Effect of the Nucleophile's Nature on Chloroacetanilide Herbicides Cleavage Reaction Mechanism. A DFT Study.

In this study, the degradation mechanism of chloroacetanilide herbicides in the presence of four different nucleophiles, namely: Br-, I-, HS-, and S2O3-2, was theoretically evaluated using the dispersion-corrected hybrid functional wB97XD and the DGDZVP as a basis set. The comparison of computed activation energies with experimental data shows an excellent correlation (R2 = 0.98 for alachlor and 0.97 for propachlor). The results suggest that the best nucleophiles are those where a sulfur atom performs the nucleophilic attack, whereas the other species are less reactive. Furthermore, it was observed that the different R groups of chloroacetanilide herbicides have a negligible effect on the activation energy of the process. Further insights into the mechanism show that geometrical changes and electronic rearrangements contribute 60% and 40% of the activation energy, respectively. A deeper analysis of the reaction coordinate was conducted, employing the evolution chemical potential, hardness, and electrophilicity index, as well as the electronic flux. The charge analysis shows that the electron density of chlorine increases as the nucleophilic attack occurs. Finally, NBO analysis indicates that the nucleophilic substitution in chloroacetanilides is an asynchronous process with a late transition state for all models except for the case of the iodide attack, which occurs through an early transition state in the reaction.

In silico study of the potential interactions of 4'-acetamidechalcones with protein targets in SARS-CoV-2.

The sanitary emergency generated by the pandemic COVID-19, instigates the search for scientific strategies to mitigate the damage caused by the disease to different sectors of society. The disease caused by the coronavirus, SARS-CoV-2, reached 216 countries/territories, where about 20 million people were reported with the infection. Of these, more than 740,000 died. In view of the situation, strategies involving the development of new antiviral molecules are extremely important. The present work evaluated, through molecular docking assays, the interactions of 4'-acetamidechalcones with enzymatic and structural targets of SARS-CoV-2 and with the host's ACE2, which is recognized by the virus, facilitating its entry into cells. Therefore, it was observed that, regarding the interactions of chalcones with Main protease (Mpro), the chalcone N-(4'[(2E)-3-(4-flurophenyl)-1-(phenyl)prop-2-en-1-one]) acetamide (PAAPF) has the potential for coupling in the same region as the natural inhibitor FJC through strong hydrogen bonding. The formation of two strong hydrogen bonds between N-(4[(2E)-3-(phenyl)-1-(phenyl)-prop-2-en-1-one]) acetamide (PAAB) and the NSP16-NSP10 heterodimer methyltransferase was also noted. N-(4[(2E)-3-(4-methoxyphenyl)-1-(phenyl)prop-2-en-1-one]) acetamide (PAAPM) and N-(4-[(2E)-3-(4-ethoxyphenyl)-1-(phenyl)prop-2-en-1-one]) acetamide (PAAPE) chalcones showed at least one strong intensity interaction of the SPIKE protein. N-(4[(2E)-3-(4-dimetilaminophenyl)-1-(phenyl)-prop-2-en-1-one]) acetamide (PAAPA) chalcone had a better affinity with ACE2, with strong hydrogen interactions. Together, our results suggest that 4'-acetamidechalcones inhibit the interaction of the virus with host cells through binding to ACE2 or SPIKE protein, probably generating a steric impediment. In addition, chalcones have an affinity for important enzymes in post-translational processes, interfering with viral replication.

An efficient synthetic route to O-(2-O-benzyl-3,4-di-O-acetyl-α/ß-l-fucopyranosyl)-trichloroacetimidate.

An efficient synthetic route to prepare O-(2-O-benzyl-3,4-di-O-acetyl-α/ß-l-fucopyranosyl)-trichloroacetimidate from l-fucose was developed by introducing the thiophenyl group at the anomeric center and the benzylidene functional group to protect the 3 and 4 positions. Although three approaches were considered, the best result was obtained when, after the 2-hydroxyl benzylation, both protective groups were simultaneously removed by using acetic anhydride and perchloric acid supported on silica as catalyst. Selective deacetylation of the obtained tri-O-acetate followed by the reaction of the resultant hemiacetal with trichloroacetonitrile and DBU afforded the trichloroacetimidate with an overall yield of 56% from the l-fucose.

68Ga-Labeled bismacrocyclic methylene phosphonate as potential bone seeking PET radiopharmaceutical.

