Conformation of the LL and LD hairpin bends with internal hydrogen bonds in proteins and peptides

The conformation of three linked peptide units having an internal 4 → 1 type of hydrogen bond has been studied in detail, and the low energy conformations are listed. These conformations all lead to the reversal of the chain direction, and may therefore be called as “hairpin bends” or “U-bends”. Since this bend can occur at the end of two chains hydrogen-bonded in the antiparallel β-conformation, it is also known as the “β-bend”. Two types of conformation are possible when the residues at the second and third Cα atoms are both of type L (the LL bend), while only one type is possible for the LD and the DL bend. The LL bend can also accommodate the sequences LG, GL, GG (G = glycine), while the LD bend can accommodate the sequences LG, GD and GG. The conformations for the sequences DD and DL are exact inverses (or mirror images) of those for the sequences LL and LD, respectively, and have dihedral angles (phi2, ψ2), (phi3, ψ3) of the same magnitudes, but of opposite signs as those for the former types, which are listed, along with the characteristics (length, angle and energy) of the hydrogen bonds. A comparison of the theoretical predictions with experimental data (from X-ray diffraction and NMR studies) on proteins and peptides, show reasonably good agreement. However, a systematic trend is observable in the experimental data, slightly deviating from theory, which indicates that some deformations occur in the shapes of the peptide units forming the bend, differing from that of the standard planar peptide unit.

The 310 Helical Conformation of the Amino Terminal Decapeptide of Suzukacillin. 270 MHz 'H NMR Evidence for Eight Intramolecular Hydrogen Bonds

The amino terminal suzukacillin decapeptide fragment, Boc-Aib-Pro-Val-Aib-Val-Ala-Aib-Ala-Aib-Aitbh-eO Me, two pentapeptides Boc-AibPrc-Val-AibVal-OMe and Boc-Ala-AibAla-AibAibOMe, and the tripeptide Boc-Ala-AibAibOMe have been studied by 270-MHz 'H NMR spectroscopy. By use of solvent dependence of chemical shifts in a CDC13-(CD3),S0 system and temperature dependence of amide NH chemical shifts in (CD3),S0, the intramolecularly hydrogen bonded NH groups in these peptides have been identified. The tripeptide possesses one hydrogen bond, both pentapeptides show evidence for three intramolecular hydrogen bonds, and the decapeptide has eight NH groups participating in hydrogen bonding. An Ala( 1)-Aib(2) @ turn is proposed for the tripeptide. Both pentapeptides favor 310 helical conformations composed of three consecutive B turns. The decapeptide adopts a 310 helical conformation with some flexibility at the Va1(5)-Ala(6) segment. The proposed conformations are consistent with the known stereochemical preferences of Aib residues.

Growth and physical properties of a new chiral open-framework crystal for NLO applications: Cesium hydrogen l-malate monohydrate

Cesium hydrogen l-malate monohydrate, CsH(C4H4O5)·H2O, is a new chiral open-framework semi-organic crystalline material with a second-harmonic generation efficiency one order of magnitude greater than KDP. Single crystals of this new material have been grown by the conventional slow cooling technique from aqueous solution. Grown crystals display both platy and prismatic morphologies depending on the imposed supersaturation. Hardness values measured using Vickers hardness indenter show considerable anisotropy. The resistivity behavior at room temperature and above, places the crystal between an ionic conductor and a dielectric. The single-crystal SHG efficiency estimated through Maker fringes experiment gives deff which is 4.24 times that of KDP. Single and multiple shot experiments performed on the grown crystals for the fundamental and second harmonic of pulsed Nd:YAG laser (1064 and 532 nm) show that it exhibits a high laser damage threshold which is a favorable property for nonlinear optical applications.

Layer-by-layer self-assembly of modified hyaluronic acid/chitosan based on hydrogen bonding

The fabrication of hydrogen bonded polymer self-assembly for drug delivery has been accomplished via layer-by-layer sequential assembly from aqueous solution. In this study, the self-assembly was constructed based on hydrogen bonding between DNA base (adenine and thymine) pairs substituted on the backbone of chitosan and hyaluronic acid. Chitosan was modified with adenine, whereas hyaluronic acid was modified with thymine. Subsequently, these two polymers were sequentially absorbed on flat substrate by taking advantage of interactions of DNA base pairs via hydrogen bonding. Interlayer hydrogen bonding of these two polymers produces stable multilayer film without using any cross-linking agent. Thin film formation on quartz substrate has been monitored with UV-vis spectra and an AFM study. Formation of multilayer hydrogen-bonded thin film has been further confirmed with SEM. Encapsulation and release behavior of the therapeutic drug from the multilayer thin film at different conditions has been illustrated using UV-vis spectra. Cell viability of modified polymers using MTT assay confirmed no cytotoxic effect.

