Searching for the Achilles' Heel of Urethane Linkage-An Energetic Perspective.

A sudden increase in polyurethane (PU) production necessitates viable recycling methods for the waste generated. PU is one of the most important plastic materials with a wide range of applications; however, the stability of the urethane linkage is a major issue in chemical recycling. In this work, termination reactions of a model urethane molecule, namely methyl N-phenyl carbamate (MPCate), are investigated using G3MP2B3 composite quantum chemical method. Our main goal was to gain insights into the energetic profile of urethane bond termination and find an applicable chemical recycling method. Hydrogenation, hydrolysis, methanolysis, peroxidation, glycolysis, ammonolysis, reduction with methylamine and termination by dimethyl phosphite were explored in both gas and condensed phases. Out of these chemicals, degradation by H2, H2O2 and CH3NH2 revealed promising results with lower activation barriers and exergonic pathways, especially in water solvation. Implementing these effective PU recycling methods can also have significant economic benefits since the obtained products from the reactions are industrially relevant substances. For example, aniline and dimethyl carbonate could be reusable in polymer technologies serving as potential methods for circular economy. As further potential transformations, several ionizations of MPCate were also examined including electron capture and detachment, protonation/deprotonation and reaction with OH-. Alkaline digestion against the model urethane MPCate was found to be promising due to the relatively low activation energy. In an ideal case, the transformation of the urethane bond could be an enzymatic process; therefore, potential enzymes, such as lipoxygenase, were also considered for the catalysis of peroxidation, and lipases for methanolysis.

Understanding the Molecular Mechanism of Anesthesia: Effect of General Anesthetics and Structurally Similar Non-Anesthetics on the Properties of Lipid Membranes.

General anesthesia can be caused by various, chemically very different molecules, while several other molecules, many of which are structurally rather similar to them, do not exhibit anesthetic effects at all. To understand the origin of this difference and shed some light on the molecular mechanism of general anesthesia, we report here molecular dynamics simulations of the neat dipalmitoylphosphatidylcholine (DPPC) membrane as well as DPPC membranes containing the anesthetics diethyl ether and chloroform and the structurally similar non-anesthetics n-pentane and carbon tetrachloride, respectively. To also account for the pressure reversal of anesthesia, these simulations are performed both at 1 bar and at 600 bar. Our results indicate that all solutes considered prefer to stay both in the middle of the membrane and close to the boundary of the hydrocarbon domain, at the vicinity of the crowded region of the polar headgroups. However, this latter preference is considerably stronger for the (weakly polar) anesthetics than for the (apolar) non-anesthetics. Anesthetics staying in this outer preferred position increase the lateral separation between the lipid molecules, giving rise to a decrease of the lateral density. The lower lateral density leads to an increased mobility of the DPPC molecules, a decreased order of their tails, an increase of the free volume around this outer preferred position, and a decrease of the lateral pressure at the hydrocarbon side of the apolar/polar interface, a change that might well be in a causal relation with the occurrence of the anesthetic effect. All these changes are clearly reverted by the increase of pressure. Furthermore, non-anesthetics occur in this outer preferred position in a considerably smaller concentration and hence either induce such changes in a much weaker form or do not induce them at all.

A Simplified and Efficient Method for Production of Manganese Ferrite Magnetic Nanoparticles and Their Application in DNA Isolation.

A simplified, fast, and effective production method has been developed for the synthesis of manganese ferrite (MnFe2O4) magnetic nanoparticles (MNPs). In addition to the wide applicability of MnFe2O4 MNPs, this work also reports their application in DNA isolation for the first time. An ultrasonic-cavitation-assisted combustion method was applied in the synthesis of MnFe2O4 MNPs at different furnace temperatures (573 K, 623 K, 673 K, and 773 K) to optimize the particles' properties. It was shown that MnFe2O4 nanoparticles synthesized at 573 K consist of a spinel phase only with adequate size and zeta potential distributions and superparamagnetic properties. It was also demonstrated that superparamagnetic manganese ferrite nanoparticles bind DNA in buffer with a high NaCl concentration (2.5 M), and the DNA desorbs from the MNPs by decreasing the NaCl concentration of the elution buffer. This resulted in a DNA yield comparable to that of commercial DNA extraction products. Both the DNA concentration measurements and electrophoresis confirmed that a high amount of isolated bacterial plasmid DNA (pDNA) with adequate purity can be extracted with MnFe2O4 (573 K) nanoparticles by applying the DNA extraction method proposed in this article.

