Molecular Rate Constants Research Articles

Biomolecular interactions on densely coated nanoparticles: a single-molecule perspective.

DNA-modified gold nanoparticles (AuNPs) play a pivotal role in bio-nanotechnology, driving advancements in bio-sensing, bio-imaging, and drug delivery. Synthetic protocols have focused on maximizing the receptor density on particles by fine-tuning chemical conditions, particularly for DNA. Despite their significance, the understanding of hybridization kinetics on functionalized AuNPs is lacking, particularly how this kinetics depends on DNA density and to what extent it varies from particle-to-particle. This study explores the molecular mechanisms of DNA hybridization on densely coated AuNPs by employing a combination of single-molecule microscopy and coarse-grained molecular dynamics simulations providing a quantification of the molecular rate constants for single particles. Our findings demonstrate that DNA receptor density and the presence of spacer strands profoundly impact association kinetics, with short spacers enhancing association rates by up to ∼15-fold. In contrast, dissociation kinetics are largely unaffected by receptor density within the studied range. Single-particle analysis directly reveals variability in hybridization kinetics, which is analyzed in terms of intra- and inter-particle heterogeneity. A coarse-grained DNA model that quantifies hybridization kinetics on densely coated surfaces further corroborates our experimental results, additionally shedding light on how transient base pairing within the DNA coating influences kinetics. This integrated approach underscores the value of single-molecule studies and simulations for understanding DNA dynamics on densely coated nanoparticle surfaces, offering guidance for designing DNA-functionalized nanoparticles in sensor applications.

RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons

DNA transcription initiates after an RNA polymerase (RNAP) molecule binds to the promoter of a gene. In bacteria, the canonical picture is that RNAP comes from the cytoplasmic pool of freely diffusing RNAP molecules. Recent experiments suggest the possible existence of a separate pool of polymerases, competent for initiation, which freely slide on the DNA after having terminated one round of transcription. Promoter-dependent transcription reinitiation from this pool of posttermination RNAP may lead to coupled initiation at nearby operons, but it is unclear whether this can occur over the distance and timescales needed for it to function widely on a bacterial genome in vivo. Here, we mathematically model the hypothesized reinitiation mechanism as a diffusion-to-capture process and compute the distances over which significant interoperon coupling can occur and the time required. These quantities depend on molecular association and dissociation rate constants between DNA, RNAP, and the transcription initiation factor σ70; we measure these rate constants using single-molecule experiments in vitro. Our combined theory/experimental results demonstrate that efficient coupling can occur at physiologically relevant σ70 concentrations and on timescales appropriate for transcript synthesis. Coupling is efficient over terminator-promoter distances up to ∼1,000 bp, which includes the majority of terminator-promoter nearest neighbor pairs in the Escherichia coli genome. The results suggest a generalized mechanism that couples the transcription of nearby operons and breaks the paradigm that each binding of RNAP to DNA can produce at most one messenger RNA.

A ReaxFF molecular dynamics and RRKM ab initio based study on degradation of indene

The degradation of indene is investigated using molecular dynamics (MD) with the ReaxFF force field and RRKM theory. Microcanonical rate constants are obtained over a broad energy range (8–25 eV). There is agreement between the results of the molecular dynamics and RRKM calculations at the lower energies, while the molecular dynamics rate constants are larger at the higher energies. At the lower energies there is also agreement with values obtained by using expressions for photodegradation of polyaromatic hydrocarbons from the literature. Values from those expressions however increase even faster with energy than our molecular dynamics rate constants do. At the same time those values are lower than an experimental result at 6.4 eV. This suggests that astrochemical models employing those values may result in unreliable polycyclic aromatic hydrocarbons abundances.

Conformational Dynamics of Human ALKBH2 Dioxygenase in the Course of DNA Repair as Revealed by Stopped-Flow Fluorescence Spectroscopy

