Klassische und ab initio Molekulardynamik-Untersuchungen zu Germaniumdioxidschmelzen

Germaniumdioxid (GeO2) ist ein Glasbildner, der wie das homologe SiO2 ein ungeordnetes tetraedrisches Netzwerk ausbildet. In dieser Arbeit werden mit Hilfe von Molekulardynamik-Computersimulationen die Struktur und Dynamik von GeO2 in Abhängigkeit von der Temperatur untersucht. Dazu werden sowohl Simulationen mit einem klassischen Paarpotentialmodell von Oeffner und Elliott als auch ab initio-Simulationen gemäß der Car-Parrinello-Molekulardynamik (CPMD), bei der elektronische Freiheitsgrade mittels Dichtefunktionaltheorie beschrieben werden, durchgeführt. In der klassischen Simulation werden dazu ein Temperaturen zwischen 6100 K und 2530 K betrachtet. Darüberhinaus ermöglichen Abkühlläufe auf T=300 K das Studium der Struktur des Glases. Zum Vergleich werden CPMD-Simulationen für kleinere Systeme mit 60 bzw. 120 Teilchen bei den Temperaturen 3760 K und 3000 K durchgeführt. In den klassischen Simulationen kann die im Experiment bis 1700 K nachgewiesene, im Vergleich zu SiO2 starke, Temperaturabhängigkeit der Dichte auch bei höheren Temperaturen beobachtet werden. Gute Übereinstimmungen der Simulationen mit experimentellen Daten zeigen sich bei der Untersuchung verschiedener struktureller Größen, wie z.B. Paarkorrelationsfunktionen, Winkelverteilungen, Koordinationszahlen und Strukturfaktoren. Es können leichte strukturelle Abweichungen der CPMD-Simulationen von den klassischen Simulationen aufgezeigt werden: 1. Die Paarabstände in CPMD sind durchweg etwas kleiner. 2. Es zeigt sich, daß die Bindungen in den ab initio-Simulationen weicher sind, was sich auch in einer etwas stärkeren Temperaturabhängigkeit der strukturellen Größen im Vergleich zu den klassischen Simulationen niederschlägt. 3. Für CPMD kann ein vermehrtes Auftreten von Dreierringstrukturen gezeigt werden. 4. In der CPMD werden temperaturabhängige Defektstrukturen in Form von Sauerstoffpaaren beobachtet, die vor allem bei 3760 K, kaum jedoch bei 3000 K auftreten. Alle strukturellen Unterschiede zwischen klassischer und CPMD-Simulation sind eindeutig nicht auf Finite-Size-Effekte aufgrund der kleinen Systemgrößen in den CPMD-Simulationen zurückzuführen, d.h. sie sind tatsächlich methodisch bedingt. Bei der Dynamik von GeO2 wird in den klassischen Simulationen ebenfalls eine gute Übereinstimmung mit experimentellen Daten beobachtet, was ein Vergleich der Diffusionskonstanten mit Viskositätsmessungen bei hohen Temperaturen belegt. Die Diffusionskonstanten zeigen teilweise ein verschiedenes Verhalten zum homologen SiO2. Sie folgen in GeO2 bei Temperaturen unter 3000 K einem Arrheniusgesetz mit einer deutlich niedrigeren Aktivierungsenergie. Darüberhinaus werden die Möglichkeiten der Parametrisierung eines neuen klassischen Paarpotentials mittels der Kräfte entlang der CPMD-Trajektorien untersucht. Es zeigt sich, daß derartige Parametrisierungen sehr stark von den gewählten Startparametern abhängen. Ferner führen sämtliche an die Schmelze parametrisierten Potentiale zu zu hohen Dichten im Vergleich zum Experiment. Zum einen liegt dies sehr wahrscheinlich daran,daß für das System GeO2 Kraftdaten allein nicht ausreichen, um grundlegende strukturelle Größen, wie z.B. Paarkorrelationen und Winkelverteilungen, der CPMD-Simulationen gut reproduzieren zu können. Zum anderen ist wohl die Beschreibung mittels Paarpotentialen nicht ausreichend und es ist erforderlich, Merkörperwechselwirkungen in Betracht zu ziehen.

