Volume 133, Issue 12, 28 September 2010

Phtalocyanine compounds deserved a considerable interest in recent times, particularly because of their possible use in the field of nanoelectronics. In particular, the charge mobility (of both electrons and holes) in phtalocyanine stacked arrangements has been recently extensively investigated. The present work focuses on the study of the holetransfer mechanism between two phtalocyanine monomers. For an interdisk distance larger than 4.5 bohrs, the eclipsed dimer exhibits a mixedvalence behavior, with a saddle point transition state separating two equivalent minima. This behavior, however, is strongly dependent on the relative angle between the disks. In particular, the mixedvalence character of the compound is strongly enhanced for arrangements that are far from the eclipsed geometry. Moreover, for values of the angle close to and , the ground and excited transition states have exactly the same energy, thus implying the presence of a conical intersection. These results can have deep implication in the charge transfer along phtalocyanine chains.
 ARTICLES

 Theoretical Methods and Algorithms

Transitiondensityfragment interaction approach for excitoncoupled circular dichroism spectra
View Description Hide DescriptionA transitiondensityfragment interaction (TDFI) method for excitoncoupled circular dichroism (ECCD) spectra is proposed. The TDFI method was previously developed for excitationenergy transfer, which led to the successful estimation of the electronic coupling energy between donor and accepter molecules in xanthorhodopsin [K. J. Fujimoto and S. Hayashi, J. Am. Chem. Soc.131, 14152 (2009)]. In the present study, the TDFI scheme is extended to the ECCD spectral calculation based on the matrix method and is applied to a dimerized retinal (alltrans retinylideneLalanine Schiff base) chromophore. Compared with the dipoledipole and transition charge from ESP methods, TDFI has a much improved description of the electronic coupling. In addition, the matrix method combined with TDFI can reduce the computational costs compared with the full quantummechanical calculation. These advantages of the present method make it possible to accurately evaluate the CD Cotton effects observed in experiment.

A truncation hierarchy of coupled cluster models of strongly correlated systems based on perfectpairing references: The models
View Description Hide DescriptionPaired, activespace treatments of static correlation are augmented with additional amplitudes to produce a hierarchy of parsimonious and efficient cluster truncations that approximate the total energy. The number of parameters introduced in these models grow with system size in a tractable way: two powers larger than the static correlation model it is built upon: for instance cubic for the models built on perfect pairing, fourth order for a perfect quadruples (PQ) reference, and fifth order for the models built on perfect hextuples. These methods are called (SD) corrections to perfect pairing, PQ, perfect hextuples, and two variants are explored. An implementation of the SD methods is compared to benchmark results for and dissociation problems, the and model systems, and the insertion of beryllium into hydrogen. In the cases examined even the quartic number of parameters associated with PQSD is able to provide results which meaningfully improve on coupledcluster singles doubles (CCSD) (which also has quartic amplitudes) and compete with existing multireference alternatives.

The barrier method: A technique for calculating very long transition times
View Description Hide DescriptionIn many dynamical systems, there is a large separation of time scales between typical events and “rare” events which can be the cases of interest. Rareevent rates are quite difficult to compute numerically, but they are of considerable practical importance in many fields, for example, transition times in chemical physics and extinction times in epidemiology can be very long, but are quite important. We present a very fast numerical technique that can be used to find long transition times (very small rates) in lowdimensional systems, even if they lack detailed balance. We illustrate the method for a bistable nonequilibrium system introduced by Maier and Stein and a twodimensional (in parameter space) epidemiology model.

