Quantum Dynamical Investigation of Dihydrogen-Hydride Exchange in a Transition-Metal Polyhydride Complex.

The ongoing shift toward clean, sustainable energy is a primary driving force behind hydrogen fuel research. Safe and effective storage of hydrogen is a major challenge (particularly for mobile applications) and requires a detailed understanding of the atomic level interactions of hydrogen with its host materials. The light mass of hydrogen, however, implies that quantum effects are important, so a quantum dynamical treatment is required to properly account for these effects in computational simulations. As one such example, we describe herein the hydrogen exchange dynamics between a hydride and a dihydrogen ligand in the [FeH(H2)(PH3)4]+ model complex. A global three-dimensional (3D) potential energy surface (PES) was constructed by fitting to and interpolating from a discrete set of grid points computed using density functional theory; exact quantum dynamical calculations were then carried out on the 3D PES using discrete variable representation basis sets. Energy levels and their quantum tunneling splittings were computed up to 3000 cm-1 above the ground state. Within that energy range, all three fundamentals have been identified using wave function plots, as well as the first three overtones of the exchange (reaction coordinate) motion and several of its combination bands. From the tunneling splittings, the Boltzmann-averaged tunneling rates were computed. The Arrhenius plot of the total exchange rate shows a clear transition around 150 K, below which the activation energy is essentially zero and above which it is less than half of the electronic structure barrier. This indicates that exchange rates are governed by quantum tunneling throughout the relevant temperature range with the low-temperature regime dominated by a single quantum (ground) state. This work is the first-ever fully quantum dynamical study to investigate the hydrogen exchange dynamics between hydride and dihydrogen ligands coordinated to a transition-metal complex.

Hydrogen bond dynamics and conformational flexibility in antipsychotics.

Effective treatment of disorders of the central nervous system can often be achieved using bioactive molecules of similar moieties to those known to be tolerable. A better understanding of the solid-state characteristics of such molecules could thereby create new opportunities for research on pharmaceutical preparations and drug prescriptions, while information about their rich intramolecular dynamics may well add an important aspect in the field of in silico drug discovery. We have therefore investigated three different antipsychotic drugs: haloperidol (C21H23ClFNO2, HAL), aripiprazole (C23H27Cl2N3O2, APZ) and quetiapine hemifumarate (C21H25N3O2S·0.5C4H4O4, QTP) based on similarities either in their structures, hydrophobic and hydrophilic moieties, or in their modes of action, typical or atypical. Our aim was to test the structural and molecular stability of these three different antipsychotics. To this end, we compared the molecular vibrations observed by inelastic neutron spectroscopy of these systems with those from theoretical periodic calculations of the crystalline antipsychotics using the Vienna ab initio simulation package (VASP). While most of the observed features in the lattice region were reasonably well represented by the calculations, the overall spectra were relatively complex, and hence traditional assignment procedures for the approximately 600 normal modes in the unit cell were not possible. These results indicate that in the search for new drug candidates, not only analysis of the flexibility of the receptor, but also the dynamics of the active molecules play a role in improving the prediction of binding affinities.

A quantum dynamical study of the rotation of the dihydrogen ligand in the Fe(H)2(H2)(PEtPh2)3 coordination complex.

Progress in the hydrogen fuel field requires a clear understanding and characterization of how materials of interest interact with hydrogen. Due to the inherently quantum mechanical nature of hydrogen nuclei, any theoretical studies of these systems must be treated quantum dynamically. One class of material that has been examined in this context are dihydrogen complexes. Since their discovery by Kubas in 1984, many such complexes have been studied both experimentally and theoretically. This particular study examines the rotational dynamics of the dihydrogen ligand in the Fe(H)2(H2)(PEtPh2)3 complex, allowing for full motion in both the rotational degrees of freedom and treating the quantum dynamics (QD) explicitly. A "gas-phase" global potential energy surface is first constructed using density functional theory with the Becke, 3-parameter, Lee-Yang-Parr functional; this is followed by an exact QD calculation of the corresponding rotation/libration states. The results provide insight into the dynamical correlation of the two rotation angles as well as a comprehensive analysis of both ground- and excited-state librational tunneling splittings. The latter was computed to be 6.914 cm-1-in excellent agreement with the experimental value of 6.4 cm-1. This work represents the first full-dimensional ab initio exact QD calculation ever performed for dihydrogen ligand rotation in a coordination complex.