An Ab Initio Investigation on Relevant Oligomerization Reactions of Toluene Diisocyanate (TDI).

2,4- and 2,6-isomers of toluene diisocyanates (2,4-TDI and 2,6-TDI) are important raw materials in the polyurethane industry. These reactive compounds associate even under ambient conditions to form oligomers, changing the physicochemical properties of the raw material. Kinetically and thermodynamically relevant dimerization reactions were selected based on G3MP2B3 calculations from all possible dimers of phenyl isocyanate using these isocyanates as proxies. As it turned out, only the formation of the diazetidine-2,4-dione ring (11-dimer, uretdione) resulted in a species having an exothermic enthalpy of formation (-30.4 kJ/mol at 298.15 K). The oxazetidin-2-one ring product (1-2-dimer) had a slightly endothermic standard enthalpy of formation (37.2 kJ/mol at 298.15 K). The mechanism of the relevant cyclodimerization reactions was investigated further for 2,4-TDI and 2,6-TDI species using G3MP2B3 and SMD solvent model for diazetidine as well as oxazetidin-2-one ring formation. The formation of the uretdione ring structures, from the 2,4-TDI dimer with both NCO groups in the meta position for each phenyl ring and one methyl group in the para and one in the meta position, had the lowest-lying transition state (Δ#E0= 94.4 kJ/mol) in the gas phase. The one- and two-step mechanisms of the TDI cyclotrimerization were also studied based on the quasi-G3MP2B3 (qG3MP2B3) computational protocol. The one-step mechanism had an activation barrier as high as 149.0 kJ/mol, while the relative energies in the two-step mechanism were significantly lower for both transition states in the gas phase (94.7 and 60.5 kJ/mol) and in ODCB (87.0 and 54.0 kJ/mol).

Computational Elucidation of the Solvent-Dependent Addition of 4-Hydroxy-2-nonenal (HNE) to Cysteine and Cysteinate Residues.

The lipid peroxidation end product, 4-hydroxy-2-nonenal (HNE), is a secondary mediator of oxidative stress due to its strong ability to form adducts to the side chains of lysine, histidine, and cysteine residues (Cys) at increasing reactivities. This reaction can take place in various cellular environments and may be dependent on solvent. Moreover, approximately 10% of cysteine residues within the cells exist as the negatively charged cysteinate, which may also have a distinct reactivity toward HNE. In this study, quantum chemical calculations are used to investigate the reactivity of HNE toward Cys and cysteinate in three distinct solvent environments to mimic the aqueous, polar, and hydrophobic regions within the cell. Water enhances the reactivity of HNE to cysteine compared to that of the polar and hydrophobic solvents, and the reactivity of HNE is further augmented when Cys is first ionized to cysteinate. This is also confirmed by the transition state rate constant calculations. This study reveals the role of solvent polarity in these reactions and how cysteinate can account for the seemingly high reactivity of HNE toward Cys compared to other amino acid residues and demonstrates how a strong nucleophile can enhance the reactivity of an antioxidant analogue of the Cys residue.

A Theoretical Study on the Phosgenation of 2,4-Toluenediamine (2,4-TDA).

Industrially relevant phosgenation mechanisms of 2,4-toluenediamine (2,4-TDA) were investigated using G3MP2B3 model chemistry. Six reaction pathways had been explored, which resulted in the formation of toluene diisocyanate (2,4-TDI) including different scenarios of the 'phosgenations first' and 'consecutive phosgenations' mechanisms in both gas and condensed phases. Two possible 'phosgenations first' mechanisms show superior to the others in terms of energy, regardless of which phases are considered. Due to the o-dichlorobenzene (ODCB) solvation, the reaction barriers are dramatically reduced compared to the gas-phase reaction mechanism and the solvent effect can be described by linear relationship. Standard enthalpy of formation value was also recommended for 2,4-TDA (59.3 kJ/mol) and 2,4-TDI (-94.1 kJ/mol), as well as for the gas-phase intermediates (IM).