Phosphonates-based agents are well-known bone-seeking radiopharmaceuticals with application in detection and therapy. With higher sensitivity and resolution offered by Positron Emission Tomography (PET), tracers based on this technique are gaining huge attention. 68Ga-based generator and radiotracers render independence from the on-site cyclotron. We report the development of 68Ga-labeled DOTA-based bismacrocyclic phosphonate derivative, for bone PET imaging. The synthesis and characterization of 68Ga- DO3P-AME-DO3P was carried out in > 95% purity. The radiotracer displayed high stability and low binding affinity (<3%) to blood serum. High in vitro binding affinity were observed for synthetic hydroxyapatite, SAOS-2, osteoclast and osteoblast cells. In vivo pharmacokinetics revealed fast washout with biphasic release pattern. The deposition of radiotracer in osseous tissues was high (Bone/Muscle ratio:18), as studied from the biodistribution studies. In vivo PET/CT and biodistribution analyses revealed the ability of 68Ga-DO3P-AME-DO3P to target and accumulate in bone, thus displaying its potential as a PET bone imaging agent.

Potential of 2-Chloro-N-(4-fluoro-3-nitrophenyl)acetamide Against Klebsiella pneumoniae and In Vitro Toxicity Analysis.

Klebsiella pneumoniae causes a wide range of community and nosocomial infections. The high capacity of this pathogen to acquire resistance drugs makes it necessary to develop therapeutic alternatives, discovering new antibacterial molecules. Acetamides are molecules that have several biological activities. However, there are no reports on the activity of 2-chloro-N-(4-fluoro-3-nitrophenyl)acetamide. Based on this, this study aimed to investigate the in vitro antibacterial activity of this molecule on K. pneumoniae, evaluating whether the presence of the chloro atom improves this effect. Then, analyzing its antibacterial action more thoroughly, as well as its cytotoxic and pharmacokinetic profile, in order to contribute to future studies for the viability of a new antibacterial drug. It was shown that the substance has good potential against K. pneumoniae and the chloro atom is responsible for improving this activity, stabilizing the molecule in the target enzyme at the site. The substance possibly acts on penicillin-binding protein, promoting cell lysis. The analysis of cytotoxicity and mutagenicity shows favorable results for future in vivo toxicological tests to be carried out, with the aim of investigating the potential of this molecule. In addition, the substance showed an excellent pharmacokinetic profile, indicating good parameters for oral use.

Anxiolytic-like effect of chalcone N-{4'[(2E)-3-(3-nitrophenyl)-1-(phenyl)prop-2-en-1-one]} acetamide on adult zebrafish (Danio rerio): Involvement of the 5-HT system.

The action of anxiolytic compounds that act on selective serotonin receptors (SSRIs) have been scarcely evaluated. Serotonergic drugs have been shown to be effective in treating anxiety without presenting adverse effects as benzodiazepines. However, the anxiolytic effects take days to occur. This study aimed to evaluate the anxiolytic effect of the synthetic chalcone, 4'-[(2E) -3- (3-nitrophenyl) -1- (phenyl) prop-2-en-1-one] acetamide (PAAMNBA), and its possible mechanism of action in adult zebrafish (Danio rerio). PAAMNBA was synthesized with a yield of 51.3% and its chemical structure was determined by 1H and 13C NMR. Initially, PAAPMNBA was intraperitoneally administered to zebrafish (n = 6/group) at doses of 4, 12, or 40 mg/kg, and the animals were subsequently subjected to acute and open field toxicity tests. PAAMNBA was administered to the other groups (n = 6/group) for analyzing its effect in the light and dark test. The involvement of the serotonergic (5HT) system was also evaluated using 5-HTR 1, 5-HTR 2A/2C, and 5-HTR 3A/3B receptor antagonists, namely, pizotifeo, granizetron, and ciproeptadina, respectively. Molecular coupling was performed using the 5-HT1 receptor. PAAMNBA was found to be non-toxic, reduced the locomotor activity, and had an anxiolytic effect in adult zebrafish. The effect was reduced by pretreatment with pizotifene and was not reversed by treatment with granizetron and cyproeptadine. A previous in vivo molecular coupling study indicated that chalcones interact with the 5-HT1 receptor. The results suggested that the chalcone, PAAPMNBA, has anxiolytic activity, that is mediated by the serotonergic system via the 5-HT1 receptor. The interaction of PAAPMNBA with the 5-HT1 receptor was confirmed by molecular docking studies.

