A method has been developed to investigate the sensitivity of solutions large sets coupled nonlinear rate equations uncertainties in coefficients. This is based on varying all coefficients simultaneously through introduction a parameter such way that output concentrations become periodic functions this at any given time t. The chemical species are then Fourier analyzed We show via an application Weyl's ergodic theorem subset related 〈∂ci/∂kl〉, change concentration i with respect constant for...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiffusion of Brownian spheres in semidilute polymer solutionsR. I. CukierCite this: Macromolecules 1984, 17, 2, 252–255Publication Date (Print):February 1, 1984Publication History Published online1 May 2002Published inissue 1 February 1984https://pubs.acs.org/doi/10.1021/ma00132a023https://doi.org/10.1021/ma00132a023research-articleACS PublicationsRequest reuse permissionsArticle Views1437Altmetric-Citations303LEARN ABOUT THESE METRICSArticle Views...

In Parts I and II of this series [J. Chem. Phys. 59, 3873, 3879 (1973)] we developed a new method sensitivity analysis for large sets coupled nonlinear equations with many parameters. developing theory in carrying out the computer calculations involved made number approximations. We present here quantitative these approximations and, where applicable, develop rigorous error bounds. Our shows that can specify which enter into our so as to obtain measures known accuracy. On basis feel...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotoinduced electron transfer mediated by a hydrogen-bonded interfaceClaudia Turro, Chi K. Chang, George E. Leroi, Robert I. Cukier, and Daniel G. NoceraCite this: J. Am. Chem. Soc. 1992, 114, 10, 4013–4015Publication Date (Print):May 1, 1992Publication History Published online1 May 2002Published inissue 1 1992https://pubs.acs.org/doi/10.1021/ja00036a081https://doi.org/10.1021/ja00036a081research-articleACS PublicationsRequest reuse...

A recent theory [Cukier, R. I. J. Phys. Chem. 1995, 99, 16101] that predicts the rate of a proton-coupled electron transfer (PCET) reaction is developed further. In PCET, and proton may consecutively, (ET) followed by (PT), designated as ET/PT, or they concertedly, in one tunnel event, ETPT. Since charge coupled to solvent dipoles fashion similar electron−solvent coupling, effect solvation on shape potential energy surface must be known order evaluate PCET constant. We show how dielectric...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMechanism for Proton-Coupled Electron-Transfer ReactionsR. I. CukierCite this: J. Phys. Chem. 1994, 98, 9, 2377–2381Publication Date (Print):March 1, 1994Publication History Published online1 May 2002Published inissue 1 March 1994https://pubs.acs.org/doi/10.1021/j100060a027https://doi.org/10.1021/j100060a027research-articleACS PublicationsRequest reuse permissionsArticle Views689Altmetric-Citations136LEARN ABOUT THESE METRICSArticle Views are the...

A theory for proton-coupled electron-transfer (PCET) reactions (Cukier, R. I.; Nocera, D. Ann. Rev. Phys. Chem. 1998, 49, 337) is generalized to also apply hydrogen-atom transfer (HAT) reactions. PCET was described as a concerted of an electron and proton, with both species weakly coupled between their respective initial final states, nonadiabatic regime proton. Here, we treat the adiabatically, asserting that it strongly proton can span adiabatic regimes. rate constant expression obtained...

Adenylate kinase from E. coli (AKE) is studied with molecular dynamics. AKE undergoes large-scale motions of its Lid and AMP-binding domains when open form closes over substrates, AMP Mg2+-ATP. The third domain, the Core, relatively stable during closing. resulting trajectory analyzed a principal component analysis method that decomposes atom into modes ordered by their decreasing contributions to total protein fluctuation. Simulations at 303 K (normal T) 500 (high reveal both temperatures...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolymer attached metallocenes. Evidence for site isolationR. Grubbs, C. P. Lau, R. Cukier, and Brubaker Jr.Cite this: J. Am. Chem. Soc. 1977, 99, 13, 4517–4518Publication Date (Print):June 1, 1977Publication History Published online1 May 2002Published inissue 1 June 1977https://doi.org/10.1021/ja00455a059Request reuse permissionsArticle Views122Altmetric-Citations66LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text...

A large domain motion in adenylate kinase from E. coli (AKE) is studied with molecular dynamics. AKE undergoes a large-scale rearrangement of its lid and AMP-binding domains when the open form closes over substrates, AMP, Mg2+-ATP, whereby come closer to core. The third domain, core, relatively stable during this motion. reaction coordinate that monitors distance between core selected be able compare results energy transfer experiments. Sampling along carried out by using replica exchange...

