1,724 research outputs found
Dynamics of Proton Transfer in Mesoscopic Clusters
Proton transfer rates and mechanisms are studied in mesoscopic, liquid-state,
molecular clusters. The proton transfer occurs in a proton-ion complex solvated
by polar molecules comprising the cluster environment. The rates and mechanisms
of the reaction are studied using both adiabatic and non-adiabatic molecular
dynamics. For large molecular clusters, the proton-ion complex resides
primarily on the surface of the cluster or one layer of solvent molecules
inside the surface. The proton transfer occurs as the complex undergoes
orientational fluctuations on the cluster surface or penetrates one solvent
layer into the cluster leading to solvent configurations that favor the
transfer. For smaller clusters the complex resides mostly on the surface of the
cluster and proton transfer is observed only when the complex penetrates the
cluster and solvent configurations that favor the proton transfer are achieved.
Quantitative information on the cluster reaction rate constants is also
presented.Comment: To appear in JCP (March). Postscript figures available on request
([email protected]
An interpretation of fluctuations in enzyme catalysis rate, spectral diffusion, and radiative component of lifetimes in terms of electric field fluctuations
Time-dependent fluctuations in the catalysis rate ({delta}k(t)) observed in single-enzyme experiments were found in a particular study to have an autocorrelation function decaying on the same time scale as that of spectral diffusion {delta}{omega}0(t). To interpret this similarity, the present analysis focuses on a factor in enzyme catalysis, the local electrostatic interaction energy (E) at the active site and its effect on the activation free energy barrier. We consider the slow fluctuations of the electrostatic interaction energy ({delta}E(t)) as a contributor to {delta}k(t) and relate the latter to {delta}{omega}0(t). The resulting relation between {delta}k(t) and {delta}{omega}0(t) is a dynamic analog of the solvatochromism used in interpreting solvent effects on organic reaction rates. The effect of the postulated {delta}E(t) on fluctuations in the radiative component ({delta}{gamma}Formula(t)) of the fluorescence decay of chromophores in proteins also is examined, and a relation between {delta}{gamma}Formula(t) and {delta}{omega}0(t) is obtained. Experimental tests will determine whether the correlation functions for {delta}k(t), {delta}{omega}0(t), and {delta}{gamma}Formula are indeed similar for any enzyme. Measurements of dielectric dispersion, {varepsilon}({omega}), for the enzyme discussed elsewhere will provide further insight into the correlation function for {delta}E(t). They also will determine whether fluctuations in the nonradiative component {gamma}Formula of the lifetime decay has a different origin, fluctuations in distance for example
Three applications of path integrals: equilibrium and kinetic isotope effects, and the temperature dependence of the rate constant of the [1,5] sigmatropic hydrogen shift in (Z)-1,3-pentadiene
Recent experiments have confirmed the importance of nuclear quantum effects
even in large biomolecules at physiological temperature. Here we describe how
the path integral formalism can be used to describe rigorously the nuclear
quantum effects on equilibrium and kinetic properties of molecules.
Specifically, we explain how path integrals can be employed to evaluate the
equilibrium (EIE) and kinetic (KIE) isotope effects, and the temperature
dependence of the rate constant. The methodology is applied to the [1,5]
sigmatropic hydrogen shift in pentadiene. Both the KIE and the temperature
dependence of the rate constant confirm the importance of tunneling and other
nuclear quantum effects as well as of the anharmonicity of the potential energy
surface. Moreover, previous results on the KIE were improved by using a
combination of a high level electronic structure calculation within the
harmonic approximation with a path integral anharmonicity correction using a
lower level method.Comment: 9 pages, 4 figure
Kinetics and mechanism of proton transport across membrane nanopores
We use computer simulations to study the kinetics and mechanism of proton
passage through a narrow-pore carbon-nanotube membrane separating reservoirs of
liquid water. Free energy and rate constant calculations show that protons move
across the membrane diffusively in single-file chains of hydrogen-bonded water
molecules. Proton passage through the membrane is opposed by a high barrier
along the effective potential, reflecting the large electrostatic penalty for
desolvation and reminiscent of charge exclusion in biological water channels.
At neutral pH, we estimate a translocation rate of about 1 proton per hour and
tube.Comment: 4 pages, 4 figure
A network model to investigate structural and electrical properties of proteins
One of the main trend in to date research and development is the
miniaturization of electronic devices. In this perspective, integrated
nanodevices based on proteins or biomolecules are attracting a major interest.
In fact, it has been shown that proteins like bacteriorhodopsin and azurin,
manifest electrical properties which are promising for the development of
active components in the field of molecular electronics. Here we focus on two
relevant kinds of proteins: The bovine rhodopsin, prototype of GPCR protein,
and the enzyme acetylcholinesterase (AChE), whose inhibition is one of the most
qualified treatments of Alzheimer disease. Both these proteins exert their
functioning starting with a conformational change of their native structure.
