Dissimilar Molecules Research Articles

Prediction of fluid-phase behavior of symmetrical binary Yukawa fluids using transition matrix Monte Carlo

Binary fluid mixtures display a wide array of fluid phase behavior ranging from simple vapor-liquid equilibrium diagrams to more complicated topology like azeotropy and heteroazeotropy. As a first step towards understanding the phenomena of equilibrium of binary molecular systems, the properties of binary monoatomic fluids have been studied in this work. An additional simplification made in this work is that of a symmetrical binary system where all similar molecules interact via the hard-core Yukawa (HCY) potential, u(r), while the dissimilar molecules interact via a potential, δu(r) where δ is a scalar parameter. The value of δ here is 0.75, which leads to the dissimilar molecules showing a tendency to dislike one another and the resulting phase diagram is such that the mixing-demixing line intersects the vapor-liquid equilibrium curve away from the vapor-liquid critical point. The effect of the variable potential range parameter of the HCY potential on the topology of the phase diagrams is investigated using grand canonical transition matrix Monte Carlo simulations and the conditions of temperature and pressure at which the system exhibits azeotropy and heteroazeotropy are ascertained. We find that the densities of the mixtures, as predicted by our simulation at equimolar concentrations, are in close agreement with the self-consistent Ornstein-Zernike approximation results of Schöll-Paschinger and co-workers.

Bioactivity of permselective PVA hydrogels with mixed ECM analogues.

The presentation of multiple biological cues, which simulate the natural in vivo cell environment within artificial implants, has recently been identified as crucial for achieving complex cellular functions. The incorporation of two or more biological cues within a largely synthetic network can provide a simplified model of multifunctional ECM presentation to encapsulated cells. Therefore, the aim of this study was to examine the effects of simultaneously and covalently incorporating two dissimilar biological molecules, heparin and gelatin, within a PVA hydrogel. PVA was functionalized with 7 and 20 methacrylate functional groups per chain (FG/c) to tailor the permselectivity of UV photopolymerized hydrogels. Both heparin and gelatin were covalently incorporated into PVA at an equal ratio resulting in a final PVA:heparin:gelatin composition of 19:0.5:0.5. The combination of both heparin and gelatin within a PVA network has proven to be stable over time without compromising the PVA base characteristics including its permselectivity to different proteins. Most importantly, this combination of ECM analogues supplemented PVA with the dual functionalities of promoting cellular adhesion and sequestering growth factors essential for cellular proliferation. Multi-functional PVA hydrogels with synthetically controlled network characteristics and permselectivity show potential in various biomedical applications including artificial cell implants.

Excess molar enthalpies of R-fenchone + propan-1-ol or +propan-2-ol. Modeling with COSMO-RS and UNIFAC

In this paper, experimental excess molar enthalpies for the binary mixtures of R-fenchone with propan-1-ol or propan-2-ol, at four temperatures (283.15, 298.15, 313.15 and 328.15)K and atmospheric pressure are reported over the entire composition range. They have been fitted to the Redlich–Kister equation at each temperature. Excess molar enthalpies are positive in all cases, being greater for the mixture with propan-2-ol than for the mixture with propan-1-ol. These positive values of the excess enthalpy suggest the predominance of the effect due to hydrogen bond breaking over the interaction between dissimilar molecules in the mixture. Finally UNIFAC (Dortmund) method and the Quantum Continuum Method COSMO-RS have been used to predict the excess molar enthalpies. Better predictions are obtained in the case of UNIFAC model.

Anesthetics act in quantum channels in brain microtubules to prevent consciousness.

The mechanism by which anesthetic gases selectively prevent consciousness and memory (sparing non-conscious brain functions) remains unknown. At the turn of the 20(th) century Meyer and Overton showed that potency of structurally dissimilar anesthetic gas molecules correlated precisely over many orders of magnitude with one factor, solubility in a non-polar, 'hydrophobic' medium akin to olive oil. In the 1980s Franks and Lieb showed anesthetics acted in such a medium within proteins, suggesting post-synaptic membrane receptors. But anesthetic studies on such proteins yielded only confusing results. In recent years Eckenhoff and colleagues have found anesthetic action in microtubules, cytoskeletal polymers of the protein tubulin inside brain neurons. 'Quantum mobility' in microtubules has been proposed to mediate consciousness. Through molecular modeling we have previously shown: (1) olive oil-like non-polar, hydrophobic quantum mobility pathways ('quantum channels') of tryptophan rings in tubulin, (2) binding of anesthetic gas molecules in these channels, and (3) capabilities for π-electron resonant energy transfer, or exciton hopping, among tryptophan aromatic rings in quantum channels, similar to photosynthesis protein quantum coherence. Here, we show anesthetic molecules can impair π-resonance energy transfer and exciton hopping in tubulin quantum channels, and thus account for selective action of anesthetics on consciousness and memory.

