A5015471372- Spectroscopy and Quantum Chemical Studies
- Protein Structure and Dynamics
- Advanced Chemical Physics Studies
- Lipid Membrane Structure and Behavior
- Metal-Organic Frameworks: Synthesis and Applications
- Zeolite Catalysis and Synthesis
- DNA and Nucleic Acid Chemistry
- Machine Learning in Materials Science
- Catalysis and Oxidation Reactions
- Advanced NMR Techniques and Applications
- Analytical Chemistry and Chromatography
- Covalent Organic Framework Applications
- Quantum, superfluid, helium dynamics
- Glycosylation and Glycoproteins Research
- Enzyme Structure and Function
- Nanopore and Nanochannel Transport Studies
- Computational Drug Discovery Methods
- Mesoporous Materials and Catalysis
- Crystallography and molecular interactions
- Enhanced Oil Recovery Techniques
- Magnetism in coordination complexes
- Molecular spectroscopy and chirality
- Thermodynamic properties of mixtures
- Neuroscience and Neuropharmacology Research
- NMR spectroscopy and applications
Ghent University
2015-2024
Instituto de Tecnología Química
2015
Universitat Politècnica de València
2015
National Institutes of Health
2008-2014
National Heart Lung and Blood Institute
2008-2014
University of California, Berkeley
2013
University of South Florida
2011
KU Leuven
2008
Q Chem (United States)
2008
Laboratoire de Physique et Modélisation des Milieux Condensés
2006
A summary of the technical advances that are incorporated in fourth major release Q-Chem quantum chemistry program is provided, covering approximately last seven years. These include developments density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster perturbation theories, for electronically excited open-shell species, tools treating extended environments, algorithms walking on potential surfaces, analysis tools, energy...
TAMkin is a program for the calculation and analysis of normal modes, thermochemical properties chemical reaction rates. At present, output from frequently applied software programs ADF, CHARMM, CPMD, CP2K, Gaussian, Q-Chem, VASP can be analyzed. The normal-mode performed using broad variety advanced models, including standard full Hessian, Mobile Block Partial Hessian Vibrational approach, Subsystem Analysis with or without mass matrix correction, Elastic Network Model, other combinations....
Methylations of ethene, propene, and butene by methanol over the acidic microporous H-ZSM-5 catalyst are studied means state art computational techniques, to derive Arrhenius plots rate constants from first principles that can directly be compared with experimental data. For these key elementary reactions in hydrocarbons (MTH) process, direct kinetic data became available only recently [J. Catal.2005, 224, 115−123; J. 234, 385−400]. At 350 °C, apparent activation energies 103, 69, 45 kJ/mol...
Abstract The functional significance of ordered nanodomains (or rafts) in cholesterol rich eukaryotic cell membranes has only begun to be explored. This study exploits the correspondence cellular rafts and liquid ( L o ) phases three-component lipid bilayers examine permeability. Molecular dynamics simulations phase dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), show that oxygen water transit a leaflet through DOPC boundaries hexagonally packed DPPC microdomains,...
In this paper, three barostat coupling schemes for pressure control, which are commonly used in molecular dynamics simulations, critically compared to characterize the rigid MOF-5 and flexible MIL-53(Al) metal–organic frameworks. We investigate performance of barostats, Berendsen, Martyna–Tuckerman–Tobias–Klein (MTTK), Langevin methods, reproducing cell parameters versus volume behavior isothermal–isobaric simulations. A thermodynamic integration method is construct free energy profiles as a...
In this paper the authors develop a method to accurately calculate localized vibrational modes for partially optimized molecular structures or containing link atoms. The avoids artificially introduced imaginary frequencies and keeps track of invariance under global translations rotations. Only subblock Hessian matrix has be constructed diagonalized, leading serious reduction computational time frequency analysis. mobile block approach (MBH) proposed in work can regarded as an extension...
An efficient procedure for normal-mode analysis of extended systems, such as zeolites, is developed and illustrated the physisorption chemisorption n-octane isobutene in H-ZSM-22 H-FAU using periodic DFT calculations employing Vienna Ab Initio Simulation Package. Physisorption entropies resulting from partial Hessian vibrational (PHVA) differ at most 10 J mol(-1) K(-1) those full analysis, even PHVA schemes which only a very limited number atoms are considered free. To acquire...
The diffusion of olefins through 8-ring solid acid microporous zeolites is investigated using molecular dynamics simulations techniques and a newly developed flexible force field. Within the context methanol-to-olefin (MTO) process observed product distribution, knowledge paths essential to obtain level control over conditions. Eight-ring zeotype materials are favorably used for MTO as they give selective distribution toward low-carbon olefins. To investigate how composition, acidity,...
The UiO-66 metal organic framework is one of the most thermally and chemically stable hybrid materials reported to date. However, it also accepted that material contains structurally embedded defects, which may be engineered enhance properties towards specific applications such as catalysis, sensing, etc. synthesis conditions determine a large extent level perfection additionally catalytic activity enhanced by post-synthesis activation at high temperature under vacuum, in defect coordinating...
A Bayesian-based methodology is developed to estimate diffusion tensors from molecular dynamics simulations of permeants in anisotropic media, and applied oxygen lipid bilayers. By a separation variables the Smoluchowski equation, multidimensional reduced coupled one-dimensional problems that are treated by discretization. The resulting diffusivity profiles characterize membrane transport as function position across membrane, discriminating between normal parallel membrane. first validated...
