Autonomous University of Mexico State
Cuernavaca, Mexico
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Galindo-Murillo R.,University of Utah | Barroso-Flores J.,Autonomous University of Mexico State
Physical Chemistry Chemical Physics | Year: 2017

In vivo inclusion of unnatural base pairs (UBPs) into functional DNA was recently reported for compounds 2,6-dimethyl-2H-isoquiniline-1-thione (d5SICS, X) and 2-methoxy-3-methylnaphthalene (dNaM, Y) in a modified E. coli strand, for which high-fidelity replication was observed. Yet, little is known about possible genetic consequences they have in largely substituted DNA. Using a converged microsecond long molecular dynamics (MD) simulation of the sequences 5′-GCGCAAXTTGCGC-3′ and 5′-GCGCXAXTXGCGC-3′, where X represents the UBP, we show that in the system with only a single XY UBP pair present, the global RMS deviation from canonical B-DNA in our control simulations is ∼3 and a fully converged ensemble is achieved within 2 s. With three UBPs, deviation increases to ∼5 and convergence is not achieved within 10 s of sampling time. With five UBPs, no convergence is observed and the double helix collapses into a globular structure. A fully optimized structure of the trimer d(GXC) was obtained using the density functional theory method B97D/cc-pVTZ and resulted in an RMSD value of ∼2 when compared to the most populated structure obtained from the MD simulations. Their calculated interaction energy is -3.7 kcal mol-1. It is thus unlikely that d5SICS and dNaM could be useful as tools in DNA manipulation. This theoretical methodology can be used in the de novo design of UBPs. © 2017 the Owner Societies.

Heinze J.,Albert Ludwigs University of Freiburg | Frontana-Uribe B.A.,Autonomous University of Mexico State | Frontana-Uribe B.A.,National Autonomous University of Mexico | Ludwigs S.,Albert Ludwigs University of Freiburg
Chemical Reviews | Year: 2010

A study on electrochemistry of conducting polymers (CP), their persistent models and new concepts was reported. A central point of electrochemical research is the analysis of the doping process, which corresponds to redox reactions in the polymer matrix. Starting with the electrochemical formation mechanism of CPs, it has been clarified that oligomerization occurs in solution in front of the electrode and is preferably based on succeeding dimerization steps of ionic (radicalic) species. Deposition of the oligomers involves nucleation, growth, and solid state coupling processes. The results of the oligomer approach prove that the redox charging of conjugated systems is due to potential-dependent successive redox steps, which may overlap, causing a faradaic plateau current. Conceivable applications such as electrocatalysis, electronic devices, solar cells, or electrochromic windows are just a few challenges which have motivated researchers to refine strategies in preparing materials with tailor-made properties.

Martinez S.S.,Autonomous University of the State of Morelos | Uribe E.V.,Autonomous University of Mexico State
Ultrasonics Sonochemistry | Year: 2012

The degradation of azure B dye (C15H16ClN 3S; AB) has been studied by Fenton, sonolysis and sono-electroFenton processes employing ultrasound at 23 kHz and the electrogeneration of H 2O2 at the reticulated vitreous carbon electrode. It was found that the dye degradation followed apparent first-order kinetics in all the degradation processes tested. The rate constant was affected by both the pH of the solution and initial concentration of Fe2+, with the highest degradation obtained at pH between 2.6 and 3. The first-order rate constant decreased in the following order: sono-electroFenton > Fenton > sonolysis. The rate constant for AB degradation by sono-electroFenton is ∼10-fold that of sonolysis and ∼2-fold the one obtained by Fenton under silent conditions. The chemical oxygen demand was abated ∼68% and ∼85% by Fenton and sono-electroFenton respectively, achieving AB concentration removal over 90% with both processes. © 2011 Elsevier B.V. All rights reserved.

Alejo-Molina A.,Autonomous University of Mexico State | Hingerl K.,Johannes Kepler University | Hardhienata H.,Johannes Kepler University | Hardhienata H.,Bogor Agricultural University
Journal of the Optical Society of America B: Optical Physics | Year: 2015

We report a comprehensive study of the fourth rank tensor describing third harmonic generation (THG) and electric field induced second harmonic (EFISH) in centrosymmetric material from two different viewpoints: group theory and the simplified bond hyperpolarizability model (SBHM). We show that the fourth rank tensor related to THG and direct current EFISH can be reduced to two independent elements, whereas SBHM always gives only one, reproducing perfectly well EFISH experimental results in a metal oxide semiconductor. We argue that it is possible to reduce the fourth rank tensor describing EFISH to a third rank tensor and further deliver a classical explanation of EFISH regarding symmetry breaking, where the term containing r3 in the potential immediately leads to second harmonic generation. © 2015 Optical Society of America.

