Adsorption of Ciprofloxacin on Clay Minerals in Argentinian Santa Rosa-Corrientes Soils.

The presence of antibiotics in soils is increasing drastically in last decades due to the intensive farming industry and excessive human consumption. Clay minerals are one of the soil components with great adsorption capacity for organic pollutants. The study of interactions between antibiotics and mineral surfaces will give us scientific knowledge of these pollutants through soils. In this work, we study the adsorption of the antibiotic ciprofloxacin in the clay mineral fraction of soils from the Argentinian zone of Santa Rosa (Corrientes), in a collaborative research of experiments and atomistic modelling calculations of the intercalation of ciprofloxacin in the interlayer space of montmorillonite. Adsorption and desorption isotherms were performed and compared with different isotherm models. Additionally, enthalpy, entropy, and free energy were determined from equilibrium constants at a function of temperature. All these experiments and calculations lead to the conclusions that two adsorption types of ciprofloxacin are found on clay minerals: one weakly sorbed that is released during the desorption experiments, and other one strongly joined that remains in the soil.

Effect of Iron Isomorphic Substitution in Mg:Al and Zn:Al-Layered Double-Hydroxide Structures by Means of First Principle Calculations.

Layered double hydroxides (LDHs) are important components in terrestrial and extra-terrestrial environments. The presence of iron in these minerals provides them a wide potential application in environmental and materials sciences. In this work, the role of Fe in the crystallographic properties of LDHs M2+:M3+ 2:1 with Mg:(Fe,Al), Mg:Fe, Zn:(Fe,Al), and Zn:Fe is investigated by means of quantum mechanical calculations based on the density functional theory (DFT). Several relative proportions of Fe are studied. The cation ordering of these LDHs has been explored, finding useful insights for experimental synthetic paths of these minerals. The a and b cell parameters increase with the iron concentration. Some diffraction lines at high angle decrease in angle and increase in intensity with the increasing iron concentration. All of them agree with the experimental results. The iron substitutions tend to aggregate.

Modeling of the adsorption of a protein-fragment on kaolinite with potential antiviral activity.

This work aimed at studying the potentiality of interactions between kaolinite surfaces and a protein-fragment (350-370 amino acid units) extracted from the glycoprotein E1 in the transmembrane domain (TMD) of hepatitis C virus capsid. A computational work was performed for locating the potential electrostatic interaction sites between kaolinite aluminol and siloxane surfaces and the residues of this protein-fragment ligand, monitoring the possible conformational changes. This hydrated neutralized kaolinite/protein-fragment system was simulated by means of molecular modeling based on atomistic force fields based on empirical interatomic potentials and molecular dynamic (MD) simulations. The MD calculations indicated that the studied protein-fragment interacted with the kaolinite surfaces with an exothermic process and structural distortions were observed, particularly with the hydrophilic aluminol surface by favorable adsorption energy. The viral units isolation or trapping by the adsorption on the kaolinite nanoparticles producing structural distortion of the peptide ligands could lead to the blockage of the entry on the receptor and hence a lack of viral activity would be produced. Therefore, these findings with the proposed insights could be an useful information for the next experimental and development studies in the area of discovering inhibitors of the global challenged hepatitis and other pathogenic viruses based on the phyllosilicate surface activity. These MD studies can be extended to other viruses like the COVID-19 interacting with silicate minerals surfaces.

Compressibility of 2M1 muscovite-phlogopite series minerals.

Muscovite (Ms) and phlogopite (Phl) belong to the 2:1 dioctahedral and trioctahedral layer silicates, respectively, and are the end members of Ms-Phl series minerals. This series was studied in the 2M1 polytype and modeled by the substitution of three Mg2+ cations in the Phl octahedral sites by two Al3+ and one vacancy, increasing the substitution up to reach the Ms. The series was computationally examined at DFT level as a function of pressure to 9 GPa. Cell parameters as a function of pressure and composition, and bulk moduli as a function of the composition agrees with the existing experimental results. The mixing Gibbs free energy was calculated as a function of composition. From these data, approximated solvi were calculated at increasing pressure. A gap of solubility is found, decreasing the gap of solubility at high pressure.

Theoretical study of the gas-phase thermolysis reaction of 3,6-dimethyl-1,2,4,5-tetroxane. Methyl and axial-equatorial substitution effects.

