Index of content:
Volume 138, Issue 3, 21 January 2013
We report spontaneous translocation of small interfering RNA (siRNA) inside carbon nanotubes (CNTs) of various diameters and chirality using all atom molecular dynamics simulations with explicit solvent. We use umbrella sampling method to calculate the free energy landscape of the siRNA entry and translocation event. Free energy profiles show that siRNA gains free energy while translocating inside CNT, and barrier for siRNA exit from CNT ranges from 40 to 110 kcal/mol depending on CNT chirality and salt concentration. The translocation time τ decreases with the increase of CNT diameter with a critical diameter of 24 Å for the translocation. In contrast, double strand DNA of the same sequence does not translocate inside CNT due to large free energy barrier for the translocation. This study helps in understanding the nucleic acid transport through nanopores at microscopic level and may help designing carbon nanotube based sensor for siRNA.
- Theoretical Methods and Algorithms
Optimal scale-free network with a minimum scaling of transport efficiency for random walks with a perfect trap138(2013); http://dx.doi.org/10.1063/1.4774269View Description Hide Description
Average trapping time (ATT) is central in the trapping problem since it is a key indicator characterizing the efficiency of the problem. Previous research has provided the scaling of a lower bound of the ATT for random walks in general networks with a deep trap. However, it is still not well understood in which networks this minimal scaling can be reached. Particularly, explicit quantitative results for ATT in such networks, even in a specific network, are lacking, in spite that such networks shed light on the design for optimal networks with the highest trapping efficiency. In this paper, we study the trapping problem taking place on a hierarchical scale-free network with a perfect trap. We focus on four representative cases with the immobile trap located at the root, a peripheral node, a neighbor of the root with a single connectivity, and a farthest node from the root, respectively. For all the four cases, we obtain the closed-form formulas for the ATT, as well as its leading scalings. We show that for all the four cases of trapping problems, the dominating scalings of ATT can reach the predicted minimum scalings. This work deepens the understanding of behavior of trapping in scale-free networks, and is helpful for designing networks with the most efficient transport process.
Reactive adsorption of ammonia and ammonia/water on CuBTC metal-organic framework: A ReaxFF molecular dynamics simulation138(2013); http://dx.doi.org/10.1063/1.4774332View Description Hide Description
We report ReaxFF molecular dynamics simulations for reactive adsorption of NH3 on dehydrated CuBTC metal-organic framework. If the temperature is moderate (up to 125 °C), the dehydrated CuBTC demonstrates a good hydrostatic stability for water concentrations up to 4.0 molecules per copper site. However, if the temperature increases to 550 K, the dehydrated CuBTC will collapse even at a small water concentration, 1.0 H2O molecule per copper site. When NH3 molecules are adsorbed in the channel and micropores of CuBTC, they prefer to chemisorb to the copper sites rather than forming a dimer with another NH3 molecule. The formation of equimolar Cu 2(NH2)4 and (NH4)3BTC structures is observed at 348 K, which is in good agreement with previous experimental findings. The dehydrated CuBTC framework is partially collapsed upon NH3 adsorption, while the Cu–Cu dimer structure remains stable under the investigated conditions. Further calculations reveal that the stability of CuBTC is related to the ammonia concentration. The critical NH3 concentration after which the dehydrated CuBTC starts to collapse is determined to be 1.0 NH3 molecule per copper site. Depending on whether NH3 concentration is below or above the critical value, the dehydrated CuBTC can be stable to a higher temperature, 378 K, or can collapse at a lower temperature, 250 K. H2O/NH3 mixtures have also been studied, and we find that although water molecules do not demonstrate a strong interaction with the copper sites of CuBTC, the existence of water molecules can substantially prevent ammonia from interacting with CuBTC, and thus reduce the amount of chemisorbed NH3 molecules on CuBTC and stabilize the CuBTC framework to some extent.
Multicanonical molecular dynamics by variable-temperature thermostats and variable-pressure barostats138(2013); http://dx.doi.org/10.1063/1.4773435View Description Hide Description
Sampling from flat energy or density distributions has proven useful in equilibrating complex systems with large energy barriers. Several thermostats and barostats are presented to sample these flat distributions by molecular dynamics. These methods use a variable temperature or pressure that is updated on the fly in the thermodynamic controller. These methods are illustrated on a Lennard-Jones system and a structure-based model of proteins.
