Vapor-phase Beckmann rearrangement of oxime molecules over H-Faujasite zeolite.

The Beckmann rearrangement (BR) plays an important role in a variety of industries. The mechanism of this reaction rearrangement of oximes with different molecular sizes, specifically, the oximes of formaldehyde (H₂C?NOH), Z‐acetaldehyde (CH₃HC?NOH), E‐acetaldehyde (CH₃HC?NOH) and acetone (CH₃)₂C?NOH, catalyzed by the Faujasite zeolite is investigated by both the quantum cluster and embedded cluster approaches at the B3LYP level of theory using the 6‐31G (d,p) basis set. To enhance the energetic properties, single point calculations are undertaken at MP2/6‐311G(d,p). The rearrangement step, using the bare cluster model, is the rate determining step of the entire reaction of these oxime molecules of which the energy barrier is between 50–70 kcal mol^?1. The more accurate embedded cluster model, in which the effect of the zeolitic framework is included, yields as the rate determining step, the formaldehyde oxime reaction rearrangement with an energy barrier of 50.4 kcal mol^?1. With the inclusion of the methyl substitution at the carbon‐end of formaldehyde oxime, the rate determining step of the reaction becomes the 1,2 H‐shift step for Z‐acetaldehyde oxime (30.5 kcal mol^?1) and acetone oxime (31.2 kcal mol^?1), while, in the E‐acetaldehyde oxime, the rate determining step is either the 1,2 H‐shift (26.2 kcal mol^?1) or the rearrangement step (26.6 kcal mol^?1). These results signify the important role that the effect of the zeolite framework plays in lowering the activation energy by stabilizing all of the ionic species in the process. It should, however, be noted that the sizeable turnover of a reaction catalyzed by the Brønsted acid site might be delayed by the quantitatively high desorption energy of the product and readsorption of the reactant at the active center.     

Comprehensive Analysis of DNA Strand Breaks at the Guanosine Site Induced by Low‐Energy Electron Attachment

To elucidate the role of guanosine in DNA strand breaks caused by low‐energy electrons (LEEs), theoretical investigations of the LEE attachment‐induced C? O σ‐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 C? O 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 C? O bond cleavage to 1.06–3.56 kcal mol^?1. These low‐energy barriers ensure that either C_5′? O_5′ or C_3′? O_3′ 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 C? O 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.     

Oxidative Dehydrogenation of Propane over a VO2‐Exchanged MCM‐22 Zeolite: A DFT Study

The adsorption and the mechanism of the oxidative dehydrogenation (ODH) of propane over VO₂‐exchanged MCM‐22 are investigated by DFT calculations using the M06‐L functional, which takes into account dispersion contributions to the energy. The adsorption energies of propane are in good agreement with those from computationally much more demanding MP2 calculations and with experimental results. In contrast, B3LYP binding energies are too small. The reaction begins with the movement of a methylene hydrogen atom to the oxygen atom of the VO₂ group, which leads to an isopropyl radical bound to a HO? V? O intermediate. This step is rate determining with the apparent activation energy of 30.9 kcal mol^?1, a value within the range of experimental results for ODH over other silica supports. In the propene formation step, the hydroxyl group is the more reactive group requiring an apparent activation energy of 27.7 kcal mol^?1 compared to that of the oxy group of 40.8 kcal mol^?1. To take the effect of the extended framework into account, single‐point calculations on 120T structures at the same level of theory are performed. The apparent activation energy is reduced to 28.5 kcal mol^?1 by a stabilizing effect caused by the framework. Reoxidation of the catalyst is found to be important for the product release at the end of the reaction.     

