Near-quantitative Agreement Research Articles

At What Size Do Neutral Gold Clusters Turn Three-Dimensional?

Recent experiments and calculations have established the transition from two-dimensional (2D) to three-dimensional (3D) structures at a cluster size of 8 and 12 atoms for gold cluster cations and anions. For neutral gold clusters, however, experimental data are scarce, and existing theoretical studies disagree on the 2D–3D crossover point. We present the results of global structure optimizations of neutral gold clusters Aun for n = 9–13 using a genetic algorithm and meta-generalized density functional theory. The relative energies of the lowest-lying isomers are computed using the revTPSS functional and the random phase approximation (RPA). Thermal, scalar relativistic, and spin–orbit effects are included, and basis set extrapolations are performed for the RPA calculations. For the 2D–3D transition of gold cluster cations and anions, this methodology yields near-quantitative agreement with cross section and electron diffraction measurements. For neutral gold clusters, the 2D and 3D structures are predicte...

Induced Polarization Influences the Fundamental Forces in DNA Base Flipping.

Base flipping in DNA is an important process involved in genomic repair and epigenetic control of gene expression. The driving forces for these processes are not fully understood, especially in the context of the underlying dynamics of the DNA and solvent effects. We studied double-stranded DNA oligomers that have been previously characterized by imino proton exchange NMR using both additive and polarizable force fields. Our results highlight the importance of induced polarization on the base flipping process, yielding near-quantitative agreement with experimental measurements of the equilibrium between the base-paired and flipped states. Further, these simulations allow us to quantify for the first time the energetic implications of polarization on the flipping pathway. Free energy barriers to base flipping are reduced by changes in dipole moments of both the flipped bases that favor solvation of the bases in the open state and water molecules adjacent to the flipping base.

Anomalies in bulk supercooled water at negative pressure.

Water anomalies still defy explanation. In the supercooled liquid, many quantities, for example heat capacity and isothermal compressibility κT, show a large increase. The question arises if these quantities diverge, or if they go through a maximum. The answer is key to our understanding of water anomalies. However, it has remained elusive in experiments because crystallization always occurred before any extremum is reached. Here we report measurements of the sound velocity of water in a scarcely explored region of the phase diagram, where water is both supercooled and at negative pressure. We find several anomalies: maxima in the adiabatic compressibility and nonmonotonic density dependence of the sound velocity, in contrast with a standard extrapolation of the equation of state. This is reminiscent of the behavior of supercritical fluids. To support this interpretation, we have performed simulations with the 2005 revision of the transferable interaction potential with four points. Simulations and experiments are in near-quantitative agreement, suggesting the existence of a line of maxima in κT (LMκT). This LMκT could either be the thermodynamic consequence of the line of density maxima of water [Sastry S, Debenedetti PG, Sciortino F, Stanley HE (1996) Phys Rev E 53:6144-6154], or emanate from a critical point terminating a liquid-liquid transition [Sciortino F, Poole PH, Essmann U, Stanley HE (1997) Phys Rev E 55:727-737]. At positive pressure, the LMκT has escaped observation because it lies in the "no man's land" beyond the homogeneous crystallization line. We propose that the LMκT emerges from the no man's land at negative pressure.

Metal/nanowire contacts, quantum confinement, and their roles in the generation of new, gigantic actions in nanowire transistors

A distinctly new route for the design, modeling and electrical behavior of very short-channel (5–10 nm in channel length) nanowire field-effect transistors (FETs) has been presented. Essential elements of the approach entail a drain current determined by thermionic emission, but not by carrier mobility in the channel of the transistor. A basic understanding of the fundamental physics and the concepts of Schottky-barrier-based design for the proposed route have been described. Quantum confinement in the nanowire channel together with Schottky barrier tailing and temperature-dependent fluctuations of applied biases has been taken into account for the development of the model. Both current–voltage characteristics and transconductance of FETs have been studied. The calculated results are in near-quantitative agreement with the available experiments. Measured data show very diverse (e.g., exponential, linear, saturating, and non-linear non-exponential non-saturating) nanowire transistor characteristics. The model explains these characteristics well and reveals a number of new transistor actions. It highlights the impacts of quantum confinement and Schottky contacts for these new transistor actions. It also quantifies the significant enhancement of the drain–source current and transconductance. With new findings thus achieved, suggestions for the realization of very high-performance, small-diameter (preferably 2 nm), small-Schottky-barrier-height, high-operating temperature, ultra-short-channel-length, nanowire transistors have been made. Optimized design of these transistors has been suggested. And the range (in terms of device and technological parameters) of the proposed model has been elucidated.

