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1.  Microfluidic Channels on Nanopatterned Substrates: Monitoring Protein Binding to Lipid Bilayers with Surface-Enhanced Raman Spectroscopy 
Chemical physics letters  2010;489(1-3):121-126.
We used Surface Enhanced Raman Spectroscopy (SERS) to detect binding events between streptavidin and biotinylated lipid bilayers. The binding events took place at the surface between microfluidic channels and anodized aluminum oxide (AAO) with the latter serving as substrates. The bilayers were incorporated in the substrate pores. It was revealed that non-bound molecules were easily washed away and that large suspended cells (Salmonella enterica) are less likely to interfere with the monitoring process: when focusing to the lower surface of the channel, one may resolve mostly the bound molecules.
doi:10.1016/j.cplett.2010.02.053
PMCID: PMC4053208  PMID: 24932024
2.  How do proteins locate specific targets in DNA? 
Chemical physics letters  2013;570:10.1016/j.cplett.2013.03.035.
Many aspects of biology depend on the ability of DNA-binding proteins to locate specific binding sites within the genome. Interest in this target search problem has been reinvigorated through the recent development of microscopy-based technologies capable of tracking individual proteins in real-time as they search for binding sites. In this review we discuss how two different proteins, lac repressor and RNA polymerase, have solved the target search problem through seemingly different mechanisms, with an emphasis on how recent in vitro single-molecule studies have influenced our understanding of these reactions.
doi:10.1016/j.cplett.2013.03.035
PMCID: PMC3810971  PMID: 24187380
3.  Quenching of p-Cyanophenylalanine Fluorescence by Various Anions 
Chemical physics letters  2013;563:93-96.
To expand the spectroscopic utility of the non-natural amino acid p-cyanophenylalanine (PheCN), we examine the quenching efficiencies of a series of commonly encountered anions toward its fluorescence. We find that iodide exhibits an unusually large Stern-Volmer quenching constant, making it a convenient choice in PheCN fluorescence quenching studies. Indeed, using the villin headpiece subdomain as a testbed we demonstrate that iodide quenching of PheCN fluorescence offers a convenient means to reveal protein conformational heterogeneity. Furthermore, we show that the amino group of PheCN strongly quenches its fluorescence, suggesting that PheCN could be used as a local pH sensor.
doi:10.1016/j.cplett.2013.02.015
PMCID: PMC3640566  PMID: 23645934
4.  Numerical Poisson-Boltzmann Model for Continuum Membrane Systems 
Chemical physics letters  2012;555:274-281.
Membrane protein systems are important computational research topics due to their roles in rational drug design. In this study, we developed a continuum membrane model utilizing a level set formulation under the numerical Poisson-Boltzmann framework within the AMBER molecular mechanics suite for applications such as protein-ligand binding affinity and docking pose predictions. Two numerical solvers were adapted for periodic systems to alleviate possible edge effects. Validation on systems ranging from organic molecules to membrane proteins up to 200 residues, demonstrated good numerical properties. This lays foundations for sophisticated models with variable dielectric treatments and second-order accurate modeling of solvation interactions.
doi:10.1016/j.cplett.2012.10.081
PMCID: PMC3579545  PMID: 23439886
membrane proteins; continuum membrane model; Poisson-Boltzmann; implicit solvation
5.  Effect of Surface Coating on the Toxicity of Silver Nanomaterials on Human Skin Keratinocytes 
Chemical physics letters  2010;487(1-3):10.1016/j.cplett.2010.01.027.
As nanotechnology field continues to develop, assessing nanoparticle toxicity is very important for advancing nanoparticles for daily life application. In this Letter, we report the effect of surface coating on cyto, geno and photo-toxicity of silver nanomaterials of different shapes on human skin HaCaT keratinocytes. We found that the citrate coated colloidal silver nanoparticles at 100 µg/mL level are not geno-, cyto- and phtotoxic. On the other hand, citrate coated powder form of the silver nanoparticles are toxic. We have demonstrated that coating of the silver nanoparticles with a biodegradable polymer prevents the toxicity of the powder. Toxicity mechanism has been discussed.
doi:10.1016/j.cplett.2010.01.027
PMCID: PMC3812814  PMID: 24187379
6.  Ultrafast E to Z photoisomerization dynamics of the Cph1 phytochrome 
Chemical physics letters  2012;549:86-92.
