Linear oligopeptides: 65′. Conformational analysis of the N-protected aromatic α-amino acid N-tert-butyloxycarbonyl-l-phenylalanine by X-ray diffraction and infrared absorption

The X-ray diffraction and i.r. absorption conformational analysis of $\text{N}\text{-tert-butyloxycarbonyl-}\text{l}\text{-phenylalanine}$ has showed the absence of intramolecularly hydrogen-bonded peptide conformations in the solid state. The molecules are held together in rows of ‘cyclic dimer’ motifs through intermolecular NH … OC (acid) and OH … OC {urethane} hydrogen bonds, the secondary amide-like group of the urethane moiety being in the unusual cis conformation, whereas the carboxylic acid group in the common syn conformation. The two molecules in the unit cell present a centrosymmetric set of ?, ψ¹, and ψ² values. In polar solvents solvated species largely predominate. In saturated hydrocarbon solution non-associated and associated (mostly involving the carboxylic acid CO as the proton acceptor) species simultaneously occur. The extent of association decreases with dilution. The amount of intramolecularly hydrogen-bonded oxy-C₇ and C₅ forms if any, should be extremely small. The type of association at saturation seems to differ from that found in the crystalline compound obtained by precipitation with saturated aliphatic hydrocarbons (from a diethyl ether solution).     

Ruthenium(II) complexes derived from 2-(methylamino)pyridine

2-(Methylamino)pyridine reacts with RuCl₂(CO)₃ to give a carbamoyl complex, [$\text{Ru(C(O)N(CH}{}_3\text{)(C}{}_5\text{H}{}_4\text{N}$)Cl(CO)₂], which yields with pyridine (py) and acetylacetone (Hacac), respectively, [$\text{Ru(C(O)N(CH}{}_3\text{)C}{}_5\text{H}{}_4\text{N}$)Cl(CO)₂(py)] and [$\text{Ru(C(O)N(CH}{}_3\text{)C}{}_5\text{H}{}_4\text{N}$)(CO)₂(acac)]. These complexes are characterized spectroscopically. The amino group of the ligand is carbonylated and the resulted carbamoyl ligand is chelating through a pyridine ring-N and a carbamoyl-C atom. 2-Aminopyridine and 2-aminopyrimidine react similarly with RuCl₂(CO)₃ to give the corresponding carbamoyl complexes.     

Studies on the conformations and interactions of elastin. Proton magnetic resonance of the repeating tetramer

Proton magnetic resonance studies at 220 MHz were carried out on synthetic polymers of the repeating tetrapeptide of elastin. Temperature dependence and solvent-mixture dependence of peptide proton chemical shifts were determined for both linear polymers, N-formyl-(Val-Pro-Gly₁-Gly₂)_n-Val OMe where n ? 8 and 40, and for cyclic polymers (Val-Pro-Gly₁-Gly₂)_n, where n = 3 and 4. The Gly₂ NH was found to be solvent shielded. In addition, by studying the polymers Boc-Val-Pro-Gly₁-Gly₂-OH, H-Pro-Gly₁-Gly₂-Val OMe, H(Pro-Gly₁-Gly₂-Val)₃OH, and others, it was demonstrated that the Val C–O immediately preceding the Gly₂ NH in the sequence was required for solvent shielding. Also the Gly₂ NH resonance is found at higher field than the Gly₁ NH resonance. This provides the basis for proposing a β turn in which the Pro and Gly₁ residues form the corners, i.e., residues i + 1 and i + 2, and in which the Gly₂ NH, residue i + 3 hydrogen bonds to the carbonyl of residue i, the Val residue. Studies on methanol–water solvent systems indicated retention of the β turn as a significant conformational feature. This suggests that the β turn occurs in the elastic fiber, which contains about 60% water but which utilizes association of hydrophobic groups as a primary force in fibrogenesis.     