Vapor-Liquid Equilibrium Study of the Monochlorobenzene-4,6-Dichloropyrimidine Binary System.

The number of newly synthesized and produced organic chemicals has increased extremely quickly. However, the measurements of their physical properties, including their vapor-liquid equilibrium (VLE) data, are time-consuming. It so happens that there is no physical property data about a brand-new chemical. Therefore, the importance of calculating their physicochemical properties has been playing a more and more important role. 4,6-Dichloropyrimidine (DCP) is also a relatively new molecule of high industrial importance with little existing data. Therefore, their measurements and the comparison with the calculated data are of paramount concern. DCP is a widespread heterocyclic moiety that is present in synthetic pharmacophores with biological activities as well as in numerous natural products. Isobaric VLE for the binary system of 4,6-dichloropyrimidine and its main solvent monochlorobenzene (MCB) was measured using a vapor condensate and liquid circulation VLE apparatus for the first time in the literature. Density functional-based VLE was calculated using the COSMO-SAC protocol to verify the laboratory results. The COSMO-SAC calculation was found to be capable of representing the VLE data with high accuracy. Adequate agreement between the experimental and calculated VLE data was acquired with a minimal deviation of 3.0 × 10-3, which allows for broader use of the results.

Computer simulation investigation of the adsorption of acetamide on low density amorphous ice. An astrochemical perspective.

The adsorption of acetamide on low density amorphous (LDA) ice is investigated by grand canonical Monte Carlo computer simulations at the temperatures 50, 100, and 200 K, characteristic of certain domains of the interstellar medium (ISM). We found that the relative importance of the acetamide-acetamide H-bonds with respect to the acetamide-water ones increases with decreasing temperature. Thus, with decreasing temperature, the existence of the stable monolayer, characterizing the adsorption at 200 K, is gradually replaced by the occurrence of marked multilayer adsorption, preceding even the saturation of the first layer at 50 K. While isolated acetamide molecules prefer to lay parallel to the ice surface to maximize their H-bonding with the surface water molecules, this orientational preference undergoes a marked change upon saturation of the first layer due to increasing competition of the adsorbed molecules for H-bonds with water and to the possibility of their H-bond formation with each other. As a result, molecules stay preferentially perpendicular to the ice surface in the saturated monolayer. The chemical potential value corresponding to the point of condensation is found to decrease linearly with increasing temperature. We provide, in analogy with the Clausius-Clapeyron equation, a thermodynamic explanation of this behavior and estimate the molar entropy of condensed phase acetamide to be 34.0 J/mol K. For the surface concentration of the saturated monolayer, we obtain the value 9.1 ± 0.8 µmol/m2, while the heat of adsorption at infinitely low surface coverage is estimated to be -67.8 ± 3.0 kJ/mol. Our results indicate that the interstellar formation of peptide chains through acetamide molecules, occurring at the surface of LDA ice, might well be a plausible process in the cold (i.e., below 50 K) domains of the ISM; however, it is a rather unlikely scenario in its higher temperature (i.e., 100-200 K) domains.

Reaction kinetics of 1,4-cyclohexadienes with OH radicals: an experimental and theoretical study.

