Self-consistent implementation of a nonlocal van der Waals density functional with a Gaussian basis set

Nearly all common density functional approximations fail to properly describe dispersion interactions responsible for binding in van der Waals complexes. Empirical corrections can fix some of the failures but cannot fully grasp the complex physics and may not be reliable for systems dissimilar to the fitting set. In contrast, the recently proposed nonlocal van der Waals density functional (vdW-DF) was derived from first principles, describes dispersion interactions in a seamless fashion, and yields the correct asymptotics. Implementation of this functional is somewhat cumbersome: Nonlocal dependence on the electron density requires numerical double integration over the space variables and functional derivatives are nontrivial. This paper shows how vdW-DF can be implemented self-consistently with Gaussian basis functions. The gradients of the energy with respect to nuclear displacements have also been derived and coded, enabling efficient geometry optimizations. We test the vdW-DF correlation functional in combination with several exchange approximations. We also study the sensitivity of the method to the basis set size and to the quality of the numerical quadrature grid. For weakly interacting systems, acceptable accuracy in semilocal exchange is achieved only with fine grids, whereas for nonlocal vdW-DF correlation even rather coarse grids are sufficient. The current version of vdW-DF is not well suited for pairing with Hartree-Fock exchange, leading to considerable overbinding.     

Gas phase spectra of all-benzenoid polycyclic aromatic hydrocarbons: triphenylene

The jet-cooled laser-induced fluorescence and dispersed fluorescence spectra of the S1(A1')<--S0(A1') transition of triphenylene are reported. The spectra exhibit false origins of e' symmetry which are modeled by performing calculations of Herzberg-Teller coupling using time-dependent density functional theory. It is found that this level of theory reproduces the main features of the observed spectra. The oscillator strength of the strongest band is calculated to be f=7x10(-4). From a combination of theory and the observed upper state lifetime of 41 ns, an estimate of the fluorescence yield is made of PhiF=0.084, in agreement with previous studies in the condensed phase.     

Low variance energy estimators for systems of quantum Drude oscillators: treating harmonic path integrals with large separations of time scales

In the effort to develop atomistic models capable of accurately describing nanoscale systems with complex interfaces, it has become clear that simple treatments with rigid charge distributions and dispersion coefficients selected to generate bulk properties are insufficient to predict important physical properties. The quantum Drude oscillator model, a system of one-electron pseudoatoms whose "pseudoelectrons" are harmonically bound to their respective "pseudonuclei," is capable of treating many-body polarization and dispersion interactions in molecular systems on an equal footing due to the ability of the pseudoatoms to mimic the long-range interactions that characterize real materials. Using imaginary time path integration, the Drude oscillator model can, in principle, be solved in computer operation counts that scale linearly with the number of atoms in the system. In practice, however, standard expressions for the energy and pressure, including the commonly used virial estimator, have extremely large variances that require untenably long simulation times to generate converged averages. In this paper, low-variance estimators for the internal energy are derived, in which the large zero-point energy of the oscillators does not contribute to the variance. The new estimators are applicable to any system of harmonic oscillators coupled to one another (or to the environment) via an arbitrary set of anharmonic interactions. The variance of the new estimators is found to be much smaller than standard estimators in three example problems, a one-dimensional anharmonic oscillator and quantum Drude models of the xenon dimer and solid (fcc) xenon, respectively, yielding 2-3 orders of magnitude improvement in computational efficiency.     

Polyaniline-coated nanoelectrospray emitters treated with hydrophobic polymers at the tip

In nanoelectrospray ionization (nanoESI) techniques, the hydrophilic character of the emitters generally produces large bases for the Taylor cones, thereby generating relatively large droplet sizes and consequently reduced sensitivity. In order to minimize this 'wetting' effect in nanoESI, a model hydrophobic polymer (an acrylic paint) was coated at the tip of commercial polyaniline (PANI)-coated emitters, and their performance was compared with that of unmodified PANI emitters using oxytocin and neuropeptide Y (NPY) solutions. In experiments with oxytocin, the hydrophobic emitter produced higher signal intensities (up to 3.6 times) as well as higher signal-to-noise ratios (33% increase) than those from the unmodified PANI emitter. In addition, the hydrophobic emitter showed reusability and a slightly wider linear dynamic range (10 nM to 50 microM, r2=0.9938) than that from the unmodified PANI emitter (10 nM to 10 microM, r2=0.9904). In the case of NPY, the hydrophobic emitter also enabled an approximately 350-fold overall increase in sensitivity than the unmodified PANI emitter (70 zmol vs. 25 amol). The enhanced performance of the hydrophobic emitter clearly indicates potential for further increases in nanoESI sensitivity using emitters with tailored hydrophobic overcoatings.     

Some upper and lower bounds on PSD-rank

Positive semidefinite rank (PSD-rank) is a relatively new complexity measure on matrices, with applications to combinatorial optimization and communication complexity. We first study several basic properties of PSD-rank, and then develop new techniques for showing lower bounds on the PSD-rank. All of these bounds are based on viewing a positive semidefinite factorization of a matrix M as a quantum communication protocol. These lower bounds depend on the entries of the matrix and not only on its support (the zero/nonzero pattern), overcoming a limitation of some previous techniques. We compare these new lower bounds with known bounds, and give examples where the new ones are better. As an application we determine the PSD-rank of (approximations of) some common matrices.     