Arylboronic acids inhibit P2X7 receptor function and the acute inflammatory response.

The P2X7 receptor (P2X7R) is an ion channel which is activated by interactions with the extracellular ATP molecules. The molecular complex P2X7R/ATP induces conformational changes in the protein subunits, opening a pore in the ion channel macromolecular structure. Currently, the P2X7R has been studied as a potential therapeutic target of anti-inflammatory drugs. Based on this, a series of eight boronic acids (NO) analogs were evaluated on the biologic effect of this pharmacophoric group on the human and murine P2X7R. The boronic acids derivatives NO-01 and NO-12 inhibited in vitro human and murine P2X7R function. These analogs compounds showed effect better than compound BBG and similar to inhibitor A740003 for inhibiting dye uptake, in vitro IL-1ß release and ATP-induced paw edema in vivo. In both, in vitro and in vivo assays the compound NO-01 showed to be the hit compound in the present series of the arylboronic acids analogs. The molecular docking suggests that the NO derivatives bind into the upper body domain of the P2X7 pore and that the main intermolecular interaction with the two most active NO derivatives occur with the residues Phe 95, 103 and 293 by hydrophobic interactions and with Leu97, Gln98 and Ser101 by hydrogen bonds.. These results indicate that the boronic acid derivative NO-01 shows the lead compound characteristics to be used as a scaffold structure to the development of new P2X7R inhibitors with anti-inflammatory action.

Fenton-based electrochemical degradation of metolachlor in aqueous solution by means of BDD and Pt electrodes: influencing factors and reaction pathways.

This work explores the role of electrode material and the oxidation ability of electrochemical advanced oxidation processes (EAOPs), such as electro-oxidation (EO) with or without H2O2 production, electro-Fenton (EF), and UVA photoelectron-Fenton (PEF), in the degradation of metolachlor. The performance of the EAOPs using Boron-doped diamond (BDD) or Pt as anode has been compared from the analysis of decay kinetics, mineralization profile, and energy consumption using small undivided batch cell. Metolachlor concentration always decays following a pseudo-first-order kinetics. Using the Pt anode, none of the processes reaches 30% mineralization, including PEF. In contrast, the BDD anode showed a higher mineralization rate allowing almost total mineralization in PEF due to the synergetic action of UVA light and oxidant hydroxyl radicals formed in the bulk from Fenton's reaction, as well as in the BDD, which has large reactivity to oxidize the pollutants. The increase in current density and decrease in metolachlor concentration accelerated the mineralization in PEF, although lower current efficiency and higher energy consumption was obtained. The GC-MS and HPLC analysis allowed the identification of up to 17 aromatics intermediates and 7 short-chain carboxylic acids. Finally, a reaction pathway for metolachlor mineralization by EAOPs is proposed. PEF with BDD allowed total removal of the herbicide in real water matrix and a high mineralization (83.82%).

Thiophenacetamide as a potential modulator to NF-κB: structure and dynamics study using in silico and molecular biology assays.

Nuclear factor kappa B (NF-κB) plays critical roles in the regulation of many pathophysiological processes, including inflammation and immune responses, cell growth and apoptosis. This DNA-binding protein receptor is considered an important molecular target to treat many diseases through host-directed therapy. In this line, several drugs containing thiophene cores have been extensively evaluated due to their ability to interfere on NF-κB translocation to the nucleus. In this work, assays using drug affinity responsive target stability (DARTS) revealed that the parent compound N-(Aryl)-2-thiophen-2-ylacetamide referred to as thiophenacetamide (TAA) specifically binds to the p65 subunit of the NF-κB. Since no experimental binding mode of TAA with p65 is available, we explored TAA within putative sites in silico to gain insights into its possible binding mode and behavior. The binding mode of TAA found in Site 1 formed hydrogen bonds with Lys37 and Asp125 on p65, important residues near DNA-binding region. Molecular dynamics simulations showed the stability of this mode of binding in contrast to the other also tested modes. Our results suggest that TAA binding could occur in regions close to residues responsible for DNA binding, increasing NF-κB protein rigidity and affecting the association between DNA and NF-κB. Communicated by Ramaswamy H. Sarma.

