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The decay paths on the singlet excited-state surface of 9H-adenine and the associated energy barriers have been calculated at the CAS-PT2//CASSCF level. There are three fundamental paths for the photophysics: two paths for the ¹Lb state which are virtually barrierless at the present level of theory and correspond to formation of the (n,π*) intermediate and direct decay to the ground state and a third path for ground-state decay of the (n,π*) state with an activation barrier of approximately 0.1 eV. The ¹La state, which has the largest oscillator strength, either decays directly to the ground state or contributes indirectly to the excited-state lifetime by populating the two other states. The results are used to interpret the photophysics in terms of an excited-state plateau for the ¹Lb state that corresponds to the short-lived excited- state component (approximately 0.1 ps) and a well (i.e., a proper minimum) for the (n,π*) state that gives rise to the long component (1 ps or more). The direct decay to the ground state of the ¹Lb state is probably the decay channel invoked to explain the experimental wavelength dependence of the relative amplitudes of the two components. In addition to that, the excited-state component in the nanosecond range detected in the time-resolved photoelectron spectrum is proposed to be a triplet (π,π*) state formed after intersystem crossing from the singlet (n,π*) state. [ABSTRACT FROM AUTHOR]

Presents a study which employed the use of the Hartee-Fock/density functional theory, second-order perturbation theory and the coupled-cluster method to examine the benzene potential energy hyperface. Mechanism for the topomerization of benzene; Thermochemical corrections and thermal topomerization of benzene; Details on theories used in study.

We report the first preparation of a stable aminothioketyl radical, CH3C•(SH)NHCH3 (1), by fast electron transfer to protonated thioacetamide in the gas phase. The radical was characterized by neutralization-reionization mass spectrometry and ab initio calculations at high levels of theory. The unimolecular dissociations of 1 were elucidated with deuterium-labeled radicals CH3C•(SD)NHCH3 (1a), CH3C•(SH)NDCH3 (1b), CH3C•(SH)NHCD3 (1c), and CD3C•(SH)NHCH3 (1d). The main dissociations of 1 were a highly specific loss of the thiol H atom and a specific loss of the N-methyl group, which were competitive on the potential energy surface of the ground electronic state of the radical. RRKM calculations on the CCSD(T)/aug-cc-pVTZ potential energy surface indicated that the cleavage of the S-H bond in 1 dominated at low internal energies, Eint < 232 kJ mol-1. The cleavage of the N-CH3 bond was calculated to prevail at higher internal energies. Loss of the thiol hydrogen atom can be further enhanced by dissociations originating from the B excited state of 1 when accessed by vertical electron transfer. Hydrogen atom addition to the thioamide sulfur atom is calculated to have an extremely low activation energy that may enable the thioamide group to function as a hydrogen atom trap in peptide radicals. The electronic properties and reactivity of the simple aminothioketyl radical reported here may be extrapolated and applied to elucidate the chemistry of thioxopeptide radicals and cation radicals of interest to protein structure studies. [ABSTRACT FROM AUTHOR]

The potential energy surface of the rearrangement of 3-vinylmethylenecyclobutane to 4-methylenecyclohexene has been studied computationally using density functional theory (B3LYP) and complete active space ab initio methods (CASSCF and CASPT2). The parent reaction is nonconcerted and occurs through several parallel diradical pathways. Transition structures and diradical intermediates are highly comparable in energy, with no deep potential energy well on the potential energy surface. In the substituted system, stereoelectronic effects of the trialkylsiloxy group regulate torquoselectivity in the bond-breaking processes and this, combined with low barriers to cyclization, leads to a stepwise Cope rearrangement that is, nevertheless, stereoselective. [ABSTRACT FROM AUTHOR]

Photolysis (λ > 472 nm) of 2-diazo-3-pentyne (11) affords triplet 1,3-dimethylpropynylidene (MeC3Me, ³3), which was characterized spectroscopically in cryogenic matrices. The infrared, electronic absorption, and electron paramagnetic resonance spectra of MeC3Me (³3) are compared with those of the parent system (HC3H) to ascertain the effect of alkyl substituents on delocalized carbon chains of this type. Quantum chemical calculations (CCSD(T)/ANO1) predict an unsymmetrical equilibrium structure for triplet MeC3Me (³3), but they also reveal a very shallow potential energy surface. The experimental IR spectrum of triplet MeC3Me (³3) is best interpreted in terms of a quasilinear, axially symmetric structure. EPR spectra yield zero-field splitting parameters that are typical for triplet carbenes with axial symmetry (|D/hc| = 0.63 cm-1, |E/hc| = ~ 0 cm-1), while theoretical analysis suggests that the methyl substituents confer significant spin polarization to the carbon chain. Upon irradiation into the near-UV electronic absorption (λmax 350 nm), MeC3Me (³3) undergoes 1,2-hydrogen migration to yield pent-1-en-3-yne (4), a photochemical reaction that is typical of carbenes bearing a methyl substituent. This facile process apparently precludes photoisomerization to other interesting C5H6 isomers, in contrast to the rich photochemistry of the parent C3H2 system. [ABSTRACT FROM AUTHOR]