Studies on the metal-amide bond. XX. A structural comparison of an unusual dimeric cobalt(III) complex,fac-[Co2(bpen)3]·12H2O,with the free ligand N,N′-Bis(2′-pyridinecarboxamide)-1,2-ethane,bpenH2

The crystal and molecular structures of the ligand bpenH₂ (N,N′-bis(2′-pyridinecarboxamide)-1,2-ethane) and its deprotonated dimeric cobalt(III) complex fac-[Co₂(bpen)₃]·12H₂O have been determined by single-crystal X-ray diffraction methods. Crystal data: (a) bpenH₂, C₁₄H₁₄N₄O₂, orthorhombic, space group Pccn, a=9.638(1), b= 15.288(1), c = 8.684(1) Å, Z=4; (b) Co₂(bpen)₃· 12H₂O, C₄₂H₆₀N₁₂O₁₈Co₂, triclinic, space group P$\text{1}$, a = 11.128(3), b = 14.316(5), c = 16.466(4) Å, α= 92.02(2)°, β = 95.21(2)°, γ = 99.30(2)°, Z = 2.The structures were refined to R 0.034 and 0.053 for 1064 and 7748 independent reflexions, respectively. The bpenH₂ molecule has a space group imposed centre of symmetry, with the amide group adopting a trans configuration in the closely planar picolinamide moiety. The cobalt complex is dimeric in which three bpen ligands, acting each as a bis(N₂-bidentate), bridge the two metal atoms. Each cobalt atom is octahedral with CoN_py 1.944(3) and Co N_am 1.933(3) Å. The Co··Co separation is 5.493(1) Å. The symmetry of the dimeric molecule is D₃ which is consistent with that indicated from solution NMR studies.     

Preparation and structural characterization of di-μ-azido-bis[azido(2-aminopyridine)aquo]dicopper(II), [Cu(2-ampy)(N3)2(H2O)]2

Di-μ-azido-bis[azido(2-aminopyridine)aquo]dicopper(II), [Cu(2-ampy)(N₃)₂(H₂O)]₂, was synthesized and characterized by X-ray crystallography. The crystals are triclinic, space group P$\text{1}$, with a = 7.142(1), b = 7.812(1), c = 9.727(1) Å, a = 96.52(1), β = 95.52(1), γ = 113.47(1)°, and Z = 1. The structure was refined to R_F = 0.030 for 1960 observed MoKα diffractometer data. The dimeric molecule, which possesses a crystallographic inversion center, contains both terminal and μ(1)-bridging azido groups. Each copper(II) atom is further coordinated by a 2-aminopyridine ligand (via its ring N atom) and a water molecule to give a distorted square pyramid, with the metal atom raised by 0.17 Å above the N₄ basal plane [CuN (ring) = 2.001(2), CuN (azide) = 1.962(3)–2.018(2) Å] towards the apical aquo ligand [CuO = 2.371(2) Å]. Each water molecule forms an intramolecular O?HN (amine) acceptor hydrogen bond, and is linked by two OH?N (terminal azide) intermolecular donor hydrogen bonds to adjacent dimeric complexes to yield a layer structure parallel to (001). Infrared and electronic spectral data are presented and discussed.     

Metal ions in biological systems. vol. XVIII. Circulation of metals in the environment : Edited by Helmut Sigel,Marcel Dekker,New York and Basle, 1984, 397 pp.

The solvent, pressure and temperature dependencies of the lowest energy metal to ligand charge transfer absorption bands were studied for a series of complexes of the type Mo(CO)₄(N$\text{N}$), where N$\text{N}$ = 2,2′-bipyridine, 1,10-phenanthroline and biacetylbis(phenylimine). Throughout the series of complexes the absorption bands shift to shorter wavelength in more polar solvents or on increasing the pressure in a particular solvent, but to longer wavelengths on increasing temperature. These main tendencies can be accounted for in terms of solvent polarity and its dependence on pressure and temperature.     

N(4)-amino-and N(4)-hydroxycytosines as base analogue mutagens

N(4)-Aminocytosine [N(4)NH₂C] and N(4)-amino-2′-deoxycytidine [N(4)NH₂dC] are highly mutagenic for Escherichia coli and phage φ 80 but not for T₄. There is some evidence that they are incorporated into the φ 80 DNA but $\text{[}{}^{14}\text{C}\text{]-N(4)}\text{NH}{}_2\text{C}$ could not be detected in the bacterial DNA.N(4)-Hydroxy-5,6-dihydro-6-hydroxylaminodeoxycytidine (di-NHOH-dC) is mutagenic for φ 80 and E. coli, but N(4)-hydroxydeoxycytidine [N(4)OH-dC] only has a strong inactivating effect.     

