A mechanistic study of electron transfer from the distal termini of electrode-bound, single-stranded DNAs

Electrode-bound, redox-reporter-modified oligonucleotides play roles in the functioning of a number of electrochemical biosensors, and thus the question of electron transfer through or from such molecules has proven of significant interest. In response, we have experimentally characterized the rate with which electrons are transferred between a methylene blue moiety on the distal end of a short, single-stranded polythymine DNA to a monolayer-coated gold electrode to which the other end of the DNA is site-specifically attached. We find that this rate scales with oligonucleotide length to the -1.16 ± 0.09 power. This weak, approximately inverse length dependence differs dramatically from the much stronger dependencies observed for the rates of end-to-end collisions in single-stranded DNA and through-oligonucleotide electron hopping. It instead coincides with the expected length dependence of a reaction-limited process in which the overall rate is proportional to the equilibrium probability that the end of the oligonucleotide chain approaches the surface. Studies of the ionic strength and viscosity dependencies of electron transfer further support this "chain-flexibility" mechanism, and studies of the electron transfer rate of methylene blue attached to the hexanethiol monolayer suggest that heterogeneous electron transfer through the monolayer is rate limiting. Thus, under the circumstances we have employed, the flexibility (i.e., the equilibrium statistical properties) of the oligonucleotide chain defines the rate with which an attached redox reporter transfers electrons to an underlying electrode, an observation that may be of utility in the design of new biosensor architectures.     

RATE OF INTRAMOLECULAR CONTACT FORMATION IN PROTEINS

In this paper, we estimate the rate of contact formation between two residues in the interior of the proteins using the Szabo, Schulten, and Schulten formula with the probability distribution P(r) based on 375 proteins from PDB (Protein Data Bank). The probability distribution for residue pair in proteins is different from the Gaussian distribution, especially for short distance between two residues in proteins. The rate of contact formation in the interior of protein is discussed as a function of distance n (=|j-i|) between two residues, and it decreases monotonically with n and follows the scaling relationship of k∞n-γwithγ= 1.43 for the contact radius a= 0.40 nm andγ= 1.05 for a = 0.50 nm. The diffusion coefficient for the relative diffusion of two residues in the interior of proteins is estimated as D = 6.4×10-6 cm2/s, which is close to the result that is found for monomer diffusion.     

Cluster shape anisotropy in irreversibly aggregating particulate systems

The results for cluster shape anisotropy over a broad range (10)(-3)-10(-1)) of monomer volume fractions, fv values, are presented for both two- (2d) and three-dimensional (3d) simulations of diffusion-limited (DLCA), ballistic-limited (BLCA), and reaction-limited (RLCA) cluster-cluster aggregation classes. We find that all three aggregation classes have different dilute-limit shape anisotropies, with the diffusion-limited model having the largest value of anisotropy and the reaction-limited model having the smallest. The simulation result for the cluster shape anisotropy for each of the three aggregation classes is slightly less than the corresponding prediction of the hierarchial model. In addition, we find excellent agreement between the 2d DLCA simulation results and experimental measurements of shape anisotropy. At late times, shape anisotropy decreases from the dilute-limit value.     

Phase separation mechanism in gelling aqueous biopolymer mixture probed by light scattering

Using time-resolved static and dynamic light scattering (DLS) we have studied the kinetics of phase separation in an aqueous gelatin/maltodextrin mixture upon fast cooling. The time evolution of the droplet radius is modelled for the monodisperse case under reaction-limited and diffusion-limited conditions and compared with the observed evolution of the mode associated with the droplet diffusion. For quenches to above the gelatin ordering temperature, nucleation and rather reaction-limited than diffusion-limited growth and late-stage coalescence of droplets with diameters up to 90 μm were concluded. Quenches to well below the gelatin ordering temperature seem to induce diffusion-limited growth or (delayed) spinodal decomposition (SD) to a phase-separated microstructure with slow late-stage coarsening. In deep quenches, a second slow SD or diffusion-limited cluster aggregation (DLCA) process becomes apparent from the evolution of the static structure factor; the process seems to be related to the maltodextrin gelation in the composite.     

