Volume 131, Issue 14, 14 October 2009
Index of content:
chemical-shift tensors of organic single crystals with plane waves" title="Intermolecular shielding contributions studied by modeling the chemical-shift tensors of organic single crystals with plane waves" />
In order to predict accurately the chemical shift of NMR-active nuclei in solid phase systems, magnetic shielding calculations must be capable of considering the complete lattice structure. Here we assess the accuracy of the density functional theory gauge-including projector augmented wave method, which uses pseudopotentials to approximate the nodal structure of the core electrons, to determine the magnetic properties of crystals by predicting the full chemical-shift tensors of all nuclides in 14 organic single crystals from which experimental tensors have previously been reported. Plane-wave methods use periodic boundary conditions to incorporate the lattice structure, providing a substantial improvement for modeling the chemical shifts in hydrogen-bonded systems. Principal tensor components can now be predicted to an accuracy that approaches the typical experimental uncertainty. Moreover, methods that include the full solid-phase structure enable geometry optimizations to be performed on the input structures prior to calculation of the shielding. Improvement after optimization is noted here even when neutron diffraction data are used for determining the initial structures. After geometry optimization, the isotropic shift can be predicted to within 1 ppm.
- Theoretical Methods and Algorithms
131(2009); http://dx.doi.org/10.1063/1.3243863View Description Hide Description
A simple computational technique is introduced for generating atomic electron densities using an iterated stockholder procedure. It is proven that the procedure is always convergent and leads to unique atomic densities. The resulting atomic densities are shown to have chemically intuitive and reasonable charges, and the method is used to analyze the hydrogen bonding in the minimum energy configuration of the water dimer and charge transfer in the borazane molecule.
Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach131(2009); http://dx.doi.org/10.1063/1.3242274View Description Hide Description
A model nanometer-sized hydrophobic receptor-ligand system in aqueous solution is studied by the recently developed level-set variational implicit solvent model (VISM). This approach is compared to all-atom computer simulations. The simulations reveal complex hydration effects within the (concave) receptor pocket, sensitive to the distance of the (convex) approaching ligand. The ligand induces and controls an intermittent switching between dry and wet states of the hosting pocket, which determines the range and magnitude of the pocket-ligand attraction. In the level-set VISM, a geometric free-energy functional of all possible solute-solvent interfaces coupled to the local dispersion potential is minimized numerically. This approach captures the distinct metastable states that correspond to topologically different solute-solvent interfaces, and thereby reproduces the bimodal hydration behavior observed in the all-atom simulation. Geometrical singularities formed during the interface relaxation are found to contribute significantly to the energy barrier between different metastable states. While the hydration phenomena can thus be explained by capillary effects, the explicit inclusion of dispersion and curvature corrections seems to be essential for a quantitative description of hydrophobically confined systems on nanoscales. This study may shed more light onto the tight connection between geometric and energetic aspects of biomolecular hydration and may represent a valuable step toward the proper interpretation of experimental receptor-ligand binding rates.
The quantum normal form approach to reactive scattering: The cumulative reaction probability for collinear exchange reactions131(2009); http://dx.doi.org/10.1063/1.3245402View Description Hide Description
The quantum normal form approach to quantum transition state theory is used to compute the cumulative reaction probability for collinear exchange reactions. It is shown that for heavy-atom systems such as the nitrogen-exchange reaction, the quantum normal form approach gives excellent results and has major computational benefits over full reactive scattering approaches. For light atom systems such as the hydrogen-exchange reaction however, the quantum normal approach is shown to give only poor results. This failure is attributed to the importance of tunneling trajectories in light atom reactions that are not captured by the quantum normal form as indicated by the only very slow convergence of the quantum normal form for such systems.
Benchmarking density-functional-theory calculations of rotational tensors and magnetizabilities using accurate coupled-cluster calculations131(2009); http://dx.doi.org/10.1063/1.3242081View Description Hide Description
An accurate set of benchmark rotational tensors and magnetizabilities are calculated using coupled-cluster singles-doubles (CCSD) theory and coupled-cluster single-doubles-perturbative-triples [CCSD(T)] theory, in a variety of basis sets consisting of (rotational) London atomic orbitals. The accuracy of the results obtained is established for the rotational tensors by careful comparison with experimental data, taking into account zero-point vibrational corrections. After an analysis of the basis sets employed, extrapolation techniques are used to provide estimates of the basis-set-limit quantities, thereby establishing an accurate benchmark data set. The utility of the data set is demonstrated by examining a wide variety of density functionals for the calculation of these properties. None of the density-functional methods are competitive with the CCSD or CCSD(T) methods. The need for a careful consideration of vibrational effects is clearly illustrated. Finally, the pure coupled-cluster results are compared with the results of density-functional calculations constrained to give the same electronic density. The importance of current dependence in exchange–correlation functionals is discussed in light of this comparison.
