Density-functional expansion methods: generalization of the auxiliary basis

The formulation of density-functional expansion methods is extended to treat the second and higher-order terms involving the response density and spin densities with an arbitrary single-center auxiliary basis. The two-center atomic orbital products are represented by the auxiliary functions centered about those two atoms, and the mapping coefficients are determined from a local constrained variational procedure. This two-center variational procedure allows the mapping coefficients to be pretabulated and splined as a function of internuclear separation for efficient look up. The splines of mapping coefficients have a range no longer than that of the overlap integrals, and the auxiliary density appears as a single point-multipole expansion to all nonoverlapping atoms, thus allowing for the trivial implementation of a linear-scaling algorithm. The method is tested using Gaussian multipole expansions, and the effect of angular and radial completeness is explored. Several auxiliary basis sets are parametrized and compared to an auxiliary basis analogous to that used in the self-consistent-charge density-functional tight-binding model, and the method is demonstrated to greatly improve the representation of the density response with respect to a reference expansion model that does not use an auxiliary basis.     

Density-functional expansion methods: evaluation of LDA, GGA, and meta-GGA functionals and different integral approximations

We extend the Kohn-Sham potential energy expansion (VE) to include variations of the kinetic energy density and use the VE formulation with a 6-31G* basis to perform a "Jacob's ladder" comparison of small molecule properties using density functionals classified as being either LDA, GGA, or meta-GGA. We show that the VE reproduces standard Kohn-Sham DFT results well if all integrals are performed without further approximation, and there is no substantial improvement in using meta-GGA functionals relative to GGA functionals. The advantages of using GGA versus LDA functionals becomes apparent when modeling hydrogen bonds. We furthermore examine the effect of using integral approximations to compute the zeroth-order energy and first-order matrix elements, and the results suggest that the origin of the short-range repulsive potential within self-consistent charge density-functional tight-binding methods mainly arises from the approximations made to the first-order matrix elements.     

Unimolecular rectifiers: methods and challenges

Six unimolecular rectifiers have been studied at the University of Alabama: Langmuir-Blodgett (LB) or Langmuir-Schaefer (LS), or self-assembled monolayers of these molecules show asymmetric electrical conductivity between Au or Al electrodes. These molecules are gamma-hexadecylquinolinium tricyanoquinodimethanide (Fig. 1, 2), 2,6-di[dibutylamino-phenylvinyl]-l-butylpyridinium iodide, 3, dimethylanilino-aza[C60]-fullerene, 4, fullerene-bis-[4-diphenylamino-4'-(N-ethyl-N-2-ethyl)-amino-1,4-diphenyl-1,3 -butadiene] malonate, 5, N-(10-nonadecyl)-N-(2-ferrocenyl-ethyl)-pyrenyl-methyl)pery-lene-3,4,9,10-bis(dicarboxyimide), 6, and 4,5-dipentyl-5'-methyltetrathiaful-valen-4'-methyl-oxy-2,4,5-trinitro-9-dicyanomethylenefluorene-7-(3-sulfonylpropionate), 7. Many ancillary experiments must be performed before unimolecular rectification can be fully understood. This review will focus on the fabrication techniques and the analytical tools that can help understand the asymmetric current-voltage (IV) curves. These tools include molecular orbital calculations, cyclic voltammetry, ultraviolet photoelectron spectroscopy, scanning tunneling microscopy, contact angle goniometry, ultraviolet-visible-near-infrared spectroscopy, grazing-angle Fourier transform infrared spectroscopy, surface plasmon resonance, spectroscopic ellipsometry, grazing-incidence X-ray reflectometry, core-level and valence-band X-ray photoelectron spectroscopy.     