Kinetics of loop formation in polymer chains

We investigate the kinetics of loop formation in ideal flexible polymer chains (the Rouse model), and polymers in good and poor solvents. We show for the Rouse model, using a modification of the theory of Szabo, Schulten, and Schulten, that the time scale for cyclization is tau(c) approximately tau(0)N(2) (where tau(0) is a microscopic time scale and N is the number of monomers), provided the coupling between the relaxation dynamics of the end-to-end vector and the looping dynamics is taken into account. The resulting analytic expression fits the simulation results accurately when a, the capture radius for contact formation, exceeds b, the average distance between two connected beads. Simulations also show that when a < b, tau(c) approximately N(alpha)(tau), where 1.5 < alpha(tau) < or = 2 in the range 7 < N < 200 used in the simulations. By using a diffusion coefficient that is dependent on the length scales a and b (with a < b), which captures the two-stage mechanism by which looping occurs when a < b, we obtain an analytic expression for tauc that fits the simulation results well. The kinetics of contact formation between the ends of the chain are profoundly effected when interactions between monomers are taken into account. Remarkably, for N < 100, the values of tau(c) decrease by more than 2 orders of magnitude when the solvent quality changes from good to poor. Fits of the simulation data for tau(c) to a power law in N (tau(c) approximately N(alpha)(tau)) show that alpha(tau) varies from about 2.4 in a good solvent to about 1.0 in poor solvents. The effective exponent alpha(tau) decreases as the strength of the attractive monomer-monomer interactions increases. Loop formation in poor solvents, in which the polymer adopts dense, compact globular conformations, occurs by a reptation-like mechanism of the ends of the chain. The time for contact formation between beads that are interior to the chain in good solvents changes nonmonotonically as the loop length varies. In contrast, the variation in interior loop closure time is monotonic in poor solvents. The implications of our results for contact formation in polypeptide chains, RNA, and single-stranded DNA are briefly outlined.     

Computer simulation of selective aggregation in binary colloids

The morphology of clusters formed by selective aggregation of binary colloids is studied in a two-dimensional Monte Carlo simulation for a large range of number fractions (200:1, 100:1, 10:1, 2:1). We find remarkable similarity in morphology to those observed in experiments, from the formation of closed "micelles" to large branched clusters. Quantitative studies of the fractal dimension, kinetics, and cluster size distribution are also carried out and compared with diffusion-limited cluster aggregation and reaction-limited cluster aggregation models.     

Transformation between α‐helix and β‐sheet structures of one and two polyglutamine peptides in explicit water molecules by replica‐exchange molecular dynamics simulations

Aggregation of polyglutamine peptides with β‐sheet structures is related to some important neurodegenerative diseases such as Huntington's disease. However, it is not clear how polyglutamine peptides form the β‐sheets and aggregate. To understand this problem, we performed all‐atom replica‐exchange molecular dynamics simulations of one and two polyglutamine peptides with 10 glutamine residues in explicit water molecules. Our results show that two polyglutamine peptides mainly formed helix or coil structures when they are separated, as in the system with one‐polyglutamine peptide. As the interpeptide distance decreases, the intrapeptide β‐sheet structure sometimes appear as an intermediate state, and finally the interpeptide β‐sheets are formed. We also find that the polyglutamine dimer tends to form the antiparallel β‐sheet conformations rather than the parallel β‐sheet, which is consistent with previous experiments and a coarse‐grained molecular dynamics simulation. © 2014 Wiley Periodicals, Inc.     

Kinetics of transient end-to-end contact of single-stranded DNAs

The formation of the pyrene (Py) dimer radical cation (Py(2)(*+)) was used to measure the kinetics of the intrastrand end-to-end contact rates of single-stranded DNAs (ssDNAs) in the 10 nanoseconds to the tens of microseconds time range. ssDNAs labeled with Py at both ends with the lengths of 3, 6, and 9 mer were synthesized, and the two-photon ionization method was employed to generate a Py(*+), which enables the measurements of the end-to-end contact rates from 10 ns. The formation rate of Py(2)(*+) depended on the length and the sequence of the ssDNAs, and about 1 order of magnitude faster rates were observed for the T-rich ssDNAs compared to those for the corresponding length of A-rich ssDNAs, showing that ssDNA made from adenines is much more rigid than that composed of thymidines. As for the T-rich ssDNAs, the formation of Py(2)(*+) attributed to the misfolded structures was also observed, which is consistent with the configurational diffusion model suggested by Ansari and co-workers.     