Computational study of inelastic neutron scattering vibrational spectra of water clusters and their relevance to hydration water in proteins.

BACKGROUND: Inelastic neutron scattering (INS) vibrational spectra for hydration water in proteins can be obtained from spectral differences, but their interpretation has mainly been limited to comparisons with various forms of ice at high hydration levels without making use of available structural information from neutron protein crystallography. METHODS: The INS vibrational spectra of free and partially constrained water clusters (up to n=17) were calculated with DFT methods using published energy-minimized structures. RESULTS: Reference is made to neutron diffraction studies of hydrated proteins, which contain a wealth of structural information both on individual water molecules and small clusters in the inner "shell" in order to select representative clusters to serve as models for bound, rather than free clusters as they would occur in a protein. CONCLUSIONS: INS spectra of the water librational region calculated for a combination of model bound clusters provide a qualitative account of the essentially featureless experimental spectra on water in proteins at very low hydration levels, but do indicate that the well-known rise in intensity near 500cm-1 is connected to increasing numbers of four-coordinate water molecules in larger clusters. GENERAL SIGNIFICANCE: The combination of structural information of hydration water from neutron protein crystallography with much more sophisticated computational methods than used herein should lead to a much more detailed picture of the hydration of proteins. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.

The rotational dynamics of H2 adsorbed in covalent organic frameworks.

A combined inelastic neutron scattering (INS) and theoretical study was carried out on H2 adsorbed in two covalent organic framework (COF) materials: COF-1 and COF-102. These COFs are synthesized from self-condensation reactions of 1,4-benzenediboronic acid (BDBA) and tetra(4-(dihydroxy)borylphenyl)methane (TBPM) molecules, respectively. Molecular simulations of H2 adsorption in COF-1 revealed that the H2 molecules occupy the region between two eclipsed layers of the COF. The most favorable H2 binding site in COF-1 is located between two B3O3 clusters of the eclipsed layers. Two distinct H2 binding sites were identified in COF-102 from the simulations: the B3O3 clusters and the phenyl rings of the tetraphenylmethyl units. Two-dimensional quantum rotation calculations for H2 adsorbed at the considered sites in both COFs resulted in rotational transitions that are in good agreement with those that appear in the corresponding INS spectra. Such calculations were important for interpreting the INS spectra in these materials. Calculation of the rotational potential energy surface for H2 bound at the most favorable adsorption site in COF-1 and COF-102 revealed unusually high rotational barriers that are attributed to the nature of the B3O3 rings. The values for these barriers to rotation are greater than or comparable to those observed in some metal-organic frameworks (MOFs) that possess open-metal sites. This study demonstrates the power of using INS experiments in conjunction with theoretical calculations to gain valuable insights into the nature of the binding sites and, for the first time, the rotational dynamics of H2 adsorbed in COFs.

Dynamics of H2 adsorbed in porous materials as revealed by computational analysis of inelastic neutron scattering spectra.

The inelastic scattering of neutrons from adsorbed H2 is an effective and highly sensitive method for obtaining molecular level information on the type and nature of H2 binding sites in porous materials. While these inelastic neutron scattering (INS) spectra of the hindered rotational and translational excitations on the adsorbed H2 contain a significant amount of information, much of this can only be reliably extracted by means of a detailed analysis of the spectra through the utilization of models and theoretical calculations. For instance, the rotational tunneling transitions observed in the INS spectra can be related to a value for the barrier to rotation for the adsorbed H2 with the use of a simple phenomenological model. Since such an analysis is dependent on the model, it is far more desirable to use theoretical methods to compute a potential energy surface (PES), from which the rotational barriers for H2 adsorbed at a particular site can be determined. Rotational energy levels and transitions for the hindered rotor can be obtained by quantum dynamics calculations and compared directly with experiment with an accuracy subject only to the quality of the theoretical PES. In this paper, we review some of the quantum and classical mechanical calculations that have been performed on H2 adsorbed in various porous materials, such as clathrate hydrates, zeolites, and metal-organic frameworks (MOFs). The principal aims of these calculations have been the interpretation of the INS spectra for adsorbed H2 along with the extraction of atomic level details of its interaction with the host. We describe calculations of the PES used for two-dimensional quantum rotation as well as rigorous five-dimensional quantum coupled translation-rotation dynamics, and demonstrate that the combination of INS measurements and computational modeling can provide important and detailed insights into the molecular mechanism of H2 adsorption in porous materials.