This work presents the OH-initiated oxidation kinetics of 1,4-cyclochexadiene (1,4-CHD). The temperature dependence of the reaction was investigated by utilizing a laser flash photolysis flow reactor and laser-induced fluorescence (LPFR/LIF) technique over the temperature range of 295-438 K and a pressure of ∼50 torr. The kinetics of the reaction was followed by measuring the LIF signal of OH radicals near 308 nm. The reaction of OH radicals with 1,4-CHD exhibited a clear negative temperature dependence. To discern the role of various channels, ab initio and RRKM-based ME calculations (RRKM-ME) were performed over temperatures of 200-2000 K and pressures of 0.76-7600 torr. The computed energy profile revealed that the reaction proceeds via the formation of a pre-reaction van der Waals complex at the entrance channel. The complex was found to be more stable than that usually seen in other alkenes + OH reactions. Both the addition channel and the abstraction reaction of allylic hydrogen were found to have negative energy barriers. Interestingly, the abstraction reaction exhibited a negative temperature dependence at low temperatures and contributed significantly (∼37%) to the total rate coefficients even under atmospheric conditions. At T ≥ 900 K, the reaction was found to proceed exclusively (>95%) via the abstraction channel. Due to the competing channels, the reaction of OH radicals with 1,4-CHD displays complicated kinetic behaviours, reflecting the salient features of the energy profile. The role of competing channels was fully characterized by our kinetic model. The calculated rate coefficients showed excellent agreement with the available experimental data.

Description of the Interfacial Behavior of Benzonitrile at Icy Surfaces by Grand Canonical Monte Carlo Simulations.

The adsorption of benzonitrile at the surface of crystalline (Ih) and low-density amorphous (LDA) ice has been investigated by grand canonical Monte Carlo simulations at temperatures ranging from 50 to 200 K. It is found that, in spite of its rather large dipole moment of 4.5 D, benzonitrile molecules can only form a highly unsaturated monolayer on LDA ice, reaching not more than 50% of the surface concentration of the saturated monolayer even at the lowest temperature considered, and they practically do not adsorb on Ih ice. In spite of the observed weak ability of the benzonitrile molecules for being adsorbed, the estimated heat of adsorption at an infinitely low surface concentration of -66.8 ± 2.2 kJ/mol is rather large. This value includes the contribution of roughly -30 to -35 kJ/mol of a benzene ring, about -10 kJ/mol of a large molecular dipole moment, and about -20 to -25 kJ/mol of a benzonitrile-water H-bond, as estimated from comparisons with the heat of adsorption values of similar molecules. The surprisingly weak ability of benzonitrile for adsorption is thus attributed to the unusually strong cohesion between the molecules, considerably exceeding their adhesion to ice, as reflected in the 70-80 kJ/mol difference of the lateral and ice contributions to the binding energy of surface benzonitrile molecules in the presence of condensed benzonitrile.

Optical Study of Solvatochromic Isocyanoaminoanthracene Dyes and 1,5-Diaminoanthracene.

Isocyanoaminoarenes (ICAAr-s) are a novel and versatile group of solvatochromic fluorophores. Despite their versatile applicability, such as antifungals, cancer drugs and analytical probes, they still represent a mostly unchartered territory among intramolecular charge-transfer (ICT) dyes. The current paper describes the preparation and detailed optical study of novel 1-isocyano-5-aminoanthrace (ICAA) and its N-methylated derivatives along with the starting 1,5-diaminoanthracene. The conversion of one of the amino groups of the diamine into an isocyano group significantly increased the polar character of the dyes, which resulted in a significant 50-70 nm (2077-2609 cm-1) redshift of the emission maximum and a broadened solvatochromic range. The fluorescence quantum yield of ICAAs is strongly influenced by the polarity of the solvent. The starting anthracene-diamine is highly fluorescent in every solvent (√f = 12-53%), while the isocyano derivatives are practically nonfluorescent in solvents more polar than dioxane. This phenomenon implies the potential application of ICAAs to probe the polarity of the medium and is favorable in practical applications, such as cell-staining, resulting in a reduced background fluorescence. The ICT character of the emission states of ICAAs are in good agreement with the computational findings presented in TD-DFT calculations and molecular electrostatic potential (MESP) isosurfaces.

The kinetics of the reactions of Br atoms with the xylenes: an experimental and theoretical study.

