Experimental and computational studies of the kinetics of the reaction of hydrogen peroxide with the amidogen radical.

The pulsed-laser photolysis/laser-induced fluorescence method is used to study the kinetics of the reaction of NH2 with H2O2 to yield a second-order rate constant of (2.42 ± 0.55) × 10-14 cm3 molecule-1 s-1 at 412 K in 10-22 mbar of Ar bath gas. There are no prior measurements for comparison. To check this value and enable reliable extrapolation to other temperatures, we also compute thermal rate constants for this process over the temperature range 298-3000 K via multi-structural canonical variational transition-state theory with small-curvature multidimensional tunneling (MS-CVT/SCT). The CVT/SCT rate constants are derived using a dual-level direct dynamics approach utilizing single-point CCSD(T)-F12b/cc-pVQZ-F12 energies-corrected for core-valence and scalar relativistic effects-and M06-2X/MG3S geometries, gradients, and Hessians-for all stationary and non-stationary points along the reaction path. The multistructural method with torsional anharmonicity, based on a coupled torsional potential, is then employed to calculate correction factors for the rate constants, accounting for the comprehensive effects of torsional anharmonicity on the kinetics of this reaction system. The final MS-CVT/SCT rate constants are found to be in good agreement with our measurements and can be expressed in modified Arrhenius form as 2.13 × 10-15 (T/298 K)4.02 exp(-513 K/T) cm3 molecule-1 s-1 over the temperature range of 298-3000 K.

1-Deoxysphingolipids.

Sphingolipids (SLs) are fundamental components of eukaryotic cells. 1-Deoxysphingolipids differ structurally from canonical SLs as they lack the essential C1-OH group. Consequently, 1-deoxysphingolipids cannot be converted to complex sphingolipids and are not degraded over the canonical catabolic pathways. Pathologically elevated 1-deoxySLs are involved in several disease conditions. Within this review, we will provide an up-to-date overview on the metabolic, physiological and pathophysiological aspects of this enigmatic class of "headless" sphingolipids.

Elevation of plasma 1-deoxy-sphingolipids in type 2 diabetes mellitus: a susceptibility to neuropathy?

BACKGROUND AND PURPOSE: Diabetic distal sensorimotor polyneuropathy (DSPN) is a frequent, disabling complication of diabetes mellitus. There is increasing evidence that sphingolipids play a role in insulin resistance and type 2 diabetes (T2DM). Whether neurotoxic 1-deoxy-sphingolipids are elevated in DSPN patients' plasma and whether levels correlate to the DSPN stage were examined. METHODS: The plasma profile of 12 sphingoid bases in patients with DSPN and T2DM(n = 39) were cross-sectionally compared to other nerve disorders including chronic inflammatory demyelinating polyneuropathy (CIDP) (n = 13), transthyretin-related familial amyloid polyneuropathy (FAP) (n = 10), amyotrophic lateral sclerosis (ALS) (n = 13) and small fibre neuropathy (n = 12) by liquid chromatography mass spectrometry. Correlations to the DSPN stage were additionally performed. Furthermore, the sphingoid base distribution in sural nerve specimens was measured in patients with DSPN (n = 6) compared to CIDP (n = 3). RESULTS: A significantly increased amount of 1-deoxy-sphingolipids [1-deoxy-sphinganine (0.11 ± 0.06 µmol/l), 1-deoxy-sphingosine (0.24 ± 0.16 µmol/l)] in patients with DSPN was observed compared to age-matched healthy controls (0.06 ± 0.03 µmol/l; 0.12 ± 0.05 µmol/l) and to the other groups. (Para)clinical parameters including sensory loss, neuropathic pain, weakness, vibration perception, nerve conduction velocity, sensory nerve action potentials (sural nerve) and duration of T2DM did not correlate with plasma 1-deoxy-sphingolipid levels, neither did the clinical stage according to the Dyck classification for DSPN. Sphingolipid levels in sural nerve biopsies showed no differences between DSPN and CIDP. Contrarily, patients with a small fibre neuropathy had decreased C20-sphingosine plasma levels. CONCLUSION: 1-deoxy-sphingolipid plasma levels are significantly elevated in DSPN. They are already detectable in early disease stages but do not correlate with the clinical course. Further knowledge on 1-deoxy-sphingolipids might lead to a better pathophysiological understanding and future treatment options in DSPN.

Computational study of the thermochemistry of N2O5 and the kinetics of the reaction N2O5 + H2O → 2 HNO3.

