scholarly journals Comments on Identification of a hydrogen bond in the Phe-M197→Tyr mutant reaction center of the photosynthetic purple bacterium Rhodobacter sphaeroides by X-ray crystallography and FTIR spectroscopy (FEBS 23044)

FEBS Letters ◽  
2000 ◽  
Vol 477 (3) ◽  
pp. 283-283
Author(s):  
Eliane Nabedryk ◽  
Jacques Breton
Keyword(s):  
Hydrogen Bond ◽  
Ftir Spectroscopy ◽  
Reaction Center ◽  
Rhodobacter Sphaeroides ◽  
Purple Bacterium ◽  
X Ray ◽  
X Ray Crystallography

Identification of a hydrogen bond in the Phe M197→Tyr mutant reaction center of the photosynthetic purple bacterium Rhodobacter sphaeroides by X-ray crystallography and FTIR spectroscopy1

FEBS Letters ◽  
1999 ◽  
Vol 463 (1-2) ◽  
pp. 169-174 ◽  
Author(s):  
Andreas Kuglstatter ◽  
Petra Hellwig ◽  
Günter Fritzsch ◽  
Josef Wachtveitl ◽  
Dieter Oesterhelt ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Reaction Center ◽  
Rhodobacter Sphaeroides ◽  
Purple Bacterium ◽  
X Ray ◽  
X Ray Crystallography

Configurational and conformational studies on condensation products of biogenic amines with 2,5-anhydro-D-mannose

1985 ◽  
Vol 63 (11) ◽  
pp. 2915-2921 ◽  
Author(s):  
Ian M. Piper ◽  
David B. MacLean ◽  
Romolo Faggiani ◽  
Colin J. L. Lock ◽  
Walter A. Szarek
Keyword(s):  
Hydrogen Bond ◽  
Intermolecular Hydrogen Bond ◽  
Direct Methods ◽  
Conformational Studies ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Twist Conformation ◽  
Cell Dimensions ◽  
Internal Hydrogen Bond

The products of a Pictet–Spengler condensation of tryptamine and of histamine with 2,5-anhydro-D-mannose have been studied by X-ray crystallography to establish their absolute configuration. 1(S)-(α-D-Arabinofuranosyl)-1,2,3,4-tetrahydro-β-carboline (1), C16H20N20O4, is monoclinic, P21 (No. 4), with cell dimensions a = 13.091(4), b = 5.365(1), c = 11.323(3) Å, β = 115.78(2)°, and Z = 2. 4-(α-D-Arabinofuranosyl)imidazo[4,5-c]-4,5,6,7-tetrahydropyridine (3), C11H17N3O4, is orthorhombic, P212121 (No. 19), with cell dimensions a = 8.118(2), b = 13.715(4), c = 10.963(3) Å, and Z = 4. The structures were determined by direct methods and refined to R1 = 0.0514, R2 = 0.0642 for 3210 reflections in the case of 1, and to R1 = 0.0312, R2 = 0.0335 for 1569 reflections in the case of 3. Bond lengths and angles within both molecules are normal and agree well with those observed in related structures. In 3 the base and sugar adopt a syn arrangement, which is maintained by an internal hydrogen bond between O(2′) and N(3). The sugar adopts a normal 2T3 twist conformation. The sugar has the opposite anti arrangement in the β-carboline 1 and the conformation of the sugar is unusual; it is close to an envelope conformation with O(4′) being the atom out of the plane. This conformation is caused by a strong intermolecular hydrogen bond from O(5′) in a symmetry-related molecule to O(4′). Both compounds are held together in the crystal by extensive hydrogen-bonding networks. The conformations of the compounds in solution have been investigated by 1H nmr spectroscopy, and the results obtained were compared with those obtained by X-ray crystallography for 1 and 3.

