Volume 138, Issue 11, 21 March 2013
Index of content:
- Theoretical Methods and Algorithms
138(2013); http://dx.doi.org/10.1063/1.4794424View Description Hide Description
We reported a developed methodology to design superhard materials for given chemical systems under external conditions (here, pressure). The new approach is based on the CALYPSO algorithm and requires only the chemical compositions to predict the hardness vs. energy map, from which the energetically preferable superhard structures are readily accessible. In contrast to the traditional ground state structure prediction method where the total energy was solely used as the fitness function, here we adopted hardness as the fitness function in combination with the first-principles calculation to construct the hardness vs. energy map by seeking a proper balance between hardness and energy for a better mechanical description of given chemical systems. To allow a universal calculation on the hardness for the predicted structure, we have improved the earlier hardness model based on bond strength by applying the Laplacian matrix to account for the highly anisotropic and molecular systems. We benchmarked our approach in typical superhard systems, such as elemental carbon, binary B-N, and ternary B-C-N compounds. Nearly all the experimentally known and most of the earlier theoretical superhard structures have been successfully reproduced. The results suggested that our approach is reliable and can be widely applied into design of new superhard materials.
138(2013); http://dx.doi.org/10.1063/1.4794425View Description Hide Description
Singlet fission, a spin-allowed energy transfer process generating two triplet excitons from one singlet exciton, has the potential to dramatically increase the efficiency of organic solar cells. However, the dynamical mechanism of this phenomenon is not fully understood and a complete, microscopic theory of singlet fission is lacking. In this work, we assemble the components of a comprehensive microscopic theory of singlet fission that connects excited state quantum chemistry calculations with finite-temperature quantum relaxation theory. We elaborate on the distinction between localized diabatic and delocalized exciton bases for the interpretation of singlet fission experiments in both the time and frequency domains. We discuss various approximations to the exact density matrix dynamics and propose Redfield theory as an ideal compromise between speed and accuracy for the detailed investigation of singlet fission in dimers, clusters, and crystals. Investigations of small model systems based on parameters typical of singlet fission demonstrate the numerical accuracy and practical utility of this approach.
Microscopic theory of singlet exciton fission. II. Application to pentacene dimers and the role of superexchange138(2013); http://dx.doi.org/10.1063/1.4794427View Description Hide Description
We apply our theoretical formalism for singlet exciton fission, introduced in the previous paper [T. C. Berkelbach, M. S. Hybertsen, and D. R. Reichman, J. Chem. Phys.138, 114102 (Year: 2013)]10.1063/1.4794425 to molecular dimers of pentacene, a widely studied material that exhibits singlet fission in the crystal phase. We address a longstanding theoretical issue, namely whether singlet fission proceeds via two sequential electron transfer steps mediated by charge-transfer states or via a direct two-electron transfer process. We find evidence for a superexchange mediated mechanism, whereby the fission process proceeds through virtual charge-transfer states which may be very high in energy. In particular, this mechanism predicts efficient singlet fission on the sub-picosecond timescale, in reasonable agreement with experiment. We investigate the role played by molecular vibrations in mediating relaxation and decoherence, finding that different physically reasonable forms for the bath relaxation function give similar results. We also examine the competing direct coupling mechanism and find it to yield fission rates slower in comparison with the superexchange mechanism for the dimer. We discuss implications for crystalline pentacene, including the limitations of the dimer model.
138(2013); http://dx.doi.org/10.1063/1.4794686View Description Hide Description
A recently introduced method for coarse-graining standard continuous Metropolis Monte Carlo simulations of atomic or molecular fluids onto a rigid lattice of variable scale [X. Liu, W. D. Seider, and T. Sinno, Phys. Rev. E86, 026708 (Year: 2012)]10.1103/PhysRevE.86.026708 is further analyzed and extended. The coarse-grained Metropolis Monte Carlo technique is demonstrated to be highly consistent with the underlying full-resolution problem using a series of detailed comparisons, including vapor-liquid equilibrium phase envelopes and spatial density distributions for the Lennard-Jones argon and simple point charge water models. In addition, the principal computational bottleneck associated with computing a coarse-grained interaction function for evolving particle positions on the discretized domain is addressed by the introduction of new closure approximations. In particular, it is shown that the coarse-grained potential, which is generally a function of temperature and coarse-graining level, can be computed at multiple temperatures and scales using a single set of free energy calculations. The computational performance of the method relative to standard Monte Carlo simulation is also discussed.