The multistructural method for torsional anharmonicity (MS-T) is employed to compute anharmonic conformationally averaged partition functions which then serve as the basis for the calculation of thermochemical parameters for N2O5 over the temperature range 0-3000 K, and thermal rate constants for the hydrolysis reaction N2O5 + H2O → 2 HNO3 over the temperature range 180-1800 K. The M06-2X hybrid meta-GGA density functional paired with the MG3S basis set is used to compute the properties of all stationary points and the energies, gradients, and Hessians of nonstationary points along the reaction path, with further energy refinement at stationary points obtained via single-point CCSD(T)-F12a/cc-pVTZ-F12 calculations including corrections for core-valence and scalar relativistic effects. The internal rotations in dinitrogen pentoxide are found to generate three structures (conformations) whose contributions are included in the partition function via the MS-T formalism, leading to a computed value for S°(298.15)(N2O5) of 353.45 J mol(-1) K(-1).This new estimate for S°(298.15)(N2O5) is used to reanalyze the equilibrium constants for the reaction NO3 + NO2 = N2O5 measured by Osthoff et al. [Phys. Chem. Chem. Phys. 2007, 9, 5785-5793] to arrive at ΔfH °(298.15) (N2O5) = 14.31 ± 0.53 kJ mol(-1)via the third law method, which compares well with our computed ab initio value of 13.53 ± 0.56 kJ mol(-1). Finally, multistructural canonical variational-transition-state theory with multidimensional tunneling (MS-CVT/MT) is used to study the kinetics for hydrolysis of N2O5 by a single water molecule, whose rate constant can be summarized by the Arrhenius expression 9.51 × 10(-17) (T/298 K)(3.354) e(-7900K/T) cm3 molecule(-1) s(-1) over the temperature range 180-1800 K.

Biofuel combustion. Energetics and kinetics of hydrogen abstraction from carbon-1 in n-butanol by the hydroperoxyl radical calculated by coupled cluster and density functional theories and multistructural variational transition-state theory with multidimensional tunneling.

Multistructural canonical variational transition-state theory with small-curvature multidimensional tunneling (MS-CVT/SCT) is employed to calculate thermal rate constants for hydrogen-atom abstraction from carbon-1 of n-butanol by the hydroperoxyl radical over the temperature range 250-2000 K. The M08-SO hybrid meta-GGA density functional was validated against CCSD(T)-F12a explicitly correlated wave function calculations with the jul-cc-pVTZ basis set. It was then used to compute the properties of all stationary points and the energies and Hessians of a few nonstationary points along the reaction path, which were then used to generate a potential energy surface by the multiconfiguration Shepard interpolation (MCSI) method. The internal rotations in the transition state for this reaction (like those in the reactant alcohol) are strongly coupled to each other and generate multiple stable conformations, which make important contributions to the partition functions. It is shown that neglecting to account for the multiple-structure effects and torsional potential anharmonicity effects that arise from the torsional modes would lead to order-of-magnitude errors in the calculated rate constants at temperatures of interest in combustion.

Computational study of the reactions of methanol with the hydroperoxyl and methyl radicals. 2. Accurate thermal rate constants.

Multistructural canonical variational-transition-state theory with multidimensional tunneling (MS-CVT/MT) is employed to calculate thermal rate constants for the abstraction of hydrogen atoms from both positions of methanol by the hydroperoxyl and methyl radicals over the temperature range 100-3000 K. The M08-HX hybrid meta-generalized gradient approximation density functional and M08-HX with specific reaction parameters, both with the maug-cc-pVTZ basis set, were validated in part 1 of this study (Alecu, I. M.; Truhlar, D. G. J. Phys. Chem. A2011, 115, 2811) against highly accurate CCSDT(2)(Q)/CBS calculations for the energetics of these reactions, and they are used here to compute the properties of all stationary points and the energies, gradients, and Hessians of nonstationary points along each considered reaction path. The internal rotations in some of the transition states are found to be highly anharmonic and strongly coupled to each other, and they generate multiple structures (conformations) whose contributions are included in the partition function. It is shown that the previous estimates for these rate constants used to build kinetic models for the combustion of methanol, some of which were based on transition state theory calculations with one-dimensional tunneling corrections and harmonic-oscillator approximations or separable one-dimensional hindered rotor treatments of torsions, are appreciably different than the ones presently calculated using MS-CVT/MT. The rate constants obtained from the best MS-CVT/MT calculations carried out in this study, in which the important effects of corner cutting due to small and large reaction path curvature are captured via a microcanonical optimized multidimensional tunneling (µOMT) treatment, are recommended for future refinement of the kinetic model for methanol combustion.

