222 research outputs found
Hydrophobic aggregation and collective absorption of dioxin into lipid membranes: insights from atomistic simulations
Dioxins are a highly toxic class of chlorinated aromatic chemicals. They have been extensively studied, but several molecular-level details of their action are still missing. Here we present molecular dynamics simulations of their absorption and diffusion through cell membranes. We show that, due to their hydrophobic character, dioxins can quickly penetrate into a lipid membrane, both as single molecules and as aggregates. We find clear evidence for their ability to accumulate in cell membranes. Our free energy calculations indicate that subsequent transport into the cell is unlikely to be a simple diffusive process
Hydrogen Bonds Involving Metal Centers
Vodikova veza u kojoj atom metala sudjeluje kao donor ili akceptor vodika samo je jedan oblik interakcije vodika s metalnim centrom, pa je stoga vodikovu vezu s metalom teško razlikovati od drugih vodikovih interakcija, posebice agostičkih. U ovom pregledu razmatraju se specifična obilježja vodikovih veza u kojima sudjeluje metal, i to sa stajališta strukturne kemije te molekularne spektroskopije (IR, NMR). Prikazane su vodikove veze tipa M···H-D i M-H···A u kompleksima teških metala (Pt, Pd, Ir, Co, Rh, Ni, Cu, Ag, Os) s aromatskim (naftalenskim, kinuklidinskim, benzokinolinskim) i nearomatskim ligandima (ugljikov monoksid, tricijanofosfin) kao i u sendvičnim i polusendvičnim spojevima.Hydrogen bonds involving metal center as a hydrogen donor or hydrogen acceptor are only a specific type of metal-hydrogen interactions; it is therefore not easy to differentiate hydrogen bond from other metal-hydrogen interactions, especially agostic ones. The first part of the review is therefore devoted to the results of structural chemistry and molecular spectroscopy (NMR, IR), as a tool for differentiating hydrogen bondings from other hydrogen interactions. The classical examples of Pt···H-N, Pt···H-O, Pt···H-C, and Pd···H-N hydrogen bonds were discussed as well as hydrogen bonds involving half-sandwich complexes (η5-C5R5)ML2, where M stays for Co, Ir or Rh, R for H or CH3, and L for CO, PMe3 or C2H4. The paper deals also with metal donating (M-H···A) and bifurcated hydrogen bonds. The hydrogen interactions in complexes of other heavy metals (Ni, Cu, Ag, Os) were also briefly discussed
Hydrogen Bonds Involving Metal Centers
Vodikova veza u kojoj atom metala sudjeluje kao donor ili akceptor vodika samo je jedan oblik interakcije vodika s metalnim centrom, pa je stoga vodikovu vezu s metalom teško razlikovati od drugih vodikovih interakcija, posebice agostičkih. U ovom pregledu razmatraju se specifična obilježja vodikovih veza u kojima sudjeluje metal, i to sa stajališta strukturne kemije te molekularne spektroskopije (IR, NMR). Prikazane su vodikove veze tipa M···H-D i M-H···A u kompleksima teških metala (Pt, Pd, Ir, Co, Rh, Ni, Cu, Ag, Os) s aromatskim (naftalenskim, kinuklidinskim, benzokinolinskim) i nearomatskim ligandima (ugljikov monoksid, tricijanofosfin) kao i u sendvičnim i polusendvičnim spojevima.Hydrogen bonds involving metal center as a hydrogen donor or hydrogen acceptor are only a specific type of metal-hydrogen interactions; it is therefore not easy to differentiate hydrogen bond from other metal-hydrogen interactions, especially agostic ones. The first part of the review is therefore devoted to the results of structural chemistry and molecular spectroscopy (NMR, IR), as a tool for differentiating hydrogen bondings from other hydrogen interactions. The classical examples of Pt···H-N, Pt···H-O, Pt···H-C, and Pd···H-N hydrogen bonds were discussed as well as hydrogen bonds involving half-sandwich complexes (η5-C5R5)ML2, where M stays for Co, Ir or Rh, R for H or CH3, and L for CO, PMe3 or C2H4. The paper deals also with metal donating (M-H···A) and bifurcated hydrogen bonds. The hydrogen interactions in complexes of other heavy metals (Ni, Cu, Ag, Os) were also briefly discussed
Early Stages of Homopolymer Collapse
Interest in the protein folding problem has motivated a wide range of
theoretical and experimental studies of the kinetics of the collapse of
flexible homopolymers. In this Paper a phenomenological model is proposed for
the kinetics of the early stages of homopolymer collapse following a quench
from temperatures above to below the theta temperature. In the first stage,
nascent droplets of the dense phase are formed, with little effect on the
configurations of the bridges that join them. The droplets then grow by
accreting monomers from the bridges, thus causing the bridges to stretch.
