V. Van Speybroeck

Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules

A. Ghysels, V. Van Speybroeck, E. Pauwels, D. Van Neck, B.R. Brooks, M. Waroquier
Journal of Chemical Theory and Computation (JCTC)
5 (5), 1203-1215
2009
A1

Abstract 

In an earlier work, the authors developed a new method, the mobile block Hessian (MBH) approach, to accurately calculate vibrational modes for partially optimized molecular structures [ J. Chem. Phys. 2007, 126 (22), 224102.]. It is based on the introduction of blocks, consisting of groups of atoms, that can move as rigid bodies. The internal geometry of the blocks need not correspond to an overall optimization state of the total molecular structure. The standard MBH approach considers free blocks with six degrees of freedom. In the extended MBH approach introduced herein, the blocks can be connected by one or two adjoining atoms, which further reduces the number of degrees of freedom. The new approach paves the way for the normal-mode analysis of biomolecules such as proteins. It rests on the hypothesis that low-frequency modes of proteins can be described as pure rigid-body motions of blocks of consecutive amino acid residues. The method is validated for a series of small molecules and further applied to alanine dipeptide as a prototype to describe vibrational interactions between two peptide units; to crambin, a small protein with 46 amino acid residues; and to ICE/caspase-1, which contains 518 amino acid residues.

Nucleophile-dependent regioselective ring opening of 2-substituted N,N-dibenzylaziridinium ions: bromideversushydride

S. Young Yun, S. Catak, W. Koo Lee, M. D'Hooghe, N. De Kimpe, V. Van Speybroeck, M. Waroquier, Y. Kim, H-J. Ha
Chemical Communications
(18), 2508-2510
2009
A1

Abstract 

The ring opening of 2-substituted N,N-dibenzylaziridinium ions by bromide exclusively occurs at the substituted aziridine carbon atom in a stereospecific way, whereas the opposite regioselectivity was observed for hydride-induced ring opening at the unsubstituted position; furthermore, this unprecedented hydride-promoted reactivity was validated by means of Density Functional Theory (DFT) calculations.

Bond Dissociation Enthalpies of Large Aromatic Carbon-Centered Radicals

K. Hemelsoet, V. Van Speybroeck, M. Waroquier
Journal of Physical Chemistry A
112 (51), 13566-13573
2008
A1

Abstract 

Carbon−hydrogen bond dissociation enthalpy (BDE) values are computed for the class of benzylic radicals. An extended and representative set of large methylated polyaromatics has been submitted to an accurate computational study using various levels of theory. The hybrid B3P86 as well as two contemporary functionals (BMK and M05-2X) are applied. For a selection of species, the suitability of the DFT methods is validated through comparison with high-level G3(MP2)-RAD and SCS-ROMP2 results. The influence of the polyaromatic environment on the BDE results is thoroughly discussed. The results are compared with other hydrocarbon radical types in order to obtain a generalized radical stability scale. In order to complete this investigation, also carbon−carbon BDE values have been calculated, giving information about the influence of the local environment on removing the methyl group from the polyaromatic.

MD-TRACKS: A Productive Solution for the Advanced Analysis of Molecular Dynamics and Monte Carlo simulations

T. Verstraelen, M. Van Houteghem, V. Van Speybroeck, M. Waroquier
Journal of Chemical Information and Modeling (JCIM)
48 (12), 2414–2424
2008
A1

Abstract 

In this paper, we present MD-TRACKS, an advanced statistical analysis toolkit for Molecular Dynamics and Monte Carlo simulations. The program is compatible with different molecular simulation codes, and the analysis results can be loaded into spreadsheet software and plotting tools. The analysis is performed with commands that operate on a binary trajectory database. These commands process not only plain trajectory data but also the output of other MD-TRACKS commands, which enables complex analysis work flows that are easily programmed in shell scripts. The applicability, capabilities, and ease of use of MD-TRACKS are illustrated by means of examples, that is, the construction of vibrational spectra and radial distribution functions from a molecular dynamics run is discussed in the case of tetrahydrofuran. These properties are compared with the experimental data available in the literature. MD-TRACKS is open-source software distributed at http://molmod.ugent.be/code/.

