1,721,232 research outputs found
Polaritonic Chemistry: Hindering and Easing Ground State Polyenic Isomerization via Breakdown of σ-π Separation
Full text linkThe ground state conformational isomerization in polyenes is a symmetry allowed process. Its low energy barrier is governed by electron density transfer from the formal single bond that is rotated to the nearby formal double bonds. Along the reaction pathway, the transition state is therefore destabilized. The rules of polaritonic chemistry, i.e., chemistry in a nanocavity with reflecting windows, are barely beginning to be laid out. The standing electric field of the nanocavity couples strongly with the molecular wave function and modifies the potential energy curve in unexpected ways. A quantum electrodynamics approach, applied to the torsional degree of freedom of the central bond of butadiene, shows that formation of the polariton mixes the sigma-pi frameworks thereby stabilizing/destabilizing the planar, reactant-like conformations. The values of the fundamental mode of the cavity field used in the absence of the cavity do not trigger this mechanism
Hydrodynamic fluctuations in the presence of one parameter Mittag-Leffler friction
Full text linkThe effects of hydrodynamic fluctuations on the subdiffusive motion of a particle subject to one parameter Mittag-Leffler friction are examined by means of the fractional Langevin equation. The particle experiences an overall additive colored noise formed by, on the one hand, the hydrodynamic back flow effects and, on the other hand, an additional contribution predicted by fluctuation dissipation relation. Particle motion may or may not be subject to a restoring force. All possible combinations of forces exerted on the test particle are being studied, and for each of them the generalized response function in terms of multinomial Mittag-Leffler functions is provided. Mean square displacement, normalized velocity and position auto-correlation functions are furnished as special cases of the generalized response function, and their short and long time limits are analytically given. In addition, for the same measures analytical expressions valid for time windows much broader than the usual asymptotic limit are provided, and can be used to fit real life data. We demonstrate that normalized velocity and position auto-correlation functions are the main sources providing information on the effect of hydrodynamic fluctuations on particle motion. Actually, they oppose to friction and to restoring force, and smooth out the anti-persistent character of the motion
Electric-field perturbations of ring currents in π systems
No full textIpsocentric distributed-gauge calculations are used to map differential ring currents induced in [4n+2] and [4n] π systems by simultaneous application of an axial magnetic and electric field (field gradient). In benzene, electric fields and gradients produce stratified first-order π ring currents, opposing/reinforcing the intrinsic diatropic current, according to the height profile of charge depletion/enhancement induced by the electric perturbation. In (planarised) cyclooctatetraene, action of a uniform electric field is similarly rationalised, but response to the (totally symmetric) field gradient is dominated by a specific orbital effect, closing/widening of the small HOMO-LUMO gap leading to reinforcement/reduction of the intrinsic paratropic current. © 2005 Elsevier B.V. All rights reserved
Role of the intracellular cavity in potassium channel conductivity
No full textThe role of several fragments of the potassium channel KcsA has been examined by the Poisson-Nernst-Planck (PNP) theory. The efficiency of the computational method allowed comparing a large number of channel models, with different intracellular gate openings, partial atomic charges, and amino acid sequences. Perhaps counter-intuitively, the calculated ion current decreases when the mean radius of the entrance cavity increases. Widening of the vestibule, in fact, increases the volume accessible to water, which is the volume with a high dielectric constant. In turn, water screens the attractive charges of the P-loop backbone. The backbone charges of the M2 helixes instead oppose the entrance of potassium ions through a complicated mechanism that can be separated in the activity of two interfering dipoles. The conductance of the KcsA models increased when two neutral residues in M2 were mutated to glutamic acid, in agreement with experimental results (Brelidze, T. I.; Niu, X.; Magleby, K. L. PNAS 2003, 100, 9017-9022). As a general conclusion, a relation between channel conductance and potassium concentration in the intracellular cavity emerged. Although the ion transport is the result of the fine balance of a number of different effects, the experimental results can be reproduced quantitatively only on the basis of electrostatic forces, which are the only driving forces modeled by the PNP theory
Dynamic Self-Organization and Catalysis: Periodic versus Random Driving Forces
No full textDynamic
self-assembly is an emerging area of research where properly
designed self-assembly elements can be used reversibly to trigger
and control some tasks at the molecular level. The interactions between
decorated nanoparticles, NPs, are experimentally modifiable by a variety
of stimuli that can also vary in time periodically or randomly. In
coarse-grained simulations, we activate a switch, either periodically
or randomly, which assembles–disassembles clusters of NPs.
