Volume 143, Issue 20, 28 November 2015

We demonstrate that the enantiomers of chiralmacromolecules at an aqueous interface can be distinguished with monolayer sensitivity using heterodynedetected vibrational sumfrequency generation (VSFG). We perform VSFG spectroscopy with a polarization combination that selectively probes chiral molecular structures. By using frequencies far detuned from electronic resonances, we probe the chiral macromolecular structures with high surface specificity. The phase of the sumfrequency light generated by the chiral molecules is determined using heterodyne detection. With this approach, we can distinguish righthanded and lefthanded helical peptides at a waterair interface. We thus show that heterodynedetected VSFG is sensitive to the absolute configuration of complex, interfacial macromolecules and has the potential to determine the absolute configuration of enantiomers at interfaces.
 COMMUNICATIONS


Communication: Probing the absolute configuration of chiral molecules at aqueous interfaces
View Description Hide DescriptionWe demonstrate that the enantiomers of chiralmacromolecules at an aqueous interface can be distinguished with monolayer sensitivity using heterodynedetected vibrational sumfrequency generation (VSFG). We perform VSFG spectroscopy with a polarization combination that selectively probes chiral molecular structures. By using frequencies far detuned from electronic resonances, we probe the chiral macromolecular structures with high surface specificity. The phase of the sumfrequency light generated by the chiral molecules is determined using heterodyne detection. With this approach, we can distinguish righthanded and lefthanded helical peptides at a waterair interface. We thus show that heterodynedetected VSFG is sensitive to the absolute configuration of complex, interfacial macromolecules and has the potential to determine the absolute configuration of enantiomers at interfaces.

Communication: Polarizable polymer chain under external electric field in a dilute polymer solution
View Description Hide DescriptionWe study the conformational behavior of polarizable polymer chain under an external homogeneous electric field within the Flory type selfconsistent field theory. We consider the influence of electric field on the polymer coil as well as on the polymer globule. We show that when the polymer chain conformation is a coil, application of external electric field leads to its additional swelling. However, when the polymer conformation is a globule, a sufficiently strong field can induce a globulecoil transition. We show that such “fieldinduced” globulecoil transition at the sufficiently small monomer polarizabilities goes quite smoothly. On the contrary, when the monomer polarizability exceeds a certain threshold value, the globulecoil transition occurs as a dramatic expansion in the regime of firstorder phase transition. The developed theoretical model can be applied to predicting polymer globule density change under external electric field in order to provide more efficient processes of polymer functionalization, such as sorption, dyeing, and chemical modification

 ARTICLES

 Theoretical Methods and Algorithms

Permutation blocking path integral Monte Carlo approach to the uniform electron gas at finite temperature
View Description Hide DescriptionThe uniform electron gas (UEG) at finite temperature is of high current interest due to its key relevance for many applications including dense plasmas and laser excited solids. In particular, density functional theory heavily relies on accurate thermodynamic data for the UEG. Until recently, the only existing firstprinciple results had been obtained for N = 33 electrons with restricted path integral Monte Carlo (RPIMC), for low to moderate density, . These data have been complemented by configuration path integral Monte Carlo (CPIMC) simulations for rs ≤ 1 that substantially deviate from RPIMC towards smaller rs and low temperature. In this work, we present results from an independent third method—the recently developed permutation blocking path integral Monte Carlo (PBPIMC) approach [T. Dornheim et al., New J. Phys. 17, 073017 (2015)] which we extend to the UEG. Interestingly, PBPIMC allows us to perform simulations over the entire density range down to half the Fermi temperature (θ = kBT/EF = 0.5) and, therefore, to compare our results to both aforementioned methods. While we find excellent agreement with CPIMC, where results are available, we observe deviations from RPIMC that are beyond the statistical errors and increase with density.