Our guess is that such a change should be accompanied with a detectable
variation of their electrical properties. To investigate this conjecture, we
present an impedance network model of proteins, able to estimate the different
electrical response associated with the different configurations. The model
resolution of the electrical response is found able to monitor the structure
and the conformational change of the given protein. In this respect, rhodopsin
exhibits a better differential response than AChE. This result gives room to
different interpretations of the degree of conformational change and in
particular supports a recent hypothesis on the existence of a mixed state
already in the native configuration of the protein.Comment: 25 pages, 12 figure
First-principles calculations of the structural, electronic, vibrational and magnetic properties of C_{60} and C_{48}N_{12}: a comparative study
In this work, we perform first-principles calculations of the structural,
electronic, vibrational and magnetic properties of a novel azafullerene. Full geometrical optimization shows that is characterized by several distinguishing features: only
one nitrogen atom per pentagon, two nitrogen atoms preferentially sitting in
one hexagon, symmetry, 6 unique nitrogen-carbon and 9 unique
carbon-carbon bond lengths. The highest occupied molecular orbital of is a doubly degenerate level of symmetry and its
lowest unoccupied molecular orbital is a nondegenerate level of
symmetry. Vibrational frequency analysis predicts that has in total 116 vibrational modes: 58 infrared-active and 58
Raman-active modes. is also characterized by 8
and 2 NMR spectral signals. Compared to , shows an enhanced third-order optical
nonlinearities which implies potential applications in optical limiting and
photonics.Comment: a long version of our manuscript submitted to J.Chem.Phy
GPU.proton.DOCK: Genuine Protein Ultrafast proton equilibria consistent DOCKing
GPU.proton.DOCK (Genuine Protein Ultrafast proton equilibria consistent DOCKing) is a state of the art service for in silico prediction of proteinâprotein interactions via rigorous and ultrafast docking code. It is unique in providing stringent account of electrostatic interactions self-consistency and proton equilibria mutual effects of docking partners. GPU.proton.DOCK is the first server offering such a crucial supplement to protein docking algorithmsâa step toward more reliable and high accuracy docking results. The code (especially the Fast Fourier Transform bottleneck and electrostatic fields computation) is parallelized to run on a GPU supercomputer. The high performance will be of use for large-scale structural bioinformatics and systems biology projects, thus bridging physics of the interactions with analysis of molecular networks. We propose workflows for exploring in silico charge mutagenesis effects. Special emphasis is given to the interface-intuitive and user-friendly. The input is comprised of the atomic coordinate files in PDB format. The advanced user is provided with a special input section for addition of non-polypeptide charges, extra ionogenic groups with intrinsic pKa values or fixed ions. The output is comprised of docked complexes in PDB format as well as interactive visualization in a molecular viewer. GPU.proton.DOCK server can be accessed at http://gpudock.orgchm.bas.bg/
Modified reaction centers from Rhodobacter sphaeroides R26
Incubation of photosynthetic reaction centers from Rhodobacter sphaeroides R26 with exogenous 132-OH-bacteriochlorophyll ap or aGG according to Scheer et al. (1987) results in the exchange of endogenous bacteriochlorophyll ap. The exchange amounts to less-than-or-equals, slant 50% according to HPLC analysis, corresponding to a complete replacement of the âmonomericâ bacteriochlorophylls, bm and bl, by exogenous pigment. The absorption spectra show small, but distinct changes in the Qx-region of the bacteriochlorophylls, and bleaching of the modified reaction centers is retained. The corresponding binding sites must be accessible from the exterior, and allow for the introduction of a polar residue at C-132. This is supported by the observation of side reactions of the endogenous âmonomericâ bacteriochlorophylls within the reaction center pigments, e.g. epimerization and hydroxylation at C-132
Dynamical transition, hydrophobic interface, and the temperature dependence of electrostatic fluctuations in proteins
Molecular dynamics simulations have revealed a dramatic increase, with
increasing temperature, of the amplitude of electrostatic fluctuations caused
by water at the active site of metalloprotein plastocyanin. The increased
breadth of electrostatic fluctuations, expressed in terms of the reorganization
energy of changing the redox state of the protein, is related to the formation
of the hydrophobic protein/water interface allowing large-amplitude collective
fluctuations of the water density in the protein's first solvation shell. On
the top of the monotonic increase of the reorganization energy with increasing
temperature, we have observed a spike at 220 K also accompanied by a
significant slowing of the exponential collective Stokes shift dynamics. In
contrast to the local density fluctuations of the hydration-shell waters, these
spikes might be related to the global property of the water solvent crossing
the Widom line.Comment: 9 pages, 8 figure
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