Monitoring gold nanorod synthesis by localized surface plasmon resonance

Surfactants can direct the growth of gold nanoparticles to create anisotropic structures in high yield by simple means, yet the exact roles of surfactants and other reactants are not entirely understood. Here we show that one can exploit the geometrical dependence of the localized surface plasmon resonant extinction spectrum of gold nanorods to monitor their synthesis kinetics. By using quantitative measurements of nanorod extinction cross sections, Gans' theory for the spectral extinction of prolate spheroids can be normalized to provide values for the nanorod length and diameter from extinction spectra measured during growth. The nanorod length growth rate was first observed at 0.15 nm/s and decayed during the growth reaction. The rate dependence on nanorod size did not correspond to any simple reaction-limited or diffusion-limited growth mechanisms.     

Neutron reflectivity characterization of the photoacid reaction-diffusion latent and developed images of molecular resists for extreme ultraviolet lithography

Lithographic feature size requirements have approached a few radius of gyration of photoresist polymers used in thin-film patterning. Furthermore, the feature dimensions are commensurate with the photoacid diffusion length that defines the underlying latent image. Smaller imaging building blocks may enable reduced feature sizes; however, resolution limits are also dependent upon the spatial extent of the photoacid-catalyzed reaction diffusion front and subsequent dissolution mechanism. The reaction-diffusion front was characterized by neutron reflectivity for ccc stereoisomer-purified, deuterium-labeled tert-butoxycarbonyloxy calix[4]resorcinarene molecular resists. The spatial extent of the reaction front exceeds the size of the molecular resist with an effective diffusion constant of (0.13 ± 0.06) nm(2)/s for reaction times longer than 60 s, with the maximum at shorter times. Comparison to a mean-field reaction-diffusion model shows that a photoacid trapping process provides bounds to the spatial and extent of reaction via a reaction-limited mechanism whereas the ratio of the reaction rate to trapping rate constants recovers the effective diffusion peak. Under the ideal step-exposure conditions, surface roughness was observed after either positive- or negative-tone development. However, negative-tone development follows a surface-restructuring mechanism rather than etch-like dissolution in positive-tone development.     

Rotational transfer rates and propensity rule in nitric oxide-rare gas collisions

In the first application of the technique of multistep ionization to the measurement of rotational transfer rates within an electronically excited molecular state, we have observed a propensity to even ΔJ in NO colliding with rare gased and have measured a number of transfer rates with high accuracy. A propensity to even ΔJ has been predicted but no observation of it has been previously reported.     

Inherent Conformational Preferences of Ac‐Gln‐Gln‐NHBn: Sidechain Hydrogen Bonding Supports a β‐Turn in the Gas Phase

Gas‐phase single‐conformation spectroscopy is used to study Ac‐Gln‐Gln‐NHBn in order to probe the interplay between sidechain hydrogen bonding and backbone conformational preferences. This small, amide‐rich peptide offers many possibilities for backbone–backbone, sidechain–backbone, and sidechain–sidechain interactions. The major conformer observed experimentally features a type‐I β‐turn with a canonical 10‐membered ring C=O—H?N hydrogen bond between backbone amide groups. In addition, the C=O group of each Gln sidechain participates in a seven‐membered ring hydrogen bond with the backbone NH of the same residue. Thus, sidechain hydrogen‐bonding potential is satisfied in a manner that is consistent with and stabilizes the β‐turn secondary structure. This turn‐forming propensity may be relevant to pathogenic amyloid formation by polyglutamine segments in human proteins.     

