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Free Energy Barriers (free + energy_barrier)
Selected AbstractsFirst-principle studies of intermolecular and intramolecular catalysis of protonated cocaineJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2005Chang-Guo Zhan Abstract We have performed a series of first-principles electronic structure calculations to examine the reaction pathways and the corresponding free energy barriers for the ester hydrolysis of protonated cocaine in its chair and boat conformations. The calculated free energy barriers for the benzoyl ester hydrolysis of protonated chair cocaine are close to the corresponding barriers calculated for the benzoyl ester hydrolysis of neutral cocaine. However, the free energy barrier calculated for the methyl ester hydrolysis of protonated cocaine in its chair conformation is significantly lower than for the methyl ester hydrolysis of neutral cocaine and for the dominant pathway of the benzoyl ester hydrolysis of protonated cocaine. The significant decrease of the free energy barrier, ,4 kcal/mol, is attributed to the intramolecular acid catalysis of the methyl ester hydrolysis of protonated cocaine, because the transition state structure is stabilized by the strong hydrogen bond between the carbonyl oxygen of the methyl ester moiety and the protonated tropane N. The relative magnitudes of the free energy barriers calculated for different pathways of the ester hydrolysis of protonated chair cocaine are consistent with the experimental kinetic data for cocaine hydrolysis under physiologic conditions. Similar intramolecular acid catalysis also occurs for the benzoyl ester hydrolysis of (protonated) boat cocaine in the physiologic condition, although the contribution of the intramolecular hydrogen bonding to transition state stabilization is negligible. Nonetheless, the predictability of the intramolecular hydrogen bonding could be useful in generating antibody-based catalysts that recruit cocaine to the boat conformation and an analog that elicited antibodies to approximate the protonated tropane N and the benzoyl O more closely than the natural boat conformer might increase the contribution from hydrogen bonding. Such a stable analog of the transition state for intramolecular catalysis of cocaine benzoyl-ester hydrolysis was synthesized and used to successfully elicit a number of anticocaine catalytic antibodies. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 980,986, 2005 [source] Computer simulations of protein translocationPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 9 2006Serdal Kirmizialtin Many biological processes involve translocation of protein molecules across pores. Shown in the cover picture of this issue is a snapshot from a computer simulation of the protein ubiquitin that is forced mechanically to enter a narrow cylindrical pore. As the force f applied at one end of the molecule pulls it along the pore, the confinement within the pore causes the protein to unfold. The ensuing changes in the protein's entropy and energy lead to a free energy barrier, which has to be surmounted for the translocation to occur. The magnitude of this barrier is estimated by Kirmizialtin et al. in the article [1]. The plot was generated by using the PyMol software. This paper is a presentation from the 1st Institute for the Theory of Advanced Materials in Information Technology Workshop on Computational Materials and Electronics held 20,22 October 2005 in Austin, USA. The present issue has been guest-edited by James Chelikowsky and Alex Demkov. The background of the cover shows a photograph of the tower of the University of Texas at Austin. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] A Theoretical Study on the Mechanism of C2H4 Oxidation over a Neutral V3O8 ClusterCHEMPHYSCHEM, Issue 8 2010Yan-Ping Ma Dr. Abstract Density functional theory (DFT) calculations are used to investigate the reaction mechanism of V3O8+C2H4. The reaction of V3O8 with C2H4 produces V3O7CH2+HCHO or V3O7+CH2OCH2 overall barrierlessly at room temperature, whereas formation of hydrogen-transfer products V3O7+CH3CHO is subject to a tiny overall free energy barrier (0.03 eV), although the formation of the last-named pair of products is thermodynamically more favorable than that of the first two. These DFT results are in agreement with recent experimental observations. The (Ob)2V(OtOt). (b=bridging, t=terminal) moiety containing the oxygen radical in V3O8 is the active site in the reaction with C2H4. Similarities and differences between the reactivities of (Ob)2V(OtOt). in V3O8 and the small VO3 cluster [(Ot)2VOt.] are discussed. Moreover, the effect of the support on the reactivity