Toxicity assessment of nanomaterials: methods and challenges

The increasing use of nanomaterials in consumer and industrial products has aroused global concern regarding their fate in biological systems, resulting in a demand for parallel risk assessment. A number of studies on the effects of nanoparticles in in vitro and in vivo systems have been published. However, there is still a need for further studies that conclusively establish their safety/toxicity, due to the many experimental challenges and issues encountered when assessing the toxicity of nanomaterials. Most of the methods used for toxicity assessment were designed and standardized with chemical toxicology in mind. However, nanoparticles display several unique physicochemical properties that can interfere with or pose challenges to classical toxicity assays. Recently, some new methods and modified versions of pre-existing methods have been developed for assessing the toxicity of nanomaterials. This review is an attempt to highlight some important methods employed in nanomaterial toxicology and to provide a critical analysis of the major issues/challenges faced in this emerging field.     

Density-functional methods for the study of the ground-state vibrations of the guanidinium ion

Sixteen density functional methods (including four hybrid methods) with the 3–21G and the 6–31G(d, p) basis set of atomic functions are used to predict the structure and vibrations of the guanidinium ion [C(NH₂)₃]⁺. The study was done with the ion both in a vacuum and in an aqueous solution. To account for the solvation effect on the vibrating behavior of the ion, the solvent was modeled in two ways of increasing complexity: First, the guanidinium was inserted into a cavity of a continuous medium (dielectric constant ϵ = 78) and, second, six explicit water molecules were considered around the ion and the whole aggregate inserted into the cavity of the continuum. The conformation corresponding to the energy minimum is predicted to have D₃ symmetry rather than D_3h. The harmonic vibrational frequencies obtained have a mean absolute deviation from the experimental data of about one-half the value achieved by pure Hartree-Fock methods. Isotopic substitution calculations were also carried out and shifts obtained are in good agreement with experience and so are the assignments of the observed bands to the vibrational normal modes. The study of the solvent effect shows the existence of modes that are not affected by hydration and some improvement in the values predicted, especially for low-frequency vibrations. © 1997 John Wiley & Sons, Inc.     

Poor quality drugs: grand challenges in high throughput detection, countrywide sampling, and forensics in developing countries

Throughout history, poor quality medicines have been a persistent problem, with periodical crises in the supply of antimicrobials, such as fake cinchona bark in the 1600s and fake quinine in the 1800s. Regrettably, this problem seems to have grown in the last decade, especially afflicting unsuspecting patients and those seeking medicines via on-line pharmacies. Here we discuss some of the challenges related to the fight against poor quality drugs, and counterfeits in particular, with an emphasis on the analytical tools available, their relative performance, and the necessary workflows needed for distinguishing between genuine, substandard, degraded and counterfeit medicines.     

Some convergence aspects of the one-center expansion methods

Among the methods that may be used to carry out multicenter integrals over STOS, the one-center two-range expansion is probably the oldest one. However, the convergence of the leading series is generally slow and, hence, time-consuming. Therefore, it was the aim of the present work to show that the so-called nonlinear sequence transformations may be of substantial help for improving the rate of convergence of such series. © 1994 John Wiley & Sons, Inc.     

Density-functional theory for polymer-carbon dioxide mixtures: A perturbed-chain SAFT approach

We propose a density-functional theory (DFT) describing inhomogeneous polymer-carbon dioxide mixtures based on a perturbed-chain statistical associating fluid theory equation of state (PC-SAFT EOS). The weight density functions from fundamental measure theory are used to extend the bulk excess Helmholtz free energy to the inhomogeneous case. The additional long-range dispersion contributions are included using a mean-field approach. We apply our DFT to the interfacial properties of polystyrene-CO(2) and poly(methyl methacrylate) CO(2) systems. Calculated values for both solubility and interfacial tension are in good agreement with experimental data. In comparison with our earlier DFT based on the Peng-Robinson-SAFT EOS, the current DFT produces quantitatively superior agreement with experimental data and is free of the unphysical behavior at high pressures (>35 MPa) in the earlier theory.     