131(2009); http://dx.doi.org/10.1063/1.3243080View Description Hide Description
To extract mechanistic information of activated processes, we propose to decompose potential energy and free energy differences between configurations into contributions from individual atoms, functional groups, or residues. Decomposition is achieved by calculating the mechanical work associated with the displacements and forces of each atom along a path that connects two states, i.e., following the flow of work. Specifically, we focus on decomposing energy or free energy differences along representative pathways such as minimum energy paths (MEPs) and minimum free energy paths (MFEPs), and a numerical metric is developed to quantify the required accuracy of the reaction path. A statistical mechanical analysis of energy decomposition is also presented to illustrate the generality of this approach. Decomposition along MEP and MFEP is demonstrated on two test cases to illustrate the ability to derive quantitative mechanistic information for different types of activated processes. First, the MEP of alanine dipeptideisomerization in vacuum and the MFEP of isomerization in explicit water is studied. Our analysis shows that carbonyl oxygen and amide hydrogen contribute to most of the energetic cost for isomerization and that explicit water solvation modulates the free energy landscape primarily through hydrogen bonding with these atoms. The second test case concerns the formation of tetrahedral intermediate during a transesterification reaction. Decomposition analysis shows that water molecules not only have strong stabilization effects on the tetrahedral intermediate but also constitute a sizable potential energy barrier due to their significant structural rearrangement during the reaction. We expect that the proposed method can be generally applied to develop mechanistic understanding of catalytic and biocatalytic processes and provide useful insight for strategies of molecular engineering.
Density matrix treatment of combined instantaneous and delayed dissipation for an electronically excited adsorbate on a solid surface131(2009); http://dx.doi.org/10.1063/1.3246168View Description Hide Description
The interaction of an excited adsorbate with a medium undergoing electronic and vibrational transitions leads to fast dissipation due to electronic energy relaxation and slow (or delayed) dissipation from vibrational energy relaxation. A theoretical and computational treatment of these phenomena has been done in terms of a reduced density matrix satisfying a generalized Liouville–von Neumann equation, with instantaneous dissipation constructed from state-to-state transition rates, and delayed dissipation given by a memory term derived from the time-correlation function (TCF) of atomic displacements in the medium. Two representative applications are presented here, where electronic excitation may enhance vibrational relaxation of an adsorbate. They involve femtosecond excitation of (a) a CO molecule adsorbed on the Cu(001) metal surface and (b) a metal cluster on a semiconductor surface, , both electronically excited by visible light and undergoing electron transfer and dissipative dynamics by electronic and vibrational relaxations. Models have been parametrized in both cases from electronic structure calculations and known TCFs for the medium, which are slowly decaying in case (a) and fast decaying in case (b). This requires different numerical procedures in the solution of the integrodifferential equations for the reduced density matrix, which have been solved with an extension of the Runge–Kutta algorithm. Results for the populations of vibronic states versus time show that they oscillate due to vibrational coupling through dissipative interaction with the substrate and show quantum coherence. The total population of electronic states is, however, little affected by vibrational motions. Vibrational relaxation is important only at very long times to establish thermal equilibrium.
131(2009); http://dx.doi.org/10.1063/1.3244562View Description Hide Description
In this work a replica exchange Monte Carlo scheme which considers an extended isobaric-isothermal ensemble with respect to pressure is applied to study hard spheres (HSs). The idea behind the proposal is expanding volume instead of increasing temperature to let crowded systems characterized by dominant repulsive interactions to unblock, and so, to produce sampling from disjoint configurations. The method produces, in a single parallel run, the complete HS equation of state. Thus, the first order fluid-solid transition is captured. The obtained results well agree with previous calculations. This approach seems particularly useful to treat purely entropy-driven systems such as hard body and nonadditive hard mixtures, where temperature plays a trivial role.
