Showing papers on "Transition state published in 1994"
TL;DR: In this paper, the optimal interaction energies were found to be 1.5-2.0 kcal/mol more favorable for hydrogen bonding to the oxygen or nitrogen in the transition states than for the dienophiles.
Abstract: Ab initio molecular orbital calculations reveal enhanced hydrogen bonding of a water molecule to the transition states for the Diels-Alder reactions of cyclopentadiene with methyl vinyl ketone (MVK) and acrylonitrile. The optimal interaction energies are found to be 1.5-2.0 kcal/mol more favorable for hydrogen bonding to the oxygen or nitrogen in the transition states than for the dienophiles. This support the assertion from a prior simulation study that the observed rate accelerations for Diels-Alder reactions in aqueous solution arise from this hydrogen-bonding effect in addition to a relatively constant hydrophobic term
139 citations
TL;DR: In this article, aldol addition with a variety of aldehydes at room temperature without the need for catalysts was investigated, revealing a competition between 1,2-and 1,Caddition favoring the former.
Abstract: O(Silacyclobuty1) ketene acetals derived from esters, thiol esters, and amides underwent facile aldol addition with a variety of aldehydes at room temperature without the need for catalysts. The uncatalyzed aldol addition reaction of O(silacyclobuty1) ketene acetals displayed the following characteristics: (1) the rate of reaction was highly dependent on the spectator substituent on silicon and the geometry of the ketene acetal, (2) the 0,O-ketene acetal of E configuration afforded the syn aldol products with high diastereoselectivity (93/7 to 99/1), (3) conjugated aldehydes reacted more rapidly than aliphatic aldehydes, and (4) the reaction was mildly sensitive to solvent. In addition, the aldol reaction was found to be efficiently catalyzed by metal alkoxides. Labeling experiments revealed that the thermal aldol reaction proceeds by direct intramolecular silicon group transfer, while the alkoxide-catalyzed version probably proceeds via in situ generated metal enolates. Computational modeling of the transition states suggests that the boat transition structures are preferred, supporting the observed syn selectivity of the thermal aldol reaction. Both thermal and alkoxide-catalyzed Michael additions were investigated, revealing a competition between 1,2- and 1 ,Caddition favoring the former.
130 citations
TL;DR: In this article, high-level ab initio calculations at the QCISD/6-311G∗∗ + ZPVE level have been carried out to study the addition reactions of CH, CHOH∗, and CHCN∗ radicals to the substituted alkenes CH=CHX (X = H, NH, F, CI, CHO, and CN) and the results analyzed with the aid of the curve-crossing model.
Abstract: High-level ab initio calculations at the QCISD/6-311G∗∗ + ZPVE level have been carried out to study the addition reactions of CH∗, CHOH∗, and CHCN∗ radicals to the substituted alkenes CH=CHX (X = H, NH, F, CI, CHO, and CN) and the results analyzed with the aid of the curve-crossing model. We find that the reactivity of CH∗ is primarily governed by enthalpy effects, whereas both enthalpy and polar effects are important for the reactions of CHOH∗ and CHCN∗ There is no general barrier height-enthalpy correlation for the latter two radicals because of the presence in some cases of polar effects that stabilize the transition states without a corresponding stabilization of the products. The polar effects are not sufficient, however, to significantly shift the location of the transition states, so a general structure-enthalpy correlation is observed.
102 citations
TL;DR: In this article, it was shown that if a hydride ion is split off from the paraffin, then the transition state resembles the adsorbed carbonium ion and the reaction results in molecular hydrogen and in formation of the surface alkoxy group.
Abstract: HF-21G quantum-chemical analysis of the protolytic attack of acid protons in zeolites at the C-H bonds in methane and ethane indicated that the resulting transition states depend on the sign of the bond polarization. If a hydride ion is split off from the paraffin, then the transition state resembles the adsorbed carbonium ion and the reaction results in molecular hydrogen and in formation of the surface alkoxy group. The case, when a proton tends to split off from the paraffin, corresponds to the hetero-isotope exchange of paraffins with surface OH groups. This is a concerted acid-base reaction with a transition state different from adsorbed carbonium ion.
75 citations
TL;DR: In this article, the Hartree-Fock-level energy profiles for base-catalysed hydrolysis (i.e., attack by OH−) of dimethyl and ethylene phosphate are determined at the Hartrees-FOCK level and with MP2 correlation corrections.