Unexpected Chemistry from the Reaction of Naphthyl and Acetylene at Combustion‐Like Temperatures

The hydrogen abstraction/acetylene addition (HACA) mechanism has long been viewed as a key route to aromatic ring growth of polycyclic aromatic hydrocarbons (PAHs) in combustion systems. However, doubt has been drawn on the ubiquity of the mechanism by recent electronic structure calculations which predict that the HACA mechanism starting from the naphthyl radical preferentially forms acenaphthylene, thereby blocking cyclization to a third six‐membered ring. Here, by probing the products formed in the reaction of 1‐ and 2‐naphthyl radicals in excess acetylene under combustion‐like conditions with the help of photoionization mass spectrometry, we provide experimental evidence that this reaction produces 1‐ and 2‐ethynylnaphthalenes (C₁₂H₈), acenaphthylene (C₁₂H₈) and diethynylnaphthalenes (C₁₄H₈). Importantly, neither phenanthrene nor anthracene (C₁₄H₁₀) was found, which indicates that the HACA mechanism does not lead to cyclization of the third aromatic ring as expected but rather undergoes ethynyl substitution reactions instead.     

Spectroscopy and thermochemistry of a jet-cooled open-shell polyene: 1,4-pentadienyl radical

The 1,4-pentadienyl (vinylallyl) radical has been observed for the first time by optical spectroscopy. An excitation spectrum is recorded on m/z 67 by resonant two-color two-photon ionization spectroscopy. Several bands are observed with the origin transition identified at 19 449 cm(-1). The spectrum is assigned by a comparison with ab initio frequencies calculated at the CASPT2/cc-pVTZ level of theory, with an accompanying Franck-Condon calculation of the excitation spectrum, including Dushinsky mixing. The b(1) and a(2) outer C-C bond torsional modes are calculated to halve in frequency upon electronic excitation, bringing about their appearance in the excitation spectrum. This can be readily understood by considering the torsional sensitivity of the frontier molecular orbital energies. High-level quantum chemical calculations of the radical stabilization energy, resulting in a value of nearly 120 kJ mol(-1), provide quantitative confirmation that this radical is highly stabilized.     

Polymerized planar suspended lipid bilayers for single ion channel recordings: comparison of several dienoyl lipids

The stabilization of suspended planar lipid membranes, or black lipid membranes (BLMs), through polymerization of mono- and bis-functionalized dienoyl lipids was investigated. Electrical properties, including capacitance, conductance, and dielectric breakdown voltage, were determined for BLMs composed of mono-DenPC, bis-DenPC, mono-SorbPC, and bis-SorbPC both prior to and following photopolymerization, with diphytanoyl phosphocholine (DPhPC) serving as a control. Poly(lipid) BLMs exhibited significantly longer lifetimes and increased the stability of air-water transfers. BLM stability followed the order bis-DenPC > mono-DenPC ≈ mono-SorbPC > bis-SorbPC. The conductance of bis-SorbPC BLMs was significantly higher than that of the other lipids, which is attributed to a high density of hydrophilic pores, resulting in relatively unstable membranes. The use of poly(lipid) BLMs as matrices for supporting the activity of an ion channel protein (IC) was explored using α-hemolysin (α-HL), a model IC. Characteristic i-V plots of α-HL were maintained following photopolymerization of bis-DenPC, mono-DenPC, and mono-SorbPC, demonstrating the utility of these materials for preparing more durable BLMs for single-channel recordings of reconstituted ICs.     

Desmoplakin is important for proper cardiac cell-cell interactions

Normal cardiac function is maintained through dynamic interactions of cardiac cells with each other and with the extracellular matrix. These interactions are important for remodeling during cardiac growth and pathophysiological conditions. However, the precise mechanisms of these interactions remain unclear. In this study we examined the importance of desmoplakin (DSP) in cardiac cell-cell interactions. Cell-cell communication in the heart requires the formation and preservation of cell contacts by cell adhesion junctions called desmosome-like structures. A major protein component of this complex is DSP, which plays a role in linking the cytoskeletal network to the plasma membrane. Our laboratory previously generated a polyclonal antibody (1611) against the detergent soluble fraction of cardiac fibroblast plasma membrane. In attempting to define which proteins 1611 recognizes, we performed two-dimensional electrophoresis and identified DSP as one of the major proteins recognized by 1611. Immunoprecipitation studies demonstrated that 1611 was able to directly pulldown DSP. We also demonstrate that 1611 and anti-DSP antibodies co-localize in whole heart sections. Finally, using a three-dimensional in vitro cell-cell interaction assay, we demonstrate that 1611 can inhibit cell-cell interactions. These data indicate that DSP is an important protein for cell-cell interactions and affects a variety of cellular functions, including cytokine secretion.