New Insight into the Chloroacetanilide Herbicide Degradation Mechanism through a Nucleophilic Attack of Hydrogen Sulfide.

The nucleophilic attack of hydrogen sulfide (HS-) on six different chloroacetanilide herbicides was evaluated theoretically using the dispersion-corrected hybrid functional wB97XD and the 6-311++G(2d,2p) Pople basis sets. The six evaluated substrates were propachlor (A), alachlor (B), metolachlor (C), tioacetanilide (D), ß-anilide (E), and methylene (F). Three possible mechanisms were considered: (a) bimolecular nucleophilic substitution (SN²) reaction mechanism, (b) oxygen assistance, and (c) nitrogen assistance. Mechanisms based on O- and N-assistance were discarded due to a very high activation barrier in comparison with the corresponding SN² mechanism, with the exception of compound F. The N-assistance mechanism for compound F had a free activation energy of 23.52 kcal/mol, which was close to the value for the corresponding SN² mechanism (23.94 kcal/mol), as these two mechanisms could occur in parallel reactions with almost 50% of each one. In compounds A to D, an important electron-withdrawing effect of the C=O and C=S groups was seen, and consequently, the activation free energies in these SN² reactions were smaller, with a value of approximately 18 kcal/mol. Instead, compounds E and F, which have a CH2 group in the ß-position, presented a higher activation free energy (≈22 kcal/mol). Good agreement was found between experimental and theoretical values for all cases, and a reaction force analysis was performed on the intrinsic reaction coordinate profile in order to gain more details about the reaction mechanism. Finally, from the natural bond orbital (NBO) analysis, it was possible to evaluate the electronic reorganization through the reaction pathway where all the transition states were early in nature in the reaction coordinate (δBav < 50%); the transition states corresponding to compounds A to D turned out to be more synchronous than those for compounds E and F.

Th1-Biased Immunomodulation and In Vivo Antitumor Effect of a Novel Piperine Analogue.

Natural products have an important role as prototypes in the synthesis of new anticancer drugs. Piperine is an alkaloid amide with antitumor activity and significant toxicity. Then, the N-(p-nitrophenyl)acetamide piperinoate (HE-02) was synthesized, and tested for toxicological and antitumor effects. The toxicity was evaluated in vitro (on RAW 264.7 cells and mice erythrocytes) and in vivo (acute toxicity in mice). The Ehrlich ascites carcinoma model was used to evaluate the antitumor activity of HE-02 (6.25, 12.5 or 25 mg/kg, intraperitoneally, i.p.), as well as toxicity. HE-02 induced only 5.01% of hemolysis, and reduced the viability of RAW 264.7 cells by 49.75% at 1000 µg/mL. LD50 (lethal dose 50%) was estimated at around 2000 mg/kg (i.p.). HE-02 reduced Ehrlich tumor cell viability and peritumoral microvessels density. There was an increase of Th1 helper T lymphocytes cytokine profile levels (IL-1ß, TNF-α, IL-12) and a decrease of Th2 cytokine profile (IL-4, IL-10). Moreover, an increase was observed on reactive oxygen species and nitric oxide production. Weak in vivo toxicological effects were recorded. Our data provide evidence that the piperine analogue HE-02 present low toxicity, and its antitumor effect involves modulation of immune system to a cytotoxic Th1 profile.

Chemometric optimization of the extraction and derivatization of parabens for their determination in water samples by rotating-disk sorptive extraction and gas chromatography mass spectrometry.

A combination of rotating disk sorptive extraction (RDSE) using Oasis® HLB as the sorbent phase and gas chromatography mass spectrometry (GC-MS) has been performed for the determination of four of the most widely used parabens: methylparaben, ethylparaben, propylparaben and n-butylparaben. The extraction and derivatization of the analytes in water samples were optimized by using factorial (screening) and Doehlert designs, thus reducing the number of analyses with the concomitant reduction of time, reagents, waste, samples and cost. Thus, a RDSE method using 20mL of sample was performed. The disk was rotated at 2900rpm for 70min at room temperature. After a desorption step and evaporation of solvent, a derivatization method using 5µL of N-methyl-N-(trimethylsilyl)trifluoroacetamide (MSTFA) for 15min at room temperature was used previously to inject the final extract into GC-MS. The detection limits and precision (%RSD) were lower than 0.05µgL- 1 and 9.7% for the studied compounds, respectively. Recoveries were studied using effluent samples of a wastewater treatment plant (WWTP), with values higher than 80% being obtained. The applicability and reliability of this methodology were confirmed through the analysis of tap water and influents from Santiago, Chile, with concentration values ranging from 0.57 to 0.83µgL- 1 in influents. The main advantage of the present RDSE method is that it is significantly faster than its counterpart by SBSE and requires a considerable lower volume of derivatizing agent.

