Index of content:
Volume 140, Issue 7, 21 February 2014
Weak van der Waals adsorption of π-conjugated hydrocarbon molecules onto the gold surface, Au(111), is one of the essential processes in constructing organic-metal interfaces in organic electronics. Here we provide a first direct observation of adsorption geometry of a single π-conjugated hydrocarbon molecule on Au(111) using an atomically resolved scanning tunneling microscopy study combined with van der Waals density functional methodology. For the purpose, we utilized a highly symmetric π-conjugated hydrocarbon molecule, dehydrobenzoannulene (DBA), which has a definite three-fold symmetry, the same as the Au(111) surface. Interestingly, our observations on an atomically resolved scale clearly indicate that the DBA molecule has only one adsorption configuration on Au(111) in spite of the weak van der Waals adsorption system. Based on the precisely determined adsorption geometry of DBA/Au(111), our calculation results imply that even a very small contribution of the interfacial orbital interaction at the organic-metal interface can play a decisive role in constraining the adsorption geometry even in the van der Waals adsorption system of a π-conjugated hydrocarbon molecule on the noblest Au(111) surface. Our observations provide not only deeper insight into the weak adsorption process, but also new perspectives to organic electronics using π-conjugated hydrocarbon molecules on the Au surface.
- Theoretical Methods and Algorithms
140(2014); http://dx.doi.org/10.1063/1.4865750View Description Hide Description
Eckart frame is a unique embedding in the theory of molecular vibrations and rotations. It is defined by the condition that the Coriolis coupling of the reference structure of the molecule is zero for every choice of the shape coordinates. It is far from trivial to set up Eckart kinetic energy operators (KEOs), when the shape of the molecule is described by curvilinear coordinates. In order to obtain the KEO, one needs to set up the corresponding contravariant metric tensor. Here, I derive explicitly the Eckart frame rotational measuring vectors. Their inner products with themselves give the rotational elements, and their inner products with the vibrational measuring vectors (which, in the absence of constraints, are the mass-weighted gradients of the shape coordinates) give the Coriolis elements of the contravariant metric tensor. The vibrational elements are given as the inner products of the vibrational measuring vectors with themselves, and these elements do not depend on the choice of the body-frame. The present approach has the advantage that it does not depend on any particular choice of the shape coordinates, but it can be used in conjunction with allshape coordinates. Furthermore, it does not involve evaluation of covariant metric tensors, chain rules of derivation, or numerical differentiation, and it can be easily modified if there are constraints on the shape of the molecule. Both the planar and non-planar reference structures are accounted for. The present method is particular suitable for numerical work. Its computational implementation is outlined in an example, where I discuss how to evaluate vibration-rotation energies and eigenfunctions of a general N-atomic molecule, the shape of which is described by a set of local polyspherical coordinates.
140(2014); http://dx.doi.org/10.1063/1.4864200View Description Hide Description
Energy transfer between a macromolecule or supramolecular assembly and a host medium is considered from the perspective of Newton's equations and Lie-Trotter factorization. The development starts by demonstrating that the energy of the molecule evolves slowly relative to the time scale of atomic collisions-vibrations. The energy is envisioned to be a coarse-grained variable that coevolves with the rapidly fluctuating atomistic degrees of freedom. Lie-Trotter factorization is shown to be a natural framework for expressing this coevolution. A mathematical formalism and workflow for efficient multiscale simulation of energy transfer is presented. Lactoferrin and human papilloma virus capsid-like structure are used for validation.
