Volume 138, Issue 15, 21 April 2013
 COMMUNICATIONS


Communication: Collective dynamics of roomtemperature ionic liquids and their Li ion solutions studied by highresolution inelastic Xray scattering
View Description Hide DescriptionHighresolution inelastic Xray scattering (IXS) measurements were performed for roomtemperature ionic liquids (ILs) of 1ethyl3methylimidazolium bis(trifluoromethanesulfonyl)amide and bis(fluorosulfonyl)amide, [C_{2}mIm^{+}][TFSA^{−}] and [C_{2}mIm^{+}][FSA^{−}], respectively, at ambient temperature. The observed spectra as a function of Q of 1.4–6 nm^{−1} can be ascribed to quasielastic and inelastic scatterings, so that they are well represented with the fitting by using the Lorentz and the damped harmonic oscillator model functions to yield the dynamic structure factors. It was found in the intermediate scattering function, F(Q, t) that both ILs show the relaxation at t < 10 ps. The IXS measurements were also made on [C_{2}mIm^{+}][TFSA^{−}] and [C_{2}mIm^{+}][FSA^{−}] solutions dissolving Li salt. It is suggested that the adding of Li salt to IL significantly prolongs the relaxation time.

Communication: Chemical bonding in carbon dimer isovalent series from the natural orbital functional theory perspective
View Description Hide DescriptionThe natural orbital functional theory admits two unique representations in the orbital space. On the one hand, we have the natural orbitals themselves that minimize the energy functional, and which afford for a diagonal oneparticle reduced density matrix but not for a diagonal Lagrangian orbital energy multipliers matrix. On the other hand, since it is possible to reverse the situation but only once the energy minimization has been achieved, we have the socalled canonical representation, where the Lagrangian orbital energy multipliers matrix is diagonal but the oneparticle reduced density matrix is not. Here it is shown that the former representation, the natural orbital representation, accounts nicely for the quadrupole bond character of the ground states of C_{2}, BN, CB^{−}, and CN^{+}, and for the double bond order character of the isovalent state of Si_{2}. Similarly, the canonical orbital representation accounts correctly for the ionization spectra of all these species.

Communication: Fullerene resolution by the magnetic circular dichroism
View Description Hide DescriptionThe similarity in shape makes separation and identification of fullerenes difficult. In this work, the magnetic circular dichroism (MCD) spectroscopy is presented as a useful tool for this purpose. Experimental C_{60} and C_{70} spectra were obtained and reproduced with the aid of density functional computations and the complex polarization propagator method. Theoretical spectra of other fullerenes revealed distinctive patterns extremely sensitive to molecular structure as well. Requiring tiny amounts of the sample, the MCD technique thus appears as a useful for detailed fullerene studies.
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 ARTICLES

 Theoretical Methods and Algorithms

Basis set converged weak interaction energies from conventional and explicitly correlated coupledcluster approach
View Description Hide DescriptionInteraction energies for seven weakly bound dimers involving helium, argon, water, and methane are computed using large correlationconsistent basis sets augmented with bond functions. The estimates of the coupledcluster singles, doubles, and noniterative triples [CCSD(T)] complete basis set limit are obtained using both the conventional approach and several variants of the explicitly correlated CCSD(T)F12 method. It is shown that both bond functions and the F12 approach significantly speed up the convergence of the CCSD(T)/augccpVXZ interaction energies with the basis set cardinal number X. However, the extent of improvement provided by each technique varies with the character of the interactions—the F12 method works best for polar, electrostaticsbound dimers, while for dispersiondominated complexes the addition of bond functions is more efficient. The convergence rate afforded by different coupledcluster variants is fairly consistent across the entire attractive region of the potential curve, while the improvement provided by the F12 correction increases along the repulsive wall. The use of large basis sets and the agreement between conventional and explicitly correlated approaches allow us to assess the importance of different residual approximations present in the popular CCSD(T)F12 implementations.