Abstract: Quantum-mechanical and solvation-effect calculations of the hydrolysis mechanism of dimethyl and ethylene phosphate, which are model compounds for the hydrolysis of DNA and RNA, respectively, are reported and used to explain the fact that in solution, five-membered-ring cyclic phosphates hydrolyse 106–108 times faster than acyclic esters. Ab initio energy profiles for the base-catalysed hydrolysis (i.e. attack by OH–) of dimethyl and ethylene phosphate are determined at the Hartree–Fock level and with MP2 correlation corrections. The reaction proceeds through the formation of a pentacovalent phosphorane transition state with attack by the hydroxide ion as the rate-determining step; stable phosphorane intermediates are not observed in the gas phase. A detailed analysis is made of the ring strain in the cyclic phosphate reactant, which had been proposed as the origin of the observed rate effect and the results for the reactants are compared with those for the transition state. Although there is strain in the ground state of the cyclic reactant, it does not contribute to the rate acceleration because of dihedral angle constraints present in the cyclic transition state. An estimate of solvation effects indicates that most of the rate acceleration observed in solution arises from differential solvation of the transition states.
64 citations
TL;DR: In this article, it was shown that the path of a chemical reaction of the potential energy surface of a system can only be a gradient line between two critical points, and existing rules of symmetry conservation along the reaction path were analyzed to establish their consistence with published experimental data and with ab initio calculations.
Abstract: We show that the path of a chemical reaction of the potential energy surface of a chemical system can only be a gradient line between two critical points. Existing rules of symmetry conservation along the reaction path are analysed to establish their consistence with published experimental data and with ab initio calculations. In some systems the possible existence of reaction paths consisting of several gradients lines (both equivalent and nonequivalent) has been demonstrated. The relationship between the reaction mechanisms and the corresponding paths on the potential energy surface is discussed. The bibliography includes 238 references.
64 citations
TL;DR: In this article, the addition reaction of ieri-butyl radical to a set of substituted alkenes, CH═CHX (X = H, NH, F, Cl, CHO, and CN), was analyzed with the aid of the curve-crossing model.
Abstract: High-level ab initio calculations at the QCISD/6-311G** + ZPVE level have been carried out to study the addition reactions of ieri-butyl radical to a set of substituted alkenes, CH═CHX (X = H, NH, F, Cl, CHO, and CN), and the results analyzed with the aid of the curve-crossing model. The reactivity of the tert-butyl radical is found to be governed by a combination of enthalpy and polar factors. The polar factor leads to tert-butyl radical displaying strong nucleophilic character which stabilizes the transition states by 20-25 kJ mol compared with those for the relatively nonpolar reactions of methyl radical. Consequently, barrier heights are significantly lower for radical addition reactions of tert-butyl (1.9-21.6 kJ mol) than for methyl (24.3-39.8 kJ mol). A transition state structure-enthalpy correlation is found for the addition reactions of tert-butyl radical but is shifted slightly from the correlation line previously found for the CH, CHOH, and ChCN radicals, reflecting the increasing importance of polar contributions.
55 citations
TL;DR: In this article, secondary tritium and primary 14C kinetic isotope effects were measured for the hydrolysis of a substrate promoted with retention or inversion of configuration according to the enzyme catalyst.
55 citations
54 citations
TL;DR: In this paper, three different pathways for ethylene decomposition were investigated and it was shown that due to the excess energy available in the photochemical experiments, all three mechanisms can give rise to rotationally hot H2 when proper account is taken of the transverse vibrational modes along the reaction paths.
Abstract: Ab initio quantum chemical methods are applied to the study of ethylene decomposition to acetylene and molecular hydrogen in the ground electronic state. Results are reported on three different pathways for ethylene decomposition—two stepwise processes involving a hydrogen transfer followed by 1,1 elimination of H2, or vice versa, and a 1,2 elimination. The latter proceeds through an energy maximum with two imaginary frequencies, rather than one as for conventional transition states. Ethylidene and vinylidene are predicted to be stationary points on the C2H4 and C2H2 potential energy surfaces, respectively. Recent photochemical studies have observed rotationally hot H2. It is shown that due to the excess energy available in the photochemical experiments, all three mechanisms can give rise to rotationally hot H2 when proper account is taken of the transverse vibrational modes along the reaction paths.