Femtosecond photodynamics of the reverse (15EPfr→15ZPr) reaction of the red/far-red phytochrome Cph1 from Synechocystis were resolved with visible broadband transient absorption spectroscopy. Multi-phasic dynamics were resolved and separated via global target analysis into a fast-decaying (260 fs) excited-state population that bifurcates to generate the isomerized Lumi-F primary photoproduct and a non-isomerizing vibrationally excited ground state that relaxes back into the 15EPfr ground state on a 2.8-ps time scale. Relaxation on a 1-ms timescale results in the loss of red absorbing region, but not blue region, of Lumi-F, which indicates that formation of 15ZPr occurs on slower timescales.
doi:10.1016/j.cplett.2012.08.044
PMCID: PMC3611326  PMID: 23554514
7.  Fluorescent Polyelectrolyte Capped Silver Nanoclusters: Optimization and Spectroscopic Evaluation 
Chemical physics letters  2012;549:72-76.
In the present work, we have synthesized water soluble Ag nanoclusters using PMAA as a template with different Ag+: COO-ratios, to optimize it for highest brightness using less UV exposure time. Fluorescence polarization was 0.30 for and was found to vary with excitation and emission wavelength with few hundred picoseconds average fluorescence lifetime. Fluorescence Correlation Spectroscopy data depicts slower diffusion at red excitation compared to blue excitation in confocal volume than conventionally synthesized colloids proving presence of multiple sizes. The optical properties of the particles are dependent upon the excitation wavelength used and the emission wavelength collected.
doi:10.1016/j.cplett.2012.08.042
PMCID: PMC3678839  PMID: 23772092
Metal Nanoclusters; Fluorescent Ag Nanoclusters; Polymethylacrylic Acid; Polarization; FCS
8.  Controlling the femtosecond laser-driven transformation of dicyclopentadiene into cyclopentadiene 
Chemical physics letters  2013;558:1-7.
Dynamics of the chemical transformation of dicyclopentadiene into cyclopentadiene in a supersonic molecular beam is elucidated using femtosecond time-resolved degenerate pump–probe mass spectrometry. Control of this ultrafast chemical reaction is achieved by using linearly chirped frequency modulated pulses. We show that negatively chirped femtosecond laser pulses enhance the cyclopentadiene photo-product yield by an order of magnitude as compared to that of the unmodulated or the positively chirped pulses. This demonstrates that the phase structure of femtosecond laser pulse plays an important role in determining the outcome of a chemical reaction.
doi:10.1016/j.cplett.2012.10.054
PMCID: PMC3790071  PMID: 24098059
9.  Metal-enhanced intrinsic fluorescence of nucleic acids using platinum nanostructured substrates 
Chemical physics letters  2012;548:45-50.
We investigated the feasibility of using platinum nanostructures to accomplish the metal-enhanced fluorescence (MEF) in the UV spectral region. We examine the possibility for detection of the intrinsic fluorescence from nucleotides and G-quadruplex DNA on platinum nanoparticles. Guanosine monophosphate (GMP) showed significant increases (~20-fold) in fluorescence intensities in the presence of platinum nanostructures when compared to quartz controls. G-quadruplex DNA demonstrated ~5-fold increase in fluorescence intensity and higher photostability in the presence of Pt nanostructures. We performed finite element method simulations to explore how Pt nanoparticles interact with plane waves and conformed that the Pt nanostructures are promising for enhancing the fluorescence emission in the UV region.
doi:10.1016/j.cplett.2012.08.020
PMCID: PMC3446211  PMID: 23002289
Intrinsic fluorescence of nucleotides; metal-enhanced fluorescence (MEF); plasmonics; metallic nanoparticles; finite element calculations
10.  Challenge in Understanding Size and Shape Dependent Toxicity of Gold Nanomaterials in Human Skin Keratinocytes 
Chemical physics letters  2008;463(1-3):145-149.
As the nanotechnology field continues to develop, assessing nanoparticle toxicity is very important for advancing nanoparticles for biomedical application. Here we report cytotoxicity of gold nanomaterial of different size and shape using MTT test, absorption spectroscopy and TEM. Spherical gold nanoparticles with different sizes are not inherently toxic to human skin cells, but gold nanorods are highly toxic due to the presence of CTAB as coating material. Due to CTAB toxicity, and aggregation of gold nanomaterials in the presence of cell media, it is a real challenge to study the cytotoxicity of gold nanomaterials individually.
doi:10.1016/j.cplett.2008.08.039
PMCID: PMC3780398  PMID: 24068836
11.  Gold Nanoparticle Based Surface Enhanced Fluorescence For Detection of Organophosphorus Agents 
Chemical physics letters  2008;460(1-3):187-190.