This work reports the temperature dependence of the rate coefficients for the reactions of atomic bromine with the xylenes that are determined experimentally and theoretically. The experiments were carried out in a Pyrex chamber equipped with fluorescent lamps to measure the rate coefficients at temperatures from 295 K to 346 K. Experiments were made at several concentrations of oxygen to assess its potential kinetic role under atmospheric conditions and to validate comparison of our rate coefficients with those obtained by others using air as the diluent. Br2 was used to generate Br atoms photolytically. The relative rate method was used to obtain the rate coefficients for the reactions of Br atoms with the xylenes. The reactions of Br with both toluene and diethyl ether (DEE) were used as reference reactions where the loss of the organic reactants was measured by gas chromatography. The rate coefficient for the reaction of Br with diethyl ether was also measured in the same way over the same temperature range with toluene as the reference reactant. The rate coefficients were independent of the concentration of O2. The experimentally determined temperature dependence of the rate coefficients of these reactions can be given in the units cm3 molecule-1 s-1 by: o-xylene + Br, log10(k) = (-10.03 ± 0.35) - (921 ± 110)/T; m-xylene + Br, log10(k) = (-10.78 ± 0.09) - (787 ± 92/T); p-xylene + Br, log10(k) = (-9.98 ± 0.39) - (956 ± 121)/T; diethyl ether + Br, log10(k) = (-7.69 ± 0.55) - (1700 ± 180)/T). This leads to the following rate coefficients, in the units of cm3 molecule-1 s-1, based on our experimental measurements: o-xylene + Br, k(298 K) = 7.53 × 10-14; m-xylene + Br, k(298 K) = 3.77 × 10-14; p-xylene + Br, k(298 K) = 6.43 × 10-14; diethyl ether + Br, k(298 K) = 4.02 × 10-14. Various ab initio methods including G3, G4, CCSD(T)/cc-pV(D,T)Z//MP2/aug-cc-pVDZ and CCSD(T)/cc-pV(D,T)Z//B3LYP/cc-pVTZ levels of theory were employed to gain detailed information about the kinetics as well as the thermochemical quantities. Among the ab initio methods, the G4 method performed remarkably well in describing the kinetics and thermochemistry of the xylenes + Br reaction system. Our theoretical calculations revealed that the reaction of Br atoms with the xylenes proceeds via a complex forming mechanism in an overall endothermic reaction. The rate determining step is the intramolecular rearrangement of the pre-reactive complex leading to the post-reactive complex. After lowering the relative energy of the corresponding transition state by less than 1.5 kJ mol-1 for this step in the reaction of each of the xylenes with Br, the calculated rate coefficients are in very good agreement with the experimental data.

Preparation of highly effective carbon black supported Pd-Pt bimetallic catalysts for nitrobenzene hydrogenation.

Carbon black (CB) supported palladium-platinum catalysts were prepared with and without nickel(II) oxide or iron(III) oxide promoter materials. By applying ultrasonic cavitation highly efficient CB supported catalysts were created. The designed catalyst preparation is a one-step procedure, as post-treatments (e.g. calcination, hydrogen activation) are not necessary. The activation of the catalysts occurs during their preparation due to the ultrasonic cavitation. Thus, a fast and simple catalyst preparation procedure have been developed. The activity of the catalysts was compared in nitrobenzene hydrogenation at different temperatures in the range of 283-323 K at 20 bar hydrogen pressure. In terms of selectivity and aniline yield, no significant differences were detected even when promoters were present. By using the NiO promoter, the activation energy was extremely low (7.6 ± 0.7 kJ mol-1). The selectivity was over 99% in every case, and 99.6% aniline yield was achieved without any promoters (99.7% with NiO), while less than 1.0% by-products were formed. The reaction rate was high with every catalyst, and no significant differences were detected. All in all, the prepared catalysts show excellent catalytic activity in the hydrogenation of nitrobenzene.

Transmembrane penetration mechanism of cyclic pollutants inspected by molecular dynamics and metadynamics: the case of morpholine, phenol, 1,4-dioxane and oxane.