Efficient stochastic thermostatting of path integral molecular dynamics
View Description Hide DescriptionThe path integral molecular dynamics (PIMD) method provides a convenient way to compute the quantum mechanical structural and thermodynamic properties of condensed phase systems at the expense of introducing an additional set of high frequency normal modes on top of the physical vibrations of the system. Efficiently sampling such a wide range of frequencies provides a considerable thermostatting challenge. Here we introduce a simple stochastic path integral Langevin equation (PILE) thermostat which exploits an analytic knowledge of the free path integral normal mode frequencies. We also apply a recently developed colored noise thermostat based on a generalized Langevin equation (GLE), which automatically achieves a similar, frequencyoptimized sampling. The sampling efficiencies of these thermostats are compared with that of the more conventional Nosé–Hoover chain (NHC) thermostat for a number of physically relevant properties of the liquid water and hydrogeninpalladium systems. In nearly every case, the new PILE thermostat is found to perform just as well as the NHC thermostat while allowing for a computationally more efficient implementation. The GLE thermostat also proves to be very robust delivering a nearoptimum sampling efficiency in all of the cases considered. We suspect that these simple stochastic thermostats will therefore find useful application in many future PIMD simulations.

Imaging mesoscopic nuclear spin noise with a diamond magnetometer
View Description Hide DescriptionMagnetic resonance imaging can characterize and discriminate among tissues using their diverse physical and biochemical properties. Unfortunately, submicrometer screening of biological specimens is presently not possible, mainly due to lack of detection sensitivity. Here we analyze the use of a nitrogenvacancy center in diamond as a magnetic sensor for nanoscale nuclear spinimaging and spectroscopy. We examine the ability of such a sensor to probe the fluctuations of the “classical” dipolar field due to a large number of neighboring nuclear spins in a densely protonated sample. We identify detection protocols that appropriately take into account the quantum character of the sensor and find a signaltonoise ratio compatible with realistic experimental parameters. Through various example calculations we illustrate different kinds of image contrast. In particular, we show how to exploit the comparatively long nuclear spincorrelation times to reconstruct a local, highresolution sample spectrum.

Accurate onedimensional potential energy curve of the linear cluster
View Description Hide DescriptionWe present a sub0.3 K accuracy, groundstate onedimensional potential energy curve of the metastable linear configuration of the cluster calculated exclusively with explicitly correlated Gaussian functions with shifted centers. The internuclear distance is kept at the isolated vibrational groundstate average value of 1.448 736 bohr and the intermonomer separation is varied between 2 and 100 bohrs. The analytical gradient of the energy with respect to the nonlinear parameters of the Gaussians (i.e., the exponents and the coordinates of the shifts) has been employed in the variational optimization of the wave function. Procedures for enlarging the basis set and for adjusting the centers of the Gaussians to the varying intermonomer separation have been developed and used in the calculations.

Reference state for the generalized Yvon–Born–Green theory: Application for coarsegrained model of hydrophobic hydration
View Description Hide DescriptionCoarsegrained (CG) models provide a computationally efficient means for investigating phenomena that remain beyond the scope of atomically detailed models. Although CG models are often parametrized to reproduce the results of atomistic simulations, it is highly desirable to determine accurate CG models from experimental data. Recently, we have introduced a generalized Yvon–Born–Green (gYBG) theory for directly (i.e., noniteratively) determining variationally optimized CG potentials from structural correlation functions. In principle, these correlation functions can be determined from experiment. In the present work, we introduce a reference state potential into the gYBG framework. The reference state defines a fixed contribution to the CG potential. The remaining terms in the potential are then determined, such that the combined potential provides an optimal approximation to the manybody potential of mean force. By specifying a fixed contribution to the potential, the reference state significantly reduces the computational complexity and structural information necessary for determining the remaining potentials. We also validate the quantitative accuracy of the proposed method and numerically demonstrate that the reference state provides a convenient framework for transferring CG potentials from neat liquids to more complex systems. The resulting CG model provides a surprisingly accurate description of the two and threeparticle solvation structures of a hydrophobic solute in methanol. This work represents a significant step in developing the gYBG theory as a useful computational framework for determining accurate CG models from limited experimental data.