50 citations
TL;DR: In this paper, the formation of a ball-and-chain model adduct through a Diels-Alder reaction between 2,3-dimethylidene-bicyclo[2.2]octane (C 10 H 14 ) and buckminsterfullerene (C 60 ) has been studied theoretically by means of the AM1 semi-empirical method.
TL;DR: In this paper, the isotope exchange reactions of D 2 and CD 4 with a zeolite model were analyzed using ab initio calculations using an ionic character for the transmitted moieties, H - and CH 3 -, respectively.
Abstract: The isotope-exchange reactions of D 2 and CD 4 with a zeolite model are analyzed using ab initio calculations. It is concluded that these exchange reactions could occur with activation energies in the 25-40 kcal/mol region. The mechanisms for these exchanges are different than those encountered in previous modeling studies of the addition of ethylene, acetylene, and formaldehyde to the acidic sites of zeolites. The addition mechanisms come close to conceptually involving ZO - ,HR + -like transition states. However, the exchange-reaction transition states have anionic character for the transmitted moieties, H - and CH 3 - , respectively, and two protons are strongly attached to the oxygen of the zeolite model
TL;DR: In this article, a chemical model for the avoided crossing state (ACS) of the chemical reaction has been proposed for ground-state and excited-state reactivities of electrophile-nucleophile combinations.
Abstract: A chemical model has been constructed for the transition state (TS) that is otherwise defined only by mathematical terms as a saddle point on the potential-energy surface. The proposed model is the avoided crossing state (ACS) of the chemical reaction. Unlike the TS that is a priori unknown, the ACS possesses a wavefunction that is prescribed by the constraints of the avoided crossing and is explicit in terms of the participating VB configurations. These VB configurations provide simultaneously a generalized TS description along with lucid information about the chemical nature of the TS. Ab initio computations demonstrate that, for nine SN2 and nucleophilic addition reactions, the ACS is an excellent approximation for the TS. This proximity between the two structures means in turn, that the bottleneck of the reaction may be associated with the chemically well defined ACS. VB mixing ideas are used to articulate the ACS paradigm and derive electronic properties of this state and its antibonding companion state. Applications to ground-state and excited-state reactivities of electrophile–nucleophile combinations are discussed.
TL;DR: In this review, the prospects for application of probes exhibiting electron transfer, proton transfer, molecular rotations and isomerizations are presented and discussed and the general problem of photochemical modeling of biochemical reactions is discussed.
TL;DR: In this paper, the activation free energy of the identity SN2 reaction Cl− + CH3Cl → ClCH3 + Cl− in solution is examined theoretically, where two diabatic valence bond states, ψ1[Cl−1/CH3Cl] and ψ2[ClCH3/Cl−], are employed within the framework of the Kim-Hynes theory of solvation.
TL;DR: In this paper, the transition states for dissociation of NO and CO have been located and optimized for several reaction paths on cluster models of the copper (100) and (111) surfaces using density functional theory.
TL;DR: In this paper, an approach for including solvent effects in variational transition state theory calculations of rate constants for activated chemical reactions in solution is presented, and the focus is on methods capable of first-principles predictions of reaction rate constants from interatomic potential energy surfaces.
Abstract: An approach is outlined for including solvent effects in variational transition state theory calculations of rate constants for activated chemical reactions in solution. The focus is on methods capable of first-principles predictions of reaction rate constants from interatomic potential energy surfaces. The approach separates the system into a cluster model that is treated explicitly and the ‘solvent’ that is treated approximately, and includes both equilibrium solvation effects on interaction energies and non-equilibrium effects that enter through a solvent friction model. We discuss methods used to included quantum-mechanical effects on bound vibrational motions and quantum-mechanical effects on motion along a reaction coordinate (e.g. quantum tunnelling).