The enantioselective Pd-catalyzed redox-relay Heck arylation of acyclic alkenyl alcohols allows access to various useful chiral building blocks from simple olefinic substrates. Mechanistically, after the initial migratory insertion, a succession of β-hydride elimination and migratory insertion steps yields a saturated carbonyl product instead of the more general Heck product, an unsaturated alcohol. Here, we investigate the reaction mechanism, including the relay function, yielding the final carbonyl group transformation. M06 calculations predict a ΔΔG of 1 kcal/mol for the site selectivity and 2.5 kcal/mol for the enantioselectivity, in quantitative agreement with experimental results. The site selectivity is controlled by a remote electronic effect, where the developing polarization of the alkene in the migratory insertion transition state is stabilized by the C–O dipole of the alcohol moiety. The enantioselectivity is controlled by steric repulsion between the oxazoline substituent and the alcohol-bearing alkene substituent. The relay efficiency is due to an unusually smooth potential energy surface without high barriers, where the hydroxyalkyl-palladium species acts as a thermodynamic sink, driving the reaction toward the carbonyl product. Computational predictions of the relative reactivity and selectivity of the double bond isomers are validated experimentally. [ABSTRACT FROM AUTHOR]

Photochromic compounds efficiently transduce photonic energy to potential energy for excited-state bond-breaking and bond-forming reactions. A critical feature of this reaction is the nature of the electronic excited-state potential energy surface and how this surface facilitates large nuclear displacements and rearrangements. We have prepared two photochromic ruthenium sulfoxide complexes that feature two isomerization reactions following absorption of a single photon. We show by femtosecond transient absorption spectroscopy that this reaction is complete within a few hundred picoseconds and suggest that isomerization occurs along a conical intersection seam formed by the ground-state and excited-state potential energy surfaces. [ABSTRACT FROM AUTHOR]

State-of-the-art quantum simulations on a full-dimensional ab initio potential energy surface are used to characterize the properties of the water hexamer. The relative populations of the different isomers are determined over a wide range of temperatures. While the prism isomer is identified as the global minimum-energy structure, the quantum simulations, which explicitly include zero-point energy and quantum thermal motion, predict that both the cage and prism isomers are present at low temperature down to almost 0 K. This is largely consistent with the available experimental data and, in particular, with very recent measurements of broadband rotational spectra of the water hexamer recorded in supersonic expansions. [ABSTRACT FROM AUTHOR]

Transition-state theory (TST) is a widely accepted paradigm for rationalizing the kinetics of chemical reactions involving one potential energy surface (PES). Multiple PES reaction rate constants can also be estimated within semiclassical approaches provided the hopping probability between the quantum states is taken into account when determining the transmission coefficient. In the Marcus theory of electron transfer, this hopping probability was historically calculated with models such as Landau-Zener theory. Although the hopping probability is intimately related to the question of the transition from the fully quantum to the semiclassical description, this issue is not adequately handled in physicochemical models commonly in use. In particular, quantum nuclear effects such as decoherence or dephasing are not present in the rate constant expressions. Retaining the convenient semiclassical picture, we include these effects through the introduction of a phenomenological quantum decoherence function. A simple modification to the usual TST rate constant expression is proposed: in addition to the electronic coupling, a characteristic decoherence time τdec now also appears as a key parameter of the rate constant. This new parameter captures the idea that molecular systems, although intrinsically obeying quantum mechanical laws, behave semiclassically after a finite but nonzero amount of time (τdec). This new degree of freedom allows a fresh look at the underlying physics of chemical reactions involving more than one quantum state. The ability of the proposed formula to describe the main physical lines of the phenomenon is confirmed by comparison with results obtained from density functional theory molecular dynamics simulations for a triplet to singlet transition within a copper dioxygen adduct relevant to the question of dioxygen activation by copper monooxygenases. [ABSTRACT FROM AUTHOR]