Generalizing the self-healing diffusion Monte Carlo approach to finite temperature: A path for the optimization of low-energy many-body bases140(2014); http://dx.doi.org/10.1063/1.4861222View Description Hide Description
A statistical method is derived for the calculation of thermodynamic properties of many-body systems at low temperatures. This method is based on the self-healing diffusion Monte Carlo method for complex functions [F. A. Reboredo, J. Chem. Phys.136, 204101 (2012)] and some ideas of the correlation function Monte Carlo approach [D. M. Ceperley and B. Bernu, J. Chem. Phys.89, 6316 (1988)]. In order to allow the evolution in imaginary time to describe the density matrix, we remove the fixed-node restriction using complex antisymmetric guiding wave functions. In the process we obtain a parallel algorithm that optimizes a small subspace of the many-body Hilbert space to provide maximum overlap with the subspace spanned by the lowest-energy eigenstates of a many-body Hamiltonian. We show in a model system that the partition function is progressively maximized within this subspace. We show that the subspace spanned by the small basis systematically converges towards the subspace spanned by the lowest energy eigenstates. Possible applications of this method for calculating the thermodynamic properties of many-body systems near the ground state are discussed. The resulting basis can also be used to accelerate the calculation of the ground or excited states with quantum Monte Carlo.
140(2014); http://dx.doi.org/10.1063/1.4864759View Description Hide Description
The response of an arbitrary closed quantum system to a partially coherent electric field is investigated, with a focus on the transient coherences in the system. As a model we examine, both perturbatively and numerically, the coherences induced in a three level V system. Both rapid turn-on and pulsed turn-on effects are investigated. The effect of a long and incoherent pulse is also considered, demonstrating that during the pulse the system shows a coherent response which reduces after the pulse is over. Both the pulsed scenario and the thermally broadened CW case approach a mixed state in the long time limit, with rates dictated by the adjacent level spacings and the coherence time of the light, and via a mechanism that is distinctly different from traditional decoherence. These two excitation scenarios are also explored for a minimal “toy” model of the electronic levels in pigment protein complex PC645 by both a collisionally broadened CW laser and by a noisy pulse, where unexpectedly long transient coherence times are observed and explained. The significance of environmentally induced decoherence is noted.
140(2014); http://dx.doi.org/10.1063/1.4865229View Description Hide Description
It is shown that the diagonal components of the mixed electric-magnetic dipole polarizability tensor, used to rationalize the optical rotatory power of chiral molecules, are origin independent, if they are referred to the coordinate system defined by the eigenvectors of the dynamic electric dipole polarizability, for a given value ω of the frequency of a monochromatic wave impinging on an ordered sample. Within this reference frame, the individual diagonal components of the mixed electric-magnetic dipole polarizability are separately measurable properties. The theoretical method is applied via a test calculation to the cyclic 1,2-M enantiomer of the dioxin molecule, using a large Gaussian basis set to estimate near Hartree-Fock values within a series of dipole length, velocity, and acceleration representations.
140(2014); http://dx.doi.org/10.1063/1.4865339View Description Hide Description
We present a full quantum evaluation of the water second virial coefficient B(T) based on the Takahashi-Imada second order approximation. As the associated trace is performed in the coordinate representation, it does also include contribution from the whole continuum, i.e., resonances and collision pairs of monomers. This approach is compared to a Path Integral Monte Carlo evaluation of this coefficient by Schenter [J. Chem. Phys.117, 6573 (2002)] for the TIP4P potential and shown to give extremely close results in the low temperature range (250–450 K) reported. Using a recent ab initio flexible potential for the water dimer, this new formulation leads to very good agreement with experimental values over the whole range of temperatures available. The virial coefficient is then used in the well known relation K p (T) = −(B(T) − b M )/RT where the excluded volume b M is assimilated to the second virial coefficient of pure water monomer vapor and approximated from the inner repulsive part of the interaction potential. This definition, which renders b M temperature dependent, allows us to retrieve the 38 cm3 mol−1 value commonly used, at room temperature. The resulting values for K p (T) are in agreement with available experimental data obtained from infrared absorption spectra of water vapor.
