Hydrogen molecule in the small dodecahedral cage of a clathrate hydrate: quantum five-dimensional calculations of the coupled translation-rotation eigenstates

We report quantum five-dimensional (5D) calculations of the energy levels and wave functions of the hydrogen molecule, para-H2 and ortho-H2, confined inside the small dodecahedral (H2O)20 cage of the sII clathrate hydrate. All three translational and the two rotational degrees of freedom of H2 are included explicitly, as fully coupled, while the cage is treated as rigid. The 5D potential energy surface (PES) of the H2-cage system is pairwise additive, based on the high-quality ab initio 5D (rigid monomer) PES for the H2-H2O complex. The bound state calculations involve no dynamical approximations and provide an accurate picture of the quantum 5D translation-rotation dynamics of H2 inside the cage. The energy levels are assigned with translational (Cartesian) and rotational quantum numbers, based on calculated root-mean-square displacements and probability density plots. The translational modes exhibit negative anharmonicity. It is found that j is a good rotational quantum number, while the threefold degeneracy of the j = 1 level is lifted completely. There is considerable translation-rotation coupling, particularly for excited translational states.     

H2, HD, and D2 inside C60: coupled translation-rotation eigenstates of the endohedral molecules from quantum five-dimensional calculations

We have performed rigorous quantum five-dimensional (5D) calculations of the translation-rotation (T-R) energy levels and wave functions of H(2), HD, and D(2) inside C(60). This work is an extension of our earlier investigation of the quantum T-R dynamics of H(2)@C(60) [M. Xu et al., J. Chem. Phys. 128, 011101 (2008)] and uses the same computational methodology. Two 5D intermolecular potential energy surfaces (PESs) were employed, differing considerably in their well depths and the degree of confinement of the hydrogen molecule. Our calculations revealed pronounced sensitivity of the endohedral T-R dynamics to the differences in the interaction potentials, and to the large variations in the masses and the rotational constants of H(2), HD, and D(2). The T-R levels vary significantly in their energies and ordering on the two PESs, as well as from one isotopomer to another. Nevertheless, they all display the same distinctive patterns of degeneracies, which can be qualitatively understood and assigned in terms the model which combines the isotropic three-dimensional harmonic oscillator, the rigid rotor, and the coupling between the orbital and the rotational angular momenta of H(2)/HD/D(2). The quantum number j associated with the rotation of H(2), HD, and D(2) was found to be a good quantum number for H(2) and D(2) on both PESs, while most of the T-R levels of HD exhibit strong mixing of two or more rotational basis functions with different j values.     

Hydrogen adsorption strength and sites in the metal organic framework MOF5: Comparing experiment and model calculations

Hydrogen adsorption in porous, high surface area, and stable metal organic frameworks (MOF’s) appears a novel route towards hydrogen storage materials [N.L. Rosi, J. Eckert, M. Eddaoudi, D.T. Vodak, J. Kim, M. O’Keeffe, O.M. Yaghi, Science 300 (2003) 1127; J.L.C. Rowsell, A.R. Millward, K. Sung Park, O.M. Yaghi, J. Am. Chem. Soc. 126 (2004) 5666; G. Ferey, M. Latroche, C. Serre, F. Millange, T. Loiseau, A. Percheron-Guegan, Chem. Commun. (2003) 2976; T. Loiseau, C. Serre, C. Huguenard, G. Fink, F. Taulelle, M. Henry, T. Bataille, G. Férey, Chem. Eur. J. 10 (2004) 1373]. A prerequisite for such materials is sufficient adsorption interaction strength for hydrogen adsorbed on the adsorption sites of the material because this facilitates successful operation under moderate temperature and pressure conditions. Here we report detailed information on the geometry of the hydrogen adsorption sites, based on the analysis of inelastic neutron spectroscopy (INS). The adsorption energies for the metal organic framework MOF5 equal about 800 K for part of the different sites, which is significantly higher than for nanoporous carbon materials (550 K) [H.G. Schimmel, G.J. Kearley, M.G. Nijkamp, C.T. Visser, K.P. de Jong, F.M. Mulder, Chem. Eur. J. 9 (2003) 4764], and is in agreement with what is found in first principles calculations [T. Sagara, J. Klassen, E. Ganz, J. Chem. Phys. 121 (2004) 12543; F.M. Mulder, T.J. Dingemans, M. Wagemaker, G.J. Kearley, Chem. Phys. 317 (2005) 113]. Assignments of the INS spectra is realized using comparison with independently published model calculations [F.M. Mulder, T.J. Dingemans, M. Wagemaker, G.J. Kearley, Chem. Phys. 317 (2005) 113] and structural data [T. Yildirim, M.R. Hartman, Phys. Rev. Lett. 95 (2005) 215504].     