Study of dipolar association in polar–polar system of ethyl methyl ketone (EMK) and carboxylic acids vis-à-vis molecular interaction

Dielectric constant of binary mixtures of ethyl methyl ketone (EMK) with some carboxylic acid, namely, acetic acid, propionic acid, and butyric acid, is measured at 303.16 K and 455 kHz. The data are used to compute the mutual correlation factor, gab, excess molar polarization, ΔP, and excess Gibbs free energy, ΔG, of mixing to study the molecular interaction. The study reveals that interaction is maximum in EMK + butyric acid system and microheterogeneous β-clusters with antiparallel orientation of dissimilar molecules predominate in it.

Ebulliometric determination of vapor–liquid equilibria for binary mixtures of NMP with some cyclic compounds

Vapor–liquid equilibrium results of the binary systems of N-methyl-2-pyrrolidone with cyclohexylamine, cyclohexanol, and cyclohexene at the local atmospheric pressure of 95.3kPa are experimentally obtained in the entire composition range of the component liquids using Swietoslawski ebulliometer. The experimental data are correlated with Wilson model. The investigated systems show positive and negative deviations from Raoult's law, and also indicate the non-formation of azeotropic mixtures. The liquid phase activity coefficients are estimated considering the non-ideal behavior of the mixtures. Computed vapor phase mole fractions, activity coefficients, and the values of excess Gibbs energy with the optimum Wilson parameters are presented and the results are correlated to the molecular interactions between the dissimilar molecules of the binary mixtures.

“Partial pressures” of humid air in wide pressure and temperature ranges

“Partial pressure” in humid air is a question very much concerned by scientists and no satisfactory answer has been found to date. This paper proposes a novel method to obtain the “partial pressures” of the water vapor and dry air in humid air. The results obtained by the proposed method are quite different from that obtained by Dalton’s partial pressure law. The fundamental behaviors of water vapor and dry air are studied in depth in wide pressure and temperature ranges. Semi-permeable membrane models are proposed and applied for both saturated and unsaturated humid air. “Improvement factors” are developed to quantitatively describe the magnitude of the interaction between dissimilar molecules. One discovery is that the “partial pressure” of the water vapor in saturated humid air equals Ps, rather than (f·Ps) which was formerly believed. The other is that the interaction between dissimilar molecules may be omitted when temperature is above “cutting-off temperature” for unsaturated humid air. This paper satisfactorily answers the quest of “partial pressures” in humid air from a new perspective.

New calculation method for thermodynamic properties of humid air in humid air turbine cycle – The general model and solutions for saturated humid air

The article proposes a new calculation method for thermodynamic properties (i.e. specific enthalpy, specific entropy and specific volume) of humid air in humid air turbine cycle. The research pressure range is from 0.1 MPa to 5 MPa. The fundamental behaviors of dry air and water vapor in saturated humid air are explored in depth. The new model proposes and verifies the relationship between total gas mixture pressure and gas component pressures. This provides a good explanation of the fundamental behaviors of gas components in gas mixture from a new perspective. Another discovery is that the water vapor component pressure of saturated humid air equals PS, always smaller than its partial pressure (f·PS) which was believed in the past researches. In the new model, “Local Gas Constant” describes the interaction between similar molecules. “Improvement Factor” is proposed for the first time by this article, and it quantitatively describes the magnitude of interaction between dissimilar molecules. They are combined to fully describe the real thermodynamic properties of humid air. The average error of Revised Dalton's Method is within 0.1% compared to experimentally-based data.

Revised Dalton's method for calculation of thermodynamic properties of unsaturated humid air and gas mixture after combustion in humid air turbine cycle

The article applies Revised Dalton's method for calculation of thermodynamic properties (i.e. specific enthalpy, specific entropy and specific volume) of unsaturated humid air and gas mixture after combustion in humid air turbine cycle. The research temperature range is from 280 K to 1600 K and pressure range from 0.1 MPa to 5 MPa. “Improvement Factor” and “Cutting Off Temperature” for unsaturated humid air are explored in depth. Two “Improvement Factor” formulas are proposed. The discovery of the changing trends of “Improvement Factors” reveals the fundamental behaviors of dry air and water vapor in unsaturated humid air. Another discovery is “Cutting Off Temperature”. It is a crucial temperature point, above which the interaction of dissimilar molecules may be omitted. Revised Dalton's method may also be applied to gas mixture after combustion. The thermodynamic properties of unsaturated humid air and gas mixture after combustion are calculated by the Revised Dalton's method. The average error of Revised Dalton's method is within 0.1% compared to experimental data.

