Chemical similarity of molecules with physiological response

Measuring the similarity among molecules is an important task in various chemically oriented problems. This elusive concept is hard to define and quantify. Moreover, the complexity of the problem is elevated by bifurcating the notion of molecular similarity to structural and chemical similarity. While the structural similarity of molecules is being extensively researched, the so-called chemical similarity is being mentioned scarcely. Here, we propose a way of converting the physico-chemical properties into molecular fingerprints. Then, using the apparatus of measuring the structural similarity, the chemical similarity can be assessed. The proof of a concept is demonstrated on a set of molecules that induce diverse physiological responses.

Modified Born method for modeling melting temperature using ab initio molecular dynamics

The prediction of a material's melting point through computational methods is a very difficult problem due to system size requirements, computational efficiency and accuracy within current models. In this work, we have used a newly developed metric to analyze the trends within the elastic tensor elements as a function of temperature to determine the melting point of Au, Na, Ni, SiO2 and Ti within 20 K. This work uses our previously developed method of calculating the elastic constants at finite temperatures, as well as leveraging those calculations into a modified Born method for predicting melting point. While this method proves to be computationally expensive, the level of accuracy of these predictions is very difficult to reach using other existing computational methods.&#xD.

Experimental and theoretical study of the physicochemical properties of the novel imidazole-based eutectic solvent

Novel solvents and their applications are experiencing an increasing interest by the scientific community. Imidazole has been utilized as a major component in many successful ionic liquids. However, very limited studies were reported for using it as a hydrogen bond acceptor in the synthesis of eutectic solvents. In this work, a novel eutectic solvent composed of Imidazole and Monoethanolamine (MEA) is synthesized at different molar ratios. The basic physicochemical properties such as melting point, density, viscosity, and refractive index were measured at different temperatures and modeled as a function of molar composition and temperature. FTIR and ¹H NMR analyses were conducted and, the nature and strength of the molecular interaction between the two solvent molecules were investigated by conducting combined molecular dynamics (MD) simulations and density functional theory (DFT) calculations. The study revealed the electrostatic H-bonding nature of interaction with strength related to their bond distances. The binding energy between the two DES ingredients is proportional to the amount of MEA in the DES due to increasing the H-bonding interactions between Imidazole and MEA molecules. These findings suggest that DES might be used in a variety of chemical and industrial applications.

Development of a novel rheological method for determining melting properties of gelatin-based gummies

In this study, a novel rheometer-based method was explored to determine the melting point of gummy, which is one of the most consumed confectionery products. The new method is based on the vertical deformation of a solid sample since melting points of the products were determined by performing onset analysis on the graph of gap values against temperature. Peltier system heating rate and sample thickness parameters were used to develop the method. To verify the obtained melting points, time sweep tests in the rheometer at constant temperature, conventional oven and water bath analysis, thermograms of the samples obtained from differential scanning calorimetry (DSC) and their microstructures at various temperatures with polarized light microscopy (PLM) were examined. Herein, it can be realized that the developed method detects the melting point of a gummy with a sensitivity of 1 °C when temperature increase rate and thickness values were 1 °C/min and 4000 μm, respectively. As a result of the application of the novel method for the commercial samples, the melting points of C1 and C2 gummy samples were determined as 45 °C and verified by other experiments with one unit of precision. Therefore, the method has brought a different perspective to the melting temperature analysis with ease of use and short-term detection by sensitive and reproducible results. Besides, it has come to the forefront as it allows the studied materials to be used in solid form in the rheometer.

Model prediction of herbicide residues in soybean oil: Relationship between physicochemical properties and processing factors

The distribution and processing factors (PFs) of herbicides in cold-/hot-pressed soybean samples (n = 3) were studied on the laboratory scale. The hot-pressing process was found to have a significant effect on herbicide degradation in soybean samples. Specifically, for highly water-soluble pesticides with pK_ow > 2 in soybean oil, the PF values were generally > 1. Nonlinear curve fitting revealed that the PFs of herbicides in soybean oil were positively correlated with their octanol-water partition coefficients, but negatively correlated with their water solubility and melting points. A principal component analysis confirmed the dominant parameters among the herbicide PFs during soybean oil production. Using the physicochemical parameters of pesticides, the developed multiple linear regression model gave a fitting accuracy of ≥0.80 for predicting the theoretical PF values of pesticides in soybean oil products (0.39 < RMSE < 0.58). Thus, this model may be applicable for safety risk assessments and establishing maximum residue limits for pesticides in processed products.