The multicopper oxidases (MCOs) utilize a blue type 1 (T1) copper site and a trinuclear Cu cluster composed of a type 2 (T2) and a binuclear type 3 (T3) site that together catalyze the four-electron reduction of O2 to H2O. Reaction of the fully reduced enzyme with O2 proceeds via two sequential two- electron steps generating the peroxy intermediate (PI) and the native intermediate (NI). While a detailed description of the geometric and electronic structure of NI has been developed, this has been more elusive for PI largely due to the diamagnetic nature of its ground state. Density functional theory (DFT) calculations have been used to correlate to spectroscopic data to generate a description of the geometric and electronic structure of PI. A highly conserved carboxylate residue near the T2 site is found to play a critical role in stabilizing the P1 structure, which induces oxidation of the T2 and one T3 Cu center and strong super exchange stabilization via the peroxide bridge, allowing irreversible binding of O2 at the trinuclear Cu site. Correlation of PI to NI is achieved using a two-dimensional potential energy surface generated to describe the catalytic two-electron reduction of the peroxide O-O bond by the MCOs. It is found that the reaction is thermodynamically driven by the relative stability of NI and the involvement of the simultaneous two-electron-transfer process. A low activation barrier (calculated ∼5-6 kcal/mol and experimental ∼3-5 kcal/mol) is produced by the triangular topology of the trinuclear Cu cluster site, as this symmetry provides good donor-acceptor frontier molecular orbital (FMO) overlap. Finally, the O-O bond cleavage in the trinuclear Cu cluster can be achieved via either a proton-assisted or a proton-unassisted process, allowing the MCOs to function over a wide range of pH. It is found that while the proton helps to stabilize the acceptor O22- σ*orbital in the proton-assisted process for better donor-acceptor FMO overlap, the third oxidized Cu center in the trinuclear site assumes the role as a Lewis acid in the proton-unassisted process for similarly efficient O-O bond cleavage. [ABSTRACT FROM AUTHOR]

Experimental and density functional theory show that the reaction of acetonitrile with a zerovalent nickel bis(dialkylphosphino)ethane fragment (alkyl = methyl, isopropyl) proceeds via initial exothermic formation of an η2-nitrile complex. Three well-defined transition states have been found on the potential energy surface between the η2-nitrile complex and the activation products. The lowest energy transition state is an η3-acetonitrile complex, which connects the η2-nitrile to a higher energy η3-acetonitrile intermediate with an agostic C--H bond, while the other two lead to cleavage of either the C--H or the C--CN bonds. Gas-phase calculations show C--CN bond activation to be endothermic, which contradicts the observation of thermal C--CN activation in THF. Therefore, the effect of solvent was taken into consideration by using the polarizable continuum model (PCM), whereupon the activation of the C--CN bond was found to be exothermic. Furthermore the C--CN bond activation was found to be favored exclusively over C--H bond activation due to the strong thermodynamic driving force and slightly lower kinetic barrier. [ABSTRACT FROM AUTHOR]

The role of anharmonic effects in the vibrational spectroscopy of the dark state and two major chromophore intermediates of the photoactive yellow protein (PYP) photocycle is examined via ab initio vibrational self-consistent field (VSCF) calculations and time-resolved resonance Raman spectroscopy. For the first time, anharmonicity is considered explicitly in calculating the vibrational spectra of an ensemble consisting of the PYP chromophore surrounded by model compounds used as mimics of the important active-site residues. Predictions of vibrational frequencies on an ab initio corrected semiempirical potential energy surface show remarkable agreement with experimental frequencies for all three states, thus shedding light on the potential along the reaction path. For example, calculated frequencies for vibrational modes of the red-shifted intermediate, PYPL, exhibit an overall average error of 0.82% from experiment. Upon analysis of anharmonicity patterns in the PYP modes we observe a decrease in anharmonicity in the C8-C9 stretching mode ν29 (trans-cis isomerization marker mode) with the onset of the cis configuration in PYPL. This can be attributed to the loss of the hydrogen-bonding character of the adjacent C9-O2 to the methylamine (Cys69 backbone). For several of the modes, the anharmonicity is mostly due to mode-mode coupling, while for others it is mostly intrinsic. This study shows the importance of the inclusion of anharmonicity in theoretical spectroscopic calculations, and the sensitivity of experiments to anharmonicity. The characterization of protein active-site residues by small molecular mimics provides an acceptable chemical structural representation for biomolecular spectroscopy calculations. [ABSTRACT FROM AUTHOR]

