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.
 ARTICLES

 Theoretical Methods and Algorithms

Optimal scalefree network with a minimum scaling of transport efficiency for random walks with a perfect trap
View Description Hide DescriptionAverage 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 scalefree 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 closedform 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 scalefree networks, and is helpful for designing networks with the most efficient transport process.

Reactive adsorption of ammonia and ammonia/water on CuBTC metalorganic framework: A ReaxFF molecular dynamics simulation
View Description Hide DescriptionWe report ReaxFF molecular dynamics simulations for reactive adsorption of NH_{3} on dehydrated CuBTC metalorganic 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 H_{2}O molecule per copper site. When NH_{3} 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 NH_{3} molecule. The formation of equimolar Cu _{2}(NH_{2})_{4} and (NH_{4})_{3}BTC structures is observed at 348 K, which is in good agreement with previous experimental findings. The dehydrated CuBTC framework is partially collapsed upon NH_{3} 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 NH_{3} concentration after which the dehydrated CuBTC starts to collapse is determined to be 1.0 NH_{3} molecule per copper site. Depending on whether NH_{3} 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. H_{2}O/NH_{3} 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 NH_{3} molecules on CuBTC and stabilize the CuBTC framework to some extent.

Multicanonical molecular dynamics by variabletemperature thermostats and variablepressure barostats
View Description Hide DescriptionSampling 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 LennardJones system and a structurebased model of proteins.

Direct determination of exciton couplings from subsystem timedependent densityfunctional theory within the Tamm–Dancoff approximation
View Description Hide DescriptionIn subsystem timedependent 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 intersubsystem matrix elements in subsystem TDA can, in contrast to the full subsystemTDDFT 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 fixednode diffusion Monte Carlo to investigate the effects of rotationvibration coupling in highly fluxional asymmetric top molecules: Application to H_{2}D^{+}
View Description Hide DescriptionA fixednode diffusion Monte Carlo approach for obtaining the energies and wave functions of the rotationally excited states of asymmetric top molecules that undergo large amplitude, zeropoint 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 zeropoint, vibrationally averaged rotational constants. Using H_{2}D^{+} 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 fixednode diffusion Monte Carlo approach to provide insights into the nature and strength of the rotationvibration 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.

An efficient and near linear scaling pair natural orbital based local coupled cluster method
View Description Hide DescriptionIn 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 orbitalcoupledcluster single double (LPNOCCSD) 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 10^{5}–10^{6} 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 LPNOCCSD 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 LPNOCCSD 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 DLPNOCCSD (“domain based LPNOCCSD”). The method is nearly linear scaling with respect to system size. The original LPNOCCSD 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 realspace cutoffs. Single excitations are truncated using singlesspecific 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 LPNOCCSD predecessor, the method is completely of black box character and does not require any user adjustments. It is shown here that DLPNOCCSD is as accurate as LPNOCCSD 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 LPNOCCSD step took less time than the preceding HartreeFock 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.

Molecular diffusion between walls with adsorption and desorption
View Description Hide DescriptionThe 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 surfacetovolume 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 timedependent diffusion coefficient between two confining walls in the presence of adsorption and desorption. We show that they strongly modify the timedependency 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

Multiple populationperiod transient spectroscopy (MUPPETS) in excitonic systems
View Description Hide DescriptionTimeresolved experiments with more than one period of incoherent time evolution are becoming increasingly accessible. When applied to a twolevel system, these experiments separate homogeneous and heterogeneous contributions to kinetic dispersion, i.e., to nonexponential relaxation. Here, the theory of twodimensional (2D) multiple populationperiod 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

Attachment crosssections of protonated and deprotonated water clusters
View Description Hide DescriptionAttachment crosssections of water molecules onto size selected protonated (H_{2}O)_{ n }H^{+} and deprotonated (H_{2}O)_{ n − 1}OH^{−} 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 crosssections 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 H_{2}O isolated lines: Complementary tests of the partially correlated speeddependent KeilsonStorer model
View Description Hide DescriptionComplementary tests of the partially correlated speeddependent KeilsonStorer (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 selfbroadened H_{2}O lines in the 1.6 μm region at room temperature and for pressures from 0.5 to 15 Torr. Furthermore, the H_{2} ^{18}O 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 collisioninduced velocity changes, the speed dependences of the broadening and shifting coefficients as well as the partial correlation between velocity and rotationalstate changes. All parameters of the model have been fixed at values previously determined, except for a scaling factor applied to the input speeddependent 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 conversion
View Description Hide DescriptionChallenges 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 firstprinciples computations, we demonstrate that these fuels, composed of organic photoisomers bound to inexpensive carbonbased templates, can reversibly store solar energy at densities comparable to Liion 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 solartoheat conversion. Our work suggests that the solar thermal fuels concept can be translated into a practical and highly customizable energy storage and conversion technology.