Reorganization energy of electron transfer processes in ionic fluids: A molecular Debye-Hückel approach138(2013); http://dx.doi.org/10.1063/1.4794790View Description Hide Description
The reorganization energy of electron transfer processes in ionic fluids is studied under the linear response approximation using a molecule Debye-Hückel theory. Reorganization energies of some model reactants of electron transfer reactions in molten salts are obtained from molecular simulations and a molecule Debye-Hückel approach. Good agreements between simulation results and the results from our theoretical calculations using the same model Hamiltonian are found. Applications of our theory to electron transfer reactions in room temperature ionic liquids further demonstrate that our theoretical approach presents a reliable and accurate methodology for the estimation of reorganization energies of electron transfer reactions in ionic fluids.
138(2013); http://dx.doi.org/10.1063/1.4794995View Description Hide Description
It is known that Belousov-Zhabotinsky (BZ) reaction can be applied to chemical computation, e.g., image processing, computational geometry, logical computation, and so on. In the field of logical computation, some basic logic gates and basic combinational logic circuits, such as adder, counter, memory cell, have already been implemented in simulations or in chemical experiments. In this paper, we focus on another important combinational logic circuit, binary decoder. Integrating AND gate and NOT gate, we first design and implement a one-bit binary decoder through numerical simulation. Then we show that one-bit decoder can be extended to design two-bit, three-bit, or even higher bit binary decoders by a cascade method. The simulation results demonstrate the effectiveness of these devices. The chemical realization of decoders can guide the construction of more sophisticated functions based on BZ reaction; meanwhile, the cascade method can facilitate the design of other combinational logic circuits.
138(2013); http://dx.doi.org/10.1063/1.4795158View Description Hide Description
We present frequency-dependent polarizabilities and C 6 dipole-dipole dispersion coefficients for a wide range of fullerene molecules including C60, C70, C78, C80, C82, and C84. The static and dynamic polarizabilities at imaginary frequencies are computed using time-dependent Hartree-Fock, B3LYP, and CAM-B3LYP ab initio methods by employing the complex linear polarization propagator and are subsequently utilized to determine the C 6 coefficients using the Casimir-Polder relation. Overall, the C60 and C70 average static polarizabilities agree to better than 2% with linear-response coupled-cluster single double and experimental benchmark results, and the C 6 coefficient of C60 agrees to better than 1% with the best accepted value. B3LYP provides the best agreement with benchmark results with deviations less than 0.1% in and C 6. We find that the static polarizabilities and the C 6 coefficients are non-additive, and scale, respectively, as N 1.2 and N 2.2 with the number of carbon atoms in the fullerene molecule. The exponent for C 6 power-dependence on N is much smaller than the value predicted recently based on a classical-metallic spherical-shell approximation of the fullerenes.
138(2013); http://dx.doi.org/10.1063/1.4794856View Description Hide Description
A theoretical model based on the phenomenon of dipolar truncation is proposed to explain the nuances of polarization transfer from abundant to less-abundant nuclei in cross-polarization (CP) NMR experiments. Specifically, the transfer of polarization from protons to carbons (in solids) in strongly coupled systems is described in terms of effective Hamiltonians based on dipolar truncation. Through suitable model spin systems, the important role of dipolar truncation in the propagation of spin polarization in CP experiments is outlined. We believe that the analytic theory presented herein provides a convenient framework for modeling polarization transfer in strongly coupled systems.