Molecular dynamics simulation of 1-methyl-4,5-dinitroimidazole (MDNI)/1-methyl-3,4,5-trinitropyrazole (MTNP) eutectic mixtures

1-Methyl-4,5-dinitroimidazole (MDNI)/1-methyl-3,4,5-trinitropyrazole (MTNP) mixtures with different mass ratios were investigated by a combination of theory and experiment. The melting points were predicted using the relationships of specific volume versus temperature, non-bond energy versus temperature, and diffusion coefficient versus temperature, and compared with the experimental values. It was found that the melting point values obtained from the three relationships were in good agreement with the experimentally measured melting points with little error. The interactions between MDNI/MTNP were analyzed by binding energy and RDF, and the results showed that, as the temperature increased, the intermolecular interactions weakened, the binding energy decreased, and the stability of the system decreased. The comprehensive results show that mixture 4 (MDNI/MTNP = 60/40) has a low melting point value and good compatibility, and the detonation velocity and density are improved compared with TNT and MDNI, which is expected to be further applied in melt-cast explosives.

Thermal shift assay: Strengths and weaknesses of the method to investigate the ligand-induced thermostabilization of soluble guanylyl cyclase

Thermal shift assay is a fluorescence dye based biochemical method to determine the melting point of a protein. It can be used to investigate the ligand-induced stabilization of proteins and helps to increase the likelihood of crystallization in biological samples. Dimeric proteins like soluble guanylyl cyclase (sGC) have specific structural and functional properties which may pose a challenge in thermal shift measurements. In this paper, thermal shift assay was used to examine ligand-induced thermostabilization of the dimeric heme-containing protein soluble guanylyl cyclase. Adjustment of the parameters buffer solution, pH, protein / dye ratio and protein amount per well yielded a one-phase melting curve of sGC with a sharp transition and high reproducibility. We found that thermal shift measurement is not affected by heme state or heme content of the enzyme preparation. We used the method to investigate the thermostabilization of sGC induced by the heme-mimetic activator drugs cinaciguat, BAY 60-2770 and BR 11257 in combination with non-hydrolyzable nucleotides. Measurements with the dicarboxylic drugs cinaciguat and BAY 60-2770 yielded steep melting curves with high amplitudes. In contrast, in the presence of the monocarboxylic sGC activator BR 11257, melting curves appear flattened in the dye-based measurements. In the present paper, we show that activity-based thermostability measurements are superior to dye-based measurements in detecting the thermostabilizing influence of sGC activator drugs.

Communication versus waterproofing: the physics of insect cuticular hydrocarbons

Understanding the evolution of complex traits is among the major challenges in biology. One such trait is the cuticular hydrocarbon (CHC) layer in insects. It protects against desiccation and provides communication signals, especially in social insects. CHC composition is highly diverse within and across species. To understand the adaptive value of this chemical diversity, we must understand how it affects biological functionality. So far, CHCs have received ample research attention, but their physical properties were little studied. We argue that these properties determine their biological functionality, and are vital to understanding how CHC composition affects their adaptive value. We investigated melting behaviour and viscosity of CHCs from 11 ant species using differential scanning calorimetry and a novel microrheological technique. CHCs began melting below -45°C, and often were entirely liquid only above 30°C. Thus, they formed a solid-liquid mixture under ambient conditions, which contrasts to previous assumptions of entirely solid layers in many species. This may be adaptive as only biphasic CHC layers ensure uniform coating of the insect body, which is necessary for waterproofing. CHC viscosity was mostly between 0.1 and 0.2 Pa s^-1, thus similar to motor oils. Surprisingly, chemically different CHC profiles had similar viscosities, suggesting that a certain viscosity level is adaptive and ensures that communication signals can be perceived. With this study, we draw attention to the importance of studying the physics of CHC layers. Only by understanding how chemical and physical mechanisms enable CHC functionality can we understand the causes and consequences of CHC diversification.

Measurement and Evaluation of Local Surface Temperature Induced by Irradiation of Nanoscaled or Microscaled Electron Beams

Electron beams (e-beams) have been applied as detecting probes and clean energy sources in many applications. In this work, we investigated several approaches for measurement and estimation of the range and distribution of local temperatures on a subject surface under irradiation of nano-microscale e-beams. We showed that a high-intensity e-beam with current density of 105-6 A/cm2 could result in vaporization of solid Si and Au materials in seconds, with a local surface temperature higher than 3000 K. With a lower beam intensity to 103-4 A/cm2, e-beams could introduce local surface temperature in the range of 1000-2000 K shortly, causing local melting in metallic nanowires and Cr, Pt, and Pd thin films, and phase transition in metallic Mg-B films. We demonstrated that thin film thermocouples on a freestanding Si3N4 window were capable of detecting peaked local surface temperatures up to 2000 K and stable, and temperatures in a lower range with a high precision. We discussed the distribution of surface temperatures under e-beams, thermal dissipation of thick substrate, and a small converting ratio from the high kinetic energy of e-beam to the surface heat. The results may offer some clues for novel applications of e-beams.