C-H bond activation of methane in aqueous solution: a hybrid quantum mechanical/effective fragment potential study

In this study, we investigated the C? H bond activation of methane catalyzed by the complex [PtCl₄]^2?, using the hybrid quantum mechanical/effective fragment potential (EFP) approach. We analyzed the structures, energetic properties, and reaction mechanism involved in the elementary steps that compose the catalytic cycle of the Shilov reaction. Our B3LYP/SBKJC/cc‐pVDZ/EFP results show that the methane activation may proceed through two pathways: (i) electrophilic addition or (ii) direct oxidative addition of the C? H bond of the alkane. The electrophilic addition pathway proceeds in two steps with formation of a σ‐methane complex, with a Gibbs free energy barrier of 24.6 kcal mol^?1, followed by the cleavage of the C? H bond, with an energy barrier of 4.3 kcal mol^?1. The activation Gibbs free energy, calculated for the methane uptake step was 24.6 kcal mol^?1, which is in good agreement with experimental value of 23.1 kcal mol^?1 obtained for a related system. The results shows that the activation of the C? H bond promoted by the [PtCl₄]^2? catalyst in aqueous solution occurs through a direct oxidative addition of the C? H bond, in a single step, with an activation free energy of 25.2 kcal mol^?1, as the electrophilic addition pathway leads to the formation of a σ‐methane intermediate that rapidly undergoes decomposition. The inclusion of long‐range solvent effects with polarizable continuum model does not change the activation energies computed at the B3LYP/SBKJC/cc‐pVDZ/EFP level of theory significantly, indicating that the large EFP water cluster used, obtained from Monte Carlo simulations and analysis of the center‐of‐mass radial pair distribution function, captures the most important solvent effects. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Kinetics and mechanism of the interaction of adenosine with cis‐diaqua(cis‐1,2‐diaminocyclohexane)platinum(II) perchlorate in aqueous medium

The kinetics of the interaction of adenosine with cis‐[Pt(cis‐dach)(OH₂)₂]²⁺ (dach = diaminocyclohexane) was studied spectrophotometrically as a function of [cis‐[Pt(cis‐dach)(OH₂)₂]²⁺], [adenosine], and temperature at a particular pH (4.0), where the substrate complex exists predominantly as the diaqua species and the ligand adenosine exists as a neutral molecule. The substitution reaction shows two consecutive steps: the first is the ligand‐assisted anation followed by a chelation step. The activation parameters for both the steps have been evaluated using Eyring equation. The low negative value of ΔH^≠₁ (43.1 ± 1.3 kJ mol^?1) and the large negative value of ΔS^≠₁ (?177 ± 4 J K^?1 mol^?1) along with ΔH^≠₂ (47.9 ± 1.8 kJ mol^?1) and ΔS^≠₂ (?181 ± 6 J K^?1 mol^?1) indicate an associative mode of activation for both the aqua ligand substitution processes. The kinetic study was substantiated by infrared and electrospray ionization mass spectroscopic analysis. © 2011 Wiley Peiodicals, Inc. Int J Chem Kinet 43: 219–229, 2011     

Kinetics of the substitution reactions of some Pt(II) complexes with 5′‐GMP and L‐histidine

The reactions of platinum(II) complexes, [PtCl₂(dach)] (dach = (1R,2R)‐1,2‐diaminocyclohexane) and [PtCl₂(en)] (en = ethylenediamine) with biologically relevant ligands such as 5′‐GMP (guanosine‐5′‐monophosphate) and l ‐His (l ‐histidine) were studied by UV–vis spectrophotometry, ¹H NMR spectroscopy, and high‐performance liquid chromatography (HPLC). Spectrophotometrically, these reactions were investigated under pseudo‐first‐order conditions at 310 K in 25 mM Hepes buffer (pH 7.2) and 10 mM NaCl to prevent the hydrolysis of the complexes. The [PtCl₂(en)] complex reacts faster than [PtCl₂(dach)] in the reaction with studied nucleophiles. This confirms the fact that the reactivity of studied Pt(II) complexes depends on the structure of the inert bidentate ligand. Also, the substitution reactions with l ‐His are always faster than the reactions with nucleotide 5′‐GMP. The reactions of [PtCl₂(dach)] and [PtCl₂(en)] complexes with l ‐histidine are studied by ¹H NMR spectroscopy. The obtained rate constants are in agreement with those obtained by UV–vis. The same reactions were studied by HPLC comparing the obtained chromatograms during the reaction. The changes in intensity of signals of the free and coordinated ligand show that after a few days there is only one dominant product in the system. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 43: 99–106, 2011     

Photolysis and Thermolysis of Platinum(IV) 2,2′‐Bipyridine Complexes Lead to Identical Platinum(II)–DNA Adducts