During these two stages the overall dimensions of the chain decrease only
weakly. Further growth of the droplets is accomplished by the shortening of the
bridges, which causes the shrinking of the overall dimensions of the chain. The
characteristic times of the three stages respectively scale as the zeroth, 1/5
and 6/5 power of the the degree of polymerization of the chain.Comment: 11 pages, 3 figure
Pyrazolium- versus imidazolium-based ionic liquids: Structure, dynamics and physicochemical properties
Ionic liquids (ILs) composed of two different pyrazolium cations with dicyanamide and bis(trifluoromethanesulfonyl)imide anions have been synthesized and characterized by NMR, Kamlet-Taft solvatochromic parameters, conductivity and rheological measurements, as well as ab initio calculations. Density functional calculations for the two pyrazolium cations, 1-butyl-2- methylpyrazolium [bmpz] and 1-butyl-2,3,5-trimethylpyrazolium [bm 3pz], provide a full picture of their conformational states. Homo- and heteronuclear NOE show aggregation motives sensitive to steric hindrance and the anions' nature. Self-diffusion coefficients D for the anion and the cation have been measured by pulsed field gradient spin-echo NMR (PGSE-NMR). The ionic diffusivity is influenced by their chemical structure and steric hindrance, giving the order Dcation > Danion for all of the examined compounds. The measured ion diffusion coefficients, viscosities, and ionic conductivity follow the Vogel-Fulcher-Tammann (VFT) equation for the temperature dependencies, and the best-fit parameters have been determined. Solvatochromic parameters indicate an increased ion association upon going from bis(trifluoromethanesulfonyl)imide to dicyanamide-based pyrazolium salts, as well as specific hydrogen bond donor capability of H atoms on the pyrazolium ring. All of these physical properties are compared to those of an analogous series of imidazolium-based ILs
Electron transport in crystalline PCBM-like fullerene derivatives: a comparative computational study
We present an extensive study of electron transport (ET) in several crystal forms of phenyl-C61-butyric acid methyl ester (PCBM) and 1-thienyl-C61-butyric acid methyl ester (ThCBM) fullerene derivatives. Our calculations are based on a localized representation of the electronic states. Orbital couplings, site energies and reorganization energies have been calculated using various density functional and semi-empirical techniques and used within the Landau–Zener, Marcus and Marcus–Levich–Jortner expressions to evaluate electron transfer rates. Electron mobilities have been then estimated by kinetic Monte Carlo (KMC) simulations. The adiabaticity of electron transfer directions within the different crystal structures has also been verified using the Landau–Zener expression. Finally, the role of low energy virtual orbitals of the fullerene molecules has been investigated using charge transport networks of increasing complexities. Our results show that these molecules may form one-, two- or three-dimensional percolation networks and that their higher energy orbitals often participate in ET. The highest mobility values were obtained for the crystal structure of ThCBM and are comparable to experimental values
An integral equation approach to effective interactions between polymers in solution
We use the thread model for linear chains of interacting monomers, and the
``polymer reference interaction site model'' (PRISM) formalism to determine the
monomer-monomer pair correlation function for dilute and
semi-dilute polymer solutions, over a range of temperatures from very high
(where the chains behave as self-avoiding walks) to below the
temperature, where phase separation sets in. An inversion procedure, based on
the HNC integral equation, is used to extract the effective pair potential
between ``average'' monomers on different chains. An accurate relation between
, [the pair correlation function between the polymer
centers of mass (c.m.)], and the intramolecular form factors is then used to
determine , and subsequently extract the effective c.m.-c.m. pair
potential by a similar inversion procedure. depends on
temperature and polymer concentration, and the predicted variations are in
reasonable agreement with recent simulation data, except at very high
temperatures, and below the temperature.Comment: 13 pages, 13 figures, revtex ; revised versio
Sensing with the Motor Cortex
The primary motor cortex is a critical node in the network of brain regions responsible for voluntary motor behavior. It has been less appreciated, however, that the motor cortex exhibits sensory responses in a variety of modalities including vision and somatosensation. We review current work that emphasizes the heterogeneity in sensorimotor responses in the motor cortex and focus on its implications for cortical control of movement as well as for brain-machine interface development
Ready Both to Your and to My Hands: Mapping the Action Space of Others
To date, mutual interaction between action and perception has been investigated mainly by focusing on single individuals. However, we perceive affording objects and acts upon them in a surrounding world inhabited by other perceiving and acting bodies. Thus, the issue arises as to whether our action-oriented object perception might be modulated by the presence of another potential actor. To tackle this issue we used the spatial alignment effect paradigm and systematically examined this effect when a visually presented handled object was located close either to the perceiver or to another individual (a virtual avatar). We found that the spatial alignment effect occurred whenever the object was presented within the reaching space of a potential actor, regardless of whether it was the participant's own or the other's reaching space. These findings show that objects may afford a suitable motor act when they are ready not only to our own hand but also, and most importantly, to the other's hand. Our proposal is that this effect is likely to be due to a mapping of our own and the other's reaching space and we posit that such mapping could play a critical role in joining our own and the other's action
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