A statistical mechanical theory of proton transport kinetics in hydrogenbonded networks based on population correlation functions with applications to acids and bases
View Description Hide DescriptionExtraction of relaxation times, lifetimes, and rates associated with the transport of topological charge defects in hydrogenbonded networks from molecular dynamics simulations is a challenge because proton transfer reactions continually change the identity of the defect core. In this paper, we present a statistical mechanical theory that allows these quantities to be computed in an unbiased manner. The theory employs a set of suitably defined indicator or population functions for locating a defect structure and their associated correlation functions. These functions are then used to develop a chemical master equation framework from which the rates and lifetimes can be determined. Furthermore, we develop an integral equation formalism for connecting various types of population correlation functions and derive an iterative solution to the equation, which is given a graphical interpretation. The chemical master equation framework is applied to the problems of both hydronium and hydroxide transport in bulk water. For each case it is shown that the theory establishes direct links between the defect’s dominant solvation structures, the kinetics of charge transfer, and the mechanism of structural diffusion. A detailed analysis is presented for aqueous hydroxide, examining both reorientational time scales and relaxation of the rotational anisotropy, which is correlated with recent experimental results for these quantities. Finally, for it is demonstrated that the “dynamical hypercoordination mechanism” is consistent with available experimental data while other mechanistic proposals are shown to fail. As a means of going beyond the linear rate theory valid from short up to intermediate time scales, a fractional kinetic model is introduced in the Appendix in order to describe the nonexponential longtime behavior of timecorrelation functions. Within the mathematical framework of fractional calculus the power law decay , where is a parameter of the model and depends on the dimensionality of the system, is obtained from Mittag–Leffler functions due to their longtime asymptotics, whereas (stretched) exponential behavior is found for short times.
 Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Charge transfer and mixedvalence behavior in phtalocyaninedimer cations
View Description Hide DescriptionPhtalocyanine compounds deserved a considerable interest in recent times, particularly because of their possible use in the field of nanoelectronics. In particular, the charge mobility (of both electrons and holes) in phtalocyanine stacked arrangements has been recently extensively investigated. The present work focuses on the study of the holetransfer mechanism between two phtalocyanine monomers. For an interdisk distance larger than 4.5 bohrs, the eclipsed dimer exhibits a mixedvalence behavior, with a saddle point transition state separating two equivalent minima. This behavior, however, is strongly dependent on the relative angle between the disks. In particular, the mixedvalence character of the compound is strongly enhanced for arrangements that are far from the eclipsed geometry. Moreover, for values of the angle close to and , the ground and excited transition states have exactly the same energy, thus implying the presence of a conical intersection. These results can have deep implication in the charge transfer along phtalocyanine chains.

Dynamical (e, 2e) studies using tetrahydrofuran as a DNA analog
View Description Hide DescriptionTriple differential cross sections for the electronimpact ionization of the outer valence orbital of tetrahydrofuran have been measured using the (e, 2e) technique. The measurements have been performed with coplanar asymmetric kinematics, at an incident electron energy of 250 eV and at an ejected electron energy of 10 eV, over a range of momentum transfers. The experimental results are compared with theoretical calculations carried out using the molecular threebody distorted wave model. The results obtained are important for gaining an understanding of electron driven processes at a molecular level and for modeling energy deposition in living tissue.

Highresolution electron momentum spectroscopy of valence satellites of carbon disulfide
View Description Hide DescriptionThe binding energy spectrum of carbon disulphide in the energy range of 9–23 eV has been measured by a highresolution spectrometer employing asymmetric noncoplanar kinematics at an impact energy of 2500 eV plus the binding energy. Taking the advantage of the high energy resolution of 0.54 eV, four main peaks and five satellites in the outervalence region are resolved. The assignments and pole strengths for these satellite states are achieved by comparing the experimental electron momentum profiles with the corresponding theoretical ones calculated using Hartree–Fock and density functional theory methods. The results are also compared in detail with the recent SACCI generalR calculations. General agreement is satisfactory, while the present experiment suggests cooperative contributions from , states to satellite 2 and , states to satellite 3. Besides, relatively low pole strength for state is obtained which contradicts all the theoretical calculations [2phTDA, ADC(3), SACCI generalR, ADC(4)] so far.