Two Pt^IV and two Pt^II complexes containing a 2,2′‐bipyridine ligand were treated with a short DNA oligonucleotide under light irradiation at 37 °C or in the dark at 37 and 50 °C. Photolysis and thermolysis of the Pt^IV complexes led to spontaneous reduction of the Pt^IV to the corresponding Pt^II complexes and to binding of Pt^II 2,2′‐bipyridine complexes to N7 of guanine. When the reduction product was [Pt(bpy)Cl₂], formation of bis‐oligonucleotide adducts was observed, whereas [Pt(bpy)(MeNH₂)Cl]⁺ gave monoadducts, with chloride ligands substituted in both cases. Neither in the dark nor under light irradiation was the reductive elimination process of these Pt^IV complexes accompanied by oxidative DNA damage. This work raises the question of the stability of photoactivatable Pt^IV complexes toward moderate heating conditions.     

Thermochemical properties for n‐propyl,iso‐propyl,and tert‐butyl nitroalkanes,alkyl nitrites,and their carbon‐centered radicals

Density functional theory (DFT) based calculations are performed on a series of alkyl nitrites and nitroalkanes representing large‐scale primary, secondary, and tertiary nitro compounds and their radicals resulting from the loss of their skeletal hydrogen atoms. Geometries, vibration frequencies, and thermochemical properties [S°(T) and C°_p(T) (10 K ? T ? 5000 K)] are calculated at the B3LYP/6‐31G(d,p) DFT level. Δ_fH°₂₉₈ values are from B3LYP/6‐31G(d,p), B3LYP/6‐31+G(2d,2p), and the composite CBS‐QB3 levels. Potential energy barriers for the internal rotations have been computed at the B3LYP/6‐31G(d,p) level of theory, and the lower barrier contributions are incorporated into entropy and heat capacity data. The standard enthalpies of formation at 298 K are evaluated using isodesmic reaction schemes with several work reactions for each species. Recommended values derived from the most stable conformers of respective nitro‐ and nitrite isomers include ?30.57 and ?28.44 kcal mol^?1 for n‐propane‐, ?33.89 and ?32.32 kcal mol^?1 for iso‐propane‐, ?42.78 and ?41.36 kcal mol^?1 for tert‐butane‐nitro compounds and nitrites, respectively. Entropy and heat capacity values are also reported for the lower homologues: nitromethane, nitroethane, and corresponding nitrites. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 181–199, 2010     

Enthalpy of formation and bond energies on unsaturated oxygenated hydrocarbons using G3MP2B3 calculation methods

Enthalpies of unsaturated oxygenated hydrocarbons and radicals corresponding to the loss of hydrogen atoms from the parent molecules are intermediates and decomposition products in the oxidation and combustion of aromatic and polyaromatic species. Enthalpies (Δ_fH⁰₂₉₈) are calculated for a set of 27 oxygenated and nonoxygenated, unsaturated hydrocarbons and 12 radicals at the G3MP2B3 level of theory and with the commonly used B3LYP/6‐311g(d,p) density functional theory (DFT) method. Standard enthalpies of formation (Δ_fH⁰₂₉₈) are determined from the calculated enthalpy of reaction (ΔH⁰_rxn,298) using isodesmic work reactions with reference species that have accurately known Δ_fH⁰₂₉₈ values. The deviation between G3MP2B3 and B3LYP methods is under ±0.5 kcal mol^?1 for 9 species, 18 other species differs by less than ±1 kcal mol^?1 , and 11 species differ by about 1.5 kcal mol^?1. Under them are 11 radicals derived from the above‐oxygenated hydrocarbons that show good agreement between G3MP2B3 and B3LYP methods. G3 calculations have been performed to further validate enthalpy values, where a discrepancy of more than 2.5 kcal mol^?1 exists between the G3MP3B3 and density functional results. Surprisingly the G3 calculations support the density functional calculations in these several nonagreement cases. © 2005 Wiley Periodicals, Inc. Int J Chem Kinet 37: 633–648, 2005     