Molecular force fields for aqueous electrolytes: SPC/Ecompatible charged LJ sphere models and their limitations
View Description Hide DescriptionThirteen of the most common aqueous NaCl solution force fields based on the SPC/E water solvent are examined with respect to their prediction at ambient conditions of the concentration dependence of the total electrolyte chemical potential and the solution density. We also calculate the salt solubility and the chemical potential and density of the NaCl crystalline solid. We obtain the solution chemical potential in a computationally efficient manner using our recently developed Osmotic Ensemble Monte Carlo method [F. Moučka, M. Lísal, and W. R. Smith, J. Phys. Chem. B116, 5468 (Year: 2012)10.1021/jp301447z]. We find that the results of the force fields considered are scattered over a wide range of values, and none is capable of producing quantitatively accurate results over the entire concentration range, with only two of them deemed to be acceptable. Our results indicate that several force fields exhibit precipitation at concentrations below the experimental solubility limit, thus limiting their usefulness. This has important implications, both in general and for their use in biomolecular simulations carried out in the presence of counterions. We conclude that either different parameter fitting techniques taking highconcentration properties into account must be used when determining force field model parameters, or that the class of models considered here is intrinsically incapable of the task and more sophisticated mathematical forms must be used.

Diffusive spatiotemporal noise in a firstpassage time model for intracellular calcium release
View Description Hide DescriptionThe intracellular release of calcium from the endoplasmic reticulum is controlled by ion channels. The resulting calcium signals exhibit a rich spatiotemporal signature, which originates at least partly from microscopic fluctuations. While stochasticity in the gating transition of ion channels has been incorporated into many models, the distribution of calcium is usually described by deterministic reactiondiffusion equations. Here we test the validity of the latter modeling approach by using two different models to calculate the frequency of localized calcium signals (calcium puffs) from clustered IP_{3} receptor channels. The complexity of the full calcium system is here limited to the basic opening mechanism of the ion channels and, in the mathematical reduction simplifies to the calculation of a first passage time. Two models are then studied: (i) a hybrid model, where channel gating is treated stochastically, while calcium concentration is deterministic and (ii) a fully stochastic model with noisy channel gating and Brownian calcium ion motion. The second model utilises the recently developed tworegime method [M. B. Flegg, S. J. Chapman, and R. Erban, “The tworegime method for optimizing stochastic reactiondiffusion simulations,” J. R. Soc., Interface9, 859–868 (Year: 2012)]10.1098/rsif.2011.0574 in order to simulate a large domain with precision required only near the Ca^{2+} absorbing channels. The expected time for a first channel opening that results in a calcium puff event is calculated. It is found that for a large diffusion constant, predictions of the interpuff time are significantly overestimated using the model (i) with a deterministic nonspatial calcium variable. It is thus demonstrated that the presence of diffusive noise in local concentrations of intracellular Ca^{2+} ions can substantially influence the occurrence of calcium signals. The presented approach and results may also be relevant for other cellphysiological firstpassage time problems with small ligand concentration and high cooperativity.

Singlefile diffusion in an interval: First passage properties
View Description Hide DescriptionWe investigate the longtime behavior of the survival probability of a tagged particle in a singlefile diffusion in a finite interval. The boundary conditions are of two types: (1) one boundary is absorbing the second is reflecting and (2) both boundaries are absorbing. For each type of the boundary conditions we consider two types of initial conditions: (a) initial number of particles N is given and (b) initial concentration of particles is given (N is random). In all four cases the taggedparticle survival probability exhibits different asymptotic behavior. When the both boundaries are absorbing we also consider a case of a random interval length (singlefile diffusion on a line with randomly distributed traps). In the latter setting, the initial concentration of particles has the same effect on the asymptotic decay of the survival probability as the concentration of traps.