An Intrinsic Radical Stability Scale from the Perspective of Bond Dissociation Enthalpies: A Companion to Radical Electrophilicities

F. De Vleeschouwer, V. Van Speybroeck, M. Waroquier, P. Geerlings, F. De Proft
Journal of Organic Chemistry
73 (22) 9109-9120
2008
A1

Abstract 

Bond dissociation enthalpies (BDEs) of a large series of molecules of the type A−B, where a series of radicals A ranging from strongly electrophilic to strongly nucleophilic are coupled with a series of 8 radicals (CH2OH, CH3, NF2, H, OCH3, OH, SH, and F) also ranging from electrophilic to nucleophilic, are computed and analyzed using chemical concepts emerging from density functional theory, more specifically the electrophilicities of the individual radical fragments A and B. It is shown that, when introducing the concept of relative radical electrophilicity, an (approximately) intrinsic radical stability scale can be developed, which is in good agreement with previously proposed stability scales. For 47 radicals, the intrinsic stability was estimated from computed BDEs of their combinations with the strongly nucleophilic hydroxymethyl radical, the neutral hydrogen atom, and the strongly electrophilic fluorine atom. Finally, the introduction of an extra term containing enhanced Pauling electronegativities in the model improves the agreement between the computed BDEs and the ones estimated from the model, resulting in a mean absolute deviation of 16.4 kJ mol−1. This final model was also tested against 82 experimental values. In this case, a mean absolute deviation of 15.3 kJ mol−1 was found. The obtained sequences for the radical stabilities are rationalized using computed spin densities for the radical systems.

A DFT-Based Investigation of Hydrogen Abstraction Reactions from Methylated Polycyclic Aromatic Hydrocarbons

K. Hemelsoet, V. Van Speybroeck, M. Waroquier
ChemPhysChem
9 (16), 2349-2358
2008
A1

Abstract 

The growth of polycyclic aromatic hydrocarbons (PAHs) is in many areas of combustion and pyrolysis of hydrocarbons an inconvenient side effect that warrants an extensive investigation of the underlying reaction mechanism, which is known to be a cascade of radical reactions. Herein, the focus lies on one of the key reaction classes within the coke formation process: hydrogen abstraction reactions induced by a methyl radical from methylated benzenoid species. It has been shown previously that hydrogen abstractions determine the global PAH formation rate. In particular, the influence of the polyaromatic environment on the thermodynamic and kinetic properties is the subject of a thorough exploration. Reaction enthalpies at 298 K, reaction barriers at 0 K, rate constants, and kinetic parameters (within the temperature interval 700–1100 K) are calculated by using B3LYP/6-31+G(d,p) geometries and BMK/6-311+G(3df,2p) single-point energies. This level of theory has been validated with available experimental data for the abstraction at toluene. The enhanced stability of the product benzylic radicals and its influence on the reaction enthalpies is highlighted. Corrections for tunneling effects and hindered (or free) rotations of the methyl group are taken into account. The largest spreading in thermochemical and kinetic data is observed in the series of linear acenes, and a normal reactivity–enthalpy relationship is obtained. The abstraction of a methyl hydrogen atom at one of the center rings of large methylated acenes is largely preferred. Geometrical and electronic aspects lie at the basis of this striking feature. Comparison with hydrogen abstractions leading to arylic radicals is also made.

Synthesis of Tricyclic Phosphonopyrrolidines via IMDAF: Experimental and Theoretical Investigation of the Observed Stereoselectivity

D.D. Claeys, K. Moonen, B.I. Roman, V.N. Nemykin, V.V. Zhdankin, M. Waroquier, V. Van Speybroeck, C.V. Stevens
Journal of Organic Chemistry
73 (20), 7921-7927
2008
A1

Abstract 

During the synthesis of tricyclic phosphonopyrrolidines via intramolecular Diels−Alder reactions of 1-acylamino(furan-2-yl)methyl phosphonates, two isomers are formed in most cases. The presence of a short three-atom tether together with spectroscopic data, including difference NOE, revealed that the cycloaddition occurred exo, but the phosphonate substituent on the tether had an exo or endo orientation. This was confirmed via X-ray analysis. A thermodynamic preference for the product with the phosphonate function in the endo position was observed experimentally and was confirmed theoretically. Density functional theory methods and several high-level post Hartree−Fock procedures were used to rationalize the observed isomer ratio of the IMDAF-reactions. This was done for two different types of reagents: with the activating carbonyl group in the tether or as a substituent on the tether. For the first type of molecules there is a large steric hindrance of the bulky tether substituents that disfavors the exo-isomer. In the latter case, there was a very small energy difference between the transition states causing a mixture of epimers being formed.