Thermochemistry and Kinetics of the Thermal Decomposition of 1‐Chlorohexane

A theoretical kinetic study of the thermal decomposition of 1‐chlorohexane in gas phase between 600 and 1000 K was performed. Transition‐state theory and unimolecular reaction rate theory were combined with molecular information provided by quantum chemical calculations. Particularly, the B3LYP, BMK, M05–2X, and M06–2X formulations of the density functional theory (DFT) and the high‐level ab initio methods G3B3 and G4 were employed. The possible reaction channels for the thermal decomposition of 1‐chlorohexane were investigated, and the reaction takes place through the elimination of HCl with the formation of 1‐hexene. The derived high‐pressure limit rate coefficients are k _∞(600–1000 K) = (8 ± 5) × 10¹³ exp[‐((56.7 ± 0.4) kcal mol⁻¹/RT )] s⁻¹. The pressure effect over the reaction was analyzed from the calculation of the low‐pressure limit rate coefficients and the falloff curves. In addition, the standard enthalpies of formation at 298 K of −46.9 ± 1.5 kcal mol⁻¹ for 1‐chlorohexane and 5.8 ± 1.5 kcal mol⁻¹ for C₆H₁₃ radical were derived from isodesmic and isogiric reactions at high levels of theory.     

Formic acid catalyzed gas-phase reaction of H2O with SO3 and the reverse reaction: a theoretical study

The formic acid catalyzed gas‐phase reaction between H₂O and SO₃ and its reverse reaction are respectively investigated by means of quantum chemical calculations at the CCSD(T)//B3LYP/cc‐pv(T+d)z and CCSD(T)//MP2/aug‐cc‐pv(T+d)z levels of theory. Remarkably, the activation energy relative to the reactants for the reaction of H₂O with SO₃ is lowered through formic acid catalysis from 15.97 kcal mol^?1 to ?15.12 and ?14.83 kcal mol^?1 for the formed H₂O ??? SO₃ complex plus HCOOH and the formed H₂O ??? HCOOH complex plus SO₃, respectively, at the CCSD(T)//MP2/aug‐cc‐pv(T+d)z level. For the reverse reaction, the energy barrier for decomposition of sulfuric acid is reduced to ?3.07 kcal mol^?1 from 35.82 kcal mol^?1 with the aid of formic acid. The results show that formic acid plays a strong catalytic role in facilitating the formation and decomposition of sulfuric acid. The rate constant of the SO₃+H₂O reaction with formic acid is 10⁵ times greater than that of the corresponding reaction with water dimer. The calculated rate constant for the HCOOH+H₂SO₄ reaction is about 10^?13 cm³ molecule^?1 s^?1 in the temperature range 200–280 K. The results of the present investigation show that formic acid plays a crucial role in the cycle between SO₃ and H₂SO₄ in atmospheric chemistry.     

Mechanism for the gas‐phase hydrogen fluoride‐mediated decomposition of peroxyacetyl nitrate (PAN) studied by DFT method

Density functional theory has been used to study the mechanism of the decomposition of peroxyacetyl nitrate (CH₃C(O)OONO₂) in hydrogen fluoride clusters containing one to three hydrogen fluoride molecules at the B3LYP/6‐311++G(d,p) and B3LYP/6‐311+G(3df,3pd) levels. The calculations clarify some of the uncertainties in the mechanism of PAN decomposition in the gas phase. The energy barrier decreases from 30.5 kcal mol^?1 (single hydrogen fluoride) to essentially 18.5 kcal mol^?1 when catalyzed by three hydrogen fluoride molecules. As the size of the hydrogen fluoride cluster is increased, PAN shows increasing ionization along the O? N bond, consistent with the proposed predissociation in which the electrophilicity of the nitrogen atom is enhanced. This reaction is found to proceed through an attack of a fluorine to the PAN nitrogen in concert with a proton transfer to a PAN oxygen. On the basis of our calculations, an alternative reaction mechanism for the decomposition of PAN is proposed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Kinetics and Mechanism of the Reaction of Chloroplatinum(II) Complexes with Alkyl Radicals

