Dataset Information

Formamide reaction network in gas phase and solution via a unified theoretical approach: Toward a reconciliation of different prebiotic scenarios.

ABSTRACT: Increasing experimental and theoretical evidence points to formamide as a possible hub in the complex network of prebiotic chemical reactions leading from simple precursors like H2, H2O, N2, NH3, CO, and CO2 to key biological molecules like proteins, nucleic acids, and sugars. We present an in-depth computational study of the formation and decomposition reaction channels of formamide by means of ab initio molecular dynamics. To this aim we introduce a new theoretical method combining the metadynamics sampling scheme with a general purpose topological formulation of collective variables able to track a wide range of different reaction mechanisms. Our approach is flexible enough to discover multiple pathways and intermediates starting from minimal insight on the systems, and it allows passing in a seamless way from reactions in gas phase to reactions in liquid phase, with the solvent active role fully taken into account. We obtain crucial new insight into the interplay of the different formamide reaction channels and into environment effects on pathways and barriers. In particular, our results indicate a similar stability of formamide and hydrogen cyanide in solution as well as their relatively facile interconversion, thus reconciling experiments and theory and, possibly, two different and competing prebiotic scenarios. Moreover, although not explicitly sought, formic acid/ammonium formate is produced as an important formamide decomposition byproduct in solution.

SUBMITTER: Pietrucci F

PROVIDER: S-EPMC4679036 | biostudies-other | 2015 Dec

REPOSITORIES: biostudies-other

ACCESS DATA

Similar Datasets

Project description:The potential energy surface (PES) of the C6H5 + NH2 reaction has been investigated by using ab initio CCSD(T)//B3LYP/6-311++G(3df,2p) calculations. The conventional transition-state theory (TST) and the variable reaction coordinate-TST (VRC-TST) have been used to predict the rate constants for the channels possessing tight and barrierless transition states, respectively. The Rice-Ramsperger-Kassel-Marcus/Master equation (RRKM/ME) theory has been utilized to determine the pressure-dependent rate constants for these reactions. The PES shows that the reaction begins with an exothermic barrierless addition of NH2 to C6H5 producing the vital intermediate state, namely, aniline (C6H5NH2, IS1). Once IS1 is generated, it can further isomerize to various intermediate states, which can give rise to different products, including PR4 (4,5,6-trihydro-1-amino phenyl + H2), PR5 (3,4,5,6-tetrahydro phenyl + NH3), PR6 (2,3,5,6-tetrahydro-1-imidogen phenyl + H2), PR9 (3,4,5,6-tetrahydro-1-imidogen phenyl + H2), and PR10 (2,5,6-trihydro-1-amino phenyl + H2), of which the most stable product, PR5, was formed by the most favorable channel going through the two advantageous transition states T1/11 (-28.9 kcal/mol) and T11P5 (-21.5 kcal/mol). The calculated rate constants for the low-energy channel, 1.37 × 10-9 and 2.16 × 10-11 cm3 molecule-1 s-1 at T = 300, P = 1 Torr and T = 2000 K, P = 760 Torr, respectively, show that the title reaction is almost pressure- and temperature-dependent. The negative temperature-dependent rate coefficients can be expressed in the modified Arrhenius form of k 1 = 8.54 × 1013 T -7.20 exp (-7.07 kcal·mol-1/RT) and k 2 = 2.42 × 1015 T -7.61 exp (-7.75 kcal·mol-1/RT) at 1 and 10 Torr, respectively, and in the temperature range of 300-2000 K. The forward and reverse rate coefficients as well as the high-pressure equilibrium constants of the C6H5 + NH2 ↔ IS1 process were also predicted; their values revealed that its kinetics do not depend on pressure at low temperature but strongly depend on pressure at high temperature. Moreover, the predicted formation enthalpies of reactants and the enthalpy changes of some channels are in good agreement with the experimental results.

Project description:[1] This study attempts to reconcile the conflicting results reported in the literature concerning the behavior of peak-over-threshold (POT) daily rainfall extremes and their distribution. By using two worldwide data sets, the impact of threshold selection and record length on the upper tail behavior of POT observations is investigated. The rainfall process is studied within the framework of generalized Pareto (GP) exceedances according to the classical extreme value theory (EVT), with particular attention paid to the study of the GP shape parameter, which controls the heaviness of the upper tail of the GP distribution. A twofold effect is recognized. First, as the threshold decreases, and nonextreme values are progressively incorporated in the POT samples, the variance of the GP shape parameter reduces and the mean converges to positive values denoting a tendency to heavy tail behavior. Simultaneously, the EVT asymptotic hypotheses are less and less realistic, and the GP asymptote tends to be replaced by the Weibull penultimate asymptote whose upper tail is exponential but apparently heavy. Second, for a fixed high threshold, the variance of the GP shape parameter reduces as the record length (number of years) increases, and the mean values tend to be positive, thus denoting again the prevalence of heavy tail behavior. In both cases, i.e., threshold selection and record length effect, the heaviness of the tail may be ascribed to mechanisms such as the blend of extreme and nonextreme values, and fluctuations of the parent distributions. It is shown how these results provide a link between previous studies and pave the way for more comprehensive analyses which merge empirical, theoretical, and operational points of view. This study also provides several ancillary results, such as a set of formulae to correct the bias of the GP shape parameter estimates due to short record lengths accounting for uncertainty, thus avoiding systematic underestimation of extremes which results from the analysis of short time series. Citation: Serinaldi, F., and C. G. Kilsby (2014), Rainfall extremes: Toward reconciliation after the battle of distributions, Water Resour. Res., 50, 336-352, doi:10.1002/2013WR014211.

Dataset Information

Formamide reaction network in gas phase and solution via a unified theoretical approach: Toward a reconciliation of different prebiotic scenarios.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets