Descripción: Recent experimental and theoretical methods allowed the efficient investigation of highly excited rovibrational states of molecular systems. At these levels of excitation the correspondence principle holds, and then classical mechanics can provide intuitive views of the involved processes. In this respect, we have recently shown that for completely hyperbolic systems, homoclinic motions, which are known to organize the classical chaotic region in Hamiltonian systems, imprint a clear signature in the corresponding highly excited quantum spectra. In this Communication we show that this result also holds in mixed systems, by considering an application to the floppy LiNCLiCN molecular system. © 2005 American Institute of Physics.

Descripción: This paper describes a matrix formulation for the correlated hole theory within the framework of the domain-averaged model in many electron systems (atoms, molecules, condensed matter, etc.). General relationships between this quantity and one-particle reduced density matrices for any independent particle or correlated state functions are presented. This formulation turns out to be suitable for computational purposes due to the straightforward introduction of cumulants of two-particle reduced density matrices within the quantum field structure. Numerical calculations in selected simple molecular systems have been performed in order to determine preliminary correlated values for such a quantity.

Descripción: In this paper we propose a functional of the many-body cumulant of the second-order reduced density matrix within the spin-free formalism of quantum chemistry which quantifies the idea of electron correlation and allows one to detect spin entanglement. Its properties are rigorously stated and discussed for spin-adapted pure states. Numerical determinations are performed for both equilibrium conformations and dissociation processes in molecular systems. © 2010 American Institute of Physics.

Descripción: A novel appropriate definition for the density matrix for an interacting Coulombic driven atomic or molecular system with non-integer number of particles is given. Our approach leads to a direct derivation of the proposal reported by Perdew [Phys. Rev. Lett. 49, 1691 (1982)]10.1103/PhysRevLett.49.1691 and points out its suitability and perspective advances. © 2012 American Institute of Physics.

Descripción: Grand-canonical like descriptions of many electron atomic and molecular open systems which are characterized by a non-integer number of electrons are presented. Their associated reduced density matrices (RDMs) are obtained by introducing the contracting mapping for this type of distributions. It is shown that there is loss of information when connecting RDMs of different order by partial contractions. The energy convexity property of these systems simplifies the description. Consequently, this formulation opens the possibility to a new look for chemical descriptors such as chemical potential and reactivity among others. Examples are presented to discuss the theoretical aspects of this work. © 2013 AIP Publishing LLC.

Descripción: This article is a continuation of our previous paper on schemes of energy decompositions of molecular systems in the real space [D. R. Alcoba, J. Chem. Phys. 122, 074102 (2005)] now using correlated state functions. We study, according to physical arguments, the appropriate management of the density cumulant arising from the second-order reduced density matrix at correlated level, whose contributions can be assigned to one-center or to two-center terms in the energy partitioning. Our treatments are applied within two physical space partitioning schemes: the Bader partitioning into atomic basins and the fuzzy atom procedure. The results obtained in selected molecules are analyzed and discussed in detail. © 2007 American Institute of Physics.

Descripción: This work describes simple decompositions of the energy of molecular systems according to schemes that partition the three-dimensional space. The components of those decompositions depend on one and two atomic domains thus providing a meaningful chemical information about the nature of different bondings among the atoms which compose the system. Our algorithms can be applied at any level of theory (correlated or uncorrelated wave functions). The results reported here, obtained at the Hartree-Fock level in selected molecules, show a good agreement with the chemical picture of molecules and require a low computational cost in comparison with other previously reported decompositions.

Descripción: This work studies the partitioning of the electron density into two contributions which are interpreted as the paired and the effectively unpaired electron densities. The topological features of each density field as well as of the total density are described localizing the corresponding critical points in simple selected molecules (local formalism). The results show that unpaired electron-density concentrations occur out of the topological bonding regions whereas the paired electron densities present accumulations inside those regions. A comparison of these results with those arising from population analysis techniques (nonlocal or integrated formalisms) is reported. © 2005 American Institute of Physics.

Descripción: 1. 1. By chromatography through Sephadex G-200 of increasing amounts of partially purified pig liver ALA-D, different profiles were obtained, showing that species of molecular weights ranging from 140,000 to 560,000 might exist in equilibrium, but their relative ratio was dependent on the total amount of protein sampled. In all cases, however, the main peak (60-70%) corresponded to the 280,000 MW oligomer, that is the octamer. 2. 2. It was found that elution profiles were also dependent on column dimensions and on the purity of the enzyme preparation. 3. 3. K+ ions affected both catalytic activity and aggregation of the enzyme. 4. Results here reported add further support to the proposal of the existence of a minimal functional dimer. © 1980.

