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Styrene energetics and characterization of its conjugate base: An example of isotopic labeling gone awry
, Article International Journal of Mass Spectrometry ; 2016 ; 13873806 (ISSN) ; Lis, L ; Kass, S. R ; Sharif University of Technology
Elsevier
Abstract
The equilibrium acidity of styrene was measured (δH°acid(PhCHCH2)=390.6±0.5kcalmol-1) and its deprotonation site was revised from the ortho position on the aromatic ring to the α-hydrogen atom based upon deuterium-labeling studies and extensive computations. Somewhat surprisingly, the nature of the anionic base plays a critical role in properly determining the ionization site and avoiding misleading results due to extraordinary hydrogen-deuterium exchange. Bracketing the electron affinity of α-styryl radical (PhC CH2, 23.1±3.4kcalmol-1) enabled the α-CH bond dissociation energy (100.1±3.4kcalmol-1) of styrene and the effect of a phenyl substituent at an sp2-hybridized carbon to be...
Styrene energetics and characterization of its conjugate base: An example of isotopic labeling gone awry
, Article International Journal of Mass Spectrometry ; Volume 413 , 2017 , Pages 163-167 ; 13873806 (ISSN) ; Lis, L ; Kass, S. R ; Sharif University of Technology
Elsevier B.V
2017
Abstract
The equilibrium acidity of styrene was measured (ΔH°acid(PhCH[dbnd]CH2) = 390.6 ± 0.5 kcal mol−1) and its deprotonation site was revised from the ortho position on the aromatic ring to the α-hydrogen atom based upon deuterium-labeling studies and extensive computations. Somewhat surprisingly, the nature of the anionic base plays a critical role in properly determining the ionization site and avoiding misleading results due to extraordinary hydrogen–deuterium exchange. Bracketing the electron affinity of α-styryl radical (PhC[rad][dbnd]CH2, 23.1 ± 3.4 kcal mol−1) enabled the α-C[sbnd]H bond dissociation energy (100.1 ± 3.4 kcal mol−1) of styrene and the effect of a phenyl substituent at an...
Phenylcyclopropane energetics and characterization of its conjugate base: Phenyl substituent effects and the C-H bond dissociation energy of cyclopropane
, Article Journal of Organic Chemistry ; Volume 81, Issue 19 , 2016 , Pages 9175-9179 ; 00223263 (ISSN) ; Lis, L ; Kass, S. R ; Sharif University of Technology
American Chemical Society
Abstract
The α-C-H bond dissociation energy (BDE) of phenylcyclopropane (1) was experimentally determined using Hess' law. An equilibrium acidity determination of 1 afforded ΔH°acid = 389.1 ± 0.8 kcal mol-1, and isotopic labeling established that the α-position of the three-membered ring is the favored deprotonation site. Interestingly, the structure of the base proved to be a key factor in correctly determining the proper ionization site (i.e., secondary amide ions are needed, and primary ones and OH- lead to incorrect conclusions since they scramble the deuterium label). An experimental measurement of the electron affinity of 1-phenylcyclopropyl radical (EA = 17.5 ± 2.8 kcal mol-1) was combined...
Carbon dioxide reforming of methane by pulsed glow discharge at atmospheric pressure: the effect of pulse compression
, Article Journal of Applied Physics ; Volume 101, Issue 12 , 2007 ; 00218979 (ISSN) ; Modarresi, H ; Sharif University of Technology
2007
Abstract
Methane reforming by carbon dioxide in pulsed glow discharge at atmospheric pressure is examined. The plasma pulse is compressed to less than 50 ns. This compression enables one to work at higher frequencies, over 3 kHz, without glow-arc transition. The main products of the reaction are synthetic gases (H2, CO) and C2 hydrocarbons. Approximately 42% of plasma energy goes to the chemical dissociation, when the reactant ratio is C O2 C H4 =1. At this point, the energy expense is less than 3.8 eV per converted molecule while reactant conversions are relatively high reaching to 55% (C H4) and 42% (C O2). The reactor energy performance even gets better at higher C O2 C H4 ratios. While energy...
The formation and dissociation energy of vacancies in cementite: A first-principles study
, Article Nuclear Instruments and Methods in Physics Research, Section B: Beam Interactions with Materials and Atoms ; Volume 502 , 2021 , Pages 157-163 ; 0168583X (ISSN) ; Amirhossein Feghhi, S ; Samadfam, M ; Sharif University of Technology
Elsevier B.V
2021
Abstract
Because of the possibility of various types of vacancies in cementite due to its crystalline structure, the focus of this paper was only on vacancies. In this regard, the formation energies of single, two, three and four vacancies of over than 120 different cases were calculated using first-principles method. For the case of single vacancy, the results were in three values of ~1.63, 1.39 and 0.78 eV according to iron vacancies at general positions, iron vacancies located on mirror planes and carbon vacancies in the interstitial positions, respectively. The results for the case of two, three and four vacancies were between from 2.10 to 3.34 eV, from 3.92 to 5.10 eV and from 4.77 to 6.33 eV,...