Effect of N-alkyl-N,N,N-trimethylammonium ions on phosphatidylcholine model membrane structure as studied by 31P-NMR

The interaction of |C_nH_2n+1N⁺(CH₃)₃| · I^? (n = 3, 6, 9, 12, 14, 16 or 18) with egg-yolk phosphatidylcholine-water dispersions has been studied by ³¹P-NMR spectroscopy. It is shown that the effective anisotropy of ³¹P chemical shift (?Δσ_eff) of the lamellar phospholipid liquid-crystalline phase L_α increases with increasing concentration and alkyl chain length of the drug. Addition of $\text{|}\text{C}{}_6\text{H}{}_{13}\text{N}{}^{\mathrm{+}}\text{(CH}{}_3\text{)}{}_3\text{| ·I}{}^{\mathrm{?}}$ or |C₉H₁₉N⁺(CH₃)₃|·I^? to the phospholipid-water dispersion at a molar ratio ammonium salt:phospholipid > 0.8 induces in the dispersion a structure with an effective isotropic phospholipid motion. This structure is unstable and slowly transforms into the hexagonal phase. These effects have not been observed in phospholipid-water dispersions mixed with the ammonium derivatives with the longer alkyl chains n  12, 14, 16 or 18. It is proposed that these results might explain the effects of the investigated drugs on the nerve, muscle and bacterial cells.     

Acylated des-(Ala1-Gly2)-somatostatin analogs: prolonged inhibition of growth hormone secretion

The following eight analogs of somatostatin were synthesized by solid phase: des-[Ala¹-Gly²]-somatostatin (I); des-[Ala¹-Gly²]-H₂somatostatin (II); $\text{N}$-acetyl-Cys³-somatostatin (III); $\text{N}$-acetyl-Cys³-H₂somatostatin (IV); $\text{N}$-pyvalyl-Cys³-H₂somatostatin (V); $\text{N}$-acrylyl-Cys³-H₂somatostatin (VI); $\text{N}$-benzoyl-Cys³-H₂somatostatin (VII); $\text{N}$-hexanoyl-Cys³-H₂somatostatin (VIII). Deletion of the N-terminal dipeptide Ala¹-Gly² is compatible with high biological activity. A single s.c. injection of these analogs as a microsuspension in saline inhibits for 24–72 hours (depending on the compound) the secretion of growth hormone normally stimulated in rats by pentobarbital.     

Hydrogen bonds in the tripeptide Pro-Leu-Gly-NH217O and 1H studies

¹⁷ONMR measurements of labeled Pro-Leu-Gly-NH₂ were carried out at different pH levels and in mixed solvents of water/acetonitrile. Complementary studies of the amide protons were carried out in acetonitrile-d₃. Only the prolyl $\text{C}\text{=}{}^{17}\text{O}$ group was sensitive to the pH level. Protonation of the amine group resulted in an upfield chemical shift of 18 ppm. The chemical shifts of each of the three oxygen sites was sensitive to the ratio water: acetonitrile. Solvent composition dependence of the chemical shift and linewidth suggests that the prolyl $\text{C}\text{=}{}^{17}\text{O}$ is involved in intramolecular hydrogen bond formation when Pro-Leu-Gly-NH₂ is dissolved in acetonitrile, while in water there is no intramolecular H bond.     

Comformation and absolute configuration of -methyllanthionine

If the bicyclic peptide ring proposed by Gross $\text{et}$$\text{al}$. (1,2) does in fact exist in nisin and related antibiotics, then the unusual β-methyllanthionine component must be significantly distorted from its conformation in the free state, as determined by x-ray structure analysis. The torsion angles about the SC_β bonds are 50–100° from the torsion angles in models of the sulfur-bridged peptide ring proposed for nisin. The chirality of the methylated β-carbon atom is (S). The conformation of the amino acid differs from that of $\text{meso}$-lanthionine only by a 180° rotation of a carboxyl group about the $\text{C}{}_{\mathrm{\alpha }}{}^{\mathrm{D}}\text{C}{}_{\mathrm{\beta }}\text{(CH}{}_3\text{)}$ bond.     