Hydrogen molecule in the small dodecahedral cage of a clathrate hydrate: quantum translation-rotation dynamics at higher excitation energies

Higher-lying five-dimensional translation-rotation (T-R) eigenstates of a single p-H2 and o-D2 molecule confined inside the small dodecahedral (512) cage of the structure II clathrate hydrate are calculated rigorously, as fully coupled, with the cage assumed to be rigid. The calculations cover the excitation energies up to and beyond the j=2 rotational level of the free molecule, 356 cm(-1) for H2 and 179 cm(-1) for D2. It is found that j is a good quantum number for all the T-R states of p-H2, j=0 and j=2, considered. The same is not true for o-D2, where a number of T-R states in the neighborhood of the j=2 level show significant mixing of j=0 and j=2 rotational basis functions. The 5-fold degeneracy of the j=2 level of p-H2 is lifted completely due to the anisotropy of the cage environment, as is the 3-fold degeneracy of the j=1 level of o-H2 studied by us previously. Pure translational mode excitations with up to four quanta display negative anharmonicity, which was observed earlier for the translational fundamentals and their first overtones. The issues of assigning the combination states of p-H2 with excitations of two or all three translational modes, and of the strength of the mode coupling as a function of the excitation energy, are studied carefully for a range of quantum numbers. The average T-R energy of the encapsulated p-H2 is calculated as a function of temperature from 0 to 150 K.     

Regularity of low-lying quantum eigenstates in a classically mixing system

Low-lying quantum energy eigenstates of the classically mixing stadium system are shown to be highly regular and to be well described by an adiabatic separable Hamiltonian. The results clearly demonstrate quantum regularity in an energy regime of extreme classical chaos.     

Accuracy of gates in a quantum computer based on vibrational eigenstates

A model is developed to study the properties of a quantum computer that uses vibrational eigenstates of molecules to implement the quantum information bits and shaped laser pulses to apply the quantum logic gates. Particular emphasis of this study is on understanding how the different factors, such as properties of the molecule and of the pulse, can be used to affect the accuracy of quantum gates in such a system. Optimal control theory and numerical time-propagation of vibrational wave packets are employed to obtain the shaped pulses for the gates NOT and Hadamard transform. The effects of the anharmonicity parameter of the molecule, the target time of the pulse and of the penalty function are investigated. Influence of all these parameters on the accuracy of qubit transformations is observed and explained. It is shown that when all these parameters are carefully chosen the accuracy of quantum gates reaches 99.9%.     

Hydrogen physisorption on the organic linker in metal organic frameworks: ab initio computational study

Research for materials offering efficient hydrogen storage and transport has recently received increased attention. Metal organic frameworks (MOFs) provide one promising group of materials where several recent advances were reported in this direction. In this computational study ab initio methods are employed to study the physisorption of hydrogen on conjugated systems. These systems are used as models for the organic linker within MOFs. Here, we focus on the adsorption sites related to the organic linker with special attention to the edge site, which was only recently reported to exist as the weakest adsorbing site in MOFs. We also investigate chemically modified models of the organic connector that result in enforcing this adsorption site. This may be crucial for improving the uptake properties of these materials to the goal defined by DOE for efficient hydrogen transport materials.     

Dynamics of photochemical reactions: Simulation by quantum calculations for transition metal hydrides

The photodissociation dynamics of some organometallic molecules in the lowest repulsive electronically states are reported for the following concurrent primary reactions: (i) the homolysis of a metal–hydrogen bond vs. the heterolytic loss of a carbonyl ligand in HCo(CO)₄; (ii) the photoinduced elimination of molecular hydrogen vs. the loss of a carbonyl ligand in H₂Fe(CO)₄; and (iii) the photoinduced elimination of molecular hydrogen vs. the loss of a mesithylene ligand in H₂Os(CO)Mes (Mes = C₆H₃(CH₃))₃. The dynamics are simulated quantum mechanically using a time-dependent wavepacket propagation technique on potential energy surfaces obtained from CASSCF /CCI calculations for HCo(CO)₄ and H₂Fe(CO)₄ and from SCF -INO /MRCI calculations for H₂Os(CO)Mes. This approach gives a rather detailed view of some important elementary processes that contribute to the photochemistry of these complexes. The nature of the photoactive excited states is determined without ambiguity, as well as the time scales, the branching ratio of the different primary dissociation pathways, and some features of the absorption spectra. © 1994 John Wiley & Sons, Inc.     