Theoretical investigation on antioxidant activity of bromophenols from the marine red alga Rhodomela confervoides: H-atom vs electron transfer mechanism
, Article Journal of Agricultural and Food Chemistry ; Volume 61, Issue 7 , 2013 , Pages 1534-1541 ; 00218561 (ISSN) ; Javan, M. J ; Tehrani, Z. A ; Sharif University of Technology
2013
Abstract
Bromophenols are known as antioxidant radical scavengers for some biomolecules such as those in marine red alga. Full understanding of the role played by bromophenols requires detailed knowledge of the radical scavenging activities in probable pathways, a focus of ongoing research. To gain detailed insight into two suggested pathways, H-atom transfer and electron transfer, theoretical studies employing first principle quantum mechanical calculations have been carried out on selected bromophenols. Detailed investigation of the aforementioned routes revealed that upon H-atom abstraction or the electron transfer process, bromophenols cause an increase in radical species in which the unpaired...
, M.Sc. Thesis Sharif University of Technology ; Fattahi, Alireza (Supervisor)
Abstract
It is believed that intramolecular hydrogen bonding and also conjugation can affect the acidity power of organic molecules. But simultaneous effects of intramolecular hydrogen bonding and conjugation have not investigated systematically yet. In this project, we choose Ascorbic acid as a basic structure. Then we have changed its structure conveniently, and have explored the roles of hydrogen bonding and conjugation on the acidity of this molecule by using B3LYP functional with the 6-311++G(d,p) basis set. After that we similarly investigate these effects on the acidity of three different systems, including enols, enamines and alcohols. In this project we probe the effect of different hydrogen...
Electrostatically defying cation-cation clusters: Can likes attract in a low-polarity environment?
, Article Journal of Physical Chemistry A ; Volume 117, Issue 38 , 2013 , Pages 9252-9258 ; 10895639 (ISSN) ; Ramezani, M ; Fattahi, A ; Kass, S. R ; Sharif University of Technology
2013
Abstract
Like-charge ion pairing is commonly observed in protein structures and plays a significant role in biochemical processes. Density functional calculations combined with the conductor-like polarizable continuum model were employed to study the formation possibilities of doubly charged noncovalently linked complexes of a series of model compounds and amino acids in the gas phase and in solution. Hydrogen bond interactions were found to offset the Coulombic repulsion such that cation-cation clusters are minima on the potential energy surfaces and neither counterions nor solvent molecules are needed to hold them together. In the gas phase the dissociation energies are exothermic, and the...
Bonding, structural and thermodynamic analysis of dissociative adsorption of H3O+ ion onto calcite (10 1 ¯ 4) surface: CPMD and DFT calculations
, Article Journal of Molecular Modeling ; Volume 23, Issue 12 , 2017 ; 16102940 (ISSN) ; Koleini, M. M ; Sharif University of Technology
Abstract
We used density functional theory (DFT) and Car-Parrinello molecular dynamics (CPMD) simulation to investigate the adsorption and bond formation of hydronium ion (H3O+) onto a (10 1 ¯ 4) calcite surface. For surface coverage of 25% to 100%, the nature of H3O+ interaction was explored through electron density and energetics in the context of bond critical points. The adsorbate–adsorbent structure was studied by simulation of pair correlation function. The results revealed that dissociation into water molecule(s) and proton(s) complements H3O+ ion(s) adsorbtion. The H2O molecule adsorbs onto the surface via its O atom, and interacts with surface calcium in a closed-shell mode; the H+ ion makes...
Gold at crossroads of radical generation and scavenging at density functional theory level: Nitrogen and oxygen free radicals versus their precursors in the face of nanogold
, Article Journal of Physical Organic Chemistry ; Volume 34, Issue 1 , 2021 ; 08943230 (ISSN) ; Kassaee, M. Z ; Ayoubi Chianeh, M ; Fattahi, A ; Sharif University of Technology
John Wiley and Sons Ltd
2021
Abstract
In our previous report (J. Phys. Org. Chem., 2017), we discussed the dual behavior of gold nanocluster (Au3 NC), where it scavenged reactive oxygen species (ROS) while promoted their generation to a lesser extent. Continuing this quest, we investigate the effects of Au3 NC on common reactive nitrogen species (RNS: O=N˙ and O=N-O) and their precursors (O=N-H and O=N-O-H, respectively), at B3LYP/LACVP+* level of theory. We compare the results with those of prevalent ROS (H-O˙ and H-O-O˙) and their precursors (H-O-H and H-O-O-H, respectively). To this end, various parameters are probed such as binding energy (Eb), bond dissociation energy (BDE), bond lengths, Mullikan spin density (MSD),...