138(2013); http://dx.doi.org/10.1063/1.4795159View Description Hide Description
We use numerically exact iterative path integral methods to investigate the decoherence and entanglement dynamics of a tunneling pair of two coupled qubits (spins) system interacting with a dissipative bath. We find that decoherence is generally accompanied by the destruction of entanglement, although the specifics of this destruction depend sensitively on the parameters of the Hamiltonian (qubit-qubit coupling and/or energy bias), the strength of dissipation, the temperature, and the choice of initial condition. We also observe that dissipation can in some cases generate a substantial amount of entanglement. Finally, if an entangled eigenstate exists which does not couple to the environment, the long-time entanglement can significantly exceed the value corresponding to the Boltzmann equilibrium state.
138(2013); http://dx.doi.org/10.1063/1.4795236View Description Hide Description
The Jarzynski identity can be applied to instances when a microscopic system is pulled repeatedly but quickly along some coordinate, allowing the calculation of an equilibrium free energy profile along the pulling coordinate from a set of independent non-equilibrium trajectories. Using the formalism of Wiener stochastic path integrals in which we assign temperature-dependent weights to Langevin trajectories, we derive exact formulae for the temperature derivatives of the free energy profile. This leads naturally to analytical expressions for decomposing a free energy profile into equilibrium entropy and internal energy profiles from non-equilibrium pulling. This decomposition can be done from trajectories evolved at a unique temperature without repeating the measurement as done in finite-difference decompositions. Three distinct analytical expressions for the entropy-energy decomposition are derived: using a time-dependent generalization of the weighted histogram analysis method, a quasi-harmonic spring limit, and a Feynman-Kac formula. The three novel formulae of reconstructing the pair of entropy-energy profiles are exemplified by Langevin simulations of a two-dimensional model system prototypical for force-induced biomolecular conformational changes. Connections to single-molecule experimental means to probe the functionals needed in the decomposition are suggested.
138(2013); http://dx.doi.org/10.1063/1.4795319View Description Hide Description
In this work we propose a multidimensional free energy perturbation scheme that allows the evaluation of the free energy difference between a state sampled based on importance sampling and almost any state that can be constructed by the reduction of the number of molecules in the system and the change of either the interaction energy or the thermodynamic state variable (e.g., the temperature) of the system. We show that via this approach it is possible to evaluate any thermodynamic property included but not limited to free energy, chemical potential, and pressure, along a series of isotherms from a single molecular simulation.
- Advanced Experimental Techniques
138(2013); http://dx.doi.org/10.1063/1.4795001View Description Hide Description
The nuclear magnetic resonance of paramagnetic solids is usually characterized by the presence of large chemical shifts and shift anisotropies due to hyperfine interactions. Frequently the resulting spectra cover a frequency range of several megahertz, which is greater than the bandwidth of commercially available radio-frequency (RF) probes, making it impossible to acquire the whole spectrum in a single experiment. In these cases it common to record a series of spectra, in which the probe is tuned to a different frequency for each, and then sum the results to give the “true” spectrum. While this method is very widely used on static samples, the application of frequency stepping under magic-angle spinning (MAS) is less common, owing to the increased complexity of the spin dynamics when describing the interplay of the RF irradiation with the mechanical rotation of the shift tensor. In this paper, we present a theoretical description, based on the jolting frame formalism of Caravatti et al. [J. Magn. Reson.55, 88 (Year: 1983)10.1016/0022-2364(83)90279-2], for describing the spin dynamics of a powder sample under MAS when subjected to a selective pulse of low RF-field amplitude. The formalism is used to describe the frequency stepping method under MAS, and under what circumstances the true spectrum is reproduced. We also present an experimental validation of the methodology under ultra-fast MAS with the paramagnetic materials LiMnPO4 and TbCsDPA.