An improved long-range corrected hybrid functional with vanishing Hartree–Fock exchange at zero interelectronic distance (LC2gau-BOP)131(2009); http://dx.doi.org/10.1063/1.3243819View Description Hide Description
We present a new long-range corrected (LC) density functional theory(DFT) scheme, named “LC2gau,” which combines the best features of our two recently developed hybrid functionals, “LCgau” [J.-W. Song et al., J. Chem. Phys.127, 154109 (2007)] and “LCgau-core” [J.-W. Song et al., J. Chem. Phys.129, 184113 (2008)]. By introducing a flexible mixing of Hartree–Fock and DFT exchange in the LCgau scheme, we showed that a DFT functional could simultaneously achieve high accuracy in the reproduction of thermochemicalproperties, molecular geometries, as well as charge transfer and valence-Rydberg excitation energies. With an alternative mixing of short-range exchange, LCgau-core can reproduce core excitations with high accuracy, especially in the C, N, and O atoms, but at the expense of slightly higher atomization energy errors. We now show that LC2gau can simultaneously perform well for all types of excitations, as well as thermochemistry. In contrast to the previously proposed LC functionals, a notable feature is the inclusion of 100% DFT exchange as the interelectronic distance vanishes, showing that pure DFT approximations can be successfully used at short range, and the importance of including an appropriate correction in the midrange. This is achieved using two Gaussian functions in combination with the error function to describe the exchange partitioning. We rationalize the success of LC2gau by demonstrating a near-linear behavior of the total energies of the C atom as a function of the fractional number of electrons, both in the valence and core regions, which indicates an alleviation of significant self-interaction errors observed with other functionals.
- Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry
The molecular dissociation of formaldehyde at medium photoexcitation energies: A quantum chemistry and direct quantum dynamics study131(2009); http://dx.doi.org/10.1063/1.3242082View Description Hide Description
The mechanisms of radiationless decay involved in the photodissociation of formaldehyde into and CO have been investigated using complete active space self-consistent field (CASSCF) calculations and direct dynamics variational multiconfiguration Gaussian (DD-vMCG) quantum dynamics in the , , and states. A commonly accepted scheme involves Fermi Golden Rule internal conversion from followed by dissociation of vibrationally hot in . We recently proposed a novel mechanism [M. Araujo et al., J. Phys. Chem. A112, 7489 (2008)] whereby internal conversion and dissociation take place in concert through a seam of conical intersection between and after the system has passed through an transition barrier. The relevance of this mechanism depends on the efficiency of tunneling in . At lower energy, an alternative scheme to internal conversion involves intersystem crossing via to regenerate the reactant before the barrier to dissociation. We propose here a previously unidentified mechanism leading directly to and CO products via . This channel opens at medium energies, near or above the barrier to dissociation and still lower than the barrier, thus making a possible shortcut to molecular dissociation.
131(2009); http://dx.doi.org/10.1063/1.3242294View Description Hide Description
In a recent mass spectrometry/photoelectron spectroscopy study on the reactions between and water, Jarrold and co-workers [J. Chem. Phys.130, 124314 (2009)] observed interesting differences in the reactivity of the different cluster ions. Particularly noteworthy is the observation that the only product with the incorporation of hydrogens is a single peak corresponding to . As reactions between metal oxide clusters and small molecules such as water have high potential for catalytic applications, we carried out a careful study to obtain a mechanistic understanding of this observed reactivity. Using electronic structure calculations, we identified and characterized multiple modes of reactivity between unsaturated tungsten oxide clusters [ ] and water. By calculating the free energy corrected reaction profiles, our results provide an explanation for the formation of . We propose a mechanism in which water reacts with a metal oxide cluster and eliminates . The results from our calculations show that this is nearly a barrierless process for all suboxide clusters with the exception of .
131(2009); http://dx.doi.org/10.1063/1.3245859View Description Hide Description
Photoelectron spectra of cold (10 K) size selected water cluster anions and have been measured in the size range . A new isomer with a higher binding energy than the so-called isomer I has been identified, which appears in the size range and for becomes dominant at . Magic numbers observed in the mass spectra of the cluster anions provide evidence that this new isomer class consists of clusters with an internal electron.
Probing royal demolition explosive (1,3,5-trinitro-1,3,5-triazocyclohexane) by low-energy electrons: Strong dissociative electron attachment near 0 eV131(2009); http://dx.doi.org/10.1063/1.3230116View Description Hide Description
Low energy electron attachment to gas phase royal demolition explosive (RDX) (and RDX-A3) has been performed by means of a crossed electron-molecular beam experiment in an electron energy range from 0 to 14 eV with an energy resolution of . The most intense signals are observed at 102 and 46 amu and assigned to and , respectively. Anion efficiency curves of 16 anions have been measured. Product ions are observed mainly in the low energy region, near 0 eV arising from surprisingly complex reactions associated with multiple bond cleavages and structural and electronic rearrangement. The remarkable instability of RDX to electron attachment with virtually thermal electrons reflects the highly explosive nature of this compound. The present results are compared to other explosive aromatic nitrocompounds studied in our laboratory recently.