Exceptional H2 sorption characteristics in a Mg(2+)-based metal-organic framework with small pores: insights from experimental and theoretical studies.

Experimental sorption measurements, inelastic neutron scattering (INS), and theoretical studies of H2 sorption were performed in α-[Mg3(O2CH)6], a metal-organic framework (MOF) that consists of a network of Mg(2+) ions coordinated to formate ligands. The experimental H2 uptake at 77 K and 1.0 atm was observed to be 0.96 wt%, which is quite impressive for a Mg(2+)-based MOF that has a BET surface area of only 150 m(2) g(-1). Due to the presence of small pore sizes in the MOF, the isosteric heat of adsorption (Qst) value was observed to be reasonably high for a material with no open-metal sites (ca. 7.0 kJ mol(-1)). The INS spectra for H2 in α-[Mg3(O2CH)6] is very unusual for a porous material, as there exist several different peaks that occur below 10 meV. Simulations of H2 sorption in α-[Mg3(O2CH)6] revealed that the H2 molecules sorbed at three principal locations within the small pores of the framework. It was discovered through the simulations and two-dimensional quantum rotation calculations that different groups of peaks correspond to particular sorption sites in the material. However, for H2 sorbed at a specific site, it was observed that differences in the positions and angular orientations led to distinctions in the rotational tunnelling transitions; this led to a total of eight identified sites. An extremely high rotational barrier was calculated for H2 sorbed at the most favorable site in α-[Mg3(O2CH)6] (81.59 meV); this value is in close agreement to that determined using an empirical phenomenological model (75.71 meV). This rotational barrier for H2 exceeds those for various MOFs that contain open-metal sites and is currently the highest yet for a neutral MOF. This study highlights the synergy between experiment and theory to extract useful and important atomic level details on the remarkable sorption mechanism for H2 in a MOF with small pore sizes.

Low voltage transmission electron microscopy of graphene.

The initial isolation of graphene in 2004 spawned massive interest in this two-dimensional pure sp(2) carbon structure due to its incredible electrical, optical, mechanical, and thermal effects. This in turn led to the rapid development of various characterization tools for graphene. Examples include Raman spectroscopy and scanning tunneling microscopy. However, the one tool with the greatest prowess for characterizing and studying graphene is the transmission electron microscope. State-of-the-art (scanning) transmission electron microscopes enable one to image graphene with atomic resolution, and also to conduct various other characterizations simultaneously. The advent of aberration correctors was timely in that it allowed transmission electron microscopes to operate with reduced acceleration voltages, so that damage to graphene is avoided while still providing atomic resolution. In this comprehensive review, a brief introduction is provided to the technical aspects of transmission electron microscopes relevant to graphene. The reader is then introduced to different specimen preparation techniques for graphene. The different characterization approaches in both transmission electron microscopy and scanning transmission electron microscopy are then discussed, along with the different aspects of electron diffraction and electron energy loss spectroscopy. The use of graphene for other electron microscopy approaches such as in-situ investigations is also presented.

Investigating H2 Sorption in a Fluorinated Metal-Organic Framework with Small Pores Through Molecular Simulation and Inelastic Neutron Scattering.

Simulations of H2 sorption were performed in a metal-organic framework (MOF) consisting of Zn(2+) ions coordinated to 1,2,4-triazole and tetrafluoroterephthalate ligands (denoted [Zn(trz)(tftph)] in this work). The simulated H2 sorption isotherms reported in this work are consistent with the experimental data for the state points considered. The experimental H2 isosteric heat of adsorption (Qst) values for this MOF are approximately 8.0 kJ mol(-1) for the considered loading range, which is in the proximity of those determined from simulation. The experimental inelastic neutron scattering (INS) spectra for H2 in [Zn(trz)(tftph)] reveal at least two peaks that occur at low energies, which corresponds to high barriers to rotation for the respective sites. The most favorable sorption site in the MOF was identified from the simulations as sorption in the vicinity of a metal-coordinated H2O molecule, an exposed fluorine atom, and a carboxylate oxygen atom in a confined region in the framework. Secondary sorption was observed between the fluorine atoms of adjacent tetrafluoroterephthalate ligands. The H2 molecule at the primary sorption site in [Zn(trz)(tftph)] exhibits a rotational barrier that exceeds that for most neutral MOFs with open-metal sites according to an empirical phenomenological model, and this was further validated by calculating the rotational potential energy surface for H2 at this site.