Gold at crossroads of radical generation and scavenging at density functional theory level: Nitrogen and oxygen free radicals versus their precursors in the face of nanogold
, Article Journal of Physical Organic Chemistry ; Volume 34, Issue 1 , 2021 ; 08943230 (ISSN) ; Kassaee, M.Z ; Ayoubi-Chianeh, M ; Fattahi, A ; Sharif University of Technology
John Wiley and Sons Ltd
2021
Abstract
In our previous report (J. Phys. Org. Chem., 2017), we discussed the dual behavior of gold nanocluster (Au3 NC), where it scavenged reactive oxygen species (ROS) while promoted their generation to a lesser extent. Continuing this quest, we investigate the effects of Au3 NC on common reactive nitrogen species (RNS: O=N˙ and O=N-O) and their precursors (O=N-H and O=N-O-H, respectively), at B3LYP/LACVP+* level of theory. We compare the results with those of prevalent ROS (H-O˙ and H-O-O˙) and their precursors (H-O-H and H-O-O-H, respectively). To this end, various parameters are probed such as binding energy (Eb), bond dissociation energy (BDE), bond lengths, Mullikan spin density (MSD),...
What roles do boron substitutions play in structural, tautomeric, base pairing and electronic properties of uracil? NBO & AIM analysis
, Article Journal of Physical Organic Chemistry ; Volume 25, Issue 9 , 2012 , Pages 787-796 ; 08943230 (ISSN) ; Abedin, A ; Shakourian Fard, M ; Fattahi, A ; Sharif University of Technology
Wiley
2012
Abstract
The synthesis of modified versions of deoxyribonucleic acid is an area that is receiving much attention. The replacement of the nitrogen atom on the nucleobases with boron atom has provided insight into deoxyribonucleic acid and ribonucleic acid stability, recognition, and replication at the atomic level. In the present research, we investigated a detailed density functional theory study of the structural, tautomeric, base-pairing ability, bond dissociation energy, and electronic properties of two boron analogues (i.e., boron substitutions at 4-position and 5-position of uracil) of uracil nucleobase. The effects of these modifications on theirs acid-base properties have been considered. Our...
Adsorption of carbon monoxide on SixGe4-x(x = 0-4) nano-clusters: A hybrid meta density functional study
, Article Molecular Physics ; Volume 108, Issue 10 , 2010 , Pages 1317-1327 ; 00268976 (ISSN) ; Gobal, F ; Sharif University of Technology
2010
Abstract
Theoretical study of carbon monoxide adsorption on SixGe4 - x(x = 0-4) nano-clusters has been carried out using advanced hybrid meta density functional method of Truhlar (MPW1B95). MG3 semi-diffuse (MG3S) and correlation consistent valence basis sets with relativistic core potential were employed to improve the results. The agreement of the calculated ionization and dissociation energies with experimental values validates the reported structures of nano-clusters and justifies the use of hybrid meta density functional method. The geometry, adsorption energy, charge distribution, and vibrational frequency of CO adsorption on all possible structures were investigated. The maximum vibrational...
Origin of the correlation of the rate constant of substrate hydroxylation by nonheme iron(IV)-oxo complexes with the bond-dissociation energy of the C-H bond of the substrate
, Article Chemistry - A European Journal ; Volume 15, Issue 27 , 2009 , Pages 6651-6662 ; 09476539 (ISSN) ; Bagherzadeh, M ; De Visser, S ; Sharif University of Technology
Wiley-VCH Verlag
2009
Abstract
Mononuclear nonheme iron containing systems are versatile and vital oxidants of substrate hydroxylation reactions in many biosystems, whereby the rate constant of hydroxylation correlates with the strength of the C-H bond that is broken in the process. The thermodynamic reason behind these correlations, however, has never been established. In this work results of a series of density functional theory calculations of substrate hydroxylation by a mononuclear nonheme iron(IV)-oxo oxidant with a 2 His/ 1Asp structural motif analogous to aketoglutarate dependent dioxygenases are presented. The calculations show that these oxidants are very efficient and able to hydroxylate strong C-H bonds,...
Electronic structure of some thymol derivatives correlated with the radical scavenging activity: Theoretical study
, Article Food Chemistry ; Vol. 165, issue , Dec , 2014 , p. 451-459 ; Jebeli Javanb, M ; Sharif University of Technology
Abstract
Molecules acting as antioxidants capable of scavenging reactive oxygen species (ROS) are of upmost importance in the living cell. Thymol derivatives exhibit various antioxidant activities and potential health benefits. Exploration of structure-radical scavenging activity (SAR) was approached with a wide range of thymol derivatives. To accomplish this task, the DPPH experimental assay along with quantum-chemical calculations were also employed for these compounds. By comparing the structural properties of the derivatives of interest, their antioxidant activity was explained by the formation of an intramolecular hydrogen bond and the presence of unsaturated double bond (–CHdouble bond; length...