of the (Ob)2V(OtOt). active site is evaluated by investigating the reactivity of the cluster VX2O8, which is obtained by replacing the V atoms in the (Ob)3VOt support moieties of V3O8 with X atoms (X=P, As, Sb, Nb, Ta, Si, and Ti). Support X atoms with different electronegativities influence the oxidative reactivity of the (Ob)2V(OtOt). active site through changing the net charge of the active site. These theoretical predictions of the mechanism of V3O8+C2H4 and the effect of the support on the active site may be helpful for understanding the reactivity and selectivity of reactive O. species over condensed-phase catalysts. [source] A Combined Theoretical and Experimental Research Project into the Aminolysis of ,-Lactam Antibiotics: The Importance of Bifunctional CatalysisEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 21 2003Natalia Dķaz Abstract This paper reports the results of experimental work on the aminolysis of penicillin (6-APA) and monobactam (aztreonam) antibiotics by propylamine or ethanolamine. In general, aztreonam is slightly more reactive than 6-APA, despite the common assumption that the amide bond should be less activated in monobactams. Intriguingly, when ethanolamine acts as the nucleophile, the corresponding rate law has a kinetic term proportional to [RNH2][RNH3+]. To complement the experimental observations, the rate-determining free energy barriers in aqueous solution for various mechanistic pathways were computed by standard quantum chemical methodologies. From previous theoretical work it was assumed that the aminolysis of ,-lactams proceeds through mechanisms in which either a water molecule or a second amine molecule may act as bifunctional catalysts, assisting proton transfer from the attacking amine molecule to the leaving amino group. The energy barriers as computed have moderate values (ca. 26,34 kcal·mol,1) and reproduce most of the experimentally observed kinetic trends. Furthermore, the calculations predict that positively charged ethanolamine molecules can act as bifunctional catalysts as well, thus explaining the presence of the kinetic term proportional to [RNH2][RNH3+] in the rate law. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Copper-catalyzed phosphinidene transfer to ethylene, acetylene, and carbon monoxide: A computational studyINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 9 2010Matthew J. Amme Abstract A DFT study of phosphinidene transfer by copper model catalysts is reported. PR-transfer pathways are highly exergonic with respect to catalyst and phosphinidene transfer reagent. Calculated free energy barriers by which (dhpe)Cu(PMe) active species yields functionalized products are reasonable for modeled substrates,ethylene, acetylene, and carbon monoxide. Calculations suggest a (dhpe)CuI(-PMe·,) formulation as more appropriate than (dhpe)CuII(=PMe2,). The preferred pathway for production of phosphirane (phosphirene) is via direct [1 + 2] addition of ethylene (acetylene) to the PMe group of (dhpe)Cu(PMe), which contrasts the [2 + 2] mechanism for the reaction of ethylene with Ni0 -phosphinidenes. In light of simulations for neutral and cationic models, it is concluded that the extra electron in copper destabilizes [2 + 2] pathways. Calculated energetics for (dhpe)Cu(PMe) versus (en)Cu(PMe), dhpe = 1,2- bis(dihydrophosphino)ethane, en = ethylenediamine, indicate that the former is a more potent for PR-transfer. Thus, it is inferred that modifications that result in a more electron deficient metal center will yield better group transfer catalysts. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Models for the adsorption and self-assembly of ethanol and 1-decanethiol on Au(111) surfaces.INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 2 2010A comparative study by computer simulation Abstract Results from computer simulations, based on different models to study theadsorption and self-assembly of the ethanol and 1-decanethiol on gold surfaces, Au(111), are presented. Canonical ensemble Monte Carlo simulations were performed at 298 K using two different force fields. One from DFT calculations, where the gold electrode has an explicit structure (corrugated electrode), and the other representing an electrode, in which the structure is taken into account on an average way (flat electrode). The behavior of the ethanol adsorption on gold surfaces, with and without the 1-decanethiol presence, is analyzed. The introduction of molecular flexibility is also discussed. The relative surface density for the ethanol oxygen, adsorbed on gold, and the density profiles, in different conditions, show that the structure of the surface has a fundamental role on the way the adsorption