Biomedical subjects

George C Schatz

Publications and source records attributed to George C Schatz.

At least 19 recordsLinked to original sources

PubMed2007

Nanoscale fracture mechanics.

Theoretical calculations on undefected nanoscale materials predict impressive mechanical properties. In this review we summarize the status of experimental efforts to directly measure the fracture strengths of inorganic and carbon nanotubes and discuss possible explanations for the deviations between the predicted and observed values. We also summarize the role of theory in understanding the molecular-level origin of these deviations. In particular, we consider the role of defects such as vacancies, Stone-Wales defects, adatoms and ad-dimers, chemical functionalization, and oxidative pitting.

Carbon↗

PubMed2006

Steered molecular dynamics studies of the potential of mean force of a Na+ or K+ ion in a cyclic peptide nanotube.

Potential of mean force (PMF) profiles of a single Na+ or K+ ion passing through a cyclic peptide nanotube, cyclo[-(D-Ala-Glu-D-Ala-Gln)2-], in water are calculated to provide insight into ion transport and to understand the conductance difference between these two ions. The PMF profiles are obtained by performing steered molecular dynamics (SMD) simulations that are based on the Jarzynski equality. The computed PMF profiles for both ions show barriers of around 2.4 kcal/mol at the channel entrances and exits and energy wells in the middle of the tube. The energy barriers, so-called dielectric energy barriers, arise due to the desolvation of water molecules when ions move across the nanotube, and the energy wells appear as a result of attractive interactions between the cations and negatively charged carbonyl oxygens on the backbone of the tube. We find more and deeper energy wells in the PMF profile for Na+ than for K+, which suggests that Na+ ions have a longer residence time inside the nanotube and that permeation of Na+ ions is reduced compared to K+ ions. Calculations of the radial distribution functions (RDF) between the ions and oxygens in the water molecules and in carbonyl groups on the tube and an investigation of the orientations of the carbonyl groups show that, in contrast with the dynamic carbonyl groups observed in the selectivity filter of the KcsA ion channel, the carbonyl groups in the cyclic peptide nanotube are relatively rigid, with only slight reorientation of the carbonyl groups as the cations pass through. The rigidity of the carbonyl groups in the cyclic peptide nanotube can be attributed to their role in hydrogen bonding, which is responsible for the tube structure. Comparison of the PMF profiles with the electrostatic energy profiles calculated from the Poisson-Boltzmann (PB) equation, a dielectric continuum model, reveals that the dielectric continuum model breaks down in the confined region within the tube that governs ion transport.

Nanotechnology↗

PubMed2006

Direct dynamics simulations of O(3P) + HCl at hyperthermal collision energies.

The dynamics of the O(3P) + HCl reaction at hyperthermal collision energies were investigated using the quasiclassical trajectory method. Stationary points on the OClH 3A" and 3A' potential energy surfaces (PESs) were also examined. The lowest transition state leading to OCl + H on the 3A" surface is 2.26 eV above the reagents at the CCSD(T)/cc-pVTZ level of theory. This saddle point is bent and product-like. Direct dynamics calculations at the MP2/cc-pVTZ level of theory were used to investigate the excitation functions for OH + Cl, OCl + H, and O + H + Cl formation. OCl is formed mainly from small-impact-parameter collisions, and the OCl + H excitation function peaks around 5 eV, where it is similar in magnitude to the OH + Cl excitation function. The shape of the OCl + H excitation function is discussed, and features are identified that should be general to hyperthermal collision dynamics.

Journal Article↗

PubMed2006

TDDFT studies of absorption and SERS spectra of pyridine interacting with Au20.