Organic peroxides are interesting compounds with a broad range of properties from antimalarial and antimicrobial activities to explosive character. In this work the gas-phase thermolysis reaction mechanism of the 3,6-dimethyl-1,2,4,5-tetroxane (DMT) is studied by DFT calculations, considering axial-axial, axial-equatorial, and equatorial-equatorial position isomers. The critical points of the singlet (S) and triplet (T) potential energy surfaces (PES) are calculated. Three mechanisms are considered: i) S-concerted, ii) S-stepwise, and iii) T-stepwise. The first intermediate of the reaction through S-stepwise-PES is a diradical open structure, o, yielding, as products, two molecules of acetaldehyde and one of O2 in the S state. The S-stepwise-mechanism gives exothermic reaction energies (Er) in the three position isomers. The S-concerted mechanism yields very high activation energies (Ea) in comparison with those of the S-stepwise mechanism. In the T-stepwise mechanism, a triplet open structure (T-o) is first considered, yielding an Er 12 kcal mol-1 more exothermic than that of the S-mechanisms. The S-o and T-o are similar in structure and energies; therefore, a crossing from the S- to T-PES is produced at the o intermediate as a consequence of a spin-orbit coupling. The highest Ea is the first step after o intermediate, and thus it is considered the rate limiting step. Therefore, the Er at the T-PES is more in agreement with the Er of the exothermic experimental diperoxide products. Ea, Er, and O···O distances are studied as a function of the number of methyl groups and the position isomerization.

A DFT study of the adsorption of glycine in the interlayer space of montmorillonite.

The adsorption properties of clay minerals have been widely studied in several technological areas, due to their versatility, absorption capacity and catalytic properties. The interaction of amino acids with clay surfaces can be interesting due to their role in prebiotic scenarios. Different degrees of hydration and the adsorption of the glycine molecule and glycinium cation in the interlayer space of montmorillonite were investigated by means of calculations based on density functional theory (DFT). Our calculations show that the cation exchange of K+ by glycinium in the interlayer of hydrated K-montmorillonite is highly possible and exothermic. This supports previous experimental results by explaining the possible adsorption of glycine as a molecule and cation. Glycine is adsorbed in a zwitterionic form in the interlayer without being solvated with water. Besides, glycine and glycinium are highly exothermically adsorbed in the interlayer. The interlayer spacings under different conditions were in agreement with the experimental values. Hydrogen bonds and electrostatic interactions between molecules and surface atoms are responsible for this exothermicity. The IR spectra were calculated and compared with the experimental results showing interesting frequency shifts depending on the intermolecular interactions in the interlayer space of montmorillonite.

Molecular modeling and infrared and Raman spectroscopy of the crystal structure of the chiral antiparasitic drug Praziquantel.

Anthelmintic praziquantel (PZQ) and its molecular and crystal lattice structures were studied by means of atomistic calculations based on empirical interatomic potentials and quantum mechanical methods (DFT). This chiral drug presents several crystal polymorphs due to the enantiomers (either R or S) or the racemic crystal, and different molecular conformations. The relative configurations of the carbonyl groups in PZQ define these conformations that produce different polymorphs. The polarity of these conformers is quite different and their relative population can vary in media with different polarity. Crystal structures of PZQ were studied by infrared and Raman spectroscopy and their spectroscopical properties were calculated by quantum mechanical methods, assigning many of their bands, and finding a good agreement with experimental data.

Theoretical study of the hydrogen bonding and infrared spectroscopy in the cis-vacant polymorph of dioctahedral 2:1 phyllosilicates.

The spatial geometry and local environment of hydroxyl groups of the cis-vacant (cv) crystal polymorph of dioctahedral 2:1 phyllosilicates are studied by computational methods, doing especial emphasis on the hydrogen bonds and electrostatic interactions of the hydroxyl groups with the neighbor atoms. Different types of phyllosilicates are explored: with only tetrahedral charge, with only octahedral charge, with simultaneous octahedral and tetrahedral substitution, and with different interlayer cation (IC). The effect of these interactions on the spectroscopic properties of these hydroxyl groups is also studied. All results are compared with the trans-vacant (tv) crystal forms of these minerals. Frequency differences between cv and tv polymorphs are smaller than those due to the local environments of these OH groups. This means that the changes in the interactions of the different local environments of each OH group are greater than the cv/tv differences.

Theoretical study of the gas-phase thermolysis of 3-methyl-1,2,4,5-tetroxane.

