B. van de Graaf

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.

A consistent molecular mechanics force field for all-silica zeolites

Abstract A consistent molecular mechanics force field has been developed for all-silica structures including α-quartz and several zeolites that predicts geometry, heat of formation, and the vibrational frequencies reasonably well. The force field consists of a bonding term, a bending term, and long-range interactions. Results are given for α-quartz and the all-silica analogs of the zeolites Nu-10, mordenite, ZSM-5, and faujasite.

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.

Molecular mechanics studies on MFI-typezeolites: Part 4. Energetics of crystal growth directing agents

Abstract A biquat (hexapropyl-1, 6-hexanediammonium) has been used as a crystal growth directing templatein the MFI synthesis. The crystals obtained show a relatively small a/b ratio. Molecular mechanics calculations show that this biquat occupies preferentially the straight channels of the MFI framework, giving information about the mechanism of template inclusion during crystal growth. Several other biquats have been examined as possible templates and have been studied with molecular mechanics.

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.

The Pristane Formation Index, a new molecular maturity parameter. A simple method to assess maturity by pyrolysis/evaporation-gas chromatography of unextracted samples

A set of eleven samples from the Handil borehole, Mahakam delta, Indonesia, has been analyzed to test the hypothesis that the Pristane Formation Index (PFI = [pristane]/{[pristane]+ [pristenes]}) can be used as a molecular maturation parameter. By pyrolysis/evaporation-gas chromatography (py/ev-GC) of unextracted samples the amounts of the product (pristane) and of the precursor(s) (measured as pristenes) of the pristane formation reaction(s) were measured simultaneously. PFI shows very high correlations with maturity parameters such as vitrinite reflectance, Carbon Preference Index (CPI), T-max and with burial depth. Calculation of the pseudo-kinetic parameters of the Arrhenius equation k = A exp(−ERT), using published values for effective time of burial (teff) and temperature gradient, yields values of 59 kJ mol−1 and2.2∗10−7 s−1 for E and A, respectively. The value of E is not very sensitive to variations in the assumed values of teff and temperature gradient; the value of A is extremely low in all cases. The values of the pseudo-kinetic parameters are much lower than those of the isomerization and aromatization reactions and thus offer interesting possibilities for the reconstruction of thermal histories of basins.

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.

The mass spectrometry of iso and anteiso monoenoic fatty acids.

The normal, iso, and anteiso Δ8- and Δ9-17:1 fatty acid methyl esters were synthesized and their electron impact-induced fragmentation was studied by mass spectrometry. The mass spectra of the preterminal branched monoenoic fatty acid methyl esters present characteristic fragment ions, now understood to be indicative of the position of the methyl group. These fragment ions are in the iso compound m/e 227 [M-55]+, m/e 195 [M-87]+, and m/e 177 [M-105]+, while in the anteiso compound these fragments are shifted by 14 mass units to m/e 213, m/e 181, and m/e 163. The 15-D-iso Δ8- and Δ9-17:1 methyl esters were synthesized because the characteristic fragment ions in the methyl branched compounds indicated a key role of the tertiary hydrogen atom in the rearrangement process. A fragmentation mechanism consisting of a double bond migration triggered by the tertiary hydrogen and an allylic cleavage assuming a displacement mechanism is proposed.

Ab initio studies on four alkyl nitric esters

Abstract Ab initio calculations at various levels have been performed to investigate the geometries and electronic structures of methyl, ethyl, propyl and butyl nitrates. The calculated results at various levels are compared with the available experimental results and with each other. The geometrical parameters of methyl and ethyl nitrates calculated by MP2/6-311G ∗ are in very good agreement with the experimental gas-phase results.