The presence of industrially produced chemicals in water is often not monitored, while their passive transport and accumulation can cause serious damage in living cells. Molecular dynamics simulations are an effective way to understand the mechanism of the action of these pollutants. In this paper, the passive membrane transport of 1,4-dioxane, phenol, oxane and morpholine was investigated and analyzed thoroughly from structural and energetic points of view. Free energy profiles for pollutant and water penetration into the bilayer were obtained from well-tempered metadynamics (WT-MD) simulations and a mass density-based approach. It was found that all four investigated compounds can penetrate biological membranes and affect the free energy profile of water penetration. Out of the investigated species, oxane has the thermodynamically most preferred position in the bilayer center, leading to a lower free energy barrier of water molecules by 3 kJ mol-1, resulting in 5 times more water molecules in the bilayer center. The concentration dependence of free energy was tested at two different phenol concentrations using WT-MD, and it was found that the higher phenol concentration lowers the main barrier by 3 kJ mol-1. Density-based free energy calculations were found to reproduce the results of WT-MD within the limits of chemical accuracy.

Theoretical Design, Synthesis, and In Vitro Neurobiological Applications of a Highly Efficient Two-Photon Caged GABA Validated on an Epileptic Case.

In this paper, we present an additional, new cage-GABA compound, called 4-amino-1-(4'-dimethylaminoisopropoxy-5',7'-dinitro-2',3'-dihydro-indol-1-yl)-1-oxobutane-γ-aminobutyric acid (iDMPO-DNI-GABA), and currently, this compound is the only photoreagent, which can be applied for GABA uncaging without experimental compromises. By a systematic theoretical design and successful synthesis of several compounds, the best reagent exhibits a high two-photon efficiency within the 700-760 nm range with excellent pharmacological behavior, which proved to be suitable for a complex epileptic study. Quantum chemical design showed that the optimal length of the cationic side chain enhances the two-photon absorption by 1 order of magnitude due to the cooperating internal hydrogen bonding to the extra nitro group on the core. This feature increased solubility while suppressing membrane permeability. The efficiency was demonstrated in a systematic, wide range of in vitro single-cell neurophysiological experiments by electrophysiological as well as calcium imaging techniques. Scalable inhibitory ion currents were elicited by iDMPO-DNI-GABA with appropriate spatial-temporal precision, blocking both spontaneous and evoked cell activity with excellent efficiency. Additionally, to demonstrate its applicability in a real neurobiological study, we could smoothly and selectively modulate neuronal activities during artificial epileptic rhythms first time in a neural network of GCaMP6f transgenic mouse brain slices.

Computational Study of Catalytic Urethane Formation.

Polyurethanes (PUs) are widely used in different applications, and thus various synthetic procedures including one or more catalysts are applied to prepare them. For PU foams, the most important catalysts are nitrogen-containing compounds. Therefore, in this work, the catalytic effect of eight different nitrogen-containing catalysts on urethane formation will be examined. The reactions of phenyl isocyanate (PhNCO) and methanol without and in the presence of catalysts have been studied and discussed using the G3MP2BHandHLYP composite method. The solvent effects have also been considered by applying the SMD implicit solvent model. A general urethane formation mechanism has been proposed without and in the presence of the studied catalysts. The proton affinities (PA) were also examined. The barrier height of the reaction significantly decreased (∆E0 > 100 kJ/mol) in the presence of the studied catalysts, which proves the important effect they have on urethane formation. The achieved results can be applied in catalyst design and development in the near future.

Membrane Flash Index: Powerful and Perspicuous Help for Efficient Separation System Design.

There are different factors and indices to characterize the performance of a pervaporation membrane, but none of them gives information about their capabilities in the area of liquid separation compared to the most convenient alternative, which is distillation. Membrane flash index (MFLI) can be considered the first and only one that shows if the membrane is more efficient or not than distillation and quantifies this feature too. Therefore, the MFLI helps select the best separation alternative in the case of process design. In this study, the evaluation and capabilities of membrane flash index are comprehensively investigated in the cases of six aqueous mixtures: methyl alcohol-water, ethyl alcohol-water, isobutyl alcohol-water, tetrahydrofuran-water, N-butyl alcohol-water, and isopropanol-water. It must be concluded that the separation capacity of organophilic type membranes is remarkably lower than hydrophilic membranes in all cases of separation. The study of the MFLI is extended with the consideration of other binary interaction parameters like separation factor, permeation flux, selectivity, and pervaporation separation index (PSI) in order to find a descriptive relationship between them. For the same membrane material type, descriptive function can be determined between feed concentration and MFLI and PSI and separation factor, which can be used to calculate each other's value. On the basis of the indices and especially the MFLI, a significant help can be given to the process design engineer to select the right liquid separation alternative and, in the case of pervaporation, find the most appropriate membrane.