Abstract: Combined experimental and theoretical studies of the reactions and were carried out in the present work. The rate constant of reaction (1) was investigated in the temperature range 293 K ⩽ T ⩽612 K using the laser photolysis continuous-wave laser-induced fluorescence technique for the production and detection of NH 2 . The results are well described by k 1 ( T )=5.43× T −4.02 exp(−1034 K/T ) cm 3 molecule −1 s −1 . Stationary points on the potential energy surface were characterized using the gaussian -2 (G2) ab initio method. The surface is complex, with hydrogen-atom transfers and cis—trans isomerization connecting five stable adduct species. The product distribution of reaction (2) was studied at room temperature using the discharge flow technique with mass spectrometric detection of the reaction products. Measured branching fractions for the production of N 2 O+H(D) were k 2a / k 2 = 0.84±0.4 for NH+NO and k 2a / k 2 = 0.87±0.17 for ND+NO. Stationary points on the ground 2 A′ surface were calculated using the G2 method. The transition state energy for the dissociation of the cis isomer into H+N 2 O was found to be lower than the transition state energy for dissociation into OH+N 2 . Additionally, trans -HNNO was found to isomerize to cis -HNNO before dissociation. For reaction (3), the molecular properties of all relevant intermediates and transition states on the ground state potential energy surface were determined using the G2 method. The results predict the formation of three intermediates, H 2 NO, trans -HNOH and cis -HNOH, all exothermic relative to the reactants. The transition states separating these intermediates from one another and their products (H 2 +NO, H+HNO( 1 A′) or NH+OH) were also characterized, several for the first time.
TL;DR: Strong evidence has been presented for a stepwise mechanism where both the rate of proton abstraction and one or both of the later transition states, i.e., those associated with hydroxide loss and product release, limit the overall reaction rate.
Abstract: Enolase catalyzes the interconversion of 2-phosphoglycerate and phosphoenolpyruvate. Kinetic isotope effects have been used to determine whether abstraction of the proton from C-2 and loss of hydroxide from C-3 of 2-phosphoglycerate occur in a concerted reaction or as sequential processes and whether these steps are kinetically significant for the enolase-catalyzed reaction. Enolase exhibits a significant primary deuterium isotope effect, as well as catalyzing the relatively rapid exchange of the C-2 proton with solvent water. Secondary C-3 deuterium isotope effects are also reported, both when the C-2 carbon carries a hydrogen and when this center is deuterated. These results provide information about the kinetic significance and timing of the transition state(s) associated with the loss of H+ and OH-. Strong evidence has been presented for a stepwise mechanism where both the rate of proton abstraction and one or both of the later transition states, i.e., those associated with hydroxide loss and product release, limit the overall reaction rate. If a concerted reaction were to be invoked, the presence of a small secondary 2H isotope effect in combination with the observed rate of exchange of the C-2 proton require the intrinsic secondary 2H kinetic isotope effect to be effectively unity. For the concerted mechanism, an intrinsic effect of unity would be consistent only with an extremely asymmetric transition state that is dominated by C-H bond cleavage.
TL;DR: The observation that the discriminating power of an antibody for enantiomeric transition states can far exceed simple binding discrimination for ground state molecules suggests a promising future for catalytic antibodies as enantioselective catalysts.
Abstract: The hydrolysis of alkyl enol ethers to their corresponding carbonyl compounds proceeds by acid-catalyzed, rate-determining protonation on the /?-carbon to form an oxocarbonium ion intermediate (Kresge, A. J.; Chang, Y. J. Chem. SOC. B 1967, 53). Antibody 14D9 (anti-1) catalyzes the hydrolysis of enol ethers 4 and 5 with very high enantioselectivity of protonation (Reymond, J.-L.; Janda, K. D.; Lerner, R. A. J. Am. Chem. SOC. 1992, 114, 2257). Catalysis involves participation of an antibody side chain as a general acid, as well as pyramidalization of the enol ether's c Jahangiri, G. K.; Stoudt, C.; Lerner, R. A. J. Am. Chem. SOC. 1993, 115, 3909). The present study addresses the question of the origin of the enantioselectivity of this catalyst. First, enantioselectivity and substrate tolerance, which are most remarkable in antibody 14D9, are shown to be recurrent features for anti-1 or anti-2 antibodies. Four antibodies were studied, and all enantioselectively deliver a proton on the re face of enol ethers to produce (5')-configured carbonyl products, while stereoselectively binding to analogs of the (S,S)-hapten 1. The orientation of the enol ether at the transition state relative to the hapten is then established by comparing the effect of alkyl substitutions at the /?-carbon on antibody catalysis with the effect of equivalent substitutions on antibody binding to hapten analogs. For antibody 14D9 (anti-1), the results show that the alkyl substituent of the enol ether's /?-carbon binds to the N-methyl site of the hapten at the transition state. Substitution of ethyl for methyl at that position results in a 20-fold drop in transition state binding and a 3-7-fold drop in affinity for inhibitors. The orientation is such that the cyclic substrates do not fit in the site complementary to the piperidine ring of the hapten at the transition state. The antibody-catalyzed hydrolysis of the cyclopentanone enol ether 6, which produces exclusively (9-7, is 40 times more efficient than for the cyclohexanone enol ether 10. By contrast, no binding selectivity is found for the individual enantiomers of the corresponding ketone products 7 and 18, which are neutral transition state analogs for re- or si-selective protonation of 6 or 10. The enantioselectivity of 14D9 appears only for the transition state, which suggests that it contains a dynamic component, probably the strict geometrical constraint that the enol ether be aligned with the antibody residue acting as a general acid catalyst during proton transfer. The enantioselectivity of antibody 14D9 thus results from an unexpected combination of binding and catalysis. This study establishes the relationship between hapten and transition states in unprecedented details. The observation that the discriminating power of an antibody for enantiomeric transition states can far exceed simple binding discrimination for ground state molecules suggests a promising future for catalytic antibodies as enantioselective catalysts.