Milestoning with coarse memory
View Description Hide DescriptionMilestoning is a method used to calculate the kinetics of molecular processes occurring on timescales inaccessible to traditional molecular dynamics (MD) simulations. In the method, the phase space of the system is partitioned by milestones (hypersurfaces), trajectories are initialized on each milestone, and short MD simulations are performed to calculate transitions between neighboring milestones. Long trajectories of the system are then reconstructed with a semiMarkov process from the observed statistics of transition. The procedure is typically justified by the assumption that trajectories lose memory between crossing successive milestones. Here we present Milestoning with Coarse Memory (MCM), a generalization of Milestoning that relaxes the memory loss assumption of conventional Milestoning. In the method, milestones are defined and sample transitions are calculated in the standard Milestoning way. Then, after it is clear where trajectories sample milestones, the milestones are broken up into distinct neighborhoods (clusters), and each sample transition is associated with two clusters: the cluster containing the coordinates the trajectory was initialized in, and the cluster (on the terminal milestone) containing trajectory's final coordinates. Long trajectories of the system are then reconstructed with a semiMarkov process in an extended state space built from milestone and cluster indices. To test the method, we apply it to a process that is particularly ill suited for Milestoning: the dynamics of a polymer confined to a narrow cylinder. We show that Milestoning calculations of both the mean first passage time and the mean transit time of reversal—which occurs when the endtoend vector reverses direction—are significantly improved when MCM is applied. Finally, we note the overhead of performing MCM on top of conventional Milestoning is negligible.

Calculation of nonadiabatic coupling vectors in a localorbital basis set
View Description Hide DescriptionMost of today's moleculardynamics simulations of materials are based on the BornOppenheimer approximation. There are many cases, however, in which the coupling of the electrons and nuclei is important and it is necessary to go beyond the BornOppenheimer approximation. In these methods, the nonadiabatic coupling vectors are fundamental since they represent the link between the classical atomic motion of the nuclei and the time evolution of the quantum electronic state. In this paper we analyze the calculation of nonadiabatic coupling vectors in a basis set of local orbitals and derive an expression to calculate them in a practical and computationally efficient way. Some examples of the application of this expression using a localorbital density functional theory approach are presented for a few simple molecules: H_{3}, formaldimine, and azobenzene. These results show that the approach presented here, using the Slater transitionstate density, is a very promising way for the practical calculation of nonadiabatic coupling vectors for large systems.

Hydrodynamically enforced entropic Brownian pump
View Description Hide DescriptionTransport of overdamped Brownian particles in a finite hydrodynamical channel is investigated in the presence of the ac driving force and the pressuredriven flow. The system is bounded by two particle reservoirs. With the help of the FickJacobs method, we obtain the directed current of Brownian particles and the pumping capacity of the system. The directed transport is determined by the competitions among the asymmetry of the channel, the ac driving force, the pressuredriven flow, and the concentration difference. Their interplays can exhibit the peculiar properties. Remarkably, the particles can be pumped through the channel from the lower concentration reservoir to the higher concentration one, or from the lower pressure side to the higher pressure one. In addition, due to the existence of the pressure drop, ac driving force still plays the significant role on directed transport even in a completely symmetric channel. Our results could be implemented in constrained structures with narrow channels or pores where the particles are suspended in a solvent.

Multistate reweighting and configuration mapping together accelerate the efficiency of thermodynamic calculations as a function of molecular geometry by orders of magnitude
View Description Hide DescriptionWe present an approach to calculate free energy and other thermodynamic property differences between molecules which have very little or no overlap in configuration space, but where a onetoone mapping between the molecule geometries exists. The approach combines multistate reweighting with remapping of phase space between simulated states. We apply this method to calculate the free energy differences between nonoverlapping, truncated harmonic oscillators, the free energy, enthalpy, and entropy differences between different parameterizations of rigid water, and differences in free energy of solvation between dipoles of different lengths. Previously difficult or impossible problems become either trivially easy or are improved in efficiency by two to five orders of magnitude.