Nature of Noncovalent Interactions in Catenane Supramolecular Complexes: Calibrating the MM3 Force Field with ab Initio, DFT, and SAPT Methods

The design and assembly of mechanically interlocked molecules, such as catenanes and rotaxanes, are dictated by various types of noncovalent interactions. In particular, [C-H···O] hydrogen-bonding and π-π stacking interactions in these supramolecular complexes have been identified as important noncovalent interactions. With this in mind, we examined the [3]catenane 2·4PF6 using molecular mechanics (MM3), ab initio methods (HF, MP2), several versions of density functional theory (DFT) (B3LYP, M0X), and the dispersion-corrected method DFT-D3. Symmetry adapted perturbation theory (DFT-SAPT) provides the highest level of theory considered, and we use the DFT-SAPT results both to calibrate the other electronic structure methods, and the empirical potential MM3 force field that is often used to describe larger catenane and rotaxane structures where [C-H···O] hydrogen-bonding and π-π stacking interactions play a role. Our results indicate that the MM3 calculated complexation energies agree qualitatively with the energetic ordering from DFT-SAPT calculations with an aug-cc-pVTZ basis, both for structures dominated by [C-H···O] hydrogen-bonding and π-π stacking interactions. When the DFT-SAPT energies are decomposed into components, we find that electrostatic interactions dominate the [C-H···O] hydrogen-bonding interactions, while dispersion makes a significant contribution to π-π stacking. Another important conclusion is that DFT-D3 based on M06 or M06-2X provides interaction energies that are in near-quantitative agreement with DFT-SAPT. DFT results without the D3 correction have important differences compared to DFT-SAPT, while HF and even MP2 results are in poor agreement with DFT-SAPT.

Characterization of the internal dynamics and conformational space of zinc-bound amyloid β peptides by replica-exchange molecular dynamics simulations

Amyloid β (Aβ) peptides and metal ions have been associated with the pathogenesis of Alzheimer's disease. The conformational space of Aβ fragments of different length with and without binding of metal ions has been extensively investigated by replica-exchange molecular dynamics (REMD) simulation. However, only trajectories extracted at relatively low temperatures have been used for this analysis. The capability of REMD simulations to characterize the internal dynamics of such intrinsically disordered proteins (IDPs) as Aβ has been overlooked. In this work, we use an approach recently developed by Xue and Skrynnikov (J Am Chem Soc 133:14614-14628, 2011) to calculate NMR observables, including (15)N relaxation rates and (15)N-(1)H nuclear Overhauser enhancement (NOE), from the high-temperature trajectory of REMD simulations for zinc-bound Aβ peptides. The time axis of the trajectory was rescaled to correct for the effect of the high temperature (408K) compared with the experimental temperature (278K). Near-quantitative agreement between simulated values and experimental results was obtained. When the structural properties and free-energy surfaces of zinc-bound Aβ(1-40) and Aβ(1-42) were compared at the physiological temperature 310K it was found that zinc-bound Aβ(1-42) was more rigid than Aβ(1-40) at the C terminus, and its conformational transitions were also more preferred. The self-consistent results derived from trajectories at high and low temperatures demonstrate the capability of REMD simulations to capture the internal dynamics of IDPs.

