Abiotic synthesis of organic molecules from minerals containing traces of dissolved H2O, CO2 and N2 part II: Experimental data

1984 ◽  
Vol 14 (1-4) ◽  
pp. 197-204 ◽  
Author(s):  
Rolt Knobel ◽  
Herbert Breuer ◽  
Friedemann Freund
Keyword(s):  
Experimental Data ◽  
Organic Molecules ◽  
Abiotic Synthesis

scholarly journals Abiotic Synthesis of Methane and Organic Compounds in Earth’s Lithosphere

Elements ◽  
2020 ◽  
Vol 16 (1) ◽  
pp. 25-31 ◽  
Author(s):  
Eoghan P. Reeves ◽  
Jens Fiebig
Keyword(s):  
Organic Matter ◽  
Organic Compounds ◽  
Molecular Hydrogen ◽  
Inorganic Carbon ◽  
Organic Molecules ◽  
Laboratory Simulations ◽  
Abiotic Synthesis ◽  
Extensive Analysis ◽  
Isotope Analyses ◽  
Ubiquitous Presence

Accumulation of molecular hydrogen in geologic systems can create conditions energetically favorable to transform inorganic carbon into methane and other organic compounds. Although hydrocarbons with a potentially abiotic origin have been proposed to form in a number of crustal settings, the ubiquitous presence of organic compounds derived from biological organic matter presents a challenge for unambiguously identifying abiotic organic molecules. In recent years, extensive analysis of methane and other organics in diverse geologic fluids, combined with novel isotope analyses and laboratory simulations, have, however, yielded insights into the distribution of specific abiotic organic molecules in Earth’s lithosphere and the likely conditions and pathways under which they form.

Ab-Initio Molecular Dynamics of Organic Compounds on a Massively Parallel Computer

1995 ◽  
Vol 408 ◽  
Author(s):  
François Gygi
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Organic Compounds ◽  
Organic Molecules ◽  
Curvilinear Coordinates ◽  
Parallel Computer ◽  
Massively Parallel ◽  
Dynamics Simulations

AbstractWe present results of ab-initio electronic structure calculations and molecular dynamics simulations of organic molecules carried out using adaptive curvilinear coordinates, within the local density approximation of density functional theory. This approach allows for an accurate treatment of first-row elements, which makes it particularly suitable for investigations of organic compounds. A recent formulation of this method relies on a real-space approach which combines the advantages of finite-difference methods with the accuracy of adaptive coordinates, and is well suited for implementation on massively parallel computers. We used molecular dynamics simulations to obtain the fully relaxed structures of nitrosyl fluoride (FNO), and of the aromatic heterocycles furan and pyrrole. The equilibrium geometries obtained show excellent agreement with experimental data. The harmonic vibrational frequencies of furan and pyrrole were calculated by diagonalization of their dynamical matrix and are found to agree with experimental data within an rms error of 25 cm-1 and 28 cm-1 for furan and pyrrole respectively. This accuracy is comparable to that attained for smaller organic molecules using elaborate quantum chemistry methods.

Internal rotation in some organic molecules containing methyl, amino, hydroxyl, and formyl groups

1972 ◽  
Vol 25 (8) ◽  
pp. 1601 ◽  
Author(s):  
L Radom ◽  
WA Lathan ◽  
WJ Hehre ◽  
JA Pople
Keyword(s):  
Experimental Data ◽  
Ab Initio ◽  
Internal Rotation ◽  
Molecular Orbital ◽  
Organic Molecules ◽  
Experimental Information ◽  
Molecular Orbital Theory ◽  
Orbital Theory ◽  
Moderate Agreement ◽  
Theoretical Results

Ab initio molecular orbital theory is used to study internal rotation in 20 organic molecules of the types X-Y, X-CH2-Y, X-SH-Y, X-O-Y, and X-CO-Y-where X and Y are methyl, amino, hydroxy, or formyl groups. In some of these molecules, internal rotation about two bonds is possible. The theoretical results are generally in moderate agreement with available experimental data and, in addition, lead to a number of predictions for molecules for which experimental information is lacking.

scholarly journals Calculation of the Vapour Pressure of Organic Molecules by Means of a Group-Additivity Method and Their Resultant Gibbs Free Energy and Entropy of Vaporization at 298.15 K

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 1045
Author(s):  
Rudolf Naef ◽  
William E. Acree
Keyword(s):  
Experimental Data ◽  
Free Energy ◽  
Correlation Coefficient ◽  
Gibbs Free Energy ◽  
Vapour Pressure ◽  
Organic Molecules ◽  
Group Additivity ◽  
Standard Entropy ◽  
Absolute Deviation ◽  
Entropy Of Vaporization

