Ab Initio Quantum Chemical Studies on Neutral-Radical Reactions of Ethynyl (C2H) and Cyano (CN) with Unsaturated Hydrocarbons

An Ab Initio/RRKM study of the reaction mechanism and product branching ratios of neutral-radical ethynyl (C2H) and cyano (CN) radical species with unsaturated hydrocarbons is performed. The reactions studied apply to cold conditions such as planetary atmospheres including Titan, the Interstellar Medium (ISM), icy bodies and molecular clouds. The reactions of C2H and CN additions to gaseous unsaturated hydrocarbons are an active area of study. NASA’s Cassini/Huygens mission found a high concentration of C2H and CN from photolysis of ethyne (C2H2) and hydrogen cyanide (HCN), respectively, in the organic haze layers of the atmosphere of Titan. The reactions involved in the atmospheric chemistry of Titan lead to a vast array of larger, more complex intermediates and products and may also serve as a chemical model of Earth’s primordial atmospheric conditions. The C2H and CN additions are rapid and exothermic, and often occur barrierlessly to various carbon sites of unsaturated hydrocarbons. The reaction mechanism is proposed on the basis of the resulting potential energy surface (PES) that includes all the possible intermediates and transition states that can occur, and all the products that lie on the surface. The B3LYP/6-311g(d,p) level of theory is employed to determine optimized electronic structures, moments of inertia, vibrational frequencies, and zero-point energy. They are followed by single point higher-level CCSD(T)/cc-vtz calculations, including extrapolations to complete basis sets (CBS) of the reactants and products. A microcanonical RRKM study predicts single-collision (zero-pressure limit) rate constants of all reaction paths on the potential energy surface, which is then used to compute the branching ratios of the products that result. These theoretical calculations are conducted either jointly or in parallel to experimental work to elucidate the chemical composition of Titan’s atmosphere, the ISM, and cold celestial bodies.

Full-dimensional analytical ab initio potential energy surface of the ground state of HOI

Extensive ab initio calculations using a complete active space second-order perturbation theory wavefunction, including scalar and spin-orbit relativistic effects with a quadruple-zeta quality basis set were used to construct an analytical potential energy surface (PES) of the ground state of the [H, O, I] system. A total of 5344 points were fit to a three-dimensional function of the internuclear distances, with a global root-mean-square error of 1.26 kcal mol(-1). The resulting PES describes accurately the main features of this system: the HOI and HIO isomers, the transition state between them, and all dissociation asymptotes. After a small adjustment, using a scaling factor on the internal coordinates of HOI, the frequencies calculated in this work agree with the experimental data available within 10 cm(-1). (C) 2011 American Institute of Physics. [doi: 10.1063/1.3615545]

Recent advances in the preparation and utilization of carbon nanotubes for hydrogen storage

Recent progress in the production, purification, and experimental and theoretical investigations of carbon nanotubes for hydrogen storage are reviewed. From the industrial point of view, the chemical vapor deposition process has shown advantages over laser ablation and electric-arc-discharge methods. The ultimate goal in nanotube synthesis should be to gain control over geometrical aspects of nanotubes, such as location and orientation, and the atomic structure of nanotubes, including helicity and diameter. There is currently no effective and simple purification procedure that fulfills all requirements for processing carbon nanotubes. Purification is still the bottleneck for technical applications, especially where large amounts of material are required. Although the alkali-metal-doped carbon nanotubes showed high H-2 Weight uptake, further investigations indicated that some of this uptake was due to water rather than hydrogen. This discovery indicates a potential source of error in evaluation of the storage capacity of doped carbon nanotubes. Nevertheless, currently available single-wall nanotubes yield a hydrogen uptake value near 4 wt% under moderate pressure and room temperature. A further 50% increase is needed to meet U.S. Department of Energy targets for commercial exploitation. Meeting this target will require combining experimental and theoretical efforts to achieve a full understanding of the adsorption process, so that the uptake can be rationally optimized to commercially attractive levels. Large-scale production and purification of carbon nanotubes and remarkable improvement of H-2 storage capacity in carbon nanotubes represent significant technological and theoretical challenges in the years to come.

