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Bifurcated H-bond systems are common in alpha-helical transmembrane proteins between the backbone amide C=O of residue i as the H-bond acceptor and two H-bond donors from residue i + 4: the backbone amide N−H and a side-chain hydroxyl or thiol H +. The energy preference of the bifurcated H-bond hydroxyl or thiol system is -3.4 kcal/mol or -2. ...
The alpha helix is also commonly called a: Pauling–Corey–Branson α-helix (from the names of three scientists who described its structure); 3.6 13-helix because there are 3.6 amino acids in one ring, with 13 atoms being involved in the ring formed by the hydrogen bond (starting with amidic hydrogen and ending with carbonyl oxygen)
Most importantly, the N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier; this repeated i + 5 → i hydrogen bonding defines a π-helix. Similar structures include the 3 10 helix (i + 3 → i hydrogen bonding) and the α-helix (i + 4 → i hydrogen bonding).
The structure of the molecule of urea is O=C(−NH 2) 2.The urea molecule is planar when in a solid crystal because of sp 2 hybridization of the N orbitals. [8] [9] It is non-planar with C 2 symmetry when in the gas phase [10] or in aqueous solution, [9] with C–N–H and H–N–H bond angles that are intermediate between the trigonal planar angle of 120° and the tetrahedral angle of 109.5°.
In the proposed transition state, one of the thiourea N–H donors is coordinated to the Michael acceptor and will stabilize the negative charge buildup. The basic nitrogen lone pair acts as a hydrogen-bond acceptor to coordinate the nucleophile, but in the transition state acts as a general base to promote the nucleophilic enolate addition.
For example, residue i may form hydrogen bonds to residues j − 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The hydrogen bond arrangement in parallel beta sheet resembles that in an amide ring motif with 11 atoms.
A simple example of a polyatomic ion is the hydroxide ion, which consists of one oxygen atom and one hydrogen atom, jointly carrying a net charge of −1; its chemical formula is O H −. In contrast, an ammonium ion consists of one nitrogen atom and four hydrogen atoms, with a charge of +1; its chemical formula is N H + 4.
Most examples are cationic transition metals complexes with octahedral geometry. Upon complexation, the H−H bond is extended to 0.81–0.82 Å as indicated by neutron diffraction, about a 10% extension relative to the H−H bond in free H 2. Some complexes containing multiple hydrogen ligands, i.e. polyhydrides, also exhibit short H−H contacts.