Molecular dynamics simulations of silicate and borate glasses and melts : structure, diffusion dynamics and vibrational properties

Molecular dynamics simulations of silicate and borate glasses and melts: Structure, diffusion dynamics and vibrational properties. In this work computer simulations of the model glass formers SiO2 and B2O3 are presented, using the techniques of classical molecular dynamics (MD) simulations and quantum mechanical calculations, based on density functional theory (DFT). The latter limits the system size to about 100−200 atoms. SiO2 and B2O3 are the two most important network formers for industrial applications of oxide glasses. Glass samples are generated by means of a quench from the melt with classical MD simulations and a subsequent structural relaxation with DFT forces. In addition, full ab initio quenches are carried out with a significantly faster cooling rate. In principle, the structural properties are in good agreement with experimental results from neutron and X-ray scattering, in all cases. A special focus is on the study of vibrational properties, as they give access to low-temperature thermodynamic properties. The vibrational spectra are calculated by the so-called ”frozen phonon” method. In all cases, the DFT curves show an acceptable agreement with experimental results of inelastic neutron scattering. In case of the model glass former B2O3, a new classical interaction potential is parametrized, based on the liquid trajectory of an ab initio MD simulation at 2300 K. In this course, a structural fitting routine is used. The inclusion of 3-body angular interactions leads to a significantly improved agreement of the liquid properties of the classical MD and ab initio MD simulations. However, the generated glass structures, in all cases, show a significantly lower fraction of 3-membered planar boroxol rings as predicted by experimental results (f=60%-80%). The largest boroxol ring fraction of f=15±5% is observed in the full ab initio quenches from 2300 K. In case of SiO2, the glass structures after the quantum mechanical relaxation are the basis for calculations of the linear thermal expansion coefficient αL(T), employing the quasi-harmonic approximation. The striking observation is a change change of sign of αL(T) going along with a temperature range of negative αL(T) at low temperatures, which is in good agreement with experimental results.

Structure and thermodynamics of H3O+(H2O)8 clusters: A combined molecular dynamics and quantum mechanics approach

We have studied the structure and stability of (H3O+)(H2O)8 clusters using a combination of molecular dynamics sampling and high-level ab initio calculations. 20 distinct oxygen frameworks are found within 2 kcal/mol of the electronic or standard Gibbs free energy minimum. The impact of quantum zero-point vibrational corrections on the relative stability of these isomers is quite significant. The box-like isomers are favored in terms of electronic energy, but with the inclusion of zero-point vibrational corrections and entropic effects tree-like isomers are favored at higher temperatures. Under conditions from 0 to 298.15 K, the global minimum is predicted to be a tree-like structure with one dangling singly coordinated water molecule. Above 298.15 K, higher entropy tree-like isomers with two or more singly coordinated water molecules are favored. These assignments are generally consistent with experimental IR spectra of (H3O+)(H2O)8 obtained at 150 K.

Excited state properties of formamide in water solution: An ab initio study

We present ab initio quantum calculation of the optical properties of formamide in vapor phase and in water solution. We employ time dependent density functional theory for the isolated molecule and many-body perturbation theory methods for the system in solution. An average over several molecular dynamics snapshots is performed to take into account the disorder of the liquid. We find that the excited stateproperties of the gas-phase formamide are strongly modified by the presence of the water solvent: the geometry of the molecule is distorted and the electronic and optical properties are severely modified. The important interaction among the formamide and the water molecules forces us to use fully quantum methods for the calculation of the excited stateproperties of this system. The excitonic wave function is localized both on the solute and on part of the solvent.

Supramolecular Organization of Heptapyrenotide Oligomers—An in Depth Investigation by Molecular Dynamics Simulations

We present a molecular modeling study based on ab initio and classical molecular dynamics calculations, for the investigation of the tridimensional structure and supramolecular assembly formation of heptapyrenotide oligomers in water solution. Our calculations show that free oligomers self-assemble in helical structures characterized by an inner core formed by π- stacked pyrene units, and external grooves formed by the linker moieties. The coiling of the linkers has high ordering, dominated by hydrogen-bond interactions among the phosphate and amide groups. Our models support a mechanism of longitudinal supramolecular oligomerization based on interstrand pyrene intercalation. Only a minimal number of pyrene units intercalate at one end, favoring formation of very extended longitudinal chains, as also detected by AFM experiment. Our results provide a structural explanation of the mechanism of chirality amplification in 1:1 mixtures of standard heptapyrenotides and modified oligomers with covalently linked deoxycytidine, based on selective molecular recognition and binding of the nucleotide to the groove of the left-wound helix.

