Average Number Of Hydrogen Bonds Research Articles

Application of green deep eutectic solvents for anthocyanins extraction from grape pomace: Optimization, stability, antioxidant activity, and molecular dynamic simulation

The wine-making industry produces a large amount of grape pomace, which is rich in anthocyanins. To avoid wasting these resources, choline chloride: lactic acid (molar ratio of 1:2) (DES-1) was selected as the optimal solvent. The optimal extraction conditions were as follows: temperature 60°C, time 60 min, water content 25%. The anthocyanins yield was 5.73 mg (cyanidin-3-glucoside) equivalent/ g under the optimal conditions, which was significantly higher than that obtained by DES-3 (Choline chloride: 1,4 butanediol), DES-5 (Choline chloride: 1,2 propylene glycol), and ethanol. The DES-1 extract showed significant higher color stability and antioxidant activities compared with the anthocyanins extracted by DES-3, DES-5, and ethanol. A total of eight individual anthocyanin compounds were identified in each extract, with delphinidin 3-O-glucoside, peonidin 3-O- glucoside, petunidin, and delphinidin as the dominant compounds. Molecular dynamics simulation confirmed that DES-1 system showed a larger average number of hydrogen bonds (11.63), average lifetime of hydrogen bonds (364.21 ps) and with a reduced total interaction energy (-706.82 kJ/moL), thus improving the extraction efficiency and stability of anthocyanins. This study would provide new protocols for the extraction of anthocyanins from grape pomace.

Molecular dynamics simulation on the variations in characteristics of aqueous solution with diverse additives: Inspirations for binary ice preparation

Ice slurry, as a novel energy storage medium, possesses the superiority of high energy storage density. The freezing point inhibitors are employed to regulate the supercooling phenomenon of water, while the macroscopic experiments are complicated to elucidate the action mechanism. Consequently, this paper adopts molecular dynamic simulation method to investigate the mean square displacement, radial distribution function, hydrogen bonds types, hydrogen bonds number and length of water at various concentrations of ethanol, NaCl, and SiO2 additives. The results indicate that the average number of hydrogen bonds of the system composed with 600 pure water molecules is 1127.24, and the average length of hydrogen bonds is 2.33 Å. Moreover, the addition of alcoholics and chlorides inhibits the hydrogen bonds between water and water molecules, and promotes the generation of hydrogen bonds, thus weakening the diffusion motion of water molecules. Whereas, it is observed that the addition of nanoparticles leads to agglomeration in pure water system, resulting an increase in the viscosity and a decrease in the diffusion rate of the system. The proposed microscopic model can effectively depict the potential interaction mechanisms of additives and water, which is contributing to develop effective freezing point inhibitors and improve the energy utilization efficiency.

Demulsification of W/O emulsions induced by terahertz pulse electric fields-driven hydrogen bond disruption of water molecules

Demulsifying highly stable W/O emulsions, composed of heavy oil and water, is crucial for simplifying crude oil processing, reducing production costs, and mitigating environmental pollution. In these emulsions, aromatic components in the oil phase stack via π-π interactions, while hydrogen bonds stabilize the water phase. This leads to the creation of a strong oil-water interface through electrostatic attraction, ultimately hindering water droplet coalescence and oil-water separation. In this study, a 1.0 THz pulse electric field is introduced to effectively disrupt the hydrogen bond network among water molecules by inducing hydrogen bond resonance. This disruption contributes to increased water mobility in the oil phase, weakened stability of the oil-water interface film, and facilitates efficient water droplet coalescence in the oil phase. The results show that throughout the demulsification process, the average number of hydrogen bonds per water molecule rapidly decreases from 1.41 to 1.08 within 100 ps. The upper and lower limits of hydrogen bond lifetimes decrease by 8.12 ps and 3.24 ps, respectively. This indicates a significant disruption in the stability of hydrogen bonds between water molecules. Concurrently, the terahertz pulse electric field disrupts the initially stable oil-water interface film of the emulsion system, leading to a noteworthy reduction in the oil-water interface tension from 54.3 to 39.2 mN·m−1. The self-diffusion coefficient of water molecules increases from 1.33 to 2.62 Å2·ps−1, signifying that water molecules are more inclined to penetrate the interfacial region between the two phases. Additionally, the terahertz pulse electric field induces alterations in the arrangement of water molecules, resulting in the rearrangement of electrons in the water phase and disrupting the originally stable electrical double layer structure of the oil-water interface. This study provides novel insights into the development of efficient and environmentally friendly electric demulsification technologies, holding significant potential for widespread industrial applications.

The MD study of water short-range order during liquid-liquid transition: Toward the second critical point

Full-scale thermodynamic experimental investigations of the liquid-liquid transition and different water phases remain challenging due to spontaneous crystallization and the complexity of studies on the nanosecond time scale. Moreover, the specific position of the second critical point in water is still unclear. This study used molecular dynamics to reproduce the structural properties of both low- and high-density waters and to characterize changes in the order parameters, average number of hydrogen bonds, and ordering of neighboring molecules during liquid-liquid transitions and in regimes of supercooled waters. A rapid change in calculated parameters under increased pressure could be attributed to a first-order phase transition. In addition, we provided evidence that low-density water becomes dissolved in high-density water inclusions as the temperature or pressure increases. The presumed location of the second critical point has been identified as TC ≈ 220 K, PC ≈ 1.5 kbar, and ρC ≈ 1.02 g/cm3.