takes place, not only on the preferential adsorption sites of the surface but also on the ethanol distribution over the electrodes. Potentials of mean force have also been calculated for the two surface models, giving the free energy barriers to the 1-decanethiol crossing of the solvent adsorption layers. The average tilt angle, obtained with a single thiol molecule in the simulation box, presents the values: ,26° for the rigid molecule model and 74° ± 18° for the flexible one. These differences are analyzed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] First-principle studies of intermolecular and intramolecular catalysis of protonated cocaineJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2005Chang-Guo Zhan Abstract We have performed a series of first-principles electronic structure calculations to examine the reaction pathways and the corresponding free energy barriers for the ester hydrolysis of protonated cocaine in its chair and boat conformations. The calculated free energy barriers for the benzoyl ester hydrolysis of protonated chair cocaine are close to the corresponding barriers calculated for the benzoyl ester hydrolysis of neutral cocaine. However, the free energy barrier calculated for the methyl ester hydrolysis of protonated cocaine in its chair conformation is significantly lower than for the methyl ester hydrolysis of neutral cocaine and for the dominant pathway of the benzoyl ester hydrolysis of protonated cocaine. The significant decrease of the free energy barrier, ,4 kcal/mol, is attributed to the intramolecular acid catalysis of the methyl ester hydrolysis of protonated cocaine, because the transition state structure is stabilized by the strong hydrogen bond between the carbonyl oxygen of the methyl ester moiety and the protonated tropane N. The relative magnitudes of the free energy barriers calculated for different pathways of the ester hydrolysis of protonated chair cocaine are consistent with the experimental kinetic data for cocaine hydrolysis under physiologic conditions. Similar intramolecular acid catalysis also occurs for the benzoyl ester hydrolysis of (protonated) boat cocaine in the physiologic condition, although the contribution of the intramolecular hydrogen bonding to transition state stabilization is negligible. Nonetheless, the predictability of the intramolecular hydrogen bonding could be useful in generating antibody-based catalysts that recruit cocaine to the boat conformation and an analog that elicited antibodies to approximate the protonated tropane N and the benzoyl O more closely than the natural boat conformer might increase the contribution from hydrogen bonding. Such a stable analog of the transition state for intramolecular catalysis of cocaine benzoyl-ester hydrolysis was synthesized and used to successfully elicit a number of anticocaine catalytic antibodies. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 980,986, 2005 [source] The mechanism of alkaline hydrolysis of amides: a comparative computational and experimental study of the hydrolysis of N -methylacetamide, N -methylbenzamide, and acetanilideJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 6 2009Diana Cheshmedzhieva Abstract Theoretical computations and experimental kinetic measurements were applied in studying the mechanistic pathways for the alkaline hydrolysis of three secondary amides: N -methylbenzamide, N -methylacetamide, and acetanilide. Electronic structure methods at the HF/6-31+G(d,p) and B3LYP/6-31+G(d,p) levels of theory are employed. The energies of the stationary points along the reaction coordinate were further refined via single point computations at the MP2/6-31+G(d,p) and MP2/6-311++G(2d,2p) levels of theory. The role of water in the reaction mechanisms is examined. The theoretical results show that in the cases of N -methylbenzamide and N -methylacetamide the process is catalyzed by an ancillary water molecule. The influence of water is further assessed by predicting its role as bulk solvent. The alkaline hydrolysis process in aqueous solution is characterized by two distinct free energy barriers: the formation of a tetrahedral adduct and its breaking to products. The results show that the rate-determining stage of the process is associated with the second transition state. The entropy terms evaluated from theoretical computations referring to gas-phase processes are significantly overestimated. The activation barriers for the alkaline hydrolysis of N -methylbenzamide and acetanilide were experimentally determined. Quite satisfactory agreement between experimental values and computed activation enthalpies was obtained. Copyright © 2008 John Wiley & Sons, Ltd. [source] | ||||||||||