Practical methods for including torsional anharmonicity in thermochemical calculations on complex molecules: the internal-coordinate multi-structural approximation.

Many methods for correcting harmonic partition functions for the presence of torsional motions employ some form of one-dimensional torsional treatment to replace the harmonic contribution of a specific normal mode. However, torsions are often strongly coupled to other degrees of freedom, especially other torsions and low-frequency bending motions, and this coupling can make assigning torsions to specific normal modes problematic. Here, we present a new class of methods, called multi-structural (MS) methods, that circumvents the need for such assignments by instead adjusting the harmonic results by torsional correction factors that are determined using internal coordinates. We present three versions of the MS method: (i) MS-AS based on including all structures (AS), i.e., all conformers generated by internal rotations; (ii) MS-ASCB based on all structures augmented with explicit conformational barrier (CB) information, i.e., including explicit calculations of all barrier heights for internal-rotation barriers between the conformers; and (iii) MS-RS based on including all conformers generated from a reference structure (RS) by independent torsions. In the MS-AS scheme, one has two options for obtaining the local periodicity parameters, one based on consideration of the nearly separable limit and one based on strongly coupled torsions. The latter involves assigning the local periodicities on the basis of Voronoi volumes. The methods are illustrated with calculations for ethanol, 1-butanol, and 1-pentyl radical as well as two one-dimensional torsional potentials. The MS-AS method is particularly interesting because it does not require any information about conformational barriers or about the paths that connect the various structures.

Computational study of the reactions of methanol with the hydroperoxyl and methyl radicals. 1. Accurate thermochemistry and barrier heights.

The reactions of CH(3)OH with the HO(2) and CH(3) radicals are important in the combustion of methanol and are prototypes for reactions of heavier alcohols in biofuels. The reaction energies and barrier heights for these reaction systems are computed with CCSD(T) theory extrapolated to the complete basis set limit using correlation-consistent basis sets, both augmented and unaugmented, and further refined by including a fully coupled treatment of the connected triple excitations, a second-order perturbative treatment of quadruple excitations (by CCSDT(2)(Q)), core-valence corrections, and scalar relativistic effects. It is shown that the M08-HX and M08-SO hybrid meta-GGA density functionals can achieve sub-kcal mol(-1) agreement with the high-level ab initio results, identifying these functionals as important potential candidates for direct dynamics studies on the rates of these and homologous reaction systems.

How Well Can Modern Density Functionals Predict Internuclear Distances at Transition States?

We introduce a new database called TSG48 containing 48 transition state geometrical data (in particular, internuclear distances in transition state structures) for 16 main group reactions. The 16 reactions are the 12 reactions in the previously published DBH24 database (which includes hydrogen transfer reactions, heavy-atom transfer reactions, nucleophilic substitution reactions, and association reactions plus one unimolecular isomerization) plus four H-transfer reactions in which a hydrogen atom is abstracted by the methyl or hydroperoxyl radical from the two different positions in methanol. The data in TSG48 include data for four reactions that have previously been treated at a very high level in the literature. These data are used to test and validate methods that are affordable for the entire test suite, and the most accurate of these methods is found to be the multilevel BMC-CCSD method. The data that constitute the TSG48 database are therefore taken to consist of these very high level calculations for the four reactions where they are available and BMC-CCSD calculations for the other 12 reactions. The TSG48 database is used to assess the performance of the eight Minnesota density functionals from the M05-M08 families and 26 other high-performance and popular density functionals for locating transition state geometries. For comparison, the MP2 and QCISD wave function methods have also been tested for transition state geometries. The MC3BB and MC3MPW doubly hybrid functionals and the M08-HX and M06-2X hybrid meta-GGAs are found to have the best performance of all of the density functionals tested. M08-HX is the most highly recommended functional due to the excellent performance for all five subsets of TSG48, as well as having a lower cost when compared to doubly hybrid functionals. The mean absolute errors in transition state internuclear distances associated with breaking and forming bonds as calculated by the B2PLYP, MP2, and B3LYP methods are respectively about 2, 3, and 5 times larger than those calculated by MC3BB and M08-HX.

Computational Thermochemistry: Scale Factor Databases and Scale Factors for Vibrational Frequencies Obtained from Electronic Model Chemistries.