Descripción: Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such a continuum approach in a density functional theory framework using plane-wave basis sets and periodic boundary conditions. Our work stems from a recent model designed for Car-Parrinello simulations of quantum solutes in a dielectric medium [D. A. Scherlis, J. Chem. Phys. 124, 074103 (2006)], for which the permittivity of the solvent is defined as a function of the electronic density of the solute. This strategy turns out to be inadequate for systems extended in two dimensions: the dependence of the dielectric function on the electronic density introduces a new term in the Kohn-Sham potential, which becomes unphysically large at the interfacial region, seriously affecting the convergence of the self-consistent calculations. If the dielectric medium is properly redefined as a function of the atomic coordinates, a good convergence is obtained and the constant of motion is conserved during the molecular dynamics simulations. The Poisson problem is solved using a multigrid method, and in this way Car-Parrinello molecular dynamics simulations of solid-liquid interfaces can be performed at a very moderate computational cost. This scheme is employed to investigate the acid-base equilibrium at the TiO2 -water interface. The aqueous behavior of titania surfaces has stimulated a large amount of experimental research, but many open questions remain concerning the molecular mechanisms determining the chemistry of the interface. Here we make an attempt to answer some of them, putting to the test our continuum model. © 2009 American Institute of Physics.

Descripción: An information theory description of finite systems explicitly evolving in time is presented. We impose a MaxEnt variational principle on the Shannon entropy at a given time while the constraints are set at a former time. The resulting density matrix contains explicit time odd components in the form of collective flows. As a specific application we consider the dynamics of the expansion in connection with heavy ion experiments. Lattice gas and classical molecular dynamics simulations are shown. © 2007 American Institute of Physics.

Descripción: We investigate classical Hamiltonian models for particles interacting with steep differential repulsive barriers both in coordinate and momentum space. The final aim is to define a classical system of many particles behaving as fermions in many respects. In this paper we examine the appearance of the phase portrait of one- or two-particle systems to skim the essential features that would later be transcribed to the basic rules of a molecular dynamics algorithm. One of the remarkable properties of the phase portrait is the flow from states that start far away with a wide range of momentum towards a narrow region in momentum-a virtual locking of momentum-in the vicinity of the steepest part of the barrier in momentum space. The central ideas are developed through two examples in one and two dimensions. © 1995 The American Physical Society.

Descripción: In this work we studied the effect of NaCl on the thermodynamic and dynamic properties of supercooled water, for salt concentrations between 0.19 and 1.33mol kg-1, using molecular dynamic simulations for TIP5PE water model and ion parameters specially designed to be used in combination with this potential. We studied the isobaric heat capacity (Cp) temperature dependence and observed a maximum in Cp, occurring at Tm, that moves to lower temperature values with increasing salt concentration. Many characteristic changes were observed at scaled temperature TTm ∼ 0.96, namely a minimum in the density of the system, a reduction of the slope of the number of hydrogen bonds vs. temperature, and a crossover from Vogel-Tamman-Fulcher to Arrhenius dynamics. Finally, at low temperatures we observed that water dynamics become heterogeneous with an apparently common relationship between the fraction of immobile molecules and T/Tm for all studied systems. © 2011 American Institute of Physics.

Descripción: The photophysical behaviour of phloxine B adsorbed onto microcrystalline cellulose was evaluated by reflectance spectroscopy and laser induced time-resolved luminescence in the picosecond-nanosecond and microsecond- millisecond ranges. Analysis of the absorption spectral changes with concentration points to a small tendency of the dye to aggregate in the range of concentrations under study. Prompt fluorescence, phosphorescence and delayed fluorescence spectral decays were measured at room temperature and 77 K, without the need of sample degassing because cellulose protects triplet states from oxygen quenching. In all cases, spectral changes with time and lifetime distribution analysis were consistent with the dye coexisting in two different environments: dyes tightly entrapped between polymer chains in crystalline regions of cellulose showed longer fluorescence and phosphorescence lifetimes and more energetic triplet states, while dyes adsorbed in more amorphous regions of the support showed shorter lifetimes and less energetic triplet states. This behaviour is discussed in terms of the different dye-support interactions in both kinds of adsorption sites.

Descripción: The competition between chemical equilibrium, for example protonation, and physical interactions determines the molecular organization and functionality of biological and synthetic systems. Charge regulation by displacement of acid-base equilibrium induced by changes in the local environment provides a feedback mechanism that controls the balance between electrostatic, van der Waals, steric interactions and molecular organization. Which strategies do responsive systems follow to globally optimize chemical equilibrium and physical interactions? We address this question by theoretically studying model layers of end-grafted polyacids. These layers spontaneously form self-assembled aggregates, presenting domains of controlled local pH and whose morphologies can be manipulated by the composition of the solution in contact with the film. Charge regulation stabilizes micellar domains over a wide range of pH by reducing the local charge in the aggregate at the cost of chemical free energy and gaining in hydrophobic interactions. This balance determines the boundaries between different aggregate morphologies. We show that a qualitatively new form of organization arises from the coupling between physical interactions and protonation equilibrium. This optimization strategy presents itself with polyelectrolytes coexisting in two different and well-defined protonation states. Our results underline the need of considering the coupling between chemical equilibrium and physical interactions due to their highly nonadditive behavior. The predictions provide guidelines for the creation of responsive polymer layers presenting self-organized patterns with functional properties and they give insights for the understanding of competing interactions in highly inhomogeneous and constrained environments such as those relevant in nanotechnology and those responsible for biological cells function.