Bending rigidities of surfactant bilayers using selfconsistent field theory
View Description Hide DescriptionSelfconsistent field (SCF) theory is used to find bending moduli of surfactant and lipid bilayers. Recently, we successfully applied lowmemory search methods to solve the SCF equations. Using these we are now able to directly evaluate the Gaussian bending modulus for molecularly detailed models of bilayers by evaluating the excess Helmholtz energy of tensionless bilayers in a (part of the) Im3m cubic phase. The result prompted us to reconsider the protocol that has been used thus far to find the mean bending modulus k _{ c } and Gaussian bending modulus . With respect to previous predictions, the value of k _{ c } is reduced by a factor of two and the Gaussian bending modulus is less negative and much closer to zero. In line with experimental data we now find that can also become positive. In this paper we use the nonionic surfactants series of the type C_{ n }E_{ m } for illustration.
 Advanced Experimental Techniques

A novel technique for measurement of thermal rate constants and temperature dependences of dissociative recombination: CO_{2} ^{+}, CF_{3} ^{+}, N_{2}O^{+}, C_{7}H_{8} ^{+}, C_{7}H_{7} ^{+}, C_{6}H_{6} ^{+}, C_{6}H_{5} ^{+}, C_{5}H_{6} ^{+}, C_{4}H_{4} ^{+}, and C_{3}H_{3} ^{+}
View Description Hide DescriptionA novel technique using a flowing afterglowLangmuir probe apparatus for measurement of temperature dependences of rate constants for dissociative recombination (DR) is presented. Low (∼10^{11} cm^{−3}) concentrations of a neutral precursor are added to a noble gas/electron afterglow plasma thermalized at 300–500 K. Charge exchange yields one or many cation species, each of which may undergo DR. Relative ion concentrations are monitored at a fixed reaction time while the initial plasma density is varied between 10^{9} and 10^{10} cm^{−3}. Modeling of the decrease in concentration of each cation relative to the nonrecombining noble gas cation yields the rate constant for DR. The technique is applied to several species (O_{2} ^{+}, CO_{2} ^{+}, CF_{3} ^{+}, N_{2}O^{+}) with previously determined 300 K values, showing excellent agreement. The measurements of those species are extended to 500 K, with good agreement to literature values where they exist. Measurements are also made for a range of C_{n}H_{m} ^{+} (C_{7}H_{7} ^{+}, C_{7}H_{8} ^{+}, C_{5}H_{6} ^{+}, C_{4}H_{4} ^{+}, C_{6}H_{5} ^{+}, C_{3}H_{3} ^{+}, and C_{6}H_{6} ^{+}) derived from benzene and toluene neutral precursors. C_{n}H_{m} ^{+} DR rate constants vary from 8–12 × 10^{−7} cm^{3} s^{−1} at 300 K with temperature dependences of approximately T^{−0.7}. Where prior measurements exist these results are in agreement, with the exception of C_{3}H_{3} ^{+} where the present results disagree with a previously reported flat temperature dependence.

Nonlinear femtosecond laser induced scanning tunneling microscopy
View Description Hide DescriptionWe demonstrate ultrafast laser driven nonlinear scanning tunneling microscopy (STM), under ambient conditions. The design is an adaptation of the recently introduced crosspolarized double beat method, whereby zpolarized phase modulated fields are tightly focused at a tunneling junction consisting of a sharp tungsten tip and an optically transparent gold film as substrate. We demonstrate the prerequisites for ultrafast timeresolved STM through an operative mechanism of nonlinear laser fielddriven tunneling. The spatial resolution of the nonlinear laser driven STM is determined by the local field intensity. Resolution of 0.3 nm–10 nm is demonstrated for the intensity dependent, exponential tunneling range. The demonstration is carried out on a junction consisting of tungsten tip and gold substrate. Nanostructured gold is used for imaging purposes, to highlight junction plasmon controlled tunneling in the conductivity limit.
 Atoms, Molecules, and Clusters

A global potential energy surface for the H_{2} + OH ↔ H_{2}O + H reaction using neural networks
View Description Hide DescriptionA global potential energy surface for the H_{2} + OH ↔ H_{2}O + H reaction has been constructed using the neural networks method based on ∼17 000 ab initio energies calculated at UCCSD(T)F12a/AVTZ level of theory. Timedependent wave packet calculations showed that the new potential energy surface is very well converged with respect to the number of ab initio data points, as well as to the fitting process. Various tests revealed that the new surface is considerably more smooth and accurate than the existing YZCL2 and XXZ surfaces, representing the best available potential energy surface for the benchmark fouratom system. Equally importantly, the number of ab initio energies required to obtain the well converged potential energy surface is rather limited, indicating the neural network fitting is a powerful method to construct accurate potential energy surfaces for polyatomic reactions.