The influence of solid state information and descriptor selection on statistical models of temperature dependent aqueous solubility

Predicting the equilibrium solubility of organic, crystalline materials at all relevant temperatures is crucial to the digital design of manufacturing unit operations in the chemical industries. The work reported in our current publication builds upon the limited number of recently published quantitative structure-property relationship studies which modelled the temperature dependence of aqueous solubility. One set of models was built to directly predict temperature dependent solubility, including for materials with no solubility data at any temperature. We propose that a modified cross-validation protocol is required to evaluate these models. Another set of models was built to predict the related enthalpy of solution term, which can be used to estimate solubility at one temperature based upon solubility data for the same material at another temperature. We investigated whether various kinds of solid state descriptors improved the models obtained with a variety of molecular descriptor combinations: lattice energies or 3D descriptors calculated from crystal structures or melting point data. We found that none of these greatly improved the best direct predictions of temperature dependent solubility or the related enthalpy of solution endpoint. This finding is surprising because the importance of the solid state contribution to both endpoints is clear. We suggest our findings may, in part, reflect limitations in the descriptors calculated from crystal structures and, more generally, the limited availability of polymorph specific data. We present curated temperature dependent solubility and enthalpy of solution datasets, integrated with molecular and crystal structures, for future investigations.

Thermoanalytical study of sweetener myo-inositol: α and β polymorphs

This work investigates the thermal behavior of α and β myo-inositol polymorphs. The inositol is a natural compound widely used in the food industry due to its presence in carbohydrate metabolism and its sweet taste. The occurrence of polymorphism could change some physico-chemical properties, such as melting and sublimation temperatures, and solubility. Therefore, the thermal study of polymorphism is important to ensure better conditions for synthesis, storage, and transportation of food that contains the myo-inositol. Simultaneous Termogravimetry-Differential Thermal Analysis, Photovisual Differential Scanning Calorimetry, Polarized Light Thermomicroscopy, and Powder X-ray Diffraction were used in investigation. The data show a new thermal event associated to β myo-inositol melting at 221.43°C, suggesting that the solid-solid transition at 185.68°C was incomplete. The kinetics data made it possible to determine the transition lifetime of myo-inositol to occur 5% of solid-solid transition at 20°C and 37°C: 126 and 8years, respectively.

Effect of Drug Carrier Melting Points on Drug Release of Dexamethasone-Loaded Microspheres

Here, we examined the effect of melting point of drug carriers on drug release of dexamethasone (Dex)-loaded microspheres. We prepared poly(L-lactide-ran-ε-caprolactone) (PLC) copolymers with varying compositions of poly(ε-caprolactone) (PCL) and poly(L-lactide) (PLLA). As the PLLA content increased, the melting points of PLC copolymers decreased from 61 to 43 °C. PLC copolymers in vials solubilized at 40-50 °C according to the incorporation of PLLA into the PCL segment. Dexamethasone (Dex)-loaded PLC (MCxLy) microspheres were prepared by the oil-in-water (O/W) solvent evaporation/extraction method. The preparation yields were above 70%, and the mean particle size ranged from 30 to 90 μm. The MCxLy microspheres also showed controllable melting points in the range of 40-60 °C. Dex-loaded MCxLy microspheres showed similar in vitro and in vivo sustained release patterns after the initial burst of Dex. The in vitro and in vivo order of the Dex release was MC80L20 > MC90L10 > MC95L5, which agreed well with the melting point order of the drug carrier. Using in vivo fluorescence imaging of fluorescein (FI)-loaded microspheres implanted in animals, we confirmed the sustained release of FI over an extended period. In vivo inflammation associated with the PLC microsphere implants was less pronounced than that associated with Poly(lactide-co-glycolide) (PLGA). In conclusion, we successfully demonstrated that it is possible to control Dex release using Dex-loaded MCxLy microspheres with different melting points.