Electrostatic force between a charged sphere and a planar surface: A general solution for dielectric materials140(2014); http://dx.doi.org/10.1063/1.4862897View Description Hide Description
Using the bispherical coordinate system, an analytical solution describing the electrostatic force between a charged dielectric sphere and a planar dielectric surface is presented. This new solution exhibits excellent numerical convergence, and is sufficiently general as to allow for the presence of charge on both the sphere and the surface. The solution has been applied to two examples of sphere-plane interactions chosen from the literature, namely, (i) a charged lactose sphere interacting with a neutral glass surface and (ii) a charged polystyrene sphere interacting with a neutral graphite surface. Theory suggests that in both cases the electrostatic force makes a major contribution to the experimentally observed attraction at short sphere-plane separations, and that the force is much longer ranged than previously suggested.
Computational efficiency improvement with Wigner rotation technique in studying atoms in intense few-cycle circularly polarized pulses140(2014); http://dx.doi.org/10.1063/1.4865747View Description Hide Description
We show that by introducing Wigner rotation technique into the solution of time-dependent Schrödinger equation in length gauge, computational efficiency can be greatly improved in describing atoms in intense few-cycle circularly polarized laser pulses. The methodology with Wigner rotation technique underlying our openMP parallel computational code for circularly polarized laser pulses is described. Results of test calculations to investigate the scaling property of the computational code with the number of the electronic angular basis function l as well as the strong field phenomena are presented and discussed for the hydrogen atom.
140(2014); http://dx.doi.org/10.1063/1.4865220View Description Hide Description
Transition paths characterize chemical reaction mechanisms. In this paper, we present a new method to find mean reaction paths based on the free energy. A nudged elastic band (NEB) is optimized using gradients and Hessians of the free energy, which are obtained from umbrella integration. The transition state can be refined by a Newton–Raphson search starting from the highest point of the NEB path. All optimizations are done using Cartesian coordinates. Independent molecular dynamics (MD) runs are performed at each image used to discretize the path. This makes the method intrinsically parallel. In contrast to other free energy methods, the algorithm does not become more expensive when including more degrees of freedom in the active space. The method is applied to the alanine-dipeptide as a test case and compared to pathways that have been derived from metadynamics and forward flux sampling.
The FADE mass-stat: A technique for inserting or deleting particles in molecular dynamics simulations140(2014); http://dx.doi.org/10.1063/1.4865337View Description Hide Description
The emergence of new applications of molecular dynamics (MD) simulation calls for the development of mass-statting procedures that insert or delete particles on-the-fly. In this paper we present a new mass-stat which we term FADE, because it gradually “fades-in” (inserts) or “fades-out” (deletes) molecules over a short relaxation period within a MD simulation. FADE applies a time-weighted relaxation to the intermolecular pair forces between the inserting/deleting molecule and any neighbouring molecules. The weighting function we propose in this paper is a piece-wise polynomial that can be described entirely by two parameters: the relaxation time scale and the order of the polynomial. FADE inherently conserves overall system momentum independent of the form of the weighting function. We demonstrate various simulations of insertions of atomic argon, polyatomic TIP4P water, polymer strands, and C60 Buckminsterfullerene molecules. We propose FADE parameters and a maximum density variation per insertion-instance that restricts spurious potential energy changes entering the system within desired tolerances. We also demonstrate in this paper that FADE compares very well to an existing insertion algorithm called USHER, in terms of accuracy, insertion rate (in dense fluids), and computational efficiency. The USHER algorithm is applicable to monatomic and water molecules only, but we demonstrate that FADE can be generally applied to various forms and sizes of molecules, such as polymeric molecules of long aspect ratio, and spherical carbon fullerenes with hollow interiors.