- Atoms, Molecules, and Clusters
138(2013); http://dx.doi.org/10.1063/1.4795007View Description Hide Description
This paper studies Xe-insertion ethylene and ethane compounds, i.e., HXeC2H3 and HXeC2H5. The structures, harmonic frequencies, and energetics for both molecules have been calculated at the MP2(full)/6-311++G(2d,2p) level. Our theoretical results predict the existence of HXeC2H3 and the instability of HXeC2H5. Natural bond orbital (NBO) analysis shows a strong ionic bond between the xenon atom and hydrocarbon radical. In addition, the interaction between the donor (Xe lone pair) and acceptor (the C–C antibonding orbital, i.e., π*(C–C)) increases the stability of HXeC2H3.
138(2013); http://dx.doi.org/10.1063/1.4795101View Description Hide Description
Here, we show how a copper atom in a copperphthalocyanine (CuPc) molecule can be decoupled from its environment. This is realized by trapping the CuPc molecule between two adjacent nanowires that are 1.6 nm apart. Using low-temperature scanning tunnelling microscopy and spectroscopy, the structural and electronic properties of CuPc in the stable “molecular bridge” configuration have been studied. Constant current and differential conductivity maps are recorded to reveal the spatial variation of the electronic structure of the cores and the lobes of CuPc molecules. The core of CuPc molecule is dim at low voltages, but suddenly becomes bright at a voltage of 5 V. Time-resolved scanning tunnelling microscopy measurements show that some of the CuPc lobes are very stable, while other lobes are very dynamic.
138(2013); http://dx.doi.org/10.1063/1.4795235View Description Hide Description
The infrared absorption spectra of the H2O, HDO, and D2O monomers isolated in solid N2 have been recorded at various temperatures between 4 and 30 K. A study of the absorption features of the ν1, ν2, and ν3 vibrational modes for each monomer shows their optical line shapes to be strongly temperature dependent. For all three modes, a decrease in the absorption amplitude and a proportional broadening of the linewidth was observed with increasing temperature, while the integrated absorbance remained constant. These observations were explained in terms of phonon coupling, by which high frequency intramolecular modes decay by exciting matrix phonons. Fits of the linewidth for the lowest frequency ν2 vibrational mode to the predicted vibrational relaxation rate in a solid medium gave average phonon mode frequencies consistent with the Debye frequency for solid N2.
Rotational spectroscopy of antipyretics: Conformation, structure, and internal dynamics of phenazone138(2013); http://dx.doi.org/10.1063/1.4794693View Description Hide Description
The conformational and structural preferences of phenazone (antipyrine), the prototype of non-opioid pyrazolone antipyretics, have been probed in a supersonic jet expansion using rotational spectroscopy. The conformational landscape of the two-ring assembly was first explored computationally, but only a single conformer was predicted, with the N-phenyl and N-methyl groups on opposite sides of the pyrazolone ring. Consistently, the microwave spectrum evidenced a rotational signature arising from a single molecular structure. The spectrum exhibited very complicated fine and hyperfine patterns (not resolvable with any other spectroscopic technique) originated by the simultaneous coupling of the methyl group internal rotation and the spins of the two 14N nuclei with the overall rotation. The internal rotation tunnelling was ascribed to the C–CH3 group and the barrier height established experimentally (7.13(10) kJ mol−1). The internal rotation of the N–CH3 group has a lower limit of 9.4 kJ mol−1. The structure of the molecule was determined from the rotational parameters, with the phenyl group elevated ca. 25° with respect to the average plane of the pyrazolic moiety and a phenyl torsion of ca. 52°. The origin of the conformational preferences is discussed in terms of the competition between intramolecular C–H⋯N and C–H⋯O weak hydrogen bonds.