Pinhole Effect on the Melting Behavior of Ag@Al2O3 SERS Substrates

High-temperature surface-enhanced Raman scattering (SERS) sensing is significant for practical detections, and pinhole-containing (PC) metal@oxide structures possessing both enhanced thermal stability and superior SERS sensitivity are served as promising SERS sensors at extreme sensing conditions. Through tuning the Al2O3 precursors' exposure time during atomic layer deposition (ALD), Al2O3 shells with different amount of pinholes were covered over Ag nanorods (Ag NRs). By virtue of these unique PC Ag@Al2O3 nanostructures, herein we provide an excellent platform to investigate the relationship between the pinhole rate of Al2O3 shells and the melting behavior, high-temperature SERS performances of these core-shell nanostructures. Pinhole effect on the melting procedures of PC Ag@Al2O3 substrates was characterized in situ via their reflectivity variations during heating, and the specific melting point was quantitatively estimated. It is found that the melting point of PC Ag@Al2O3 raised along with the decrement of pinhole rate, and substrates with less pinholes exhibited better thermal stability but sacrificed SERS efficiency. This work achieved highly reliable and precise control of the pinholes over Al2O3 shells, offering sensitive SERS substrates with intensified thermal stability and superior SERS performances at extreme sensing conditions.

Estimation of melting points of large set of persistent organic pollutants utilizing QSPR approach

The presence of polyhalogenated persistent organic pollutants (POPs), such as Cl/Br-substituted benzenes, biphenyls, diphenyl ethers, and naphthalenes has been identified in all environmental compartments. The exposure to these compounds can pose potential risk not only for ecological systems, but also for human health. Therefore, efficient tools for comprehensive environmental risk assessment for POPs are required. Among the factors vital for environmental transport and fate processes is melting point of a compound. In this study, we estimated the melting points of a large group (1419 compounds) of chloro- and bromo- derivatives of dibenzo-p-dioxins, dibenzofurans, biphenyls, naphthalenes, diphenylethers, and benzenes by utilizing quantitative structure-property relationship (QSPR) techniques. The compounds were classified by applying structure-based clustering methods followed by GA-PLS modeling. In addition, random forest method has been applied to develop more general models. Factors responsible for melting point behavior and predictive ability of each method were discussed.

Effect of inorganic salts and glucose additives on dose-response, melting point and mass density of genipin gel dosimeters

Genipin gel dosimeters are hydrogels infused with a radiation-sensitive material which yield dosimetric information in three dimensions (3D). The effect of inorganic salts and glucose on the visible absorption dose-response, melting points and mass density of genipin gel dosimeters has been experimentally evaluated using 6-MV LINAC photons. As a result, the addition of glucose with optimum concentration of 10% (w/w) was found to improve the thermal stability of the genipin gel and increase its melting point (Tm) by 6 °C accompanied by a slight decrease of dose-response. Furthermore, glucose helps to adjust the gel mass density to obtain the desired tissue-equivalent properties. A drop of Tm was observed when salts were used as additives. As the salt concentration increased, gel Tm decreased. The mass density and melting point of the genipin gel could be adjusted using different amounts of glucose that improved the genipin gel suitability for 3D dose measurements without introducing additional toxicity to the final gel.

Development of quantitative structure property relationships for predicting the melting point of energetic materials

The accurate prediction of the melting temperature of organic compounds is a significant problem that has eluded researchers for many years. The most common approach used to develop predictive models entails the derivation of quantitative structure-property relationships (QSPRs), which are multivariate linear relationships between calculated quantities that are descriptors of molecular or electronic features and a property of interest. In this report the derivation of QSPRs to predict melting temperatures of energetic materials based on descriptors calculated using the AM1 semiempirical quantum mechanical method are described. In total, the melting points and experimental crystal structures of 148 energetic materials were analyzed. Principal components analysis was performed in order to assess the relative importance and roles of the descriptors in our QSPR models. Also described are the results of k means cluster analysis, performed in order to identify natural groupings within our study set of structures. The QSPR models resulting from these analyses gave training set R(2) values of 0.6085 (RMSE = ± 15.7 °C) and 0.7468 (RMSE = ± 13.2 °C). The test sets for these clusters had R(2) values of 0.9428 (RMSE = ± 7.0 °C) and 0.8974 (RMSE = ± 8.8 °C), respectively. These models are among the best melting point QSPRs yet published for energetic materials.