Near-Quantitative Agreement of Model-Free DFT-MD Predictions with XAFS Observations of the Hydration Structure of Highly Charged Transition-Metal Ions

First-principles dynamics simulations (DFT, PBE96, and PBE0) and electron scattering calculations (FEFF9) provide near-quantitative agreement with new and existing XAFS measurements for a series of transition-metal ions interacting with their hydration shells via complex mechanisms (high spin, covalency, charge transfer, etc.). This analysis does not require either the development of empirical interparticle interaction potentials or structural models of hydration. However, it provides consistent parameter-free analysis and improved agreement with the higher-R scattering region (first- and second-shell structure, symmetry, dynamic disorder, and multiple scattering) for this comprehensive series of ions. DFT+GGA MD methods provide a high level of agreement. However, improvements are observed when exact exchange is included. Higher accuracy in the pseudopotential description of the atomic potential, including core polarization and reducing core radii, was necessary for very detailed agreement. The first-principles nature of this approach supports its application to more complex systems.

Molecule‐specific determination of atomic polarizabilities with the polarizable atomic multipole model

Recently, many polarizable force fields have been devised to describe induction effects between molecules. In popular polarizable models based on induced dipole moments, atomic polarizabilities are the essential parameters and should be derived carefully. Here, we present a parameterization scheme for atomic polarizabilities using a minimization target function containing both molecular and atomic information. The main idea is to adopt reference data only from quantum chemical calculations, to perform atomic polarizability parameterizations even when relevant experimental data are scarce as in the case of electronically excited molecules. Specifically, our scheme assigns the atomic polarizabilities of any given molecule in such a way that its molecular polarizability tensor is well reproduced. We show that our scheme successfully works for various molecules in mimicking dipole responses not only in ground states but also in valence excited states. The electrostatic potential around a molecule with an externally perturbing nearby charge also exhibits a near-quantitative agreement with the reference data from quantum chemical calculations. The limitation of the model with isotropic atoms is also discussed to examine the scope of its applicability.

Barrierless photoisomerisation of the “simplest cyanine”: Joining computational and femtosecond optical spectroscopies to trace the full reaction path

The photoisomerisation of 1,1'-diethyl-2,2'-pyridocyanine, regarded by Brooker as the simplest cyanine, is examined in methanol by time-resolved experiments and PCM/TD-CAM-B3LYP calculations. Femtosecond transient absorption, fluorescence upconversion, and stimulated Raman scattering, all with broadband coverage, provide a panoramic view of the photoreaction. On the computational side, evolving distributions on an S(1) minimum-energy path are obtained by solving the Smoluchowski equation for drift and diffusion of torsional motion. Absorption and fluorescence bandshapes are calculated and compared to the observations; near-quantitative agreement implies that the entire S(1) path has been observed. Most importantly the global S(1) minimum, i.e. the perpendicular "phantom state" P*, can be identified and characterized in this way. Internal conversion of P* (3.7 ps), assisted by solvent equilibration, leads to the hot ground state. Within 5 ps, vibrational bands of cis and trans isomers are recognized with the help of calculated Raman spectra. The differences between observed and simulated spectra are discussed.

Nano-indentation of a room-temperature ionic liquid film on silica: a computational experiment

We investigate the structure of the [bmim][Tf(2)N]/silica interface by simulating the indentation of a thin (4 nm) [bmim][Tf(2)N] film by a hard nanometric tip. The ionic liquid/silica interface is represented in atomistic detail, while the tip is modelled by a spherical mesoscopic particle interacting via an effective short-range potential. Plots of the normal force (F(z)) on the tip as a function of its distance from the silica surface highlight the effect of weak layering in the ionic liquid structure, as well as the progressive loss of fluidity in approaching the silica surface. The simulation results for F(z) are in near-quantitative agreement with new AFM data measured on the same [bmim][Tf(2)N]/silica interface under comparable thermodynamic conditions.

Motion of a Disordered Polypeptide Chain as Studied by Paramagnetic Relaxation Enhancements,15N Relaxation, and Molecular Dynamics Simulations: How Fast Is Segmental Diffusion in Denatured Ubiquitin?

