Faculty Opinions recommendation of Selective stabilization of the chorismate mutase transition state by a positively charged hydrogen bond donor.

2003 ◽  
Author(s):  
Arieh Warshel
Keyword(s):  
Hydrogen Bond ◽  
Transition State ◽  
Chorismate Mutase ◽  
Hydrogen Bond Donor ◽  
Selective Stabilization ◽  
Positively Charged

Structure and activity of the tyrosy1-tRNA synthetase: the hydrogen bond in catalysis and specificity

1986 ◽  
Vol 317 (1540) ◽  
pp. 305-320 ◽  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Transition State ◽  
Binding Site ◽  
Electrostatic Interactions ◽  
Bacillus Stearothermophilus ◽  
Trna Synthetase ◽  
Binding Energies ◽  
Hydrogen Bond Donor ◽  
Differential Binding

The role ofhydrogen bonding in specificity, binding and catalysis by the tyrosyl-tRNA synthetase from Bacillus stearothermophilus has been investigated by systematic mutation of residues which form hydrogen bonds with substrates during the reaction between ATP and tyrosine to form tyrosyl adenylate. Data on hydrogen bonding as a determinant of biological specificity are summarized thus: deletion of an hydrogen-bond donor or acceptor between the enzyme and substrate to leave an unpaired but uncharged acceptor or donor weakens binding by only 2-7 kJ mol -1 ; but deletion to leave an unpaired but charged acceptor or donor weakens binding by some 17 kJ mol -1 or so. Hydrogen bonding is found to have a profound role in catalysis by mediating the differential binding of substrates, transition states and products. The formation of tyrosyl adenylate is not catalysed by classical mechanisms of acid-base or nucleophilic catalysis but the enhancement of rate is solely a result of a combination ofhydrogen bonding and electrostatic interactions which stabilize the transition state of the substrates relative to their ground states. The binding energy of ATP increases by more than 29 kJ mol -1 as it passes through the transition state, enhancing the rate by more than a factor of 10 5 . The residues involved in differential binding are spread over the molecule, away from the seat of reaction. The catalysis is delocalized over the whole binding site and not restricted to one or two specific residues. Some regions of the binding site are complementary in structure to the intermediate, tyrosyl adenylate. The apparent binding energies of certain side chains increase as the reaction proceeds, being weakest in the enzyme—substrate complex, stronger in the enzyme-transition-state complex and strongest in the enzyme-intermediate complex. This converts the unfavourable equilibrium constant for the formation of tyrosyl adenylate in solution to a favourable value for the enzyme-bound reagents and helps sequester the reactive tyrosyl adenylate.

Three Hydrogen Bond Donor Catalysts: Oxyanion Hole Mimics and Transition State Analogues

2012 ◽  
Vol 134 (45) ◽  
pp. 18534-18537 ◽  
Author(s):  
Evgeny V. Beletskiy ◽  
Jacob Schmidt ◽  
Xue-Bin Wang ◽  
Steven R. Kass
Keyword(s):  
Hydrogen Bond ◽  
Transition State ◽  
Hydrogen Bond Donor ◽  
Oxyanion Hole ◽  
Transition State Analogues

Aliphatic Carboxylic Acid as Hydrogen-Bond Donor for Converting CO2 and Epoxide into Cyclic Carbonate under Mild Conditions

2021 ◽  
Author(s):  
Zheng Wang ◽  
Yajun Wang ◽  
Qianjie Xie ◽  
Zhiying Fan ◽  
Yehua Shen
Keyword(s):  
Hydrogen Bond ◽  
Carboxylic Acid ◽  
Value Added ◽  
Cyclic Carbonate ◽  
Hydrogen Bond Donor ◽  
Title Reaction ◽  
Aliphatic Carboxylic Acid ◽  
Mild Conditions ◽  
Atmospheric Carbon

The coupling of CO2 and epoxide is promising way to reduce atmospheric carbon by converting it into value-added cyclic carbonate. Pursuing efficient catalysts is highly attractive for the title reaction....

Role of the hydrogen bond donor component for a proper development of novel hydrophobic deep eutectic solvents

2019 ◽  
Vol 281 ◽  
pp. 423-430 ◽  
Author(s):  
Matteo Tiecco ◽  
Federico Cappellini ◽  
Francesco Nicoletti ◽  
Tiziana Del Giacco ◽  
Raimondo Germani ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Deep Eutectic Solvents ◽  
Hydrogen Bond Donor

Crystal structure of ziprasidone hydrochloride monohydrate, C21H22Cl2N4OS(H2O)

2015 ◽  
Vol 30 (3) ◽  
pp. 192-198
Author(s):  
James A. Kaduk ◽  
Kai Zhong ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Powder Diffraction ◽  
Density Functional ◽  
Minimum Energy ◽  
Strong Hydrogen Bond ◽  
Powder Diffraction File ◽  
X Ray ◽  
Hydrochloride Monohydrate ◽  
Positively Charged

The crystal structure of ziprasidone hydrochloride monohydrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Ziprasidone hydrochloride monohydrate crystallizes in space group P-1 (#2) with a = 7.250 10(3), b = 10.986 66(8), c = 14.071 87(14) Å, α = 83.4310(4), β = 80.5931(6), γ = 87.1437(6)°, V = 1098.00(1) Å3, and Z = 2. The ziprasidone conformation in the solid state is very close to the minimum energy conformation. The positively-charged nitrogen in the ziprasidone makes a strong hydrogen bond with the chloride anion. The water molecule makes two weaker bonds to the chloride, and acts as an acceptor in an N–H⋯O hydrogen bond. The powder pattern is included in the Powder Diffraction File™ as entry 00-064-1492.

Identifying Selective Host–Guest Interactions Based on Hydrogen Bond Donor–Acceptor Pattern in Functionalized Al-MIL-53 Metal–Organic Frameworks

2013 ◽  
Vol 117 (39) ◽  
pp. 19991-20001 ◽  
Author(s):  
Julia Wack ◽  
Renée Siegel ◽  
Tim Ahnfeldt ◽  
Norbert Stock ◽  
Luís Mafra ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Metal Organic Frameworks ◽  
Hydrogen Bond Donor ◽  
Donor Acceptor ◽  
Metal Organic

6,9-Dibromo-2a,10b-diphenyl-2a,5,10,10b-tetrahydro-2H,3H-2,3,4a,10a-tetraazabenzo[g]cyclopenta[cd]azulene-1,4-dione monohydrate

2006 ◽  
Vol 62 (5) ◽  
pp. o1754-o1755
Author(s):  
Neng-Fang She ◽  
Sheng-Li Hu ◽  
Hui-Zhen Guo ◽  
An-Xin Wu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Title Compound ◽  
Supramolecular Structure ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor ◽  
Compound C ◽  
Bifurcated Hydrogen Bond

The title compound, C24H18Br2N4O2·H2O, forms a supramolecular structure via N—H...O, O—H...O and C—H...O hydrogen bonds. In the crystal structure, the water molecule serves as a bifurcated hydrogen-bond acceptor and as a hydrogen-bond donor.

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