Toon Verstraelen

TAMkin: A Versatile Package for Vibrational Analysis and Chemical Kinetics

TAMkin is a program for the calculation and analysis of normal modes, thermochemical properties and chemical reaction rates. At present, the output from the frequently applied software programs ADF, CHARMM, CPMD, CP2K, Gaussian, Q-Chem, and VASP can be analyzed. The normal-mode analysis can be performed using a broad variety of advanced models, including the standard full Hessian, the Mobile Block Hessian, the Partial Hessian Vibrational approach, the Vibrational Subsystem Analysis with or without mass matrix correction, the Elastic Network Model, and other combinations. TAMkin is readily extensible because of its modular structure. Chemical kinetics of unimolecular and bimolecular reactions can be analyzed in a straightforward way using conventional transition state theory, including tunneling corrections and internal rotor refinements. A sensitivity analysis can also be performed, providing important insight into the theoretical error margins on the kinetic parameters. Two extensive examples demonstrate the capabilities of TAMkin: the conformational change of the biological system adenylate kinase is studied, as well as the reaction kinetics of the addition of ethene to the ethyl radical. The important feature of batch processing large amounts of data is highlighted by performing an extended level of theory study, which TAMkin can automate significantly.

Vibrational modes in partially optimized molecular systems

In this paper the authors develop a method to accurately calculate localized vibrational modes for partially optimized molecular structures or for structures containing link atoms. The method avoids artificially introduced imaginary frequencies and keeps track of the invariance under global translations and rotations. Only a subblock of the Hessian matrix has to be constructed and diagonalized, leading to a serious reduction of the computational time for the frequency analysis. The mobile block Hessian approach (MBH) proposed in this work can be regarded as an extension of the partial Hessian vibrational analysis approach proposed by Head [Int. J. Quantum Chem. 65, 827 (1997)]. Instead of giving the nonoptimized region of the system an infinite mass, it is allowed to move as a rigid body with respect to the optimized region of the system. The MBH approach is then extended to the case where several parts of the molecule can move as independent multiple rigid blocks in combination with single atoms. The merits of both models are extensively tested on ethanol and di-n-octyl-ether.

The electronegativity equalization method and the split charge equilibration applied to organic systems: Parametrization, validation, and comparison

An extensive benchmark of the electronegativity equalization method (EEM) and the split charge equilibration (SQE) model on a very diverse set of organic molecules is presented. These models efficiently compute atomic partial charges and are used in the development of polarizable force fields. The predicted partial charges that depend on empirical parameters are calibrated to reproduce results from quantum mechanical calculations. Recently, SQE is presented as an extension of the EEM to obtain the correct size dependence of the molecular polarizability. In this work, 12 parametrization protocols are applied to each model and the optimal parameters are benchmarked systematically. The training data for the empirical parameters comprise of MP2/Aug-CC-pVDZ calculations on 500 organic molecules containing the elements H, C, N, O, F, S, Cl, and Br. These molecules have been selected by an ingenious and autonomous protocol from an initial set of almost 500,000 small organic molecules. It is clear that the SQE model outperforms the EEM in all benchmark assessments. When using Hirshfeld-I charges for the calibration, the SQE model optimally reproduces the molecular electrostatic potential from the ab initio calculations. Applications on chain molecules, i.e., alkanes, alkenes, and alpha alanine helices, confirm that the EEM gives rise to a divergent behavior for the polarizability, while the SQE model shows the correct trends. We conclude that the SQE model is an essential component of a polarizable force field, showing several advantages over the original EEM.

Hirshfeld-E Partitioning: AIM Charges with an Improved Trade-off between Robustness and Accurate Electrostatics

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.

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

A force field is proposed for the flexible metal-organic framework MIL-53(Al), which is calibrated using density functional theory calculations on nonperiodic 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 nonperiodic 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 behavior 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. J. Am. Chem. Soc.2008, 120, 11813]. The relative stability of the two phases critically depends on the vdW parameters, and the MM3 dispersion interaction has the tendency to overstabilize the np phase.

QuickFF: a program for a quick and easy derivation of force fields for metal-organic frameworks from ab initio input

QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal‐organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three‐step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal‐organic frameworks (MOFs), QuickFF is used to determine force fields for MIL‐53(Al) and MOF‐5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort.