The reaction between certain platinum(II) complexes and alky radicals produces an unstable organoplatinum(III) intermediate, {Pt^III -R}. The kinetics of this step were evaluated by laser flash photolysis with ABTS² (2,2′-azinobis(3-ethylbenzothiazoline-6-sulfonate) ion) and TMPD (tetramethylphenylenediamine) as kinetic probes. The rate constants for PtCl₄^2? are: k_Pt/10⁸ L mol^?1 s^?1 = 5.2, 2.8 and 0.27 for CH_3, C₂H₅, and CH₂Cl in aqueous solution at pH 1. Those with cis-Pt(NH₃)₂Cl₂ are somewhat smaller, and those for Pt(NH₃)₄²⁺ too small to measure will) this technique. The product analysis indicates that the decomposition of organoplatinum takes place by hydrolysis and (for R = C₂H₅ only) by β-elimination, The kinetic isotope effect on die β-elimination of DCH₂CH₂PtC₄,^2? is k_H/k_D = 1.2. The β-elimination step produces a Pt^III-hydride that releases hydrogen gas and forms {Pt_III-OH}. The short-lived Pt(III) intermediate may disproportionate or oxidize the Co^II complex that is produced in the radical-generating step.     

Evaluation of DFT Methods and Implicit Solvation Models for Anion‐Binding Host‐Guest Systems

Although supramolecular chemistry is traditionally an experimental discipline, computations have emerged as important tools for the understanding of supramolecules. We have explored how well commonly used density functional theory quantum mechanics and polarizable continuum solvation models can calculate binding affinities of host‐guest systems. We report the calculation of binding affinities for eight host–guest complexes and compare our results to experimentally measured binding free energies that span the range from ?2.3 to ?6.1 kcal mol^?1. These systems consist of four hosts (biotin[6]uril, triphenoxymethane, cryptand, and bis‐thiourea) with different halide ions (F^?, Cl^?, Br^?) in various media including organic and aqueous. The mean average deviation (MAD) of calculated from measured ΔG_a is 2.5 kcal mol^?1 when using B3LYP‐D3 with either CPCM or PCM. This MAD value lowers even more by eliminating two outliers: 1.1 kcal mol^?1 for CPCM and 1.2 kcal mol^?1 for PCM. The best DFT and implicit solvation model combination that we have studied is B3LYP?D3 with either CPCM or PCM.     

Frontside versus Backside SN2 Substitution at Group 14 Atoms: Origin of Reaction Barriers and Reasons for Their Absence

We have theoretically studied the gas‐phase nucleophilic substitution at group‐14 atoms (S_N2@A) in the model reactions of Cl^?+AH₃Cl (A=C, Si, Ge, Sn, and Pb) using relativistic density functional theory (DFT) at ZORA‐OLYP/TZ2P. Firstly, we wish to explore and understand how the reaction coordinate ζ, and potential energy surfaces (PES) along ζ, vary as the center of nucleophilic attack changes from carbon to the heavier group‐14 atoms. Secondly, a comparison between the more common backside reaction (S_N2‐b) and the frontside pathway (S_N2‐f) is performed. The S_N2‐b reaction is found to have a central barrier for A=C, but none for the other group‐14 atoms, A=Si–Pb. Relativistic effects destabilize reactant complexes and transition species by up to 10 kcal mol^?1 (for S_N2‐f@Pb), but they do not change relative heights of barriers. We also address the nature of the transformation in the frontside S_N2‐f reactions in terms of turnstile rotation versus Berry‐pseudorotation mechanism.     

Reaction mechanism of platinum dimer cation with ammonia based on the relativistic density functional study

The gas‐phase reactions between Pt and NH₃ have been investigated using the relativistic density functional approach (ZORA‐PW91/TZ2P). The quartet and doublet potential energy surfaces of Pt + NH₃ have been explored. The minimum energy reaction path proceeds through the following steps: Pt(⁴Σ_u) + NH₃ → q‐1 → d‐2 → d‐3 → d‐4 → d‐Pt₂NH⁺ + H₂. In the whole reaction pathway, the step of d‐2 → d‐3 is the rate‐determining step with a energy barrier of 36.1 kcal/mol, and exoergicity of the whole reaction is 12.0 kcal/mol. When Pt₂NH⁺ reacts with NH₃ again, there are two rival reaction paths in the doublet state. One is degradation of NH and another is loss of H₂. In the case of degradation of NH, the activation energy is only 3.4 kcal/mol, and the overall reaction is exothermic by 8.9 kcal/mol. Thus, this reaction is favored both thermodynamically and kinetically. However, in the case of loss of H₂, the rate‐determining step's energy barrier is 64.3 kcal/mol and the overall reaction is endothermic by 8.5 kcal/mol, so it is difficult to take place. Predicted relative energies and barriers along the suggested reaction paths are in reasonable agreement with experimental observations. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Formation of a Thymine‐HgII‐Thymine Metal‐Mediated DNA Base Pair: Proposal and Theoretical Calculation of the Reaction Pathway