Organophosphorus agents (OPA) represent a serious concern to public safety as nerve agents and pesticides. Here we report the development of gold nanoparticle based surface enhanced fluorescence (NSEF) spectroscopy for rapid and sensitive screening of organophosphorus agents. Fluorescent from Eu3+ ions that are bound within the electromagnetic field of gold nanoparticles exhibit a strong enhancement. In the presence of OPA, Eu3+ ions are released from the gold nanoparticle surface and thus a very distinct fluorescence signal change was observed. We discussed the mechanism of fluorescence enhancement and the role of OPA for fluorescence intensity change in the presence of gold nanoparticles.
doi:10.1016/j.cplett.2008.05.082
PMCID: PMC3768136  PMID: 24031096
12.  On-the-fly free energy parameterization via temperature accelerated molecular dynamics 
Chemical physics letters  2012;547:114-119.
We discuss a method for parametric calculation of free energy functions in arbitrary collective variables using molecular simulations. The method uses a variant of temperature accelerated molecular dynamics to evolve on-the-fly the parameters of the free energy function to their optimum values by minimization of a cumulative gradient error. We illustrate how the method performs using simple examples and discuss its application in the derivation of effective pairwise potentials for multiscale molecular simulations.
doi:10.1016/j.cplett.2012.07.064
PMCID: PMC3512107  PMID: 23226688
13.  MDMS: Molecular Dynamics Meta-Simulator for evaluating exchange type sampling methods 
Chemical physics letters  2012;545:118-124.
Replica exchange methods have become popular tools to explore conformational space for small proteins. For larger biological systems, even with enhanced sampling methods, exploring the free energy landscape remains computationally challenging. This problem has led to the development of many improved replica exchange methods. Unfortunately, testing these methods remains expensive. We propose a Molecular Dynamics Meta-Simulator (MDMS) based on transition state theory to simulate a replica exchange simulation, eliminating the need to run explicit dynamics between exchange attempts. MDMS simulations allow for rapid testing of new replica exchange based methods, greatly reducing the amount of time needed for new method development.
doi:10.1016/j.cplett.2012.07.015
PMCID: PMC3472454  PMID: 23087450
14.  Ion selectivity from local configurations of ligands in solutions and ion channels 
Chemical physics letters  2010;485(1-3):1-7.
Probabilities of numbers of ligands proximal to an ion lead to simple, general formulae for the free energy of ion selectivity between different media. That free energy does not depend on the definition of an inner shell for ligand-counting, but other quantities of mechanistic interest do. If analysis is restricted to a specific coordination number, then two distinct probabilities are required to obtain the free energy in addition. The normalizations of those distributions produce partition function formulae for the free energy. Quasi-chemical theory introduces concepts of chemical equilibrium, then seeks the probability that is simplest to estimate, that of the most probable coordination number. Quasi-chemical theory establishes the utility of distributions of ligand-number, and sharpens our understanding of quasi-chemical calculations based on electronic structure methods. This development identifies contributions with clear physical interpretations, and shows that evaluation of those contributions can establish a mechanistic understanding of the selectivity in ion channels.
doi:10.1016/j.cplett.2009.12.013
PMCID: PMC3674792  PMID: 23750043
15.  Quantifying accumulation or exclusion of H+, HO−, and Hofmeister salt ions near interfaces 
Chemical physics letters  2008;467(1-3):1-8.
Recently, surface spectroscopies and simulations have begun to characterize the non-uniform distributions of salt ions near macroscopic and molecular surfaces. The thermodynamic consequences of these non-uniform distributions determine the often-large ion-specific effects of Hofmeister salts on a very wide range of processes in water. For uncharged surfaces, where these nonuniform ion distributions are confined to the first few layers of water at the surface, a two-state approximation to the distributions of water and ions, called the salt ion partitioning model (SPM) has both molecular and thermodynamic signiicance. Here, we summarize SPM results quantifying the local accumulation of H+, exclusion of HO−, and range of partitioning behavior of Hofmeister anions and cations near macroscopic and molecular interfaces. These results provide a database to interpret or predict Hofmeister salt effects on aqueous processes in terms of structural information regarding amount and composition of the surface exposed or buried in these processes.
doi:10.1016/j.cplett.2008.10.090
PMCID: PMC3673785  PMID: 23750042
16.  Detection of some stable species during the oxidation of methane by coupling a jet-stirred reactor (JSR) to cw-CRDS 
Chemical physics letters  2012;534:1-7.