Experimental and Computational Study of the Conrotatory Ring Opening of Various 3-Chloro-2-azetines

S. Mangelinckx, V. Van Speybroeck, P. Vansteenkiste, M. Waroquier, N. De Kimpe
Journal of Organic Chemistry
73 (14) 5481-5488
2008
A1

Abstract 

A combined experimental and theoretical study is presented on 2-azetines, a class of azaheterocyclic compounds, which are difficult to access but have shown a unique reactivity as strained cyclic enamines. New highly substituted 2-azetines bearing aryl substituents at the 2- and 4-position were synthesized from 3,3-dichloroazetidines. Whereas 2-aryl-3,3-dichloroazetidines gave stable 2-aryl-3-chloro-2-azetines upon treatment with sodium hydride in DMSO, 2,4-diaryl-3,3-dichloroazetidines showed a remarkably different reactivity in that they afforded benzimidoyl-substituted alkynes under similar mild treatment with base. The formation of the alkynes involves electrocyclic ring opening of intermediate 2,4-diaryl-3-chloro-2-azetines and elimination of hydrogen chloride. Ab initio theoretical calculations confirmed the experimental findings and demonstrated that the 4-aryl substituent is responsible for this remarkably enhanced reactivity of 2-azetines toward electrocyclic conrotatory ring opening by a significant decrease in reaction barrier of about 30 kJ/mol. This activation effect by an aryl group in the allylic position toward electrocyclic ring opening of unsaturated four-membered rings is of general importance since a similar increased reactivity of 4-aryloxetes, 4-arylthiete-1,1-dioxides, and 3-arylcyclobutenes has been reported in literature as well.

ZEOBUILDER: A GUI Toolkit for the Construction of Complex Molecular Structures on the Nanoscale with Building Blocks

T. Verstraelen, V. Van Speybroeck, M. Waroquier
Journal of Chemical Information and Modeling (JCIM)
48 ( 7), 1530-1541
2008
A1

Abstract 

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.

Temperature study of a glycine radical in the solid state adopting a DFT periodic approach: vibrational analysis and comparison with EPR experiments

E. Pauwels, T. Verstraelen, H. De Cooman, V. Van Speybroeck, M. Waroquier
Journal of Physical Chemistry B
112 (25), 7618-7630
2008
A1

Abstract 

The major radiation-induced radical in crystalline glycine is examined using DFT calculations, in which both molecular environment and temperature are accounted for. This is achieved by molecular dynamics simulations of the radical embedded in a supercell under periodic boundary conditions. At 100 and 300 K, a vibrational analysis is performed based on Fourier transformation of the atomic velocity autocorrelation functions. By the use of a novel band-pass filtering approach, several vibrational modes are identified and associated with experimental infrared and Raman assignments. Decomposition of the calculated spectra in terms of radical motion reveals that several vibrational modes are unique to the radical, the most prominent one at 702 cm(-1) corresponding to out-of-plane motion of the paramagnetic center, inversely coupled with similar motion of the carboxyl carbon. A hybrid periodic/cluster scheme is used to evaluate the EPR properties of the glycine radical along the MD trajectories resulting in temperature dependent magnetic properties. These are compared with available experimental data conducted at 77 K and room temperature. Ground state or low temperature calculations yield very good agreement with 77 K experimental EPR properties. From the 300 K simulations, an important improvement is achieved on the isotropic hyperfine coupling of the (13)C tensor, which becomes closer to the value measured at room temperature. It is established that this is the result of a nonlinear relation between the planarity of the radical center and the isotropic couplings of the nuclei bound to it. Finally, a critical reevaluation of the experimental (14)N hyperfine tensor data strongly suggests that an erroneous tensor was reported in literature. It is convincingly shown that from the same experimental data set a different tensor can be derived, which is in substantially better agreement with all calculations.

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