Biomedical subjects

M Waroquier

Publications and source records attributed to M Waroquier.

At least 19 recordsLinked to original sources

PubMed2007

Spin-polarized conceptual density functional theory study of the regioselectivity in ring closures of radicals.

The regioselectivity of ring-forming radical reactions is investigated within the framework of the so-called spin-polarized conceptual density functional theory. Two different types of cyclizations were studied. First, a series of model reactions of alkyl- and acyl-substituted radicals were investigated. Next, attention was focused on the radical cascade cyclizations of N-alkenyl-2-aziridinylmethyl radicals (a three-step mechanism). In both of these reactions, the approaching radical (carbon or nitrogen centered) adds to a carbon-carbon double bond within the same molecule to form a radical ring compound. In this process, the number of electrons is changing from a local point of view (a charge transfer occurs from one part of the molecule to another one) at constant global spin number Ns (both the reactant and the product ring compound are in the doublet state). It is shown that the experimentally observed regioselectivities for these ring-closure steps can be predicted using the spin-polarized Fukui functions for radical attack, f0NN(r).

Cyclization↗

PubMed2006

X- (X = O, S) ions in alkali halide lattices through density functional calculations. 1. Substitutional defect models.

Monoatomic X- (X = O, S) chalcogen centers in MZ (M = Na, K, Rb and Z = Cl, Br, I) alkali halide lattices are investigated within the framework of density functional theory with the principal aim to establish defect models. In electron paramagnetic resonance (EPR) experiments, X- defects with tetragonal, orthorhombic, and monoclinic g-tensor symmetry have been observed. In this paper, models in which X- replaces a single halide ion, with a next nearest neighbor and a nearest neighbor halide vacancy, are validated for the X- centers with tetragonal and orthorhombic symmetry, respectively. As such defect models are extended, the ability to reproduce experimental data is a stringent test for various computational approaches. Cluster in vacuo and embedded cluster schemes are used to calculate energy and EPR parameters for the two vacancy configurations. The final assignment of a defect structure is based on the qualitative and quantitative reproduction of experimental g and (super)hyperfine tensors.

Journal Article↗

PubMed2006

X- (X = O, S, Se) Ions in alkali halide lattices through density functional calculations. 2. Interstitial defect models.

Density functional theory techniques are used to investigate the defect structure of X- (X = O, S, Se) ions in MZ (M = Na, K, Rb and Z = Cl, Br) alkali halides which exhibit monoclinic-I g-tensor symmetry, using cluster in vacuo, embedded cluster, and periodic embedding schemes. Although a perturbed interstitial defect model was suggested from electron paramagnetic resonance experiments (EPR), the nature of the perturbation is still unknown. An appropriate defect model is developed theoretically by comparing structural and energetical properties of various defect configurations. Further validation is achieved by cross referencing experimental and computed EPR data. On the basis of the computational results, the following defect model is proposed: the X- ion is located interstitially with a charge compensating halide vacancy in its first coordination shell.

Journal Article↗

PubMed2006

Density functional investigation of high-spin XY (X = Cr, Mo, W and Y = C, N, O) molecules.

The performance of a density functional theory approach in calculating the equilibrium bond length, dipole moment, and harmonic vibrational frequency in a series of group 6 (Cr, Mo, W) transition metal-containing diatomic molecules is evaluated. Using flexible basis sets comprised of Slater type functions, a wide range of exchange-correlation functionals is investigated. Comparing with known experimental values and published results from high-level theoretical calculations, the most suitable functional form is selected. The importance of relativistic effects is checked, and predictions are made for several unknown dipole moments. The best agreement with experimental parameters is obtained when using a general gradient approximation, while special and hybrid functional forms give less accurate results.

Journal Article↗

PubMed2006

An extended hindered-rotor model with incorporation of Coriolis and vibrational-rotational coupling for calculating partition functions and derived quantities.

Large-amplitude motions, particularly internal rotations, are known to affect substantially thermodynamic functions and rate constants of reactions in which flexible molecules are involved. Up to now all methods for computing the partition functions of these motions rely on the Pitzer approximation of more than 50 years ago, in which the large-amplitude motion is treated in complete independence of the other (vibrational) degrees of freedom. In this paper an extended hindered-rotor model (EHR) is developed in which the vibrational modes, treated harmonically, are correctly separated from the large-amplitude motion and in which relaxation effects (the changes in the kinetic-energy matrix and potential curvature) are taken into account as one moves along the large-amplitude path. The model also relies on a specific coordinate system in which the Coriolis terms vanish at all times in the Hamiltonian. In this way an increased level of consistency between the various internal modes is achieved, as compared with the more usual hindered-rotor (HR) description. The method is illustrated by calculating the entropies and heat capacities on 1,3-butadiene and 1-butene (with, respectively, one and two internal rotors) and the rate constant for the addition reaction of a vinyl radical to ethene. We also discuss various variants of the one-dimensional hindered-rotor scheme existing in the literature and its relation with the EHR model. It is argued why in most cases the HR approach is already quite successful.

Journal Article↗

PubMed2005

Rules for generating conformers and their relative energies in n-alkanes with a heteroelement O or S: ethers and alcohols, or sulfides and thiols.

