Bastiaan van de Graaf

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.

Extending and simplifying the electronegativity equalization method

Abstract The Electronegativity Equalization Method (EEM), developed by Mortier et al. [J.W. Mortier, S.K. Ghosh, S. Shankar, J. Am. Chem. Soc., 108 (1986) 4315; G.O.A. Janssens, B.G. Baekelandt, H. Toufar, W.J. Mortier, R.A. Schoonheydt, J. Phys. Chem., 99 (1995) 3251], is extended with a shielded external potential to improve its accuracy. EEM is also simplified in the sense that one type of hydrogen atom is used to describe positively as well as negatively charged hydrogen atoms instead of two as in the original formula. The parameters are calibrated to sets of Mulliken charges obtained from STO-3G and STO-3G* calculations, containing Al, C, H, N, O and Si atoms, and also Ge and Ti atoms for which no parameters were found in literature yet. Furthermore, the parameters (Ge and Ti excluded) are also calibrated to a set of potential derived charges (Merz–Kollman–Singh scheme). It seems that the EEM formalism, after appropriate parameterization, can reproduce the results of different charge partitioning schemes applied to calculations with different basis sets. Extending the EEM formula leads to a better reproduction of the charges. However, the parameters are highly correlated and, therefore, depend strongly on the calibration set used. All charges are well reproduced, except on titanium. A sensitivity analysis of the charges with the original and extended EEM formalism shows that their results differ, but are strongly correlated. The applicability of the EEM approach and the parameters derived is shown in a molecular dynamics calculation on ethene absorbed in H-ZSM-5. It appears that the EEM approach in such calculations can help to understand chemical reactivity in zeolites.

A consistent molecular mechanics force field for aluminophosphates

A consistent molecular mechanics force field has been developed for aluminophosphate structures including berlinite and several molecular sieve structures, which predicts the 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. Charges are calculated using the electronegativity equalization method of Mortier et al.(W. J. Mortier, S. K. Ghoshand and S. Shankar, J. Am. Chem. Soc., 1986, 108, 4315), modified with the relative permittivity. The parameters for oxygen are transferable with the all-silica force field recently developed. Results are given for berlinite, AlPO-5 (AFI), AlPO-8 (AET), AlPO-11 (AEL), AlPO-18 (AEI), AlPO-25 (ATV), AlPO-35 (LEV), AlPO-37 (FAU) and VPI-5 (VFI), as well as for the hydrated structures of variscite and VPI-5 (six-fold coordination around aluminium) and the structures of AlPO-18 and AlPO-21 (ATO) with extra-framework oxygen (five-fold coordinated aluminium). Atomic positions of the AlPO-35 structure (both DLS and energy minimized), which have not been reported before, are also given.

On the origin of the band at 960 cm−1 in the vibrational spectra of Ti-substituted zeolites

Abstract Molecular dynamics was applied to calculate the vibrational spectra of Ti-substituted orthorhombic MFI structures. In good agreement with experimental data a new band at 935 cm −1 appears in the calculated infrared and Raman spectra upon Ti incorporation into the lattice. Results of the calculations allow to assign the band to the localized stretching SiO vibration in SiOTi bridges due to the inequivalence of the SiO and TiO bonds.

A kinetic calculation method of homohopanoid maturation: Applications in the reconstruction of burial histories of sedimentary basins

Abstract Hydrous pyrolysis, performed at relatively low temperatures, of an immature marl yielded artificial maturation data on changes in homohopane isomer compositions. At higher temperatures enhanced amounts of 17α,21β(H)- and 17β,21α-hopanes over 17β,21β(H)-hopanes are observed. The amounts of 22S epimers increase relative to those of their 22R counterparts with increasing temperature. These experimental data, as well as sedimentary data on homohopane concentrations, have been reproduced using a kinetic calculation method, based on the thermodynamic stabilities determined by molecular mechanics calculation, using a full isomerization scheme rather than a single direct chiral isomerization step. We need to caution, however, that agreement between the predictions from a theoretical scheme and quantitative measurements is not an unequivocal proof for the chosen kinetic model. Good reproduction of the maturation data was obtained even for those obtained at the highest pyrolysis temperatures, at which significant destruction of hopane isomers was apparent. These results indicate that the kinetic calculation method can be used to model diagenetic and catagenetic reactions affecting biomarker ratios in sediments. Further computer simulations indicate that hopane-hopane interconversion reactions probably only have a minor influence on hopane isomer ratios.

Automated Extraction of Pure Mass Spectra from Gas Chromatographic/Mass Spectrometric Data†

An algorithm is described that extracts pure mass spectra from gas chromatographic/mass spectrometric (GC/MS) data. It is based on backfolding, a method described previously to enhance chromatographic resolution in GC/MS data. The ability to extract pure mass spectra was evaluated with both simulated and real GC/MS data and the algorithm was compared with two other methods described recently. It is shown that the algorithm presented gives good results, even when the chromatographic resolution is poor and the spectra are very similar. No a priori knowledge concerning the composition of the data is required.

Consistent implementation of the electronegativity equalization method in molecular mechanics and molecular dynamics

An approach for the inclusion of geometry-dependent charges in molecular mechanics (MM) and molecular dynamics (MD) calculations on the basis of the electronegativity equalization method (EEM) is proposed and tested. It is shown that for a consistent implementation of EEM, the force field has to be extended with charge-dependent intraatomic terms. This extension simplifies MD and MM calculations on both molecular and supramolecular systems. Compared with calculations with fixed charges the present approach leads only to a modest increase in the computational overhead.

Molecular mechanics studies of TBA and TPA in MEL and MFI

Abstract The interactions of the template ions TPA and TBA with the all-silica zeolite structure types MFI and MEL are studied by molecular mechanics calculations with complete structural relaxation of both the zeolite framework and the template ions. MFI as well as MEL can accommodate only two TBA ions per unit cell because overcrowding occurs when TBA ions occupy adjacent channel intersections. With two TBA ions MEL is more stable than MFI. Both zeolite structures can accommodate four TPA ions per unit cell. In this case MFI is the more stable structure. This result is explained by the fact that MEL has two different types of intersections. One type can accommodate tetraalkylammonium ions in their most favorable conformation. Accommodation of such a template in the other type of intersection, however, introduces considerable strain in both the zeolite and the template ion. The preference of MEL for TBA ions as template and of MFI for TPA ions as template agrees with experimental experience. The empty, relaxed MEL structure exhibits Imm2 symmetry. This is in agreement with NMR data at 268 K.

Study of methane adsorption in MFI and MEL zeolites by combination of the electronegativity equalization method and molecular dynamics

Characteristics of methane molecules adsorbed in MFI and MEL zeolites have been studied by a combination of the electronegativity equalization method and molecular dynamics (CIEEM MD, see preceding paper). The inclusion of polarization in the MD calculations is shown to reproduce important features of the host–guest interactions and gives additional information on the reactivity of the adsorbed species and on the active regions in the zeolite pore systems. The data obtained on the molecular electronegativity and the induced dipole moments indicate that the edges of the intersections of the channels are the active sites. The polarization of the methane molecules in the MEL structure is larger than that in MFI. This is largely related to the topology of the lattices. For the MFI structure the calculated dependence of the molecular dipole moment on the position of the molecules in the framework is in excellent agreement with the silicalite electrostatic potential obtained by periodical Hartree–Fock calculations (J. C. White and A. C. Hess, J. Phys. Chem., 1993, 97, 8703).

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.