We present time dependent density functional theory (TDDFT) calculations for a tetrahedral Au20 complex interacting with pyridine for the purpose of modeling absorption and surface enhanced Raman scattering, with emphasis on chemical and electrodynamic enhancement effects. These calculations are done using the ADF code with the BP86 functional, the zeroth-order regular approximation and with the resonant electronic response modeled using a short time approximation expression for the perturbed density matrix, with a damping factor that is empirically chosen. The absorption spectrum of bare Au20 shows strong intraband (sp-sp) and interband (sp-d) coupling with a low-energy peak at 2.89 eV that is mostly intraband and other peaks at 3.94 and 4.70 eV that have mixed intra- and interband character. SERS spectra are calculated for pyridine/Au20 for both vertex (V) and surface (S) configurations at their respective lowest energy absorption maxima (near 2.89 eV), and we find that the V configuration has higher intensities that correspond to SERS enhancements of 10(3)-10(4), whereas S has an enhancement of 10(2)-10(3). These enhancement values are significantly lower than the analogous results for pyridine/Ag20 primarily because of reduced oscillator strength associated with the intraband transition in Au20. Decomposition of the pyridine/Au20 enhancement factor into chemical and electromagnetic contributions (through an analysis of the static SERS intensities) shows enhanced chemical enhancements compared to Ag20 but reduced electromagnetic enhancements.

Journal Article↗

PubMed2006

Theories of reactive scattering.

This paper is an overview of the theory of reactive scattering, with emphasis on fully quantum mechanical theories that have been developed to describe simple chemical reactions, especially atom-diatom reactions. We also describe related quasiclassical trajectory applications, and in all of this review the emphasis is on methods and applications concerned with state-resolved reaction dynamics. The review first provides an overview of the development of the theory, including a discussion of computational methods based on coupled channel calculations, variational methods, and wave packet methods. Choices of coordinates, including the use of hyperspherical coordinates are discussed, as are basis set and discrete variational representations. The review also summarizes a number of applications that have been performed, especially the two most comprehensively studied systems, H+H2 and F+H2, along with brief discussions of a large number of other systems, including other hydrogen atom transfer reactions, insertion reactions, electronically nonadiabatic reactions, and reactions involving four or more atoms. For each reaction we describe the method used and important new physical insight extracted from the results.

Journal Article↗

PubMed2006

Nanografting: modeling and simulation.

We present a simple phenomenological model of the nanografting process with an emphasis on the formation of binary self-assembled monolayers. This model includes dynamical processes that are involved in natural growth experiments, including molecular deposition, surface diffusion, and the phase transition from physisorption to chemisorption, and we show that it predicts domain formation in ungrafted deposition that matches experiment. The one-order-of-magnitude faster kinetics that is found in the nanografting experiments compared to natural self-assembly (or unconstrained self-assembly) is described with a key assumption that the deposition rate is greatly enhanced in the small region confined between the back side of the AFM tip and the edge of the previously deposited self-assembled monolayer. Monte Carlo simulations based on this model reproduce experimental observations concerning the variation of SAM heterogeneity with AFM tip speed. Our simulations demonstrate that the faster the AFM tip displaces adsorbed molecules in a monolayer, the more heterogeneous are the monolayers formed behind the tip, as this allows space and time for the formation of phase-segregated domains.

Journal Article↗

PubMed2006

Resonance surface plasmon spectroscopy: low molecular weight substrate binding to cytochrome p450.

A new detection mechanism has been developed for low molecular weight substrate binding to heme proteins based on resonance localized surface plasmon spectroscopy. Cytochrome P450 has strong electronic transitions in the visible wavelength region. Upon binding of a substrate molecule (e.g., camphor), the absorption band of cytochrome P450 shifts to shorter wavelength. The event of camphor binding to a nanoparticle surface modified with cytochrome P450 protein receptors is monitored using UV-vis spectroscopy. It is observed for the first time that the binding of the substrate molecules to the protein receptor induces a blue-shift in the localized surface plasmon resonance (LSPR) of the nanosensors. The coupling between the molecular resonance of the substrate-free and substrate-bound cytochrome P450 proteins and the nanoparticles' LSPR leads to a highly wavelength-dependent LSPR response. When the LSPR of the nanoparticles is located at a wavelength distant from the cytochrome P450 resonance, an average of approximately 19 nm red-shift is observed upon cytochrome P450 binding to the nanoparticles and a approximately 6 nm blue-shift is observed upon camphor binding However, this response is significantly amplified approximately 3 to 5 times when the LSPR of the nanoparticles is located at a slightly longer wavelength than the cytochrome P450 resonance, that is, a 66.2 nm red-shift upon cytochrome P450 binding and a 34.7 nm blue-shift upon camphor binding. This is the first example of the detection of small molecules binding to a protein modified nanoparticle surface on the basis of LSPR.