140(2014); http://dx.doi.org/10.1063/1.4864356View Description Hide Description
The vibrational Hamiltonian involves two high dimensional operators, the kinetic energy operator (KEO), and the potential energy surface (PES). Both must be approximated for systems involving more than a few atoms. Adaptive approximation schemes are not only superior to truncated Taylor or many-body expansions (MBE), they also allow for error estimates, and thus operators of predefined precision. To this end, modified sparse grids (SG) are developed that can be combined with adaptive MBEs. This MBE/SG hybrid approach yields a unified, fully adaptive representation of the KEO and the PES. Refinement criteria, based on the vibrational self-consistent field (VSCF) and vibrational configuration interaction (VCI) methods, are presented. The combination of the adaptive MBE/SG approach and the VSCF plus VCI methods yields a black box like procedure to compute accurate vibrational spectra. This is demonstrated on a test set of molecules, comprising water, formaldehyde, methanimine, and ethylene. The test set is first employed to prove convergence for semi-empirical PM3-PESs and subsequently to compute accurate vibrational spectra from CCSD(T)-PESs that agree well with experimental values.
Optimization of the Jastrow factor using the random-phase approximation and a similarity-transformed Hamiltonian: Application to band-structure calculation for some semiconductors and insulators140(2014); http://dx.doi.org/10.1063/1.4865500View Description Hide Description
Based on the random-phase approximation and the transcorrelated (TC) method, we optimize the Jastrow factor together with one-electron orbitals in the Slater determinant in the correlated wave function with a new scheme for periodic systems. The TC method is one of the promising wave function theories for first-principles electronic structure calculation, where the many-body wave function is approximated as a product of a Slater determinant and a Jastrow factor, and the Hamiltonian is similarity-transformed by the Jastrow factor. Using this similarity-transformed Hamiltonian, we can optimize the one-electron orbitals without evaluating 3N-dimensional integrations for the N-electron system. In contrast, optimization of the Jastrow factor within the framework of the TC method is computationally much more expensive and has not been performed for solid-state calculations before. In this study, we also benefit from the similarity-transformation in optimizing the Jastrow factor. Our optimization scheme is tested in applications to some solids from narrow-gap semiconductors to wide-gap insulators, and it is verified that the band gap of a wide-gap insulator and the lattice constants of some solids are improved by this optimization with reasonable computational cost.
- Advanced Experimental Techniques
Coherent superposition of M-states in a single rovibrational level of H2 by Stark-induced adiabatic Raman passage140(2014); http://dx.doi.org/10.1063/1.4865131View Description Hide Description
We prepare an ensemble of isolated rovibrationally excited (v = 1, J = 2) H2 molecules in a phase-locked superposition of magnetic sublevels M using Stark-induced adiabatic Raman passage with linearly polarized single-mode pump (at 532 nm, ∼6 ns pulse duration, 200 mJ/pulse) and Stokes (699 nm, ∼4 ns pulse duration, 20 mJ/pulse) laser excitation. A biaxial superposition state, given by , is prepared with linearly but cross-polarized pump and Stokes laser pulses copropagating along the quantization z-axis. The degree of phase coherence is measured by using the O(2) line of the H2 E,F-X (0,1) band via 2 + 1 resonance enhanced multiphoton ionization (REMPI) at 210.8 nm by recording interference fringes in the REMPI signal in a time-of-flight mass spectrometer as the direction of the UV laser polarization is rotated using a half-wave plate. Nearly 60% population transfer from H2 (v = 0, J = 0) ground state to the superposition state in H2 (v = 1, J = 2) is measured from the depletion of the Q(0) line of the E,F-X (0,0) band as the Stokes frequency is tuned across the (v = 0, J = 0) → (v = 1, J = 2) Raman resonance.