Experimental investigation of colloidal gel structures

We investigate experimentally the structural properties of colloidal gels, formed under both diffusion-limited and reaction-limited aggregation conditions, using light scattering measurements and compare the results with the literature Monte Carlo (MC) simulations. The scattering structure factors have been measured for the two classes of gels in the range of the particle volume fractions between 0.02 and 0.07. From these, the corresponding fractal dimension values have been estimated. These have been found to be in good agreement with those estimated from the structure factors computed from MC simulated gels. On the basis of our previous research (Lattuada et al. Langmuir 2003, 19, 6312), this confirms that the scattering structure factor of a gel provides erroneously a small fractal dimension value, which decreases as the particle volume fraction increases. Furthermore, it is observed that the average size of the fractal clusters is larger in real gels than in simulated gels.     

Adaptive steered molecular dynamics: validation of the selection criterion and benchmarking energetics in vacuum

The potential of mean force (PMF) for stretching decaalanine in vacuum was determined earlier by Park and Schulten [J. Chem. Phys. 120, 5946 (2004)] in a landmark article demonstrating the efficacy of combining steered molecular dynamics and Jarzynski's nonequilibrium relation. In this study, the recently developed adaptive steered molecular dynamics (ASMD) algorithm [G. Ozer, E. Valeev, S. Quirk, and R. Hernandez, J. Chem. Theory Comput. 6, 3026 (2010)] is used to reproduce the PMF of the unraveling of decaalanine in vacuum by averaging over fewer nonequilibrium trajectories. The efficiency and accuracy of the method are demonstrated through the agreement with the earlier work by Park and Schulten, a series of convergence checks compared to alternate SMD pulling strategies, and an analytical proof. The nonequilibrium trajectories obtained through ASMD have also been used to analyze the intrapeptide hydrogen bonds along the stretching coordinate. As the decaalanine helix is stretched, the initially stabilized i → i + 4 contacts (α-helix) is replaced by i → i + 3 contacts (3(10)-helix). No significant formation of i → i + 5 hydrogen bonds (π-helix) is observed.     

Charge transport through polyene self-assembled monolayers from multiscale computer simulations

We combine first-principles density-functional theory with matrix Green's function calculations to predict the structures and charge transport characteristics of self-assembled monolayers (SAMs) of four classes of systems in contact with Au(111) electrodes: conjugated polyene chains (n = 4, 8, 12, 16, and 30) thiolated at one or both ends and saturated alkane chains (n = 4, 8, 12, and 16) thiolated at one or both ends. For the polyene SAMs, we find no decay in the current as a function of chain length and conclude that these 1-3 nm long polyene SAMs act as metallic wires. We also find that the polyene-monothiolate leads to a contact resistance only 2.8 times higher than that for the polyene-dithiolate chains, indicating that the device conductance is dominated by the properties of the molecular connector with less importance in having a second molecule-electrode contact. For the alkane SAMs, we observe the normal exponential decay in the current as a function of the chain length with a decay constant of beta(n) = 0.82 for the alkane-monothiolate and 0.88 for the alkane-dithiolate. We find that the contact resistance for the alkane-monothiolate is 12.5 times higher than that for the alkane-dithiolate chains, reflecting the extra resistance due to the weak contact on the nonthiolated end. These contrasting charge transport characteristics of alkane and polyene SAMs and their contact dependence are explained in terms of the atomic projected density of states.     

DNA polymorphism as an origin of adenine-thymine tract length-dependent threading intercalation rate

Binuclear ruthenium complexes that bind DNA by threading intercalation have recently been found to exhibit an exceptional kinetic selectivity for long polymeric adenine-thymine (AT) DNA. A series of oligonucleotide hairpin duplexes containing a central tract of 6-44 alternating AT base pairs have here been used to investigate the nature of the recognition mechanism. We find that, above a threshold AT tract length corresponding to one helix turn of B-DNA, a dramatic increase in threading intercalation rate occurs. In contrast, such length dependence is not observed for rates of unthreading. Intercalation by any mechanism that depends on the open end of the hairpin was found not to be important in the series of oligonucleotides used, as verified by including in the study a hairpin duplex cyclized by a copper-catalyzed "click" reaction. Our observations are interpreted in terms of a conformational pre-equilibrium, determined by the length of the AT tract. We finally find that mismatches or loops in the oligonucleotide facilitate the threading process, of interest for the development of mismatch-recognizing probes.     