We then introduce a single catalytic NP(C) covered with catalytic
moieties, C, and leave all remaining NP(R)s decorated with reactive
moieties, R. The catalytic reaction that converts R into products
P depends on the encounter of C and R. Particle-based simulations
are here used to study the catalytic activity and reaction yields
of decorated nanoparticles that aggregate/disaggregate with the application
of time-varying perturbations. Static aggregation is not catalytically
efficient because it traps the catalyst. The application of random
perturbations that vary in time in the form of colored noises improves
the reaction yields and can provide opportunities for more efficient
catalytic activity. The work can also allow us to understand how in
Nature many biological processes are affected or driven by random/noisy
fluctuations of the environment
Exploiting Blood Transport Proteins as Carborane Supramolecular Vehicles for Boron Neutron Capture Therapy
Full text linkCarboranes are promising agents for applications in boron neutron capture therapy (BNCT), but their hydrophobicity prevents their use in physiological environments. Here, by using reverse docking and molecular dynamics (MD) simulations, we identified blood transport proteins as candidate carriers of carboranes. Hemoglobin showed a higher binding affinity for carboranes than transthyretin and human serum albumin (HSA), which are well-known carborane-binding proteins. Myoglobin, ceruloplasmin, sex hormone-binding protein, lactoferrin, plasma retinol-binding protein, thyroxine-binding globulin, corticosteroid-binding globulin and afamin have a binding affinity comparable to transthyretin/HSA. The carborane@protein complexes are stable in water and characterized by favorable binding energy. The driving force in the carborane binding is represented by the formation of hydrophobic interactions with aliphatic amino acids and BH-π and CH-π interactions with aromatic amino acids. Dihydrogen bonds, classical hydrogen bonds and surfactant-like interactions also assist the binding. These results (i) identify the plasma proteins responsible for binding carborane upon their intravenous administration, and (ii) suggest an innovative formulation for carboranes based on the formation of a carborane@protein complex prior to the administration
CNT-Catalyzed Oxidative Dehydrogenation of Ethylbenzene to Styrene: DFT Calculations Disclose the Pathways
No full textOxygen atoms, in the form of epoxy or carbonyl groups present at the edges of carbon nanotubes, trigger oxidative dehydrogenation of ethylbenzene to styrene. DFT calculations reveal that the process can occur along three pathways. The first two bifurcate from the initial transformation of an epoxide into a hydroxyl group, which occurs via a biradical transition state and the formation of a benzyl-like intermediate. The epoxide can further react to release styrene and form a water molecule, as observed experimentally, via a highly exothermic process. Alternatively, in the presence of a second adjacent epoxide, styrene is also produced without water formation along a less exothermic pathway that leaves two hydroxyl groups on the nanotube surface. Along the third pathway, two adjacent carbonyl groups (quinone functionality) also promote the formation of styrene, with energy barriers similar to those calculated in the presence of epoxy groups. These are in the range 36–37 kcal mol −1 . These values that can be easily surmounted at the working temperature used in the experiment (between 450 and 550 °C)
Oriented External Electric Fields Affect Rate and Stereoselectivity of Electrocyclic Reactions
No full textWe carried out a computational investigation at the density functional theory (M06-2X) level on the effects of oriented external electric fields (OEEF) on activation barriers and stereochemical output of the thermal ring opening of 3-substituted cyclobutenes (C4H5X) to butadienes. It is well known that with π-electron-donor substituents (X = CH3, NH2), the conrotatory outward rotation is preferred, while with π-electron-acceptor substituents (X = CHO, NO, BH2), the conrotatory inward process becomes favored. In the presence of the OEEF applied along the three axes x, y, and z in either positive or negative direction, for both π-donor and π-acceptor substituents, we observed either catalysis or inhibition. Both effects were consistent with the change of the induced dipole along the direction of the applied field. An interesting effect was observed for X = CHO and NO. The simultaneous catalysis and inhibition of the outward and inward transformation leads to a reversed ratio between outward and inward transformation, with the former being favored (stereochemical inversion). Such effect was not observed for X = BH2 (the strongest π-acceptor examined here). In this case, in the absence of the applied field, the difference between the inward and outward barriers is too large and the simultaneous catalysis and inhibition of the outward and inward transformation is not capable of determining the stereochemical inversion
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