Cyclic organic peroxides are a broad and highly sought-after class of peroxide compounds that present high reactivity and even explosive character. The unusually high reactivity of these peroxides can generally be attributed to the rupture of O-O bonds. Cyclic diperoxides are a very interesting series of substituted compounds in which tetroxane is the most prominent member. Gas-phase thermolysis of the simplest substituted member of the series [3-methyl-1,2,4,5-tetroxane or methylformaldehyde diperoxide (MFDP)] has been observed to yield one acetaldehyde, one formaldehyde, and one oxygen molecule as reaction products. DFT at the 6-311 + G** level of theory using the BHANDHLYP correlation-exchange functional was applied via the Gaussian09 program to calculate the critical points of the potential energy surface (PES) of this reaction. Equatorial and axial isomers were studied. The singlet state PES of MFDP was calculated, and an open diradical structure was found to be the first intermediate in a stepwise reaction. Two PESs were subsequently obtained: singlet state (S) and triplet state (T) PESs. After that, two alternative stepwise reactions were found to be possible: 1) one in which either an acetaldehyde, or 2) formaldehyde molecule is initially formed. For second one, exothermic reactions were observed for both the S and T PESs. The reaction products include a oxygen molecule in either S or T state, with the T reaction being the most exothermic. When calculations were performed at the CASSCF(10,10)/6-311 + G** level, spin-orbit coupling permitted S to T crossing at the open diradical intermediate stage, a non-adiabatic reaction was observed, and lower activation energies and higher exothermicity were generally seen for the T PES than for the S PES. These results were compared with the corresponding results for tetroxane. The spin-orbit coupling of MFDP and tetroxane yielded identical values, so it appears that the methyl substituent does not have any effect on this coupling.

DFT study of the mechanism of the reaction of aminoguanidine with methylglyoxal.

We have studied the mechanism of the reaction between aminoguanidine (AG) and methylglyoxal (MG) by carrying out Dmol3/DFT calculations, obtaining intermediates, transition-state structures, and free-energy profiles for all of the elementary steps of the reaction. Designed models included explicit water solvent, which forms hydrogen-bond networks around the reactants and intermediate molecules, facilitating intramolecular proton transfer in some steps of the reaction mechanism. The reaction take place in four steps, namely: (1) formation of a guanylhydrazone-acetylcarbinol adduct by condensation of AG and MG; (2) dehydration of the adduct; (3) formation of an 1,2,4-triazine derivative by ring closure; and (4) dehydration with the formation of 5-methyl 3-amino-1,2,4-triazine as the final product. From a microkinetic point of view, the first dehydration step was found to be the rate-determining step for the reaction, with the reaction having an apparent activation energy of 12.65 kcal mol⁻¹. Additionally, some analogous structures of intermediates and transition states for the reaction between AG and 2,3-dicarbonyl-phosphatidylethanolamine, a possible intermediate in Amadori-glycated phosphatidylethanolamine (Amadori-PE) autooxidation, were obtained to evaluate the reaction above a phosphatidylethanolamine (PE) surface. Our results are in agreement with experimental results obtaining by other authors, showing that AG is efficient at trapping dicarbonyl compounds such as methylglyoxal, and by extension these compounds joined to biomolecules such as PE in environments such as surfaces and their aqueous surroundings.

A Tuned LRC-DFT Design of Ambipolar Diketopyrrolopyrrole-Containing Quinoidal Molecules Interesting for Molecular Electronics.

This work presents a Density Functional Theory (DFT) study on the charge transport related properties of two quinoidal diketopyrrolopyrrole (DPP) based systems. System A, recently synthesized, shows high efficiency as n-type organic semiconductor material while system B, not synthesized yet, has a linking benzothiadiazole (BT) unit between DPP moieties and would display an ambipolar character. The use of tuned, long-range corrected (LRC) functionals allows one to predict HOMO, LUMO, and charge transport properties for compound A in concordance with those experimentally observed. The use of BT building blocks allows for a conclusion that compound B is expected to display balanced and efficient charge injection along with high mobilities both for holes and electrons, which points to its potential to obtain high performances as an ambipolar semiconductor.

Vibrations of H+(D+) in stoichiometric LiNbO3 single crystal.

A first principles quantum mechanical calculation of the vibrational energy levels and transition frequencies associated with protons in stoichiometric LiNbO(3) single crystal has been carried out. The hydrogen contaminated crystal has been approximated by a model one obtains by translating a supercell, i.e., a cluster of LiNbO(3) unit cells containing a single H(+) and a Li(+) vacancy. Based on the supercell model an approximate Hamiltonian operator describing vibrations of the proton sublattice embedded in the host crystal has been derived. It is further simplified to a sum of uncoupled Hamiltonian operators corresponding to different wave vectors (ks) and each describing vibrations of a quasi-particle (quasi-proton). The three dimensional (3D) Hamiltonian operator of k=0 has been employed to calculate vibrational levels and transition frequencies. The potential energy surface (PES) entering this Hamiltonian operator has been calculated point wise on a large set of grid points by using density functional theory, and an analytical approximation to the PES has been constructed by non-parametric approximation. Then, the nuclear motion Schrödinger equation has been solved by employing the method of discrete variable representation. It has been found that the (quasi-)H(+) vibrates in a strongly anharmonic PES. Its vibrations can be described approximately as a stretching, and two orthogonal bending vibrations. The theoretically calculated transition frequencies agree within 1% with those experimentally determined, and they have allowed the assignment of one of the hitherto unassigned bands as a combination of the stretching and the bending of lower fundamental frequency.