The docosahedral metallacarboranes 4,4-(PMe2Ph)2-4,1,6-closo-PtC2B10H12, 4,4-(PMe2Ph)2-4,1,10-closo-PtC2B10H12, and [N(PPh3)2][4,4-cod-4,1,10-closo-RhC2B10H12] were prepared by reduction/metalation of either 1,2-closo-C2B10H12 or 1,12-closo-C2B10H12. All three species were fully characterized, with a particular point of interest of the latter being the conformation of the {ML2} fragment relative to the carborane ligand face. Comparison with conformations previously established for six other ML2C2B10 species of varying heteroatom patterns (4,1,2-MC2B10, 4,1,6-MC2B10, 4,1,10-MC2B10, and 4,1,12-MC2B10) reveals clear preferences. In all cases a qualitative understanding of these was afforded by simple MO arguments applied to the model heteroarene complexes [(PH3)2PtC2B4H6]2- and [(PH3)2PtCB5H6]3-. Moreover, DFT calculations on [(PH3)2PtC2B4H6]2- in its various isomeric forms approximately reproduced the observed conformations in the 4,1,2-, 4,1,6-, and 4,1,10-MC2B10 species, although analogous calculations on [(PH3)2PtCB5H6]3- did not reproduce the conformation observed in the 4,1,12-MC2B10 metallacarborane. DFT calculations on (PH3)2PtC2B10H12 yielded good agreement with experimental conformations in all four isomeric cases. Apparent discrepancies between observed and computed Pt-C distances were probed by further refinement of the 4,1,2-model to 1,2-(CH2)3-4,4-(PMe3)2-4,1,2-closo-PtC2B10H10. This still has a more distorted structure than measured experimentally for 1,2-(CH2)3-4,4-(PMe2Ph)2-4,1,2-closo-PtC2B10H10, but the structural differences lie on a very shallow potential energy surface. For the model compound a henicosahedral transition state was located 8.3 kcal mol-1 above the ground-state structure, consistent with the fluxionality of 1,2-(CH2)3-4,4-(PMe2Ph)2-4,1,2-closo-PtC2B10H10 in solution. [ABSTRACT FROM AUTHOR]

(4/4)CASSCF and CASPT2 calculations have been performed to understand the reason that addition of a second pair of geminal fluorines to methylenecyclopropane lowers the barrier to rearrangement by 6.7 kcal/mol more than addition of the first pair. Our calculations duplicate this experimental finding by Dolbier and co-workers. Our computational results confirm Dolbier's conjecture, that the non-additive lowering of Ea for the rearrangement of 2,2,3,3-tetrafluoromethylenecyclopropane (9) to 1-(difluoromethylene)-2,2-difluorocyclopropane (11) is due to destabilization of 9 by the presence of the vicinal CF2 groups in this fluorocarbon. In the course of exploring the potential energy surface for the rearrangement of 9, we have located a bond-stretch isomer (21)) that differs from 9 by inversion of both CF2 groups. The enthalpy of 20 is computed to be 21.9 kcal/mol higher than that of 9, but direct interconversion of these two ‘bond-stretch invertomers’ requires passage over a TS whose enthalpy is calculated to be 11.7 kcal/mol higher than that of 20. [ABSTRACT FROM AUTHOR]

Vibrational corrections (zero-point and temperature dependent) of the H–D spin–spin coupling constant JHD for six transition metal hydride and dihydrogen complexes have been computed from a vibrational average of JHD as a function of temperature. Effective (vibrationally averaged) H–D distances have also been determined. The very strong temperature dependence of JHD for one of the complexes, [lr(dmpm)Cp H2]² + (dmpm = bis(dimethylphosphino)methane) can be modeled simply by the Boltzmann average of the zero-point vibrationally averaged JHD of two isomers. For this complex and four others, the vibrational corrections to JHD are shown to be highly significant and lead to improved agreement between theory and experiment in most cases. The zero-point vibrational correction is important for all complexes. Depending on the shape of the potential energy and J-coupling surfaces, for some of the complexes higher vibrationally excited states can also contribute to the vibrational corrections at temperatures above 0 K and lead to a temperature dependence. We identify different classes of complexes where a significant temperature dependence of JHD may or may not occur for different reasons. A method is outlined by which the temperature dependence of the HD spin–spin coupling constant can be determined with standard quantum chemistry software. Comparisons are made with experimental data and previously calculated values where applicable. We also discuss an example where a low-order expansion around the minimum of a complicated potential energy surface appears not to be sufficient for reproducing the experimentally observed temperature dependence. [ABSTRACT FROM AUTHOR]

Calculations employing density functional theory indicate that, rather than undergoing fragmentation, dicationic clusters of benzene, hexafluorobenzene, and naphthalene produced by sequential one-electron or sudden double-ionization experiments on the neutrals can relax via the formation of inter-ring covalent C-C bonds, along with a series of proton transfers that enable a substantial reduction of inter- and intramolecular Coulomb repulsions. The theoretically predicted chemically bound structures correspond to deep local energy minima on the potential energy surface pertaining to the lowest electronic state of the dications and can therefore be regarded as metastable (kinetically long-lived) species. This discovery invalidates on theoretical grounds the liquid-droplet model of multiply charged clusters and sheds very unexpected light on possible consequences in chemistry of the intermolecular Coulornbic decay (ICD) mechanism [Cederbaum, L. S.; et al. Phys. Rev. Lett. 1997, 79, 4778; Jahnke, T.; et al. Phys. Rev. Lett 2004, 93, 163401] for deep inner-valence ionized states. Propagation of charge rearrangement reactions and proton transfers to several monomers may eventually lead to the formation of rather extended dicationic assemblies. [ABSTRACT FROM AUTHOR]

