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Activation Barriers (activation + barrier)
Selected AbstractsActivation barriers for DNA alkylation by carcinogenic methane diazonium ionsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2006Kaushalya S. Ekanayake Abstract Methylation reactions of the DNA bases with the methane diazonium ion, which is the reactive intermediate formed from several carcinogenic methylating agents, were examined. The SN2 transition states of the methylation reactions at N7, N3, and O6 of guanine; N7, N3, and N1 of adenine; N3 and O2 of cytosine; and O2 and O4 of thymine were calculated using the B3LYP density functional method. Solvation effects were examined using the conductor-like polarizable continuum method and the combined discrete/SCRF method. The transition states for reactions at guanine N3, adenine N7, and adenine N1 are influenced by steric interactions between the methane diazonium ion and exocyclic amino groups. Both in the gas phase and in aqueous solution, the methylation reactions at N atoms have transition states that are looser, and generally occur earlier along the reaction pathways than reactions at O atoms. The forming bonds in the transition states in water are 0.03 to 0.13 Å shorter than those observed in the gas phase, and the activation energies are 13 to 35 kcal/mol higher. The combined discrete/SCRF solvation energy calculations using base-water complexes with three water molecules yield base solvation energies that are larger than those obtained from the CPCM continuum method, especially for cytosine. Reactivities calculated using barriers obtained with the discrete/SCRF method are consistent with the experimentally observed high reactivity at N7 of guanine. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 277,286, 2006 [source] Olefin epoxidation by dioxiranes and percarboxylic acids: an analysis of activation energies calculated by a density functional methodJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 6 2001Philip Gisdakis Abstract The activity of dioxiranes, R2CO2, and percarboxylic acids, RCO(O2)H, in olefin epoxidation reactions can be rationalized by a frontier orbital interaction. Barrier heights of these oxygen transfer reactions, as calculated by a density functional method, depend linearly on the energy of the olefin HOMO orbital , (C,C) and of the peroxide LUMO orbital ,*(O,O). Activation barriers can be predicted from linear relationships with the proton affinity of a dioxirane (as measured by the hydrogen fluoride association energy) or the pKa value of a percarboxylic acid. Copyright © 2001 John Wiley & Sons, Ltd. [source] Quantum Chemical Analysis of the Enantiomerisation Mechanism of Complexes of the Type [MII(XU)4]F+ (M = Pt, Pd, Ni; X = S, Se, Te;U = urea)EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 20 2006Ralph Puchta Abstract The enantiomerisation pathway for {[Pt(thiourea)4]}F+ [a model for the C4 -symmetric [Pt(SU)4]SiF6 (SU = thiourea) complex] and derivatives is explored by density functional theory (B3LYP/LANL2DZp) und the activation barrier for the one-step process from C4 to C4, via a C4 transition state is computed. The substitution of Pt2+ by Pd2+ and Ni2+ and the exchange of selenourea and tellurourea increase the barrier. ({[Pt(thiourea)4]}F+: 4.2 kcal/mol, {[Pd(thiourea)4]}F+: 4.5 kcal/mol, {[Ni(thiourea)4]}F+: 7.6 kcal/mol, {[Pt(selenourea)4]}F+: 5.3 kcal/mol, {[Pt(tellurourea)4]}F+: 8.8 kcal/mol). (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] Synthesis and Dynamic Features of (Chloro)zirconocene Cations Stabilised by Pendant (Diarylphosphanyl)alkyl and (Dimethylamino)alkyl Substituents at Their Cyclopentadienyl Ring SystemsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 8 2003Steve Döring Abstract Treatment of the substituted (diarylphosphanyl)methyl group-4 metallocene complexes [(C5H4,CR1R2,PAr2)2ZrCl2] (2: R1/R2 = CH3/CH3, H/CH3, H/aryl) with Li[B(C6F5)4] in dichloromethane solution results in chloride ligand abstraction (with LiCl precipitation) to yield the complexes [(C5H4,CR1R2,PAr2)2Zr,Cl+] (5), with both phosphanyl groups internally coordinated to the metal centre. Three possible diastereoisomers are observed in the case of 5c (R1 = H; R2 = CH3), while bulkier R2 substituents give higher selectivities. The thermally induced (reversible) cleavage of the Zr,phosphane linkage results in dynamic NMR behaviour. Gibbs activation energies of ,G,(298 K) = 14.8 ± 0.5 and 14.5 ± 0.5 kcal/mol were obtained for these intramolecular equilibration processes in the complexes trans - 5d (R1 = H; R2 = Ph) and trans - 5e (R1 = H; R2 = ferrocenyl), respectively. Treatment of the substituted (dimethylamino)methyl metallocene complexes [(C5H4,CR1R2,NMe2)2ZrCl2] (6a, 6b) with Li[B(C6F5)4] proceeds analogously to yield the cation systems [{C5H4,C(CH3)2,NMe2}2ZrCl+] (12a) and [{C5H4,CH(CH3),NMe2}2ZrCl+] (12b, three possible diastereoisomers). Both complexes have their pairs of amino groups coordinated to the metal centre. The complexes exhibit dynamic NMR spectra. Selective equilibration of the diastereotopic N(CH3)A(CH3)B resonances of complex 12a is observed [,G,(233 K) = 11.5 ± 0.2 kcal/mol], whereas the adjacent C(CH3)A(CH3)B methyl groups remain diastereotopic. The dynamic equilibration of the latter was observed at a markedly higher temperature [,G,(333 K) = 17.3 ± 0.2 kcal/mol]. Treatment of [{C5H4,C(CH3)2,NMe2}CpZrCl2] (10) with Li[B(C6F5)4] resulted in the formation of complex [{C5H4,C(CH3)2,NMe2}CpZr,Cl+] (11), which shows the internal ,N(CH3)A(CH)B equilibration proceeding with a markedly higher activation barrier [,G,(333 K) = 17.6 ± 0.2 kcal/mol] than in 12a, and a stereochemical memory effect indicative of solvent coordination to the metal centre of the resulting highly electrophilic chlorozirconocene cation intermediate. Complex 11 was characterised by an X-ray crystal structure analysis, which shows the internal Zr,amine coordination. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Aliphatic Thiocarbonyl Ylides and Thiobenzophenone: Experimental Study of Regiochemistry and Methylene Transfer in CycloadditionsEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 8 2005Rolf Huisgen Abstract 1,3-Dipolar cycloadditions of aliphatic or alicyclic thiocarbonyl ylides 3A-D , sterically hindered at least at one terminus , with thiobenzophenone produce both regioisomeric 1,3-dithiolanes 4 and 5. According to quantum-chemical calculations (preceding paper), a concerted cycloaddition furnishing 2,4-substituted dithiolanes 4 competes with the formation of an intermediate C,C -biradical 9 which cyclizes to the more crowded 4,5-substituted dithiolanes 5. When steric hindrance of 3 increases, the cycloaddition is superseded by ,methylene transfer', i.e., the transfer of the less hindered terminus of 3E-J to the S-atom of thiobenzophenone. The thiobenzophenone S -alkylide 11, thus formed, rapidly reacts with a second molecule ofthiobenzophenone to generate the 4,4,5,5-tetraphenyl-1,3-dithiolane 12 via the highly stabilized C,C -biradical 10. Methylene transfer occurs when the cyclization of the mixed C,C -biradical 9 requires a higher activation barrier than its dissociation to aliphatic thioketone + 11; the threshold is surprisingly well reproduced by calculations. The structural assignment of sixteen 1,3-dithiolanes is based on their formation from corresponding reactant pairs as well as on 1H and 13C chemical shifts. X-ray diffraction analyses of three spiro-1,3-dithiolanes reveal the van der Waals strain in non-bonded interactions, folding angles, shearing forces, and bond lengths. Comparison of the mass spectra of many 1,3-dithiolanes allows the reconstruction of major fragmentation pathways. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Interaction of atoms with graphenic-type surfaces for the chemistry of the interstellar medium: New properties of H dimers on the surfaceINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 12 2010D. Teillet-Billy Abstract Following the works of Rougeau et al. (Chem Phys Lett 2006, 431,135) and Ferro et al. (Phys Rev B 2008, 78, 085417) on the one-sided double chemisorption of H atoms on graphenic platelets, we investigate the two-sided double chemisorption using DFT-GGA PW91 calculations. Equilibrium characteristics and potential energy curves for chemisorption are reported for the ortho, meta, para, and bottom positions. Contrary to the one-sided case, the two-sided ortho chemisorption, as well as the bottom position, is barrier-less, whereas the two-sided para chemisorption exhibits an activation barrier. The highest occupied Kohn-Sham orbital (HOKSO) of the H-graphene radical is shown to signal the privileged barrier-less double chemisorption sites. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Mechanism of the Asymmetric Sulfoxidation in the Esomeprazole Process: Effects of the Imidazole Backbone for the EnantioselectionADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 6 2009Muthu Seenivasaperumal Abstract The asymmetric sulfoxidation reaction of imidazole-based prochiral sulfides was studied to explore the mechanistic details of the highly efficient esomeprazole process, which is one of the few industrial scale catalytic asymmetric procedures. The synthetic studies revealed that the smallest subunit governing the selectivity in the esomeprazole process is an imidazole ring. Thus, by using the esomeprazole procedure methyl imidazole sulfide could be oxidized as efficiently as its several functionalized derivatives, including pyrmetazol. However, alkylation of the imidazole nitrogen led to a major drop of the enantioselectivity. Our atmospheric pressure chemical ionization-mass spectrometry (APCI/MS) studies indicate that addition of small amounts of water to the reaction mixture facilitates the formation of mononuclear titanium species, which are the active catalytic intermediates of the selective oxidation reaction. One of the most important features of the esomeprazole procedure is that amine additives increase the enantioselectivity of the oxidation process. The NMR studies of the presumed reaction intermediates show that under catalytic conditions the amines are able to coordinate to titanium and dissociate the coordinated imidazole substrate. The density functional theory (DFT) modelling studies provided new insights in the mechanism of the asymmetric induction. It was found that the oxidation requires a lower activation energy if the imidazole sulfide precursor does not coordinate to titanium. Two possible reaction paths were explored for this out of sphere oxidation mechanism. The most important interaction governing the enantioselection is hydrogen bonding between the NH of the imidazole ring and the chiral tartrate ligand on titanium. Furthermore, the oxidation reaction imposes an important structural constraint to the TS structure involving a linear arrangement of the peroxide oxygens and the sulfur atom. This constraint and the N coordination of imidazole leads to a very strained structure for the inner sphere mechanism of the oxidation, which leads to a much higher activation barrier than the corresponding out of sphere process, and therefore it is unlikely. [source] A theoretical study on the catalytic mechanism of Mus musculus adenosine deaminaseJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2010Xian-Hui Wu Abstract The catalytic mechanism of Mus musculus adenosine deaminase (ADA) has been studied by quantum mechanics and two-layered ONIOM calculations. Our calculations show that the previously proposed mechanism, involving His238 as the general base to activate the Zn-bound water, has a high activation barrier of about 28 kcal/mol at the proposed rate-determining nucleophilic addition step, and the corresponding calculated kinetic isotope effects are significantly different from the recent experimental observations. We propose a revised mechanism based on calculations, in which Glu217 serves as the general base to abstract the proton of the Zn-bound water, and the protonated Glu217 then activates the substrate for the subsequent nucleophilic addition. The rate-determining step is the proton transfer from Zn-OH to 6-NH2 of the tetrahedral intermediate, in which His238 serves as a proton shuttle for the proton transfer. The calculated kinetic isotope effects agree well with the experimental data, and calculated activation energy is also consistent with the experimental reaction rate. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] First-principle calculations on CO oxidation catalyzed by a gold nanoparticleJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2010Hsin-Tsung Chen Abstract We have elucidated the mechanism of CO oxidation catalyzed by gold nanoparticles through first-principle density-functional theory (DFT) calculations. Calculations on selected model show that the low-coordinated Au atoms of the Au29 nanoparticle carry slightly negative charges, which enhance the O2 binding energy compared with the corresponding bulk surfaces. Two reaction pathways of the CO oxidation were considered: the Eley,Rideal (ER) and Langmuir,Hinshelwood (LH). The overall LH reaction O2(ads) + CO(gas) , O2(ads) + CO(ads) , OOCO(ads) , O(ads) + CO2(gas) is calculated to be exothermic by 3.72 eV; the potential energies of the two transition states (TSLH1 and TSLH2) are smaller than the reactants, indicating that no net activation energy is required for this process. The CO oxidation via ER reaction Au29 + O2(gas) + CO(gas) , Au29,O2(ads) + CO(gas) , Au29,CO3(ads) , Au29,O(ads) + CO2(gas) requires an overall activation barrier of 0.19 eV, and the formation of Au29,CO3(ads) intermediate possesses high exothermicity of 4.33 eV, indicating that this process may compete with the LH mechanism. Thereafter, a second CO molecule can react with the remaining O atom via the ER mechanism with a very small barrier (0.03 eV). Our calculations suggest that the CO oxidation catalyzed by the Au29 nanoparticle is likely to occur at or even below room temperature. To gain insights into high-catalytic activity of the gold nanoparticles, the interaction nature between adsorbate and substrate is also analyzed by the detailed electronic analysis. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Looking for a contribution of the non-equilibrium solvent polarization to the activation barrier of the SN2 reactionJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 6 2002Jan S. Jaworski Abstract The solvent effect on the activation free energy of the Finkelstein reaction between methyl iodide and Cl, ions was analysed in terms of the recent Marcus theory unifying the SN2 and the electron transfer reactions. The homolytic bond dissociation energy and the related resonance energy of interaction of the states seem to be almost solvent independent. The sum of the work term wr and the solvent reorganization energy ,0/4 depends strongly on the solvent acidity parameter, e.g. ETN, describing the solvation/desolvation of anions. However, after removing the contribution of the specific solvation the linear increase of the remaining part of ,0/4 with the Pekar factor, describing the non-equilibrium solvent polarization, was observed for six aprotic solvents. Copyright © 2002 John Wiley & Sons, Ltd. [source] Influence of Sn doping upon the phase change characteristics of Ge2Sb2Te5PHYSICA STATUS SOLIDI (A) APPLICATIONS AND MATERIALS SCIENCE, Issue 14 2004K. Wang Abstract The influence of Sn doping upon the phase change characteristics of Ge2Sb2Te5 alloys has been investigated using four-point-probe electrical resistance measurements, grazing incidence X-ray diffraction (XRD), X-ray reflectometry (XRR) and variable incident angle spectroscopic ellipsometry (VASE), a static tester and atomic force microscopy (AFM). For a Ge2Sb2Te5 alloy doped with 4% Sn, two transition temperatures are observed in the temperature dependent sheet resistance measurements at 125 °C and 250 °C, respectively. The evolution of structures upon annealing, investigated by XRD, reveals that the first transition is caused by the crystallization of the amorphous film to a NaCl-type structure, while the second transition is related to the transition to a hexagonal structure. The density values of 6.02 ± 0.05 g cm,3, 6.38 ± 0.05 gcm,3 and 6.42 ± 0.05 gcm,3 are measured by XRR for the film in the amorphous, NaCl-type and hexagonal structure, respectively. Ultra-fast crystallization, which is correlated with a single NaCl-structure phase and the reduced activation barrier, is demonstrated. Sufficient optical contrast is exhibited and can be correlated with the density change upon crystallization. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Controlled Ge quantum dots positioning with nano-patterned Si(001) substratesPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 15 2006A. Bavard Abstract A square nanometric patterned substrate (period 20 nm) is obtained by direct twist bonding of two twin Si(001) surfaces, thinning and preferential chemical etching. Molecular beam epitaxy of Ge is carried out on a sample having heterogeneous trench depths to analyse islands positioning as a function of the surface morphology. Scanning electron microscopy observations show that small single dots per mesa or large dots covering several mesas can be observed. It highlights the influence of the mesa aspect ratio on the control of Ge islands self-organization, and suggests the occurrence of an effective activation barrier depending on the surface profile. The position-dependent energy stored in a dot for a given surface profile is estimated from a very simple model based on the balance between capillarity and elastic relaxation terms. By choosing a cycloid-like profile, experimental observations can be explained without fitting parameters. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] From discrete protein kinetics to continuous Brownian dynamics: A new perspectivePROTEIN SCIENCE, Issue 1 2002Hong Qian Abstract This article presents a comparative analysis of two sets of data from recent experiments on kinetics of (i) protein unfolding by mechanical force and (ii) channel gating with membrane electric potential. Both situations necessitate a continuous Brownian-dynamic view of protein conformational kinetics. We show that the discrete approach traditional to biochemical kinetics is insufficient for understanding dynamics of protein molecules in an aqueous solution or lipid membrane with varying conditions under which the major activation barrier can disappear. A semiquantitative analysis based on Brownian dynamics in a continuous energy landscape offers a more comprehensive description for motions of biological macromolecules. [source] Single-molecule pair studies of the interactions of the ,-GalNAc (Tn-antigen) form of porcine submaxillary mucin with soybean agglutininBIOPOLYMERS, Issue 9 2009Marit Sletmoen Abstract Mucins form a group of heavily O -glycosylated biologically important glycoproteins that are involved in a variety of biological functions, including modulating immune response, inflammation, and adhesion. Mucins are also involved in cancer and metastasis and often express diagnostic cancer antigens. Recently, a modified porcine submaxillary mucin (Tn-PSM) containing GalNAc,1- O -Ser/Thr residues was shown to bind to soybean agglutinin (SBA) with ,106 -fold enhanced affinity relative to GalNAc,1- O -Ser, the pancarcinoma carbohydrate antigen. In this study, dynamic force spectroscopy is used to investigate molecular pairs of SBA and Tn-PSM. A number of force jumps that demonstrate unbinding or rebinding events were observed up to a distance equal to 2.0 ,m, consistent with the length of the mucin chain. The unbinding force increased from 103 to 402 pN with increasing force loading rate. The position of the activation barrier in the energy landscape of the interaction was 0.1 nm. The lifetime of the SBA,TnPSM complex in the absence of applied force was determined to be in the range 1.3,1.9 s. Kinetic parameters describing the rate of dissociation of other sugar lectin interactions are in the range 3.3 × 10,3,2.5 × 10,3 s. The long lifetime of the SBA-TnPSM complex is compatible with a binding model in which lectin molecules "bind and jump" from ,-GalNAc residue to ,-GalNAc residue along the polypeptide chain of Tn-PSM before dissociating. These findings have important implications for the molecular recognition properties of mucins. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 719,728, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Preparation of Imidazolin-2-iminato Molybdenum and Tungsten Benzylidyne Complexes: A New Pathway to Highly Active Alkyne Metathesis CatalystsCHEMISTRY - A EUROPEAN JOURNAL, Issue 29 2010Birte Haberlag Dipl.-Chem. Abstract The reaction of [PhCMBr3(dme)] (dme=1,2-dimethoxyethane) with the hexafluoro- tert- butoxides LiX or KX [X=OC(CF3)2Me] afforded the benzylidyne complexes [PhCMX3(dme)] (2,a: M=W, 2,b: M=Mo), which further reacted with the lithium reagent Li(ImtBuN), generated with MeLi from 1,3-di- tert -butylimidazolin-2-imine (ImtBuNH), to form the imidazolin-2-iminato complexes [PhCMX2(ImtBuN)] (3,a: M=W, 3,b: M=Mo). The propylidyne complex [EtCMoX2(NImtBu)] (4) was obtained by treatment of 3,b with an excess of 3-hexyne. Complexes 3,a and 3,b are able to efficiently catalyse alkyne cross metathesis of various 3-pentynyl benzyl ethers 5 and benzoic esters 7 at room temperature, to afford 2-butyne and the corresponding diethers 6 and diesters 8. The tungsten complex 3,a proved to be a superior catalyst for ring-closing alkyne metathesis, and the [10]cyclophanes 10 and 12 were synthesised in high yield from 1,3-bis(3-pentynyloxymethyl)benzene (9) and bis(3-pentynyl) phthalate (11), respectively. The molecular structures of compounds 2,a, 2,b, 3,a, 3,b, 4, and 12 were determined by single-crystal X-ray diffraction. DFT calculations have been carried out for catalyst systems based on the imidazolin-2-iminato tungsten and molybdenum complexes 3,a and 3,b by choosing the alkyne metathesis of 2-butyne as the model reaction; the studies revealed a lower activation barrier for the tungsten system. [source] Multiple Reaction Pathways in Rhodium-Catalyzed Hydrosilylations of KetonesCHEMISTRY - A EUROPEAN JOURNAL, Issue 43 2009Nathanaëlle Schneider Dr. Abstract A detailed density functional theory (DFT) computational study (using the BP86/SV(P) and B3LYP/TZVP//BP86/SV(P) level of theory) of the rhodium-catalyzed hydrosilylation of ketones has shown three mechanistic pathways to be viable. They all involve the generation of a cationic complex [LnRhI]+ stabilized by the coordination of two ketone molecules and the subsequent oxidative addition of the silane, which results in the Rh,silyl intermediates [LnRhIII(H)SiHMe2]+. However, they differ in the following reaction steps: in two of them, insertion of the ketone into the RhSi bond occurs, as previously proposed by Ojima et,al., or into the SiH bond, as proposed by Chan et,al. for dihydrosilanes. The latter in particular is characterized by a very high activation barrier associated with the insertion of the ketone into the SiH bond, thereby making a new, third mechanistic pathway that involves the formation of a silylene intermediate more likely. This "silylene mechanism" was found to have the lowest activation