The utility of the 13C-methacetin breath test in predicting the long-term survival of patients with decompensated cirrhosis.

AIM: The 13C-methacetin breath test (13C-MeBT) is a noninvasive tool that allows evaluation of the functional activity of the liver and the prediction of liver cirrhosis. Nevertheless, there is no information on its potential utility to predict long-term survival in patients with liver disease. METHODS: Patients with cirrhosis were selected. All patients underwent a complete clinical assessment, standard biochemical tests, and 13C-MeBT at the beginning of the study. Death was recorded during the three years of follow-up. Survival curves were calculated by the Kaplan-Meier method, and Cox proportional risk models were used to identify predictive factors. The ability to classify the overall risk was assessed by the C statistic. RESULTS: One hundred and twenty-three patients were included. A significant inverse correlation was found between delta over baseline at the 15 min point (DOB15) after ingestion of 13C-methacetin and the Child-Pugh score (r = -0.411, p < 0.001). In multivariate analysis, DOB15 ≤ 4.5‰ was associated with mortality, [HR = 2.58 95% CI (1.17-5.69)]. In conclusion, our results confirm the utility of 13C-MeBT as a simple, noninvasive tool to quantitatively assess the liver's functional reserve and as a potential predictor of long-term survival in patients with decompensated cirrhosis.

Synthesis of a 2-N,N-dibenzylamino glucopyranosyl trichloroacetimidate glycosyl donor and evaluation of its utility in stereoselective glycosylation.

The 2-N,N-dibenzylamino glucopyranosyl trichloroacetimidate donor was synthesized and an extensive investigation of its glycosyl donor properties was conducted. Coupling studies incorporated a variety of glycosyl promoters and a range of acceptor alcohols representing different reactivities and protecting group patterns. Various reaction temperatures, solvents and glycosylation protocols were also examined. Exclusive ß-stereoselectivity was obtained in moderate to good yields with eight novel glycosides being produced, by probable neighbouring group participation via the formation of an aziridinium ion intermediate. Plausible reaction mechanisms were proposed based on the results obtained.

Organomineral Interactions and Herbicide Sorption in Brazilian Tropical and Subtropical Oxisols under No-Tillage.

We evaluated the effects of the soil organic matter (SOM) composition, distribution between soil aggregates size, and their interactions with the mineral phase on herbicide sorption (alachlor, bentazon, and imazethapyr) in tropical and subtropical Oxisols under no-till systems (NT). Using soil physical fractionation approach, sorption experiments were performed on whole soils and their aggregates. SOM chemistry was assessed by CP/MAS (13)C NMR. The lower sorption observed in tropical soils was attributed to the greater blockage of SOM sorption sites than in subtropical soils. When these sites were exposed upon physical fractionation, sorption of the three herbicides in tropical soils increased, especially for imazethapyr. High amounts of poorly crystallized sesquioxides in these soils may have contributed to masking of sorption sites, indicating that organomineral interactions may lead to blockage of sorption sites on SOM in tropical soils.

A molecularly imprinted polymer as the sorptive phase immobilized in a rotating disk extraction device for the determination of diclofenac and mefenamic acid in wastewater.