With the aid of density functional theory calculations, all conformers of several single-chain alcohols, thiols, ethers, and sulfides are investigated. Starting from earlier computational works on n-alkanes, we construct an extended set of general rules for predicting the number and occurrence of conformers in these oxygen- or sulfur-containing compounds. In alcohols and thiols, it is found that only the conformers generated by internal rotations in the HXCH(2)CH(2)CH(2) (X = O or S) top are distinctive from those in n-alkanes. In ethers and sulfides, the primary influence of the heteroelement also extends up to three internal rotations, but many more conformers are possible. However, a number of double gauche sequences are forbidden, and therefore, several conformers can be eliminated. These exclusions in particular make up a set of rules for eventually deducing all possible conformers. Furthermore, on the basis of only an exact calculation of these gg conformations in addition to single gauche conformers, it is possible to make an accurate estimate of the relative energy. This two-dimensional approximation scheme constitutes an effective tool for adequately describing the relative energies of all possible conformers at a minimal computational cost.

Alcohols↗

PubMed2005

N-Alkenyl-2-aziridinylmethyl radicals and N-alkenylaminyl radicals in cascade cyclizations to pyrrolizidines and indolizidines.

[reaction: see text] The radical cascade cyclizations of N-alkenyl-2-aziridinylmethyl radicals to pyrrolizidines and indolizidines were examined using density functional theory (DFT) calculations. A large preference for cyclization to pyrrolizidines was found. These predictions corroborated very well with experimental results, leading to an efficient synthesis of pyrrolizidines. No radical cascade cyclization to indolizidines could be performed in practice as only ring opening of N-alkenyl-2-aziridinylmethyl radicals to N-allyl-N-alkenylamines occurred.

Journal Article↗

PubMed2005

Ab initio study of free-radical polymerizations: cost-effective methods to determine the reaction rates.

The addition of carbon-centered radicals to ethene, which are important in free-radical polymerization processes, are studied from a theoretical point of view. Experimental data for the rate constants are only available for the addition of methyl, ethyl, propyl and butyl radicals. The latter reactions are taken as model systems to derive a cost-effective method for the addition of alkyl radicals to ethene. The proposed model must be accurate and computationally feasible for additions in which larger radicals are involved. Accuracy is validated by direct comparison of theoretical and experimental rate constants in the temperature range from 300 to 600 K. A variety of electronic-structure methods were tested ranging from Hartree-Fock and post-Hartree-Fock methods to pure and hybrid density functional theory methods. Molecular partition functions were refined by treating large amplitude vibrations beyond the harmonic oscillator approximation.

Journal Article↗

PubMed2004

Density functional theory as a tool for the structure determination of radiation-induced bioradicals.

The use of density functional methods for the elucidation of the structure of radiation-induced bio-radicals by comparison of computed and experimental EPR properties is discussed. Three case studies, radiation induced radicals of the amino acid alanine, steroid hormones and beta-D-fructose, with increasing degree of uncertainty about the proposed radical structures, are investigated. Next to the analysis of the isotropic and anisotropic components of the hyperfine tensor, also the direction cosines of the principal axes of this tensor were investigated in greater detail in the case of the beta-D-fructose radicals. Since all radicals considered in this contribution are formed in a solid matrix, also the question as to how to incorporate the effect of the molecular environment is addressed. It is concluded that the methodology outlined represents a powerful tool to aid experimentalists in the assignment of the contributions of various radicals contributing to the observed EPR spectra.

Alanine↗

PubMed2003

Saturation of nuclear matter and short-range correlations.

A fully self-consistent treatment of short-range correlations in nuclear matter is presented. Different implementations of the determination of the nucleon spectral functions for different interactions are shown to be consistent with each other. The resulting saturation densities are closer to the empirical result when compared with (continuous choice) Brueckner-Hartree-Fock values. Arguments for the dominance of short-range correlations in determining the nuclear matter saturation density are presented. A further survey of the role of long-range correlations suggests that the inclusion of pionic contributions to ring diagrams in nuclear matter leads to higher saturation densities than empirically observed. A possible resolution of the nuclear matter saturation problem is suggested.

Journal Article↗

PubMed2001

Ab initio and experimental study on thermally degradable polycarbonates: the effect of substituents on the reaction rates.

Thermal elimination reactions on polycarbonates are investigated from both theoretical and experimental points of view, to obtain insight into the microscopic aspects that influence the reaction mechanism and rates. In particular, attention is focused on the influence of the type of substituents in the polymer chain on the reaction rates. Ab initio density functional theory calculations are performed on a series of model compound systems for the polycarbonates under study, in particular carbonates differing by the groups attached at the alpha and beta carbon atoms. Reactants, products, and transition states are optimized at the B3LYP/6-311g level of theory. The structures of the activated complex give insight into the mechanistic details of this type of E(i) elimination reactions. The C(alpha)-O bond dissociates before the C(beta)-H bond, developing some carbocation character in the transition state on the C(alpha) atom. The kinematics of the thermal decomposition reactions have been studied by means of transition state theory by construction of the microscopic partition functions. It turns out that the rates of the E(i) elimination reactions are increased by the presence of those substituents on the C(alpha) and C(beta) carbon atoms which are stabilizing the carbocation character in the transition state. In a second part, degradation temperatures have been experimentally measured for some polycarbonates through thermogravimetric analysis. It is investigated whether the relative rates of the model compound carbonate systems are representative of the behavior of the thermal degradation temperatures in polycarbonates. The study as presented here proves that ab initio calculations on small model systems, which are representative for the active area of the degradation process in polycarbonates, can provide insight into the principal ingredients that govern the reaction rates.

Journal Article↗

PubMed1996