T. Verstraelen

Hirshfeld-E partitioning: AIM charges with an improved trade-off between robustness and accurate electrostatics

T. Verstraelen, P.W. Ayers, V. Van Speybroeck, M. Waroquier
Journal of Chemical Theory and Computation (JCTC)
9 (5), 2221–2225
2013
A1

Abstract 

For the development of ab-initio derived force fields, atomic charges must be computed from electronic structure computations, such that (i) they accurately describe the molecular electrostatic potential (ESP) and (ii) they are transferable to the force-field application of interest. The Iterative Hirshfeld (Hirshfeld-I or HI) scheme meets both requirements for organic molecules. For inorganic oxide clusters, however, Hirshfeld-I becomes ambiguous because electron densities of nonexistent isolated anions are needed as input. Herein, we propose a simple Extended Hirshfeld (Hirshfeld-E or HE) scheme to overcome this limitation. The performance of the new HE scheme is compared to four popular atoms-in-molecules schemes, using two tests involving a set of 248 silica clusters. These tests show that the new HE scheme provides an improved trade-off between the ESP accuracy and the transferability of the charges. The new scheme is a generalization of the Hirshfeld-I scheme and it is expected that its improvements are to a large extent applicable to molecular systems containing elements from the entire periodic table.

Diphosphonylation of Aromatic Diazaheterocycles and Theoretical Rationalization of Product Yields

A. De Blieck, S. Catak, W. Debrouwer, J. Drabowicz, K. Hemelsoet, T. Verstraelen, M. Waroquier, V. Van Speybroeck, C. Stevens
European Journal of Organic Chemistry
2013 (6), 1058-1067
2013
A1

Abstract 

Diphosphonylated diazaheterocyclic compounds were synthesized in a one-step reaction by using dimethyl trimethylsilyl phosphite (DMPTMS) under acidic conditions. The reaction of DMPTMS with 1,5-naphthyridine yielded the corresponding diphosphonylated product through a tandem 1,4–1,2 addition under microwave conditions. This tandem 1,4–1,2 addition was also evaluated for other substrates, namely, 1,10-phenanthroline, 1,7-phenanthroline and 4,7-phenanthroline. Reactions under reflux and microwave conditions were compared. 1,5-Naphthyridine and the phenanthroline derived substrates are less reactive than previously investigated quinolines. The experimental trends in reactivity were rationalized by means of theoretical calculations. The intrinsic properties, such as aromaticity and proton affinities, showed distinct differences for the various substrates. Furthermore, the calculated free energies of activation for the rate-determining step of the tandem addition reaction enabled us to rationalize the differences in product yields. Both the theoretical and the experimental results show the substantial influence of the position of the nitrogen atoms in the (poly)aromatic compounds on the reaction outcome.

ACKS2: Atom-Condensed Kohn-Sham DFT approximated to second order

T. Verstraelen, P.W. Ayers, V. Van Speybroeck, M. Waroquier
Journal of Chemical Physics
138 (7), 07408
2013
A1

Abstract 

A new polarizable force field (PFF), namely atom-condensed Kohn-Sham density functional theory approximated to second order (ACKS2), is proposed for the efficient computation of atomic charges and linear response properties of extended molecular systems. It is derived from Kohn-Sham density functional theory (KS-DFT), making use of two novel ingredients in the context of PFFs: (i) constrained atomic populations and (ii) the Legendre transform of the Kohn-Sham kinetic energy. ACKS2 is essentially an extension of the Electronegativity Equalization Method (EEM) [W. J. Mortier, S. K. Ghosh, and S. Shankar, J. Am. Chem. Soc. 108, 4315 (1986)]10.1021/ja00275a013 in which two major EEM shortcomings are fixed: ACKS2 predicts a linear size-dependence of the dipole polarizability in the macroscopic limit and correctly describes the charge distribution when a molecule dissociates. All ACKS2 parameters are defined as atoms-in-molecules expectation values. The implementation of ACKS2 is very similar to that of EEM, with only a small increase in computational cost.

Open Access version available at UGent repository

The Conformational Sensitivity of Iterative Stockholder Partitioning Schemes

T. Verstraelen, P.W. Ayers, V. Van Speybroeck, M. Waroquier
Chemical Physics Letters
545, 138-143
2012
A1

Abstract 

Chemical interpretation and empirical modeling of partial charges requires a robust partitioning scheme to derive these charges from the molecular electronic density. The degree of undesirable conformational sensitivity is assessed for three iterative stockholder partitioning schemes: Hirshfeld-I (HI), Iterative Stockholder Analysis (ISA) and a new Gaussian ISA variant (GISA). GISA has fewer degrees of freedom than ISA and enforces monotonically decaying pro-atoms. These improvements accelerate the converge of GISA as compared to ISA. However, the conformational sensitivity of the charges does not decrease and is still large compared to HI.