Molecular dynamics (MD) simulations have been widely used to analyze dynamic conformational equilibria of folded proteins, especially in relation to NMR observables. However, this approach found little use in the studies of disordered proteins, where the sampling of vast conformational space presents a serious problem. In this paper, we demonstrate that the latest advances in computation technology make it possible to overcome this limitation. The experimentally validated (calibrated) MD models allow for new insights into structure/dynamics of disordered proteins. As a test system, we have chosen denatured ubiquitin in solution with 8 M urea at pH 2. High-temperature MD simulations in implicit solvent have been carried out for the wild-type ubiquitin as well as MTSL-tagged Q2C, D32C, and R74C mutants. To recalibrate the MD data (500 K) in relation to the experimental conditions (278 K, 8 M urea), the time axes of the MD trajectories were rescaled. The scaling factor was adjusted such as to maximize the agreement between the simulated and experimental (15)N relaxation rates. The resulting effective length of the trajectories, 311 μs, ensures good convergence properties of the MD model. The constructed MD model was validated against the array of experimental data, including additional (15)N relaxation parameters, multiple sets of paramagnetic relaxation enhancements (PREs), and the radius of gyration. In each case, a near-quantitative agreement has been obtained, suggesting that the model is successful. Of note, the MD-based approach rigorously predicts the quantities that are inherently dynamic, i.e., dependent on the motional correlation times. This cannot be accomplished, other than in empirical fashion, on the basis of static structural models (conformational ensembles). The MD model was further used to investigate the relative translational motion of the MTSL label and the individual H(N) atoms. The derived segmental diffusion coefficients proved to be nearly uniform along the peptide chain, averaging to D = 0.49-0.55 × 10(-6) cm(2)/s. This result was verified by direct analysis of the experimental PRE data using the recently proposed Ullman-Podkorytov model. In this model, MTSL and H(N) moieties are treated as two tethered spheres undergoing mutual diffusion in a harmonic potential. The fitting of the experimental data involving D as a single adjustable parameter leads to D = 0.45 × 10(-6) cm(2)/s, in good agreement with the MD-based analyses. This result can be compared with the range of estimates obtained from the resonance energy transfer experiments, D = 0.2-6.0 × 10(-6) cm(2)/s.

Implicit-Solvent Models for Micellization: Nonionic Surfactants and Temperature-Dependent Properties

We have investigated micellization properties of surfactants using a recently developed implicit-solvent model and grand canonical Monte Carlo simulations. The original model had been parametrized for ionic surfactants at a single temperature; it is extended here to aqueous solutions of nonionic surfactants and given an explicit temperature dependence. Specifically, we have developed an implicit-solvent model of polyethylene glycol (PEG) surfactants and obtained the critical micelle concentrations (cmc's) and micellar aggregation numbers at low surfactant loadings. Various combinations of ethoxy and hydrocarbon tail segments were investigated in order to explore the predictive capabilities of the model. For the temperature dependence of the micellization properties, we have utilized thermodynamic approaches to quantify the hydrophobic attraction at temperatures ranging from 280 to 365 K. The temperature dependence of the cmc and the aggregate sizes were obtained for various ionic and nonionic surfactants, specifically sodium dodecyl sulfate, dodecyltrimethylammonium bromide and chloride, and PEG surfactants. For all systems studied, the model yields cmc and aggregation sizes that are in near-quantitative agreement with experimental results.

Plasmon excitations on a single-wall carbon nanotube by external charges: Two-dimensional two-fluid hydrodynamic model

We present a quantization of the hydrodynamic model to describe the excitation of plasmons in a single-walled carbon nanotube by a fast point charge moving near its surface at an arbitrary angle of incidence. Using a two-dimensional electron gas represented by two interacting fluids, which takes into account the different nature of the $\ensuremath{\sigma}$ and $\ensuremath{\pi}$ electrons, we obtain plasmon energies in near-quantitative agreement with experiment. Further, the implemented quantization procedure allows us to study the probability of exciting various plasmon modes, as well as the stopping force and energy loss spectra of the incident particle.

