Energetics of Polar Side-Chain Interactions in Helical Peptides:  Salt Effects on Ion Pairs and Hydrogen Bonds†

Biochemistry ◽  
1998 ◽  
Vol 37 (1) ◽  
pp. 33-40 ◽  
Author(s):  
Jeni S. Smith ◽  
J. Martin Scholtz
Keyword(s):  
Hydrogen Bonds ◽  
Ion Pairs ◽  
Side Chain ◽  
Salt Effects ◽  
Helical Peptides

4-(Piperidin-1-yl)pyridinium hexafluorophosphate at 150 K

2003 ◽  
Vol 59 (11) ◽  
pp. o622-o624 ◽  
Author(s):  
Bruce D. James ◽  
Siti Mutrofin ◽  
Brian W. Skelton ◽  
Allan H. White
Keyword(s):  
Hydrogen Bonds ◽  
Structural Characterization ◽  
Title Compound ◽  
Ion Pairs ◽  
Piperidine Ring ◽  
Torsion Angles ◽  
Compound C ◽  
Counter Ions

Structural characterization of the title compound, C10H15N2 +·PF6 −, shows it to be ionic, with the pyridine rather than the piperidine N atom being protonated and forming hydrogen bonds to the counter-ions, resulting in two independent ion pairs. A number of unusual features are noted, in particular the remarkably close inter-ring hydrogen contacts [1.97 (3)–2.00 (3) Å] and the considerable differences in the pair of cations, in respect of the torsion angles within the piperidine ring involving the bonds to either side of the N atom.

Structure, stability and folding of the α-helix

2001 ◽  
Vol 68 ◽  
pp. 95-110 ◽  
Author(s):  
Andrew J. Doig ◽  
Charles D. Andrew ◽  
Duncan A. E. Cochran ◽  
Eleri Hughes ◽  
Simon Penel ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Hydrophobic Interactions ◽  
Data Bank ◽  
Site Directed Mutagenesis ◽  
Model Systems ◽  
Side Chain ◽  
Structure Stability ◽  
Helical Peptides ◽  
Vast Number ◽  
Α Helix

Pauling first described the α-helix nearly 50 years ago, yet new features of its structure continue to be discovered, using peptide model systems, site-directed mutagenesis, advances in theory, the expansion of the Protein Data Bank and new experimental techniques. Helical peptides in solution form a vast number of structures, including fully helical, fully coiled and partly helical. To interpret peptide results quantitatively it is essential to use a helix/coil model that includes the stabilities of all these conformations. Our models now include terms for helix interiors, capping, side-chain interactions, N-termini and 310-helices. The first three amino acids in a helix (N1, N2 and N3) and the preceding N-cap are unique, as their amide NH groups do not participate in backbone hydrogen bonding. We surveyed their structures in proteins and measured their amino acid preferences. The results are predominantly rationalized by hydrogen bonding to the free NH groups. Stabilizing side-chain-side-chain energies, including hydrophobic interactions, hydrogen bonding and polar/non-polar interactions, were measured accurately in helical peptides. Helices in proteins show a preference for having approximately an integral number of turns so that their N- and C-caps lie on the same side. There are also strong periodic trends in the likelihood of terminating a helix with a Schellman or αL C-cap motif. The kinetics of α-helix folding have been studied with stopped-flow deep ultraviolet circular dichroism using synchrotron radiation as the light source; this gives a far superior signal-to-noise ratio than a conventional instrument. We find that poly(Glu), poly(Lys) and alanine-based peptides fold in milliseconds, with longer peptides showing a transient overshoot in helix content.

scholarly journals Diethyl (E)-2,3-bis[(E)-(2-methyl-2-phenylhydrazin-1-ylidene)methyl]but-2-enedioate

2014 ◽  
Vol 70 (6) ◽  
pp. o723-o723
Author(s):  
Peng Liu ◽  
Libin Yuan ◽  
Xiuqing Song ◽  
Hong Yan
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Phenyl Ring ◽  
Side Chain ◽  
Dihedral Angles ◽  
Inversion Symmetry ◽  
Compound C ◽  
Corrugated Sheets ◽  
Major Conformation

The complete molecule of the title compound, C24H28N4O4, is generated by crystallographic inversion symmetry. The ethyl side chain is disordered over two sets of sites in a 0.57 (4):0.43 (4) ratio. The dihedral angles between the methylidene group and the phenyl ring and ester side chain (major conformation) are 7.61 (8) and 86.95 (8)°, respectively. In the crystal, molecules are linkedviaC—H...O hydrogen bonds, forming corrugated sheets lying parallel to (010).