Liquid-phase characterization of molecular interactions in polyunsaturated and n-fatty acid methyl esters by (1)H low-field nuclear magnetic resonance

BACKGROUND

To identify and develop the best renewable and low carbon footprint biodiesel substitutes for petroleum diesel, the properties of different biodiesel candidates should be studied and characterized with respect to molecular structures versus biodiesel liquid property relationships. In our previous paper, (1)H low-field nuclear magnetic resonance (LF-NMR) relaxometry was investigated as a tool for studying the liquid-phase molecular packing interactions and morphology of fatty acid methyl esters (FAMEs). The technological potential was demonstrated with oleic acid and methyl oleate standards having similar alkyl chains but different head groups. In the present work, molecular organization versus segmental and translational movements of FAMEs in their pure liquid phase, with different alkyl chain lengths (10-20 carbons) and degrees of unsaturation (0-3 double bonds), were studied with (1)H LF-NMR relaxometry and X-ray, (1)H LF-NMR diffusiometry, and (13)C high-field NMR.

RESULTS

Based on density values and X-ray measurements, it was proposed that FAMEs possess a liquid crystal-like order above their melting point, consisting of random liquid crystal aggregates with void spaces between them, whose morphological properties depend on chain length and degree of unsaturation. FAMEs were also found to exhibit different degrees of rotational and translational motions, which were rationalized by chain organization within the clusters, and the degree and type of molecular interactions and temperature effects. At equivalent fixed temperature differences from melting point, saturated FAME molecules were found to have similar translational motion regardless of chain length, expressed by viscosity, self-diffusion coefficients, and spin-spin (T 2) (1)H LF-NMR. T 2 distributions suggest increased alkyl chain rigidity, and reduced temperature response of the peaks' relative contribution with increasing unsaturation is a direct result of the alkyl chain's morphological packing and molecular interactions.

CONCLUSIONS

Both the peaks' assignments for T 2 distributions of FAMEs and the model for their liquid crystal-like morphology in the liquid phase were confirmed. The study of morphological structures within liquids and their response to temperature changes by (1)H LF-NMR has a high value in the field of biodiesel and other research and applied disciplines in numerous physicochemical- and organizational-based properties, processes, and mechanisms of alkyl chains, molecular interactions, and morphologies.

Boiling point and melting point

The UPPER (Unified Physicochemical Property Estimation Relationships) model uses enthalpic and entropic parameters to estimate 20 biologically relevant properties of organic compounds. The model has been validated by Lian and Yalkowsky on a data set of 700 hydrocarbons. The aim of this work is to expand the UPPER model to estimate the boiling and melting points of polyhalogenated compounds. In this work, 19 new group descriptors are defined and used to predict the transition temperatures of an additional 1288 compounds. The boiling points of 808 and the melting points of 742 polyhalogenated compounds are predicted with average absolute errors of 13.56 K and 25.85 K, respectively.

Optimisation of gelatin extraction from Unicorn leatherjacket (Aluterus monoceros) skin waste: response surface approach

Physical properties of gelatin extracted from Unicorn leatherjacket (Aluterus monoceros) skin, which is generated as a waste from fish processing industries, were optimised using Response Surface Methodology (RSM). A Box-Behnken design was used to study the combined effects of three independent variables, namely phosphoric acid (H3PO4) concentration (0.15-0.25 M), extraction temperature (40-50 °C) and extraction time (4-12 h) on different responses like yield, gel strength and melting point of gelatin. The optimum conditions derived by RSM for the yield (10.58%) were 0.2 M H3PO4 for 9.01 h of extraction time and hot water extraction of 45.83 °C. The maximum achieved gel strength and melting point was 138.54 g and 22.61 °C respectively. Extraction time was found to be most influencing variable and had a positive coefficient on yield and negative coefficient on gel strength and melting point. The results indicated that Unicorn leatherjacket skins can be a source of gelatin having mild gel strength and melting point.

Piezo-thermal Probe Array for High Throughput Applications

Microcantilevers are used in a number of applications including atomic-force microscopy (AFM). In this work, deflection-sensing elements along with heating elements are integrated onto micromachined cantilever arrays to increase sensitivity, and reduce complexity and cost. An array of probes with 5-10 nm gold ultrathin film sensors on silicon substrates for high throughput scanning probe microscopy is developed. The deflection sensitivity is 0.2 ppm/nm. Plots of the change in resistance of the sensing element with displacement are used to calibrate the probes and determine probe contact with the substrate. Topographical scans demonstrate high throughput and nanometer resolution. The heating elements are calibrated and the thermal coefficient of resistance (TCR) is 655 ppm/K. The melting temperature of a material is measured by locally heating the material with the heating element of the cantilever while monitoring the bending with the deflection sensing element. The melting point value measured with this method is in close agreement with the reported value in literature.