Spontaneous formation of annular structures observed in molecular dynamics simulations of polyglutamine peptides

Annular structures have been observed experimentally in aggregates of polyglutamine-containing proteins and other proteins associated with diseases of the brain. Here we report the observation of annular structures in molecular-level simulations of large systems of model polyglutamine peptides. A system of 24 polyglutamine chains 16 residues long at a concentration of 5 mM spontaneously formed large beta sheets which curved to form tube-like annular structures that resemble beta barrels. This work was accomplished by extending the PRIME model to polyglutamine. PRIME is an off-lattice, unbiased, intermediate-resolution protein model based on an amino acid representation of between three and seven united atoms depending on the residue being modeled. Our results are interesting not only because of the recent discovery of tubular protofibrils in experiments on aggregation of mutant huntingtin fragments containing expanded polyglutamine tracts but also because Perutz predicted that polyglutamine forms water filled nanotubes.     

Tuning polymer melt fragility with antiplasticizer additives

A polymer-diluent model exhibiting antiplasticization has been developed and characterized by molecular dynamics simulations. Antiplasticizer molecules are shown to decrease the glass transition temperature Tg but to increase the elastic moduli of the polymeric material in the low-temperature glass state. Moreover, the addition of antiplasticizing particles renders the polymer melt a stronger glass-forming material as determined by changes in the characteristic temperatures of glass formation, the fragility parameter D from fits to the Vogel-Folcher-Tamman-Hesse equation, and through the observation of the temperature dependence of the size of cooperatively rearranging regions (strings) in each system. The length of the strings exhibits a weaker temperature dependence in the antiplasticized glass-forming system than in the more fragile pure polymer, consistent with the Adam-Gibbs model of glass formation. Unexpectedly, the strings become increasingly concentrated in the antiplasticizer particles upon cooling. Finally, we discuss several structural indicators of cooperative dynamics, and find that the dynamic propensity (local Debye-Waller factor p) does seem to provide a strong correlation with local molecular displacements at long times. The authors also consider maps of the propensity, and find that the antiplasticized system exhibits larger fluctuations over smaller length scales compared to the pure polymer.     

Correlation between HOMO alignment and contact resistance in molecular junctions: aromatic thiols versus aromatic isocyanides

Understanding electron transport in metal-molecule-metal (MMM) junctions is of great importance for the advancement of molecular electronics. Critical factors that determine conductivity in a MMM junction include the nature of metal-molecule contacts and the electronic structure of the molecular backbone. We have studied the electronic transport property and the valence electronic structure on rigid, conjugated oligoacenes of increasing length with either thiol (-S) or isocyanide (-CN) linkers using conducting probe atomic force microscopy (CP-AFM) and ultraviolet photoelectron spectroscopy (UPS). We find that for these conjugated systems the Au-CN contact is more resistive than Au-S. The difference in contact resistance correlates with UPS measurements that show the highest-occupied molecular orbital (HOMO) of the isocyanide series is lower in energy (relative to the Fermi level of Au) than the HOMO of the thiol series, indicating the presence of a higher tunneling barrier at the contact for the isocyanide-linked molecules. By contrast, the difference in the HOMO positions for the two series of molecules does not appear to affect the length dependence of the junction resistance (i.e., the beta value = 0.5 A-1).     

Physicochemical properties of anionic triple-chain surfactants in alkaline solutions

A series of novel gemini cationic surfactants alkanediyl-alpha,omega-bis (hydroxyethylmethylhexadecylammonium bromide) with polymethylene spacer chain length of 4, 6, 8, and 10 carbon atoms was synthesized and characterized. Critical micellar concentrations of the gemini surfactants in aqueous solutions as determined by the surface tension and conductance measurements were observed to be in the range 1.39-3.63 microM. The critical micellar concentration was observed to increase initially with spacer length up to 6 methylene groups and to decrease thereafter with the increase in spacer length. The micellar microstructure in aqueous solutions examined through small angle neutron scattering (SANS) revealed that the extent of aggregation growth and variation in shapes of micelles strongly depend on head group polarity, spacer chain length, and temperature. The propensity to micellar growth with spacer chain length 4 was found to be much higher than with the longer spacer lengths. The fractional charge on the micelle increases with increased spacer chain length and temperature.