Cytochrome P-450 Enzyme System↗

PubMed2006

Designing, fabricating, and imaging Raman hot spots.

We have developed a probe of the electromagnetic mechanism of surface-enhanced Raman scattering via Au nanodisk arrays generated by using on-wire lithography. In this approach, disk thickness and interparticle gap are precisely controlled from 5 nm to many micrometers. Confocal Raman microscopy demonstrates that disk thickness and gap play a crucial role in determining surface-enhanced Raman scattering intensities. Theoretical calculations also demonstrate that these results are consistent with the electromagnetic mechanism, including the surprising result that the largest enhancement does not occur for the smallest gaps.

Dimerization↗

PubMed2006

Localized surface plasmon resonance spectroscopy near molecular resonances.

The peak location of the localized surface plasmon resonance (LSPR) of noble metal nanoparticles is highly dependent upon the refractive index of the nanoparticles' surrounding environment. In this study, new phenomena are revealed by exploring the influence of interacting molecular resonances and nanoparticle resonances. The LSPR peak shift and line shape induced by a resonant molecule vary with wavelength. In most instances, the oscillatory dependence of the peak shift on wavelength tracks with the wavelength dependence of the real part of the refractive index, as determined by a Kramers-Kronig transformation of the molecular resonance absorption spectrum. A quantitative assessment of this shift based on discrete dipole approximation calculations shows that the Kramers-Kronig index must be scaled in order to match experiment.

Journal Article↗

PubMed2006

A cooperative beads-on-a-string approach to exceptionally stable DNA triplexes.

A poly(dT) oligomer can serve as the string on which synthetic hairpins possessing poly(dA) and poly(dT) arms connected by a hydrophobic perylene diimide linker are assembled like beads on a string. The synthetic hairpins form head-to-head dimers and trimers, respectively, in the absence of the poly(dT) string and in the presence of a string with inverted polarity at mid-strand. However, they assemble in cooperative head-to-tail fashion on normal poly(dT) oligomers.

Circular Dichroism↗

PubMed2006

Manipulating the optical properties of pyramidal nanoparticle arrays.

This paper reports the orientation-dependent optical properties of two-dimensional arrays of anisotropic metallic nanoparticles. These studies were made possible by our simple procedure to encapsulate and manipulate aligned particles having complex three-dimensional (3D) shapes inside a uniform dielectric environment. Using dark field or scattering spectroscopy, we investigated the plasmon resonances of 250-nm Au pyramidal shells embedded in a poly(dimethylsiloxane) (PDMS) matrix. Interestingly, we discovered that the scattering spectra of these particle arrays depended sensitively on the direction and polarization of the incident white light relative to the orientation of the pyramidal shells. Theoretical calculations using the discrete dipole approximation support the experimentally observed dependence on particle orientation with respect to incident field. This work presents an approach to manipulate--by hand--ordered arrays of particles over cm(2) areas and provides new insight into the relationship between the shape of well-defined, 3D particles and their supported plasmon resonance modes.

Journal Article↗

PubMed2006

Structures of DNA-linked nanoparticle aggregates.