131(2009); http://dx.doi.org/10.1063/1.3245401View Description Hide Description
Quantum optimal control calculations have been carried out for isotope-selective vibrational excitations of the cesium iodide (CsI) molecule on the ground-state potential energy curve. Considering a gaseous isotopic mixture of and , the initial state is set to the condition that both and are in the vibrational ground level and the target state is that is in the level while in the first-excited level . We find that, using the density-matrix formalism, perfect isotope-selective excitations for multilevel systems including more than ten lowest vibrational states can be completed in much shorter time scales than those for two-level systems. It is likely that this multilevel effect comes from the large isotope shifts in the vibrational levels of . To check the reliability of the calculation we also carry out optimal control calculations based on the conventional wave-packet formalism, where the wave-function amplitude is temporally propagated on the grid points in real space, and obtain almost the same results as those with the density-matrix formalism.
Termination of the sequential oxidation reaction: An exploration of kinetic versus thermodynamic effects131(2009); http://dx.doi.org/10.1063/1.3246833View Description Hide Description
Several mechanisms proposed and calculated for the sequential oxidation of tungsten suboxide clusters by [Mayhall et al., J. Chem. Phys.131,144302 (2009)] are evaluated using anion photoelectron spectroscopy of an apparent intermediate, . The spectrum of is consistent with the intermediate in which the initial water addition involves the interaction of the oxygen from with a tungsten atom, approaching from a direction with the least repulsion from the oxygen atoms, coupled with the interaction between a deuterium with a tungsten-tungsten bridging oxygen on the cluster. The presence of and suggests that there is insufficient internal energy in the complex to surmount the barrier for rearrangement required for tungsten hydride and hydroxide formation necessary for or evolution, which was calculated to be energetically favorable. The quality of the calculations is verified by direct comparison between experimental photoelectron spectra of and and spectral simulations generated from the lowest energy structures calculated for , and their corresponding neutrals. The results shed light on the importance of repulsion on the pathway a reaction follows under room temperature conditions.
131(2009); http://dx.doi.org/10.1063/1.3247289View Description Hide Description
The B3LYP, CAM-B3LYP, and RCCSD(T) calculations have been used to determine the ground-state geometries of the linear polyyne cations . The CASSCF method has also been used to optimize the ground and first excited states. The present results indicate that these linear cations generally have an acetylenic structure with the ground state of for even-numbered or for odd-numbered . Moreover, the bond length alternation of is less pronounced than the corresponding one of the neutral polyyne chains . The CASPT2 approach has been employed to estimate the vertical excitation energies for the dipole-allowed transitions in clusters. The predicted transitionenergies in the gas phase are 2.62, 2.14, 1.81, 1.52, 1.35, 1.22, and 1.10 eV, respectively, in excellent agreement with the corresponding observed values of 2.45, 2.07, 1.75, 1.52, 1.35, 1.20, and 1.08 eV. The present calculations show that the absorption wavelengths for the transitions exhibit notably linear size dependence, as shown in previous experimental studies, quite different from the nonlinear relationship for origin bands in .
The ejection of triatomic molecular hydrogen ions produced by the interaction of benzene molecules with ultrafast laser pulses131(2009); http://dx.doi.org/10.1063/1.3246832View Description Hide Description
The ejection process of triatomic molecular hydrogen ions produced by the interaction of benzene with ultrafast laser pulses of moderate strong intensity is studied by means of TOF mass spectrometry. The formation can only take place through the rupture of two C–H bonds and the migration of hydrogen atoms within the molecular structure. The fragments are released with high kinetic energy (typically 2–8 eV) and at laser intensities , well above that required for the double ionization of benzene, suggesting that its formation is taking place within multiply charged parent ions. The relative ejection efficiency of molecular hydrogen ions with respect to the atomic ones is found to be strongly decreasing as a function of the laser intensity and pulse duration (67–25 fs). It is concluded that the formation is only feasible within parent molecular precursors of relatively low charged states and before significant elongation of their structure takes place, while the higher multiply charged molecular ions preferentially dissociate into ions. The ejection of ions is also discussed in comparison to the production of and ions. Finally, by recording the mass spectra of two deuterium label isotopes of benzene (1,2-, 1,4-) it is verified that the ejection efficiency of some molecular fragments, such as , , is dependent on the specific position of hydrogen atoms in the molecular skeleton prior dissociation.
