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Reaction Energies (reaction + energy)
Selected AbstractsOn 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] Ab Initio Quantum Chemical Investigation of the First Steps of the Photocycle of Phototropin: A Model Study,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 1 2003Christian Neiß ABSTRACT Phototropin is a blue light,activated photoreceptor that plays a dominant role in the phototropism of plants. The protein contains two subunits that bind flavin mononucleotide (FMN), which are responsible for the initial steps of the light-induced reaction. It has been proposed that the photoexcited flavin molecule adds a cysteine residue of the protein backbone, thus activating autophosphorylation of the enzyme. In this study, the electronic properties of several FMN-related compounds in different charge and spin states are characterized by means of ab initio quantum mechanical calculations. The model compounds serve as idealized model chromophores for phototropism. Reaction energies are estimated for simple model reactions, roughly representing the addition of a cysteine residue to the flavin molecule. Excitation energies were calculated with the help of time-dependent density functional theory. On the basis of these calculations we propose the following mechanism for the addition reaction: (1) after photoexcitation of FMN out of the singlet ground state S0, excited singlet state(s) are populated; these relax to the lowest excited singlet state S1, and subsequently by intersystem crossing FMN in the lowest triplet state, T1 is formed; (2) the triplet easily removes the neutral hydrogen atom from the H,S group of the cysteine residue; and (3) the resulting thio radical is added. [source] Singlet,triplet splitting and stability of divalent five-membered ring C4H4M, C4H6M, and C4H8M (M = C, Si, Ge, Sn, and Pb)HETEROATOM CHEMISTRY, Issue 3 2008E. Vessally The sum of electronic and thermal free energy differences between singlet and triplet states (, Gt-s) is calculated for C4H4M, C4H6M, and C4H8M (M = C, Si, Ge, Sn, and Pb) at B3LYP/6-311++G (3df,2p) level. Singlet,triplet splitting (, Gt-s) is compared for three analogs C4H4M, C4H6M, and C4H8M. The change order of , Gt-s is (except for M = C) C4H6M > C4H8M > C4H4M. The results of homodesmotic reaction energies show the most stability for singlet state of C4H6M with respect to C4H4M and C4H8M. In contrast, the triplet state of C4H4M (except for M = C) is the most stable with respect to C4H6M and C4H8M. © 2008 Wiley Periodicals, Inc. Heteroatom Chem 19:245,251, 2008; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20428 [source] Assessing the performances of some recently proposed density functionals for the description of bond dissociations involving organic radicalsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 12 2010Vincent Tognetti Abstract In this article, we have assessed the performances of some recently proposed density functionals for the prediction of reaction energies involving radicals, notably bond dissociations of small organic molecules or of TEMPO-based ones, and ,-scissions, focusing on our TCA family and on range-separated hybrids. It is found that no functional belonging to these two families is able to compete with the M0x one. We have tried to improve the performances of the range-separated hybrids by the optimization of the attenuation parameter, but the improvements for one dataset lead to an unavoidable deterioration for the others. Furthermore, the differences between two different approaches to the long-range/short-range separation are discussed in terms of average enhancement factors, emphasizing the crucial choice of the approximate scheme used for the short-range part. Finally, the influence of the geometries has been considered and found to be negligible for this kind of molecular sets, validating the usual single point energies strategies developed in such benchmarking assessments. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Reaction pathways of propene pyrolysisJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2010Yena Qu Abstract The gas-phase reaction pathways in preparing pyrolytic carbon with propene pyrolysis have been investigated in detail with a total number of 110 transition states and 50 intermediates. The structure of the species was determined with density functional theory at B3PW91/6-311G(d,p) level. The transition states and their linked intermediates were confirmed with frequency and the intrinsic reaction coordinates analyses. The elementary reactions were explored in the pathways of both direct and the radical attacking decompositions. The energy barriers and the reaction energies were determined with accurate model chemistry method at G3(MP2) level after an examination of the nondynamic electronic correlations. The heat capacities and entropies were obtained with statistical thermodynamics. The Gibbs free energies at 298.15 K for all the reaction steps were reported. Those at any temperature can be developed with classical thermodynamics by using the fitted (as a function of temperature) heat capacities. It was found that the most favorable paths are mainly in the radical attacking chain reactions. The chain was proposed with 26 reaction steps including two steps of the initialization of the chain to produce H and CH3 radicals. For a typical temperature (1200 K) adopted in the experiments, the highest energy barriers were found in the production of C3 to be 203.4 and 193.7 kJ/mol. The highest energy barriers for the production of C2 and C were found 174.1 and 181.4 kJ/mol, respectively. These results are comparable with the most recent experimental observation of the apparent activation energy 201.9 ± 0.6 or 137 ± 25 kJ/mol. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Energy landscapes of nucleophilic substitution reactions: A comparison of density functional theory and coupled cluster methodsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2007Marcel Swart Abstract We have carried out a detailed evaluation of the performance of all classes of density functional theory (DFT) for describing the potential energy surface (PES) of a wide range of nucleophilic substitution (SN2) reactions involving, amongst others, nucleophilic attack at carbon, nitrogen, silicon, and sulfur. In particular, we investigate the ability of the local density approximation (LDA), generalized gradient approximation (GGA), meta-GGA as well as hybrid DFT to reproduce high-level coupled cluster (CCSD(T)) benchmarks that are close to the basis set limit. The most accurate GGA, meta-GGA, and hybrid functionals yield mean absolute deviations of about 2 kcal/mol relative to the coupled cluster data, for reactant complexation, central barriers, overall barriers as well as reaction energies. For the three nonlocal DFT classes, the best functionals are found to be OPBE (GGA), OLAP3 (meta-GGA), and mPBE0KCIS (hybrid DFT). The popular B3LYP functional is not bad but performs significantly worse than the best GGA functionals. Furthermore, we have compared the geometries from several density functionals with the reference CCSD(T) data. The same GGA functionals that perform best for the energies (OPBE, OLYP), also perform best for the geometries with average absolute deviations in bond lengths of 0.06 Å and 0.6°, even better than the best meta-GGA and hybrid functionals. In view of the reduced computational effort of GGAs with respect to meta-GGAs and hybrid functionals, let alone coupled cluster, we recommend the use of accurate GGAs such as OPBE or OLYP for the study of SN2 reactions. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] On the applicability of the HSAB principle through the use of improved computational schemes for chemical hardness evaluationJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2004Mihai V. Putz Abstract Finite difference schemes, named Compact Finite Difference Schemes with Spectral-like Resolution, have been used for a less crude approximation of the analytical hardness definition as the second-order derivative of the energy with respect to the electron number. The improved computational schemes, at different levels of theory, have been used to calculate global hardness values of some probe bases, traditionally classified as hard and soft on the basis of their chemical behavior, and to investigate the quantitative applicability of the HSAB principle. Exchange acid-base reactions have been used to test the HSAB principle assuming the reaction energies as a measure of the stabilization of product adducts. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 994,1003, 2004 [source] Improved third-order Møller,Plesset perturbation theoryJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2003Stefan Grimme Abstract Based on a partitioning of the total correlation energy into contributions from parallel- and antiparallel-spin pairs of electrons, a modified third-order Møller,Plesset (MP) perturbation theory is developed. The method, termed SCS,MP3 (SCS for spin-component-scaled) continues previous work on an improved version of MP2 (S. Grimme, J Chem Phys 2003, 118, 9095). A benchmark set of 32 isogyric reaction energies, 11 atomization energies, and 11 stretched geometries is used to assess to performance of the model in comparison to the standard quantum chemical approaches MP2, MP3, and QCISD(T). It is found, that the new method performs significantly better than usual MP2/MP3 and even outperforms the more costly QCISD method. Opposite to the usual MP series, the SCS third-order correction uniformly improves the results. Dramatic enhancements are especially observed for the more difficult atomization energies, some of the stretched geometries, and reaction and ionization energies involving transition metal compounds where the method seems to be competitive or even superior to the widely used density functional approaches. Further tests performed for other complex systems (biradicals, C20 isomers, transition states) demonstrate that the SCS,MP3 model yields often results of QCISD(T) accuracy. The uniformity with which the new approach improves for very different correlation problems indicates significant robustness, and suggests it as a valuable quantum chemical method of general use. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1529,1537, 2003 [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] Spin State, Structure, and Reactivity of Terminal Oxo and Dioxygen Complexes of the (PNP)Rh MoietyCHEMISTRY - A EUROPEAN JOURNAL, Issue 25 2008Alexander Abstract [RhIIIH{(tBu2PCH2SiMe2NSiMe2CH2PtBu{CMe2CH2})}], ([RhH(PNP*)]), reacts with O2 in the time taken to mix the reagents to form a 1:1 ,2 -O2 adduct, for which OO bond length is discussed with reference to the reducing power of [RhH(PNP*)]; DFT calculations faithfully replicate the observed O,O distance, and are used to understand the oxidation state of this coordinated O2. The reactivity of [Rh(O2)(PNP)] towards H2, CO, N2, and O2 is tested and compared to the associated DFT reaction energies. Three different reagents effect single oxygen atom transfer to [RhH(PNP*)]. The resulting [RhO(PNP)], characterized at and above ,60,°C and by DFT calculations, is a ground-state triplet, is nonplanar, and reacts, above about +15,°C, with its own tBu CH bond, to cleanly form a diamagnetic complex, [Rh(OH){N(SiMe2CH2PtBu2)(SiMe2CH2PtBu{CMe2CH2})}]. [source] Theoretical Studies of Damage to 3,-Uridine Monophosphate Induced by Electron AttachmentCHEMISTRY - A EUROPEAN JOURNAL, Issue 9 2008bo Zhang Ass. Abstract Low-energy electrons (LEE) are well known to induce nucleic acid damage. However, the damage mechanisms related to charge state and structural features remain to be explored in detail. In the present work, we have investigated the N1-glycosidic and C3,O(P) bond ruptures of 3,-UMP (UMP=uridine monophosphate) and the protonated form 3,-UMPH with ,1 and zero charge, respectively, based on hybrid density functional theory (DFT) B3,LYP together with the 6-31+G(d,p) basis set. The glycosidic bond breakage reactions of the 3,UMP and 3,UMPH electron adducts are exothermic in both cases, with barrier heights of 19,20,kcal,mol,1 upon inclusion of bulk solvation. The effects of the charge state on the phosphate group are marginal, but the C2,OH group destabilizes the transition structure of glycosidic bond rupture of 3,-UMPH in the gas phase by approximately 5.0,kcal,mol,1. This is in contrast with the C3,O(P) bond ruptures induced by LEE in which the charge state on the phosphate influences the barrier heights and reaction energies considerably. The barrier towards C3,O(P) bond dissociation in the 3,UMP electron adduct is higher in the gas phase than the one corresponding to glycosidic bond rupture and is dramatically influenced by the C2,OH group and bulk salvation, which decreases the barrier to 14.7,kcal,mol,1. For the C3,O(P) bond rupture of the 3,UMPH electron adduct, the reaction is exothermic and the barrier is even lower, 8.2,kcal,mol,1, which is in agreement with recent results for 3,-dTMPH and 5,-dTMPH (dTMPH=deoxythymidine monophosphate). Both the Mulliken atomic charges and unpaired-spin distribution play significant roles in the reactions. [source] Ionization-Induced Proton Transfer in Model DNA Base Pairs: A Theoretical Study of the Radical Ions of the 7-Azaindole DimerCHEMPHYSCHEM, Issue 12 2004Hsing-Yin Chen Dr. Abstract Proton-transfer reactions of the radical anion and cation of the 7-Azaindole (7AI) dimer were investigated by means of density functional theory (DFT). The calculated results for the dimer anion and cation were very similar. Three equilibrium structures, which correspond to the non-proton-transferred (normal), the single-proton-transferred (SPT) and the double-proton-transferred (tautomeric) forms, were found. The transition states for proton-transfer reactions were also located. The calculations showed that the first proton-transfer reaction (normal,SPT) is exothermic and almost barrier-free; therefore, it should occur spontaneously in the period of a vibration. In contrast, the second proton-transfer reaction (SPT,tautomer) was found to be far less-probable in terms of reaction energy and barrier. Hence, it was concluded that both (7AI)2and (7AI)2exist in the SPT form. The conclusion was further confirmed by the calculated electron vertical detachment energy (VDE) of the SPT form of (7AI)2, 1.33 eV, which is very close to the experimental measurement of 1.35 eV. The calculated VDEs of the normal and tautomeric (7AI)2forms were too small compared to the experimental value. The proton transfer process was found to be multidimensional in nature involving not only proton motion but also intermolecular rocking motion. In addition, IR spectra were calculated and reported. The spectra of the three structures showed very different features and, therefore, can be considered as fingerprints for future experimental identifications. The implications of these results to biology and spectroscopy are also briefly discussed. [source] | ||||||||||