A reaction mechanism that describes the substitution of two imino protons in a thymine:thymine (T:T) mismatched DNA base pair with a Hg^II ion, which results in the formation of a (T)N3‐Hg^II‐N3(T) metal‐mediated base pair was proposed and calculated. The mechanism assumes two key steps: The formation of the first Hg^II? N3(T) bond is triggered by deprotonation of the imino N3 atom in thymine with a hydroxo ligand on the Hg^II ion. The formation of the second Hg^II? N3(T) bond proceeds through water‐assisted tautomerization of the remaining, metal‐nonbonded thymine base or through thymine deprotonation with a hydroxo ligand of the Hg^II ion already coordinated to the thymine base. The thermodynamic parameters ΔG_R=?9.5 kcal mol^?1, ΔH_R=?4.7 kcal mol^?1, and ΔS_R=16.0 cal mol^?1 K^?1 calculated with the ONIOM (B3LYP:BP86) method for the reaction agreed well with the isothermal titration calorimetric (ITC) measurements by Torigoe et al. [H. Torigoe, A. Ono, T. Kozasa, Chem. Eur. J. 2010 , 16, 13218–13225]. The peculiar positive reaction entropy measured previously was due to both dehydration of the metal and the change in chemical bonding. The mercury reactant in the theoretical model contained one hydroxo ligand in accord with the experimental pK_a value of 3.6 known for an aqua ligand of a Hg^II center. The chemical modification of T:T mismatched to the T‐Hg^II‐T metal‐mediated base pair was modeled for the middle base pair within a trinucleotide B‐DNA duplex, which ensured complete dehydration of the Hg^II ion during the reaction.     

Mechanism of the Pd‐catalyzed Decarboxylative Allylation of α‐Imino Esters: Decarboxylation via Free Carboxylate Ion

The Pd‐catalyzed decarboxylative allylation of α‐(diphenylmethylene)imino esters ( 1 ) or allyl diphenylglycinate imines ( 2 ) is an efficient method to construct new C(sp³)? C(sp³) bonds. The detailed mechanism of this reaction was studied by theoretical calculations [ONIOM(B3LYP/LANL2DZ+p:PM6)] combined with experimental observations. The overall catalytic cycle was found to consist of three steps: oxidative addition, decarboxylation, and reductive allylation. The oxidative addition of 1 to [(dba)Pd(PPh₃)₂] (dba=dibenzylideneacetone) produces an allylpalladium cation and a carboxylate anion with a low activation barrier of +9.1 kcal mol^?1. The following rate‐determining decarboxylation proceeds via a solvent‐exposed α‐imino carboxylate anion rather than an O‐ligated allylpalladium carboxylate with an activation barrier of +22.7 kcal mol^?1. The 2‐azaallyl anion generated by this decarboxylation attacks the face of the allyl ligand opposite to the Pd center in an outer‐sphere process to produce major product 3 , with a lower activation barrier than that of the minor product 4 . A positive linear Hammett correlation [ρ=1.10 for the PPh₃ ligand] with the observed regioselectivity ( 3 versus 4 ) supports an outer‐sphere pathway for the allylation step. When Pd combined with the bis(diphenylphosphino)butane (dppb) ligand is employed as a catalyst, the decarboxylation still proceeds via the free carboxylate anion without direct assistance of the cationic Pd center. Consistent with experimental observations, electron‐withdrawing substituents on 2 were calculated to have lower activation barriers for decarboxylation and, thus, accelerate the overall reaction rates.     