There is a discrepancy between the observed and calculated stability of trans-cycloheptene (t-CHP). Generation of t-CHP has always led to its low-temperature (-40 °C) isomerization to cis-cycloheptene (c-CHP). However, force field and semiempirical calculations on the energy difference between the two isomers have suggested that t-CHP should be stable at room temperature. We performed a series of ab initio calculations, which predicted that the simple process of double bond rotation leading from t-CHP to c-CHP would have an activation barrier too high to permit isomerization below 100 °C (35 kcal/mol). The validity of our calculation method on this very strained system was supported by the agreement between the calculation and the dynamics of the ring flip of the unsymmetrical t-CHP ring and the observed NMR shifts and coupling constants for the system. This incompatibility between the experimental behavior of t-CHP and our calculations led to our reexamining the decay kinetics of t-CHP. We find that this decay is second order and represents an "interrupted" dimerization, where an initially formed 1 ,4-biradical rapidly changes its geometry and cleaves back to produce two c-CHP molecules. This mechanism was supported by calculations of the 1 ,4-biradical potential energy surface. [ABSTRACT FROM AUTHOR]

White phosphorus (P4) reacts with three-coordinate molybdenum(III) trisamides or molybdaziridine hydride complexes to produce either bridging or terminal phosphide (P3-) species, depending upon the ancillary ligand steric demands. Thermochemical measurements have been made that place the Mo≡P triple bond dissociation enthalpy at 92.2 kcal·mol-1. Thermochemical measurements together with computational analysis rule out simple P-atom abstraction from P4 as a step in the phosphorus activation mechanism. Kinetic measurements made by the stopped-flow method show that the reaction between the monomeric molybdenum complexes and P4 is first-order both in metal complex and in P4. cyclo-P3 complexes can be obtained when ancillary ligand steric demands are small, but kinetic measurements rule them out as monometallic intermediates in the P4 activation mechanism. Also studied by calorimetric, kinetic, and in one case variable-temperature NMR methods is the process of μ-phosphide bridge formation. Post-rate-determining steps of the P4 activation process were examined in a search for minima on the reaction's potential energy surface, leading to the proposal of two plausible, parallel, bimetallic reaction channels. [ABSTRACT FROM AUTHOR]

DFT(B3PW91) calculations show that the reaction pathways for ethylene metathesis with Re(≡CMe)(=CHMe)(X)(Y) (X/Y = CH2CH3/CH2CH3; CH2CH3/OSiH3; OSiH3/CH2CH3 ; OCH3/OCH3, CH2CH3/OCH3, and OCF3/OCF3) occur in two steps: first, the pseudo-tetrahedral d0 Re complexes distort to a trigonal pyramid to open a coordination site for ethylene, which remains far from Re (early transition state for C—C bond formation). The energy barrier, determined by the energy required to distort the catalyst, is the lowest for unsymmetrical ligands (X ≠ Y) when the apical site of the TBP is occupied by a good σ-donor ligand (X) and the basal site by a poor σ-donor (Y). Second, the formation of metallacyclobutanes (late transition state for C—C bond formation) has a tow energy barrier for any type of ligands, decreasing for poor σ-donor X and Y ligands, because they polarize the Re-C alkylidene bond as Re+δ=C-δ, which favors the reaction with ethylene, itself polarized by the metal center in the reverse way. The metallacyclobutane is also a TBP, with apical alkylidyne and Y ligands, and it is stabilized by poor σ-donor X and Y. The best catalyst will have the more shallow potential energy surface, and will thus be obtained for the unsymmetrical set of ligands with X = a good σ-donor (alkyl) and Y = a poor σ-donor (O-based ligand). This rationalizes the high efficiency of well-defined Re alkylidene supported on silica, compared to its homogeneous equivalent, Re(≡CMe)(=CH Me)(OR)2. [ABSTRACT FROM AUTHOR]