Excitonic splittings in molecular dimers: why static ab initio calculations cannot match them

After decades of research on molecular excitons, only few molecular dimers are available on which exciton and vibronic coupling theories can be rigorously tested. In centrosymmetric H-bonded dimers consisting of identical (hetero)aromatic chromophores, the monomer electronic transition dipole moment vectors subtract or add, yielding S0 → S1 and S0 → S2 transitions that are symmetry-forbidden or -allowed, respectively. Symmetry breaking by 12C/13C or H/D isotopic substitution renders the forbidden transition weakly allowed. The excitonic coupling (Davydov splitting) can then be measured between the S0 → S1 and S0 → S2 vibrationless bands. We discuss the mass-specific excitonic spectra of five H-bonded dimers that are supersonically cooled to a few K and investigated using two-color resonant two-photon ionization spectroscopy. The excitonic splittings Δcalc predicted by ab initio methods are 5–25 times larger than the experimental excitonic splittings Δexp. The purely electronic ab initio splittings need to be reduced (“quenched”), reflecting the coupling of the electronic transition to the optically active vibrations of the monomers. The so-called quenching factors Γ < 1 can be determined from experiment (Γexp) and/or calculation (Γcalc). The vibronically quenched splittings Γ·Δcalc are found to nicely reproduce the experimental exciton splittings.

Ab initio Methodology for Calculating Elastic Constant and Sound Velocity for Hydrogen and Deuterium in Molecular Solid Phase

Hydrogen isotopes play a critical role both in inertial and magnetic confinement Nuclear Fusion. Since the preferent fuel needed for this technology is a mixture of deuterium and tritium. The study of these isotopes particularly at very low temperatures carries a technological interest in other applications. The present line promotes a deep study on the structural configuration that hydrogen and deuterium adopt at cryogenic temperatures and at high pressures. Typical conditions occurring in present Inertial Fusion target designs. Our approach is aims to determine the crystal structure characteristics, phase transitions and other parameters strongly correlated to variations of temperature and pressure. With this results is possible calculated the elastic constant and sound velocity for hydrogen and deuterium in molecular solid phase.

From ab initio quantum mechanics to molecular neurobiology: A cation–π binding site in the nicotinic receptor

The nicotinic acetylcholine receptor is the prototype ligand-gated ion channel. A number of aromatic amino acids have been identified as contributing to the agonist binding site, suggesting that cation–π interactions may be involved in binding the quaternary ammonium group of the agonist, acetylcholine. Here we show a compelling correlation between: (i) ab initio quantum mechanical predictions of cation–π binding abilities and (ii) EC50 values for acetylcholine at the receptor for a series of tryptophan derivatives that were incorporated into the receptor by using the in vivo nonsense-suppression method for unnatural amino acid incorporation. Such a correlation is seen at one, and only one, of the aromatic residues—tryptophan-149 of the α subunit. This finding indicates that, on binding, the cationic, quaternary ammonium group of acetylcholine makes van der Waals contact with the indole side chain of α tryptophan-149, providing the most precise structural information to date on this receptor. Consistent with this model, a tethered quaternary ammonium group emanating from position α149 produces a constitutively active receptor.

Photodissociation of benzene under collision-free conditions: An ab initio/Rice-Ramsperger-Kassel-Marcus study

The ab initio/Rice-Ramsperger-Kassel-Marcus (RRKM) approach has been applied to investigate the photodissociation mechanism of benzene at various wavelengths upon absorption of one or two UV photons followed by internal conversion into the ground electronic state. Reaction pathways leading to various decomposition products have been mapped out at the G2M level and then the RRKM and microcanonical variational transition state theories have been applied to compute rate constants for individual reaction steps. Relative product yields (branching ratios) for C6H5+H, C6H4+H-2, C4H4+C2H2, C4H2+C2H4, C3H3+C3H3, C5H3+CH3, and C4H3+C2H3 have been calculated subsequently using both numerical integration of kinetic master equations and the steady-state approach. The results show that upon absorption of a 248 nm photon dissociation is too slow to be observable in molecular beam experiments. In photodissociation at 193 nm, the dominant dissociation channel is H atom elimination (99.6%) and the minor reaction channel is H-2 elimination, with the branching ratio of only 0.4%. The calculated lifetime of benzene at 193 nm is about 11 mus, in excellent agreement with the experimental value of 10 mus. At 157 nm, the H loss remains the dominant channel but its branching ratio decreases to 97.5%, while that for H-2 elimination increases to 2.1%. The other channels leading to C3H3+C3H3, C5H3+CH3, C4H4+C2H2, and C4H3+C2H3 play insignificant role but might be observed. For photodissociation upon absorption of two UV photons occurring through the neutral hot benzene mechanism excluding dissociative ionization, we predict that the C6H5+H channel should be less dominant, while the contribution of C6H4+H-2 and the C3H3+C3H3, CH3+C5H3, and C4H3+C2H3 radical channels should significantly increase. (C) 2004 American Institute of Physics.

Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures

Bacterial chaperonin, GroEL, together with its co-chaperonin, GroES, facilitates the folding of a variety of polypeptides. Experiments suggest that GroEL stimulates protein folding by multiple cycles of binding and release. Misfolded proteins first bind to an exposed hydrophobic surface on GroEL. GroES then encapsulates the substrate and triggers its release into the central cavity of the GroEL/ES complex for folding. In this work, we investigate the possibility to facilitate protein folding in molecular dynamics simulations by mimicking the effects of GroEL/ES namely, repeated binding and release, together with spatial confinement. During the binding stage, the (metastable) partially folded proteins are allowed to attach spontaneously to a hydrophobic surface within the simulation box. This destabilizes the structures, which are then transferred into a spatially confined cavity for folding. The approach has been tested by attempting to refine protein structural models generated using the ROSETTA procedure for ab initio structure prediction. Dramatic improvements in regard to the deviation of protein models from the corresponding experimental structures were observed. The results suggest that the primary effects of the GroEL/ES system can be mimicked in a simple coarse-grained manner and be used to facilitate protein folding in molecular dynamics simulations. Furthermore, the results Sur port the assumption that the spatial confinement in GroEL/ES assists the folding of encapsulated proteins.

Approximate ab initio calculations and the method of molecular fragments

A two stage approach to performing ab initio calculations on medium and large sized molecules is described. The first step is to perform SCF calculations on small molecules or molecular fragments using the OPIT Program. This employs a small basis set of spherical and p-type Gaussian functions. The Gaussian functions can be identified very closely with atomic cores, bond pairs, lone pairs, etc. The position and exponent of any of the Gaussian functions can be varied by OPIT to produce a small but fully optimised basis set. The second stage is the molecular fragments method. As an example of this, Gaussian exponents and distances are taken from an OPIT calculation on ethylene and used unchanged in a single SCF calculation on benzene. Approximate ab initio calculations of this type give much useful information and are often preferable to semi-empirical approaches, since the nature of the approximations involved is much better defined.

Hydrogen spillover mechanism on a pd-doped mg surface as revealed by ab initio density functional calculation

The hydrogenation kinetics of Mg is slow, impeding its application for mobile hydrogen storage. We demonstrate by ab initio density functional theory (DFT) calculations that the reaction path can be greatly modified by adding transition metal catalysts. Contrasting with Ti doping, a Pd dopant will result in a very small activation barrier for both dissociation of molecular hydrogen and diffusion of atomic H on the Mg surface. This new computational finding supports for the first time by ab initio simulationthe proposed hydrogen spillover mechanism for rationalizing experimentally observed fast hydrogenation kinetics for Pd-capped Mg materials.

Structural and electronic properties of diazonium functionalized (4, 4) single walled carbon nanotube : an ab initio study

In this work, ab initio density functional theory (DFT) calculations are performed to study the structural and electronic properties of diazonium reagent functionalized (4, 4) single-walled carbon nanotube (SWCNT). We find the aryl group covalently bonds with SWCNT and prefers to be perpendicular to the side wall of nanotube. It has a rotational barrier of 0.35 eV around the formed aryl-tube bond axis and should be thermodynamically stable at room temperature. Additionally, new peaks appeared around the Fermi energy in the density of state (DOS) due to the weak band dispersion. Increasing of the coverage of the functional group will result in significant upshift of the Fermi level.

The role of V2O5 on the dehydrogenation and hydrogenation in magnesium hydride : An ab initio study

Ab initio density functional theory calculations are performed to study the experimentally observed catalytic role of V2O5 in the recycling of hydrogen in magnesium hydride. We find that the Mg–H bond length becomes elongated when MgH2 clusters are positioned on single, two, and three coordinated oxygen sites (O1, O2, and O3) on the V2O5(001) surface. Molecular hydrogen is predicted to spontaneously form at the hole site on the V2O5(001) surface. Additionally, the activation barrier for the dissociation of hydrogen on V-doped Mg(0001) surface is 0.20 eV, which is only 1/5 of that on pure Mg(0001) surface. Our results indicate that oxygen sites on the V2O5(001)surface and the V dopant in Mg may be important facilitators for dehydrogenation and rehydrogenation, respectively. The understanding gained here will aid in the rational design and development of Mg-based hydrogen storage materials.

NMR (1H, 13C) and MO (ab initio, CNDO/2, EHT) studies on basic and N-protonated hydrazinecarbothioamide

The conformational preferences of hydrazinecarbothioamide (HCTA, H2NNHCSNH2) in its basic and N-protonated (PHCTA, H3NNNHCSNH2) forms have been studied by 1H and 13C NMR spectroscopy and by theoretical LCAO-MO methods (ab initio, CNDO/2 and EHT). The hindered rotation around the C---N bond has been investigated by a total line shape analysis for the thioamide protons and by the three MO methods. Changes in the molecular conformation and electronic structure on protonation are briefly discussed.