We present the coupling of a jet-stirred reactor to detection by cw-CRDS in the near infrared and first results obtained during the oxidation of methane. The mixture is rapidly expanded from the jet-stirred reactor into a 80 cm-long cw-CRDS cell maintained at a the pressure around 1.33 kPa, thus freezing the reaction and decreasing pressure broadening of the absorption lines. Some stable species (CH4, H2O and CH2O) have been quantified through their well structured spectra around 1506 nm, while H2O2 and HO2 radicals could not be detected.
doi:10.1016/j.cplett.2012.03.012
PMCID: PMC3662210  PMID: 23710075
17.  Influence of water on the work function of certain metals 
Chemical physics letters  2012;536:65-67.
Experiments were carried out to explore the effect of light on Au, Pt and Cu surfaces immersed in water, in order to study the changes of work function arising from the interaction between the metallic surfaces and water. The results show an action of liquid water about three times larger than that of low-temperature ice. Theoretical calculations, present in literature, have predicted values much lower than those we measured. The substantial changes in work function measured here appear to arise from the complex structure of water in the vicinity of the metal surface.
doi:10.1016/j.cplett.2012.03.094
PMCID: PMC3359016  PMID: 22639466
Metal-water interface; work function; photoelectric effect; surface double layers
18.  Solvation Structure and Energetics of Single Ions at the Aqueous Liquid-Vapor Interface 
Chemical physics letters  2012;527:22-26.
Potentials of mean force for single, nonpolarizable monovalent halide anions and alkali cations are computed for transversing the water-air interface (modeling using polarizable TIP4P-FQ and TIP4P-QDP). Iodide and bromide in TIP4P-FQ show interfacial stability, whereas chloride, bromide, and iodide show interfacial stability in TIP4P-QDP. A monotonic decrease in coordination number and an increasingly anisotropic distribution of solvating water molecules is shown to accompany movement of the ions towards vapor conditions; these effects are most noticeable with increases in ion size/decreases in magnitude of hydration free energy.
doi:10.1016/j.cplett.2011.12.061
PMCID: PMC3488351  PMID: 23136448
Ions; Polarizable Force Fields; Molecular Dynamics; TIP4P-FQ; TIP4P-QDP; Potential of Mean Force; Solvation Structure
19.  Modified Becke’05 method of nondynamic correlation in density functional theory with self-consistent implementation 
Chemical physics letters  2012;525-526:150-152.
Becke’s B05 method for nondynamic correlation is simplified for self-consistent implementation. An alternative form is proposed for the nondynamic correlation factors that do not require solving a complicated nonlinear algebraic equation. The four linear parameters of B05 are re-optimized together with one extra parameter entering a modified expression for the second-order same-spin energy contribution. The latter is co-linear with the exact-exchange energy density and does not require higher moments of the relaxed exchange hole. Preliminary tests of this method show that it leads to a slight improvement over the resolution-of-identity B05 results reported previously for atomization energies, and to a definite improvement for reaction barriers of Hydrogen abstraction.
doi:10.1016/j.cplett.2011.12.069
PMCID: PMC3367507  PMID: 22685346
20.  Modulations in restricted amide rotation by steric induced conformational trapping 
Chemical physics letters  2012;523(27):124-127.
The rotation around the amide bond in N,N-diethyl-m-toluamide (m-DEET) has been studied extensively and often used in laboratory instructions to demonstrate the phenomenon of chemical exchange. Herein, we show that a simple modification to N,N-diethyl-o-toluamide (o-DEET) significantly alters the dynamics of the restricted rotation around the amide bond due to steric interactions between the ring methyl group and the two N-ethyl groups. This alters the classic two-site exchange due to restricted rotation around the amide bond, to a three-site exchange, with the third conformation trapped at a higher-energy state compared to the other two. This often overlooked phenomenon is elucidated using variable-temperature NMR, two-dimensional exchange spectroscopy and molecular modeling studies.
doi:10.1016/j.cplett.2011.11.058
PMCID: PMC3272771  PMID: 22322969
Dynamic NMR; chemical exchange; restricted rotation
21.  Carotenoid response to retinal excitation and photoisomerization dynamics in xanthorhodopsin 
Chemical physics letters  2011;516(1-3):96-101.