TL;DR: The enzyme-stabilized transition state for AMP hydrolysis is characterized by new positive electrostatic potential in the adenine ring as a result of protonation by the enzyme, closely matched by the protonated pyrazole ring of formycin 5'-phosphate.
Abstract: AMP nucleosidase hydrolyzes the N-glycosidic bond of AMP to yield adenine and ribose 5-phosphate. Kinetic isotope effects have been used to establish an experimentally based transition-state structure for the native enzyme and a Vmax mutant [Mentch, F., Parkin, D. W., & Schramm, V. L. (1987) Biochemistry 26, 921-930; Parkin, D. W., Mentch, F., Banks, G. A., Horenstein, B. A., & Schramm, V. L. (1991) Biochemistry 30, 4586-4594]. The transition states are characterized by weak reaction coordinate bonds to C1' and substantial carbocation character in the ribose ring. The N9-C1' bond to the leaving group is nearly broken and the adenine ring is protonated at the transition state. Formycin 5'-phosphate and other purine nucleoside 5'-phosphate analogues with syn-glycosyl torsion angles bind better than substrate, supporting a syn configuration in the enzyme-substrate complex and presumably in the transition state [Giranda, V. L., Berman, H. M., & Schramm, V. L. (1988) Biochemistry 27, 5813-5818]. Access to a geometric model of the transition state permits the analysis of its molecular electrostatic potential surface as enforced by the enzyme. Comparison of the molecular electrostatic potential surfaces for AMP, formycin 5'-phosphate, and the transition state reveals a striking similarity in the surface charges of formycin 5'-phosphate and the transition state. The enzyme-stabilized transition state for AMP hydrolysis is characterized by new positive electrostatic potential in the adenine ring as a result of protonation by the enzyme. This is closely matched by the protonated pyrazole ring of formycin 5'-phosphate. The molecular electrostatic potential surfaces of formycin 5'-phosphate and the transition state for AMP are similar and are likely to be a factor in the Km/Ki value of > 10(3) for formycin 5'-phosphate as a transition-state inhibitor of AMP nucleosidase.
TL;DR: In this article, the metastable dissociation of the methoxymethyl cation and a number of its deuterium and 13C variants was examined using a reverse-geometry double-focusing mass spectrometer.
Abstract: The metastable dissociation of the methoxymethyl cation and a number of its deuterium and 13C variants was examined using a reverse-geometry double-focusing mass spectrometer. The loss of methane from the methoxymethyl cation clearly showed a composite peak shape which, when deconvoluted, revealed a bimodal kinetic energy release distribution in the resulting formyl cations. Labelling experiments revealed that the two carbon atoms and all hydrogens become equivalent on the time-scale of the unimolecular dissociation lifetime of the decomposing ion. A small deuterium isotope effect was found which can be rationalized on the basis of zero point energy effects. The bimodal kinetic energy release distribution was shown, with the aid of a four-sector instrument, to be due to the production of both formyl cation (with a large kinetic energy release) and isoformyl cation (with a much smaller kinetic energy release). The methoxymethyl cation was also prepared with a precisely defined amount of internal energy in a Fourier transform ion cyclotron resonance (FTICR) spectrometer by the reaction of methyl cation with formaldehyde. Experiments with 13C and deuterium labelling revealed that the dissociation to formyl cation of the methoxymethyl cations formed in the low-pressure FTICR cell by reaction of methyl cation with formaldehyde is accompanied by complete scrambling of the carbons and incomplete scrambling of the hydrogens. Ab initio calculations were carried out which identified and characterized each of the stable minima and transition states for the appropriate reactions. The calculations were fully consistent with the mechanism deduced on the basis of the experimental data.