N-(5-Nitro-1,3-thiazol-2-yl)-4-(trifluoromethyl)benzamide

There are two independent and conformationally dissimilar mol­ecules (A and B) in the asymmetric unit of the title compound, C11H6F3N3O3S; the dihedral angles between the benzene and thia­zole rings are 33.8 (2)° in A and 59.7 (2)° in B. The similarity of the C—N bond lengths in the amide group [1.379 (5) and 1.358 (5) Å for A, and 1.365 (5) and 1.363 (5) Å for B] indicates the presence of conjugation between the two rings. In the crystal, mol­ecules are linked by N—H⋯N hydrogen bonds, forming chains extending along [010]; weak N—H⋯Oamide inter­actions are also present in the structure.

Dissimilar stability of proteins in graphene bilayer: a molecular dynamics study

In order to study protein stability on graphene surface and in a confined space simultaneously, two parallel graphene single layers were built and two structurally dissimilar protein molecules were placed in between. Molecular dynamics simulation results showed a significant denaturing effect of graphene layers on GA module, a 3-α helices bundle protein, while another α/β structure protein, protein G, kept its NMR structure intact throughout all simulations. Such extremely different denaturation behaviours of the proteins offer a good chance to investigate the mechanism of graphene toxicity. Further analysis showed Van der Waals interaction could be the main cause of the denaturing effect. Although the solvation effect can contribute, its contribution is not comparable with the Van der Waals interaction.

Retrained Classification of Tyrosinase Inhibitors and “In Silico” Potency Estimation by Using Atom-Type Linear Indices

In this paper, the authors present an effort to increase the applicability domain (AD) by means of retraining models using a database of 701 great dissimilar molecules presenting anti-tyrosinase activity and 728 drugs with other uses. Atom-based linear indices and best subset linear discriminant analysis (LDA) were used to develop individual classification models. Eighteen individual classification-based QSAR models for the tyrosinase inhibitory activity were obtained with global accuracy varying from 88.15-91.60% in the training set and values of Matthews correlation coefficients (C) varying from 0.76-0.82. The external validation set shows globally classifications above 85.99% and 0.72 for C. All individual models were validated and fulfilled by OECD principles. A brief analysis of AD for the training set of 478 compounds and the new active compounds included in the re-training was carried out. Various assembled multiclassifier systems contained eighteen models using different selection criterions were obtained, which provide possibility of select the best strategy for particular problem. The various assembled multiclassifier systems also estimated the potency of active identified compounds. Eighteen validated potency models by OECD principles were used.

Thermodynamic properties of 1‐ETHYL‐3‐methylimidazolium methanesulphonate with aromatic sulphur, nitrogen compounds at T = 298.15–323.15 K and P = 1 bar

AbstractThis work investigates the ability of 1‐ethyl‐3‐methylimidazolium methanesulphate ([EMIM][MeSO3]) as a green and tuneable solvent for denitrification and desulphurisation studies. Experimental density, surface tension and refractive index data have been measured for the following systems: [EMIM][MeSO3] (1) + pyridine (2), [EMIM][MeSO3] (1) + pyrrole (2), [EMIM][MeSO3] (1) + quinoline (2), [EMIM][MeSO3] (1) + indoline (2), [EMIM][MeSO3] (1) + thiophene (2) and [EMIM][MeSO3] (1) + water (2) over the entire mole fraction of [EMIM][MeSO3] at T = 298.15–323.15 K and P = 1 bar. Further from experimental density, surface tension and refractive index, coefficient of thermal expansivity, excess molar volume, deviation of surface tension and refractive index deviation were also calculated. It was found that the heteroaromatic nitrogen/sulphur compounds are completely miscible in [EMIM][MeSO3]. The surface tension values were found to increase while the refractive index decreases with increasing mole fraction of [EMIM][MeSO3]. The experimental values for surface tension increased in the order: pyridine > thiophene > pyrrole > indoline > quinoline > water and for refractive index: pyridine > pyrrole > indoline > quinoline > thiophene > water. It was found that the composition of [EMIM][MeSO3] has a greater influence than temperature in deciding the surface, optical and thermodynamic properties for similar molecular interaction such as IL–thiophene and IL–pyrrole than dissimilar molecules such as IL–water. Further quantum chemical‐based COSMO‐RS tool was used to estimate the activity coefficient at different composition. © 2012 Canadian Society for Chemical Engineering