Hydrogen absorption in transition metal silicides: La3Pd5Si-hydrogen system

Pressure-composition isotherm measurements show that the ternary lanthanum palladium silicide phase La3Pd5Si absorbs reversibly up to 5 hydrogen atoms per formula unit at 550 K and 14 bar hydrogen pressure. In-situ synchrotron and neutron powder diffraction reveals three phases, an alpha-phase having the limiting composition La3Pd5SiD approximately 1.6 at low deuterium pressure (at up to 9.5 bar D2 and 550 K), a beta-phase La3Pd5SiD approximately 2.30-4 at intermediate deuterium pressure (<9.5 bar D2 and 550 K), and a relatively unstable gamma-phase La3Pd5SiD approximately 5 at high deuterium pressure (obtained at 75 bar D2 and 293 K). While the alpha and beta phases retain the symmetry of the H-free La3Pd5Si (space group Imma), the gamma-phase undergoes a symmetry lowering (a(gamma) approximately a(beta), b(gamma) approximately 3b(beta) and c(gamma) approximately c(beta), V(gamma) approximately 3V(beta), space group Pmnb). The structure of the alpha-phase contains isolated [Pd-D-Pd] fragments, which are joined into polymeric (-Pd-D-Pd-)n zig-zag chains in the beta-phase. In the gamma-phase some D sites depopulate, while new D sites are occupied, thus leading to a partial interruption of the zig-zag chains and the formation of isolated [D-Pd-D-Pd] and [D-Pd-D-Pd-D] fragments. This unexpected behavior can be attributed to the onset of repulsive Si-D and D-D interactions (Si-D > 3.0 A, D-D > 2.1 A) that divide the structure into Si-poor slabs that absorb hydrogen and Si-rich slabs that do not. The competition between silicon and deuterium which act as a transition metal ligand is further underlined by the fact that Pd atoms having one Si ligand are capable of forming Pd-D bonds, whereas Pd atoms having two Si ligands are not.     

Adsorption of organic probes on silica through Lewis interactions: a comparison of experimental results and quantum chemical calculations

The adsorption of organic probe molecules on a partly dehydroxylated silica (SiO(2)) surface has been studied in a non-aquatic and non-polar environment. These results were compared to, verified and explained by quantum chemical calculations on the same systems. Since the systems are water free and since the non-polar solvent cyclohexane is used in the experiments, the quantum chemical calculations are well comparable to the experimental results without any additional terms. The characterized surface was found to contain both Lewis acid and Lewis base sites and a good agreement between the experimentally determined and the calculated data was found.     

Vibrations of a single adsorbed organic molecule: anharmonicity matters!

Vibrational spectroscopy is a powerful tool to identify molecules and to characterise their chemical state. Inelastic electron tunnelling spectroscopy (IETS) combined with scanning tunnelling microscopy (STM) allows the application of vibrational analysis to a single molecule. Up to now, IETS was restricted to small species due to the complexity of vibration spectra for larger molecules. We extend the horizon of IETS for both experiment and theory by measuring the STM-IETS spectra of mercaptopyridine adsorbed on the (111) surface of gold and comparing it to theoretical spectra. Such complex spectra with more than 20 lines can be reliably determined and computed leading to completely new insights. Experimentally, the vibrational spectra exhibit a dependence on the specific adsorption site of the molecules. Theoretically, this dependence is only accessible if anharmonic contributions to the interaction potentials are included. These joint experimental and theoretical advances open new perspectives for structure determination of organic adlayers.     

Vibrationally excited states of DC5N: Millimeter-wave spectroscopy and coupled cluster calculations

The rotational spectrum of DC₅N has been investigated in the millimeter-wave region for 16 vibrationally excited states which approximately lie below 760 cm⁻¹, namely (v₆ v₇ v₈ v₉ v₁₀ v₁₁)=(000001), (000002), (000003), (000005), (000010), (000020), (000100) (001000), (010000), (100000), (000011), (000101), (001001), (010001), (001010), and (010010). Gas-phase copyrolysis of fully deuterated pyridine and phosphorus trichloride was used to produce the semi-stable DC₅N molecule. In addition to the usual l-type resonances, several vibrational interactions have been taken into account to fit properly the measured transition frequencies. The most important perturbations are caused by the cubic anharmonic interactions which mix the v₆ stretching state with the 2v₁₀ overtone and the v₈+v₁₁ and v₇+v₁₁ bending combination states. The analysis of the spectra was facilitated by theoretical predictions from CCSD(T) calculations with the cc-pVQZ basis.     