Polymorphism of paracetamol: a new understanding of molecular flexibility through local methyl dynamics.

This study focuses on the interplay of molecular flexibility and hydrogen bonding manifested in the monoclinic (form I) and orthorhombic (form II) polymorphs of paracetamol. By means of incoherent inelastic neutron scattering and density functional theory calculations, the relaxation processes related to the methyl side-group reorientation were analyzed in detail. Our computational study demonstrates the importance of considering quantum effects to explain how methyl reorientations and subtle conformational changes of the molecule are intertwined. Indeed, by analyzing the quasi elastic signal of the neutron data, we were able to show a unique and complex motional flexibility in form II, reflected by a coupling between the methyl and the phenyl reorientation. This is associated with a higher energy barrier of the methyl rotation and a lower Gibbs free energy when compared to form I. We put forward the idea that correlating solubility and molecular flexibility, through the relation between pKa and methyl rotation activation energy, might bring new insights to understanding and predicting drug bioavailability.

A general protocol for determining the structures of molecularly ordered but noncrystalline silicate frameworks.

A general protocol is demonstrated for determining the structures of molecularly ordered but noncrystalline solids, which combines constraints provided by X-ray diffraction (XRD), one- and two-dimensional solid-state nuclear magnetic resonance (NMR) spectroscopy, and first-principles quantum chemical calculations. The approach is used to determine the structure(s) of a surfactant-directed layered silicate with short-range order in two dimensions but without long-range periodicity in three-dimensions (3D). The absence of long-range 3D molecular order and corresponding indexable XRD reflections precludes determination of a space group for this layered silicate. Nevertheless, by combining structural constraints obtained from solid-state (29)Si NMR analyses, including the types and relative populations of distinct (29)Si sites, their respective (29)Si-O-(29)Si connectivities and separation distances, with unit cell parameters (though not space group symmetry) provided by XRD, a comprehensive search of candidate framework structures leads to the identification of a small number of candidate structures that are each compatible with all of the experimental data. Subsequent refinement of the candidate structures using density functional theory calculations allows their evaluation and identification of "best" framework representations, based on their respective lattice energies and quantitative comparisons between experimental and calculated (29)Si isotropic chemical shifts and (2)J((29)Si-O-(29)Si) scalar couplings. The comprehensive analysis identifies three closely related and topologically equivalent framework configurations that are in close agreement with all experimental and theoretical structural constraints. The subtle differences among such similar structural models embody the complexity of the actual framework(s), which likely contain coexisting or subtle distributions of structural order that are intrinsic to the material.

Methyl dynamics flattens barrier to proton transfer in crystalline tetraacetylethane.

We analyze the interplay between proton transfer in the hydrogen-bond bridge, O···H···O, and lattice dynamics in the model system tetraacetylethane (TAE) (CH(3)CO)(2)CH═CH(COCH(3))(2) using density functional theory. Lattice dynamics calculations and molecular dynamics simulations are validated against neutron scattering data. Hindrance to the cooperative reorientation of neighboring methyl groups at low temperatures gives a preferred O atom for the bridging proton. The amplitude of methyl torsions becomes larger with increasing temperature, so that the free-energy minimum for the proton becomes flat over 0.2 Å. For the isolated molecule, however, we show an almost temperature-independent symmetric double-well potential persists. This difference arises from the much higher barriers to methyl torsion in the crystal that make the region of torsional phase space that is most crucial for symmetrization poorly accessible. Consequently, the proton-transfer potential remains asymmetric though flat at the base, even at room temperature in the solid.

Hydrogen adsorbed in a metal organic framework-5: coupled translation-rotation eigenstates from quantum five-dimensional calculations.