We present a theory of solvent effects on the rate intramolecular proton-transfer (IPT) reactions. The proton tunnels between two vibrational levels double minimum potential. proton’s coupling to is modeled with an oscillator bath, appropriate reactions where charge interacts many molecules. evaluated by use Golden Rule; perturbation level splitting. IPT constant has several limiting expressions, one which activated form. activation energy related medium reorganization energy, and provides...

We present a theory of proton transfer reactions which incorporate the modulation proton’s potential surface by intermolecular vibrations and effect coupling to solvent degrees freedom. The tunnels between states corresponding it being localized in wells double minimum potential. resulting tunnel splitting depends on separation. response charge is modeled as that damped oscillator, allowing introduction friction effects dynamics. rate evaluated perturbation level splitting. find typically...

We analyze the effect of dynamical solvent effects on rate a nonadiabatic electron transfer (ET) reaction. Starting from Hamiltonian for reaction coordinate motion along potential surfaces donor and acceptor species, bath representing effects, we obtain system four coupled reduced equations elements density matrix donor/acceptor system. In this derivation dynamics are to classical Fokker–Planck operator since assume temperature is high compared with frequencies. At temperatures where nuclear...

Diffusion-controlled reactions in a nondilute sink system are rigorously studied with the aid of scaling expansion method. A space-time coarse graining is carried out manner consistent an concentration to obtain macroscopic transport equations from microscopic equations. It shown that, beyond lowest order concentration, equation for reaction–diffusion process cannot be written conventional local form space and time since nonlocal contribution becomes important. Properties fluctuations around...

We present a microscopic derivation of Fokker-Planck equation for the distribution function heavy Brownian particle in dense fluid from Liouville equation. The usual perturbation theory suffers presence secular terms familiar non-linear mechanics. employ "multiple time scale" technique developed by Frieman and Sandri to eliminate render expansions uniformly valid time. method introduces explicit variables exploit existence multiplicity scales inherent problem. Using this formalism we derive...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProton-Coupled Electron Transfer through an Asymmetric Hydrogen-Bonded InterfaceR. I. CukierCite this: J. Phys. Chem. 1995, 99, 43, 16101–16115Publication Date (Print):October 1, 1995Publication History Published online1 May 2002Published inissue 1 October 1995https://pubs.acs.org/doi/10.1021/j100043a060https://doi.org/10.1021/j100043a060research-articleACS PublicationsRequest reuse permissionsArticle Views276Altmetric-Citations69LEARN ABOUT THESE...

We formulate an effective medium theory for diffusion controlled processes among randomly distributed, stationary, reactive sinks. An implicit expression the exact ‘‘self-energy’’ of combined density field and sinks is obtained in terms propagator. The lowest order truncation this can be solved by numerical iteration self-energy. rate coefficients as a function sink concentration are extracted from also consider next which explicitly introduces pair correlation

A theory of rotational motion molecules in liquids is presented. The traditional Debye diffusion model generalized so as to include arbitrary reorientation angles by means a nonlocal master equation. Random walk models are special case this generalization. We have obtained the conditional probabilities for orientation body and vector fixed geometry. These results then specialized specific symmetries. From these we calculate correlation functions which describe large number spectroscopic...

Abstract Background During elongation, multi-subunit RNA polymerases (RNAPs) cycle between phosphodiester bond formation and nucleic acid translocation. In the conformation associated with catalysis, mobile “trigger loop” of catalytic subunit closes on nucleoside triphosphate (NTP) substrate. Closing trigger loop is expected to exclude water from active site, dehydration may contribute catalysis fidelity. absence a NTP substrate in opens, which enable Another notable structural element RNAP...

The possibility of controlling the tunneling a proton in condensed phase with use static or time varying external fields, which couple to transition dipole moment proton, is investigated. Starting from Hamiltonian, an equation motion describing tunnel dynamics as stochastically modulated, externally driven, two-level system derived under suitable restrictions. For fields that satisfy precise connection between frequency and amplitude, whereby resulting Floquet eigenvalues (quasienergies) are...

Cytochrome c oxidase (CcO) converts the energy from redox and oxygen chemistry to support proton translocation create a transmembrane DeltamuH(+) used for ATP production. Molecular dynamics (MD) simulations were carried out probe formation water chains capable of participating in translocation. Attention was focused on region between above a(3) hemes where well-defined have not been identified crystallographic studies. An arginine (R481) (Rhodobacter sphaeroides numbering), positioned...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular Dynamics and Quantum Chemistry Study of a Proton-Coupled Electron Transfer ReactionX. G. Zhao R. I. CukierCite this: J. Phys. Chem. 1995, 99, 3, 945–954Publication Date (Print):January 1, 1995Publication History Published online1 May 2002Published inissue 1 January 1995https://pubs.acs.org/doi/10.1021/j100003a017https://doi.org/10.1021/j100003a017research-articleACS PublicationsRequest reuse permissionsArticle...