations. These robust VCD bands, however, provide information for the detailed structural analysis of these smaller systems. Chirality 27:625–634, 2015 © 2015 Wiley Periodicals, Inc.     

Cα-Methyl, Cα-phenylglycine peptides: A structural study

Summary In order to obtain further information on the role played by phenyl ring position in the C^α-methylated α-amino acid side chain on peptide preferred conformation, the crystal-state structural preferences of C^α-methyl, C^α-phenylglycine peptides have been determined by X-ray diffraction. This study shows that either the fully extended conformation or the β-bend/3₁₀-helical structures are adopted by peptides characterized by this C^α-methylated, β-branched, aromatic α-amino acid.     

Comparison of multiple crystal structures with NMR data for engrailed homeodomain

Two methods are currently available to solve high resolution protein structures—X-ray crystallography and nuclear magnetic resonance (NMR). Both methods usually produce highly similar structures, but small differences between both solutions are always observed. Here the raw NMR data as well as the solved NMR structure were compared to the multiple crystal structures solved for the WT 60 residue three helix bundle engrailed homeodomain (EnHD) and single point mutants. There was excellent agreement between TALOS-predicted and crystal structure-observed dihedral angles and a good agreement for the ³ J(H ^N H ^α ) couplings for the multiple crystal structures. Around 1% of NOEs were violated for any crystal structure, but no NOE was inconsistent with all of the crystal structures. Violations usually occurred for surface residues or for residues for which multiple discreet conformations were observed between the crystal structures. Comparison of the disorder shown in the multiple crystal structures shows little correlation with dynamics under native conditions for this protein.     

Synthesis and crystal structure of a cobalt(II) coordination polymer constructed from 2,6-pyridinedicarboxylate anion and 1,3-bis(4-pyridyl)propane nitrogen ligand

The coordination polymer named {[Co(H₂O)₄(BPP)][Co(dipic)₂]·H₂O}_n (dipic = 2,6-pyridinedicarboxylate and BPP = 1,3-bis(4-pyridyl)propane) has been synthesized by the diffusion method and characterized by thermal analysis, vibrational spectroscopy and single crystal X-ray diffraction analysis. The compound is formed by an one-dimensional polymeric cationic chain, in which the BPP ligands connect the Co2 sites, and an anionic moiety formed by Co1 center and two dipic²⁻ anions. Both crystallographic independent metal sites adopt a distorted octahedral geometry. Co2 center is coordinated by two nitrogen atoms from BPP ligands and four oxygen atoms from aqua ligands, while Co1 center is coordinated by two nitrogen atoms and four oxygen atoms from two dipic²⁻ anions. The cationic and anionic moieties are connected through hydrogen bonding interactions leading to a 3D supramolecular array.     

Cladosporium carrionii and Hormoconis resinae (C. resinae): Cell Wall and Melanin Studies

Two phaeoid strains of the fungus Cladosporium carrionii (SR3 from a xerophyte species and PP8201 from a patient), and one strain of Hormoconis resinae (Cladosporium resinae), isolated from oil-impregnated soil, were analyzed for their cell wall composition by colorimetric methods, X-ray diffraction, infrared spectroscopy, and solid-state ¹³C-nuclear magnetic resonance. Results suggested that the cell walls were composed mainly of hexoses (34%–47%) as β-1,3-glucan (some galactose and mannose were also present) and melanin, chitin being absent. Electron microscopic observations suggested that melanin was found not only in the cell wall but also in intracellular bodies resembling melanosomes.     

Solid-state structure of N-o-, N-m-, and N-p-nitrophenyl-2,3,4-tri-O-acetyl-β-d-xylopyranosylamines

Comprehensive structural analyses were performed for N-o-, N-m-, and N-p-nitrophenyl-2,3,4-tri-O-acetyl-β-d-xylopyranosylamines. Single-crystal X-ray diffraction data were collected and revealed that one compound under investigation undergoes temperature-dependent polymorph transitions (crystal structures of three polymorphs were obtained). The number of molecules in the independent part of the crystal unit cells was in agreement with the number of resonances in solid-state ¹³C NMR spectra. Therefore, the compounds exist as single polymorphs at room temperature, as confirmed by powder X-ray diffraction measurements. Significant differences in ¹³C chemical shifts between solution and solid-state NMR for selected carbon atoms confirmed the existence of intra- and/or intermolecular interactions.     