Direct determination of exciton couplings from subsystem time-dependent density-functional theory within the Tamm–Dancoff approximation138(2013); http://dx.doi.org/10.1063/1.4774117View Description Hide Description
In subsystem time-dependent density functional theory (TDDFT) [J. Neugebauer, J. Chem. Phys.126, 134116 (Year: 2007)10.1063/1.2713754] localized excitations are used to calculate delocalized excitations in large chromophore aggregates. We have extended this formalism to allow for the Tamm–Dancoff approximation (TDA). The resulting response equations have a form similar to a perturbative configuration interaction singles (CIS) approach. Thus, the inter-subsystem matrix elements in subsystem TDA can, in contrast to the full subsystem-TDDFT case, directly be interpreted as exciton coupling matrix elements. Here, we present the underlying theory of subsystem TDDFT within the TDA as well as first applications. Since for some classes of pigments, such as linear polyenes and carotenoids, TDA has been reported to perform better than full TDDFT, we also report applications of this formalism to exciton couplings in dimers of such pigments and in mixed bacteriochlorophyll–carotenoid systems. The improved description of the exciton couplings can be traced back to a more balanced description of the involved local excitations.
Using fixed-node diffusion Monte Carlo to investigate the effects of rotation-vibration coupling in highly fluxional asymmetric top molecules: Application to H2D+138(2013); http://dx.doi.org/10.1063/1.4774318View Description Hide Description
A fixed-node diffusion Monte Carlo approach for obtaining the energies and wave functions of the rotationally excited states of asymmetric top molecules that undergo large amplitude, zero-point vibrational motions is reported. The nodal surfaces required to introduce rotational excitation into the diffusion Monte Carlo calculations are obtained from the roots of the asymmetric top rigid rotor wave functions calculated using the system's zero-point, vibrationally averaged rotational constants. Using H2D+ as a model system, the overall accuracy of the methodology is tested by comparing to the results of converged variational calculations. The ability of the fixed-node diffusion Monte Carlo approach to provide insights into the nature and strength of the rotation-vibration coupling present in the rotationally excited states of highly fluxional asymmetric tops is discussed. Finally, the sensitivity of the methodology to the details of its implementation, such as the choice of embedding scheme, is explored.
138(2013); http://dx.doi.org/10.1063/1.4773581View Description Hide Description
In previous publications, it was shown that an efficient local coupled cluster method with single- and double excitations can be based on the concept of pair natural orbitals (PNOs) [F. Neese, A. Hansen, and D. G. Liakos, J. Chem. Phys.131, 064103 (Year: 2009)10.1063/1.3173827]. The resulting local pair natural orbital-coupled-cluster single double (LPNO-CCSD) method has since been proven to be highly reliable and efficient. For large molecules, the number of amplitudes to be determined is reduced by a factor of 105–106 relative to a canonical CCSD calculation on the same system with the same basis set. In the original method, the PNOs were expanded in the set of canonical virtual orbitals and single excitations were not truncated. This led to a number of fifth order scaling steps that eventually rendered the method computationally expensive for large molecules (e.g., >100 atoms). In the present work, these limitations are overcome by a complete redesign of the LPNO-CCSD method. The new method is based on the combination of the concepts of PNOs and projected atomic orbitals (PAOs). Thus, each PNO is expanded in a set of PAOs that in turn belong to a given electron pair specific domain. In this way, it is possible to fully exploit locality while maintaining the extremely high compactness of the original LPNO-CCSD wavefunction. No terms are dropped from the CCSD equations and domains are chosen conservatively. The correlation energy loss due to the domains remains below <0.05%, which implies typically 15–20 but occasionally up to 30 atoms per domain on average. The new method has been given the acronym DLPNO-CCSD (“domain based LPNO-CCSD”). The method is nearly linear scaling with respect to system size. The original LPNO-CCSD method had three adjustable truncation thresholds that were chosen conservatively and do not need to be changed for actual applications. In the present treatment, no additional truncation parameters have been introduced. Any additional truncation is performed on the basis of the three original thresholds. There are no real-space cutoffs. Single excitations are truncated using singles-specific natural orbitals. Pairs are prescreened according to a multipole expansion of a pair correlation energy estimate based on local orbital specific virtual orbitals (LOSVs). Like its LPNO-CCSD predecessor, the method is completely of black box character and does not require any user adjustments. It is shown here that DLPNO-CCSD is as accurate as LPNO-CCSD while leading to computational savings exceeding one order of magnitude for larger systems. The largest calculations reported here featured >8800 basis functions and >450 atoms. In all larger test calculations done so far, the LPNO-CCSD step took less time than the preceding Hartree-Fock calculation, provided no approximations have been introduced in the latter. Thus, based on the present development reliable CCSD calculations on large molecules with unprecedented efficiency and accuracy are realized.