Type I and II β-turns prediction using NMR chemical shifts

A method for predicting type I and II β-turns using nuclear magnetic resonance (NMR) chemical shifts is proposed. Isolated β-turn chemical-shift data were collected from 1,798 protein chains. One-dimensional statistical analyses on chemical-shift data of three classes β-turn (type I, II, and VIII) showed different distributions at four positions, (i) to (i + 3). Considering the central two residues of type I β-turns, the mean values of C_ο, C_α, H_N, and N_H chemical shifts were generally (i + 1) > (i + 2). The mean values of C_β and H_α chemical shifts were (i + 1) < (i + 2). The distributions of the central two residues in type II and VIII β-turns were also distinguishable by trends of chemical shift values. Two-dimensional cluster analyses on chemical-shift data show positional distributions more clearly. Based on these propensities of chemical shift classified as a function of position, rules were derived using scoring matrices for four consecutive residues to predict type I and II β-turns. The proposed method achieves an overall prediction accuracy of 83.2 and 84.2 % with the Matthews correlation coefficient values of 0.317 and 0.632 for type I and II β-turns, indicating that its higher accuracy for type II turn prediction. The results show that it is feasible to use NMR chemical shifts to predict the β-turn types in proteins. The proposed method can be incorporated into other chemical-shift based protein secondary structure prediction methods.     

X-ray structure of a mono(1-methylthyminato) complex of cisplatin,chloro-(1-methylthyminato-N3)-cis-diammineplatinum(II) monohydrate

The crystal structure of chloro-(1-methyltyminato- N3)-cis-diammineplatinum(II) monohydrate, cis- (NH₃)₂Pt(C₆H₇N₂O₂)Cl·H₂O, is reported. The compound crystallizes in space group P$\text{1}$ with a = 6.911(2) Å, b = 8.598(3) Å, c = 11.464(4) Å, α = 100.13(3)°, β = 120.03(3)°, γ = 93.16(3)°, Z = 2. The structure was refined to R = 0.048 and R_w = 0.057. The compound contains the deprotonated 1-methylthymine ligand coordinated to Pt through N3 (1.973(10) Å). This distance represents the shortest Pt-N3(pyrimidine-2.4-dione) bond reported so far. The two PtNH₃ bond lengths differ significantly: PtNH₃ (trans to Cl) is longer (2.052(10) Å) than PtNH₃ (trans to N3 of 1-MeT) (2.002(11) Å). The PtCl distance (2.326(3) Å) is normal, as is the large dihedral angle between the Pt coordination plane and the nucleobase (76.5°).     

Crystal structure of [chloro(diethyldithiocarbamato)butyl phenyl]tin(IV)

The crystal structure of the title compound, SnCl(C₆H₅)(C₄H₉)[S₂CN(C₂H₅)₂], was determined and refined to an R factor of 3.2% for 4876 reflections. The molecule contains five-coordinate tin in a distorted trigonal bipyramidal arrangement with the tin atom lying 0.20 Å below the equatorial plane formed by one of the sulphur atoms, S(1), and the donor carbons of the butyl and phenyl groups. The chlorine and the other sulphur atom, S(2), occupy axial sites, making a S(2)SnCl angle of 156.85(1)°. The SnS(2) bond is markedly elongated (2.764(1) Å) compared to the SnCl bond (2.449(1) Å) and the SnS(1) bond (2.454(1) Å). The structure resembles those of analogues such as (C₆H₅)₂Sn(glygly) in having both hydrocarbon ligands located in the equatorial plane. Crystal data: space group P$\text{1}$: a = 8.291(2) Å, b = 14.726(3) Å, c = 9.509(2) Å, α = 96.24(2)°, β = 107.02(3)°, γ = 116.70(2)°, Z = 2, R = 3.2% for 4876 independent reflections.     

Respiration-driven proton translocation with nitrite and nitrous oxide in Paracoccus denitrificans