The room-temperature structure of DNA-linked gold nanoparticle aggregates is investigated using a combination of experiment and theory. The experiments involve extinction spectroscopy measurements and dynamic light scattering measurements of aggregates made using 60 and 80 nm gold particles and 30 base-pair DNA. The theoretical studies use calculated spectra for models of the aggregate structures to determine which structure matches the observations. These models include diffusion-limited cluster-cluster aggregation (DLCA), reaction-limited cluster-cluster aggregation (RLCA), and compact (nonfractal) cluster aggregation. The diameter of the nanoparticles used in the experiments is larger than has been considered previously, and this provides greater sensitivity of spectra to aggregate structure. We show that the best match between experiment and theory occurs for the RLCA fractal structures. This indicates that DNA hybridization takes place under irreversible conditions in the room-temperature aggregation. Some possible structural variations which might influence the result are considered, including the edge-to-edge distance between nanoparticles, variation in the diameter of the nanoparticles, underlying lattice structures of on-lattice compact clusters, and positional disorders in the lattice structures. We find that these variations do not change the conclusion that the room-temperature structure of the aggregates is fractal. We also examine the variation in extinction at 260 nm as temperature is increased, showing that the decrease in extinction at temperatures below the melting temperature is related to a morphological change from fractal toward compact structures.

DNA↗

PubMed2006

Semiclassical nonadiabatic dynamics based on quantum trajectories for the O(3P,1D) + H2 system.

The O(3P,1D) + H2 --> OH + H reaction is studied using trajectory dynamics within the approximate quantum potential approach. Calculations of the wave-packet reaction probabilities are performed for four coupled electronic states for total angular momentum J = 0 using a mixed coordinate/polar representation of the wave function. Semiclassical dynamics is based on a single set of trajectories evolving on an effective potential-energy surface and in the presence of the approximate quantum potential. Population functions associated with each trajectory are computed for each electronic state. The effective surface is a linear combination of the electronic states with the contributions of individual components defined by their time-dependent average populations. The wave-packet reaction probabilities are in good agreement with the quantum-mechanical results. Intersystem crossing is found to have negligible effect on reaction probabilities summed over final electronic states.

Journal Article↗

PubMed2006

Resonance Raman scattering of rhodamine 6G as calculated using time-dependent density functional theory.

In this work, we present the first calculation of the resonance Raman scattering (RRS) spectrum of rhodamine 6G (R6G) which is a prototype molecule in surface-enhanced Raman scattering (SERS). The calculation is done using a recently developed time-dependent density functional theory (TDDFT) method, which uses a short-time approximation to evaluate the Raman scattering cross section. The normal Raman spectrum calculated with this method is in good agreement with experimental results. The calculated RRS spectrum shows qualitative agreement with SERS results at a wavelength that corresponds to excitation of the S(1) state, but there are significant differences with the measured RRS spectrum at wavelengths that correspond to excitation of the vibronic sideband of S(1). Although the agreement with the experiments is not perfect, the results provide insight into the RRS spectrum of R6G at wavelengths close to the absorption maximum where experiments are hindered due to strong fluorescence. The calculated resonance enhancements are found to be on the order of 10(5). This indicates that a surface enhancement factor of about 10(10) would be required in SERS in order to achieve single-molecule detection of R6G.

Journal Article↗

PubMed2006

Quantum trajectory dynamics in arbitrary coordinates.

The quantum trajectory approach is generalized to arbitrary coordinate systems, including curvilinear coordinates. This allows one to perform an approximate quantum trajectory propagation, which scales favorably with system size, in the same framework as standard quantum wave packet dynamics. The trajectory formulation is implemented in Jacobi coordinates for a nonrotating triatomic molecule. Wave packet reaction probabilities are computed for the O(3P) + H2 --> OH + H reaction using the approximate quantum potential. The latter is defined by the nonclassical component of the momentum operator expanded in terms of linear and exponential functions. Unlike earlier implementations with linear functions, the introduction of the exponential function provides an accurate description of asymptotic dynamics for this system and gives good agreement of approximate reaction probabilities with accurate quantum calculations.

Journal Article↗

PubMed2006

Ion current calculations based on three dimensional Poisson-Nernst-Planck theory for a cyclic peptide nanotube.