We report rigorous quantum five-dimensional (5D) calculations of the coupled translation-rotation (T-R) eigenstates of a H(2) molecule adsorbed in metal organic framework-5 (MOF-5), a prototypical nanoporous material, which was treated as rigid. The anisotropic interactions between H(2) and MOF-5 were represented by the analytical 5D intermolecular potential energy surface (PES) used previously in the simulations of the thermodynamics of hydrogen sorption in this system [Belof et al., J. Phys. Chem. C 113, 9316 (2009)]. The global and local minima on this 5D PES correspond to all of the known binding sites of H(2) in MOF-5, three of which, α-, ß-, and γ-sites are located on the inorganic cluster node of the framework, while two of them, the δ- and ε-sites, are on the phenylene link. In addition, 2D rotational PESs were calculated ab initio for each of these binding sites, keeping the center of mass of H(2) fixed at the respective equilibrium geometries; purely rotational energy levels of H(2) on these 2D PESs were computed by means of quantum 2D calculations. On the 5D PES, the three adjacent γ-sites lie just 1.1 meV above the minimum-energy α-site, and are separated from it by a very low barrier. These features allow extensive wave function delocalization of even the lowest translationally excited T-R eigenstates over the α- and γ-sites, presenting significant challenges for both the quantum bound-state calculations and the analysis of the results. Detailed comparison is made with the available experimental data.

Investigating H2 Adsorption in Isostructural Metal-Organic Frameworks M-CUK-1 (M = Co and Mg) through Experimental and Theoretical Studies.

A combined experimental and theoretical study of H2 adsorption was carried out in Co-CUK-1 and Mg-CUK-1, two isostructural metal-organic frameworks (MOFs) that consist of M2+ ions (M = Co and Mg) coordinated to pyridine-2,4-dicarboxylate (pdc2-) and OH- ligands. These MOFs possess saturated metal centers in distorted octahedral environments and narrow pore sizes and display high chemical and thermal stability. Previous experimental studies revealed that Co-CUK-1 exhibits a H2 uptake of 183 cm3 g-1 at 77 K/1.0 atm [ Angew. Chem., Int. Ed. 2007, 46, 272-275, DOI: 10.1002/anie.200601627], while that for Mg-CUK-1 under the same conditions is 240 cm3 g-1 on the basis of the experimental measurements carried out herein. The theoretical H2 adsorption isotherms are in close agreement with the corresponding experimental measurements for simulations using electrostatic and polarizable potentials of the adsorbate. Through simulated annealing calculations, it was found that the primary binding site for H2 in both isostructural analogues is localized proximal to the center of the aromatic rings belonging to the pdc2- linkers. Inelastic neutron scattering (INS) spectroscopic studies of H2 adsorbed in both MOFs revealed a rotational tunnelling transition occurring at around 8 meV in the corresponding spectra; this peak represents H2 adsorbed at the primary binding site. Two-dimensional quantum rotation calculations for H2 localized at the primary and secondary binding sites in both MOFs yielded rotational energy levels that are in agreement with the transitions observed in the INS spectra. Even though both M-CUK-1 analogues possess different metal ions, they exhibit similar electrostatic environments, modeled structures at H2 saturation, and rotational potentials for H2 adsorbed at the most favorable adsorption site. Overall, this study demonstrates how important molecular-level details of the H2 adsorption mechanism inside MOF micropores can be derived from a combination of experimental measurements and theoretical calculations using two stable and isostructural MOFs with saturated metal centers and small pore windows as model systems.

Breathing and twisting: an investigation of framework deformation and guest packing in single crystals of a microporous vanadium benzenedicarboxylate.

The structural details of the compounds vanadium benzenedicarboxylate VO(bdc)·Guest, where the Guests are the absorbed six-ring molecules: benzene, 1,4-cyclohexadiene, 1,3-cyclohexadiene, cyclohexene and cyclohexane, have been determined from single crystal X-ray data. All of the six-ring guest molecules show a high degree of ordering inside the channels of VO(bdc). The interactions between the guests and the host framework are dominated by van der Waals bonding. The six-ring molecules are all packed in two columns in the channels, either in herringbone or close to parallel patterns. The packing changes the space group symmetry of VO(bdc) from Pnma to the noncentrosymmetric space group P2(1)2(1)2(1). The VO(bdc) framework deforms to closely adapt to the shape and thickness changes of the double columns of the guest molecules. In addition to the well studied breathing deformation, a twisting deformation mechanism that involves a cooperative rotation of the octahedral chains accompanied by bending of the bdc ligand is apparent in the detailed structural data. More quantitative information on the remarkable flexibility of the VO(bdc) framework was obtained from ab initio calculations.