Open Access version available at UGent repository

Analysis of the basis set superposition error in molecular dynamics of hydrogen-bonded liquids: application to methanol

M. Van Houteghem, T. Verstraelen, A. Ghysels, L. Vanduyfhuys, M. Waroquier, V. Van Speybroeck
Journal of Chemical Physics
137 (10), 104506
2012
A1

Abstract 

An ecient protocol is presented to compensate for the basis set superposition error (BSSE) in DFT molecular dynamics (MD) simulations using localized Gaussian basis sets. We propose a classical correction term that can be added a posteriori to account for BSSE. It is tested to what extension this term will improve radial distribution functions (RDFs). The proposed term is pairwise between certain atoms in dierent molecules and was calibrated by tting reference BSSE data points computed with the counterpoise method. It is veried that the proposed exponential decaying functional form of the model is valid. This work focuses on hydrogen-bonded liquids, i.e. methanol, and more specic on the intermolecular hydrogen bond, but in principle the method is generally applicable on any type of interaction where BSSE is significant. We evaluated the relative importance of the Grimme-dispersion versus BSSE and found that they are of the same order of magnitude, but with an opposite sign. Upon introduction of the correction, the relevant RDFs, obtained from MD, have amplitudes equal to experiment.

Open Access version available at UGent repository

Catalytic Performance of Vanadium MIL-47 and Linker-Substituted Variants in the Oxidation of Cyclohexene: A Combined Theoretical and Experimental Approach

M. Vandichel, S. Biswas, K. Leus, J. Paier, J. Sauer, T. Verstraelen, P. Van der Voort, M. Waroquier, V. Van Speybroeck
ChemPlusChem
79 (8), 1183–1197
2014
A1

Abstract 

The epoxidation of cyclohexene has been investigated on a metal–organic framework MIL-47 containing saturated V+IV sites linked with functionalized terephthalate linkers (MIL-47-X, X=OH, F, Cl, Br, CH3, NH2). Experimental catalytic tests have been performed on the MIL-47-X materials to elucidate the effect of linker substitution on the conversion. Notwithstanding the fact that these substituted materials are prone to leaching in the performed catalytic tests, the initial catalytic activity of these materials correlates with the Hammett substituent constants. In general, substituents led to an increased activity relative to the parent MIL-47. To rationalize the experimental findings, first-principles kinetic calculations were performed on periodic models of MIL-47 to determine the most important active sites by creating defect structures in the interior of the crystalline material. In a next step these defect structures were used to propose extended cluster models, which are able to reproduce in an adequate way the direct environment of the active metal site. An alkylperoxo species V+VO(OOtBu) was identified as the most abundant and therefore the most active epoxidation site. The structure of the most active site was a starting basis for the construction of extended cluster models including substituents. They were used for quantifying the effect of functionalization of the linkers on the catalytic performance of the heterogeneous catalyst MIL-47-X. Electron-withdrawing as well as electron-donating groups have been considered. The epoxidation activity of the functionalized models has been compared with the measured experimental conversion of cyclohexene. The agreement is fairly good. This combined experimental–theoretical study makes it possible to elucidate the structure of the most active site and to quantify the electronic modulating effects of linker substituents on the catalytic activity.

Automated Parametrization of AMBER Force Field Terms from Vibrational Analysis with a Focus on Functionalizing Dinuclear Zinc(II) Scaffolds

S.K. Burger, M. Lacasse, T. Verstraelen, J.A. Drewry, P.T. Gunning, P.W. Ayers
Journal of Chemical Theory and Computation (JCTC)
8 (2), 554-562
2012
A1

Abstract 

A procedure for determining force constants that is independent of the internal redundant coordinate choice is presented. The procedure is based on solving each bond and angle term separately, using the Wilson B matrix. The method only requires a single ab initio frequency calculation at the minimum energy structure and is made available in the software "parafreq". The methodology is validated with a set of small molecules, by showing it can reproduce ab initio frequencies better than other methods such as taking the diagonal terms of the Hessian in internal coordinates or by using standard AMBER force fields. Finally, the utility of the method is demonstrated by parametrizing the dizinc scaffold of bis-dipicolylamine (BDPA) bound to phosphotyrosine, which is then functionalized into promising antitumor drug proteomimetics.