The molecular structure of all silver halide monomers, Ag2X, AgX, AgX2, and AgX3, (X = F, Cl, Br, I), have been calculated at the B3LYP, MP2, and CCSD(T) levels of theory by using quasirelativistic pseudopotentials for all atoms except fluorine and chlorine. All silver monohalides are stable molecules, while the relative stabilities of the subhalides, dihalides, and trihalides considerably decrease toward the larger halogens. The ground-state structure of all Ag2X silver subhalides has C2v symmetry, and the molecules can be best described as [Ag2]+X--. Silver dihalides are linear molecules; AgF2 has a ²Σg ground state, while all of the other silver dihalides have a ground state of ²IIg symmetry. The potential energy surface (PES) of all silver trihalides has been investigated. Neither of these molecules has a D3h symmetric trigonal planar geometry, due to their Jahn--Teller distortion. The minimum energy structure of AgF3 is a T-shaped structure with C2v symmetry. For AgCI3, AgBr3, and Agl3, the global minimum is an L-shaped structure, which lies outside the Jahn--Teller PES. This structure can be considered as a donor--acceptor system, with X2 acting as donor and AgX as acceptor. Thus, except for AgF3, in the other three silver trihalides, silver is not present in the formal oxidation state 3. [ABSTRACT FROM AUTHOR]

Complex [Cp*lr(dmpm)H2]2+ (dmpm = bis(dimethylphosphino)methane) has been reported to display temperature-dependent spin-spin coupling constant (1 JHD) and isotope effect on the 1H NMR chemical shift (Δ&delta). A combined electronic structure density functional theory + quantum nuclear dynamics study is used to determine from first-principles the unusual temperature dependence of the spin-spin coupling constant. It is found that the potential energy surface describing the motion of the lr-H2 unit has a deeper minimum in the dihydride region and is characterized by important anharmonicities. These anomalies affect the nature of the vibrational states of the unit and are the main reason for the unusual temperature dependence of 1JHD and Δ&delta. These results suggest experimental tests to identify compressed dihydride transition metal complexes. [ABSTRACT FROM AUTHOR]

The nuclear vibrational wave function and zero-point vibrational energy of CH5+ are calculated using quantum diffusion Monte Carlo techniques on an interpolated potential energy surface constructed from CCSD(T)/aug'-cc-pVTZ ab initio data. From this multidimensional wave function, the vibrationally averaged rotational constants and radial distribution functions for atom-atom distances within the molecule are constructed. It is found that the distributions of all 10 H-H distances are bimodal and identical. The radial distribution functions obtained for the five C-H distances are also identical, but unimodal. The three rotational constants were found to be 3.78, 3.80, and 3.83 cm-1. These values indicate that the ground state of CH5+ is significantly more symmetric than its global minimum energy structure. We conclude that the zero-point motion of CH5+ renders all five protons equivalent in the ground state and precludes the assignment of a unique structure to the molecule. [ABSTRACT FROM AUTHOR]

Various high levels of theory have been applied to the characterization of two higher lying biradicaloid metastable singlet states of peroxynitrous acid. A singlet minimum (cis-2) was located that had an elongated 0-0 distance (2.17 Å) and was only 12.2 kcal/mol [UB3LYP/6-311 +G(3df,2p)+ZPVE] higher in energy than its ground-state precursor. A trans-metastable singlet (trans-2) was 10.9 kcal/mol higher in energy than ground-state HO-ONO. CASSCF(12,1O)/6-311+G(d,P) calculations predict the optimized geometries of these cis- and trans-metastable singlets to be close to those obtained with DFT. Optimization of cis- and trans-2 within the COSMO solvent model suggests that both exist as energy minima in polar media. Both cis- and trans-2 exist as hydrogen bonded complexes with several water molecules. These collective data suggest that solvated forms of cis-2.3H20 and trans-2.3H20 represent the elusive higher lying biradicaloid minima that were recently (J. Am. Chem. Soc. 2003, 125, 16204) advocated as the metastable forms of peroxynitrous acid (HOONO*). The involvement of metastable trans-2 in the gas phase oxidation of methane and isobutane is firmly established to take place on the unrestricted [UB3LYP/ 6-311 +G(d,p)] potential energy surface (PES) with classical activations barriers for the hydrogen abstraction step that are 15.7 and 5.9 kcal/mol lower than the corresponding activation energies for producing products methanol and tert-butyl alcohol formed on the restricted PES. The oxidation of dimethyl sulfide and dimethyl selenide, two-electron oxidations, proceeds by an SN2-like attack of the heteroatom lone pair on the 0-0 bond of ground-state peroxynitrous acid. No involvement of metastable forms of HO-ONO was discernible. [ABSTRACT FROM AUTHOR]

Laser desorption of model peptides coupled to laser spectroscopic techniques enables the gas-phase observation of genuine secondary structures of biology. Spectroscopic evidence for the formation of fl-turns in gas-phase peptide chains containing glycine and phenylalanine residues establishes the intrinsic stability of these forms and their ability to compete with other stable structures. The precise characterization of local minima on the potential energy surface from 1R spectroscopy constitutes an acute assessment for the state-of-the-art quantum mechanical calculations also presented. The observation of different types of /3-turns depending upon the residue order within the sequence is found to be consistent with the residue propensities in tums of proteins, which suggests that the prevalence of glycine in type II and II' turns stems essentially from an energetic origin, already at play under isolated conditions. [ABSTRACT FROM AUTHOR]