(1) $\text{H}$⁺/electron acceptor ratios have been determined with the oxidant pulse method for cells of denitrifying Paracoccus denitrificans oxidizing endogenous substrates during reduction of O₂, NO^?₂ or N₂O. Under optimal H⁺-translocation conditions, the ratios $\text{H}{}^{\mathrm{+}}\text{O}$, $\text{H}{}^{\mathrm{+}}\text{N}{}_2\text{O}$, $\text{H}{}^{\mathrm{+}}\text{NO}{}^{\mathrm{?}}{}_2$ for reduction to N₂ and $\text{H}{}^{\mathrm{+}}\text{NO}{}^{\mathrm{?}}{}_2$ for reduction to N₂O were 6.0–6.3, 4.02, 5.79 and 3.37, respectively. (2) With ascorbate/N,N,N′,N′-tetramethyl-p-phenylenediamine as exogenous substrate, addition of NO^?₂ or N₂O to an anaerobic cell suspension resulted in rapid alkalinization of the outer bulk medium. $\text{H}{}^{\mathrm{+}}\text{N}{}_2\text{O}$, $\text{H}{}^{\mathrm{+}}\text{NO}{}^{\mathrm{?}}{}_2$ for reduction to N₂ and $\text{H}{}^{\mathrm{+}}\text{NO}{}^{\mathrm{?}}{}_2$ for reduction to N₂O were ?0.84, ?2.33 and ?1.90, respectively. (3) The $\text{H}{}^{\mathrm{+}}\text{oxidant}$ ratios, mentioned in item 2, were not altered in the presence of $\text{valinomycin}\text{K}{}^{\mathrm{+}}$ and the triphenylmethylphosphonium cation. (4) A simplified scheme of electron transport to O₂, NO^?₂ and N₂O is presented which shows a periplasmic orientation of the nitrite reductase as well as the nitrous oxide reductase. Electrons destined for NO^?₂, N₂O or O₂ pass two H⁺-translocating sites. The $\text{H}{}^{\mathrm{+}}\text{electron}$ acceptor ratios predicted by this scheme are in good agreement with the experimental values.     

A CD and an nmr study of multiple bradykinin conformations in aqueous trifluoroethanol solutions

CD and nmr studies have been carried out on aqueous trifluoroethanol (TFE) solutions of bradykinin (BK) and a bradykinin antagonist. The CD results exhibit a striking effect of TFE on the spectra of BK, with sequence Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg, and the BK antagonist, with sequence D -Arg-Arg-Pro-Hyp-Gly-Thi-D -Ser-D -Cpg-Cpg-Arg [where Hyp is 4-hydroxy-L -proline; Thi refers to β-(2-thienyl)-L -alanine and Cpg refers to α-cyclopentylglycine]. The effect of increasing concentration of TFE in water on the difference ellipticity at 222 nm was examined and showed that BK may be a mixture of at least two different conformers, one of which largely forms when the TFE concentration is increased beyond 80%. The linear extrapolation of 100% of the difference ellipticity of BK at low TFE concentrations yields a value in agreement with that shown by the BK antagonist, indicating that the conformation of BK at the lower TFE concentrations is similar to that of the BK antagonist. The conformational analysis was carried out using both one-dimensional and two-dimensional ¹H-nmr techniques. The total correlation spectroscopy (TOCSY) spectrum of BK in a 60/40% (v/v) TFE/H₂O solution at 10°C and a nuclear Overhauser effect spectroscopy (NOESY) spectrum that shows only sequential H_α(i) – NH(i + 1) or the H_α(i) – H_δδ′(i + 1) NOEs indicate that the majority of the molecules adopt an all-trans extended conformation. The TOCSY for BK in the 95/5% (v/v) TFE/H₂O solution shows that there are two major conformations in the solution with about equal population. The NOESY experiment shows two new important cross peaks for one conformation, namely Pro²(α)-Pro³ (α) and the Pro²(α)-Gly⁴(NH), indicating a cis Pro²-Pro³ bond and a type VI β-turn between residues Arg¹ and Gly⁴ involving cis proline at position 3, respectively. The low temperature coefficient of Gly⁴ for this conformation suggests the presence of an intramolecular hydrogen bond, therefore a type VIa β-turn is present. The other conformation is all trans and extended. The BK antafonist shows difference CD spectra in TFE solutions referred to H₂O that are superficially indicative of a β-bend. However, nmr speaks against this possibility, as only one set of peaks were observed in the TOCSY and NOESY experiments, indicating an all-trans extended confirmation over the range of TFE concentrations. The BK-antagonist CD data suggest that solvent perturbation of the CD of an extended confirmation perturbation of the optical activity of the thienyl moiety of the peptide since the CD spectrum of N-acetyl-β-thienyl-L -alanine N-methylamide is strongly perturbed by TFE. The present results again demonstrate the complementary relationship between CD and nmr. © 1994 John Wiley & Sons, Inc.