The microextraction of diclofenac and mefenamic acid from water samples was performed by using rotating disk sorptive extraction (RDSE) with molecularly imprinted polymer (MIP) as the sorptive phase. The MIP was synthesized from the monomer 1-vinylimidazol (VI) together with the cross-linker divinylbenzene (DVB) using diphenylamine as the template molecule. Scanning electron microscopy (SEM) analyses of the MIP revealed clusters of spherical particles having a narrow size distribution, with diameters of approximately 1 µm. The optimized extraction conditions involved a disk rotation velocity of 3000 rpm, an extraction time of 120 min, a sample volume of 50 mL, and a sample pH of 2 as well as 25 mg of MIP immobilized in the disk. Desorption of the extracted analytes was performed with 5 mL of methanol for 10 min. Analysis by gas chromatography-mass spectrometry (GC-MS) was carried out after derivatization of the analytes with N-tert-butyldimethylsilyl-N-methyltrifluoroacetamide (MTBSTFA). Nonmolecularly imprinted polymer (NIP) was also synthesized for comparison. It was observed that under the same conditions, MIP extracted significantly more NSAIDs containing diphenylamine (or part of this molecule) in their structure than NIP. Higher significant differences between MIP and NIP were observed for diclofenac, mefenamic acid and paracetamol, clearly indicating the effect of the template on the extraction. Recoveries of the method were between 100 and 112%, with relative standard deviations of 5-6%. The limits of detection were between 60 and 223 ng L(-1). Water samples from a wastewater treatment plant (WWTP) of Santiago de Chile, were found to contain concentrations of these acidic drugs between 1.6 and 4.3 µg L(-1) and between 1.4 and 3.3 µg L(-1) in the influent and effluent, respectively.

El significado del capital social "individual" en diabéticos receptores de cuidado en un contexto urbano colombiano / The meaning of "individual" social capital for diabetics receiving care in a Colombian city / O significado do capital social "individual" em diabéticos que precisam de cuidados dentro de um contexto urbano colombiano

Comprender el significado del capital social de la diabetes tipo 2 según género, dentro un contexto urbano colombiano. Investigación cualitativa del interaccionismo simbólico. 25 mujeres y 16 hombres, diabéticos, familiares, vecinos y personal asistencial participaron en seis grupos focales. Emergieron 850 códigos que se integraron en un set de 142 códigos de códigos para el ego, el alter y alter ego. Tres categorías y veinte subcategorías fueron identificadas para el diseño del "paradigma de la codificación". El significado no es igual para hombres y mujeres. Los vínculos sociales de las redes sociales, creados cotidianamente por la confianza y la solidaridad para el cuidado, son valorados de manera diferente, debido a experiencias y hechos sociales resultantes de la autoconfianza, la autoeficacia para el apoyo social principalmente y, la autoestima frente al manejo y control de la enfermedad. Los recursos sociales de un individuo son reificados para el manejo y cuidado de la enfermedad como estrategia para disminuir las inequidades en salud.

The aim of this study was to understand the meaning of social capital in relation to type 2 diabetes according to gender, within an urban setting in Colombia, based on a qualitative design for symbolic interactionism. Twenty-four women and 16 men with diabetes, family members, and healthcare personnel participated in six focus groups. A total of 850 codes emerged that comprised a set of 142 codes for ego, alter, and alter ego. Three categories and 20 subcategories were identified for the "coding paradigm design". The meaning differed between men and women. Social ties in social networks, created daily through trust and solidarity for care, were valued differently due to the social experiences and events resulting from self-confidence, self-efficacy for social support, and mainly self-esteem vis-à-vis management and control of the disease. An individual's social resources are reified for the management and care of the disease as a strategy to mitigate health inequalities. .

Compreender o significado do capital social, diabetes tipo 2 por sexo, um contexto urbano da Colômbia. pesquisa qualitativa do interacionismo simbólico. 25 mulheres e 16 homens, diabéticos, familiares, vizinhos e cuidadores participaram seis grupos focais. 850 códigos se que foram integrados em um conjunto de 142 codes para o ego, o alter e alter ego. Três categorias e vinte subcategorias foram identificados para o projeto de "codificação de paradigma". O significado não é o mesmo para homens e mulheres. Laços sociais das redes sociais criadas diariamente pela confiança e solidariedade são valorizados cuidado diferente, porque as experiências sociais e fatos resultantes da auto-confiança, auto-eficácia e de apoio social, principalmente, auto-gestão e controle em relação a doença. Os recursos sociais de um indivíduo são reificadas para a gestão o cuidado da doença como uma estratégia para reduzir as desigualdades na saúde.

Rotational isomerism of some chloroacetamides: theoretical and experimental studies through calculations, infrared and NMR.