Imaging the nature of the modespecific chemistry in the reaction of Cl atom with antisymmetric stretchexcited
View Description Hide DescriptionFollowing up our preliminary communication [Kawamata et al., Phys. Chem. Chem. Phys.10, 4378 (2008)], the effects of the antisymmetricstretching excitation of methane on the reaction are examined here over a wide range of initial collision energy in a crossed molecular beam imaging experiment. The antisymmetric stretch of is prepared in a single rovibrational state of by direct infrared absorption, and the major product states of are probed by a timesliced velocitymap imaging method. We find that at fixed collision energies, the stretching excitation promotes reaction rate. Compared to the groundstatereaction, this vibrational enhancement factor is, however, no more effective than the translational enhancement. The correlated vibrational branching fraction shows a striking dependence on collision energies, varying from 0.7 at to about 0.2 at . This behavior resembles the previously studied , but is in sharp contrast to the and reactions. Dependences of experimental results on the probed rotational states of are also elucidated. We qualitatively interpret those experimental observations based on a conceptual framework proposed recently.

Unusual photochemical dynamics of a bridged azobenzene derivative
View Description Hide DescriptionIn a largescale simulation study of ultrafast photochemical dynamics for an azobenzene compound with an additional ethylenic bridge we have found unexpected features: while the dynamics starting from the Z isomer follow a barrierless path with steep gradients, the dynamics starting from the E isomer proceed through a different conical intersection surrounded by a rather flat potential energy landscape and then encounter a sizeable barrier in the electronic ground state that markedly influences the reaction behavior. Direct comparisons with experimental static UV spectra, quantum yields, and transient absorption spectra show good agreement and reveal signatures of this unusual behavior.

Structure and bonding in thirdrow main group dicarbides
View Description Hide DescriptionThe molecular structures of thirdrow main group dicarbides have been studied by theoretical methods. It is found that K, Ca, and Ga favor symmetric (Tshape) ground states, whereas As, Se, and Br have linear or quasilinear ground states. In the case of germanium. a very flat potential energy surface is found and an Lshape structure seems to be the ground state.Dissociation energies into are relatively high. The main features of these compounds, in particular, the preference for linear or cyclic structures, have been rationalized in terms of the most relevant interactions between the thirdrow atom and dicarbon with the help of an energy decomposition analysis.

Guided ion beam and theoretical study of the reactions of with , , and HD
View Description Hide DescriptionThe kinetic energy dependences of reactions of the thirdrow transition metal cation with , , and HD were determined using a guided ion beam tandem mass spectrometer. A flow tube ion source produces in its electronic ground state level. Corresponding statespecific reaction cross sections are obtained. The kinetic energy dependences of the cross sections for the endothermic formation of and are analyzed to give a 0 K bonddissociation energy of . Quantum chemical calculations at several levels of theory performed here generally overestimate the experimental bondenergy but results obtained using the BeckehalfandhalfLYP functional show good agreement. Theory also provides the electronic structures of these species and the reactive potential energy surfaces. Results from the reactions with HD provide insight into the reaction mechanisms and indicates that reacts via a statistical mechanism. We also compare this thirdrow transition metal system with the firstrow and secondrow congeners, and , and find that has a weaker bond. As most thirdrow transition metal hydride cation bonds exceed their lighter congeners, this trend is unusual but can be understood using promotion energy arguments.

Electronic structure and properties of isoelectronic magic clusters:
View Description Hide DescriptionThe equilibrium structure, stability, and electronic properties of the clusters have been studied using a combination of photoelectron spectroscopy experiment and density functional theory. All these clusters constitute 40 electron systems with 39 electrons contributed by the 13 Al atoms and 1 electron contributed by each of the X atom. A systematic study allows us to investigate whether all electrons contributed by the X atoms are alike and whether the structure, stability, and properties of all the magic clusters are similar. Furthermore, quantitative agreement between the calculated and the measured electron affinities and vertical detachment energies enable us to identify the ground state geometries of these clusters both in neutral and anionic configurations.

Ab initio studies of ultrafast xray scattering of the photodissociation of iodine
View Description Hide DescriptionWe computationally examine various aspects of the reaction dynamics of the photodissociation and recombination of molecular iodine. We use our recently proposed formalism to calculate timedependent xray scattering signal changes from first principles. Different aspects of the dynamics of this prototypical reaction are studied, such as coherent and noncoherent processes, features of structural relaxation that are periodic in time versus nonperiodic dissociative processes, as well as small electron density changes caused by electronic excitation, all with respect to xray scattering. We can demonstrate that wideangle xray scattering offers a possibility to study the changes in electron densities in nonperiodic systems, which render it a suitable technique for the investigation of chemical reactions from a structural dynamics point of view.

