Competitive Solvation of the Imidazolium Cation by Water and Methanol

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

SIMULATING HYDROGEN BONDED CLUSTERS AND ZEOLITE CLUSTERS FOR RENEWABLE ENERGY APPLICATIONS

Our research attention is focused on the development of new fuel cell membrane materials and new zeolites which improve biomass conversion rate to meet the increasing demand of renewable and sustainable energy. We have simulated the dynamics of amphiprotic groups (pyrazole, imidazole, 1,2,3-triazole, 1,2,4-triazole, and tetrazole, acetic acid, formic acid, sulfuric acid, and phosphoric acid) as neat liquids and tethered via linkers to aliphatic backbones, to determine how tethering and varying functional groups affect hydrogen bond networks and reorientation dynamics, both factors thought to influence proton conduction. We used the DL_Poly_2 molecular dynamics code with the GAFF force field to simulate tethered systems over the temperature range 200−900 K, and to simulate the corresponding neat liquids under liquid state temperatures at standard pressure. We computed hydrogen-bond cluster sizes; orientational order parameters and orientational correlation functions associated with functional groups, linkers, and backbones; and time scales and activation energies associated with orientational randomization. Regarding neat phosphoric acid, we find that anomalously large hydrogen-bond clusters provide a neutral-system signature of the high experimental proton conductivity in neat phosphoric acid. Regarding tethered oligomer systems, all exhibited a liquid to glassy-solid transition upon cooling, with the formic-, and acetic-based oligomers retaining liquid behavior to relatively low temperatures (~400 K); while azoles- and phosphonic-oligomers formed glassy solids around 500-600 K; and sulfonic-pentamers lost motion around 900 K as evidenced by orientational order parameters and correlation functions. Hydrogen bond cluster sizes in tethered phosphonic acid (T ≤ 500 K) remain orders of magnitude above all other tethered systems, suggesting tethered phosphonic oligomers as promising targets for new PEMs. Tethering the azoles was generally found to produce hydrogen-bond cluster sizes similar to those in untethered liquids, and to produce longer hydrogen-bond lifetimes than those in liquids. The simulated rates of functional group reorientation decreased dramatically upon tethering. The activation energies associated with orientational randomization agree well with NMR data for tethered imidazole systems at lower temperatures, and for tethered 1,2,3-triazole systems at both low- and high-temperature ranges. Overall, our simulations corroborate the notion that tethering functional groups dramatically slows the process of reorientation. We found a linear correlation between gas-phase hydrogen-bond energies and tethered-functional-group reorientation barriers for all azoles except for imidazole, which acts as an outlier because of both atomic charges and molecular structure. We have performed density functional theory (DFT) calculations to investigate the convergence of reaction barriers with respect to zeolite cluster size, for multi-step reactions catalyzed in HZSM-5 zeolite. We have constructed cluster models of HZSM-5 using the delta-cluster approach reported previously by us [ACS Catalysis 5, 2859 (2015)], which systematically treats zeolite confinement using a single neighbor-list radius. We computed barriers for several different reaction types, and with a range of reactant sizes from 2 to 13 heavy (non-hydrogen) atoms, to determine the cluster sizes and neighbor-list radii needed to fully treat zeolite confinement effects. To establish barrier convergence, we studied the acid-zeolite-catalyzed aldol reactions of acetone with aldehydes of increasing size (formaldehyde, furfural, and hydroxymethyl-furfural), modeling the acid-catalyzed aldol reaction in three steps: keto/enol tautomerization of acetone, bimolecular combination between each aldehyde and the enol, and aldol dehydration. We found that the delta cluster neighbor-list radius of 4 Å is sufficient to converge barriers with respect to cluster size for all reaction steps considered, yielding complete treatments of confinement in HZSM-5 with clusters containing up to 99 (Si, Al, O) framework atoms. For comparison, periodic DFT calculations on HZSM-5 include 288 framework atoms, requiring 19 times more CPU time in our head-to-head comparisons on a single processor. The converged acetone/formaldehyde dehydration barrier from our cluster calculations agrees quantitatively with a comparable barrier obtained by Curtiss and coworkers with periodic DFT, showing that cluster calculations can converge properties with respect to system size at a fraction of the cost of periodic DFT. Interestingly, we found that the bulkier, furan-containing aldehydes exhibit faster aldol reactivity because of charge delocalization from their aromatic rings, which significantly speeds up aldol dehydration

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

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

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

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

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 (CH₄) 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 CH₄ and 488 v/v at 77 K and 20 bar for H₂. Direct observation and quantification of the location, binding, and rotational modes of adsorbed CH₄ and H₂ 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 H₂ and CH₄ 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 CH₄ molecules and the hydroxyl groups within the pore of a material. This is different from the arrangement found in CH₄/water clathrates, the CH₄ store of nature

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

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

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

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?

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