Calculating initial-state-selected reaction probabilities from thermal flux eigenstates: a transition-state-based approach

An approach for the calculation of initial-state-selected reaction probabilities utilizing a transition-state view and the multiconfigurational time-dependent Hartree approach is presented. Using flux correlation functions, wave packets located in the transition-state region are constructed and propagated into the asymptotic region to obtain initial-state-selected reaction probabilities. A complete set of reaction probabilities is obtained from a single set of thermal flux eigenstates. Concepts previously applied with success to the calculation of k(T) or N(E) are transferred to the calculation of state-selected probabilities. The benchmark H+H(2) (J=0) reaction on the LSTH potential-energy surface is used to test the reliability of this approach.     

The structure of chlorophyll a-water complexes: insights from quantum chemistry calculations

Computations show that chlorophyll a is able to coordinate a maximum of two water molecules in hydrophobic media that form a bridge between the Mg atom and the methyl ester carbonyl group.     

Massively parallel direct SCF calculations on large metal clusters: Ni5-Ni481

Summary The convergence of the cluster model with respect to excitation energies, ionization potentials and hydrogen chemisorption energy in the four-fold hollow site of the Ni(100) surface is studied for a sequence of cluster models from Ni₅ up to Ni₁₈₁. For the largest, Ni₄₈₁, cluster studied, only the structure of the occupied levels for one state is obtained. The concept of bond-preparation is found to be essential for the evaluation of chemisorption energies also for clusters with more than 100 atoms. The cluster excitation energies show a slow decrease such that even for Ni₁₈₁ the step between the lower excited states is still 0.1–0.2 eV. The effect ofp-functions on surrounding cluster atoms is found to be 3–4 kcal/mol independent of cluster-size. The direct SCF program DISCO was parallelized using the TCGMSG toolkit in order to perform the calculations. The easy strategy utilized is analysed and exhaustive timings on the Alliant Campus/800 MPP system with 200 CPU's are presented.     

Dynamic structure of organic compounds in solution according to NMR data and quantum chemical calculations: II. Styrene

The dynamic structure of styrene has been studied with the goal of obtaining detailed information on the internal rotation parameters. A potential energy surface has been constructed for the rotation of the vinyl group about the single bond in terms of the second-order Møller–Plesset perturbation theory with aug-cc-pvtz basis functions, and conformational dependences of ⁿ J _HH have been calculated at the FPT DFT (B3LYP) level of theory with basis functions of the same type. The vibration-averaged coupling constants have been compared with the experimental values reliably determined in this work. A high efficiency of the proposed dynamic model for structural studies of organic molecules with ultrafast internal rotation dynamics has been demonstrated.     

Dynamic structure of organic compounds in solution according to NMR data and quantum mechanical calculations: I. Soman

Dynamic structure of Soman diastereoisomers has been studied with the goal of obtaining accurate information to simulate molecular mechanisms of its action on living systems. The potential energy surface for internal rotation about the single P–O and O–C bonds has been constructed in terms of the Møller–Plesset second-order perturbation theory using 6-311G(d,p) basis set. The relative contributions of different conformers have been estimated by solving the vibrational problem according to the large-amplitude vibration model. The conformational dependences of the ⁴J_CF and ³J_CP coupling constants for the S,S and S,R diastereoisomers of Soman have been calculated at the FPT DFT B3LYP/6-311++G(2df,2p) level of theory. The calculated vibrationally averaged coupling constants have been compared with the available experimental data to determine the structure of the most toxic Soman stereoisomer.     

Electron-attachment resonances of glycine zwitterions from quantum scattering calculations: modeling macrosolvation effects

A computational study of the quantum dynamics for low-energy electrons scattered by the isolated zwitterionic species of the glycine molecule is carried out using a model interaction potential described in the main text. The macroscopic effects of water solvation on the target molecule in the electron scattering problem are described through a continuum polarizable model (CPCM) which modifies the target molecular structure. In such a way, realistic molecular orbitals depicting the glycine zwitterion in solution are used to model the electron-molecule interaction. The results of the calculations indicate the presence of five different transient negative ions (TNIs) formed at energies from the threshold and up to about 6 eV. Although no nuclear motion was explicitly considered in the ensuing decay processes, the analysis of the nodal structures and density distributions for the resonant excess electron wavefunctions over the molecular space suggests possible anionic fragmentations that produce (Gly-H)-, H-, -CO2-, and -NH3. The likely consequences of such releases into the medium are briefly discussed.