The crystal structure of ethyl-Z-3-amino-2-benzoyl-2-butenoate and measurement of the barrier to E,Z-isomerization

1980 ◽  
Vol 58 (17) ◽  
pp. 1821-1828 ◽  
Author(s):  
Gary D. Fallon ◽  
Bryan M. Gatehouse ◽  
Allan Pring ◽  
Ian D. Rae ◽  
Josephine A. Weigold
Keyword(s):  
Crystal Structure ◽  
Nuclear Magnetic Resonance ◽  
Hydrogen Bond ◽  
Free Energy ◽  
Magnetic Resonance ◽  
Energy Of Activation ◽  
X Ray ◽  
X Ray Crystallography ◽  
Free Energy Of Activation ◽  
Nuclear Magnetic

Ethyl-3-amino-2-benzoyl-2-butenoate crystallizes from pentane as either the E (mp 82–84 °C) or the Z-isomer (mp 95.5–96.5 °C). The E isomer is less stable, and changes spontaneously into the Z, which bas been identified by X-ray crystallography. The structure is characterised by an N–H/ester CO hydrogen bond and a very long C2—C3 bond (1.39 Å). Nuclear magnetic resonance methods have been used to measure the rate of [Formula: see text] isomerization at several temperatures, leading to the estimate that the free energy of activation at 268 K is 56 ± 8 kJ.

scholarly journals Molecular mechanism of ATP versus GTP selectivity of adenylate kinase

2018 ◽  
Vol 115 (12) ◽  
pp. 3012-3017 ◽  
Author(s):  
Per Rogne ◽  
Marie Rosselin ◽  
Christin Grundström ◽  
Christian Hedberg ◽  
Uwe H. Sauer ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Adenylate Kinase ◽  
Function Analysis ◽  
Substrate Selectivity ◽  
Cellular Functions ◽  
X Ray ◽  
Precise Control ◽  
X Ray Crystallography ◽  
The Family ◽  
Atp Analogs

Enzymatic substrate selectivity is critical for the precise control of metabolic pathways. In cases where chemically related substrates are present inside cells, robust mechanisms of substrate selectivity are required. Here, we report the mechanism utilized for catalytic ATP versus GTP selectivity during adenylate kinase (Adk) -mediated phosphorylation of AMP. Using NMR spectroscopy we found that while Adk adopts a catalytically competent and closed structural state in complex with ATP, the enzyme is arrested in a catalytically inhibited and open state in complex with GTP. X-ray crystallography experiments revealed that the interaction interfaces supporting ATP and GTP recognition, in part, are mediated by coinciding residues. The mechanism provides an atomic view on how the cellular GTP pool is protected from Adk turnover, which is important because GTP has many specialized cellular functions. In further support of this mechanism, a structure–function analysis enabled by synthesis of ATP analogs suggests that a hydrogen bond between the adenine moiety and the backbone of the enzyme is vital for ATP selectivity. The importance of the hydrogen bond for substrate selectivity is likely general given the conservation of its location and orientation across the family of eukaryotic protein kinases.

scholarly journals Reactions and interactions between peri-groups in 1-dimethylamino-naphthalene salts: an example of a “through space” amide

2016 ◽  
Vol 88 (4) ◽  
pp. 317-331
Author(s):  
Amélie Wannebroucq ◽  
Andrew P. Jarmyn ◽  
Mateusz B. Pitak ◽  
Simon J. Coles ◽  
John D. Wallis
Keyword(s):  
Hydrogen Bond ◽  
Methyl Ester ◽  
Carbonyl Group ◽  
Dimethylamino Group ◽  
X Ray ◽  
X Ray Crystallography ◽  
Electron Donation ◽  
Protonated Cation