Optimized scale factors for calculating vibrational harmonic and fundamental frequencies and zero-point energies have been determined for 145 electronic model chemistries, including 119 based on approximate functionals depending on occupied orbitals, 19 based on single-level wave function theory, three based on the neglect-of-diatomic-differential-overlap, two based on doubly hybrid density functional theory, and two based on multicoefficient correlation methods. Forty of the scale factors are obtained from large databases, which are also used to derive two universal scale factor ratios that can be used to interconvert between scale factors optimized for various properties, enabling the derivation of three key scale factors at the effort of optimizing only one of them. A reduced scale factor optimization model is formulated in order to further reduce the cost of optimizing scale factors, and the reduced model is illustrated by using it to obtain 105 additional scale factors. Using root-mean-square errors from the values in the large databases, we find that scaling reduces errors in zero-point energies by a factor of 2.3 and errors in fundamental vibrational frequencies by a factor of 3.0, but it reduces errors in harmonic vibrational frequencies by only a factor of 1.3. It is shown that, upon scaling, the balanced multicoefficient correlation method based on coupled cluster theory with single and double excitations (BMC-CCSD) can lead to very accurate predictions of vibrational frequencies. With a polarized, minimally augmented basis set, the density functionals with zero-point energy scale factors closest to unity are MPWLYP1M (1.009), τHCTHhyb (0.989), BB95 (1.012), BLYP (1.013), BP86 (1.014), B3LYP (0.986), MPW3LYP (0.986), and VSXC (0.986).

Studies of the kinetics and thermochemistry of the forward and reverse reaction Cl + C6H6 = HCl + C6H5.

The laser flash photolysis resonance fluorescence technique was used to monitor atomic Cl kinetics. Loss of Cl following photolysis of CCl4 and NaCl was used to determine k(Cl + C6H6) = 6.4 x 10(-12) exp(-18.1 kJ mol(-1)/RT) cm(3) molecule(-1) s(-1) over 578-922 K and k(Cl + C6D6) = 6.2 x 10(-12) exp(-22.8 kJ mol(-1)/RT) cm(3) molecule(-1) s(-1) over 635-922 K. Inclusion of literature data at room temperature leads to a recommendation of k(Cl + C6H6) = 6.1 x 10(-11) exp(-31.6 kJ mol(-1)/RT) cm(3) molecule(-1) s(-1) for 296-922 K. Monitoring growth of Cl during the reaction of phenyl with HCl led to k(C6H5 + HCl) = 1.14 x 10(-12) exp(+5.2 kJ mol(-1)/RT) cm(3) molecule(-1) s(-1) over 294-748 K, k(C6H5 + DCl) = 7.7 x 10(-13) exp(+4.9 kJ mol(-1)/RT) cm(3) molecule(-1) s(-1) over 292-546 K, an approximate k(C6H5 + C6H5I) = 2 x 10(-11) cm(3) molecule(-1) s(-1) over 300-750 K, and an upper limit k(Cl + C6H5I) < or = 5.3 x 10(-12) exp(+2.8 kJ mol(-1)/RT) cm(3) molecule(-1) s(-1) over 300-750 K. Confidence limits are discussed in the text. Third-law analysis of the equilibrium constant yields the bond dissociation enthalpy D(298)(C6H5-H) = 472.1 +/- 2.5 kJ mol(-1) and thus the enthalpy of formation Delta(f)H(298)(C6H5) = 337.0 +/- 2.5 kJ mol(-1).

Thermochemistry is not a lower bound to the activation energy of endothermic reactions: a kinetic study of the gas-phase reaction of atomic chlorine with ammonia.

The rate constant for Cl + NH3 --> HCl + NH2 has been measured over 290-570 K by the time-resolved resonance fluorescence technique. Ground-state Cl atoms were generated by 193 nm excimer laser photolysis of CCl4 and reacted under pseudo-first-order conditions with excess NH3. The forward rate constant was fit by the expression k1 = (1.08 +/- 0.05) x 10(-11) exp(-11.47 +/- 0.16 kJ mol(-1)/RT) cm3 molecule(-1) s(-1), where the uncertainties in the Arrhenius parameters are +/-1 sigma and the 95% confidence limits for k1 are +/-11%. To rationalize the activation energy, which is 7.4 kJ mol(-1) below the endothermicity in the middle of the 1/T range, the potential energy surface was characterized with MPWB1K/6-31++G(2df,2p) theory. The products NH2 + HCl form a hydrogen-bonded adduct, separated from Cl + NH3 by a transition state lower in energy than the products. The rate constant for the reverse process k(-1) was derived via modified transition state theory, and the computed k(-1) exhibits a negative activation energy, which in combination with the experimental equilibrium constant yields k1 in fair accord with experiment.