Mendez-Arroyo J.,Northwestern University | Barroso-Flores J.,Autonomous University of Mexico State | Lifschitz A.M.,Northwestern University | Sarjeant A.A.,Northwestern University | And 2 more authors.
Journal of the American Chemical Society | Year: 2014

A biomimetic, ion-regulated molecular receptor was synthesized via the Weak-Link Approach (WLA). This structure features both a calix[4]arene moiety which serves as a molecular recognition unit and an activity regulator composed of hemilabile phosphine alkyl thioether ligands (P,S) chelated to a Pt(II) center. The host-guest properties of the ion-regulated receptor were found to be highly dependent upon the coordination of the Pt(II) center, which is controlled through the reversible coordination of small molecule effectors. The environment at the regulatory site dictates the charge and the structural conformation of the entire assembly resulting in three accessible binding configurations: one closed, inactive state and two open, active states. One of the active states, the semiopen state, recognizes a neutral guest molecule, while the other, the fully open state, recognizes a cationic guest molecule. Job plots and 1H NMR spectroscopy titrations were used to study the formation of these inclusion complexes, the receptor binding modes, and the receptor binding affinities (Ka) in solution. Single crystal X-ray diffraction studies provided insight into the solid-state structures of the receptor when complexed with each guest molecule. The dipole moments and electrostatic potential maps of the structures were generated via DFT calculations at the B97D/LANL2DZ level of theory. finally, we describe the reversible capture and release of guests by switching the receptor between the closed and semiopen configurations via elemental anion and small molecule effectors. © 2014 American Chemical Society.

Barrera-Diaz C.E.,Autonomous University of Mexico State | Lugo-Lugo V.,Autonomous University of Mexico State | Lugo-Lugo V.,Valle de Toluca University | Bilyeu B.,Xavier University of Louisiana
Journal of Hazardous Materials | Year: 2012

Hexavalent chromium is of particular environmental concern due to its toxicity and mobility and is challenging to remove from industrial wastewater. It is a strong oxidizing agent that is carcinogenic and mutagenic and diffuses quickly through soil and aquatic environments. It does not form insoluble compounds in aqueous solutions, so separation by precipitation is not feasible. While Cr(VI) oxyanions are very mobile and toxic in the environment, Cr(III) cations are not. Like many metal cations, Cr(III) forms insoluble precipitates. Thus, reducing Cr(VI) to Cr(III) simplifies its removal from effluent and also reduces its toxicity and mobility. In this review, we describe the environmental implications of Cr(VI) presence in aqueous solutions, the chemical species that could be present and then we describe the technologies available to efficiently reduce hexavalent chromium. © 2012 Elsevier B.V.

Zarabadi-Poor P.,University of Tehran | Badiei A.,University of Tehran | Yousefi A.A.,Iran Polymer And Petrochemical Institute | Barroso-Flores J.,Autonomous University of Mexico State
Journal of Physical Chemistry C | Year: 2013

The H-acid dye intermediate was successfully attached to the SBA-15 mesoporous silica surface in a two-step modification process. Synthesized materials were characterized using several techniques including Fourier transform infrared spectroscopy, N2 adsorption-desorption measurements, small-angle X-ray scattering, transmission electron microscopy, and thermogravimetric analysis. The fluorescent sensing properties were examined in the final product toward several metal ions and showed high selectivity for Hg2+. Computational studies were performed in order to obtain a detailed electronic description of the quenching mechanism of H-acid fluorescence by Hg2+ as well as studying the structure and bonding in the [H-acid]Hg2+ complex. © 2013 American Chemical Society.