Structure and electron paramagnetic resonance parameters of the manganese site of concanavalin A studied by density functional methods

The EPR parameters of the manganese site in the saccharide-binding protein concanavalin A have been studied by density functional methods, with an emphasis on metal (55Mn) and ligand (1H and 17O) hyperfine couplings, in comparison with high-field EPR and ENDOR data. Results for gradient-corrected and hybrid functionals with different exact-exchange admixture have been compared with experiment for the 55Mn and the 1H ligand hyperfine coupling and have been predicted for 17O hyperfine coupling based on comparison with experiment for the related [Mn(H2O)6]2+. Appreciable exact-exchange admixture in the hybrid functional is needed to obtain an adequate spin-density distribution and thus near-quantitative agreement with experimental EPR parameters. The common use of experimental proton hyperfine coupling tensors together with the point-dipole approximation for determination of bond lengths is evaluated by explicit calculations.

Cavity ring-down spectroscopy measurements of single aerosol particle extinction. I. The effect of position of a particle within the laser beam on extinction

A continuous wave distributed feedback diode laser operating in the near infrared at wavelengths close to 1650 nm has been used to measure the extinction of light by single aerosol particles. The technique of optical feedback cavity ring-down spectroscopy (CRDS) was used for measurement of CRDS events at a repetition rate of 1.25 kHz. This very high repetition rate enabled multiple measurements of the extinction of light by single aerosol particles for the first time and demonstrated the dependence of light scattering on the position of a particle within the laser beam. A model is proposed to explain quantitatively this phenomenon. The minimum detectable dimensionless extinction coefficient epsilonmin was determined to be 3x10(-6). Extinction values obtained for single spherical polymer beads from a monodisperse sample of particles of diameter of 4 microm are in near-quantitative agreement with the values calculated by the Mie scattering theory. The deviations from the Mie theory expected for measurement of extinction by CRDS using a continuous wave laser are discussed in the companion paper.

Jahn-Teller effect in CH3D+ and CD3H+: Conformational isomerism, tunneling-rotation structure, and the location of conical intersections

High-resolution pulsed-field-ionization zero-kinetic-energy photoelectron spectra of CH(3)D and CD(3)H have been recorded at rotational resolution from the adiabatic ionization energy up to 600 cm(-1) of internal energy of the respective cations. The spectra are characterized by the effects of a large-amplitude pseudorotational motion exchanging the equivalent nuclei in each molecule. With increasing internal energy, a transition from the tunneling regime with splittings of the order of 1-10 cm(-1) to the free pseudorotation regime is observed. A theoretical model that treats the simultaneous rotational and pseudorotational motions and incorporates the effects of the geometric phase has been developed. The model provides the appropriate rovibronic symmetries in the C(3v)(M) molecular symmetry group and reaches a near-quantitative agreement with the experimental data. The complete group-theoretical analysis of the rovibronic problem is also given. The analysis of the spectra has revealed the existence of two different isomers for both CH(3)D(+) and CD(3)H(+), which differ in the bond length between the carbon atom and the unique ligand atom. All isomers are subject to a fast pseudorotational motion between three equivalent minima with a period of 3-5 ps in CH(3)D(+) and 18-28 ps in CD(3)H(+). The analysis has also provided the ordering of the tunneling sublevels for each isomer, which enables the location of the twofold conical intersections on the potential energy surface that could not be determined from experiments on CH(4) (+).

Quantum Interference as the Source of Steric Asymmetry and Parity Propensity Rules in NO−Rare Gas Inelastic Scattering