Ab initio parametrized force field for the flexible metal-organic framework MIL-53(Al)

L. Vanduyfhuys, T. Verstraelen, M. Vandichel, M. Waroquier, V. Van Speybroeck
Journal of Chemical Theory and Computation (JCTC)
8 (9), 3217-3231
2012
A1

Abstract 

A force field is proposed for the flexible metal-organic framework MIL-53(Al), which is calibrated using density functional theory calculations on non-periodic clusters. The force field has three main contributions: an electrostatic term based on atomic charges derived with a modified Hirshfeld-I method, a van der Waals (vdW) term with parameters taken from the MM3 model and a valence force field whose parameters were estimated with a new methodology that uses the gradients and Hessian matrix elements retrieved from non-periodic cluster calculations. The new force field, predicts geometries and cell parameters that compare well with the experimental values both for the large and narrow pore phases. The energy profile along the breathing mode of the empty material reveals the existence of two minima, which confirms the intrinsic bistable behaviour of the MIL-53. Even without the stimulus of external guest molecules the material may transform from the large pore (lp) to the narrow pore (np) phase [Liu et al. JACS 2008, 120, 11813]. The relative stability of the two phases critically depends on the vdW parameters and MM3 dispersion interaction has the tendency to overstabilize the np phase.

Host-guest and guest-guest interactions between xylene isomers confined in the MIL-47(V) pore system

A. Ghysels, M. Vandichel, T. Verstraelen, M. van der Veen, D. De Vos, M. Waroquier, V. Van Speybroeck
Theoretical Chemistry Accounts
131 (7) 1234-1246
2012
A1

Abstract 

The porous MIL-47 material shows a selective adsorption behavior for para-, ortho-, and meta-isomers of xylenes, making the material a serious candidate for separation applications. The origin of the selectivity lies in the differences in interactions (energetic) and confining (entropic). This paper investigates the xylene–framework interactions and the xylene–xylene interactions with quantum mechanical calculations, using a dispersion-corrected density functional and periodic boundary conditions to describe the crystal. First, the strength and geometrical characteristics of the optimal xylene–xylene interactions are quantified by studying the pure and mixed pairs in gas phase. An extended set of initial structures is created and optimized to sample as many relative orientations and distances as possible. Next, the pairs are brought in the pores of MIL-47. The interaction with the terephthalic linkers and other xylenes increases the stacking energy in gas phase (−31.7 kJ/mol per pair) by roughly a factor four in the fully loaded state (−58.3 kJ/mol per xylene). Our decomposition of the adsorption energy shows various trends in the contributing xylene–xylene interactions. The absence of a significant difference in energetics between the isomers indicates that entropic effects must be mainly responsible for the separation behavior.

Open Access version available at UGent repository

Computation of charge distribution and electrostatic potential in silicates with the use of chemical potential equalization models

T. Verstraelen, S.V. Sukhomlinov, V. Van Speybroeck, M. Waroquier, K. Smirnov
Journal of Physical Chemistry C
116 (1), 490–504
2012
A1

Abstract 

New parameters for the electronegativity equalization model (EEM) and the split-charge equilibration (SQE) model are calibrated for silicate materials, based on an extensive training set of representative isolated systems. In total, four calibrations are carried out, two for each model, either using iterative Hirshfeld (HI) charges or ESP grid data computed with Density Functional Theory (DFT) as a reference. Both the static (ground state) reference quantities and their responses to uniform electric fields are included in the fitting procedure. The EEM model fails to describe the response data, while the SQE model quantitatively reproduces all the training data. For the ESP-based parameters, we found that the reference ESP data are only useful at those grid points where the electron density is lower than 10-3 a.u. The density value correlates with a distance criterion used for selecting grid points in common ESP fitting schemes. All parameters are validated with DFT computations on an independent set of isolated systems (similar to the training set), and on a set of periodic systems including dense and microporous crystalline silica structures, zirconia, and zirconium silicate. Although the transferability of the parameters to new isolated systems poses no difficulties, the atomic hardness parameters in the HI-based models must be corrected to obtain accurate results for periodic systems. The SQE/ESP model permits the calculation of the ESP with similar accuracy in both isolated and periodic systems.

Open Access version available at UGent repository

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