Refractive Index of Liquid Mixtures: Theory and Experiment

An innovative approach is presented to interpret the refractive index of binary liquid mixtures. The concept of refractive index "before mixing" is introduced and shown to be given by the volume-fraction mixing rule of the pure-component refractive indices (Arago-Biot formula). The refractive index of thermodynamically ideal liquid mixtures is demonstrated to be given by the volume-fraction mixing rule of the pure-component squared refractive indices (Newton formula). This theoretical formulation entails a positive change of refractive index upon ideal mixing, which is interpreted in terms of dissimilar London dispersion forces centred in the dissimilar molecules making up the mixture. For real liquid mixtures, the refractive index of mixing and the excess refractive index are introduced in a thermodynamic manner. Examples of mixtures are cited for which excess refractive indices and excess molar volumes show all of the four possible sign combinations, a fact that jeopardises the finding of a general equation linking these two excess properties. Refractive indices of 69 mixtures of water with the amphiphile (R,S)-1-propoxypropan-2-ol are reported at five temperatures in the range 283-303 K. The ideal and real refractive properties of this binary system are discussed. Pear-shaped plots of excess refractive indices against excess molar volumes show that extreme positive values of excess refractive index occur at a substantially lower mole fraction of the amphiphile than extreme negative values of excess molar volume. Analysis of these plots provides insights into the mixing schemes that occur in different composition segments. A nearly linear variation is found when Balankina's ratios between excess and ideal values of refractive indices are plotted against ratios between excess and ideal values of molar volumes. It is concluded that, when coupled with volumetric properties, the new thermodynamic functions defined for the analysis of refractive indices of liquid mixtures give important complementary information on the mixing process over the whole composition range.

Novel coumarin-based tyrosinase inhibitors discovered by OECD principles-validated QSAR approach from an enlarged, balanced database

The present work is devoted to the development and application of a multi-agent Quantitative Structure-Activity Relationship (QSAR) classification system for tyrosinase inhibitor identification, in which the individual QSAR outputs are the inputs of a fusion approach based on the voting mechanism. The individual models are based on TOMOCOMD-CARDD (TOpological Molecular COMputational Design-Computer Aided Rational Drug Design) atom-based bilinear descriptors and Linear Discriminant Analysis (LDA) on a novel enlarged, balanced database of 1,429 compounds within 701 greatly dissimilar molecules presenting anti-tyrosinase activity. A total of 21 adequate models are obtained taking into account the requirements of the Organization for Economic Cooperation and Development (OECD) principles for QSAR validation and present global accuracies (Q) above 84.50 and 79.27% in the training and test sets, respectively. The resulted fusion system is used for the in silico identification of synthesized coumarin derivatives as novel tyrosinase inhibitors. The 7-hydroxycoumarin (compound C07) shows potent activity for the inhibition of monophenolase activity of mushroom tyrosinase giving a value of inhibition percentage close to 100% in vitro assays, by means of spectrophotometric analysis. The current report could help to shed some clues in the identification of new chemicals that inhibit tyrosinase enzyme, for entering in the pipeline of drug discovery development.

Enantioselective interaction of carbamoylated quinine and (S)-3,5-dinitrobenzoyl alanine: theoretical and experimental circular dichroism study

The interaction between tert-butylcarbamoylquinine selector and (S)-3,5-dinitrobenzoyl alanine selectand was studied experimentally and theoretically by chiroptical methods. Using a combination of experimental and calculated circular dichroism spectra, we present the first work dealing with the interaction of two dissimilar chiral molecules interacting by diverse types of interactions: ion pairing, hydrogen bonding and π-π stacking. Conformational analysis of the free selector, free selectand and the complex of selector with selectand was carried out and the obtained conformers were optimized at the BHandH/6-31+G** and B97d/6-31+G** levels. Consequently, vibrational (VCD) and electronic (ECD) circular dichroism spectra were calculated at the BHandH/6-31+G** and B97d/6-31+G** levels for the VCD and HF/6-31++G** and CAM-B3LYP/6-31++G** levels for the ECD. Spectral patterns of the free selectand and selector together with the complexation-induced spectral changes were compared with experimental data. Despite many simplifications within the theoretical model, the calculated ECD and VCD spectra are in good agreement with experimental data, which proves that the density functional theory (DFT) methods are able to model complicated systems interacting via multiple interactions of different natures.

Graph-theoretical comparison of protein surfaces reveals potential determinants of cross-reactivity and the molecular mimicry

Different proteins, even without sequence similarity, still can contain similar surface regions involved in protein–protein interactions with common target. These regions can serve as structural determinants of cross-reactivity and molecular mimicry. Molecular mimicry, defined as the process in which structural properties of one molecule are simulated by the dissimilar molecules, is implicated in several biologically important processes, including autoimmune and allergic reactions, binding of some ligands to common receptor, and interactions in cell signaling. The problem of identification of the determinants of molecular mimicry is not completely solved at this time. We hypothesize that identification of structurally and chemically similar surface regions of two protein molecules capable of binding to the same target will allow us to identify sites involved in cross-reactivity including determinants of the molecular mimicry. We used a graph-theoretical approach in order to determine highly similar surface regions of two proteins with known three-dimensional structures. This approach uses a variation of Maximal Common Subgraph (MCS) isomorphism, where an association graph is constructed based on the surface-exposed residues of the two molecules and the matching regions are found based on the maximum cliques in the association graph. Testing the proposed method on the targets of autoantibody involved in antiphopholipid syndrome (APS) – β2-GPI, PC, thrombin, factor IX, factor X, and plasmin allowed identifying potential epitopes for antibody that can inhibit coagulation proteases. Application of this method to the Activated Protein C and factor VII Gla-domains revealed surface regions involved in EPCR and plasma membrane binding, consistent with known experimental results. Analysis of major pollen allergen that can cause food allergies through cross-reactivity found known epitopes involved in cross-reactivity and also revealed additional surface regions that can complement the list of epitopes. Taken together, our results suggest that the proposed graph-theoretical approach can identify determinants of cross-reactivity and molecular mimicry.

Atom- and Bond-Based 2D TOMOCOMD-CARDD Approach and Ligand-Based Virtual Screening for the Drug Discovery of New Tyrosinase Inhibitors

Two-dimensional atom- and bond-based TOMOCOMD-CARDD descriptors and linear discriminant analysis (LDA) are used in this report to perform a quantitative structure-activity relationship (QSAR) study of tyrosinase-inhibitory activity. A database of inhibitors of the enzyme is collected for this study, within 246 highly dissimilar molecules presenting antityrosinase activity. In total, 7 discriminant functions are obtained by using the whole set of atom- and bond-based 2D indices. All the LDA-based QSAR models show accuracies above 90% in the training set and values of the Matthews correlation coefficient (C) varying from 0.85 to 0.90. The external validation set shows globally good classifications between 89% and 91% and C values ranging from 0.75 to 0.81. Finally, QSAR models are used in the selection/identification of the 20 new dicoumarins subset to search for tyrosinase inhibitory activity. Theoretical and experimental results show good correspondence between one another. It is important to remark that most compounds in this series exhibit a more potent inhibitory activity against the mushroom tyrosinase enzyme than the reference compound, Kojic acid (IC(50) = 16.67 muM), resulting in a novel nucleus base (lead) with antityrosinase activity, and this could serve as a starting point for the drug discovery of novel tyrosinase inhibitor lead compounds. ( Journal of Biomolecular Screening 2008:1014-1024).

Salting-Out of Lysozyme and Ovalbumin from Mixtures: Predicting Precipitation Performance from Protein−Protein Interactions

Protein−protein interactions, whether desirable or not, can have direct effects on protein separations. The most obvious of these are interactions between similar molecules, which determine the thermodynamic properties and phase behavior of protein solutions. Interactions between dissimilar molecules also affect the properties and phase behavior of protein mixtures and, therefore, protein separations. Here, we seek to quantify these effects by comparing precipitation behavior from binary solutions with direct measurements of protein−protein interactions using cross-interaction chromatography, which is a variant of affinity chromatography that provides data that can be interpreted in terms of the virial cross-coefficient. First, the effects of pH, ionic strength, different precipitants and the initial protein concentrations and their ratio on the binary precipitation of lysozyme and ovalbumin were investigated. Next, self- and cross-interaction measurements were used to suggest the optimal precipitation conditions for separating lysozyme from ovalbumin. The results show that protein interactions can explain anomalies and inconsistencies that frequently confound the extraction of meaningful general trends in separations analyses.

The equation of state for gas mixtures in the canonical form

The T 0 and ρ variables, where ρ is the density and T 0 the parametric temperature depending on T and ρ, were introduced to obtain the equation of state of a mixture for the Helmholtz energy. The equation explicitly includes an analogue of a pure substance as a component. Its properties are determined by the interactions of dissimilar molecules.