Heat capacities of mass selected deprotonated water clusters
View Description Hide DescriptionHeat capacities of mass selected deprotonated water clusters (H_{2}O)_{n−1}OH^{−} have been measured in the size range n = 48–118, as a function of temperature. We have found that they undergo a meltinglike 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 naphthaleneargon complex: Applications to collisional energy transfer and matrix isolated IR spectroscopy
View Description Hide DescriptionAn explicit polarizable potential for the naphthaleneargon 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 tightbinding model for naphthalene, collisional energy transfer is studied by means of dedicated molecular dynamics simulations, nuclear quantum effects being accounted for in the pathintegral 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 zeropoint energy and the higher density of states. Using an ab initio potential for the ArAr 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.

Nonequivalent carbon atoms in the resonant inelastic soft Xray scattering map of cysteine
View Description Hide DescriptionResonant inelastic soft xray scattering (RIXS) was used to study the electronic structure of solid cysteine films. A RIXS map approach, i.e., plotting the xray emission intensity as a function of excitation and emission energy, allows us to separate the contributions of the three chemically nonequivalent 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 twodimensional FrenkelKontorova model
View Description Hide DescriptionWe demonstrate the ratchet and phase locking effects in a twodimensional overdamped FrenkelKontorova 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 ditantalum boride clusters: Ta_{2}B_{ x } ^{−} (x = 2–5)
View Description Hide DescriptionThe structural and electronic properties for ditantalum boride clusters Ta _{2}B_{ x } ^{−} (x = 2–5) were investigated using photoelectron spectroscopy and density functional calculations. The photoelectron spectra for Ta _{2}B_{ 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 lowlying isomers are compared with the experimental data. Strong boronboron bonding is found to dominate the lowest energy structures of Ta _{2}B_{ x } ^{−} and Ta _{2}B_{ 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 _{2}B_{ x } ^{−} and Ta _{2}B_{ x } for x = 2–4, whereas the Ta–Ta distance is increased significantly in Ta _{2}B_{5} ^{−} and Ta _{2}B_{5}.

Collection efficiency of photoelectrons injected into near and supercritical argon gas
View Description Hide DescriptionInjection 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 highfield data agree with the YoungBradbury model and with previous measurements below T _{ c } and at an intermediate temperature above T _{ c }. The effective, densitydependent electronatom momentum transfer scattering cross section can be deduced. However, the weakfield 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

Structural study of Al_{2}O_{3}Na_{2}OCaOP_{2}O_{5} bioactive glasses as a function of aluminium content
View Description Hide DescriptionCalcium 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 (Al_{2}O_{3})_{x} (Na _{2}O)_{0.11x}(CaO)_{0.445}(P_{2}O_{5})_{0.445}, where x = 0, 0.03, 0.05, and 0.08, were prepared by melt quenching. The atomicscale structure has been studied using neutron diffraction and solid state ^{27}Al 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. % Al_{2}O_{3} the density starts to decrease. Neutron diffraction data show a concomitant change in the aluminium speciation, which is confirmed by ^{27}Al MAS NMR studies. The NMR data reveal that aluminium is present in 4, 5, and 6fold coordination and that the relative concentrations of these environments change with increasing aluminium concentration. Materials containing aluminium in 6fold coordination tend to have higher densities than analogous materials with the aluminium found in 4fold coordination. Thus, the density changes may readily be explained in terms of an increase in the relative concentration of 4coordinated aluminium at the expense of 6fold aluminium as the Al_{2}O_{3} content is increased beyond 3 mol. %.

LandauPlaczek ratio for heat density dynamics and its application to heat capacity of liquids
View Description Hide DescriptionExact relation for contributions to heat capacity of liquids is obtained from hydrodynamic theory. It is shown from analysis of the longwavelength limit of heat density autocorrelation functions that the heat capacity of simple liquids is represented as a sum of two contributions due to “phononlike” collective excitations and heat relaxation. The ratio of both contributions being the analogy of LandauPlaczek 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 LandauPlaczek 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 NavierStokes theory: Correlations in molecular fluids with intrinsic angular momentum
View Description Hide DescriptionThe extended NavierStokes theory accounts for the coupling between the translational and rotational molecular degrees of freedom. In this paper, we generalize this theory to nonzero frequencies and wavevectors, which enables a new study of spatiotemporal 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.