Opposite regiospecific ring opening of 2-(cyanomethyl)aziridines by hydrogen bromide and benzyl bromide : experimental study and theoretical rationalization

Ring opening of 1-arylmethyl-2-(cyanomethyl)aziridines with HBr afforded 3-(arylmethyl)amino-4-bromobutyronitriles via regiospecific ring opening at the unsubstituted aziridine carbon. Previous experimental and theoretical reports show treatment of the same compounds with benzyl bromide to furnish 4-amino-3-bromobutanenitriles through ring opening at the substituted aziridine carbon. To gain insights into the regioselective preference with HBr, reaction paths have been analyzed with computational methods. The effect of solvation was taken into account by the use of explicit solvent molecules. Geometries were determined at the B3LYP/6-31++G(d,p) level of theory, and a Grimme-type correction term was included for long-range dispersion interactions; relative energies were refined with the meta-hybrid MPW1B95 functional. Activation barriers confirm preference for ring opening at the unsubstituted ring carbon for HBr. HBr versus benzyl bromide ring opening was analyzed through comparison of the electronic structure of corresponding aziridinium intermediates. Although the electrostatic picture fails to explain the opposite regiospecific nature of the reaction, frontier molecular orbital analysis of LUMOs and nucleophilic Fukui functions show a clear preference of attack for the substituted aziridine carbon in the benzyl bromide case and for the unsubstituted aziridine carbon in the HBr case, successfully rationalizing the experimentally observed regioselectivity.

Assessment of Atomic Charge Models for Gas-Phase Computations on Polypeptides.

The concept of the atomic charge is extensively used to model the electrostatic properties of proteins. Atomic charges are not only the basis for the electrostatic energy term in biomolecular force fields but are also derived from quantum mechanical computations on protein fragments to get more insight into their electronic structure. Unfortunately there are many atomic charge schemes which lead to significantly different results, and it is not trivial to determine which scheme is most suitable for biomolecular studies. Therefore, we present an extensive methodological benchmark using a selection of atomic charge schemes [Mulliken, natural, restrained electrostatic potential, Hirshfeld-I, electronegativity equalization method (EEM), and split-charge equilibration (SQE)] applied to two sets of penta-alanine conformers. Our analysis clearly shows that Hirshfeld-I charges offer the best compromise between transferability (robustness with respect to conformational changes) and the ability to reproduce electrostatic properties of the penta-alanine. The benchmark also considers two charge equilibration models (EEM and SQE), which both clearly fail to describe the locally charged moieties in the zwitterionic form of penta-alanine. This issue is analyzed in detail because charge equilibration models are computationally much more attractive than the Hirshfeld-I scheme. Based on the latter analysis, a straightforward extension of the SQE model is proposed, SQE+Q(0), that is suitable to describe biological systems bearing many locally charged functional groups.

ZEOBUILDER: A GUI toolkit for the construction of complex molecular structures on the nanoscale with building blocks.

In this paper, a new graphical toolkit, ZEOBUILDER, is presented for the construction of the most complex zeolite structures based on building blocks. Molecular simulations starting from these model structures give novel insights in the synthesis mechanisms of micro- and mesoporous materials. ZEOBUILDER is presented as an open-source code with easy plug-in facilities. This architecture offers an ideal platform for further development of new features. Another specific aspect in the architecture of ZEOBUILDER is the data structure with multiple reference frames in which molecules and molecular building blocks are placed and which are hierarchically ordered. The main properties of ZEOBUILDER are the feasibility for constructing complex structures, extensibility, and transferability. The application field of ZEOBUILDER is not limited to zeolite science but easily extended to the construction of other complex (bio)molecular systems. ZEOBUILDER is a unique user-friendly GUI toolkit with advanced plug-ins allowing the construction of the most complex molecular structures, which can be used as input for all ab initio and molecular mechanics program packages.

The Significance of Parameters in Charge Equilibration Models

Charge equilibration models such as the electronegativity equalization method (EEM) and the split charge equilibration (SQE) are extensively used in the literature for the efficient computation of accurate atomic charges in molecules. However, there is no consensus on a generic set of optimal parameters, even when one only considers parameters calibrated against atomic charges in organic molecules. In this work, the origin of the disagreement in the parameters is investigated by comparing and analyzing six sets of parameters based on two sets of molecules and three calibration procedures. The resulting statistical analysis clearly indicates that the conventional least-squares cost function based solely on atomic charges is in general ill-conditioned and not capable of fixing all parameters in a charge-equilibration model. Methodological guidelines are formulated to improve the stability of the parameters. Although in this case a simple interpretation of individual parameters is not possible, charge equilibration models remain of great practical use for the computation of atomic charges.