Permeation of many small molecules through lipid bilayers can be directly observed in molecular dynamics simulations on the nano- and microsecond timescale. While unbiased provide an unobstructed view permeation process, their feasibility for computing permeability coefficients depends various factors that differ each permeant. The present work studies three which are feasible within less than a microsecond, one hydrophobic (oxygen), hydrophilic (water), amphiphilic (ethanol). Permeabilities...
When adsorbing guest molecules, the porous metal–organic framework MIL-53(Cr) may vary its cell parameters drastically while retaining crystallinity. A first approach to thermodynamic analysis of this "framework breathing" consists comparing osmotic potential in two distinct shapes only (large-pore and narrow-pore). In paper, we propose a generic parametrized free energy model including three contributions: host energy, guest–guest interactions, host–guest interaction. Free landscapes now be...
The methanol-to-olefin process is a showcase example of complex zeolite-catalyzed chemistry. At real operating conditions, many factors affect the reactivity, such as framework flexibility, adsorption various guest molecules, and competitive reaction pathways. In this study, strength first principle molecular dynamics techniques to capture complexity shown by means two case studies. Firstly, behavior methanol water in H-SAPO-34 at 350 °C investigated. Hereby an important degree flexibility...
Silicalite-1 zeolite exhibits a characteristic pentasil framework vibration around 540−550 cm−1. In the initial stages of synthesis, however, this band is observed at much higher wavenumbers: literature shows to depend on particle size and shift over 100 cm−1 with increasing condensation. work, frequency was derived from theoretical molecular dynamics simulations obtain correct IR assignments for important nanoparticles. The spectroscopic fingerprint oligomeric five-ring containing...
A new vibrational subsystem analysis (VSA) method is presented for coupling global motion to a local while including the inertial effects of environment. The premise VSA partitioning system into smaller region interest and usually larger part referred as This allows investigation local-global coupling, more accurate estimation free energy contribution parts large system, elimination "tip effect" in elastic network model calculations. Additionally, can be used probe specific degrees freedom...
Modeling the flexibility of metal–organic frameworks (MOFs) requires computation mechanical properties from first principles, e.g., for screening materials in a database, gaining insight into structural transformations, and force field development. However, this paper shows that computations with periodic density functional theory are challenged by these materials: guidelines experience standard solid-state calculations cannot be simply transferred to flexible porous frameworks. Our test...
Partial optimization is a useful technique to reduce the computational load in simulations of extended systems. In such nonequilibrium structures, accurate calculation localized vibrational modes can be troublesome, since standard normal mode analysis becomes inappropriate. previous paper [A. Ghysels et al., J. Chem. Phys. 126, 224102 (2007)], mobile block Hessian (MBH) approach was presented deal with partially optimized MBH model, nonoptimized regions system are represented by one or...
Abstract Standard normal mode analysis becomes problematic for complex molecular systems, as a result of both the high computational cost and excessive amount information when full Hessian matrix is used. Several partial methods have been proposed in literature, yielding approximate modes. These aim at reducing load and/or calculating only relevant modes interest specific application. Each method has its own (dis)advantages application field but guidelines most suitable choice are lacking....
Abstract We present and discuss the advancements made in PyRETIS 3, third instalment of our Python library for an efficient user‐friendly rare event simulation, focused to execute molecular simulations with replica exchange transition interface sampling (RETIS) its variations. Apart from a general rewiring internal code towards more modular structure, several recently developed strategies have been implemented. These include Monte Carlo moves increase path decorrelation convergence rate, new...
The calculation of the analytical second derivative matrix (Hessian) is bottleneck for vibrational analysis in QM/MM systems when an electrostatic embedding scheme employed. Even with a small number QM atoms system, presence MM increases computational cost dramatically: long-range Coulomb interactions require that additional coupled perturbed self-consistent field (CPSCF) equations need to be solved each atom displacement. This paper presents extension Mobile Block Hessian (MBH) formalism...
The balance of normal and radial (lateral) diffusion oxygen in phospholipid membranes is critical for biological function. Based on the Smoluchowski equation inhomogeneous solubility-diffusion model, Bayesian analysis (BA) can be applied to molecular dynamics trajectories extract free energy profiles. This paper derives a theoretical formalism convert these profiles into characteristic times lengths associated with entering, escaping, or completely crossing membrane. computes mean first...
Drug discovery is usually focused on a single protein target; in this process, existing compounds that bind to related proteins are often ignored. We describe ProBiS plugin, extension of our earlier ProBiS-ligands approach, which for given structure allows prediction its binding sites and, each site, the ligands from similar Protein Data Bank. developed new database precalculated site comparisons about 290000 allow fast proteins. The plugin enables advanced viewing predicted sites, ligands'...
In an earlier paper, the authors have developed a new method, mobile block Hessian (MBH), to accurately calculate vibrational modes for partially optimized molecular structures [J. Chem. Phys. 2007, 126 (22), 224102]. The proposed procedure remedies artifact of imaginary frequencies, occurring in standard frequency calculations, when parts system are at different levels theory. Frequencies essential ingredient predicting reaction rate coefficients due their input partition functions....