Vibrationally resolved NEXAFS at C and N Kedges of pyridine, 2fluoropyridine and 2,6difluoropyridine: A combined experimental and theoretical assessment
View Description Hide DescriptionIn the present work, the near edge Xray absorption spectroscopy (NEXAFS)spectra at both C and N Kedges of pyridine, 2fluoropyridine, and 2,6difluoropyridine have been studied both experimentally and theoretically. From an electronic point of view, both transition potential density functional theory and timedependent density functional theory approaches lead to reliable results provided that suitable basis sets and density functionals are employed. In this connection, the global hybrid B3LYP functional in conjunction with the EPRIII basis set appears particularly suitable after constant scaling of the band positions. For the N Kedge, vertical energies obtained at these levels and broadened by symmetric Gaussian distributions provide spectra in reasonable agreement with the experiment. Vibronic contributions further modulate the bandshapes leading to a better agreement with the experimental results, but are not strictly necessary for semiquantitative investigations. On the other hand, vibronic contributions are responsible for strong intensity redistribution in the NEXAFS C Kedge spectra, and their inclusion is thus mandatory for a proper description of experiments. In this connection, the simple vertical gradient model is particularly appealing in view of its sufficient reliability and low computational cost. For more quantitative results, the more refined vertical Hessian approach can be employed, and its effectiveness has been improved thanks to a new leastsquares fitting approach.

Accelerating the convergence of higherorder coupled cluster methods
View Description Hide DescriptionThe problem of the generally inferior convergence behavior of higherorder coupled cluster methods, such as CCSDT and CCSDTQ, compared to CCSD is analyzed in terms of MøllerPlesset perturbation theory. A new structure for the CCSDT and CCSDTQ equations (and various approximations of these) is proposed which reorders contributions between the various cluster amplitudes and emphasizes lowerorder corrections to the energy at each iteration. Numerical testing of the proposed method compared to the widely used direct inversion in the iterative subspace convergence acceleration technique shows significant improvement in the rate of convergence and total timetosolution, especially for methods including quadruple excitations.

Comparison of the Marcus and Pekar partitions in the context of nonequilibrium, polarizablecontinuum solvation models
View Description Hide DescriptionThe Marcus and Pekar partitions are common, alternative models to describe the nonequilibrium dielectric polarization response that accompanies instantaneous perturbation of a solute embedded in a dielectric continuum. Examples of such a perturbation include vertical electronic excitation and vertical ionization of a solutionphase molecule. Here, we provide a general derivation of the accompanying polarization response, for a quantummechanical solute described within the framework of a polarizable continuum model (PCM) of electrostatic solvation. Although the nonequilibrium free energy is formally equivalent within the two partitions, albeit partitioned differently into “fast” versus “slow” polarization contributions, discretization of the PCM integral equations fails to preserve certain symmetries contained in these equations (except in the case of the conductorlike models or when the solute cavity is spherical), leading to alternative, nonequivalent matrix equations. Unlike the total equilibrium solvation energy, however, which can differ dramatically between different formulations, we demonstrate that the equivalence of the Marcus and Pekar partitions for the nonequilibrium solvation correction is preserved to high accuracy. Differences in vertical excitation and ionizationenergies are <0.2 eV (and often <0.01 eV), even for systems specifically selected to afford a large polarization response. Numerical results therefore support the interchangeability of the Marcus and Pekar partitions, but also caution against relying too much on the fast PCM charges for interpretive value, as these charges differ greatly between the two partitions, especially in polar solvents.

Large deviations of Rouse polymer chain: First passage problem
View Description Hide DescriptionThe purpose of this paper is to investigate several analytical methods of solving first passage (FP) problem for the Rouse model, a simplest model of a polymer chain. We show that this problem has to be treated as a multidimensional Kramers’ problem, which presents rich and unexpected behavior. We first perform direct and forwardflux sampling (FFS) simulations and measure the mean firstpassage time τ(z) for the free end to reach a certain distance z away from the origin. The results show that the mean FP time is getting faster if the Rouse chain is represented by more beads. Two scaling regimes of τ(z) are observed, with transition between them varying as a function of chain length. We use these simulation results to test two theoretical approaches. One is a well known asymptotic theory valid in the limit of zero temperature. We show that this limit corresponds to fully extended chain when each chain segment is stretched, which is not particularly realistic. A new theory based on the well known FreidlinWentzell theory is proposed, where dynamics is projected onto the minimal action path. The new theory predicts both scaling regimes correctly, but fails to get the correct numerical prefactor in the first regime. Combining our theory with the FFS simulations leads us to a simple analytical expression valid for all extensions and chain lengths. One of the applications of polymer FP problem occurs in the context of branched polymer rheology. In this paper, we consider the armretraction mechanism in the tube model, which maps exactly on the model we have solved. The results are compared to the MilnerMcLeish theory without constraint release, which is found to overestimate FP time by a factor of 10 or more.