Elucidation of physicochemical mechanisms of enzymatic processes is one of the main tasks of modern biology. High efficiency and selectivity of enzymatic catalysis are mostly ensured by conformational dynamics of enzymes and substrates. Here, we applied a stopped-flow kinetic analysis based on fluorescent spectroscopy to investigate mechanisms of conformational transformations during the removal of alkylated bases from DNA by ALKBH2, a human homolog of Escherichia coli AlkB dioxygenase. This enzyme protects genomic DNA against various alkyl lesions through a sophisticated catalytic mechanism supported by a cofactor (Fe(II)), a cosubstrate (2-oxoglutarate), and O2. We present here a comparative study of conformational dynamics in complexes of the ALKBH2 protein with double-stranded DNA substrates containing N1-methyladenine, N3-methylcytosine, or 1,N6-ethenoadenine. By means of fluorescent labels of different types, simultaneous detection of conformational transitions in the protein globule and DNA substrate molecule was performed. Fitting of the kinetic curves by a nonlinear-regression method yielded a molecular mechanism and rate constants of its individual steps. The results shed light on overall conformational dynamics of ALKBH2 and damaged DNA during the catalytic cycle.

Intramolecular H-bond design for efficient orange–red thermally activated delayed fluorescence based on a rigid dibenzo[f,h]pyrido[2,3-b]quinoxaline acceptor

Tune the molecular excited state and rate constants of radiative intersystem crossing by constructing intramolecular H-bonds to achieve high-efficiency orange–red TADF-OLEDs.

A Multiscale Approach to Modeling Plasmonic Nanorod Biosensors

Due to their strongly enhanced optical near-fields, plasmonic nanostructures are promising candidates as ultrasensitive label-free sensors of single molecule binding kinetics. However, the interpretation of nanoplasmonic sensing data is complicated by the spatial inhomogeneity of the near-field response and the stochastic nature of molecule-nanoparticle interactions, which makes it difficult to accurately count the number of adsorbed molecules per nanosensor. We combined electromagnetic calculations with stochastic diffusion-reaction simulations in order to investigate how these two sources of noise influence the uncertainty in measured molecular association and dissociation rate constants and concentration for the most common type of plasmonic nanosensor, the nanorod. Using this multiscale in silico tool, we show how to minimize the measurement uncertainty, and we identify the optimum nanorod aspect ratio for quantitative sensing.

Molecular Regulation of Actin Turnover at the Leading Edge of Migrating Cells

Actin couples molecular motors to extracellular adhesions and its turnover regulates cell polarization and protrusion efficiency. Actin filament turnover is regulated by polymerization and depolymerization at the ends, which is increased by severing filaments internally. To determine how these reactions affect F-actin turnover rate we simulated the molecular mechanisms revealed by experiments and determined the ODEs for changes in the average filament length and number of filaments that determine total F-actin. These results reveal the conditions that end dynamics and severing strongly cooperate to increase actin turnover and steady-state behavior. Although the molecular rate constants that regulate actin turnover have been measured in vitro in the presence of various actin regulatory proteins these constants are still unknown in vivo for most cell processes regulated by actin turnover. Importantly, these constants that regulate actin turnover at the leading edge of migrating cells remain unknown. Therefore, we modeled actin turnover as a system of these molecular mechanisms at the leading edge to investigate how actin distributions emerge and actin dynamics are regulated by migrating U251 glioma cells. We used the model to fit leading edge actin distributions of cells transfected with GFP-actin and aligned on one-dimensional tracks using model convolution microscopy. Best fits of the model yield estimates of the molecular rate constants that regulate actin turnover in vivo. We then correlated the molecular rates with the velocities of actin-network retrograde flow, cell protrusion and cell displacement of expanding, contracting and migrating cells. The quantitative analyses of our model provide in vivo estimates for the molecular rate constants that regulate actin turnover at the leading edge of cells and presents insights into the molecular mechanisms that regulate actin-based cell migration.

Potential new therapeutic modality revealed through agent-based modeling of the neuromuscular junction and acetylcholinesterase inhibition.

BackgroundOne of the leading causes of death and illness within the agriculture industry is through unintentionally ingesting or inhaling organophosphate pesticides. OP intoxication directly inhibits acetylcholinesterase, resulting in an excitatory signaling cascade leading to fasciculation, loss of control of bodily fluids, and seizures.MethodsOur model was developed using a discrete, rules-based modeling approach in NetLogo. This model includes acetylcholinesterase, the nicotinic acetylcholine receptor responsible for signal transduction, a single release of acetylcholine, organophosphate inhibitors, and a theoretical novel medical countermeasure. We have parameterized the system considering the molecular reaction rate constants in an agent-based approach, as opposed to apparent macroscopic rates used in differential equation models.ResultsOur model demonstrates how the cholinergic crisis can be mitigated by therapeutic intervention with an acetylcholinesterase activator. Our model predicts signal rise rates and half-lives consistent with in vitro and in vivo data in the absence and presence of inhibitors. It also predicts the efficacy of theoretical countermeasures acting through three mechanisms: increasing catalytic turnover of acetylcholine, increasing acetylcholine binding affinity to the enzyme, and decreasing binding rates of inhibitors.ConclusionWe present a model of the neuromuscular junction confirming observed acetylcholine signaling data and suggesting that developing a countermeasure capable of reducing inhibitor binding, and not activator concentration, is the most important parameter for reducing organophosphate (OP) intoxication.Electronic supplementary materialThe online version of this article (doi:10.1186/1742-4682-11-42) contains supplementary material, which is available to authorized users.

