J. M. A. Baas

Limited double bond isomerisation and selective hydrogenation of sterenes during early diagenesis

Abstract Relative differences in free energy of 32 cholestene isomers have been calculated by molecular mechanics using the MM2 empirical force field with adjusted increments for sp 2 hybridised carbon atoms. Based on the results and on a reinspection of the literature it has been concluded that some steps in the previously proposed early diagenetic pathways of steroid diagenesis have to be reconsidered; double bond isomerizations via secondary carbocations are not considered likely to occur in nature. To explain in an alternative way the sterene/sterane distribution patterns observed in Recent sediments a limited isomerization ( via tertiary carbocations only) occurring simultaneously with a selective reduction is proposed.

DELFT MOLECULAR MECHANICS : A NEW APPROACH TO HYDROCARBON FORCE FIELDS : INCLUSION OF A GEOMETRY-DEPENDENT CHARGE CALCULATION

A new hydrocarbon force fields for saturated and non-conjugated unsaturated hydrocarbons has been developed. The most important difference between this force field and existing ones is its ability to produce a realistic, geometry-dependent charge distribution, the charges being calculated by the geometry-dependent method of Mortier (W. J. Mortier, S. K. Ghosh and S. Shankear, J. Am. Chem. Soc., 1986, 108, 4315). The use of this charge the calculation means that polarization effects can be reproduced. charge–Charge interactions are used between all the atoms in the molecules.Results show that by using this method a good hydrocarbon force field can be constructed. Heats of formation for a hundred compounds are calculated with an average absolute difference from experimental values of 1.02 kJ mol–1. Geometries, IR Frequencies and conformational energies are also well reproduced.

Theoretical organic geochemistry. I. The thermodynamic stability of several cholestane isomers calculated by molecular mechanics

Abstract The thermodynamic stabilities of thirteen cholestane isomers have been computed using molecular mechanics. The calculated composition of a mixture of these isomers at thermodynamic equilibrium is in agreement with the composition of a cholestane isomerate. From the calculated stabilities the extent to which isomerisation reactions can proceed during maturation can be predicted. The GLC retention order on non-polar phases of 20R/S isomeric pairs has been estimated from the preferred geometries of the molecules which are also obtained by molecular mechanics.

A molecular mechanics study on rotational motions of side groups in poly(methyl methacrylate)

Abstract Molecular mechanics has been applied to model compounds of syndiotactic poly(methyl methacrylate) (PMMA). The results for the energy minimum correspond with the conformation derived in literature from wide-angle X-ray scattering. Barriers to rotation calculated for the ester and the main-chain methyl groups correspond well with available experimental data. The barrier to rotation obtained for the alkoxy group is much higher than usually expected, but the two-well potential model rules this rotation out as the molecular process responsible for the β-maximum of PMMA. The barrier to rotation obtained for the alkoxycarbonyl group is much too low to correspond to the β-maximum. Constraint of the main-chain torsion angles brings the barrier near to the activation energy of this process. We conclude that about half the experimental barrier can be attributed to matrix effects.

Chair-boat equilibria in bicyclo[3.3.1]nonane and some 3- and 3,7-substituted derivatives: Thermodynamic parameters and geometry of the conformers as obtained by molecular mechanics

Abstract ΔG-Values for conformational equilibria in 3,7-substituted bicyclo[3.3.1]nonanes have been obtained by means of epimerisation experiments ( cc α bc ) and by variable temperature 13 C NMR ( bc α bb ). The results of these experiments fit well with those of molecular mechanics using the Schleyer force field. In bicyclo[3.3.1]nonane and 3β-substituted derivatives the cc conformation predominates; however, the bulky 3β-substituent t-butyl, is found to have a destabilizing effect. A 3α-substituent forces the substituted wing into the boat conformation. For the 3α,7α-substituted derivatives the conformational preferences depend on the size of the substituents: for 3α-methyl-7α-t-butylbicyclo[3.3.1]nonane the cb and t- bb conformers are of approximately equal enthalpy. The geometries, obtained by the calculations, show that the conformers of bicyclo[3.3.1]nonane ( cc , bc and t-bb ) are all distinctly flattened. The boat wings of bc conformers are not twisted to any extent. The t-bb is the most stable bb conformation. The influence of substitution at positions 3 or 7 is discussed in detail; in general, a bulky substituent such as t-butyl, affects the geometry of both wings of the ring system. The calculated geometries are in good agreement with the conclusions of previous 1 H NMR investigations.

