Benchmark calculations of proton affinities and gas-phase basicities of molecules important in the study of biological phosphoryl transfer

2005 ◽  
Vol 7 (16) ◽  
pp. 3070 ◽  
Author(s):  
Kevin Range ◽  
Demian Riccardi ◽  
Qiang Cui ◽  
Marcus Elstner ◽  
Darrin M. York
Keyword(s):  
Gas Phase ◽  
Phosphoryl Transfer ◽  
Proton Affinities ◽  
Gas Phase Basicities

scholarly journals An Assessment of Computational Methods for Calculating Accurate Structures and Energies of Bio-Relevant Polysulfur/Selenium-Containing Compounds

Molecules ◽  
2018 ◽  
Vol 23 (12) ◽  
pp. 3323 ◽  
Author(s):  
Sahar Nikoo ◽  
Paul Meister ◽  
John Hayward ◽  
James Gauld
Keyword(s):  
Inorganic Chemistry ◽  
Bond Length ◽  
Gas Phase ◽  
Electron Correlation ◽  
Negative Charge ◽  
Basis Set ◽  
Proton Affinities ◽  
Selenium Compounds ◽  
Gas Phase Basicities

The heavier chalcogens sulfur and selenium are important in organic and inorganic chemistry, and the role of such chalcogens in biological systems has recently gained more attention. Sulfur and, to a lesser extent selenium, are involved in diverse reactions from redox signaling to antioxidant activity and are considered essential nutrients. We investigated the ability of the DFT functionals (B3LYP, B3PW91, ωB97XD, M06-2X, and M08-HX) relative to electron correlation methods MP2 and QCISD to produce reliable and accurate structures as well as thermochemical data for sulfur/selenium-containing systems. Bond lengths, proton affinities (PA), gas phase basicities (GPB), chalcogen–chalcogen bond dissociation enthalpies (BDE), and the hydrogen affinities (HA) of thiyl/selenyl radicals were evaluated for a range of small polysulfur/selenium compounds and cysteine per/polysulfide. The S–S bond length was found to be the most sensitive to basis set choice, while the geometry of selenium-containing compounds was less sensitive to basis set. In mixed chalcogens species of sulfur and selenium, the location of the sulfur atom affects the S–Se bond length as it can hold more negative charge. PA, GPB, BDE, and HA of selenium systems were all lower, indicating more acidity and more stability of radicals. Extending the sulfur chain in cysteine results in a decrease of BDE and HA, but these plateau at a certain point (199 kJ mol−1 and 295 kJ mol−1), and PA and GPB are also decreased relative to the thiol, indicating that the polysulfur species exist as thiolates in a biological system. In general, it was found that ωB97XD/6-311G(2d,p) gave the most reasonable structures and thermochemistry relative to benchmark calculations. However, nuances in performance are observed and discussed.

scholarly journals Protonated heterocyclic derivatives of cyclopropane and cyclopropanone: classical species, alternate sites, and ring fragmentation

2015 ◽  
Vol 93 (7) ◽  
pp. 708-714 ◽  
Author(s):  
Margarida S. Miranda ◽  
Darío J.R. Duarte ◽  
Joaquim C.G. Esteves da Silva ◽  
Joel F. Liebman
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Computational Study ◽  
Basis Set ◽  
Proton Affinities ◽  
Functional Theory ◽  
Heterocyclic Derivatives ◽  
Gas Phase Basicities ◽  
Derivatives Of

A computational study has been performed for protonated oxygen- or nitrogen-containing heterocyclic derivatives of cyclopropane and cyclopropanone. We have searched for the most stable conformations of the protonated species using density functional theory with the B3LYP functional and the 6-31G(2df,p) basis set. More accurate enthalpy values were obtained from G4 calculations. Proton affinities and gas-phase basicities were accordingly derived.

Gas phase basicities of fluorocarbonyl compounds. An ion cyclotron resonance investigation of the effects of fluorine and trifluoromethyl substituents on hydroxy carbonium ion stabilities

1981 ◽  
Vol 59 (18) ◽  
pp. 2689-2694 ◽  
Author(s):  
C. E. Doiron ◽  
T. B. McMahon
Keyword(s):  
Gas Phase ◽  
Carbonyl Compounds ◽  
Cyclotron Resonance ◽  
Substituent Effects ◽  
Ion Cyclotron Resonance ◽  
Proton Affinities ◽  
Resonance Investigation ◽  
Carbonium Ion ◽  
Hydrogen Bonding Interactions ◽  
Gas Phase Basicities

Gas phase proton affinities for a number of fluoro- and trifluoromethyl-substituted carbonyl compounds have been obtained using a combination of proton transfer equilibria and bracketing experiments. Absolute and relative substituent effects for F and CF3 on carbonyl basicities are determined and discussed in terms of inductive, resonance, polarization, and hydrogen bonding interactions. The data are used to interpolate basicities for HCOF and CF3CHO and are compared to theoretical ab initio calculations.

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