Urethane Formation with an Excess of Isocyanate or Alcohol: Experimental and Ab Initio Study.

A kinetic and mechanistic investigation of the alcoholysis of phenyl isocyanate using 1-propanol as the alcohol was undertaken. A molecular mechanism of urethane formation in both alcohol and isocyanate excess is explored using a combination of an accurate fourth generation Gaussian thermochemistry (G4MP2) with the Solvent Model Density (SMD) implicit solvent model. These mechanisms were analyzed from an energetic point of view. According to the newly proposed two-step mechanism for isocyanate excess, allophanate is an intermediate towards urethane formation via six-centered transition state (TS) with a reaction barrier of 62.6 kJ/mol in the THF model. In the next step, synchronous 1,3-H shift between the nitrogens of allophanate and the cleavage of the C-N bond resulted in the release of the isocyanate and the formation of a urethane bond via a low-lying TS with 49.0 kJ/mol energy relative to the reactants. Arrhenius activation energies of the stoichiometric, alcohol excess and the isocyanate excess reactions were experimentally determined by means of HPLC technique. The activation energies for both the alcohol (measured in our recent work) and the isocyanate excess reactions were lower compared to that of the stoichiometric ratio, in agreement with the theoretical calculations.

Molecular Dynamics and Metadynamics Insights of 1,4-Dioxane-Induced Structural Changes of Biomembrane Models.

1,4-Dioxane is a cytotoxic B2-type human carcinogen, a serious water pollutant produced solely by industrial activity. The effect of 1,4-dioxane on phospholipid membrane models composed of dipalmitoyl-phosphatidylcholine (DPPC) and its branched isomer (isodipalmitoyl-phosphatidylcholine, IPPC) was investigated using MD simulations. Clear and polluted membranes were compared by membrane parameters such as area per lipid (APL), volume per lipid (VPL), compressibility modulus, membrane thickness, and orderliness of lipid tails. While neat systems significantly differ from each other, the presence of the pollutant has the same effect on both types of lipid membranes. High density of dioxane appears in the vicinity of ester groups, which pushes away lipid headgroups from each other, leading to an overall change in lipid structure: APL and VPL grows, while the orderliness of lipid tails, membrane thickness, and compressibility modulus decrease. Orientational preferences of water and dioxane molecules were also investigated and different membrane regions have been specified according to the stance of water molecules. Free-energy profile for 1,4-dioxane penetration mechanism into DPPC membranes was carried out using metadynamics for two different concentrations of the pollutant (c1 = 7.51 g/dm3, c2 = 75.10 g/dm3), which showed that the higher the concentration is, the lower the free energy of penetration gets. Only a small free-energy barrier was found in the headgroup region and accumulation of dioxane is thermodynamically unfavored in the middle of the bilayer. The penetration mechanism has been described in detail based on the orientational preference of 1,4-dioxane molecules and the free-energy profiles.

Oxidatively-mediated in silico epimerization of a highly amyloidogenic segment in the human calcitonin hormone (hCT15-19).

In order to study the effects of peptide exposure to oxidative attack, we chose a model reaction in which the hydroxyl radical discretely abstracts a hydrogen atom from the α-carbon of each residue of a highly amyloidogenic region in the human calcitonin hormone, hCT15-19. Based on a combined Molecular Mechanics / Quantum Mechanics approach, the extended and folded L- and D-configuration and radical intermediate hCT15-19 peptides were optimized to obtain their compactness, secondary structure and relative thermodynamic data. The results suggest that the epimerization of residues is generally an exergonic process that can explain the cumulative nature of molecular aging. Moreover, the configurational inversion induced conformational changes can cause protein dysfunction. The epimerization of the central residue to the D-configuration induced a hairpin structure in hCT15-19, concomitant with a possible oligomerization of human calcitonin into Aß(1-42)-like amyloid fibrils present in patients suffering from Alzheimer's disease.