138(2013); http://dx.doi.org/10.1063/1.4775742View Description Hide Description
The time dependency of the diffusion coefficient of particles in porous media is an efficient probe of their geometry. The analysis of this quantity, measured, e.g., by nuclear magnetic resonance, can provide rich information pertaining to porosity, pore size distribution, permeability, and surface-to-volume ratio of porous materials. Nevertheless, in numerous if not all practical situations, transport is confined by walls where adsorption and desorption processes may occur. In this article, we derive explicitly the expression of the time-dependent diffusion coefficient between two confining walls in the presence of adsorption and desorption. We show that they strongly modify the time-dependency of the diffusion coefficient, even in this simple geometry. We finally propose several applications, from sorption rates measurements to the use as a reference for numerical implementations for more complex geometries.
- Advanced Experimental Techniques
138(2013); http://dx.doi.org/10.1063/1.4773982View Description Hide Description
Time-resolved experiments with more than one period of incoherent time evolution are becoming increasingly accessible. When applied to a two-level system, these experiments separate homogeneous and heterogeneous contributions to kinetic dispersion, i.e., to nonexponential relaxation. Here, the theory of two-dimensional (2D) multiple population-period transient spectroscopy (MUPPETS) is extended to multilevel, excitonic systems. A nonorthogonal basis set is introduced to simplify pathway calculations in multilevel systems. Because the exciton and biexciton signals have different signs, 2D MUPPETS cleanly separates the exciton and biexciton decays. In addition to separating homogeneous and heterogeneous dispersion of the exciton, correlations between the exciton and biexciton decays are measurable. Such correlations indicate shared features in the two relaxation mechanisms. Examples are calculated as both 2D time decays and as 2D rate spectra. The effect of solvent heating (i.e., thermal gratings) is also calculated in multidimensional experiments on multilevel systems.
- Atoms, Molecules, and Clusters
138(2013); http://dx.doi.org/10.1063/1.4775401View Description Hide Description
Attachment cross-sections of water molecules onto size selected protonated (H2O) n H+ and deprotonated (H2O) n − 1OH− water clusters have been measured in the size range n = 30–140 for 10 eV kinetic energy of the clusters in the laboratory frame. Within our experimental accuracy, the attachment cross-sections are found to have the same magnitude and size dependence for both species. It is shown that electrostatic interactions are likely to play a role even for the largest sizes investigated.
Velocity effects on the shape of pure H2O isolated lines: Complementary tests of the partially correlated speed-dependent Keilson-Storer model138(2013); http://dx.doi.org/10.1063/1.4774094View Description Hide Description
Complementary tests of the partially correlated speed-dependent Keilson-Storer (pCSDKS) model for the shape of isolated transition of pure water vapor[N. H. Ngo et al. , J. Chem. Phys.136, 154310 (Year: 2012)]10.1063/1.4704675 are made using new measurements. The latter have been recorded using a high sensitivity cavity ring down spectrometer, for seven self-broadened H2O lines in the 1.6 μm region at room temperature and for pressures from 0.5 to 15 Torr. Furthermore, the H2 18O spectra of [M. D. De Vizia et al. , Phys. Rev. A83, 052506 (Year: 2011)]10.1103/PhysRevA.83.052506 in the 1.38 μm region, measured at 273.15 K and for pressures from 0.3 to 3.75 Torr have also been used for comparison with the model. Recall that the pCSDKS model takes into account the collision-induced velocity changes, the speed dependences of the broadening and shifting coefficients as well as the partial correlation between velocity and rotational-state changes. All parameters of the model have been fixed at values previously determined, except for a scaling factor applied to the input speed-dependent line broadening. Comparisons between predictions and experiments have been made by looking at the results obtained when fitting the calculated and measured spectra by Voigt profiles. The good agreement obtained for all considered lines, at different temperature and pressure conditions, confirms the consistency and the robustness of the model. Limiting cases of the model have been then derived, showing the influence of different contributions to the line shape.