The calculation of the vapour pressure of organic molecules at 298.15 K is presented using a commonly applicable computer algorithm based on the group-additivity method. The basic principle of this method rests on the complete breakdown of the molecules into their constituting atoms, further characterized by their immediate neighbour atoms. The group contributions are calculated by means of a fast Gauss–Seidel fitting algorithm using the experimental data of 2036 molecules from literature. A ten-fold cross-validation procedure has been carried out to test the applicability of this method, which confirmed excellent quality for the prediction of the vapour pressure, expressed in log(pa), with a cross-validated correlation coefficient Q2 of 0.9938 and a standard deviation σ of 0.26. Based on these data, the molecules’ standard Gibbs free energy ΔG°vap has been calculated. Furthermore, using their enthalpies of vaporization, predicted by an analogous group-additivity approach published earlier, the standard entropy of vaporization ΔS°vap has been determined and compared with experimental data of 1129 molecules, exhibiting excellent conformance with a correlation coefficient R2 of 0.9598, a standard error σ of 8.14 J/mol/K and a medium absolute deviation of 4.68%.

scholarly journals Calculation of the Vapour Pressure of Organic Molecules by Means of a Group-Additivity Method and their Resultant Gibbs Free Energy and Entropy of Vaporization at 298.15K

2021 ◽  
Author(s):  
Rudolf Naef ◽  
William E. Acree Jr.
Keyword(s):  
Experimental Data ◽  
Free Energy ◽  
Correlation Coefficient ◽  
Gibbs Free Energy ◽  
Vapour Pressure ◽  
Organic Molecules ◽  
Group Additivity ◽  
Standard Entropy ◽  
Absolute Deviation ◽  
Entropy Of Vaporization

The calculation of the vapour pressure of organic molecules at 298.15K is presented using a commonly applicable computer algorithm based on the group-additivity method. The basic principle of this method rests on the complete breakdown of the molecules into their constituting atoms, further characterized by their immediate neighbour atoms. The group contributions are calculated by means of a fast Gauss-Seidel fitting algorithm using the experimental data of 2036 molecules from literature. A ten-fold cross-validation procedure has been carried out to test the applicability of this method, which confirmed excellent quality for the prediction of the vapour pressure, expressed in log(pa), with a cross-validated correlation coefficient Q2 of 0.9938 and a standard deviation  of 0.26. Based on these data, the molecules' standard Gibbs free energy G°vap has been calculated. Furthermore, using their enthalpies of vaporization, predicted by an analogous group-additivity approach published earlier, the standard entropy of vaporization S°vap has been determined and compared with experimental data of 1129 molecules, exhibiting excellent conformance with a correlation coefficient R2 of 0.9598, a standard error  of 8.14 J/mol/K and a medium absolute deviation of 4.68%.

Computer Simulations of Diffusion, Adsorption and Reaction of Organic Molecules in Pillared Clays

1987 ◽  
Vol 111 ◽  
Author(s):  
Muhammad Sahimi ◽  
Theodore T. Tsotsis ◽  
Mario L. Occelli
Keyword(s):  
Experimental Data ◽  
Monte Carlo ◽  
Organic Molecules ◽  
Effective Diffusivity ◽  
Pillared Clays ◽  
Recent Experimental Data ◽  
Accurate Data ◽  
Gas Oil ◽  
New Class ◽  
Dynamic Monte Carlo

AbstractDiffusion and reaction of large organic molecules in pillared clays, a new class of catalysts capable of converting gas oil into transportation fluids, is investigated. We first discuss some recent experimental data and point out the possible difficulties for obtaining accurate data. We, then, discuss a new model for describing diffusion and reaction of large organic molecules in pillared clays. The model employs stochastic and random walk concepts to model the diffusion process, and a dynamic Monte Carlo method for predicting various properties of interest, such as the effective diffusivity of the molecules.

Molecular geometries - Accuracy test of the PCILO method

1980 ◽  
Vol 45 (2) ◽  
pp. 321-329 ◽  
Author(s):  
Zdeněk Havlas ◽  
Petr Maloň
Keyword(s):  
Experimental Data ◽  
Quadratic Form ◽  
Organic Molecules ◽  
Molecular Geometry ◽  
Stationary Points ◽  
Small Organic Molecules ◽  
Accuracy Test ◽  
Pcilo Method ◽  
Length Determination ◽  
Energy Hypersurface

Applicability of the PCILO method for investigation of stationary points of the energy hypersurface has been tested with a set of 11 small organic molecules. From comparison of the molecular geometries, completely optimized with the use of the Payne algorithm, with experimental data and with the results obtained by the MINDO/3 and MNDO methods it follows that the PCILO method is suitable for semiquantitative estimate of molecular geometry (mean error in the bond length determination 5 . 10-3 nm, valence angles 3.4°). The Payne algorithm is little efficient, if the starting geometry is far from the stationary point and if the assumption of quadratic form of the hypersurface is not fulfilled.

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