Isotope effect in the photochemical decomposition of CO_{2} (ice) by Lymanα radiation
View Description Hide DescriptionThe photochemical decomposition of CO_{2} (ice) at 75 K by Lymanα radiation (10.2 eV) has been studied using transmission infrared spectroscopy. An isotope effect in the decomposition of the CO_{2} molecule in the ice has been discovered, favoring ^{12}CO_{2} photodecomposition over ^{13}CO_{2} by about 10%. The effect is caused by electronic energy transfer from the excited CO_{2} molecule to the ice matrix, which favors quenching of the heavier electronicallyexcited ^{13}CO_{2} molecule over ^{12}CO_{2}. The effect is similar to the MenzelGomerRedhead isotope effect in desorption from adsorbed molecules on surfaces when electronically excited. An enhancement of the rate of formation of latticetrapped CO and CO_{3} species is observed for the photolysis of the ^{12}CO_{2} molecule compared to the ^{13}CO_{2} molecule in the ice. Only 0.5% of the primary photoexcitation results in O–CO bond dissociation to produce trappedCO and trappedCO_{3} product molecules and the majority of the electronicallyexcited CO_{2} molecules return to the ground state. Here either vibrational relaxation occurs (majority process) or desorption of CO_{2} occurs (minority process) from highly vibrationallyexcited CO_{2} molecules in the ice. The observation of the ^{12}C/^{13}C isotope effect in the Lymanα induced photodecomposition of CO_{2} (ice) suggests that over astronomical time scales the isotope enrichment effect may distort historical information derived from isotope ratios in space wherever photochemistry can occur.

Lymanα photodesorption from CO_{2}(ice) at 75 K: Role of CO_{2} vibrational relaxation on desorption rate
View Description Hide DescriptionThe photodesorption of CO_{2} from CO_{2} (ice) at 75 K when irradiated by Lymanα light is strongly mediated by vibrational relaxation of highly vibrationally excited molecules produced from the electronically excited CO_{2} state. A vibrationally hot molecule can either relax (major process) in the ice or desorb (minor process). We find that isotopically pure CO_{2} ices photodesorb least efficiently due to efficient vibrational tuning between molecules in the ice. Isotopically impure CO_{2} ices are more poorly vibrationally relaxed and hence photodesorb more efficiently. Mixed CO_{2}Xe ices are still more efficiently photodesorbed due to the dilution of CO_{2}, which further reduces the rate of vibrational relaxation. Resonant interactions as well as phononassisted interactions contribute to vibrational relaxation efficiency in ices, and inversely to photodesorption efficiency. The vibrational lifetime of hot CO_{2} in its ice at 75 K is of order of 10^{−15} s. These results indicate that under astronomical conditions, the rate of photodesorption will depend inversely on the rate of vibrational quenching in the ice, which is dependent on the abundance and distance of like oscillators from each other in the ice. In rather isotopically pure ices, the minority isotopic species will photodesorb more rapidly.

