424 research outputs found

    Competitive Solvation of the Imidazolium Cation by Water and Methanol

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    Imidazolium-based ionic liquids are widely used in conjunction with molecular liquids for various applications. Solvation, miscibility and similar properties are of fundamental importance for successful implementation of theoretical schemes. This work reports competitive solvation of the 1,3-dimethylimidazolium cation by water and methanol. Employing molecular dynamics simulations powered by semiempirical Hamiltonian (electronic structure level of description), the local structure nearly imidazolium cation is described in terms of radial distribution functions. Although water and methanol are chemically similar, water appears systematically more successful in solvating the 1,3-dimethylimidazolium cation. This result fosters construction of future applications of the ternary ion-molecular systems

    Unconstrained Global Optimization of Molecules on Surfaces: From globally optimized structures to scanning-probe data

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    The adsorption of molecules on a surface plays a vital role in heterogeneous catalysis. For a proper unterstanding of the reaction mechanisms involved, the adsorption ge ometry of the molecules on the surface needs to be known. So far, experimental data from tunneling microscopes and spectroscopy, such as STM and IRAS are the main ways to obtain such knowledge. Due to the vast search space of adsorption geometries, especially for oligomers, optimizations using ab initio methods can be used to confirm the experimental data only if good initial guesses are available. Global optimization can serve two purposes in these situations. On the one hand it allows for a thorough investigation of the given search space, which can provide good initial guesses for subsequent high-level structural refinements. On the other hand, given a known reaction mechanism, it could also be used to find catalysts that influence e.g. the relevant bonds. With respect to this idea the topic of this thesis is to find a local optimization method cheap enough such that the total computational cost of global optimization does not exceed availability and yet good enough that the results are meaningful to the problem at hand. With this in mind multiple force field and semiempirical methods have been tested and evaluated mainly on benzene, acetophenone and ethyl pyruvate on Pt(111) surfaces. Some other adsorbates have also been tested shortly. In addition to these global optimization results, DFT geometry optimizations of ethyl pyruvate on Pt(111) have been performed and the structures of the best adsorption geometry from global optimization and from DFT are compared. Furthermore, from the DFT data STM images have been calculated that are compared to experimental results. The theoretical and experimental STM images agree well

    17O NMR: A "Rare and Sensitive" Probe of Molecular Interactions and Dynamics

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    This review summarizes recent developments in the area of liquid-state Nuclear Magnetic Resonance spectroscopy of the 17O nucleus. It is structured in Sections, respectively covering (a) general background information, with special emphasis on spin relaxation phenomena for quadrupolar nuclei and in paramagnetic environments, (b) methods for the calculation of 17O NMR parameters, with illustrative results, (c) applications in chemistry and materials science, (d) application to biomolecules and biological systems, (e) relaxation phenomena, including contrast agents for Magnetic Resonance Imaging (MRI). The 17O nucleus emerges as a very sensitive probe of the local environment ─ including both bonding and non-bonding interactions ─ and molecular motions

    A Perturbation Approach to Predict the Infrared Spectra of Small Molecular Clusters Applied to Methanol

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    A method for predicting splittings and shifts of bands in infrared spectra of small clusters of polyatomic molecules is presented. Based on an approach of early publications of Buckingham, the influence of the intermolecular forces on the vibrational energy levels of the constituent molecules is calculated using perturbation theory to second order. In order to describe the interaction of identical molecules, this ansatz is extended to also cover degenerate systems. In first order, a coupling of the vibrational modes of the interacting molecules occurs which leads to delocalized vibrations of all the molecules in the cluster. The second order correction of the vibrational excitation frequencies are found to be dominated by the intramolecular couplings of the normal modes due to the cubic anharmonicity of the force field. The procedures developed here are applied for the interpretation of vibrational photodissociation spectra of small methanol clusters in the region of the fundamental excitation frequency of the OH stretching mode (ν1, 3681.5 cm-1), the CH3 rocking mode (ν7, 1074.5 cm-1), and the CO stretching mode (ν8, 1033.5 cm-1). Using semiempirical models for the intermolecular potential functions, splittings and positions of the experimental bands can well be explained. The nonequivalent positions of the two molecules in the linear dimer structure give rise to two different absorption frequencies for each of the three modes of the donor and the acceptor molecule, respectively. The trimer and tetramer spectrum with only one absorption band are in agreement with the existence of symmetric planar ring structures (C3h and C4h) for these species. The pentamer spectrum which also consists of one band is explained by the occurrence of three closely spaced frequencies of an asymmetric ring. The double peak structure in the hexamer spectra can be attributed to a distorted ring structure of S6 symmetry, while the occurrence of other energetically near-degenerate isomers can be ruled out by means of their spectra