Relative stabilities of sedimentary rearranged sterenes as calculated by molecular mechanics: a key to unravel further steroid diagenesis

Abstract Molecular mechanics calculations of rearranged cholestenes revealed that diacholest-13(17)-enes with 10α stereochemistry are more stable than their 10β counterparts and that a partly rearranged sterene with a Δ 8 double bond and 10β, 14β stereochemistry (compound 7) is relatively stable at thermodynamic equilibrium. The calculated data are in good agreement with sedimentary and experimental data and thus reinforce recent propositions for early-stage diagenesis of steroids.

Synthesis of Alkyl Fructosides Using Solid Acid Catalysts. Part I: Silica-Alumina Cracking Catalysts

Abstract Silica-alumina cracking catalysts and acid clays efficiently catalyze the 2-O-alkylation of d-fructose with long chain alcohols. Under the conditions applied virtually no degradation of fructose is observed. l-Sorbose and the aldopentoses also undergo silica-alumina-catalyzed alkylation. The rate of conversion is related to the solubility of the monosaccharide and the stability of the intermediate oxocarbenium ion. Best results in fructose alkylation are obtained by applying a recirculation method with butyl fructoside as soluble intermediate.

Comparison of calculated equilibrium mixtures of alkylnaphthalenes and alkylphenanthrenes with experimental and sedimentary data; the importance of entropy calculations

Abstract Evaluation of the relative stabilities of tetramethylnaphthalenes and dimethylphenanthrenes by means of molecular mechanics calculations allows one to predict the equilibrium mixture compositions for these groups of compounds. These equilibrium compositions have been calculated at various temperatures with and without taking into account the entropy of the compounds. Comparison with experimental observations, and sedimentary data, showed that when entropy is taken into account in the calculations, agreement between the experimental and sedimentary data is much improved. A distinct temperature dependence of the equilibrium composition is predicted for the tetramethylnaphthalenes, indicating the potential of this group of compounds for burial temperature evaluations.

Molecular mechanics force field for tertiary carbocations

A new force field for tertiary carbocations has been developed, based on the Delft molecular mechanics (DMM) hydrocarbon force field (A. C. T. van Duin, J. M. A. Baas and B. van de Graaf, J. Chem. Soc., Faraday Trans., 1994, 90, 2881). As in this force field, the Mortier method (W. J. Mortier, S. K. Ghosh and S. Shankar, J. Am. Chem. Soc., 1986, 108, 4315) is used to calculate geometry-dependent charges. The force field was optimized using enthalpies of formation, solvolysis-rate data and ab initio vibration and geometry data. The ab initio vibration data were rescaled using experimental spectra from the isoelectronic alkylboranes. To check the influence of electron delocalization on the geometry of tertiary carbocations, the results of the force field were compared with crystal structures.A correlation coefficient between the calculated and the experimental solvolysis rates for alkyl bromides of 0.9881 was obtained, showing that the force field gives a good description of carbocation energies.

A molecular mechanics investigation into the mechanism of the low temperature relaxations of three poly(alkyl methacrylates)

Abstract The enthalpy curves for the rotation of the ester groups around the O-alkyl bonds in three-unit all-anti models of syndiotactic poly(ethyl methacrylate), poly(isopropyl methacrylate) and poly(cyclohexyl methacrylate) have been calculated using molecular mechanics. The abundance of conformers and the enthalpies of activation for their interconversion at 50 K have been related to the mechanical loss processes at low temperature with Hoffmans theory for a three site model with two equienergetic sites. The calculated activation energies compare well with the experimental values of the δ relaxations. The mechanical loss process is in all cases caused by the exchange of ester side chain positions by partial rotation around the O-alkyl bond.