<Emphasis Type="Italic">N</Emphasis>-Methylation of <Emphasis Type="Italic">N</Emphasis><Superscript>α</Superscript>-Acetylated,Fully C<Superscript>α</Superscript>-Ethylated,Linear Peptides

“Mono-N-methyl scan” is a rational approach for the optimization of the peptide biological properties. N-Methylation of the –CONH– functionality is also a useful tool for discriminating solvent exposed from intramolecularly H-bonded secondary amide groups in peptides. We are currently extending this reaction to linear peptides based on C^α-tetrasubstituted α-amino acids. Following our study on the synthesis and conformation of the mono-N-methylated peptides from C^α-methylated residues, in this work we investigated the N-methylation reaction on homo-peptides to the pentamer level from the C^α-ethylated residue C^α,α-diethylglycine. Under the classical experimental conditions used, exclusively mono-N-methylation (on the N-terminal, acetylated residue) takes place, as unambiguously shown by mass spectrometry, 2D-NMR, and X-ray diffraction techniques. This backbone modification does not seem to involve any significant change in the peptide conformation in the crystalline state. Dedicated to the memory of Prof. Miroslav T. Leplawy (Technical University of Łodz, Poland), who performed the first synthesis of the extremely sterically demanding C^α,α-diethylglycine peptides.     

Preformulation Study of the Inclusion Complex Irbesartan-β-Cyclodextrin

The aim of the present work was to improve the solubility and dissolution profile of Irbesartan (IRB), a poorly water-soluble drug by formation of inclusion complex with β-cyclodextrin (βCD). Phase solubility studies revealed increase in solubility of the drug upon cyclodextrin addition, showing A_L—type of graph with slope less than one indicating formation of 1:1 stoichiometry inclusion complex. The stability constant (K _s) was found to be 104.39 M⁻¹. IRB–βCD binary systems were prepared by cogrinding, kneading using alcohol, kneading using aqueous alcohol, and coevaporation methods. Characterization of the binary systems were carried out by differential scanning calorimetry, Fourier transform infrared spectroscopy, scanning electron microscopy, X-ray diffraction, and proton nuclear magnetic resonance. The dissolution profiles of inclusion complexes were determined and compared with those of IRB alone and physical mixture. Among the various methods, coevaporation was the best in which the solubility was increased and dissolution rate of the drug was the highest. The study indicated the usefulness of cyclodextrin technology to overcome the solubility problem of IRB.     

Synthesis and structural analysis of vinylogous peptides

Summary A Z-orE-ethenyl group has been inserted between the α-carbon and the carboxyl group of the proline residue by stereoselective Horner synthesis. The resulting vinylogous amino acid has been coupled with amino compounds by classical methods, and model amino acid derivatives and dipeptides containing a Z-orE-CH=CMe group have been investigated in solution by¹H-NMR and IR spectroscopy, and in the solid state by X-ray diffraction. TheE-ethenyl group gives rise to an open conformation and the Z-conformer to a folded structure with an intramolecular hydrogen bond closing a ninemembered pseudocycle.     

Determination of absolute configurations by X-ray crystallography and 1H NMR anisotropy

To determine the absolute configurations of chiral compounds, many spectroscopic and diffraction methods have been developed. Among them, X-ray crystallographic Bijvoet method, CD exciton chirality method, and the combination of vibrational circular dichroism and quantum mechanical calculations are of nonempirical nature. On the other hand, X-ray crystallography using a chiral internal reference, and 1H NMR spectroscopy using chiral anisotropy reagents are relative and/or empirical methods. In addition to absolute configurational determinations, preparations of enantiopure compounds are strongly desired. As chiral reagents useful for both the preparation of enantiopure compounds by HPLC separation and the simultaneous determination of their absolute configurations, we have developed camphorsultam dichlorophthalic acid (CSDP acid) for X-ray crystallography and 2-methoxy-2-(1-naphthyl)propionic acid (MalphaNP acid) for 1H NMR spectroscopy. In this review, the principles and applications of these X-ray and NMR methods are explained using mostly our own data.     