TL;DR: In this paper, a comparison of the radical-cation transformations of hexa-1,5-diene and semibullvalene with the degenerate rearrangements of these neutral compounds reveals that the equilibrium structure of a radical cation in each case corresponds to a symmetrical transition-state structure for the neutral molecule.
Abstract: Comparison of the radical-cation transformations of hexa-1,5-diene and semibullvalene with the degenerate rearrangements of these neutral compounds reveals that the equilibrium structure of the radical cation in each case corresponds to a symmetrical transition-state structure for the neutral molecule. Thus, the cyclohexane-1,4-diyl radical cation is formed initially by the one-electron oxidation of hexa-1,5-diene, spectroscopic proof of its delocalized chair structure being obtained by matrix-isolation studies. Similarly, it is found that the ionization of semibullvalene generates the bicyclo[3.3.0]octa-2,6-diene-4,8-diyl radical cation as a delocalized mesovalent species corresponding to the case of strong interaction between two allylic groups held in a boat conformation. Spectroscopic studies reveal that the singly occupied molecular orbitals of these diyl and diallyl radical cations are non-bonding and correspond to the respective HOMOs of the neutral transition states. Inversion of the potential-energy surface for the radical cation comes about because the difference between the ionization potentials of the neutral molecule and its transition state exceeds the activation enthalpy for the degenerate rearrangement of the neutral molecule, the low ionization potential of the transition state being attributable to the non-bonding character of its HOMO. The radical-cation rearrangements are therefore termed ‘half-Cope’ reactions since the degeneracy of the reaction coordinate is lifted in going from the neutral molecule to its radical cation. A secondary rearrangement of the cyclohexane-1,4-diyl radical cation to the cyclohexene radical cation by hydrogen transfer is accessible on account of the potential-energy minimum for the intermediate diyl radical cation. In contrast, the lack of cyclohexene formation as a side product of the neutral Cope reaction suggests that in this case there is no intermediate species with a significant potential-energy well along the reaction surface to allow this competitive path to occur.
TL;DR: In this paper, the transition states for the hetero-Diels-Alder addition of formaldehyde, formaldimine, diazene and nitrosyl hydride to cyclopentadiene were located with ab initio molecular orbital calculations.
TL;DR: Examination of the energetics of the reaction steps leading from ATP to phosphohistidine formation in E-P suggested the use of intrinsic binding energy in the synthesis of a high energy P-N linkage.
Abstract: The present study was carried out to determine the energetics of Clostridium symbiosum pyruvate phosphate dikinase (PPDK) catalyzed interconversion of adenosine 5'-triphosphate (ATP), orthophosphate (Pi), and pyruvate (pyr) with adenosine 5'-monophosphate (AMP), inorganic pyrophosphate, and phosphoenolpyruvate (PEP) [E.ATP E-PP.AMP E-PP.AMP.Pi E-P.AMP.PPi E-P.pyr E.PEP where E-PP and E-P represent the pyrophosphoryl and phosphoryl enzyme intermediates]. Thermodynamic techniques were used along with steady-state and pre-steady-state kinetic techniques to determine the rate constants for the substrate/product binding and release steps and the rate constants for the forward and reverse chemical steps. These values were used along with estimates of the cellular concentrations of the substrates and products to construct the free energy profile for the enzymatic reaction under physiological conditions. The energy profile obtained with the Mg2+/NH4(+)-activated enzyme revealed well-balanced transition states and well-balanced internal ground state energies (i.e., within 1 kcal/mol of each other). Examination of the energetics of the reaction steps leading from ATP to phosphohistidine formation in E-P suggested the use of intrinsic binding energy in the synthesis of a high energy P-N linkage. Comparison of the energy profiles of the Mg2+/NH4(+)-vs Co2+/NH4(+)-activated enzymes revealed cofactor selectivity at each of the phosphosphoryl transfer steps.
TL;DR: In this article, the potential energy surface for the loss of H 2 from ethane cations has been investigated by means of ab initio calculations and several energy minima and transition states and the reaction path connecting them have been identified.
TL;DR: In this paper, an ab initio calculation of the potential energy surface (PES) of H + OCS was performed using an extended basis set (EBS) to verify the existence of 12 transition states and 6 stable 4-body intermediates.