Crystallographic studies of human purine nucleoside phosphorylase (hPNP) with several transition-state (TS) analogues in the immucillin family showed an unusual geometric arrangement of the atoms O-5', O-4', and Op, the nucleophilic phosphate oxygen, lying in a close three-oxygen stack. These observations were corroborated by extensive experimental kinetic isotope effect analysis. We propose that protein-facilitated dynamic modes in hPNP cause this stack, centered on the ribosyl O-4' oxygen, to squeeze together and push electrons toward the purine ring, stabilizing the oxacarbenium character of the TS. As the N-ribosidic bond is cleaved during the reaction, the pKa values of N-7 and O-6 increase by the electron density expelled by the oxygen-stack compression toward the purine ring. Increased electron density in the purine ring improves electrostatic interactions with nearby residues and facilitates the abstraction of a proton from a solvent proton or an unidentified general acid, making the purine a better leaving group, and accelerating catalysis. Classical and mixed quantum/classical molecular dynamics (MD) simulations of the Michaelis complex of hPNP with the substrates guanosine and phosphate were performed to assess the existence of protein-promoting vibrations (PPVs). Analogous simulations were performed for the substrates in aqueous solution. In the catalytic site, the O-5', O-4', and Op oxygens vibrate at frequencies of ca. 125 and 465 cm-1, as opposed to 285 cm-1 in the absence of hPNP. The hybrid quantum mechanical/molecular mechanical method was used to assess whether this enzymatic vibration pushing the oxygens together is coupled to the reaction coordinate, and thus has a direct positive impact on catalysis. The potential energy surface for the phosphorolysis reaction for several snapshots taken from the classical MD simulation showed substantial differences in oxygen compression. Our calculations showed the existence of PPVs coupled to the reaction coordinate, which effect electronic alterations in the active site by pushing the three oxygen centers together in proximity, and accelerate substrate turnover in the phosphorolysis reaction catalyzed by hPNP. [ABSTRACT FROM AUTHOR]

The ultrafast N-O bond fragmentation in a series of N-methoxypyndyl radicals, formed by one-electron reduction of the corresponding N-methoxypyridiniums, has been investigated as potentially barrierless electron-transfer-initiated chemical reactions. A model for the reaction involving the electronic and geometric factors that control the shape of the potential energy surface for the reaction is described. On the basis of this model, molecular structural features appropriate for ultrafast reactivity are proposed. Femtosecond kinetic measurements on these reactions are consistent with a kinetic definition of an essentially barrierless reaction, i e., that the lifetime of the radical is a few vibrational periods of the fragmenting bond, for the p-methoxy-N-methoxypyndyl radical. [ABSTRACT FROM AUTHOR]

Variational transition state theory has been used to calculate the kinetic isotope effects affecting product ratios in the reaction between 1O2 and d6-tetramethylethylene. The minimum energy path on the potential energy surface for this process reaches a valley-ridge inflection point and then bifurcates leading to the two final products. Using canonical variational transition state theory, two distinct dynamical bottlenecks were located corresponding to the H- and the D-abstraction, respectively. The calculated KIE at 263 K turns out to be 1.126, Analogously, a H/T KIE of 1.17 at the same temperature has been found for the reaction of 1O2 with the tritiated derivative of tetramethylethylene. [ABSTRACT FROM AUTHOR]

Master equation calculations on a computational potential energy surface reveal that collisional stabilization at atmospheric pressure becomes important in the gas-phase ozonolysis of endocyclic alkenes for a carbon number between 8 and 15. Because the reaction products from endocyclic ozonolysis are tethered, this system is ideal for consideration of collisional energy transfer, as chemical activation is confined to a single reaction product. Collisional stabilization of the Criegee intermediate precedes collisional stabilization of the primary ozonide by roughly an order of magnitude in pressure. The stabilization of the Criegee intermediate leads to a dramatic transformation in the dominant oxidation pathway from a radical- forming process at low carbon number to a secondary ozonide-forming process at high carbon number. Secondary ozonide formation is important even for syn-isomer Criegee intermediates, contrary to previous speculation. We use substituted cyclohexenes as analogues for atmospherically important mono- and sesquiterpenes, which are major precursors for secondary organic aerosol formation in the atmosphere. Combining these calculations with literature experimental data, we conclude that the transformation from chemically activated to collisionally stabilized behavior most probably occurs between the mono- and sesquiterpenes, thus causing dramatically different atmospheric behavior. [ABSTRACT FROM AUTHOR]