140(2014); http://dx.doi.org/10.1063/1.4865129View Description Hide Description
In contrast to the single shock compression state that can be obtained directly via experimental measurements, the multi-shock compression states, however, have to be calculated with the aid of theoretical models. In order to determine experimentally the multiple shock states, a diagnostic approach with the Doppler pins system (DPS) and the pyrometer was used to probe multiple shocks in dense argon plasmas. Plasma was generated by a shock reverberation technique. The shock was produced using the flyer plate impact accelerated up to ∼6.1 km/s by a two-stage light gas gun and introduced into the plenum argon gas sample, which was pre-compressed from the environmental pressure to about 20 MPa. The time-resolved optical radiation histories were determined using a multi-wavelength channel optical transience radiance pyrometer. Simultaneously, the particle velocity profiles of the LiF window was measured with multi-DPS. The states of multi-shock compression argon plasma were determined from the measured shock velocities combining the particle velocity profiles. We performed the experiments on dense argon plasmas to determine the principal Hugonoit up to 21 GPa, the re-shock pressure up to 73 GPa, and the maximum measure pressure of the fourth shock up to 158 GPa. The results are used to validate the existing self-consistent variational theory model in the partial ionization region and create new theoretical models.
140(2014); http://dx.doi.org/10.1063/1.4865833View Description Hide Description
Two different samples of graphene, multi-layer flakes on Si/SiO2 substrates and single layer graphene on glass, have been examined by reflectivity contrast and spatial modulation spectroscopy measurements. For the multi-layer graphene flakes, the reflectivity contrast and spatial modulation spectroscopy measurements are in good agreement, validating the application of spatial modulation spectroscopy to two-dimensional samples. The measurements for single layer graphene on glass show features that correspond to increases and decreases in reflectivity. The features with increased reflectivity are assigned to small regions of multilayer graphene or polymer, and the features with decreased reflectivity are assigned to holes in the graphene film. Using a model for thin film reflectivity we calculate the size dependent spatial modulation signal for the holes, and find that a significant number of holes have a larger than expected signal. This could arise from the presence of multi-layers of graphene in the sample, or because of optical resonance effects for the holes.
- Atoms, Molecules, and Clusters
First principles study of the structural, electronic, and transport properties of triarylamine-based nanowires140(2014); http://dx.doi.org/10.1063/1.4864754View Description Hide Description
We investigate with state of the art density functional theory the structural, electronic, and transport properties of a class of recently synthesized nanostructures based on triarylamine derivatives. First, we consider the single molecule precursors in the gas phase and calculate their static properties, namely (i) the geometrical structure of the neutral and cationic ions, (ii) the electronic structure of the frontier molecular orbitals, and (iii) the ionization potential, hole extraction potential, and internal reorganization energy. This initial study does not evidence any direct correlation between the properties of the individual molecules and their tendency to self-assembly. Subsequently, we investigate the charge transport characteristics of the triarylamine derivatives nanowires, by using Marcus theory. For one derivative we further construct an effective Hamiltonian including intermolecular vibrations and evaluate the mobility from the Kubo formula implemented with Monte Carlo sampling. These two methods, valid respectively in the sequential hopping and polaronic band limit, give us values for the room-temperature mobility in the range 0.1–12 cm2/Vs. Such estimate confirms the superior transport properties of triarylamine-based nanowires, and make them an attracting materials platform for organic electronics.
140(2014); http://dx.doi.org/10.1063/1.4863137View Description Hide Description
Optimal control experiments can readily identify effective shaped laser pulses, or “photonic reagents,” that achieve a wide variety of objectives. An important additional practical desire is for photonic reagent prescriptions to produce good, if not optimal, objective yields when transferred to a different system or laboratory. Building on general experience in chemistry, the hope is that transferred photonic reagent prescriptions may remain functional even though all features of a shaped pulse profile at the sample typically cannot be reproduced exactly. As a specific example, we assess the potential for transferring optimal photonic reagents for the objective of optimizing a ratio of photoproduct ions from a family of halomethanes through three related experiments. First, applying the same set of photonic reagents with systematically varying second- and third-order chirp on both laser systems generated similar shapes of the associated control landscape (i.e., relation between the objective yield and the variables describing the photonic reagents). Second, optimal photonic reagents obtained from the first laser system were found to still produce near optimal yields on the second laser system. Third, transferring a collection of photonic reagents optimized on the first laser system to the second laser system reproduced systematic trends in photoproduct yields upon interaction with the homologous chemical family. These three transfers of photonic reagents are demonstrated to be successful upon paying reasonable attention to overall laser system characteristics. The ability to transfer photonic reagents from one laser system to another is analogous to well-established utilitarian operating procedures with traditional chemical reagents. The practical implications of the present results for experimental quantum control are discussed.