A comparative analysis by means of quantum molecular similarity measures of density distributions derived from conventional ab initio and density functional methods

A procedure based on quantum molecular similarity measures (QMSM) has been used to compare electron densities obtained from conventional ab initio and density functional methodologies at their respective optimized geometries. This method has been applied to a series of small molecules which have experimentally known properties and molecular bonds of diverse degrees of ionicity and covalency. Results show that in most cases the electron densities obtained from density functional methodologies are of a similar quality than post-Hartree-Fock generalized densities. For molecules where Hartree-Fock methodology yields erroneous results, the density functional methodology is shown to yield usually more accurate densities than those provided by the second order Møller-Plesset perturbation theory

Thermodynamic Stabillity of Hydrogen-Bonded Systems in Polar and Nonpolar Environments

The thermodynamic properties of a selected set of benchmark hydrogen-bonded systems (acetic acid dimer and the complexes of acetic acid with acetamide and methanol) was studied with the goal of obtaining detailed information on solvent effects on the hydrogen-bonded interactions using water, chloroform, and n-heptane as representatives for a wide range in the dielectric constant. Solvent effects were investigated using both explicit and implicit solvation models. For the explicit description of the solvent, molecular dynamics and Monte Carlo simulations in the isothermal isobaric (NpT) ensemble combined with the free energy perturbation technique were performed to determine solvation free energies. Within the implicit solvation approach, the polarizable continuum model and the conductor-like screening model were applied. Combination of gas phase results with the results obtained from the different solvation models through an appropriate thermodynamic cycle allows estimation of complexation free energies, enthalpies, and the respective entropic contributions in solution. Owing to the strong solvation effects of water the cyclic acetic acid dimer is not stable in aqueous solution. In less polar solvents the double hydrogen bond structure of the acetic acid dimer remains stable. This finding is in agreement with previous theoretical and experimental results. A similar trend as for the acetic acid dimer is also observed for the acetamide complex. The methanol complex was found to be thermodynamically unstable in gas phase as well as in any of the three solvents. (C) 2010 Wiley Periodicals, Inc. J Comput Chem 31: 2046-2055, 2010

Electronic properties of liquid hydrogen fluoride: A sequential quantum mechanical/Born-Oppenheimer molecular dynamics approach

The electronic properties of liquid hydrogen fluoride (HF) were investigated by carrying out sequential quantum mechanics/Born-Oppenheimer molecular dynamics. The structure of the liquid is in good agreement with recent experimental information. Emphasis was placed on the analysis of polarisation effects, dynamic polarisability and electronic excitations in liquid HF. Our results indicate an increase in liquid phase of the dipole moment (similar to 0.5 D) and isotropic polarisability (5%) relative to their gas-phase values. Our best estimate for the first vertical excitation energy in liquid HF indicates a blue-shift of 0.4 +/- 0.2 eV relative to that of the gas-phase monomer (10.4 eV). (C) 2010 Elsevier B.V. All rights reserved.

Ab initio study of the EFG at the N sites in imidazole

We study the nuclear quadrupole interaction at the nitrogen sites in the molecular and crystalline phases of the imidazole compound. We use PAW which is a state-of-the-art method to calculate the electronic structure and electric field gradient at the nucleus in the framework of the density functional theory. The quadrupole frequencies at both imino and amino N sites are in excellent agreement with measurements. This is the first time that the electric field gradient at crystalline imidazole is correctly treated by an ab initio theoretical approach.

Ab Initio Calculations of Structural Evolution and Conductance of Benzene-1,4-dithiol on Gold Leads

By performing at) initio density functional theory (DFT) calculations and electronic transport simulations based on the OFT nonequilibrium Green`s functions method we investigate how the conformational changes of a benzene-1,4-dithiol molecule bonded to gold affect the molecular transport as the electrodes are separated from each other. In particular we consider the full evolution of the stretching process until the Junction breaking point and compare results obtained with a standard semilocal exchange and correlation functional to those computed with a self-interaction corrected method. We conclude that the inclusion of self-interaction corrections is fundamental for describing both the molecule conductance and its stability against conformational fluctuations.

MOLECULAR DYNAMICS STUDIES OF SIMPLE MODEL FLUIDS AND WATER CONFINED IN CARBON NANOTUBE

Molecular Dynamics (MD) simulation is one of the most important computational techniques with broad applications in physics, chemistry, chemical engineering, materials design and biological science. Traditional computational chemistry refers to quantum calculations based on solving Schrodinger equations. Later developed Density Functional Theory (DFT) based on solving Kohn-Sham equations became the more popular ab initio calculation technique which could deal with ~1000 atoms by explicitly considering electron interactions. In contrast, MD simulation based on solving classical mechanics equations of motion is a totally different technique in the field of computational chemistry. Electron interactions were implicitly included in the empirical atom-based potential functions and the system size to be investigated can be extended to ~106 atoms. The thermodynamic properties of model fluids are mainly determined by macroscopic quantities, like temperature, pressure, density. The quantum effects on thermodynamic properties like melting point, surface tension are not dominant. In this work, we mainly investigated the melting point, surface tension (liquid-vapor and liquid-solid) of model fluids including Lennard-Jones model, Stockmayer model and a couple of water models (TIP4P/Ew, TIP5P/Ew) by means of MD simulation. In addition, some new structures of water confined in carbon nanotube were discovered and transport behaviors of water and ions through nano-channels were also revealed.

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.

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.

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.

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.