    Observation of Binding and Rotation of Methane and Hydrogen within a Functional Metal-Organic Framework

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    The key requirement for a portable store of natural gas is to maximize the amount of gas within the smallest possible space. The packing of methane (CH<sub>4</sub>) in a given storage medium at the highest possible density is, therefore, a highly desirable but challenging target. We report a microporous hydroxyl-decorated material, MFM-300­(In) (MFM = Manchester Framework Material, replacing the NOTT designation), which displays a high volumetric uptake of 202 v/v at 298 K and 35 bar for CH<sub>4</sub> and 488 v/v at 77 K and 20 bar for H<sub>2</sub>. Direct observation and quantification of the location, binding, and rotational modes of adsorbed CH<sub>4</sub> and H<sub>2</sub> molecules within this host have been achieved, using neutron diffraction and inelastic neutron scattering experiments, coupled with density functional theory (DFT) modeling. These complementary techniques reveal a very efficient packing of H<sub>2</sub> and CH<sub>4</sub> molecules within MFM-300­(In), reminiscent of the condensed gas in pure component crystalline solids. We also report here, for the first time, the experimental observation of a direct binding interaction between adsorbed CH<sub>4</sub> molecules and the hydroxyl groups within the pore of a material. This is different from the arrangement found in CH<sub>4</sub>/water clathrates, the CH<sub>4</sub> store of nature

    Multiple active zones in hybrid QM/MM molecular dynamics simulations for large biomolecular systems

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    A new QM/MM molecular dynamics approach that can deal with the dynamics of large real systems involving several simultaneous active zones is presented. Multiple, unconnected but interacting quantum regions are treated independently in an ordinary QM/MM approach but in a manner which converges to a unique simulation. The multiple active zones in the hybrid QM/MM molecular dynamics methodology (maz-QM/MM MD) involve molecular dynamics that is driving the whole simulation with several parallel executions of energy gradients within the QM/MM approach that merge into each MD step. The Ewald-summation method is used to incorporate long-range electrostatic interactions among the active zones in conjunction with periodic boundary conditions. To illustrate and ascertain capabilities and limitations, we present several benchmark calculations using this approach. Our results show that the maz-QM/MM MD method is able to provide simultaneous treatment of several active zones of very large proteins such as the Cu-4His-¿C* cage, a self-assembly of a 24-mer cage-like protein ferritinPeer ReviewedPostprint (published version

    Utilization of Molecular Simulation Software Gaussian 03 to Design Absorbent for CO2 Capture

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    AbstractA preliminary study on the interaction between molecules of absorbent for CO2 absorption was undertaken using Gaussian 03 molecular simulation software. The results indicate that the molecular interaction energy has strong correlations with Henry's constant. The lower interaction energy between molecules, solvent molecules form an “associated complex” more stability, and therefore the worse the effect of CO2 absorption

    Solvent as Electron Donor:  Donor/Acceptor Electronic Coupling Is a Dynamical Variable

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    We combine analysis of measurements by femtosecond optical spectroscopy, computer simulations, and the generalized Mulliken−Hush (GMH) theory in the study of electron-transfer reactions and electron donor−acceptor interactions. Our focus is on ultrafast photoinduced electron-transfer reactions from aromatic amine solvent donors to excited-state acceptors. The experimental results from femtosecond dynamical measurements fall into three categories:  six coumarin acceptors reductively quenched by N,N-dimethylaniline (DMA), eight electron-donating amine solvents reductively quenching coumarin 152 (7-(dimethylamino)-4-(trifluoromethyl)coumarin), and reductive quenching dynamics of two coumarins by DMA as a function of dilution in the nonreactive solvents toluene and chlorobenzene. Applying a combination of molecular dynamics trajectories, semiempirical quantum mechanical calculations (of the relevant adiabatic electronic states), and GMH theory to the C152/DMA photoreaction, we calculate the electron donor/acceptor interaction parameter HDA at various time frames. HDA is strongly modulated by both inner-sphere and outer-sphere nuclear dynamics, leading us to conclude that HDA must be considered as a dynamical variable

    Electronic Excitations in Nonpolar Solvents: Can the Polarizable Continuum Model Accurately Reproduce Solvent Effects?

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    In nonpolar solvents, both electrostatic and nonelectrostatic interactions play a role in tuning the electronic excitations of molecular solutes. This specificity makes the application of continuum solvation models a challenge. Here, we propose a strategy for the calculation of solvatochromic shifts on absorption spectra, using a coupling of the polarizable continuum model with a time-dependent density functional theory framework, which explicitly accounts for dispersion and repulsion, as well as for electrostatic effects. Our analysis makes a step further in the interpretation of the effects of nonpolar solvents and suggests new directions in their modeling using continuum formulations
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