Multiscale Gaussian network model (mGNM) and multiscale anisotropic network model (mANM)
View Description Hide DescriptionGaussian networkmodel (GNM) and anisotropicnetworkmodel (ANM) are some of the most popular methods for the study of protein flexibility and related functions. In this work, we propose generalized GNM (gGNM) and ANM methods and show that the GNM Kirchhoff matrix can be built from the ideal lowpass filter, which is a special case of a wide class of correlation functions underpinning the linear scaling flexibilityrigidity index (FRI) method. Based on the mathematical structure of correlation functions, we propose a unified framework to construct generalized Kirchhoff matrices whose matrix inverse leads to gGNMs, whereas, the direct inverse of its diagonal elements gives rise to FRI method. With this connection, we further introduce two multiscale elasticnetworkmodels, namely, multiscale GNM (mGNM) and multiscale ANM (mANM), which are able to incorporate different scales into the generalized Kirchhoff matrices or generalized Hessian matrices. We validate our new multiscale methods with extensive numerical experiments. We illustrate that gGNMs outperform the original GNM method in the Bfactor prediction of a set of 364 proteins. We demonstrate that for a given correlation function, FRI and gGNM methods provide essentially identical Bfactor predictions when the scale value in the correlation function is sufficiently large. More importantly, we reveal intrinsic multiscale behavior in proteinstructures. The proposed mGNM and mANM are able to capture this multiscale behavior and thus give rise to a significant improvement of more than 11% in Bfactor predictions over the original GNM and ANM methods. We further demonstrate the benefits of our mGNM through the Bfactor predictions of many proteins that fail the original GNM method. We show that the proposed mGNM can also be used to analyzeprotein domain separations. Finally, we showcase the ability of our mANM for the analysis of protein collective motions.

Linearscaling timedependent densityfunctional theory beyond the TammDancoff approximation: Obtaining efficiency and accuracy with in situ optimised local orbitals
View Description Hide DescriptionWe present a solution of the full timedependent densityfunctional theory (TDDFT) eigenvalue equation in the linear response formalism exhibiting a linearscaling computational complexity with system size, without relying on the simplifying TammDancoff approximation (TDA). The implementation relies on representing the occupied and unoccupied subspaces with two different sets of in situ optimised localised functions, yielding a very compact and efficient representation of the transition density matrix of the excitation with the accuracy associated with a systematic basis set. The TDDFT eigenvalue equation is solved using a preconditioned conjugate gradient algorithm that is very memoryefficient. The algorithm is validated on a small test molecule and a good agreement with results obtained from standard quantum chemistry packages is found, with the preconditioner yielding a significant improvement in convergence rates. The method developed in this work is then used to reproduce experimental results of the absorptionspectrum of bacteriochlorophyll in an organic solvent, where it is demonstrated that the TDA fails to reproduce the main features of the low energyspectrum, while the full TDDFT equation yields results in good qualitative agreement with experimental data. Furthermore, the need for explicitly including parts of the solvent into the TDDFT calculations is highlighted, making the treatment of large system sizes necessary that are well within reach of the capabilities of the algorithm introduced here. Finally, the linearscaling properties of the algorithm are demonstrated by computing the lowest excitation energy of bacteriochlorophyll in solution. The largest systems considered in this work are of the same order of magnitude as a variety of widely studied pigmentprotein complexes, opening up the possibility of studying their properties without having to resort to any semiclassical approximations to parts of the protein environment.