Hydrogen storage in a highly interpenetrated and partially fluorinated metal-organic framework.

A partially fluorinated metal-organic framework, Zn(bpe)(tftpa)·cyclohexanone [bpe = 1,2-bis(4-pyridyl)ethane; tftpa = tetrafluoroterephthalate], has been synthesized, and its H2 storage properties are reported. The structure is highly interpenetrated yet contains templating cyclohexanone molecules, which can be easily removed to give a porous material with fluorine atoms exposed to the pore surface. The material adsorbs 1.04 wt % H2 at 77 K and 1 atm with an adsorption enthalpy (Qst) of 6.2 kJ/mol, which represents a slight enhancement in the binding strength due to the presence of fluorine atoms over comparable metal-organic frameworks, which bind through purely physisorptive methods.

Fluxionality of hydrogen ligands in Fe(H)2(H2)(PEtPh2)3.

Extensive computational investigations along with additional quasielastic neutron scattering data were used to obtain a consistent picture of the extensive fluxionality of hydride and dihydrogen ligands in Fe(H)(2)(H(2))(PEtPh(2))(3) over a wide range of temperatures from 1.5 to 320 K. We were able to identify three different regimes in the dynamical processes based on activation energies obtained from line spectral broadening. The rotational tunneling lines (coherent exchange of the two hydrogens of the H(2) ligand) are broadened with increasing temperature by incoherent exchange up to about 80 K at which point they merge into a quasielastic spectrum from 100 K to about 225 K. The effective activation energies for the two regions are 0.14 and 0.1 kcal mol(-1), respectively. A third dynamical process with a higher activation energy of 0.44 kcal mol(-1) dominates above 225 K, which we attribute to a quantum dynamical exchange of dihydrogen and hydride ligands. Our detailed density functional theory (DFT) structural calculations involving the three functionals (B3LYP, TPSS, and wB97XD) provide a good account of the experimental structure and rotational barriers when only the hydrogen ligands are relaxed. Full relaxation of the "gas-phase" molecule, however, appears to occur to a greater degree than what is possible in the crystal structure. The classical dihydrogen-hydride exchange path involves a cis-dihydrogen and tetrahydride structure with energies of 6.49 and 7.38 kcal mol(-1), respectively. Experimental observation of this process with much lower energies would seem to suggest involvement of translational tunneling in addition to the rotational tunneling. Dynamics of this type may be presumed to be important in hydrogen spillover from metal particles, and therefore need to be elucidated in an effort to utilize this phenomenon.

The very short hydrogen bond in the pyridine N-oxide - trichloroacetic Acid complex: an inelastic neutron scattering and computational study.

We have investigated the dynamics of the very short hydrogen bond (RO...O = 2.430 Å) of the pyridine N-oxide trichloroacetic acid complex in the solid state by combining vibrational spectroscopy using inelastic neutron scattering with extensive computational studies and analysis of the vibrational spectra. The Density Functional Theory (DFT) computational models used ranged from the isolated gas phase cluster to three approaches with periodic boundary conditions, namely CRYSTAL, CPMD and VASP, all of which, however calculate frequencies in the harmonic approximation. While all but the gas phase calculation yield structural parameters for the hydrogen bond in reasonable agreement with experiment, only the periodic VASP and CPMD approaches resulted in INS spectra (calculated with the program a-climax) that adequately reproduced some of the key features of the experimental spectrum related to the in-plane and out-of-plane bending modes of the H-bond. No clear indication was found either in experiment or computational studies for OH stretching. More sophisticated and time-consuming calculations are therefore indicated to elaborate on the hydrogen bond dynamics including molecular dynamics simulations or the use of quantum dynamics on multidimensional potential energy surfaces.