138(2013); http://dx.doi.org/10.1063/1.4793744View Description Hide Description
Employing correlation consistent basis sets of quadruple-zeta quality and applying both multireference configuration interaction and single-reference coupled cluster methodologies, we studied the electronic and geometrical structure of the [V,O,H]0,+ species. The electronic structure of HVO0,+ is explained by considering a hydrogen atom approaching VO0,+, while VOH0,+ molecules are viewed in terms of the interaction of V+,2+ with OH−. The potential energy curves for H–VO0,+ and V0,+–OH have been constructed as functions of the distance between the interacting subunits, and the potential energy curves have also been determined as functions of the H–V–O angle. For the stationary points that we have located, we report energies, geometries, harmonic frequencies, and dipole moments. We find that the most stable bent HVO0,+ structure is lower in energy than any of the linear HVO0,+ structures. Similarly, the most stable state of bent VOH is lower in energy than the linear structures, but linear VOH+ is lower in energy than bent VOH+. The global minimum on the potential energy surface for the neutral species is the A″ state of bent HVO, although the A″ state of bent VOH is less than 5 kcal/mol higher in energy. The global minimum on the potential surface for the cation is the state of linear VOH+, with bent VOH+ and bent HVO+ both more than 10 kcal/mol higher in energy. For the neutral species, the bent geometries exhibit significantly higher dipole moments than the linear structures.
138(2013); http://dx.doi.org/10.1063/1.4795205View Description Hide Description
The 22Σ+ and 42Σ+ excited states of 7Li40Ca have been studied by high resolution Fourier-transform spectroscopy. The data on the lower state, 22Σ+, were obtained by analyzing the rotationally resolved spectra of the thermal emission of LiCa in the 22Σ+ → X2Σ+ band around 9500 cm−1. These data contained transitions mainly from v′ = 0 and 1 for N′ up to 92 and allowed us to derive molecular parameters describing the potential curve of the state close to its minimum. The dataset on the second state, 42Σ+, is much larger and comes from a laser-induced fluorescence experiment. The levels were excited by a single mode dye laser and the 42Σ+ → X2Σ+ fluorescence was recorded through a Fourier-transform spectrometer. For both states potential energy curves and Dunham coefficients were derived and the spin-rotation structure was evaluated. The results are compared with theoretical and experimental data from the literature.
138(2013); http://dx.doi.org/10.1063/1.4795237View Description Hide Description
In this article, the most relevant isomers of uranium tricarbide are studied through quantum chemical methods. It is found that the most stable isomer has a fan geometry in which the uranium atom is bonded to a quasilinear C3 unit. Both, a rhombic and a ring CU(C2) structures are found about 104–125 kJ/mol higher in energy. Other possible isomers including linear geometries are located even higher. For each structure, we provide predictions for those molecular properties (vibrational frequencies, IR intensities, dipole moments) that could eventually help in their experimental detection. We also discuss the possible routes for the formation of the different UC3 isomers as well as the bonding situation by means of a topological analysis of the electron density.
138(2013); http://dx.doi.org/10.1063/1.4794691View Description Hide Description
The present study focuses on the interaction of H2 Rydberg molecules with doped silicon semiconductor surfaces. Para-H2 Rydberg states with principal quantum numbers n = 17–21 and core rotational quantum number N + = 2 are populated via resonant two-colour two-photon (vacuum ultraviolet-ultraviolet) excitation and collide at grazing incidence with a surface. For small Rydberg-surface separation, the Rydberg states are ionized due to the attractive surface potential experienced by the Rydberg electron and the remaining ion-core is detectable by applying a sufficiently strong external electric field. It is found that the surface ionization profiles (ion signal vs applied field) of H2 on p-type doped Si surfaces show a higher detected ion signal than for n-type Si surfaces, while an Au surface shows lower detected ion signal than either type of Si surface. It is shown that ion detectability decreases with increasing dopant density for both types of Si surfaces. Higher-n Rydberg states show higher ion detectability than lower-n Rydberg states but this variation becomes smaller when increasing the dopant density for both p- and n-type surfaces. Theoretical trajectory simulations were developed with a 2D surface potential model and using the over-the-barrier model for the ionization distance; the results help to explain the observed variations of the experimental surface ionization profiles with dopant density and type.