Abstract: : Ab initio calculations using extended basis sets are presented for the potential energy surface (PES) of H + OCS. There are two major reaction channels on the PES; Reaction (I) is H(2S) + OCS(1(Sigma)) yields OH(2(Pi)) + CS(1(Sigma)), and Reaction (II) is H(2S) + OCS(1(Sigma)) yields SH(2(Pi)) + CO(1(Sigma)). Results of this study substantiate findings from an earlier quantum chemical study using a lower level of theory, including (1) the existence of 12 transition states and 6 stable 4-body intermediates; (2) the qualitative description of the PES (i.e., geometries, relative barriers, and well depths are similar to those in the earlier study); and (3) the entrance channel transition states leading to (II) are tight, as suggested by experiment. The results presented here also support the explanations of observed product energy distributions for (I) and (II) based on the earlier ab initio study. An additional transition state connecting the cis-HOCS and cis-HSCO minima was located, confirming a previous suggestion that Reaction (II) could result from hydrogen migration after HOCS formation. The current results show a substantial improvement in the quantitative agreement with experiment over the previously calculated values. Potential energy surface, Ab initio, MP4, QCISD(T), Electronic structure, Potential energy, Quantum chemistry.
TL;DR: In this paper, the transformation of 2-acetyl-5-substituted-tetrazoles into the corresponding 1,3,4-oxadiazoles was studied with the mopac semi-empirical and gaussian ab initio methods.
Abstract: The transformation of 2-acetyl-5-substituted-tetrazoles into the corresponding 1,3,4-oxadiazoles was studied with the mopac semiempirical and gaussian ab initio methods. Two mechanisms, one with two transition states and the other with three, were elucidated by mopac . The first mechanism supported by PM3 and MNDO has a two-step, almost concerted, mechanism for the elimination of a nitrogen molecule from the tetrazole ring and formation of the oxadiazole product from an open-chain intermediate through carbon C5 and acetyl oxygen bond formation. The second mechanism supported by AM1 and MINDO/3 breaks the elimination of the nitrogen molecule into two steps: first breaking the N4-C5 and then the N2-N3 bonds. Even when the AM1 and MINDO/3 transition state structures were optimized by PM3 and MNDO, the obtained transition states present only one bond breaking. The HF/STO-3G and HF/3-21G ab initio methods agree with the first mechanism where two bonds are breaking almost simultaneously. Despite the disagreement in the mechanism of the nitrogen elimination, the transition state that presents the product formation from open-chain intermediates is quite similar for all methods studied. The semiempirical calculation of this transition state is possible only if it is assumed that it has biradical character. The activation energies calculated by PM3 seem to be insensitive to the nature of the substituents.
TL;DR: In this article, an analytical algorithm is formulated for determining the optimal conjecture for a surmised transition state between two transition states, given the locations, the energies, and the force constants of a reactant minimum and a product minimum and assuming that no other information is available.
Abstract: Given the locations, the energies, and the force constants of a reactant minimum and a product minimum and assuming that no other information is available, an analytical algorithm is formulated for determining the optimal conjecture for a surmized transition state between them. It is based on a model surface obtained by combining the two quadratic basin approximations. The method is illustrated by applications to transition states on an analytical surface and on an ab initio surface.
TL;DR: In this paper, Hartree-Fock et al. investigated the stability of 3-methyloxadiazolinium ion and 1,2,3-oxadizoline and deter- mine the most probable thermal decomposition pathway of the oxadiazoli- ne.
Abstract: Quantum mechanical calculations were used to investigate the stability of the 3-methyloxadiazolinium ion and 1,2,3-oxadiazoline and to deter- mine the most probable thermal decomposition pathway of the oxadiazoli- ne. Ab initio RHF calculations were carried out at the 3-21G and 6-31G * basis set level to obtain the optimized SCF energies and geometries of these molecules, as well as that of the protonated 4,5-dihydro-2,3-oxa- diazoline. Only the N2-protonated oxadiazoline was found to be stable; the N1- and O-protonated oxadiazolines underwent immediate decomposi- tion. Calculations on the oxadiazolinium ion confirmed experimental re- sults regarding the most likely site of nucleophilic attack on the mo- lecule. Optimized geometries and energies for the reactant, transition state, and product molecules were obtained at post Hartree-Fock using MP2 and QCISD, as well as the density functional code, DGauss. Compari- son of the optimized geometries of the transition states from the three different bond-breakage processes revealed minor differences in these structures at the various levels of theory