scholarly journals 2-Amino-4-methylpyridinium 4-methoxybenzoate dihydrate

IUCrData ◽  
2017 ◽  
Vol 2 (5) ◽  
Author(s):  
P. Sivakumar ◽  
G. Ezhamani ◽  
S. Israel ◽  
G. Chakkaravarthi
Keyword(s):  
Hydrogen Bonds ◽  
Dihedral Angle ◽  
Ion Pairs ◽  
Three Dimensional ◽  
Water Molecules ◽  
Π Stacking ◽  
Dimensional Network ◽  
Centroid Distance ◽  
Molecular Salt

In the title hydrated molecular salt, C6H9N2+·C8H7O3−·2H2O, the cation is protonated at the pyridine N atom. The cation and anion are linked by a pair of N—H...O hydrogen bonds, which generates anR22(8) loop, and the dihedral angle between their ring planes is 16.07 (14)°. The ion pairs are linked by O—H...O hydrogen bonds involving the water molecules, generating a three-dimensional network. Weak C—H...O and aromatic π–π stacking [centroid-to-centroid distance = 3.5874 (17) Å] interactions are also observed.

scholarly journals Crystal structures of μ-oxalato-bis[azido(histamine)copper(II)] and μ-oxalato-bis[(dicyanamido)(histamine)copper(II)]

2015 ◽  
Vol 71 (11) ◽  
pp. 1379-1383 ◽  
Author(s):  
Chen Liu ◽  
Khalil A. Abboud
Keyword(s):  
Hydrogen Bonds ◽  
Copper Complexes ◽  
Copper Ions ◽  
Side Chain ◽  
Dinuclear Complexes ◽  
Compound I ◽  
Coordination Site ◽  
Oxalate Ligand ◽  
Compound Ii ◽  
Neighboring Molecule

The title compounds, μ-oxalato-κ4O1,O2:O1′,O2′-bis[[4-(2-aminoethyl)-1H-imidazole-κ2N3,N4](azido-κN1)copper(II)], [Cu2(C2O4)(N3)2(C5H9N3)2], (I), and μ-oxalato-κ4O1,O2:O1′,O2′-bis[[4-(2-aminoethyl)-1H-imidazole-κ2N3,N4](dicyanamido-κN1)copper(II)], [Cu2(C2O4)(C2N3)2(C5H9N3)2], (II), are two oxalate-bridged dinuclear copper complexes. Each CuIIion adopts a five-coordinate square-pyramidal coordination sphere where the basal N2O2plane is formed by two O atoms of the oxalate ligand and two N atoms of a bidentate chelating histamine molecule. The apical coordination site in compound (I) is occupied by a monodentate azide anion through one of its terminal N atoms. The apical coordination site in compound (II) is occupied by a monodentate dicyanamide anion through one of its terminal N atoms. The molecules in both structures are centrosymmetric. In the crystals of compounds (I) and (II), the dinuclear complexes are linked through N—H...Xand C—H...X(X= N, O) hydrogen bonds where the donors are provided by the histamine ligand and the acceptor atoms are provided by the azide, dicyanamide, and oxalate ligands. In compound (I), the coordinatively unsaturated copper ions interact with the histamine ligandviaa C—H...Cu interaction. The coordinatively unsaturated copper ions in compound (II) interactviaa weak N...Cu interaction with the dicyanamide ligand of a neighboring molecule. The side chain of the histamine ligand is disordered over three sets of sites in (II).

Supramolecular Liquid-Crystalline Side-Chain Polymers Built through a Molecular Recognition Process by Double Hydrogen Bonds

1995 ◽  
Vol 28 (26) ◽  
pp. 8875-8876 ◽  
Author(s):  
Takashi Kato ◽  
Masahisa Nakano ◽  
Tomonori Moteki ◽  
Toshiyuki Uryu ◽  
Seiji Ujiie
Keyword(s):  
Molecular Recognition ◽  
Hydrogen Bonds ◽  
Liquid Crystalline ◽  
Side Chain ◽  
Recognition Process ◽  
Double Hydrogen

(3aS,5aR,6R,8aR)-3a-Hydroxy-5a-methyl-6-[(1R,2E,4R)-1,4,5-trimethyl-2-hexen-1-yl]-3a,4,5,5a,6,7,8,8a-octahydro-2H-cyclopenta[e]benzofuran-2-one

2007 ◽  
Vol 63 (11) ◽  
pp. o4196-o4196
Author(s):  
Wen-liang Wang ◽  
Hong-wen Tao ◽  
Wei Sun ◽  
Qian-Qun Gu ◽  
Wei-Ming Zhu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Absolute Configuration ◽  
Title Compound ◽  
Optical Rotation ◽  
Side Chain ◽  
Compound C ◽  
Extended Chain ◽  
Halotolerant Fungus ◽  
The Absolute

The title compound, C21H32O3, also known as dimethylincisterol A3, was isolated from halotolerant fungus THW-18. It is composed of three fused rings and a side chain. In the crystal structure, the molecules interact with each other via O—H...O hydrogen bonds, resulting in an extended chain along the b axis. The absolute configuration was assigned from the measured optical rotation and reference to the literature.

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