An experimental and computational study has been performed to investigate the bond-forming reactivity between Ar2+ and NH3. Experimentally, we detect two previously unobserved bond-forming reactions between Ar2+ and NH3 forming ArN+ and ArNH+. This is the first experimental observation of a triatomic product ion (ArNH+) following a chemical reaction of a rare gas dication with a neutral. The intensity of ArNH+ was found to decrease with increasing collision energy, with a corresponding increase in the intensity of ArN+ indicating that ArN+ is formed by the dissociation of ArNH+ Key features on the potential energy surface for the reaction were calculated quantum chemically using CASSCF and MRCI methods. The calculated reaction mechanism, which takes place on a singlet surface, involves the initial formation of an Ar-N bond to give Ar-NH32+. This complexation is followed by proton loss via a transition state, and then loss of the two remaining hydrogen atoms in two subsequent activationless steps to give the products 3ArN+ + H+ + 2H. This calculated pathway supports the sequential formation of ArN+ from ArNH+ as suggested by the experimental data. The calculations also indicate that no bond-forming pathway exists on the ground triplet surface for this system. [ABSTRACT FROM AUTHOR]

Elucidating the role of nuclear quantum mechanical (NQM) effects in enzyme catalysis is a topic of significant current interest. Despite the great experimental progress in this field it is important to have theoretical approaches capable of evaluating and analyzing nuclear quantum mechanical contributions to catalysis. In this study, we use the catalytic reaction of lipoxygenase, which is characterized by an extremely large kinetic isotope effect, as a challenging test case for our simulation approach. This is done by applying the quantum classical path (QCP) method with an empirical valence bond potential energy surface. Our computational strategy evaluates the relevant NQM corrections and reproduces the large observed kinetic isotope effect and the temperature dependence of the H atom transfer reaction while being less successful with the D atom transfer reaction. However, the main point of our study is not so much to explore the temperature dependence of the isotope effect but rather to develop and validate an approach for calculations of nuclear quantum mechanical contributions to activation free energies. Here, we find that the deviation between the calculated and observed activation free energies is small for both H and D at all investigated temperatures. The present study also explores the nature of the reorganization energy in the enzyme and solution reactions. It is found that the outer-sphere reorganization energy is extremely small. This reflects the fact that the considered reaction involves a very small charge transfer. The implication of this finding is discussed in the framework of the qualitative vibronic model. The main point of the present study is, however, that the rigorous QCP approach provides a reliable computational tool for evaluating NQM contributions to catalysis even when the given reaction includes large tunneling contributions. [ABSTRACT FROM AUTHOR]

Microwave spectra were obtained for two distinct structural isomers of 1,1 `-dimethylferrocene, an eclipsed synperiplanar isomer (ϕ = 0°, the E0 isomer), with A = 1176.9003(2) MHz, B = 898.3343(2) MHz, C = 668.7469(2) MHz, and an eclipsed synclinal isomer (92 = 72°, the E72 isomer) with A = 1208.7117(14) MHz, B = 806.4101(12) MHz, and C = 718.7179(8) MHz. The b-dipole, asymmetric-top spectra of both structural isomers were measured in the frequency range of 5-12 GHz using a Flygare-Balle type of spectrometer. A very good fit to observed transitions, with small distortion constants, was obtained for the EO conformer, indicating that this conformer is nearly rigid. The deviations obtained in a similar least-squares fit for the E72 confomer are significantly larger, indicating possible fluxional behavior for this conformer. In addition, 7 out of the 26 transitions observed for the E72 isomer conformer clearly exhibit very small splittings, giving further evidence for internal motion. DFT calculations for the different possible conformations of 1,1'- dimethylferrocene arising from rotation of one methyl cyclopentadienyl ligand relative to the other about the nominal C[sub5] axis by an angle &phivl; (dihedral angle) were performed using the B3PW91 functional. The calculations converged and were optimized for five structures on this torsional potential energy surface corresponding to different dihedral angles ϕ three yielded energy mixima, and two gave energy maxima, corresponding to transition states. The experimental results are in very good agreement with the results of the DFT calculations. [ABSTRACT FROM AUTHOR]

Determines the molecular geometry of dimeric gold trichloride by gas-phase electron diffraction and high-level quantum chemical calculations. Occurrence of Jahn-Teller effect in gold chlorides; Separation of potential energy surface by transition state structures.

The article reports the direct spectroscopic observation of mixed valence isomers, the two alternate charge distributions of a mixed valence complex. In the normal two-state Marcus-Hush description of a symmetric mixed valence complex, electron exchange is a degenerate process, and the isomers, differing only in the position of the charge, cannot be distinguished. By introducing a slight asymmetry into a mixed valence complex, it is possible in principle to introduce a small energy difference between the two sides of the Marcus-Hush potential energy surface such that substantial Boltzmann populations of the two mixed valence isomers can exist in equilibrium.