Gas-phase reaction between calcium monocation and fluoromethane: Analysis of the potential energy hypersurface and kinetics calculations131(2009); http://dx.doi.org/10.1063/1.3247287View Description Hide Description
The gas-phase reaction between calcium monocation and fluoromethane: was theoretically analyzed. The potential energy hypersurface was explored by using density functional theory methodology with different functionals and Pople’s, Dunning’s, Ahlrichs’, and Stuttgart–Dresden basis sets. Kinetics calculations (energy and total angular momentum resolved microcanonical variational/conventional theory) were accomplished. The theoretically predicted range for the global kinetic rate constant values at 295 K agrees reasonably well with the experimental value at the same temperature . Explicit consideration of a two transition state model, where the formation of a weakly bounded prereactive complex is preceded by an outer transition state (entrance channel) and followed by an inner transition state connecting with a second intermediate that finally leads to products, is mandatory. Experimental observations on the correlation, or lack of correlation, between reaction rate constants and second ionization energies of the metal might well be rationalized in terms of this two transition state model.
131(2009); http://dx.doi.org/10.1063/1.3246840View Description Hide Description
A variety of iron oxide cluster cations is synthesized in a laser vaporization ion source. The kinetic energy dependence of the collision-induced dissociation (CID) of mass selected (, ) clusters with Xe is studied in this work using a guided ion beam tandem mass spectrometer. Examination of the general dissociation behavior over a broad collision energy range (0–15 eV) shows that iron oxide clusters can dissociate via evaporation of neutral Fe and O atoms as well as fission by loss of neutral , FeO, , , and fragments. Such fission pathways, which are not observed in the CID studies of pure Fe cluster cations and most other pure transition metal cluster cations, result from the strong iron oxygen bonds. In general, the predominant dissociation pathways are found to correlate with the oxidation state of the iron in the cluster. Thresholds for loss of neutral Fe, O, , FeO, , , and from various iron oxide cluster cations are quantitatively determined. These values are used to determine bondenergies and heats of formation for both neutral and cationic iron oxide clusters in this size range.
131(2009); http://dx.doi.org/10.1063/1.3246350View Description Hide Description
Due to the close relation of the polyenyl radicals and polyene radical cations to the neutral linear polyenes, one may suspect their excited states to possess substantial double excitation character, similar to the famous state of neutral polyenes and thus to be equally problematic for simple excited statetheories. Using the recently developed unrestricted algebraic-diagrammatic construction scheme of second order perturbation theory and the equation-of-motion coupled-cluster method, the vertical excitation energies, their corresponding oscillator strengths, and the nature of the wave functions of the lowest excited electronic states of the radicals are calculated and analyzed in detail. For the polyenyl radicals two one-photon allowed states are found as and states, with two symmetry-forbidden and states in between, while in the polyene radical cations and are allowed and is forbidden. The order of the states is conserved with increasing chain length. It is found that all low-lying excited states exhibit a significant but similar amount of doubly excited configuration in their wave functions of 15%–20%. Using extrapolation, predictions for the excitation energies of the five lowest excited states of the polyene radical cations are made for longer chain lengths.
- Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation
Spin relaxation of fullerene photoexcited triplet in molecular glasses: Evidence for onset of fast orientational motions of molecules in the matrix near 100 K131(2009); http://dx.doi.org/10.1063/1.3244983View Description Hide Description
Electron spin echo (ESE) was applied to study transversal spin relaxation of photoexcited triplet state of fullerene molecules in glassy-terphenyl and cis-/trans-decalin matrices (glass transition temperatures of 243 and 137 K, respectively). The relaxation rate was found to increase sharply above 110 K in -terphenyl and above 100 K in decalin. It is suggested that this increase arises from interaction of pseudorotation with fast molecular librations in the matrix. Both these types of motion involve atomic vibrations and are uniaxial in their nature, the known literature data on Raman light scattering and others indicate that molecular librations may be thermally activated in glasses just near 100 K. The increase in near 100 K is not observed for photoexcited triplet state of fullerene, for which pseudorotation is not uniaxial. As the fullerene molecule has a size much larger than that for glass solvent molecules, it is likely that molecular librations in the matrix are of collective nature.