NonMarkovian closure kinetics of flexible polymers with hydrodynamic interactions
View Description Hide DescriptionThis paper presents a theoretical analysis of the closure kinetics of a polymer with hydrodynamic interactions. This analysis, which takes into account the nonMarkovian dynamics of the endtoend vector and relies on the preaveraging of the mobility tensor (Zimm dynamics), is shown to reproduce very accurately the results of numerical simulations of the complete nonlinear dynamics. It is found that Markovian treatments based on a WilemskiFixman approximation significantly overestimate cyclization times (up to a factor 2), showing the importance of memory effects in the dynamics. In addition, this analysis provides scaling laws of the mean first cyclization time (MFCT) with the polymer size N and capture radius b, which are identical in both Markovian and nonMarkovian approaches. In particular, it is found that the scaling of the MFCT for large N is given by T ∼ N^{3/2}ln(N/b^{2}), which differs from the case of the Rouse dynamics where T ∼ N^{2}. The extension to the case of the reaction kinetics of a monomer of a Zimm polymer with an external target in a confined volume is also presented.
 Advanced Experimental Techniques

A dual cryogenic ion trap spectrometer for the formation and characterization of solvated ionic clusters
View Description Hide DescriptionA new experimental approach is presented in which two separate cryogenicion traps are used to reproducibly form weakly bound solvent clusters around electrosprayed ions and messengertag them for singlephoton infrared photodissociation spectroscopy. This approach thus enables the vibrational characterization of ionic clusters comprised of a solvent network around large and nonvolatile ions. We demonstrate the capabilities of the instrument by clustering water, methanol, and acetone around a protonated glycylglycine peptide. For water, cluster sizes with greater than twenty solvent molecules around a single ion are readily formed. We further demonstrate that similar water clusters can be formed around ions having a shielded charge center or those that do not readily form hydrogen bonds. Finally, infrared photodissociation spectra of D2tagged GlyGlyH^{+} ⋅ (H2O)1−4 are presented. They display wellresolved spectral features and comparisons with calculations reveal detailed information on the solvation structures of this prototypical peptide.
 Atoms, Molecules, and Clusters

Rotationally inelastic scattering of NO(A^{2}Σ^{+}) + Ar: Differential cross sections and rotational angular momentum polarization
View Description Hide DescriptionWe present the implementation of a new crossedmolecular beam, velocitymap ionimaging apparatus, optimized for collisions of electronically excited molecules. We have applied this apparatus to rotational energy transfer in NO(A^{2}Σ^{+}, v = 0, N = 0, j = 0.5) + Ar collisions, at an average energy of 525 cm^{−1}. We report differential cross sections for scattering into NO(A^{2}Σ^{+}, v = 0, N′ = 3, 5, 6, 7, 8, and 9), together with quantum scattering calculations of the differential cross sections and angle dependent rotational alignment. The differential cross sections show dramatic forward scattered peaks, together with oscillatory behavior at larger scattering angles, while the rotational alignment moments are also found to oscillate as a function of scattering angle. In general, the quantum scattering calculations are found to agree well with experiment, reproducing the forward scattering and oscillatory behavior at larger scattering angles. Analysis of the quantum scattering calculations as a function of total rotational angular momentum indicates that the forward scattering peak originates from the attractive minimum in the potential energy surface at the Nend of the NO. Deviations in the quantum scattering predictions from the experimental results, for scattering at angles greater than 10°, are observed to be more significant for scattering to odd final N′. We suggest that this represents inaccuracies in the potential energy surface, and in particular in its representation of the difference between the N and Oends of the molecule, as given by the oddorder Legendre moments of the surface.

Quantummechanical study of energies, structures, and vibrational spectra of the H(D)Cl complexed with dimethyl ether
View Description Hide DescriptionInteraction energies, molecular structure and vibrational frequencies of the binary complex formed between H(D)Cl and dimethyl ether have been obtained using quantumchemical methods. Equilibrium and vibrationally averaged structures, harmonic and anharmonic wavenumbers of the complex and its deuterated isotopomer were calculated using harmonic and anharmonic secondorder perturbation theory procedures with Density Functional Theory B3LYP and B2PLYPD and ab initio MøllerPlesset secondorder methods, and a 6311++G(3d,3p) basis set. A phenomenological model describing anharmonictype vibrational couplings within hydrogen bonds was developed to explain the unique broadening and fine structure, as well as the isotope effect of the Cl–H and Cl–D stretching IR absorption bands in the gaseous complexes with dimethyl ether, as an effect of hydrogen bond formation. Simulations of the rovibrational structure of the Cl–H and Cl–D stretching bands were performed and the results were compared with experimental spectra.