Density-functional computation of 99Ru NMR parameters

Gradient-corrected and hybrid variants of density-functional theory are used to compute the geometries and 99Ru chemical shifts of RuO4, [RuCp2], [K4Ru(CN)6], [Ru3(CO)12], [Ru(CO)3X3]- (X=Cl, I), [Ru(CO)2Cl4]2-, [Ru(bipy)3]2+, and [Ru(CO)2(iPr-DAB)(X)(Y)] [XY= Cl2, I2, MeCl, MeI, or (SnMe3)2]. For this set of compounds, substituent effects on delta(99Ru) are somewhat underestimated with the BPW91 pure density functional but are described well by the B3LYP hybrid functional, which can also be used to reproduce empirical trends in electric field gradients (EFGs) at the Ru nucleus qualitatively. In the [Ru(CO)2(iPr-DAB)XY] series, trends in the computed EFGs parallel those in the observed 99Ru NMR linewidths, in accordance with the quadrupolar relaxation mechanism expected for this nucleus. For this series of compounds, the use of X-ray-derived geometries affords a worse correlation between calculated EFGs and experimental linewidths than does the use of optimized geometries.     

Density-functional tight-binding for phosphine-stabilized nanoscale gold clusters

We report a parameterization of the second-order density-functional tight-binding (DFTB2) method for the quantum chemical simulation of phosphine-ligated nanoscale gold clusters, metalloids, and gold surfaces. Our parameterization extends the previously released DFTB2 “auorg” parameter set by connecting it to the electronic parameter of phosphorus in the “mio” parameter set. Although this connection could technically simply be accomplished by creating only the required additional Au–P repulsive potential, we found that the Au 6p and P 3d virtual atomic orbital energy levels exert a strong influence on the overall performance of the combined parameter set. Our optimized parameters are validated against density functional theory (DFT) geometries, ligand binding and cluster isomerization energies, ligand dissociation potential energy curves, and molecular orbital energies for relevant phosphine-ligated Au_n clusters (n = 2–70), as well as selected experimental X-ray structures from the Cambridge Structural Database. In addition, we validate DFTB simulated far-IR spectra for several phosphine- and thiolate-ligated gold clusters against experimental and DFT spectra. The transferability of the parameter set is evaluated using DFT and DFTB potential energy surfaces resulting from the chemisorption of a PH₃ molecule on the gold (111) surface. To demonstrate the potential of the DFTB method for quantum chemical simulations of metalloid gold clusters that are challenging for traditional DFT calculations, we report the predicted molecular geometry, electronic structure, ligand binding energy, and IR spectrum of Au₁₀₈S₂₄(PPh₃)₁₆.

We report a parameterization of the density-functional tight-binding (DFTB) method for the accurate prediction of molecular, electronic and vibrational structure of phosphine-ligated nanoscale gold clusters, metalloids, and gold surfaces.     

Density-functional theory-based molecular simulation study of liquid methanol

We present a density-functional theory based molecular dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare well with recent neutron diffraction data. We observe that, in line with infrared spectroscopic data, the hydroxyl-stretching mode is significantly redshifted in the liquid, whereas the hydroxyl bending mode shows a blueshift. A substantial enhancement of the molecular dipole moment is accompanied by significant fluctuations due to thermal motion. We compute a value of 32 for the relative permittivity, almost identical to the experimental value of 33. Our results provide valuable data for improvement of empirical potentials.     

Instrumental methods and challenges in quantifying polybrominated diphenyl ethers in environmental extracts: a review

Increased interest in the fate, transport and toxicity of polybrominated diphenyl ethers (PBDEs) over the past few years has led to a variety of studies reporting different methods of analysis for these persistent organic pollutants. Because PBDEs encompass a range of vapor pressures, molecular weights and degrees of bromine substitution, various analytical methods can lead to discrimination of some PBDE congeners. Recent improvements in injection techniques and mass spectrometer ionization methods have led to a variety of options to determine PBDEs in environmental samples. The purpose of this paper is therefore to review the available literature describing the advantages and disadvantages in choosing an injection technique, gas chromatography column and detector. Additional discussion is given to the challenges in measuring PBDEs, including potential chromatographic interferences and the lack of commercial standards for higher brominated congeners, which provides difficulties in examining degradation and debromination of BDE congeners, particularly for BDE 209.     