The geometries involved in the conformational equilibria of 2,2-dichloro-N-cyclohexyl-N-methyl-acetamide (DCCMA) and 2-chloro-N,N-dicyclohexylacetamide (CDCA) were investigated. Theoretical calculations at the B3LYP/cc-pVDZ level of theory showed that gauche forms (ClCCO) are the most stable and the predominant conformers in isolated phase. Both compounds had the conformational behavior in solvents of different polarities estimated from theoretical calculations with the PCM (Polarizable Continuum Model), at the same level of theory, using infrared data from deconvolution of the carbonyl absorption bands and (13)C NMR spectra. Their IR spectra showed two carbonyl absorptions and that the conformer with the highest dipole moment had its population increased when the most polar solvents were used, in accordance with the theoretical calculation in solution. (1)JCH coupling constants were obtained from their NMR spectra, and revealed that there was population variation of conformers with solvent exchange. Experimental data (NMR and IR) as well as calculations including the solvent effects followed the same trend.

MDWiZ: a platform for the automated translation of molecular dynamics simulations.

A variety of popular molecular dynamics (MD) simulation packages were independently developed in the last decades to reach diverse scientific goals. However, such non-coordinated development of software, force fields, and analysis tools for molecular simulations gave rise to an array of software formats and arbitrary conventions for routine preparation and analysis of simulation input and output data. Different formats and/or parameter definitions are used at each stage of the modeling process despite largely contain redundant information between alternative software tools. Such Babel of languages that cannot be easily and univocally translated one into another poses one of the major technical obstacles to the preparation, translation, and comparison of molecular simulation data that users face on a daily basis. Here, we present the MDWiZ platform, a freely accessed online portal designed to aid the fast and reliable preparation and conversion of file formats that allows researchers to reproduce or generate data from MD simulations using different setups, including force fields and models with different underlying potential forms. The general structure of MDWiZ is presented, the features of version 1.0 are detailed, and an extensive validation based on GROMACS to LAMMPS conversion is presented. We believe that MDWiZ will be largely useful to the molecular dynamics community. Such fast format and force field exchange for a given system allows tailoring the chosen system to a given computer platform and/or taking advantage of a specific capabilities offered by different software engines.

Conformational analysis of some N,N-diethyl-2-[(4'-substituted) phenylthio] acetamides.

The conformational analysis of some N,N-diethyl-2[(4'-substituted)phenylthio]acetamides bearing the substituents OMe 1, Me 2, H 3, Cl 4, Br 5 and NO26, was performed by νCO IR analysis, along with B3LYP/6-311++G(d,p) and Polarisable Continuum Model (PCM) calculations, as well as NBO analysis for 1, 3, and 6 and X-ray diffraction for 4. The results of the calculations indicated the existence of two stable conformation pairs, i.e. gauche (anti; syn) (most stable) and cis (anti; syn) in the gas phase. The gauche conformers were less polar with respect to the cis ones for 1 and 3, but more polar for 6. The most intense IR carbonyl doublet component observed at the lower frequency can be ascribed to the gauche conformers g(anti; syn) for 3-6 in n-C6H14, which is in agreement with the gauche and cis relative stabilities and frequencies resulting from the PCM calculations. Similarly, the single IR band for 1 and 2 in n-hexane may be attributed to the gauche conformers. The PCM calculations compared well with the IR data for the compounds in solution, showing that there is a progressive increase of the cis/gauche population ratio as the solvent polarity increases. The NBO analysis indicated that the gauche(anti; syn) conformation in the gas phase was stabilized by the relevant LPS4→πC2O1(∗),πC2O1→σC3S4(∗),σC3S4→πC2O1(∗),πC2O1(∗)→σC3S4(∗), and LPO1→σ(∗)C11H28 orbital interactions, which were absent in the cis(anti; syn) conformer. On the contrary, the cis conformer for derivatives 1, 3, and 6 were stabilized by the σC3-S4(∗)→σ(∗)C2N5 orbital interaction (through bond coupling), along with the additional LPO1→σ(∗)S4C10 interaction for 6. Moreover, the electrostatic repulsion between the C(δ+)S(δ-) and C(δ+)O(δ-) dipoles (Repulsive Field Effect) contributed to both the larger destabilization and increase of the νCO frequency of the cis conformer with respect to the gauche conformer. X-ray single crystal analysis indicates that compound 4 assumes the c2(anti) conformation in the solid state, which is the conformation obtained by compound 6 in the gas phase. To obtain the largest energy gain, the molecules were arranged in the crystal in a six-molecules synthon mediated by CH⋯O and Cl⋯Cl interactions, where the chlorine atoms were related by a crystallographic inversion center.