We present a comparative study of xanthorhodopsin, a proton pump with the carotenoid salinixanthin serving as an antenna, and the closely related bacteriorhodopsin. Upon excitation of retinal, xanthorhodopsin exhibits a wavy transient absorption pattern in the region between 470 and 540 nm. We interpret this signal as due to electrochromic effect of the transient electric field of excited retinal on salinixanthin. The spectral shift decreases during the retinal dynamics through the ultrafast part of the photocycle. Differences in dynamics of bacteriorhodopsin and xanthorhodopsin are discussed.
doi:10.1016/j.cplett.2011.09.062
PMCID: PMC3219219  PMID: 22102759
22.  Dielectric Boundary Forces in Numerical Poisson-Boltzmann Methods: Theory and Numerical Strategies 
Chemical physics letters  2011;514(4-6):368-373.
Continuum modeling of electrostatic interactions based upon the numerical solutions of the Poisson-Boltzmann equation has been widely adopted in biomolecular applications. To extend their applications to molecular dynamics and energy minimization, robust and efficient methodologies to compute solvation forces must be developed. In this study, we have first reviewed the theory for the computation of dielectric boundary forces based on the definition of the Maxwell stress tensor. This is followed by a new formulation of the dielectric boundary force suitable for the finite-difference Poisson-Boltzmann methods. We have validated the new formulation with idealized analytical systems and realistic molecular systems.
doi:10.1016/j.cplett.2011.08.067
PMCID: PMC3224087  PMID: 22125339
23.  Computational Study on the Conformations of Gambogic Acid 
Chemical physics letters  2011;511(4-6):405-412.
The conformations of gambogic acid were studied using force fields, MM3*, AMBER*, MMFFs and OPLS2005, and B3LYP methods. In a model molecule, only the MM3* and AMBER* methods produced the same number of conformers as B3LYP, generating two conformations for rings 1 and 2, and a single conformation for rings 3 and 4. The preferred conformations of these rings are maintained in a conformer of the actual gambogic acid generated using the AMBER* and B3LYP methods. Although this calculated conformer matches well with the crystal structure, it shows that H43, C25=C26 and C30=C31 bonds may be misassigned in the crystal structure.
doi:10.1016/j.cplett.2011.06.035
PMCID: PMC3443492  PMID: 22991483
Force field; conformation; gambogic acid; ring system
24.  Thermal stability of functionalized carbon nanotubes studied by in-situ transmission electron microscopy 
Chemical physics letters  2011;513(1-3):88-93.
The thermal stability of funtionalized carbon nanotubes (CNTs) has been studied experimentally by direct in-situ observations using a heating stage in a transmission electron microscope, from room temperature (RT) to about 1000 °C. It was found that the thermal stability of the functionalized CNTs was significantly reduced during the in-situ heating process. Their average diameter dramatically expanded from RT to about 500 °C, and then tended to be stable until about 1000 °C. The X-ray energy dispersive spectroscopy analysis suggested that the diameter expansion was associated with coalescence of the carbon structure instead of deposition with additional foreign elements during the heating process.
doi:10.1016/j.cplett.2011.07.072
PMCID: PMC3182121  PMID: 21965839
Carbon nanotubes; functionalization; in-situ; thermal stability; transmission electron microscopy
25.  The Effects of Regularly Spaced Glutamine Substitutions on Alpha-Helical Peptide Structures. A DFT/ONIOM Study 
Chemical physics letters  2011;512(4-6):255-257.
The side-chains of the residues of glutamine (Q) and asparagine (N) contain amide groups. These can H-bond to each other in patterns similar to those of the backbone amides in α-helices. We show that mutating multiple Q's for alanines (A's) in a polyalanine helix stabilizes the helical structure, while similar mutations with multiple N's do not. We suggest that modification of peptides by incorporating Q's in such positions can make more robust helices that can be used to test the effects of secondary structures in biochemical experiments linked to proteins with variable structures such as tau and α-synuclein.
doi:10.1016/j.cplett.2011.07.024
PMCID: PMC3171806  PMID: 21927063

Results 1-25 (94)