Kinetics of chemiionization reactions of lanthanide metals (Nd, Sm) from 150 to 450 K
View Description Hide DescriptionThe kinetics of chemiionization reactions of neodymium and samarium atoms with an oxygen atom to yield a metal monoxide cation and electron were studied using a flow tube apparatus over a temperature range of 150–450 K. Nd reacts efficiently with O, near the hardsphere collision limit at all temperatures, with a rate constant of 3 × 10^{−10} cm^{3} s^{−1} at 300 K and a slight positive temperature dependence. No chemiionization of Nd with N2O was observed, despite the reaction being exothermic. Chemiionization of Sm with O is slow, with a rate constant at 300 K determined to be 7 × 10^{−12} cm^{3} s^{−1}, although with large uncertainty. The Sm reaction also shows a slightly positive temperature dependence, described by a small activation energy of 60 meV. Although not definitive, the data suggest that excited states of Sm react efficiently whereas ground state Sm reacts inefficiently.

Electronic spectra of azaindole and its excited state mixing: A symmetryadapted cluster configuration interaction study
View Description Hide DescriptionElectronic structures of azaindole were studied using symmetryadapted cluster configuration interaction theory utilizing Dunning’s ccpVTZ basis set augmented with appropriate Rydbergspd functions on carbon and nitrogen atoms. The results obtained in the present study show good agreement with the available experimental values. Importantly, and contrary to previous theoretical studies, the excitation energy calculated for the important n–π^{∗} state agrees well with the experimental value. A recent study by Pratt and coworkers concluded that significant mixing of ππ^{∗} and nπ^{∗} states leads to major change in the magnitude and direction of the dipole moment of the upper state vibrational level in the 0,0 + 280 cm^{−1} band in the S1←S0 transition when compared to that of the zeropoint level of the S1 state. The present study, however, shows that all the four lowest lying excited states, ^{1}Lbππ^{∗}, ^{1}Laππ^{∗}, nπ^{∗}, and πσ^{∗}, cross each other in one way or another, and hence, significant state mixing between them is likely. The upper state vibrational level in the 0,0 + 280 cm^{−1} band in the S1←S0 transition benefits from this fourstate mixing and this can explain the change in magnitude and direction of the dipole moment of the S1 excited vibrational level. This multistate mixing, and especially the involvement of πσ^{∗} state in mixing, could also provide a route for hydrogen atom detachment reactions. The electronic spectra of benzimidazole, a closely related system, were also investigated in the present study.

Cold and ultracold dynamics of the barrierless D^{+} + H2 reaction: Quantum reactive calculations for ∼R^{−4} long range interaction potentials
View Description Hide DescriptionQuantum reactive and elastic cross sections and rate coefficients have been calculated for D^{+} + H2 (v = 0, j = 0) collisions in the energy range from 10^{−8} K (deep ultracold regime), where only one partial wave is open, to 150 K (Langevin regime) where many of them contribute. In systems involving ions, the ∼R^{−4} behavior extends the interaction up to extremely long distances, requiring a special treatment. To this purpose, we have used a modified version of the hyperspherical quantum reactive scattering method, which allows the propagations up to distances of 10^{5} a0 needed to converge the elastic cross sections. Interpolation procedures are also proposed which may reduce the cost of exact dynamical calculations at such low energies. Calculations have been carried out on the PES by Velilla et al. [J. Chem. Phys. 129, 084307 (2008)] which accurately reproduces the long range interactions. Results on its prequel, the PES by Aguado et al. [J. Chem. Phys. 112, 1240 (2000)], are also shown in order to emphasize the significance of the inclusion of the long range interactions. The calculated reaction rate coefficient changes less than one order of magnitude in a collision energy range of ten orders of magnitude, and it is found in very good agreement with the available experimental data in the region where they exist (10100 K). Statetostate reaction probabilities are also provided which show that for each partial wave, the distribution of HD final states remains essentially constant below 1 K.

