scholarly journals Controlled protonation of iron–molybdenum cofactor by nitrogenase: a structural and theoretical analysis

2001 ◽  
Vol 355 (3) ◽  
pp. 569-576 ◽  
Author(s):  
Marcus C. DURRANT
Keyword(s):  
Hydrogen Bonding ◽  
Theoretical Analysis ◽  
Proton Transfer ◽  
Water Channel ◽  
Molybdenum Cofactor ◽  
Functional Differences ◽  
Iron Molybdenum Cofactor ◽  
Transfer Channels ◽  
Protein Environment ◽  
Hydrogen Bonded

Qualitative molecular modelling has been used to identify possible routes for transfer of protons from the surface of the nitrogenase protein to the iron–molybdenum cofactor (FeMoco) and to substrates during catalysis. Three proton-transfer routes have been identified; a water-filled channel running from the protein exterior to the homocitrate ligand of FeMoco, and two hydrogen-bonded chains to specific FeMoco sulphur atoms. It is suggested that the water channel is used for multiple proton deliveries to the substrate, as well as in diffusion of products and substrates between FeMoco and the bulk solvent, whereas the two hydrogen-bonded chains each allow a single proton to be added to, and subsequently depart from, FeMoco during the catalytic cycle. Possible functional differences in the proton-transfer channels are discussed in terms of assessment of the protein environment and specific hydrogen-bonding effects. The implications of these observations are discussed in terms of the suppression of wasteful production of dihydrogen by nitrogenase and the Lowe–Thorneley scheme for dinitrogen reduction.

Effects of intermolecular hydrogen bonding on the excited-state proton transfer properties of the cinnamonitrile–methanol complex

2013 ◽  
Vol 91 (3) ◽  
pp. 229-234 ◽  
Author(s):  
Dapeng Yang ◽  
Ruiquan Qi
Keyword(s):  
Hydrogen Bonding ◽  
Excited State ◽  
Charge Transfer ◽  
Proton Transfer ◽  
Density Functional ◽  
Dft Method ◽  
Electronic Energy ◽  
Intermolecular Hydrogen Bonding ◽  
Excited State Proton Transfer ◽  
Hydrogen Bonded

The time-dependent density functional theory (TD-DFT) method was used to study the excited-state proton transfer (ESPT) properties of the hydrogen-bonded cinnamonitrile (3TPAN)–methanol (MeOH) complex (3TPAN–MeOH). The intermolecular hydrogen bonds N1···H11 in both the ground state S0 and the excited state S1 were demonstrated by the optimized geometric structures of the hydrogen-bonded 3TPAN–MeOH complex. While in the excited state S3, a new hydrogen bond H11···O1 was formed after the ESPT took place from the hydrogen-bonded MeOH molecule to the 3TPAN moiety. It was demonstrated that the electronic transitions of the S1 states for both the 3TPAN monomer (including the S3 state) and the hydrogen-bonded 3TPAN–MeOH complex should be of a localized-excited (LE) nature on the 3TPAN molecule, while the S3 state of the hydrogen-bonded 3TPAN–MeOH complex should be of charge transfer (CT) character from the hydrogen-bonded MeOH molecule (through O1···H11) to the 3TPAN moiety. The S3-state proton transfer and charge transfer due to the intermolecular hydrogen-bonding interaction should be the reasons for the remarkable redshift (0.91 eV) of the S3-state electronic energy for the hydrogen-bonded 3TPAN–MeOH complex compared with that of the 3TPAN monomer.

Stabilities in the gas phase of the hydrogen bonded complexes, YC6H4OH-X−, of substituted phenols, YC6E4OH, with the halide anions X− (Cl−, Br−, I−)

1990 ◽  
Vol 68 (11) ◽  
pp. 2070-2077 ◽  
Author(s):  
Gary J. C. Paul ◽  
Paul Kebarle
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Proton Transfer ◽  
Gas Phase ◽  
Equilibrium Constants ◽  
Substituent Effects ◽  
Closed Shell ◽  
Bond Energies ◽  
Substituted Phenols ◽  
Hydrogen Bonded

The equilibria, YPhOH + Br− = YPhOH-Br−, involving 26 differently substituted phenols, were determined with a pulsed high pressure mass spectrometer. The −ΔG0 evaluated from the equilibrium constants represent the hydrogen bond free energies in YPhOH-Br−. These data and data for X− = Cl− and I−, determined previously in this laboratory, are used to examine the substituent effects on the hydrogen bonding. It was found that the hydrogen bond energies in YPhOH-X− increase approximately linearly with the gas phase acidities of the phenols, YPhOH. This is in agreement with earlier observations that showed the bond energies in AH-B−, where AH were oxygen and nitrogen acids and B− closed shell anions, increase with increasing acidity of AH.A detailed analysis of the substituent effects, which is possible for YPhOH-X−, shows that the relationship with the acidity of AH can be divided into two parts. One is the increasing extent of actual proton transfer from AH on formation of the hydrogen bonded complex. Such proton transfer occurs in YPhOH-X− only for the series X− = Cl−. The second effect, which occurs for Cl− and is dominant for Br− and I−, is not directly related to the acidity of the phenols (or AH in general) but depends on a similarity of the substituent effects on the acidity and the stabilization of YPhOH-X− (or AH-B− in general). The dominant contribution to YPhOH-X− stabilization in this case is due to the field effects of the substituents, i.e., π delocalization plays only a small part. Therefore, the correlation with the acidity of YPhOH, where π delocalization is important, is not very close. Keywords: hydrogen bonding, substituent effects, ion–molecule equilibria, stability constants, thermochemistry.