Density-functional computation of 53Cr NMR chemical shifts

53Cr chemical shifts of CrO4(2-), Cr2O7(2-), CrO3X-, CrO2X2(X = F, Cl), and Cr(CO)5L (L = CO, PF3, CHNH2, CMeNMe2) are computed, using geometries optimized with the gradient-corrected BP86 density functional, at the gauge-including atomic orbitals (GIAO)-, BPW91-, and B3LYP levels. For this set of compounds, substituent effects on delta(53Cr) are better described with the pure BPW91 functional than with B3LYP, in contrast to most other transition-metal chemical shifts studied so far. For selected cases, 53Cr NMR line widths can be rationalized in terms of electric field gradients (EFGs) computed with the BPW91 functional, but in general other factors such as molecular correlation times appear to be dominating. 53Cr chemical shifts and EFGs are predicted for CrO3, Cr(C6H6)2, Cr(C6H6)CO3, and, with reduced reliability, for Cr2(mu2-O2CH)4.     

Density-functional study of interfacial properties of colloid-polymer mixtures

Interfacial properties of colloid-polymer mixtures are examined within an effective one-component representation, where the polymer degrees of freedom are traced out, leaving a fluid of colloidal particles interacting via polymer-induced depletion forces. Restriction is made to zero-, one-, and two-body effective potentials, and a free energy functional is used that treats colloid excluded volume correlations within Rosenfeld's fundamental measure theory, and depletion-induced attraction within first-order perturbation theory. This functional allows a consistent treatment of both ideal and interacting polymers. The theory is applied to surface properties near a hard wall, to the depletion interaction between two walls, and to the fluid-fluid interface of demixed colloid-polymer mixtures. The results of the present theory compare well with predictions of a fully two-component representation of mixtures of colloids and ideal polymers (the Asakura-Oosawa model) and allow a systematic investigation of the effects of polymer-polymer interactions on interfacial properties. In particular, the wall surface tension is found to be significantly larger for interacting than for ideal polymers, whereas the opposite trend is predicted for the fluid-fluid interfacial tension.     

Density-functional theory studies on microscopic processes of gaas growth

Results for the elementary processes of MBE growth of GaAs on the frequently used GaAs(001) substrate are reviewed. We propose a bottom-up approach, where a growth model is constructed from the results of density functional theory (DFT) calculations. The implications of such a model can be tested against the information from STM images. First, the stable surface reconstructions are reviewed. Under the most commonly used conditions for MBE growth, the arsenic-rich β2 (2 × 4) reconstruction, which contains As dimers as basic building blocks, is the most stable. Next, the adsorption and diffusion of Ga atoms and As molecules on this surface is described. The DFT calculations support the picture that adsorbed Ga atoms are quite stable against re-evaporation. Thus, their mobility determines the homogeneity of the growing layer. Incorporation of Ga atoms proceeds by splitting the As dimers. We propose a model where growth proceeds in two stages: filling of trenches in the β2 (2 × 4) reconstruction, followed by nucleation of islands on the surface regions where the trenches are filled. We demonstrate how clusters of incorporated Ga atoms act as nuclei for the process of trench filling. Concerning island formation, the role of step formation energies and attachment probabilities of mobile adatoms at steps is discussed. Knowledge of these is crucial for an understanding of island shapes. Ongoing research is aiming at understanding of the microscopic mechanisms giving rise to the transition between the step-flow mode and the island-nucleation mode of growth.     