Real-time molecular uptake and membrane-specific transport in living cells by optical microscopy and nonlinear light scattering

We show that the comparably simple and widely available technique, optical transmission microscopy (TM), can be used in a time-resolved way to independently measure uptake of any molecule (that absorbs visible light) into living cells. This technique complements second-harmonic light scattering (SHS), which can be used for time-resolved observation of adsorption and transport of small molecules, with non-zero first-order hyper-polarizability, through membranes in living cells. While either technique can be used alone, a combination of the pair allows a fully complementary and quantitative characterization of molecular uptake with membrane specificity in living cells. Specifically, TM permits detection of the changing bulk molecular concentrations within the cell, and SHS, with its inherent interface sensitivity, provides sequential differentiation of molecular density at membrane surfaces. Simultaneous global analysis of the TM and SHS observations yield molecular diffusion rate constants for all traversed cellular barriers.

Quantitative relationship between rate constants and molecular structure descriptors for the gas phase hydrogen abstraction reactions

The abstraction of hydrogen by general radicals has a wide role in environmental and also in technological processes because it results in reactive free radicals that play a vital role in atmospheric chemistry and also in biochemical processes. In addition to experimental studies, the theoretical modelling of this elementary reaction has been important for understanding and predicting respective rate constants. In this paper, molecular descriptors in the context of a QSAR approach are used to codify the relationship between molecular structure and rate constants. Unique experimental data is collected from the literature for the reaction , where are diverse radicals. The four-parameter QSAR model (n = 34, r 2 = 0.81, = 0.74, = 0.12, s 2 = 0.19) is presented for the bimolecular rate constants, accompanied with model diagnostics and analysis of descriptors in the model.

The Single-Molecule Conductance and Electrochemical Electron-Transfer Rate Are Related by a Power Law

This study examines quantitative correlations between molecular conductances and standard electrochemical rate constants for alkanes and peptide nucleic acid (PNA) oligomers as a function of the length, structure, and charge transport mechanism. The experimental data show a power-law relationship between conductances and charge transfer rates within a given class of molecules with the same bridge chemistry, and a lack of correlation when a more diverse group of molecules is compared, in contrast with some theoretical predictions. Surprisingly, the PNA duplexes exhibit the lowest charge-transfer rates and the highest molecular conductances. The nonlinear rate-conductance relationships for structures with the same bridging chemistries are attributed to differences in the charge-mediation characteristics of the molecular bridge, energy barrier shifts and electronic dephasing, in the two different experimental settings.

Molecular size dependent falloff rate constants for the recombination reactions of alkyl radicals with O2 and implications for simplified kinetics of alkylperoxy radicals

AbstractThe recombination reactions of prototypical alkyl radicals (R) with O2, R + O2 → RO2, have been investigated theoretically by using the variational transition state theory and Rice–Ramsperger–Kassel–Marcus theory/master equation calculations based on the CASPT2(7,5)/aug‐cc‐pVDZ//B3LYP/6‐311G(d,p) potential energy curves and B3LYP/6‐311G(d,p) geometries and vibrational frequencies. The calculated high‐pressure limiting rate constants well reproduced the experimental room temperature rate constants for ethyl, i‐propyl, n‐butyl, s‐butyl, and t‐butyl radicals and were nearly the same for the same class of alkyl radicals, namely for primary (ethyl and n‐butyl) and for secondary (i‐propyl and s‐butyl) radicals. Hypothetical falloff calculations ignoring the subsequent dissociation/isomerization reactions of RO2 indicated that the low‐pressure limiting (LPL) rate constants increase monotonically and systematically with the size of the molecule and are almost identical for the same‐sized C4 alkyl radicals, n‐butyl, s‐butyl, and t‐butyl. With the extended calculations for 1‐hexyl (C6H13) and 2,4,4‐trimethylpentyl (C8H17)+ O2 based on the B3LYP/6‐311G(d,p) calculations and estimated potential energy curves, class‐specific molecular size dependent falloff rate expression was proposed. The analysis of the unexpected behavior of the LPL rate constants for large alkyl radicals at high temperatures suggested the collapse of the assumption of the steady‐state dissociation or the Lindemann–Hinshelwood type of the mechanism. The analysis of the dissociation/recombination steady state suggested near‐Boltzmann distribution of RO2 in partial equilibrium with R + O2, which implies the possible simplification of the kinetic modeling by using the high‐pressure limiting rate constants for the subsequent reactions of RO2. © 2011 Wiley Periodicals, Inc. Int J Chem Kinet 44: 59–74, 2012