Interaction Site and Proton Transfer Equilibrium in the 4-Aminoantipyrine-Pentachlorophenol Hydrogen–Bonded Adduct

2002 ◽  
Vol 2002 (6) ◽  
pp. 255-256 ◽  
Author(s):  
Moustafa M. Habeeb
Keyword(s):  
Hydrogen Bonding ◽  
Proton Transfer ◽  
Crystalline Form ◽  
Hydrogen Bonding Interaction ◽  
Interaction Site ◽  
Bonding Interaction ◽  
Ft Ir ◽  
C Nmr ◽  
Hydrogen Bonded

The hydrogen-bonding interaction site between 4-aminoantipyrine (4AAP) and pentachlorophenol (PCP) was investigated in the crystalline form using FT-IR and in solution using FT-IR, UV-Vis and 1H,13C NMR spectroscopies.

scholarly journals Intramolecular hydrogen-bonding in a cobalt aqua complex and electrochemical water oxidation activity

2018 ◽  
Vol 9 (10) ◽  
pp. 2750-2755 ◽  
Author(s):  
Juliet F. Khosrowabadi Kotyk ◽  
Caitlin M. Hanna ◽  
Rebecca L. Combs ◽  
Joseph W. Ziller ◽  
Jenny Y. Yang
Keyword(s):  
Hydrogen Bonding ◽  
Proton Transfer ◽  
Water Oxidation ◽  
Intramolecular Hydrogen Bonding ◽  
Aqua Complex ◽  
Oxidation Activity ◽  
Intramolecular Hydrogen ◽  
Hydrogen Bonded

Water oxidation is catalysed in Nature by a redox cofactor embedded in a hydrogen-bonded network designed to orchestrate proton transfer throughout the challenging 4 electron reaction.

scholarly journals Three-dimensional hydrogen-bonded structures in the hydrated proton-transfer salts of isonipecotamide with the dicarboxylic oxalic and adipic acid homologues

2013 ◽  
Vol 69 (10) ◽  
pp. 1192-1195
Author(s):  
Graham Smith ◽  
Urs D. Wermuth
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Adipic Acid ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
Solvent Water ◽  
Hydrated Proton ◽  
Hydrogen Bonded

The structures of the 1:1 hydrated proton-transfer compounds of isonipecotamide (piperidine-4-carboxamide) with oxalic acid, 4-carbamoylpiperidinium hydrogen oxalate dihydrate, C6H13N2O+·C2HO4−·2H2O, (I), and with adipic acid, bis(4-carbamoylpiperidinium) adipate dihydrate, 2C6H13N2O+·C6H8O42−·2H2O, (II), are three-dimensional hydrogen-bonded constructs involving several different types of enlarged water-bridged cyclic associations. In the structure of (I), the oxalate monoanions give head-to-tail carboxylic acid O—H...Ocarboxylhydrogen-bonding interactions, formingC(5) chain substructures which extend alonga. The isonipecotamide cations also give parallel chain substructures through amide N—H...O hydrogen bonds, the chains being linked acrossband downcby alternating water bridges involving both carboxyl and amide O-atom acceptors and amide and piperidinium N—H...Ocarboxylhydrogen bonds, generating cyclicR43(10) andR32(11) motifs. In the structure of (II), the asymmetric unit comprises a piperidinium cation, half an adipate dianion, which lies across a crystallographic inversion centre, and a solvent water molecule. In the crystal structure, the two inversion-related cations are interlinked through the two water molecules, which act as acceptors in dual amide N—H...Owaterhydrogen bonds, to give a cyclicR42(8) association which is conjoined with anR44(12) motif. Further N—H...Owater, water O—H...Oamideand piperidinium N—H...Ocarboxylhydrogen bonds give the overall three-dimensional structure. The structures reported here further demonstrate the utility of the isonipecotamide cation as a synthon for the generation of stable hydrogen-bonded structures. The presence of solvent water molecules in these structures is largely responsible for the non-occurrence of the common hydrogen-bonded amide–amide dimer, promoting instead various expanded cyclic hydrogen-bonding motifs.

Theoretical study of hydrogen bonding interactions in substituted nitroxide radicals

2021 ◽  
Author(s):  
Thufail M. Ismail ◽  
Neetha Mohan ◽  
P. K. Sajith
Keyword(s):  
Hydrogen Bonding ◽  
Interaction Energy ◽  
Electrostatic Potential ◽  
Molecular Electrostatic Potential ◽  
Theoretical Study ◽  
Nitroxide Radicals ◽  
Hydrogen Bonding Interactions ◽  
Bonded Complexes ◽  
Hydrogen Bonded

Interaction energy (Eint) of hydrogen bonded complexes of nitroxide radicals can be assessed in terms of the deepest minimum of molecular electrostatic potential (Vmin).

scholarly journals Isolated iron-molybdenum cofactor of nitrogenase exists in multiple forms in its oxidized and semi-reduced states

1989 ◽  
Vol 264 (4) ◽  
pp. 1924-1927 ◽  
Author(s):  
W E Newton ◽  
S F Gheller ◽  
B J Feldman ◽  
W R Dunham ◽  
F A Schultz
Keyword(s):  
Molybdenum Cofactor ◽  
Multiple Forms ◽  
Iron Molybdenum Cofactor
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