Crystal and molecular structure of allo-4-hydroxy-L-proline dihydrate

allo-4-Hydroxy-L-proline crystallizes from an aqueous solution as the dihydrate. The crystals are orthorhombic, space group P212121, with a=7.08 (2), b=22.13 (3), c= 5"20 (2) A,. The structure was solved by direct methods and refined by block-diagonal least squares. The final R for 733 observed reflexions is 0.054. The molecule exists as a zwitterion with hydroxyl and carboxyl groups cis to the pyrrolidine ring. The latter is puckered at the fl-carbon atom, which deviates by -0.54 A, from the best plane formed by the four remaining atoms. The molecules are held together by a network of hydrogen bonds, the water molecules playing a dominant role in the stability of the structure.

Crystal and molecular structure of 15-bromolongibornane-8,9-dione

The crystal and molecular structure of the title compound (1) has been determined by the heavy-atom method from 1038 observed three-dimensional photographic data. Crystals are orthorhombic, with a = 20.07 ± 0.02, b= 10.05 ± 0.02, c= 7.31 ± 0.01 Å, space group P212121, with Z= 4. The structure was refined by block diagonal leastsquares to R 0.099. The conformation of the norbornane moiety is discussed. The seven-membered ring portion of the molecule adopts an approximate chair conformation. The packing of the molecules in the crystal is mainly a consequence of van der Waals interactions.

Structural studies of analgesics and their interactions. II. The crystal structure of a 1:1 complex between antipyrine and salicyclic acid (salipyrine)

The complex crystallizes in the space group P21/c with four formula units in a unit cell of dimensions a= 12.747, b= 7.416, c= 17.894 A and/3= 90.2 °. The structure has been solved by the symbolic addition procedure using three-dimensional photographic data and refined to an R value of 0.079 for 2019 observed reflexions. The pyramidal nature of the two hetero nitrogen atoms in the antipyrine molecule is inter:nediate between that observed in free antipyrine and in some of its metal complexes. The molecule is more polar than that in crystals of free antipyrine but less so compared with that in metal complexes. In the salicylic acid molecule, the hydroxyl group forms an internal hydrogen bond with one of the oxygen atoms in the carboxyl group. The association between the salicylic acid and the antipyrine molecules is achieved through an intermolecular hydrogen bond with the other carboxyl oxygen atom in the salicylic acid molecule as the proton donor and the carboxyl oxygen atom of the antipyrine molecule as the acceptor.

Pyridine-1-oxide complexes of lanthanide iodides

Pyridine-1-oxide complexes of lanthanide iodides of the formulaLn(PyO)8I3 whereLn=La, Pr, Nd, Tb, Dy, Er, and Yb have been prepared and characterised by analyses, molecular weight, conductance, infrared and proton NMR data. Proton NMR and IR data have shown the coordination of the ligand to the metal through the oxygen atom of the N–O group. NMR data have been interpreted in terms of a distorted square antiprismatic geometry in solution.

Structure of shock waves in partially ionized argon

The paper presents a unified picture of the structure of steady one-dimensional shock waves in partially ionized argon in the absence of external electric and magnetic fields. The study is based on a two-temperature three-fluid continuum approach using the Navier-Stokes equations as a model and taking account of nonequilibrium ionization. The analysis of the governing equations is based on the method of matched asymptotic expansions and leads to three layers: (1) a broad thermal layer dominated by electron thermal conduction; (2) an atom-ion shock structured by heavy-particle collisional dissipative mechanisms; and (3) an ionization relaxation layer in which electron-atom inelastic collisions dominate.

The nonplanar peptide unit III. Quantum chemical calculations for related compounds and experimental X-ray diffraction data

The possible nonplanar distortions of the amide group in formamide, acetamide, N-methylacetamide, and N-ethylacetamide have been examined using CNDO/2 and INDO methods. The predictions from these methods are compared with the results obtained from X-ray and neutron diffraction studies on crystals of small open peptides, cyclic peptides, and amides. It is shown that the INDO results are in good agreement with observations, and that the dihedral angles N and defining the nonplanarity of the amide unit are correlated approximately by the relation N = -2, while C is small and uncorrelated with . The present study indicates that the nonplanar distortions at the nitrogen atom of the peptide unit may have to be taken into consideration, in addition to the variation in the dihedral angles (,), in working out polypeptide and protein structures.