X-Pro peptides. A theoretical study of the hydrogen bonded conformations of (a-aminoisobutyryl-L -prolyl)n sequences

Intramolecularly hydrogen bonded conformations of (Aib-Pro)n sequences have been analysed theoretically. Both 4�1 (C10 and 3�1 (C7 hydrogen bonded regular structures are shown to be stereochemically feasible. Conformational energies for the helical structures have been estimated using classical potential energy methods. Both C10 and C7 conformations have very similar energies. Pyrrolidine ring puckering has a pronounced effect on the energies, and only Cγ-endo puckered Pro residues can be accommodated. The theoretical calculations using spectroscopic data suggest that the recently proposed novel 310 helical conformation for benzyloxycarbonyl(Aib-Pro)4-methyl ester is in solution, is indeed energetically and stereochemically favourable.

Suprahelical arrangements of hydrogen bonds in peptide helices

Abstract is not available.

Role of magnesium ion on the interaction between chromomycin A3 and deoxyribonucleic acid

Abstract is not available.

1-D hydrogen-bonded organization of hexanuclear {3d-4f-5d} complexes: evidence for slow relaxation of the magnetization for [{LMe2Ni(H2O)Ln(H2O)4.5}2{W(CN)8}2] with Ln = Tb and Dy

Heterometallic {3d-4f-5d} aggregates with formula [{LMe2Ni(H2O)Ln(H2O)4.5}2{W(CN)8}2]·15H2O, (LMe2 stands for N,N-2,2-dimethylpropylenedi(3-methoxysalicylideneiminato) Schiff-base ligand) with Ln = Gd, Tb, Dy, have been obtained by reacting bimetallic [LMe2Ni(H2O)2Ln(NO3)3] and Cs3{W(CN)8} in H2O. The hexanuclear complexes are organized in 1-D arrays by means of hydrogen bonds established between the solvent molecules coordinated to Ln and the CN ligands of an octacyanometallate moiety. The X-ray structure was solved for the Tb derivative. Magnetic behavior indicates ferromagnetic {W–Ni} and {Ni–Ln} interactions (JNiW = 18.5 cm-1, JNiGd = 1.85 cm-1) as well as ferromagnetic intermolecular interactions mediated by the H-bonds. Dynamic magnetic susceptibility studies reveal slow magnetic relaxation processes for the Tb and Dy derivatives, suggesting SMM type behavior for these compounds.

Synthesis of Azo Coupled Crown Ethers Containing Transition Metal and other Chromophoric Environments and Their Ion Complexation Properties

The crown ethers, 2,3-benzo-1,4,7,10,13-pentaoxa-cyclopentadeca-2-ene and 2,3, ll,12-dibenzo-l,4,7,10,13,16-hexaoxscyclooctadeca-2,11-diene are incorporated into H,N'-ethylenebis(acetylacetoneimino) nickel(II) and copper(II), phenol, and β-naphthol by diazo coupling reactions. The selective nature of the coupling reaction has-been demonstrated by the isolation of both asymmetric mono- and symmetric bis(glyoxalarylcrownhydrazoneimino) metal(II) complexes. An interesting binuclear complex containing two intramolecularly rearranged (glyoxal-hydrazonearylimino) metal(II) groups joined by 18-crown-6 result8 when bis(arenediazonium)-18-crown-6 is coupled with the metal(I1) Schiff bases. The substituted ethers form cationic salts with NaClO4, KCNS, NH4CNS, 14g(CNS)2 and Ca(CNS)2. All the synthesised ethers exhibit ion selectivity sequence as K+ > Na+ and Ca2+ > Mg2+.