Hybrid chromophore/template nanostructures: A customizable platform material for solar energy storage and conversion138(2013); http://dx.doi.org/10.1063/1.4773306View Description Hide Description
Challenges with cost, cyclability, and/or low energy density have largely prevented the development of solar thermal fuels, a potentially attractive alternative energy technology based on molecules that can capture and store solar energy as latent heat in a closed cycle. In this paper, we present a set of novel hybrid photoisomer/template solar thermal fuels that can potentially circumvent these challenges. Using first-principles computations, we demonstrate that these fuels, composed of organic photoisomers bound to inexpensive carbon-based templates, can reversibly store solar energy at densities comparable to Li-ion batteries. Furthermore, we show that variation of the template material in combination with the photoisomer can be used to optimize many of the key performance metrics of the fuel—i.e., the energy density, the storage lifetime, the temperature of the output heat, and the efficiency of the solar-to-heat conversion. Our work suggests that the solar thermal fuels concept can be translated into a practical and highly customizable energy storage and conversion technology.
138(2013); http://dx.doi.org/10.1063/1.4774408View Description Hide Description
Heat capacities of mass selected deprotonated water clusters (H2O)n−1OH− have been measured in the size range n = 48–118, as a function of temperature. We have found that they undergo a melting-like transition in the range 110–130 K. The transition temperature is size dependent with a strong correlation with the dissociation energy around the shell closure at n = 55.
A simple but accurate potential for the naphthalene-argon complex: Applications to collisional energy transfer and matrix isolated IR spectroscopy138(2013); http://dx.doi.org/10.1063/1.4773469View Description Hide Description
An explicit polarizable potential for the naphthalene-argon complex has been derived assuming only atomic contributions, aiming at large scale simulations of naphthalene under argon environment. The potential was parametrized from dedicated quantum chemical calculations at the CCSD(T) level, and satisfactorily reproduces available structural and energetic properties. Combining this potential with a tight-binding model for naphthalene, collisional energy transfer is studied by means of dedicated molecular dynamics simulations, nuclear quantum effects being accounted for in the path-integral framework. Except at low target temperature, nuclear quantum effects do not alter the average energies transferred by the collision or the collision duration. However, the distribution of energy transferred is much broader in the quantum case due to the significant zero-point energy and the higher density of states. Using an ab initio potential for the Ar-Ar interaction, the IR absorption spectrum of naphthalene solvated by argon clusters or an entire Ar matrix is computed via classical and centroid molecular dynamics. The classical spectra exhibit variations with growing argon environment that are absent from quantum spectra. This is interpreted by the greater fluxional character experienced by the argon atoms due to vibrational delocalization.
138(2013); http://dx.doi.org/10.1063/1.4774059View Description Hide Description
Resonant inelastic soft x-ray scattering (RIXS) was used to study the electronic structure of solid cysteine films. A RIXS map approach, i.e., plotting the x-ray emission intensity as a function of excitation and emission energy, allows us to separate the contributions of the three chemically non-equivalent carbon atoms in cysteine. In particular, we can identify orbitals localized near the photoexcited atoms, as well as orbitals that are delocalized over the entire molecule.
Ratchet effect and amplitude dependence of phase locking in a two-dimensional Frenkel-Kontorova model138(2013); http://dx.doi.org/10.1063/1.4776226View Description Hide Description
We demonstrate the ratchet and phase locking effects in a two-dimensional overdamped Frenkel-Kontorova model with a square symmetric periodic substrate when both a longitudinal dc drive and a circular ac drive are applied. Besides the harmonic steps, the large half integer steps can also clearly be seen in the longitudinal (x) direction. These half integer steps are directly correlated to the appearance of positive and negative ratchet effects in the transverse (y) direction due to the symmetry breaking in the combination of the dc and ac drives. The angle between the net displacement and the longitudinal direction is analytically obtained in a single period of the ac drive. In the examination of the amplitude dependence of the ac drive, the maxima decrease monotonically with the amplitude, while the anomalies occur for the critical depinning force and the harmonic steps due to the spatial symmetry breaking of orbits in the presence of the ac drive.
A photoelectron spectroscopy and density functional study of di-tantalum boride clusters: Ta2B x − (x = 2–5)138(2013); http://dx.doi.org/10.1063/1.4776769View Description Hide Description
The structural and electronic properties for di-tantalum boride clusters Ta 2B x − (x = 2–5) were investigated using photoelectron spectroscopy and density functional calculations. The photoelectron spectra for Ta 2B x − (x = 2–5) are obtained at several photon energies with rich spectral features. Density functional theory calculations are performed at the BP86 level to search for the global minima of both the anionic and neutral clusters. The calculated vertical electron detachment energies for the global minimum and low-lying isomers are compared with the experimental data. Strong boron-boron bonding is found to dominate the lowest energy structures of Ta 2B x − and Ta 2B x (x = 2–5), which are shown to be bipyramidal with the boron atoms forming an equatorial belt around the Ta–Ta dimer. Strong Ta–Ta bonding is observed in Ta 2B x − and Ta 2B x for x = 2–4, whereas the Ta–Ta distance is increased significantly in Ta 2B5 − and Ta 2B5.