Density Functional Theory Study of Photophysical Properties of Iridium(III) Complexes with Phenylisoquinoline and Phenylpyridine Ligands

Linear and quadratic response time-dependent density functional theory is applied to study the photophysical properties of iridium complexes with phenylisoquinoline and phenylpyridine ligands. The ground-state geometries, frontier molecular orbitals, absorption spectra, phosphorescence wavelengths, and radiative rate constants are computed to facilitate better understanding of the structure–property relationships of these iridium complexes used in organic light-emitting diodes (OLEDs) to enhance spin–orbit coupling and triplet state emission. The agreement obtained between calculated and available experimental data indicates a possibility to guide the design of phosphorescence-based OLEDs by predicting their relevant properties through quantum mechanical calculations.

Fade and quench-resistant emission in calcium phosphate nanoreactors

The fluorescence emission and photodegradation properties of fluorescein dye inside fluid-filled sphericalnanoreactors ∼ 150 nm in diameter and surrounded by a few nanometres thick layer of calcium phosphate areconsidered in detail. Steady state, stopped flow, and laser pulsed fluorescencespectroscopies, absorption spectroscopy, dynamic light scattering and electron microscopywere used to characterize the materials as a function of encapsulated dye concentration,particle concentration, illumination time, and pH. Fluorescein tends to form stableJ-aggregates inside the nanoreactors. The molecular collision rate constants between the dyeaggregates and between the dyes and soluble quenchers are greatly reduced inside thenanoreactors and are responsible for the observed resistance to photodegradationand reduced emission quenching. A model for dye behaviour in nanoreactors issuggested. Nanoreactors can be concentrated to a high suspension concentration,yielding exceptionally strong luminescence affected only by inner filter effects absentparticle–particle crosstalk. These and similar nanoreactors can be utilized as buildingblocks for three-dimensional photo-optical devices, and as versatile and resilientsupramolecular chromophores or tracers in complex fluids, cells and microfluidic systemswhere high resolution visualization is needed.

Molecular Interaction Radii and Rate Constants for Clarifying Organic Compound Physisorption on Silicon Surface

For describing the organic compound physisorption on a silicon surface, a method for systematically obtaining the physisorption and desorption rate constants of organic compounds was developed. Additionally, an equation for describing the surface concentration of organic compounds in a steady state was derived, taking into account the rate constants of physisorption and desorption and the molecular interaction radii for occupying the silicon surface. In a three-component system consisting of isopropyl alcohol, diethylphthalate, and octanol, the calculated surface concentrations showed a correlation to that of the in situ measurement using a quartz crystal microbalance. Thus, the equation obtained in this study is expected to predict an airborne organic contamination behavior in a multicomponent system.

Molecular factor analysis in self-exchange electron transfer reactions in solution

We present a systematic method to access molecular factors and rate constants for self-exchange electron transfer reactions in solution using partial least squares and a number of chosen descriptors. In this work it is shown that the log response for the set of reactions considered can be mostly described in terms of the Intersecting State Model (ISM) when the nonadiabaticity of transfers involving electrons in σ*-orbitals is considered.