Conformational characterisation of valinomycin complexation with barium salts:A nuclear magnetic resonance spectroscopic study

Conformations of valinomycin and its complexes with Perchlorate and thiocyanate salts of barium, in a medium polar solvent acetonitrile, were studied using nuclear magnetic resonance spectroscopic techniques. Valinomycin was shown to have a bracelet conformation in acetonitrile. With the doubly charged barium ion, the molecule, at lower concentrations, predominantly formed a 1:1 complex. At higher concentrations, however, apart from the 1:1, peptide as well as ion sandwich complexes were formed in addition to a :final complex:. Unlike the standard 1:1 potassium complex, where the ion was centrally located in a bracelet conformation, the a 1:1 barium complex contained the barium ion at the periphery. The a :final complex: appeared to be an open conformation with no internal hydrogen bonds and has two bound barium ions. This complex was probably made of average of many closely related conformations that were exchanging very fast (on nuclear magnetic resonance time scale) among them. The conformation of the a:final complex a: resembled the conformation obtained in the solid state. Unlike the Perchlorate anion, the thiocyanate anion seemed to have a definite role in stabilising the various complexes. While the conformation of the 1:1 complex indicated a mechanism of ion capture at the membrane interface, the sandwich complexes might explain the transport process by a relay mechanism.

Reactive state selectivity in photodimerization through micellar counter-ion effects: photodimerization of acenaphthylenes

Photodimerization of acenaphthylene and 5,6-dichloroacenaphthylene solubilized in sodium dodecylsulphate (SDS), cetyltrimethylammonium chloride (CTAC), dodecyltrimethylammonium chloride (DTAC), cetyltrimethylammonium bromide (CTAB) and Triton X-100 micelles gives a mixture of cis and trans dimers. The magnitude of the cis:trans ratio is sensitive to the type of micelle used. In CTAB micelles the heavy atom effect of the bromide counter-ions leads to an increased triplet-derived trans dimer yield, whereas in micelles with light atom counter-ions (CTAC, DTAC and SDS) the singlet-derived cis dimer predominates.

The Structure of Monosodium Phosphoenolpyruvate

CDH406P-.Na +.H20 , M r = 208.0, is monoclinic, Cc, a = 11.423 (2), b = 23.253 (5), c - 6.604 (1) A, fl = 123.63 (1) °, U = 1460.6 A 3, D x =. 1.89 Mg m -a, Z = 8, 2(Mo Ka) = 0.7107 A, p(Mo Ka) = 0.44 mm -~, F(000) = 840. Final R = 0.063 for 1697 reflections.The two crystallographically independent molecules of phosphoenolpyruvate (PEP) (A and B) are almost mirror images of each other, the mirror being the planar enolpyruvate group. The torsion angle C(3)-C(2)- O(1)-P(1) is 122.6 in A and -112.0 ° in B, in contrast to -209.1 ° in PEP.K. The enolic C(2)-O(1) has a partial double-bond character [1.401 (A), 1.386A (B)]. The high-energy P~O bond (1.595 and 1.610A) is comparable to that in PEP.K (1.612 A). Na(1) has six nearest neighbours while Na(2) has only five. The Na + ions are involved in binding only the phosphates of different molecules, in contrast to the K ÷ ion in PEP. K, which binds to both the phosphate and carboxyl ends of the same molecule. The planar carboxyl groups stack on each other at an average distance of 3.2 A instead of forming hydrogen-bonded dimers usually found in carboxylate structures.

Structural Crystallography and Crystal Chemistry

CaH406P-.K +, M r = 206.10, is orthorhombic, space group Pbca (from systematic absences), a = 14.538(4), b = 13.364(5), c = 6.880 (6)A, U = 1383.9 A 3, D x = 2.07 Mg m -a, Z = 8, ~.(Mo Ka) = 0.7107/~, p(MO Ka) = 1.015 mm -1. The final R value is 0.042 for a total of 1397 reflections. The high energy P-O(13) and the enolic C(1)-O(13) bonds are 1.612 and 1.374 A respectively. The enolpyruvate moiety is essentially planar. The orientation of the phosphate with respect to the pyruvate group in PEP.K is distinctly different from that in the PEP-cyclohexylammonium salt, the torsion angle C (2)-C (1)-O(13)- P being -209.1 in the former and -90 ° in the latter. The K + ion binds simultaneously to both the phosphate and carboxyl ends of the same PEP molecule. The ester O(13) is also a binding site for the cation. The K + ion is coplanar with the pyruvate moiety and binds to 0(22) and O(13) almost along their lone-pair directions. The carbonyl 0(22) prefers to bind to the K + ion rather than take part in the formation of hydrogen bonds usually observed in carboxylic acid structures.