Studies of phosphazenes. Part I. Reactions of octachlorocyclotetraphosphazatetraene with ethylamine

The reaction of octachlorocyclotetraphosphazatetraene, N4P4Cl8, with ethylamine has been investigated. Seven derivatives, N4P4Cl8–n(NHEt)n[n= 1, 2 (two isomers), 3, 4 (two isomers), and 8] have been isolated and their structures established by 1H and 31P n.m.r. spectroscopy. A non-geminal chlorine atom replacement scheme is observed. Attempts to prepare penta- or hexa-ethylamino derivatives were unsuccessful: only sticky, non-crystalline resins were obtained from 1 : 10 or 1 : 12 reactions. The preparation and n.m.r. spectroscopic data of mixed ethylamino(methoxy)-derivatives. N4P4(NHEt)–8-n(OMe)n[n= 6, 4 (two isomers)], and an ethylamino-(dimethylamino)-derivative, N4P4(NHEt)2(NMe2)6, are generally consistent with the proposed structures. The reaction pattern is discussed.

The perturbational treatment of the process of hydrogen abstraction by ketones

The change in energy during hydrogen abstraction by ketones is estimated for different electronic states as a function of the intermolecular orbital overlap employing perturbation theory. The results suggest that ketones preferentially undergo the in-plane reaction and abstract a hydrogen atom in their triplet nπ* state. For ketones where the triplet ππ* state lies below the triplet nπ* state, hydrogen abstraction can take place in the ππ* state owing to the crossing of the zero order reaction surfaces of the nπ* and ππ* states.

Structure of bis(thiocyanato-N)bis(thiosemicarbazide-N1,S)nickel(II): a redetermination

[Ni(NCS)2(CHsN3S)2], Mr = 356.7, monoclinic, P21/c , a = 5-297 (1), b = 7.869 (1), c - 16-078 (2) A,/3 = 91.53 (1) °, V-= 669.9 A 3, Z= 2, Om = 1"76, Dx = 1"771 g cm -3, A(Mo Ka) = 0-71069 ]k, /.~ = 19"9 cm-l, F(000) = 364, T = 295 K, final R = 0.026 for 1576 significant [F > 10g(F)] reflections. The complex lies on a crystallographic centre of symmetry. The Ni atom is octahedrally coordinated by two thiocyanates (through N atoms) and by two thiosemicarbazide molecules (through hydrazinic N and S atoms). The crystal structure is stabilized by N--H...S hydrogen bonds. Early work on this structure [Garaj & Dunaj-Jurco (1968). Chem. Commun. p. 518] used photographic data and was refined to R = 0-13 for 512 reflections.

Gabapentin: A Stereochemically Constrained gamma Amino Acid Residue in Hybrid Peptide Design

Nature has used the all-alpha-polypeptide backbone of proteins to create a remarkable diversity of folded structures. Sequential patterns of 20 distinct amino adds, which differ only in their side chains, determine the shape and form of proteins. Our understanding of these specific secondary structures is over half a century old and is based primarily on the fundamental elements: the Pauling alpha-helix and beta-sheet. Researchers can also generate structural diversity through the synthesis of polypeptide chains containing homologated (omega) amino acid residues, which contain a variable number of backbone atoms. However, incorporating amino adds with more atoms within the backbone introduces additional torsional freedom into the structure, which can complicate the structural analysis. Fortunately, gabapentin (Gpn), a readily available bulk drug, is an achiral beta,beta-disubstituted gamma amino add residue that contains a cyclohexyl ring at the C-beta carbon atom, which dramatically limits the range of torsion angles that can be obtained about the flanking C-C bonds. Limiting conformational flexibility also has the desirable effect of increasing peptide crystallinity, which permits unambiguous structural characterization by X-ray diffraction methods. This Account describes studies carried out in our laboratory that establish Gpn as a valuable residue in the design of specifically folded hybrid peptide structures. The insertion of additional atoms into polypeptide backbones facilitates the formation of intramolecular hydrogen bonds whose directionality is opposite to that observed in canonical alpha-peptide helices. If hybrid structures mimic proteins and biologically active peptides, the proteolytic stability conferred by unusual backbones can be a major advantage in the area of medicinal chemistry. We have demonstrated a variety of internally hydrogen-bonded structures in the solid state for Gpn-containing peptides, including the characterization of the C-7 and C-9 hydrogen bonds, which can lead to ribbons in homo-oligomeric sequences. In hybrid alpha gamma sequences, district C-12 hydrogen-bonded turn structures support formation of peptide helices and hairpins in longer sequences. Some peptides that include the Gpn residue have hydrogen-bond directionality that matches alpha-peptide helices, while others have the opposite directionality. We expect that expansion of the polypeptide backbone will lead to new classes of foldamer structures, which are thus far unknown to the world of alpha-polypeptides. The diversity of internally hydrogen-bonded structures observed in hybrid sequences containing Gpn shows promise for the rational design of novel peptide structures incorporating hybrid backbones.