Descripción: Lipid-protein interactions play an essential role in the regulation of biological function of integral membrane proteins; however, the underlying molecular mechanisms are not fully understood. Here we explore the modulation by phospholipids of the enzymatic activity of the plasma membrane calcium pump reconstituted in detergent-phospholipid mixed micelles of variable composition. The presence of increasing quantities of phospholipids in the micelles produced a cooperative increase in the ATPase activity of the enzyme. This activation effect was reversible and depended on the phospholipid/detergent ratio and not on the total lipid concentration. Enzyme activation was accompanied by a small structural change at the transmembrane domain reported by 1-aniline-8-naphtalenesulfonate fluorescence. In addition, the composition of the amphipilic environment sensed by the protein was evaluated by measuring the relative affinity of the assayed phospholipid for the transmembrane surface of the protein. The obtained results allow us to postulate a two-stage mechanistic model explaining the modulation of protein activity based on the exchange among non-structural amphiphiles at the hydrophobic transmembrane surface, and a lipid-induced conformational change. The model allowed to obtain a cooperativity coefficient reporting on the efficiency of the transduction step between lipid adsorption and catalytic site activation. This model can be easily applied to other phospholipid/detergent mixtures as well to other membrane proteins. The systematic quantitative evaluation of these systems could contribute to gain insight into the structure-activity relationships between proteins and lipids in biological membranes. © 2012 Dodes Traian et al.

Descripción: 1. 1. Gel filtration on Sephadex G-100 and Sepharose 4B were used to redetermine the molecular weight (MW) of porphobilinogenase, deaminase and isomerase purified from different sources, and determine the MW of these enzymes purified from Eugtena gracilis. 2. 2. Results reported here, indicate that porphobilinogenase can be found, into three different molecular forms, tetramers, dimers and monomers according to the source organism. 3. 3. It is proposed that minimal functional structure of PBGase is a hybrid protomer of MW 25,000, composed by two different domains, in a ratio of 1 mol of deaminase, MW 20,000 to 1 mol of isomerase. MW 5000. 4. 4. A model explaining the occurrence of different MW species of PBGase in nature and the possible interconversion among the various forms is postulated. © 1980.

Descripción: Although cyclophilin A (CyP-A) is a relatively abundant small immunophilin present in the cytoplasm of all mammalian cells, its general function(s) in the absence of the immunosuppressant drug cyclosporin A is not known. In contrast, the high molecular weight hsp90-binding immunophilins appear to play a role in protein trafficking in that they have been shown to link glucocorticoid receptor-hsp90 and p53-hsp90 complexes to the dynein motor protein for retrograde movement along microtubules. These immunophilins link to cytoplasmic dynein indirectly through the association of the immunophilin peptidylprolyl isomerase (PPIase) domain with dynamitin, a component of the dynein-associated dynactin complex (Galigniana, M. D., Harrell, J. M., O'Hagen, H. M., Ljungman, M., and Pratt, W. B. (2004) J. Biol. Chem. 279, 22483-22489). Here, we show that CyP-A exists in native heterocomplexes containing cytoplasmic dynein that can be formed in cell-free systems. Prolyl isomerase activity is not required for forming the dynein complex, but the PPIase domain fragment of FKBP52 blocks complex formation and CyP-A binds to dynamitin in a PPIase domain-dependent manner. CyP-A heterocomplexes containing tubulin and dynein can be formed in cytosol prepared under microtubule-stabilizing conditions, and CyP-A colocalizes in mouse fibroblasts with microtubules. Colocalization with microtubules is disrupted by overexpression of the PPIase domain fragment. Thus, we conclude that CyP-A associates in vitro and in vivo with the dynein/dynactin motor protein complex and we suggest that CyP-A may perform a general function related to the binding of cargo for retrograde movement along microtubules.

Descripción: A computational scheme was developed for a fourth-rank hyprmagnetizability tensor denoted by Xαβγδ. It was shown that this instrinsic property of diamagnetic atoms and molecules was useful to rationalize their nonlinear response to intense magnetic field. The terms connected with the fourth power of the perturbing field which represent the fourth-rank hypermagnetizability of the H2, HF, H2O, NH3, and CH4 molecules were evaluated at the coupled Hartree-Fock level of accuracy. The Gaugeless basis sets of increasing size and flexibility that adopted two different coordinate systems to estimate the degree of convergence of theoretical tensor components was employed.