Sanchez J.,Autonomous University of Mexico State | Holmgren J.,Gothenburg University
Indian Journal of Medical Research | Year: 2011

After De ́s pivotal demonstration in 1959 of a diarrhoeogenic exo-enterotoxin in cell-free culture filtrates from Vibrio cholerae (of classical biotype), much insight has been gained about cholera toxin (CT), which is arguably now the best known of all microbial toxins. The subunit structure and function of CT, its receptor (the GM1 ganglioside), and its effects on the cyclic AMP system and on intestinal secretion were defined in the 1970s, and the essential aspects of the genetic organization in the 1980s. Recent findings have generated additional perspectives. The 3D-crystal structure of CT has been established, the CT- encoding operon has been shown to be carried by a non-lytic bacteriophage, and in depth knowledge has been gained on how the bacterium controls CT gene expression in response to cell density and various environmental signals. The mode of entry into target cells and the intracellular transport of CT are becoming clearer. CT has become the prototype enterotoxin and a widely used tool for elucidating important aspects of cell biology and physiology, e.g., cell membrane receptors, the cyclic AMP system, G proteins, as well as normal and pathological ion transport mechanisms. In immunology, CT has emerged as a potent, widely used experimental adjuvant, and the strong oral-mucosal immunogenicity of the non-toxic B-subunit (CTB) has led to the use of CTB as a protective antigen together with killed vibrios in a widely licensed oral cholera vaccine. CTB has also been shown to promote immunological tolerance against certain types of mucosally co-administered antigens, preferably tissue antigens linked to the CTB molecule; this has stimulated research and development to use CTB in this context for treatment of autoimmune and allergic diseases. In summary, in the 50 years after De's discovery of CT, this molecule has emerged from being the cholera patient's "foe" to also becoming a highly useful scientist's "friend".

Galindo-Murillo R.,University of Utah | Sandoval-Salinas M.E.,Autonomous University of Mexico State | Barroso-Flores J.,Autonomous University of Mexico State
Journal of Chemical Theory and Computation | Year: 2014

The use of functionalized calix- and thia-calix[n]arenes is proposed as the basis for our in silico design of a suitable drug carrier for the tyrosine kinase inhibitor, Imatinib. Their mutual electronic properties and interaction energies, Eint, were assessed with the use of Density Functional Theory (DFT) methods under the NBODel methodology. Three structural variables for the host molecules were considered: R = {SO3H (1), t-Bu (2), i-Pr (3), COOH (4), (CH2)2OH (5), (CH2) 2NH2 (6)}; b = {CH2, S}; n = {5, 6, 8}, and two possible orientations for the insertion of Imatinib within the macrocycle cavity: pyridine moiety pointing inward (N1) and piperazine pointing inward (N2). In total, we explored 72 different assemblies. Initial molecular mechanics geometry optimizations with the UFF potential were undertaken for every host-guest complex, with further optimization at the B97D/6-31G(d,p) level of theory. Using the same optimized structures, Molecular Dynamics (MD) simulations were carried out on all 72 assemblies using the General Amber Force Field and the AMBER 12 MD package. Electronic parameters were fitted using the RESP method, and the complexes were run for 100 ns. Potential of mean force was obtained for the most stable systems using umbrella sampling and the Weighted Histogram Analysis Method. Calix[n]arenes families 1 and 5 (R = SO3H and (CH2)2OH, respectively) with n = 6 constitute the most promising candidates to become drug carriers within our parameter space due to their more negative Eint values and increased flexibility to allow the inclusion of the drug. © 2014 American Chemical Society.

Arteaga C.C.,Autonomous University of Mexico State
International Journal of Electrochemical Science | Year: 2012

Corrosion performance of stainless steel AISI-309 obtained from electrochemical noise technique and the conventional weight loss method during 5 days of exposure in 50 mol% Na2SO4-50 mol% V2O5 molten salt at 700°C is reported. Polarization curve is also presented, from which the Tafel slopes, the current density corrosion and corrosion potential were obtained. Electrochemical noise signals were analyzed in the time domain to determine the changes in corrosion activity. A statistical analysis obtaining the resistance noise and the localization index is presented as well as the determination of corrosion rates. Corrosion rates were supported by EDS analysis of corrosion products and scanning electron microscopy analysis of corroded samples. Results from optical microscope examination of the corroded samples showed that AISI-309 suffered intergranular corrosion due to the diffusion of sulfur into the matrix of the alloy through the grain boundaries. A corrosion mechanism of stainless steel AISI-309 is proposed accordingly to the noise pattern and the analysis from SEM results, showing that AISI-309 had a corrosion process of three stages, uniform corrosion, rupture and recovery of the passive film and intergranular corrosion. © 2012 by ESG.

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