ChemInform Abstract: Accurate Phase Space Theory and Molecular Dynamics Calculations of Aluminum Cluster Dissociation

Calculations of phase space theory and molecular dynamics rate constants and product energy and angular momentum distributions for Al6 and Al13 dissociation are reviewed. The molecular dynamics simulations indicate the unimolecular dynamics of these clusters are ergodic and agree with the random lifetime assumption of Rice-Ramsperger-Kassel-Marcus (RRKM) theory. With anharmonicity effects properly included, orbiting transition state theory (OTS/PST) gives rate constants and product energy and angular momentum distributions in very good agreement with those obtained from the molecular dynamics simulations.

Kinetic Characterization of OmcA and MtrC, Terminal Reductases Involved in Respiratory Electron Transfer for Dissimilatory Iron Reduction in Shewanella oneidensis MR-1

We have used scaling kinetics and the concept of kinetic competence to elucidate the role of hemeproteins OmcA and MtrC in iron reduction by Shewanella oneidensis MR-1. Second-order rate constants for OmcA and MtrC were determined by single-turnover experiments. For soluble iron species, a stopped-flow apparatus was used, and for the less reactive iron oxide goethite, a conventional spectrophotometer was used to measure rates. Steady-state experiments were performed to obtain molecular rate constants by quantifying the OmcA and MtrC contents of membrane fractions and whole cells by Western blot analysis. For reduction of soluble iron, rates determined from transient-state experiments were able to account for rates obtained from steady-state experiments. However, this was not true with goethite; rate constants determined from transient-state experiments were 100 to 1,000 times slower than those calculated from steady-state experiments with membrane fractions and whole cells. In contrast, addition of flavins to the goethite experiments resulted in rates that were consistent with both transient- and steady-state experiments. Kinetic simulations of steady-state results with kinetic constants obtained from transient-state experiments supported flavin involvement. Therefore, we show for the first time that OmcA and MtrC are kinetically competent to account for catalysis of soluble iron reduction in whole Shewanella cells but are not responsible for electron transfer via direct contact alone with insoluble iron-containing minerals. This work supports the hypothesis that electron shuttles are important participants in the reduction of solid Fe phases by this organism.

Kinetic Study of Humic Acid Ozonation in Aqueous Media

AbstractA pseudo first‐order kinetic model that describes the ozonation of two sources of humic acid (HA) in aqueous media is developed and investigated in a semi‐batch system. Further investigation shows that the degradation rates of the two HAs are highly dependent on the initial pH, temperature of the ozonation, the source of HA, and the overall kinetic rate constant, which is mainly composed of two parts, i. e., direct oxidation by molecular ozone and indirect oxidation by hydroxyl radicals (•OH). The contributions of the two pathways to HA ozonation can be traced using tert‐butanol as the radical scavenger at different pH values (3, 7, and 11), temperatures (283–303 K), and the results show that •OH oxidation is more sensitive to the operating variables than molecular ozone oxidation and exerts a contribution of ca. 50 to 60% on the overall reaction at the different operating parameters. Furthermore, the direct molecular ozone oxidation rate constant is correlated with temperature by a modified Arrhenius equation with an activation energy, Ea, of 33.57 kJ mol–1.

Effect of HCl and solution concentration on the ultrasonic degradation of aqueous solutions of poly (ethylene oxide)

The ultrasonic degradation of poly (ethylene oxide) solutions was carried out in aqueous solution of hydrogen chloride at 25°C to investigate the effect of HCl and solution concentration on the rate of degradation. The obtained limiting molecular weights and apparent rate constants indicate that the extent and rate of degradation of poly(ethylene oxide) solutions were decreased by increasing concentration of HCl from 0 to 0.3 M, and the extent and rate of degradation of poly(ethylene oxide) solutions were increased by increasing concentration of HCl from 0.3 to 0.5 M. The obtained limiting molecular weights were correlated in terms of concentration and initial intrinsic viscosity. The calculated rate constants were correlated in terms of concentration, initial intrinsic viscosity and molecular weight of polymer. This degradation behavior was interpreted in terms of initial intrinsic viscosity and concentration of polymer solutions. Intrinsic viscosity of poly (ethylene oxide) was decreased by increasing concentration of HCl from 0 to 0.3 M and the chains of polymer coiled and this caused a decrease in shear strain; therefore, the rate of degradation was decreased. But the chains of polymer were expanded by increasing concentration of HCl from 0.3 to 0.5 M and this caused an increase in shear strain; therefore, the rate of degradation was increased. As the solution concentration increased, the viscosity was increased and caused a reduction in the'cavitation efficiency, and so the rate of degradation is decreased.