barrier for the rate-determining step, the migration of a rhodium-bonded hydride to the ketone that is coordinated to the silylene ligand. This explains the previously reported rate enhancement for R2SiH2 compared to R3SiH as well as the inverse kinetic isotope effect (KIE) observed experimentally for the overall catalytic cycle because deuterium prefers to be located in the stronger bond, that is, CD versus MD. [source] Nonequilibrium solvent polarization in kinetics of SN2 reactionsINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 2 2003J. S. JaworskiArticle first published online: 21 NOV 200 The solvent effect on the experimental activation barriers for the reactions of methyl iodide with chloride and thiocyanate ions was analyzed according to the Marcus and Shaik theories, considering SN2 mechanism in terms of a single electron shift. The linear increase in the solvent reorganization energy of the Marcus theory (after removing contributions from the specific solvation) with the solvent Pekar factor, describing the effect of the nonequilibrium solvent polarization, was observed for six aprotic solvents. The direct support of the title effect based on the Shaik theory was less evident; however, in general, the calculated activation barriers in 10 solvents change parallel with the experimental ones. © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 35: 61,66, 2003 [source] Extended Hartree,Fock theory of chemical reactions.INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2009Abstract Symmetry and broken symmetry (BS) in molecular orbital description of transition structures and intermediates in oxygenation reactions have been revisited to elucidate states correlation diagrams and mechanisms for addition reactions of molecular oxygen and metal-oxo MO (M = Mn(II) and Fe(II)) species to CC double bonds. Relative stabilities between diradical (DR) and perepoxide (PE) intermediates were thoroughly investigated by several BS hybrid DFT (HDFT) methods and BS CCSD(T) method with and without spin projection. It has been found that recovery of spin symmetry, namely eliminating spin contamination error from the BS solutions, is crucial for the elucidation of reasonable state correlation diagrams and energy differences of the key structures in the oxygenation reactions because the singlet-triplet energy gap for molecular oxygen is large (22 kcal/mol). The BS HDFT followed by spin correction reproduced activation barriers for transition structures along both PE and DR reaction pathways by the use of the CASPT2 method. Basis set dependence on the relative stability between PE and DR intermediates were also examined thoroughly. Solvation effect for DR and PE intermediates was further examined with self-consistent reaction field (SCRF) and SCIPCM methods. Both BS HDFT and CASPT2 have concluded that the DR mechanism is favorable for the addition reaction of singlet oxygen to ethylene, supporting our previous conclusions. The BS HDFT with spin correction was concluded to be useful enough for theoretical investigations of mechanisms of oxygenation reactions. Implications of the computational results were discussed in relation to the theoretical framework (four configuration model) for elucidation of possible mechanisms of epoxidation reactions with Fe(IV)O cores in metalloenzymes on the basis of isolobal analogies among O, OO, and Fe(IV)O. Correspondence between magnetic coupling mode and radical pathway in oxygenations with these species was clarified based on the BS MO interaction diagrams, leading to local singlet and triplet diradical mechanisms for epoxidations. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] On the relative stability of cobalt- and nickel-based amidinate complexes against ,-migrationINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2009Jiaye Li Abstract We present a first-principles study on the relative stability of cobalt- and nickel-based amidinate complexes against ,-migration using density functional theory. Factors that influence the reactivity of these compounds were carefully addressed and the calculated molecular structures are in excellent agreement with the available crystal structural data. Reaction energies as well as activation barriers of ,-migration were evaluated. The predicted relative stability of the selected compounds is consistent with experimental observations. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] Theoretical characterizations of HAsXH (X = N, P, As, Sb, and Bi) isomers in the singlet and triplet statesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2008Chin-Hung Lai Abstract The lowest singlet and triplet potential energy surfaces for all group 15 HAsXH (X = N, P, As, Sb, and Bi) systems have been explored through ab initio calculations. The geometries of the various isomers were determined at the QCISD/LANL2DZdp level and confirmed to be minima by vibrational analysis. In the case of nitrogen, the global minimum is found to be a triplet H2NAs structure. For the phosphorus case, singlet trans -HAsPH is found to be global minima surrounded by large activation barriers, so that it should be observable. For arsenic, theoretical investigations demonstrate that the stability of HAsAsH isomers decreases in the order singlet trans -HAsAsH > triplet H2AsAs > singlet cis -HAsAsH > triplet HAsAsH > singlet H2AsAs. For antimony and bismuth, the theoretical findings suggest that the stability of HAsXH (X = Sb and Bi) systems decreases in the order triplet H2AsX , singlet trans -HAsXH > singlet cis -HAsXH > triplet HAsXH > triplet H2XAs > singlet H2AsX > singlet H2XAs. Our model calculations indicate that the relativistic effect on heavier group 15 elements should play an important role in determining the geometries as well as the stability of HAsXH molecules. The results obtained are in good agreement with the available experimental data and allow a number of predictions to be made. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Low barrier kinetics: Dependence on observables and free energy surfaceJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2006Hairong Ma Abstract Dynamics on free energy surfaces with high activation barriers are usually treated by few-state kinetics models, yielding characteristic rate coefficients and amplitudes depending on the connectivity of the states. When the barriers are low (<3 kT), the assumption of instantaneous equilibration of the transition state, and hence, the few-state kinetics treatment, break down. Langevin dynamics is used here to explore the characteristic trends that occur in such cases, as a function of barrier height, number of barriers, dimensionality of the free energy surface, and switching functions that describe how spectroscopic probes vary from reactant to product. The result is a systematic phenomenological description of low barrier kinetics and dynamics. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 125,134, 2006 [source] [2,+,3] Cycloaddition of C,C,N -triphenylnitrone to trans -substituted nitroethylenes in the light of an AM1 and AM1/COSMO computational study,JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 5 2003Andrzej Baranski Abstract AM1 calculations suggest that the [2,+,3] cycloaddition of triphenylnitrone 1 to nitroalkenes 2a,c in the gas phase takes place in a concerted manner. However, the azolidine ring bonds C3,C4 and O1,C5 are not formed fully synchronously. Kinetic factors favor the formation of cycloadducts with nitro group in position C-4 of the azolidine ring (path A). Introduction of toluene, acetone or acetonitrile as a reaction medium increases the activation barriers for both regioisomeric paths. Simultaneously, the energy profiles for path A undergo qualitative change. In this case, two transition states and an intermediate with zwitterionic character were localized by means of the AM1/COSMO method. Copyright © 2003 John Wiley & Sons, Ltd. [source] Ligand-Exchange Processes on Solvated Zinc Cations: Water Exchange on [Zn(H2O)4(L)]2+,2,H2O (L=Heterocyclic Ligand)CHEMISTRY - A EUROPEAN JOURNAL, Issue 24 2010Basam Abstract The water-exchange mechanisms of [Zn(H2O)4(L)]2+,2,H2O (L=imidazole, pyrazole, 1,2,4-triazole, pyridine, 4-cyanopyridine, 4-aminopyridine, 2-azaphosphole, 2-azafuran, 2-azathiophene, and 2-azaselenophene) have been investigated by DFT calculations (RB3LYP/6-311+G**). The results support limiting associative reaction pathways that involve the formation of six-coordinate intermediates [Zn(H2O)5(L)]2+,H2O. The basicity of the coordinated heterocyclic ligands shows a good correlation with the activation barriers, structural parameters, and stability of the transition and intermediate states. [source] Transmetalation Reactions from Fischer Carbene Complexes to Late Transition Metals: A DFT StudyCHEMISTRY - A EUROPEAN JOURNAL, Issue 35 2008Israel Fernández Dr. Abstract Transmetalation reactions from chromium(0) Fischer carbene complexes to late-transition-metal complexes (palladium(0), copper(I), and rhodium(I)) have been studied computationally by density functional theory. The computational data were compared with the available experimental data. In this study, the different reaction pathways involving the different metal atoms have been compared with each other in terms of their activation barriers and reaction energies. Although the reaction profiles for the transmetalation reactions to palladium and copper are quite similar, the computed energy values indicate that the process involving palladium as catalyst is more favorable than that involving copper. In contrast to these transformations, which occur via triangular heterobimetallic species, the transmetalation reaction to rhodium leads to a new heterobimetallic species in which a carbonyl ligand is also transferred from the Fischer carbene to the rhodium catalyst. Moreover, the structure and bonding situation of the so far elusive heterobimetallic complexes are briefly discussed. La reacción de transmetalación catalítica desde cromo(0) Fischer carbenos a metales de transición tardía (Pd0, CuIand RhI) se ha estudiado computacionalmente usando DFT. Los resultados computacionales se han comparado con los datos experimentales disponibles. Las barreras y las energías de reacción se han comparado en los caminos de reacción obtenidos para los metales considerados. Mientras que los perfiles de reacción para la transmetalación desde Cr a Pd o Cu son similares, los valores calculados indican que aquellos procesos que implican catalizadores de Pd son más favorables que los que implican Cu. En claro contraste con estas transformaciones, que ocurren a través de especies heterobimetálicas con geometría triangular, la reacción con Rh forma nuevas especies heterobimetálicas en las que se ha transferido un ligando carbonilo desde el complejo de Fischer al catalizador de Rh. Adicionalmente, se discute la estructura y la forma de enlace de éstos complejos heterobimetálicos no aislados hasta este momento. [source] Bonding and Bending in Zirconium(IV) and Hafnium(IV) HydrazidesCHEMISTRY - A EUROPEAN JOURNAL, Issue 27 2008Heike Herrmann Dr. Abstract Reaction of the dichloro complexes [M(N2TBSNpy)Cl2] (M=Zr: 1, Hf: 2; TBS: tBuMe2Si; py: pyridine) with one molar equivalent of LiNHNPh2 gave mixtures of the two diastereomeric chlorohydrazido(1,) complexes [M(N2TBSNpy)(NHNPh2)Cl] (M=Zr: 3,a,b, Hf: 4,a,b) in which the diphenylhydrazido(1,) ligand adopts a bent ,1 coordination. This mixture of isomers could be cleanly converted into the deep green diphenylhydrazido(2,) complexes [Zr(N2TBSNpy)(NNPh2)(py)] (5) and [Hf(N2TBSNpy)(NNPh2)(py)] (6), respectively, by dehydrohalogenation with lithium hexamethyldisilazide (LiHMDS) in the presence of one molar equivalent of pyridine. Both complexes contain a linearly coordinated hydrazinediide for which a DFT-based frontier orbital analysis established bonding through one , and two , orbitals. A high polarity of the MN bond was found, in accordance with the description of hydrazinediide(2,) acting as a six-electron donor ligand. The pyridine ligand in [M(N2TBSNpy)(NNPh2)(py)] (M=Zr: 5, Hf: 6) is substitutionally labile as established by line-shape analysis of the dynamic spectra (,G,=19,kcal,mol,1). A change in denticity of the hydrazido unit from ,1 to ,2 was studied by DFT methods. Both forms are calculated to be very close in energy and are only separated by shallow activation barriers, which supports the notion of a rapid ,1 to ,2 interconversion. This process is believed to happen early on in the NN scission in the presence of coupling reagents. Frontier orbital and natural population analyses suggest that a primarily charge-controlled nucleophilic attack at N, is unlikely whereas interaction with an electrophile could play an important role. This hypothesis was tested by the reaction of 5 and 6 with one molar equivalent of B(C6F5)3 to give [Zr(N2TBSNpy)(NNPh2){B(C6F5)3}] (7) and [Hf(N2TBSNpy)(NNPh2){B(C6F5)3}] (8). In these products, B(C6F5)3 becomes attached to the N, atom of the side-on bound hydrazinediide and there is an additional interaction of an ortho -F atom of a C6F5 ring with the metal centre. [source] Can [M(H)2(H2)(PXP)] Pincer Complexes (M=Fe, Ru, Os; X=N, O, S) Serve as Catalyst Lead Structures for NH3 Synthesis from N2 and H2?CHEMISTRY - A EUROPEAN JOURNAL, Issue 23 2007Markus Hölscher Dr. Abstract The potential of pincer complexes [M(H)2(H2)(PXP)] (M=Fe, Ru, Os; X=N, O, S) to coordinate, activate, and thus catalyze the reaction of N2 with classical or nonclassical hydrogen centers present at the metal center, with the aim of forming NH3 with H2 as the only other reagent, was explored by means of DF (density functional) calculations. Screening of various complexes for their ability to perform initial hydrogen transfer to coordinated N2 showed ruthenium pincer complexes to be more promising than the corresponding iron and osmium analogues. The ligand backbone influences the reaction dramatically: the presence of pyridine and thioether groups as backbones in the ligand result in inactive catalysts, whereas ether groups such as ,-pyran and furan enable the reaction and result in unprecedented low activation barriers (23.7 and 22.1,kcal,mol,1, respectively), low enough to be interesting for practical application. Catalytic cycles were calculated for [Ru(H)2(H2)(POP)] catalysts (POP=2,5-bis(dimethylphosphanylmethyl)furan and 2,6-bis(dimethylphosphanylmethyl)-,-pyran). The height of activation barriers for the furan system is somewhat more advantageous. Formation of inactive metal nitrides has not been observed. SCRF calculations were used to introduce solvent (toluene) effects. The Gibbs free energies of activation of the numerous single reaction steps do not change significantly when solvent is included. The reaction steps associated with the formation of the active catalyst from precursors [M(H)2(H2)(PXP)] were also calculated. The otherwise inactive pyridine ligand system allows for the generation of the active catalyst species, whereas the ether ligand systems show activation barriers that could prohibit practical application. Consequently the generation of the active catalyst species needs to be addressed in further studies. [source] Can Weakly Coordinating Anions Stabilize Mercury in Its Oxidation State +IV?CHEMISTRY - A EUROPEAN JOURNAL, Issue 9 2005Sebastian Riedel Dipl.-Chem. Abstract While the thermochemical stability of gas-phase HgF4 against F2 elimination was predicted by accurate quantum chemical calculations more than a decade ago, experimental verification of "truly transition-metal" mercury(IV) chemistry is still lacking. This work uses detailed density functional calculations to explore alternative species that might provide access to condensed-phase HgIV chemistry. The structures and thermochemical stabilities of complexes HgIVX4 and HgIVF2X2 (X,=AlF4,, Al2F7,, AsF6,, SbF6,, As2F11,, Sb2F11,, OSeF5,, OTeF5,) have been assessed and are compared with each other, with smaller gas-phase HgX4 complexes, and with known related noble gas compounds. Most species eliminate F2 exothermically, with energies ranging from only about ,60 kJ,mol,1 to appreciable ,180 kJ,mol,1. The lower stability of these species compared to gas-phase HgF4 is due to relatively high coordination numbers of six in the resulting HgII complexes that stabilize the elimination products. Complexes with AsF6 ligands appear more promising than their SbF6 analogues, due to differential aggregation effects in the HgII and HgIV states. HgF2X2 complexes with X,=OSeF5, or OTeF5, exhibit endothermic fluorine elimination and relatively weak interactions in the HgII products. However, elimination of the peroxidic (OEF5)2 coupling products of these ligands provides an alternative exothermic elimination pathway with energies between ,120 and ,130 kJ,mol,1. While all of the complexes investigated here thus have one exothermic decomposition channel, there is indirect evidence that the reactions should exhibit nonnegligible activation barriers. A number of possible synthetic pathways towards the most interesting condensed-phase HgIV target complexes are proposed. [source] Comprehensive Analysis of DNA Strand Breaks at the Guanosine Site Induced by Low-Energy Electron AttachmentCHEMPHYSCHEM, Issue 1 2010Jiande Gu Prof. Dr. Abstract To elucidate the role of guanosine in DNA strand breaks caused by low-energy electrons (LEEs), theoretical investigations of the LEE attachment-induced CO ,-bonds and N-glycosidic bond breaking of 2,-deoxyguanosine-3,,5,-diphosphate (3,,5,-dGMP) were performed using the B3LYP/DZP++ approach. The results reveal possible reaction pathways in the gas phase and in aqueous solutions. In the gas phase LEEs could attach to the phosphate group adjacent to the guanosine to form a radical anion. However, the small vertical detachment energy (VDE) of the radical anion of guanosine 3,,5,-diphosphate in the gas phase excludes either CO bond cleavage or N-glycosidic bond breaking. In the presence of the polarizable surroundings, the solvent effects dramatically increase the electron affinities of the 3,,5,-dGDP and the VDE of 3,,5,-dGDP,. Furthermore, the solvent,solute interactions greatly reduce the activation barriers of the CO bond cleavage to 1.06,3.56 kcal,mol,1. These low-energy barriers ensure that either C5,O5, or C3,O3, bond rupture takes place at the guanosine site in DNA single strands. On the other hand, the comparatively high energy barrier of the N-glycosidic bond rupture implies that this reaction pathway is inferior to CO bond cleavage. Qualitative agreement was found between the theoretical sequence of the bond breaking reaction pathways in the PCM model and the ratio for the corresponding bond breaks observed in the experiment of LEE-induced damage in oligonucleotide tetramer CGTA. This concord suggests that the influence of the surroundings in the thin solid film on the LEE-induced DNA damage resembles that of the solvent. [source] Analysis of Classical and Quantum Paths for Deprotonation of Methylamine by Methylamine DehydrogenaseCHEMPHYSCHEM, Issue 12 2007Kara E. Ranaghan Abstract The hydrogen-transfer reaction catalysed by methylamine dehydrogenase (MADH) with methylamine (MA) as substrate is a good model system for studies of proton tunnelling in enzyme reactions,an area of great current interest,for which atomistic simulations will be vital. Here, we present a detailed analysis of the key deprotonation step of the MADH/MA reaction and compare the results with experimental observations. Moreover, we compare this reaction with the related aromatic amine dehydrogenase (AADH) reaction with tryptamine, recently studied by us, and identify possible causes for the differences observed in the measured kinetic isotope effects (KIEs) of the two systems. We have used combined quantum mechanics/molecular mechanics (QM/MM) techniques in molecular dynamics simulations and variational transition state theory with multidimensional tunnelling calculations averaged over an ensemble of paths. The results reveal important mechanistic complexity. We calculate activation barriers and KIEs for the two possible proton transfers identified,to either of the carboxylate oxygen atoms of the catalytic base (Asp428,),and analyse the contributions of quantum effects. The activation barriers and tunnelling contributions for the two possible proton transfers are similar and lead to a phenomenological activation free energy of 16.5±0.9 kcal,mol,1 for transfer to either oxygen (PM3-CHARMM calculations applying PM3-SRP specific reaction parameters), in good agreement with the experimental value of 14.4 kcal,mol,1. In contrast, for the AADH system, transfer to the equivalent OD1 was found to be preferred. The structures of the enzyme complexes during reaction are analysed in detail. The hydrogen bond of Thr474,(MADH)/Thr172,(AADH) to the catalytic carboxylate group and the nonconserved active site residue Tyr471,(MADH)/Phe169,(AADH) are identified as important factors in determining the preferred oxygen acceptor. The protein environment has a significant effect on the reaction energetics and hence on tunnelling contributions and KIEs. These environmental effects, and the related clearly different preferences for the two carboxylate oxygen atoms (with different KIEs) in MADH/MA and AADH/tryptamine, are possible causes of the differences observed in the KIEs between these two important enzyme reactions. [source] Transition-State Energy and Position along the Reaction Coordinate in an Extended Activation Strain Model,CHEMPHYSCHEM, Issue 8 2007G. Theodoor de Jong Dr. Abstract We investigate palladium-induced activation of the CH, CC, CF, and CCl bonds in methane, ethane, cyclopropane, fluoromethane, and chloromethane, using relativistic density functional theory (DFT) at ZORA-BLYP/TZ2P. Our purpose is to arrive at a qualitative understanding, based on accurate calculations, of the trends in activation barriers and transition state (TS) geometries (e.g. early or late along the reaction coordinate) in terms of the reactants' properties. To this end, we extend the activation strain model (in which the activation energy ,E, is decomposed into the activation strain ,E,strain of the reactants and the stabilizing TS interaction ,E,int between the reactants) from a single-point analysis of the TS to an analysis along the reaction coordinate ,, that is, ,E(,)=,Estrain(,)+,Eint(,). This extension enables us to understand qualitatively, trends in the position of the TS along , and, therefore, the values of the activation strain ,E,strain=,Estrain(,TS) and TS interaction ,E,int=,Eint(,TS) and trends therein. An interesting insight that emerges is that the much higher barrier of metal-mediated CC versus CH activation originates from steric shielding of the CC bond in ethane by CH bonds. Thus, before a favorable stabilizing interaction with the CC bond can occur, the CH bonds must be bent away, which causes the metal,substrate interaction ,Eint(,) in CC activation to lag behind. Such steric shielding is not present in the metal-mediated activation of the CH bond, which is always accessible from the hydrogen side. Other phenomena that are addressed are anion assistance, competition between direct oxidative insertion (OxIn) versus the alternative SN2 pathway, and the effect of ring strain. [source] | |||||||||||||||||||||||||