Molecular Mechanics Simulations in Structure Analysis of Intercalate VOPO4·2CH3CH2OH

Molecular mechanics simulations using Cerius² combined with X-ray diffraction and supported with vibrational spectroscopy have been used to investigate the layered structure of vanadyl phosphate VOPO₄ intercalated with ethanol. This intercalated structure exhibits certain degree of disorder, which affects the diffraction diagram and obstructs the conventional structure analysis based on diffraction methods only. Present structure analysis is focused to the crystal packing in the interlayer space and layer stacking in the intercalate. The bilayer arrangement of ethanol molecules in the interlayer has been found, giving the basal spacing d = 13.21 Å, experimental d-value obtained from X-ray diffraction is 13.17 Å. One half from the total number of CH₃CH₂OH molecules is anchored with their oxygens to VOPO₄ layers to complete vanadium octahedra and their orientation is not very strictly defined. The second half of ethanoles is linked with hydrogen bridges to the anchored etahanoles and sometimes also to the layer oxygens. Positions and orientations of these unachored ethanoles with respect to VOPO₄ layers exhibit certain degree of disorder, resulting in the disorder in layer stacking. Molecular mechanics simulations revealed the character of this displacement disorder in layer stacking and enabled to determine the components of the displacement vector.     

X-ray absorption and diffraction studies of the metal binding sites in amyloid <Emphasis Type="Italic">β</Emphasis>-peptide

A major source of neurodegeneration observed in Alzheimer’s disease is believed to be caused by the toxicity from reactive oxygen species produced in the brain mediated by the Aβ protein and mainly copper species. An atomic model of an amyloid β-peptide (Aβ) Cu²⁺ complex or at least the structure of the metal binding site is of great interest. Accurate information about the Cu-binding site of Aβ protein can facilitate simulation of redox chemistry using high level quantum mechanics. Complementary X-ray diffraction and X-ray absorption techniques can be employed to obtain such accurate information. This review provides a blend of X-ray diffraction results on amyloid structures and selected works on Aβ Cu²⁺ binding based on spectroscopic measurements with emphasis on the X-ray absorption technique. Australian Society for Biophysics Special Issue: Metals and Membranes in Neuroscience.     

Strontium ranelate changes the composition and crystal structure of the biological bone-like apatite produced in osteoblast cell cultures

We evaluate the effects of strontium ranelate on the composition and crystal structure of the biological bone-like apatite produced in osteoblast cell cultures, a system that gave us the advantage of obtaining mineral samples produced exclusively during treatment. Cells were treated with strontium ranelate at concentrations of 0.05 and 0.5 mM Sr²⁺. Mineral substances were isolated and analyzed by using a combination of methods: Fourier transform infrared spectroscopy, solid-state ¹H nuclear magnetic resonance, X-ray diffraction, micro-Raman spectroscopy and energy dispersive X-ray spectroscopy. The minerals produced in all cell cultures were typical bone-like apatites. No changes occurred in the local structural order or crystal size of the minerals. However, we noticed several relevant changes in the mineral produced under 0.5 mM Sr²⁺: (1) increase in type-B CO₃ ^2? substitutions, which often lead to the creation of vacancies in Ca²⁺ and OH^? sites; (2) incorporation of Sr²⁺ by substituting slightly less than 10 % of Ca²⁺ in the apatite crystal lattice, resulting in an increase in both lattice parameters a and c; (3) change in the PO₄ ^3? environments, possibly because of the expansion of the lattice; (4) the Ca/P ratio of this mineral was reduced, but its (Ca+Sr)/P ratio was the same as that of the control, indicating that its overall cation/P ratio was preserved. Thus, strontium ranelate changes the composition and crystal structure of the biological bone-like apatite produced in osteoblast cell cultures.     

Oriented solids as a colloid suspension in nematic liquid crystal – New tool for IR-spectroscopic and structural elucidation of inorganic compounds and glasses

Possibilities of the linear-polarized infrared (IR-LD) spectroscopy of oriented colloid suspensions in nematic liquid crystals, for structural and local structural elucidation for first time are demonstrated of inorganic compounds and glasses. The advantages of the method for tellurite and borate glasses are shown. The IR-band assignment of the typical local structural units in the glasses are proposed by a comparison with the IR-characteristics of appropriate crystalline analogues as α-TeO₂, V₂O₅, MoO₃ · H₂O and its high temperature form. The IR-spectroscopic characteristics of BO₃, BO₄ and boroxol ring are elucidated, using crystalline β-BaB₂O₄, SrB₄O₇, H₃BO₃ and B₂O₃ as model systems, where the structural moieties have been refined by single crystal X-ray diffraction.