Trifurcated (four-center) hydrogen bond in solid state crystal structure of 5'-amino-5'-deoxyadenosine p-toluenesulfonate

The crystal structure of 5'-amino-5'-deoxyadenosine (5'-Am.dA) p-toluenesulfonate has been determined by X-ray crystallographic methods. It belongs to the orthorhombic space group P2(1)2(1)2(1) with a = 7.754(3)Angstrom, b = 8.065(1)Angstrom and c = 32.481(2)Angstrom. This nucleoside side shows a syn conformation about the glycosyl bond and C2'-endo-C3'-exo puckering for the ribose sugar. The orientation of N5' atom is gauche-trans about the exocyclic C4'-C5' bond. The amino nitrogen N5' forms a trifurcated hydrogen bond with N3, O9T and O4' atoms. Adenine bases form A.A.A triplets through hydrogen bonding between N6, N7 and N1 atoms of symmetry related nucleoside molecules.

2-Chloro-8-methoxyquinoline-3-carbaldehyde

In the title compound, C11H8ClNO2, the quinoline fused-ring system is almost planar (r.m.s. deviation = 0.020 angstrom). The formyl group is slightly bent out of the quinoline plane [deviation of the O atom = 0.371 (2) angstrom].

2-[2-(Cyclohexylcarbonyl)phenyl]-1-phenylethanone

The title diketone, C21H22O2, features a phenylene ring having benzoylmethyl and cyclohexanoyl substituents ortho to each other. The cyclohexyl ring adopts a chair conformation with the ketonic group occupying an equatorial position; the four-atom -C(O)-C ketonic unit is twisted out of the plane of the phenylene ring by 34.9 (1)degrees.

Interaction of substrate uridyl 3',5'-adenosine with ribonuclease A:a molecular dynamics study

A wealth of information available from x-ray crystallographic structures of enzyme-ligand complexes makes it possible to study interactions at the molecular level. However, further investigation is needed when i) the binding of the natural substrate must be characterized, because ligands in the stable enzyme-ligand complexes are generally inhibitors or the analogs of substrate and transition state, and when ii) ligand binding is in part poorly characterized. We have investigated these aspects i? the binding of substrate uridyl 3',5'-adenosine (UpA) to ribonuclease A (RNase A). Based on the systematically docked RNase A-UpA complex resulting from our previous study, we have undertaken a molecular dynamics simulation of the complex with solvent molecules. The molecular dynamics trajectories of this complex are analyzed to provide structural explanations for varied experimental observations on the ligand binding at the B2 subsite of ribonuclease A. The present study suggests that B2 subsite stabilization can be effected by different active site groups, depending on the substrate conformation. Thus when adenosine ribose pucker is O4'-endo, Gln69 and Glu111 form hydrogen-bonding contacts with adenine base, and when it is C2'-endo, Asn71 is the only amino acid residue in direct contact with this base. The latter observation is in support of previous mutagenesis and kinetics studies. Possible roles for the solvent molecules in the binding subsites are described. Furthermore, the substrate conformation is also examined along the simulation pathway to see if any conformer has the properties of a transition state. This study has also helped us to recognize that small but concerted changes in the conformation of the substrate can result in substrate geometry favorable for 2',3' cyclization. The identified geometry is suitable for intraligand proton transfer between 2'-hydroxyl and phosphate oxygen atom. The possibility of intraligand proton transfer as suggested previously and the mode of transfer before the formation of cyclic intermediate during transphosphorylation are discussed.

1-(2-Chloroacetyl)-3-methyl-2,6-diphenylpiperidin-4-one

The asymmetric unit of the title compound, C20H20ClNO2, contains two crystallographically independent molecules of similar geometry. The piperidine ring adopts a distorted boat conformation in both molecules, in which the N atom assumes an almost planar configuration.