Ion current calculations based on Poisson-Nernst-Planck (PNP) theory are performed for a synthetic cyclic peptide nanotube that consists of eight or ten cyclo[(-L-Trp-D-Leu-)4] embedded in a lipid bilayer membrane to investigate the ion transport properties of the nanotube. To explore systems with arbitrary geometries, three-dimensional PNP theory is implemented using a finite difference method. The influence of dipolar lipid molecules on the ion currents is also examined by turning on or off the charges of the lipid dipoles in dipalmitoylphosphatidylcholine (DPPC). Comparisons between the calculated and experimentally measured ion currents show that the PNP approach agrees well with the measurements at low ion concentrations but overestimates the currents at higher concentrations. Concentration profiles reveal the selectivity of the peptide nanotube to cations, which is attributed to the negatively charged carbonyl oxygens inside the nanotube. The dominant cation and the minimum anion concentrations inside the cyclic peptide nanotube suggest that these cyclic peptide nanotubes can be employed as ion sensors. In the case of the polar DPPC bilayer, smaller currents are obtained in the calculation. The variation of current with polarity of the lipids implies that both polar and nonpolar lipid bilayer membranes can be utilized to regulate ion currents in the peptide nanotube and other ion channels. Strengths and limitations of the PNP theory are also discussed.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2006

H + CD4 abstraction reaction dynamics: product energy partitioning.

This paper presents experimental and theoretical studies of the product energy partitioning associated with the H + CD4 (nu = 0) --> HD + CD3 reaction for the collision energy range 0.5-3.0 eV. The theoretical results are based on quasiclassical trajectories from (1) first principles direct dynamics calculations (B3LYP/6-31G), (2) an empirical surface developed by Espinosa-García [J. Chem. Phys. 2002, 116, 10664] (EG), and (3) two semiempirical surfaces (MSINDO and reparametrized MSINDO). We find that most of the energy appears in product translation at energies just above the reactive threshold; however, HD vibration and rotation become quite important at energies above 1 eV, each accounting for over 20% of the available energy above 1.5 eV, according to the B3LYP calculations. The barrier on the B3LYP surface, though being later than that on EG, predicts significantly higher HD vibrational excitation than EG. This deviation is contradictory to what would be expected on the basis of the Polanyi rules and derives from modest differences in the potential energy surfaces. The CD3 internal energy is generally quite low, and we present detailed rotational state distributions which show that the CD3 rotational distribution is largely independent of collision energy in the 0.75-1.95 eV range. The most populated rotational levels are N = 5 and 6 on B3LYP, with most of that excitation being associated with motion about the C2 axes, rather than C3 axis, of the CD3 product, in good agreement with the experimental results. Through our extensive studies in this and previous work concerning the scattering dynamics, we conclude that B3LYP/6-31G provides the best available description of the overall dynamics for the title reaction at relatively high collision energies.

Journal Article↗

PubMed2006

Pyridine-Ag20 cluster: a model system for studying surface-enhanced Raman scattering.

This work presents a detailed analysis of enhanced Raman scattering of the pyridine-Ag(20) model system using time-dependent density functional theory. A consistent treatment of both the chemical and electromagnetic enhancements (EM) is achieved by employing a recently developed approach based on a short-time approximation for the Raman cross section. A strong dependence of the absolute and relative intensities on the binding site and excitation wavelength is found. The analysis of the Raman scattering cross sections shows the importance of different contributions to the enhancements, including static chemical enhancements (factor of 10), charge-transfer enhancements (10(3)), and EM enhancements (10(5)). The largest enhancement found (10(5)-10(6)) is due to the EM mechanism, with a small contribution from the chemical interaction. This suggests that the enhanced Raman scattering due to atomic clusters is comparable to findings on single nanoparticles. A combination of information about the vibrational motion and the local chemical environment provides a simple picture of why certain normal modes are enhanced more than others.

Journal Article↗