Interactions of the “piano‐stool” [ruthenium(II) (η6‐arene)(en)CL]+ complexes with water and nucleobases; ab initio and DFT study

Piano stool ruthenium complexes of the composition [Ru(II)(η⁶‐arene)(en)Cl]^+/2+ (en = ethylenediamine) represent an emerging class of cisplatin‐analogue anticancer drug candidates. In this study, we use computational quantum chemistry to characterize the structure, stability and reactivity of these compounds. All these structures were optimized at DFT(B3LYP)/6‐31G(d) level and their single point properties were determined by the MP2/6‐31++G(2df,2pd) method. Thermodynamic parameters and rate constants were determined for the aquation process, as a replacement of the initial chloro ligand by water and subsequent exchange reaction of aqua ligand by nucleobases. The computations were carried out at several levels of DFT and ab initio theories (B3LYP, MP2 and CCSD) utilizing a range of bases sets (from 6‐31G(d) to aug‐cc‐pVQZ). Excellent agreement with experimental results for aquation process was obtained at the CCSD level and reasonable match was achieved also with the B3LYP/6‐31++G(2df,2pd) method. This level was used also for nucleobase‐water exchange reaction where a smaller rate constant for guanine exchange was found in comparison with adenine. Although adenine follows a simple replacement mechanism, guanine complex passes by a two‐step mechanism. At first, Ru‐O6(G) adduct is formed, which is transformed through a chelate TS2 to the Ru‐N7(G) final complex. In case of guanine, the exchange reaction is more favorable thermodynamically (releasing in total by about 8 kcal/mol) but according to our results, the rate constant for guanine substitution is slightly smaller than the analogous constant in adenine case when reaction course from local minimum is considered. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009     

Different catalysis role of in‐loop and out‐of‐loop waters in assisting HNS/HSN proton transfer isomerizations: Bridging vs. surrounding effect

In this work, a density function theory (DFT) study is presented for the HNS/HSN isomerization assisted by 1–4 water molecules on the singlet state potential energy surface (PES). Two modes are considered to model the catalytic effect of these water molecules: (i) water molecule(s) participate directly in forming a proton transfer loop with HNS/HSN species, and (ii) water molecules are out of loop (referred to as out‐of‐loop waters) to assist the proton transfer. In the first mode, for the monohydration mechanism, the heat of reaction is 21.55 kcal · mol^?1 at the B3LYP/6‐311++G** level. The corresponding forward/backward barrier lowerings are obtained as 24.41/24.32 kcal · mol^?1 compared with the no‐water‐assisting isomerization barrier T (65.52/43.87 kcal · mol^?1). But when adding one water molecule on the HNS, there is another special proton‐transfer isomerization pathway with a transition state 10T′ in which the water is out of the proton transfer loop. The corresponding forward/backward barriers are 65.89/65.89 kcal · mol^?1. Clearly, this process is more difficult to follow than the R–T–P process. For the two‐water‐assisting mechanism, the heat of reaction is 19.61 kcal · mol^?1, and the forward/backward barriers are 32.27/12.66 kcal · mol^?1, decreased by 33.25/31.21 kcal · mol^?1 compared with T. For trihydration and tetrahydration, the forward/backward barriers decrease as 32.00/12.60 (30T) and 37.38/17.26 (40T) kcal · mol^?1, and the heat of reaction decreases by 19.39 and 19.23 kcal · mol^?1, compared with T, respectively. But, when four water molecules are involved in the reactant loop, the corresponding energy aspects increase compared with those of the trihydration. The forward/backward barriers are increased by 5.38 and 4.66 kcal · mol^?1 than the trihydration situation. In the second mode, the outer‐sphere water effect from the other water molecules directly H‐bonded to the loop is considered. When one to three water molecules attach to the looped water in one‐water in‐loop‐assisting proton transfer isomerization, their effects on the three energies are small, and the deviations are not more than 3 kcal · mol^?1 compared with the original monohydration‐assisting case. When adding one or two water molecules on the dihydration‐assisting mechanism, and increasing one water molecule on the trihydration, the corresponding energies also are not obviously changed. The results indicate that the forward/backward barriers for the three in‐loop water‐assisting case are the lowest, and the surrounding water molecules (out‐of‐loop) yield only a small effect. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006