On the origin of donor O–H bond weakening in phenolwater complexes
View Description Hide DescriptionMatrix isolation infrared spectroscopy has been used to investigate intermolecular interactions in a series of binary O–H⋯O hydrogen bonded phenolwater complexes where water is the common acceptor. The interaction at the binding site has been tuned by incorporating multiple fluorine substitutions at different aromatic ring sites of the phenol moiety. The spectral effects for the aforesaid chemical changes are manifested in the infrared spectra of the complexes as systematic increase in spectral shift of the phenolic O–H stretching fundamental (ΔνO–H). While νO–H bands of the monomers of all the fluorophenols appear within a very narrow frequency range, the increase in ΔνO–H of the complexes from phenol to pentafluorophenol is very large, nearly 90%. The observed values of ΔνO–H do not show a linear correlation with the total binding energies (ΔEb) of the complexes, expected according to BadgerBauer rule. However, in the same ΔνO–H vs ΔEb plot, nice linear correlations are revealed if the complexes of orthofluorophenols are treated separately from their meta/parasubstituted analogues. The observations imply that in spite of having the same binding site (O–H⋯O) and the same chemical identities (phenolic), the complexes of ortho and nonortho fluorophenols do not belong, from the viewpoint of detailed molecular interactions, to a homologous series. Linear correlations of ΔνO–H are, however, observed with respect to the electrostatic component of ΔEb as well as the quantum mechanical charge transferinteractionenergy (ECT). From quantitative viewpoint, the latter correlation along with the associated electronic structure parameters appears more satisfactory. It has also been noted that the observed ΔνO–H values of the complexes display a linear relationship with the aqueous phase pKa values of the respective phenol derivatives.

The infrared spectrum of the Ne–C2D2 complex
View Description Hide DescriptionInfrared spectra of Ne–C2D2 are observed in the region of the ν3 fundamental band (asymmetric C–D stretch, ≈2440 cm^{−1}) using a tunable optical parametric oscillator to probe a pulsed supersonic slit jet expansion from a cooled nozzle. Like heliumacetylene, this system lies close to the free rotor limit, making analysis tricky because stronger transitions tend to pile up close to monomer (C2D2) rotationvibration transitions. Assignments are aided by predicted rotational energies calculated from a published ab initio intermolecular potential energy surface. The analysis extends up to the j = 3←2 band, where j labels C2D2 rotation within the dimer, and is much more complete than the limited infrared assignments previously reported for Ne–C2H2 and Ne–C2HD. Two previous microwave transitions within the j = 1 state of Ne–C2D2 are reassigned. Coriolis model fits to the theoretical levels and to the spectrum are compared. Since the variations observed as a function of C2D2 vibrational excitation are comparable to those noted between theory and experiment, it is evident that more detailed testing of theory will require vibrational averaging over the acetylene intramolecular modes.

Rotational dynamics of a diatomic molecular ion in a Paul trap
View Description Hide DescriptionWe present models for a heteronuclear diatomic molecular ion in a linear Paul trap in a rigidrotor approximation, one purely classical and the other where the centerofmass motion is treated classically, while rotational motion is quantized. We study the rotational dynamics and their influence on the motion of the centerofmass, in the presence of the coupling between the permanent dipole moment of the ion and the trappingelectric field. We show that the presence of the permanent dipole moment affects the trajectory of the ion and that it departs from the Mathieu equation solution found for atomic ions. For the case of quantum rotations, we also evidence the effect of the abovementioned coupling on the rotational states of the ion.

Control of multiple excited image states around segmented carbon nanotubes
View Description Hide DescriptionElectronic image states around segmented carbon nanotubes can be confined and shaped along the nanotube axis by engineering the image potential. We show how several such image states can be prepared simultaneously along the same nanotube. The interelectronic distance can be controlled a priori by engineering tubes of specific geometries. High sensitivity to external electric and magnetic fields can be exploited to manipulate these states and their mutual longrange interactions. These building blocks provide access to a new kind of tailored interacting quantum systems.