Importance of backdonation in complexes isoelectronic to
View Description Hide DescriptionIn this contribution, we study several monocarbonylmetal complexes in order to unravel the contribution of relativistic effects to the metalligand bond length and complexation energy. Using scalar density functional theory(DFT) constrained space orbital variation (CSOV) energy decomposition analysis supplemented by allelectron fourcomponent DFT computations, we describe the dependency of relativistic effects on the orbitals involved in the complexation for the isoelectronic series, namely, the fully occupied 5d orbitals and the empty 6s orbitals. We retrieve the wellknown sensitivity of gold toward relativity. For platinum and gold, the fourcomponent results illustrate the simultaneous relativistic expansion of the 5d orbitals and the contraction of the 6s orbitals. The consequences of such modifications are evidenced by CSOV computations, which show the importance of both donation and backdonation within such complexes. This peculiar synergy fades away with mercury and thallium for which coordination becomes driven by the accepting 6s orbitals only, which makes the corresponding complexes less sensitive toward the relativistic effects.

Global ab initio potential energy surfaces for the interaction
View Description Hide DescriptionCompletely ab initio global potential energy surfaces (PESs) for the singlet and triplet spin multiplicities of rigid are reported for the first time. They have been obtained by combining an accurate restricted coupled clustertheory with singles, doubles, and perturbative triple excitations [RCCSD(T)] quintet potential [Bartolomei et al.,J. Chem. Phys.128, 214304 (2008)] with complete active space second order perturbation theory (CASPT2) or, alternatively, multireference configuration interaction (MRCI) calculations of the singletquintet and tripletquintet splittings. Spherical harmonic expansions, containing a large number of terms due to the high anisotropy of the interaction, have been built from the ab initio data. The radial coefficients of these expansions are matched at long range distances with analytical functions based on recent ab initio calculations of the electric properties of the monomers [M. Bartolomei, E. CarmonaNovillo, M. I. Hernández, J. CamposMartínez, and R. HernándezLamoneda, J. Comput. Chem. (2010) (in press)]. The singlet and triplet PESs obtained from either RCCSD(T)CASPT2 or RCCSD(T)MRCI calculations are quite similar, although quantitative differences appear in specific terms of the expansion. CASPT2 calculations are the ones giving rise to larger splittings and more attractive interactions, particularly in the region of the absolute minima (in the rectangular geometry). The new singlet, triplet, and quintet PESs are tested against second virial coefficient B(T) data and, their spherically averaged components, against integral cross sections measured with rotationally hot effusive beams. Both types of multiconfigurational approaches provide quite similar results, which, in turn, are in good agreement with the measurements. It is found that discrepancies with the experiments could be removed if the PESs were slightly more attractive. In this regard, the most attractive RCCSD(T)CASPT2 PESs perform slightly better than the RCCSD(T)MRCI counterpart.

High resolution electronic spectroscopy of 9fluorenemethanol in the gas phase: New insights into the properties of hydrogen bonds
View Description Hide DescriptionRotationally resolved fluorescence excitation spectra of 9fluorenemethanol (9FM) and deuterated 9fluorenemethanol (9FMD) have been observed and assigned. Two conformers were detected; sym9FM and unsym9FM. The sym conformer has the –OH group symmetrically placed above the fluorene short axis, with its hydrogen atom pointing towards the top of an aromatic ring, whereas the unsym conformer has the –OH group tilted away from this axis, with its hydrogen atom pointing towards the side of an aromatic ring. Only the sym conformer shows a tunneling splitting associated with the torsional motion of the –OH group; the unsym conformer is “rigid.” Additionally, a third subband was observed in the spectrum of sym9FMD, evidencing secondary minima on the potential energy surfaces of the ground and excited electronic states. Studies of these surfaces along the –OH torsional coordinate provide new insights into the properties of hydrogen bonds.