A path integral influence functional for excess electron in fluids: Density-functional formulation

In this paper, we propose a path integral influence functional from a solvent to determine a self-correlation function of a quantum particle in classical simple fluid. It is shown that the influence functional is related to a grand potential functional of the pure solvent under a three-dimensional external field arising from a classical isomorphic polymer, on which the quantum particle is mapped. The influence functional can be calculated from the self-correlation function, the solute-solvent and the solvent-solvent pair correlation function. The obtained equation of the self-correlation function is applied to an excess electron problem in fluid helium. The Fourier path-integral Monte Carlo method is employed to perform the path integral of the electron. The solute-solvent pair correlation function is estimated from a reference interaction site model integral equation. These results obtained form our proposed influence functional and from that proposed by Chandler, Singh, and Richardson are compared with those provided by a path integral Monte Carlo simulation with the explicit helium solvent.     

Communication: Density-functional theory for inhomogeneous hyperbranched polymeric fluids: polydisperse effect of degree of branching

We developed a new density-functional theory (DFT) for inhomogeneous hyperbranched polymers that is able to describe the polydisperse degree of branching quantitatively. The topological contributions of the polymer chains to the Helmholtz free energy take into account the effect of triple connections that are absent in previous DFT investigations. One key advantage of the new theory is that the computational cost shows only a linear relationship with the molecular weight (rather than an exponential relationship). The practical utility of the new DFT is illustrated by investigating colloidal stability in the presence of monodisperse and polydisperse hyperbranched polymers.     

Density-functional geometry optimization of the 150,000-atom photosystem-I trimer

We present a linear-scaling method based on the use of density-functional theory (DFT) for the system-wide optimization of x-ray structural coordinates and apply it to optimize the 150,000 atoms of the photosystem-I (PS-I) trimer. The method is based on repetitive applications of a multilevel ONIOM procedure using the PW916-31G(d) DFT calculations for the high level and PM3 for the lower level; this method treats all atoms in the structure equivalently, a structure in which the majority of the atoms can be considered as part of some internal "active site." To obtain a realistic single structure, some changes to the original protein model were necessary but these are kept to a minimum in order that the optimized structure most closely resembles the original x-ray one. Optimization has profound effects on the perceived electronic properties of the cofactors, with, e.g., optimization lowering the internal energy of the chlorophylls by on average 53 kcal mol(-1) and eliminates the enormous 115 kcal mol(-1) energy spread depicted by the original x-ray heavy-atom coordinates. A highly precise structure for PS-I results that is suitable for analysis of device function. Significant qualitative features of the structure are also improved such as correction of an error in the stereochemistry of one of the chlorophylls in the "special pair" of the reaction center, as well as the replacement of a water molecule with a metal cation in a critical region on the C3 axis. The method also reveals other unusual features of the structure, leading both to suggestions concerning device functionality and possible mutations between gene sequencing and x-ray structure determination. The optimization scheme is thus shown to augment the molecular modeling schemes that are currently used to add medium-resolution structural information to the raw scattering data in order to obtain atomically resolved structures. System-wide optimization is now a feasible process and its use within protein x-ray data refinement should be considered.     

Density-functional study of two Fe4-based single-molecule magnets

We present the results of our all-electron density-functional calculations on the electronic structure and magnetic anisotropy energy of the [Fe4(OMe)6(dpm)6] and [Fe4(thme)2(dpm)6] molecular clusters, which are experimentally found to behave as single-molecule magnets. The calculated magnetic anisotropy energy barriers are 2.65 and 15.8 K, respectively, which agree with the experimental data. We also present a density-functional study on the effect of the structure distortions on the magnetic anisotropy of the [Fe(H2O)6]3+ complex. This study, together with an analysis of the projected anisotropies of each iron ion in both molecular clusters, allows us to qualitatively understand why the magnetic anisotropy energy (MAE) barrier of the second single-molecule magnet (SMM) is larger than the MAE of the first SMM.