Rotationally inelastic scattering of rare gas atoms and oriented NO molecules exhibits a remarkable alternation in the sign of steric asymmetry between even and odd changes in rotational quantum number. This effect has also been found in full quantum-mechanical scattering calculations. However, until now no physical picture has been given for the alternation. In this work, a newly developed quasi-quantum treatment (QQT) provides the first demonstration that quantum interferences between different orientations of the repulsive potential (that are present in the oriented wave function) are the source of this alternation. Further, from application of the treatment to collisions of nonoriented molecules, a previously unrecognized propensity rule is derived. The angular dependence of the cross sections for excitation to neighboring rotational states with the same parity is shown to be similar, except for a prefactor. Experimental results are presented to support this rule. Unlike conventional quantum-mechanical (or semiclassical) treatments, QQT requires no summation over the orbital angular momentum quantum number l or integration over the impact parameter b. This eliminates the need to solve large sets of coupled differential equations that couple l and rotational state channels among which interference can occur. The QQT provides a physical interpretation of the scattering amplitude that can be represented by a Legendre moment. Application of the QQT on a simple hard-shell potential leads to near-quantitative agreement with experimental observations.

Measurement and modeling of a diamond deposition reactor: Hydrogen atom and electron number densities in an Ar∕H2 arc jet discharge

A combination of experiment [optical emission and cavity ring-down spectroscopy (CRDS) of electronically excited H atoms] and two-dimensional (2D) modeling has enabled a uniquely detailed characterization of the key properties of the Ar∕H2 plasma within a ⩽10-kW, twin-nozzle dc arc jet reactor. The modeling provides a detailed description of the initial conditions in the primary torch head and of the subsequent expansion of the plasma into the lower pressure reactor chamber, where it forms a cylindrical plume of activated gas comprising mainly of Ar, Ar+, H, ArH+, and free electrons. Subsequent reactions lead to the formation of H2 and electronically excited atoms, including H(n=2) and H(n=3) that radiate photons, giving the plume its characteristic intense emission. The modeling successfully reproduces the measured spatial distributions of H(n>1) atoms, and their variation with H2 flow rate, FH20. Computed H(n=2) number densities show near-quantitative agreement with CRDS measurements of H(n=2) absorption via the Balmer-β transition, successfully capturing the observed decrease in H(n=2) density with increased FH20. Stark broadening of the Balmer-β transition depends upon the local electron density in close proximity to the H(n=2) atoms. The modeling reveals that, at low FH20, the maxima in the electron and H(n=2) atom distributions occur in different spatial regions of the plume; direct analysis of the Stark broadening of the Balmer-β line would thus lead to an underestimate of the peak electron density. The present study highlights the necessity of careful intercomparisons between quantitative experimental data and model predictions in the development of a numerical treatment of the arc jet plasma. The kinetic scheme used here succeeds in describing many disparate observations—e.g., electron and H(n=2) number densities, spatial distributions of optical emission from the plume, the variation of these quantities with added flow of H2 and, when CH4 is added, absolute number densities and temperatures of radicals such as C2 and CH. The remaining limitations of the model are discussed.

Similarity transformed semiclassical dynamics

In this article, we employ a recently discovered criterion for selecting important contributions to the semiclassical coherent state propagator [T. Van Voorhis and E. J. Heller, Phys. Rev. A 66, 050501 (2002)] to study the dynamics of many dimensional problems. We show that the dynamics are governed by a similarity transformed version of the standard classical Hamiltonian. In this light, our selection criterion amounts to using trajectories generated with the untransformed Hamiltonian as approximate initial conditions for the transformed boundary value problem. We apply the new selection scheme to some multidimensional Henon–Heiles problems and compare our results to those obtained with the more sophisticated Herman–Kluk approach. We find that the present technique gives near-quantitative agreement with the the standard results, but that the amount of computational effort is less than Herman–Kluk requires even when sophisticated integral smoothing techniques are employed in the latter.

Conservation principles in solitary impulse propagation through granular chains

An independent-collision model is advanced as a conceptually simple and computationally convenient framework for understanding non-linear impulse propagation in granular chains. In particular, conservation principles are used to show that the independent-collision model supports solitons in uniform granular chains, and exhibits an exponential dispersion of momentum and energy in tapered chains. These results are in qualitative agreement with recent detailed simulations of Hertzian spheres by Sen et al. (Physica A 299 (2001) 551). Near-quantitative agreement is achieved by renormalizing the width of an independent impulse by the solitary wave width. The model is easily extended, as we demonstrate by incorporating the effects of restitution.