138(2013); http://dx.doi.org/10.1063/1.4775594View Description Hide Description
Injection of photoelectrons into gaseous or liquid dielectrics is a widely used technique to produce cold plasmas in weakly ionized systems for investigating the transport properties of electrons. We report measurements of the collection efficiency of photoelectrons injected into dense argon gas for T = 152.7 K, close to the critical temperature T c ≈ 150.9 K, and for T = 200.0 K. The high-field data agree with the Young-Bradbury model and with previous measurements below T c and at an intermediate temperature above T c . The effective, density-dependent electron-atom momentum transfer scattering cross section can be deduced. However, the weak-field data near T c show large deviations from the theoretical model. We show that the electron behavior at weak field is influenced by electrostriction effects that are only important near the critical point.
- Liquids, Glasses, and Crystals
138(2013); http://dx.doi.org/10.1063/1.4774330View Description Hide Description
Calcium phosphate based biomaterials are extensively used in the context of tissue engineering: small changes in composition can lead to significant changes in properties allowing their use in a wide range of applications. Samples of composition (Al2O3)x (Na 2O)0.11-x(CaO)0.445(P2O5)0.445, where x = 0, 0.03, 0.05, and 0.08, were prepared by melt quenching. The atomic-scale structure has been studied using neutron diffraction and solid state 27Al MAS NMR, and these data have been rationalised with the determined density of the final glass product. With increasing aluminium concentration the density increases initially, but beyond about 3 mol. % Al2O3 the density starts to decrease. Neutron diffraction data show a concomitant change in the aluminium speciation, which is confirmed by 27Al MAS NMR studies. The NMR data reveal that aluminium is present in 4, 5, and 6-fold coordination and that the relative concentrations of these environments change with increasing aluminium concentration. Materials containing aluminium in 6-fold coordination tend to have higher densities than analogous materials with the aluminium found in 4-fold coordination. Thus, the density changes may readily be explained in terms of an increase in the relative concentration of 4-coordinated aluminium at the expense of 6-fold aluminium as the Al2O3 content is increased beyond 3 mol. %.
138(2013); http://dx.doi.org/10.1063/1.4774406View Description Hide Description
Exact relation for contributions to heat capacity of liquids is obtained from hydrodynamic theory. It is shown from analysis of the long-wavelength limit of heat density autocorrelation functions that the heat capacity of simple liquids is represented as a sum of two contributions due to “phonon-like” collective excitations and heat relaxation. The ratio of both contributions being the analogy of Landau-Placzek ratio for heat processes depends on the specific heats ratio. The theory of heat density autocorrelation functions in liquids is verified by computer simulations. Molecular dynamics simulations for six liquids having the ratio of specific heats γ in the range 1.1–2.3, were used for evaluation of the heat density autocorrelation functions and predicted Landau-Placzek ratio for heat processes. The dependence of contributions from collective excitations and heat relaxation process to specific heat on γ is shown to be in excellent agreement with the theory.
Generalized extended Navier-Stokes theory: Correlations in molecular fluids with intrinsic angular momentum138(2013); http://dx.doi.org/10.1063/1.4774095View Description Hide Description
The extended Navier-Stokes theory accounts for the coupling between the translational and rotational molecular degrees of freedom. In this paper, we generalize this theory to non-zero frequencies and wavevectors, which enables a new study of spatio-temporal correlation phenomena present in molecular fluids. To discuss these phenomena in detail, molecular dynamics simulations of molecular chlorine are performed for three different state points. In general, the theory captures the behavior for small wavevector and frequencies as expected. For example, in the hydrodynamic regime and for molecular fluids with small moment of inertia like chlorine, the theory predicts that the longitudinal and transverse intrinsic angular velocity correlation functions are almost identical, which is also seen in the molecular dynamics simulations. However, the theory fails at large wavevector and frequencies. To account for the correlations at these scales, we derive a phenomenological expression for the frequency dependent rotational viscosity and wavevector and frequency dependent longitudinal spin viscosity. From this we observe a significant coupling enhancement between the molecular angular velocity and translational velocity for large frequencies in the gas phase; this is not observed for the supercritical fluid and liquid state points.