Abstract8-Dimethylaminonaphthalene-1-carbaldehyde reacts readily at 0°C with benzoyl or pivaloyl chloride by O-acylation and formation of a N–C bond (1.566(2)–1.568(3) Å) between the peri-substituents to give a salt. The reaction is promoted by electron donation from the dimethylamino group to the carbonyl group, akin to the properties of an amide. In contrast, the corresponding methyl ester and N,N-diisopropylamide react with acid in ether by protonation of the dimethylamino group and formation of a hydrogen bond to the carbonyl group, while under similar conditions the N,N-dimethylamide undergoes ready hydrolysis to the acid. The structures of products are determined by X-ray crystallography, and from the latter hydrolysis crystals containing zwitterionic 1-dimethylammonium-naphthalene-8-carboxylate and the corresponding O-protonated cation along with dimethylammonium and triflate ions were obtained.

scholarly journals 1-[N-Methyl-N-(Phenyl)amino]-3- (4-Methylphenyl)Thiourea

Molbank ◽  
10.3390/m1052 ◽  
2019 ◽  
Vol 2019 (1) ◽  
pp. M1052 ◽  
Author(s):  
Chien Yeo ◽  
Edward Tiekink
Keyword(s):  
Hydrogen Bond ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Elemental Analysis ◽  
Title Compound ◽  
Molecular Conformation ◽  
Phenyl Hydrazine ◽  
X Ray ◽  
X Ray Crystallography

The title compound, 1-[N-methyl-N-(phenyl)amino]-3-(4-methylphenyl)thiourea (1), was synthesized by the reaction of 1-methyl-1-phenyl hydrazine and 4-tolyl isothiocyanate, and was characterized by spectroscopy (1H and 13C{1H} NMR, IR, and UV), elemental analysis as well as by single crystal X-ray crystallography. In the solid state, the molecule exists as the thioamide tautomer and features an anti-disposition of the thioamide–N–H atoms; an intramolecular N–H⋯N hydrogen bond is noted. The molecular conformation resembles that of the letter L. In the molecular packing, thioamide-N1–H⋯S1(thione) hydrogen bonds lead to centrosymmetric eight-membered {⋯HNCS}2 synthons. The dimers are assembled into a supramolecular layer in the bc-plane by phenyl- and methyl-C–H⋯π(phenyl) interactions.

scholarly journals Charting Hydrogen Bond Anisotropy

2019 ◽  
Author(s):  
Diogo Santos-Martins ◽  
Stefano Forli
Keyword(s):  
Hydrogen Bond ◽  
Chemical Biology ◽  
Solid Phase ◽  
Electronic Configuration ◽  
Interaction Energies ◽  
X Ray ◽  
X Ray Crystallography ◽  
Chemical Groups ◽  
High Degree ◽  
Context Free

<div>Hydrogen bond (HB) is an essential interaction in countless phenomena, and regulates the chemistry of life. HBs are characterized by two main features, strength and directionality, with a high degree of heterogeneity across different chemical groups. These characteristics are dependent on the electronic configuration of the atoms involved in the interaction, which, in turn, is influenced strongly by the molecular environment where they are found. Studies based on the analysis of HB in solid phase, such as X-ray crystallography, suffer from significant biases due to the packing forces. These will tend to better describe strong HBs at the expenses of weak ones, which are either distorted or under represented. Using quantum mechanics (QM), we calculated interaction energies for about a hundred acceptor and donors, in a rigorously defined set of geometries. We performed about 180,000 independent QM calculations, covering all relevant angular components, and mapping strength and directionality in a context free from external biases, with both single-site and cooperative HBs. We show that by quantifying directionality, there is not correlation with strength, and therefore these two components need to be addressed separately. Results demonstrate that there are very strong HB acceptors (e.g.,DMSO) with nearly isotropic interactions, and weak ones (e.g.,thioacetone) with a sharp directional profile. Similarly, groups can have comparable directional propensity, but be very distant in the strength spectrum (e.g., thioacetone and pyridine). These findings have implications for biophysics and molecular recognition, providing new insight for chemical biology, protein engineering, and drug design. The results require rethinking the way directionality is described, with implications for the thermodynamics of HB.</div>

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