Fouriertransform spectroscopy and description of lowlying energy levels in the B(1)^{1}Π state of RbCs
View Description Hide DescriptionThe Fourier transform spectrometer with resolution of 0.03 cm^{−1} was applied to disperse the diode laser induced B(1)^{1}Π → X ^{1}Σ^{+} fluorescence spectra of the RbCs molecule in a heat pipe. The presence of buffer gas (Ar) produced in the spectra the dense pattern of collisioninduced rotation relaxation lines, thus enlarging the B(1)^{1}Π data set, allowing to determine the Λsplitting constants and to reveal numerous local perturbations. In total, 2664 term values for ^{85}Rb^{133}Cs and ^{87}Rb^{133}Cs in the energy range from 13 770 to 15 200 cm^{−1} were obtained with accuracy about 0.01 cm^{−1}. A pointwise potential energy curve (PEC) based on inverted perturbation approach was constructed in the Rrange from 3.35 to 9.00 Å for less perturbed vibrational levels v′ ∈ [0, 35] and compared with ab initio calculations. The data included in the fit were reproduced by present PEC with standard deviation (sd) 0.95 cm^{−1}. More systematic over rotational levels J ^{′} ∈ [6, 228] data set was obtained for v′ ∈ [0, 2]. These data were reproduced by the obtained PEC with sd of 0.08 cm^{−1}. The energy of PEC’s minimum T _{ e } = 13 746.65 cm^{−1}, as well as other main molecular constants were determined.

Ab initio dynamics trajectory study of the heterolytic cleavage of H_{2} by a Lewis acid [B(C_{6}F_{5})_{3}] and a Lewis base [P(tBu)_{3}]
View Description Hide DescriptionActivation of H_{2} by a “frustrated Lewis pair” (FLP) composed of B(C_{6}F_{5})_{3} and P(tBu)_{3} species has been explored with high level direct ab initio molecular dynamics (AIMD) simulations at finite temperature (T = 300 K) in gas phase. The initial geometrical conditions for the AIMD trajectory calculations, i.e., the near attack conformations of FLP + H_{2}, were devised using the hostguest model in which suitable FLP conformations were obtained from the dynamics of the B(C_{6}F_{5})_{3}/P(tBu)_{3} pair in gas phase. AIMD trajectory calculations yielded microscopic insight into effects which originate from nuclear motion in the reacting complex, e.g., the alternating compression/elongation of the boronphosphorous distance and the change of the pyramidality of boron in B(C_{6}F_{5})_{3}. The ensemble averaged trajectory analysis has been compared with the minimum energy path (MEP) description of the reaction. Similar to MEP, AIMD shows that an attack of the acid/base pair on the H–H bond gives rise to the polarization of the H_{2} molecule and as a consequence generates a large dipole moment of the reacting complex. The MEP and AIMD portrayals of the reaction are fundamentally different in terms of the magnitude of the motion of nuclei in B(C_{6}F_{5})_{3} and P(tBu)_{3} during the H_{2} cleavage. In the AIMD trajectory simulations, geometries of B(C_{6}F_{5})_{3} and P(tBu)_{3} appear as nearly “frozen” on the short time scale of the H_{2} cleavage. This is contrary to the MEP picture. Several of the concepts which arise from this work, e.g., separation of time scales of nuclear motion and the timedependence of the donoracceptor interactions in the reacting complex, are important for the understanding of chemical reactivity and catalysis.

Electronic spectroscopy and electronic structure of diatomic IrSi
View Description Hide DescriptionThe optical spectrum of diatomic IrSi has been investigated for the first time, with transitions observed in the range from 17 178 to 23 858 cm^{−1} (582–419 nm). A rich spectrum has been recorded, consisting of 14 electronic band systems and a number of unclassified bands. Thirtyone bands have been investigated with rotational resolution, allowing the ground state to be identified as X^{2}Δ_{5/2} arising from the 1σ^{2}1π^{4}2σ^{2}1δ^{3}3σ^{2} configuration. The ground X^{2}Δ_{5/2} state is characterized by ΔG_{1/2} = 533 cm^{−1} and r_{0} = 2.0899(1) Å for the more abundant isotopic form, ^{193}Ir^{28}Si (57.8%). The measured excited electronic states have equilibrium bond lengths ranging from 2.17 to 2.25 Å and vibrational frequencies ranging from 365 to 452 cm^{−1}. Ab initio calculations were also carried out on the molecule using the complete active space selfconsistent field and multistate complete active space secondorder perturbation theory methods, with relativistic and spinorbit effects included through the restricted active space stateinteraction with spinorbit coupling method. The calculated ground state agrees with experiment, and a large number of excited states lying within 20 000 cm^{−1} of the ground state are reported.