140(2014); http://dx.doi.org/10.1063/1.4865256View Description Hide Description
We have performed large-scale Lennard-Jones molecular dynamics simulations of homogeneous vapor-to-liquid nucleation, with 109 atoms. This large number allows us to resolve extremely low nucleation rates, and also provides excellent statistics for cluster properties over a wide range of cluster sizes. The nucleation rates, cluster growth rates, and size distributions are presented in Diemand et al. [J. Chem. Phys.139, 74309 (2013)], while this paper analyses the properties of the clusters. We explore the cluster temperatures, density profiles, potential energies, and shapes. A thorough understanding of the properties of the clusters is crucial to the formulation of nucleation models. Significant latent heat is retained by stable clusters, by as much as ΔkT = 0.1ε for clusters with size i = 100. We find that the clusters deviate remarkably from spherical—with ellipsoidal axis ratios for critical cluster sizes typically within b/c = 0.7 ± 0.05 and a/c = 0.5 ± 0.05. We examine cluster spin angular momentum, and find that it plays a negligible role in the cluster dynamics. The interfaces of large, stable clusters are thinner than planar equilibrium interfaces by 10%−30%. At the critical cluster size, the cluster central densities are between 5% and 30% lower than the bulk liquid expectations. These lower densities imply larger-than-expected surface areas, which increase the energy cost to form a surface, which lowers nucleation rates.
Electronic properties of graphene nano-flakes: Energy gap, permanent dipole, termination effect, and Raman spectroscopy140(2014); http://dx.doi.org/10.1063/1.4865414View Description Hide Description
The electronic properties of graphene nano-flakes (GNFs) with different edge passivation are investigated by using density functional theory. Passivation with F and H atoms is considered: (X = F or H). We studied GNFs with 10 < N c < 56 and limit ourselves to the lowest energy configurations. We found that: (i) the energy difference Δ between the highest occupied molecular orbital and the lowest unoccupied molecular orbital decreases with N c , (ii) topological defects (pentagon and heptagon) break the symmetry of the GNFs and enhance the electric polarization, (iii) the mutual interaction of bilayer GNFs can be understood by dipole-dipole interaction which were found sensitive to the relative orientation of the GNFs, (iv) the permanent dipoles depend on the edge terminated atom, while the energy gap is independent of it, and (v) the presence of heptagon and pentagon defects in the GNFs results in the largest difference between the energy of the spin-up and spin-down electrons which is larger for the H-passivated GNFs as compared to F-passivated GNFs. Our study shows clearly the effect of geometry, size, termination, and bilayer on the electronic properties of small GNFs. This study reveals important features of graphene nano-flakes which can be detected using Raman spectroscopy.
- Liquids, Glasses, and Crystals
Melting temperatures of H2O up to 72 GPa measured in a diamond anvil cell using CO2 laser heating technique140(2014); http://dx.doi.org/10.1063/1.4865252View Description Hide Description
The melting curve of H2O from 49 to 72 GPa was determined by using a laser-heated diamond anvil cell. Double-sided CO2 laser heating technique was employed in order to heat the sample directly. Discontinuous changes of the heating efficiency attributed to the H2O melting were observed between 49 and 72 GPa. The obtained melting temperatures at 49 and 72 GPa are 1200 and 1410 K, respectively. We found that the slope of the melting curve significantly decreases with increasing pressure, only 5 K/GPa at 72 GPa while 44 K/GPa at 49 GPa. Our results suggest that the melting curve does not intersect with the isentropes of Uranus and Neptune, and hence, H2O should remain in the liquid state even at the pressure and temperature conditions found deep within Uranus and Neptune.