Influence of the alkyl and alkoxy side chains on the electronic structure and charge-transport properties of polythiophene derivatives.

Density Functional Theory has been used to study the structural, electronic and charge-transport properties of two regio-regular head-to-tail polythiophene derivatives, i.e. poly(3-hexyl-thiophene), P3HT, and poly(3-oxyhexyl-thiophene), P3OHT. The effect of substituents on the electronic structure was analyzed by means of bandwidth, bandgap, effective mass, total and partial densities of states and crystal orbital overlap populations. Electronic couplings were estimated from band diagrams as the splitting of the valence band. The neutral and cationic states of isolated oligomers were optimized using the supercell approximation. The hole-transfer rates and mobilities were evaluated according to Marcus's theory. Results provide a compelling illustration of the effect of side chains on the crystal packing, electronic structure and charge-transport properties. Thus, the hole mobility calculated for the alkyl derivative was 0.15 cm(2) V(-1) s(-1) (experimental mobility is 0.10 cm(2) V(-1) s(-1)), while the alkoxy derivative has a theoretical mobility of 0.49 cm(2) V(-1) s(-1). The obtained results hopefully could motivate experimentalists to try out P3OHT for an improved charge carrier mobility.

Exploring the rehydroxylation reaction of pyrophyllite by ab initio molecular dynamics.

We have investigated the process of rehydroxylation of pyrophyllite as a limiting factor to the dehydroxylation upon thermal treatment. Car-Parrinello molecular dynamics simulations based on density functional theory have been used along with the metadynamics algorithm. Two possible rehydroxylation mechanisms reaction have been characterized, related to two possible intermediate structures along the rehydroxylation paths, and both involve the interaction of the apical oxygen atoms. At high temperature, the rehydroxylation reaction is highly competitive (free energy barrier (DeltaF) = 1.5 kcal/mol) and inhibits the progress of the dehydroxylation reaction (DeltaF = 40 kcal/mol). In addition to the rehydroxylation of the dehydroxylated structure, the water molecule supports the interconversion of the cross and on-site intermediates as well. Thus, rehydroxylation and interconversion among intermediates can justify the wide range of transformations as a function of the temperature observed experimentally.

DFT research on the dehydroxylation reaction of pyrophyllite 2. Characterization of reactants, intermediates, and transition states along the reaction path.

We delineate the dehydroxylation reaction of pyrophyllite in detail by localizing the complete reaction path on the free energy surface obtained previously by Car-Parrinello molecular dynamics and the implemented metadynamics algorithm ( Molina-Montes et al. J. Phys. Chem. B 2008, 112, 7051 ). All intermediates were identified, and a transition state search was also undertaken with the PRFO algorithm. The characterization of this reaction and the atomic rearrangement in the intermediates and products at quantum mechanical level were performed for the two reaction paths found previously: (i) direct dehydroxylation through the octahedral hole (cross mechanism) or between contiguous hydroxyl groups (on-site mechanism) and (ii) two-step dehydroxylation assisted by apical oxygens for each of the two steps. New intermediates were found and determined structurally. The structural variations found for all intermediates and transition states are in agreement with experimental results. The formation of these structures indicates that the dehydroxylation process is much more complex than a first-order reaction and can explain the wide range of temperatures for completing the reaction, and these results can be extrapolated to the dehydroxylation of other dioctahedral 2:1 phyllosilicates.

DFT research on the dehydroxylation reaction of pyrophyllite 1. First-principle molecular dynamics simulations.

The dehydroxylation of pyrophyllite involves the reaction of OH groups and elimination of water molecules through two possible mechanisms, one involving the bridging hydroxyl groups of an octahedral Al (3+) pair and the other two hydroxyl groups reacting across the dioctahedral vacancy. First-principles molecular dynamics simulations at the density functional theory level are used together with the metadynamics algorithm to explore the free-energy surface (FES) of the initial step of the dehydroxylation. We observe that the two possible dehydroxylation mechanisms yield similar activation energies at 0 K, but at high temperatures, the cross mechanism has lower free energy than that of the on-site one. The dehydroxylation process produces different semidehydroxylated intermediates that should be taken into account. The role of the temperature in favoring a dehydroxylation nonconcerted chain mechanism over another is here elucidated, and a novel competitive mechanism, which is assisted by the structural apical oxygens in the high-temperature regime, is proposed.