Water Molecules Confined in Cryptophane Nanocages: Structures and Dynamics Driven by Hydrogen Bonding and Water Chains.

Cryptophanes (Crs) are roughly spherical organic nanocages used as vehicles for hosting xenon atoms in 129Xe NMR biosensor (XBS) structures. Crs also bind other guests, importantly water, which is abundant in biological systems. In other host cages, it has been found that the release of "high-energy" water from confinement constitutes an important contribution to the binding affinity of nonwater guests. Despite that, the role of water has received little attention in the XBS field. Based on molecular dynamics simulations in explicit water solvent, we here study the properties of confined water in three different CrA cages that have an identical interior but are functionalized with 0, 3, or 6 water solubility-enhancing, hydrophilic CH2COOH moieties. The number of the solubility groups is found to be a decisive factor for the structures and dynamics of the confined water. Formation of stable water-molecule chains is predicted within the cage with six hydrophilic groups, starting with the anchoring of one water molecule at the portal between the cage and the bulk solution. We find that the experimentally measured differences in the Xe-binding affinities of the cages can be related to the average number of hydrogen bonds per confined water molecule. The rotational dynamics of the confined water is significantly slower than that in the bulk, suggesting NMR relaxation measurements to study the intracavity water. The present findings reveal new details about the microscopic cryptophane-H2O host-guest chemistry, which will become important in the design of improved XBS devices.

Effect of Thermal and Electric Fields on Thermal Stability and Dielectric Properties of SiO2/Cellulose Composite Materials

Molecular simulation techniques are widely used to study transformer insulation material characteristics and nano-modification mechanism. However, there are numerous researches on the thermal stability and dielectric properties of nano-modified cellulose insulation paper, and few studies have combined nano-modification with the process of electrical-thermal aging. This study established SiO2/Cellulose models with different weight percentages to calculate their average number of hydrogen bonds (AHB), glass transition temperature (Tg ) and relative permittivity (RP) under electro-thermal coupling. The study indicates that the 5wt% SiO2/Cellulose model exhibits the best modification effect. Temperature is the primary factor causing aging of the cellulose insulation paper, and the introduction of an electric field accelerates the thermal aging of the cellulose insulation paper. Increasing hydrogen bond quantity and restricting molecular chain movement are key factors that enhance insulation materials anti-aging performance.

How do physicochemical properties contribute to inhibitory activity of promising peptides against Zika Virus NS3 protease?

Flavivirus diseases' cycles, especially Dengue and Yellow Fever, can be observed all over Brazilian territory, representing a great health concern. Additionally, there are no drugs available in therapy. In this scenario, in silico methodologies were applied to obtain physicochemical properties, as well as to better understand the ligand-biological target interaction mode of 20 previously reported NS2B/NS3 protease inhibitors of Dengue virus. Since catalytic site of flavivirus hold similarities, such as the same catalytic triad (His51, Asp75 e Ser135), the ability of this series of molecules to fit in Zika NS3 domains can be achieved. We performed an exploratory data analysis, using statistical methodologies, such as PCA (Principal Component Analysis) and HCA (Hierarchical Component Analysis), to assist the comprehension of how physicochemical properties impact the interaction observed by the docking studies, as well as to build a correlation between the respective ranked characteristics. Based on these previous studies, peptides were selected for the dynamics simulations, which were useful to better understand the ligand-protein interactions. Information relating to, for instance, energy, ΔG, average number of hydrogen bonds and distance from Ser135 (one of the main amino acids in the catalytic pocket) were discussed. In this sense, peptides 15 (considering ΔG value and Hbond number), 7 (ΔG and energy) and 1, 6, 7 and 15 (the proximity to Ser135 throughout the dynamics simulation) were highlighted as promising. Those interesting results could contribute to future studies regarding Zika virus drug design, since this infection represents a great concern in neglected populations. The models were constructed in the ChemDraw software. The ligand parametrization was performed in the CHEM3D 17.0, UCSF Chimera. Docking simulations were carried out in the GOLD software, after the redocking validation. We used ASP as the function score. Additionally, for dynamics simulations we applied GROMACS software, exploring, mainly, free binding energy calculations. Exploratory analysis was carried out in Minitab 17.3.1 statistical software. Prior to the exploratory analysis, data of quantum chemical properties of the peptides were collected in Microsoft Excel spreadsheet and organized to obtain Hierarchical Cluster Analysis (HCA) and Principal Component Analysis (PCA).

Investigating the properties of the water−vapor and water−graphite interfaces by PC-SAFT based density functional theory: A comparative study of different association functionals and PC-SAFT water parameter sets

In this work, we apply the perturbed-chain statistical associating fluid theory (PC-SAFT) based classical density functional theory to investigate the thermodynamics and structures of the water−vapor and water−graphite interfaces. For the water−vapor interface, we examine the surface tension as well as structural characteristics such as density profiles and hydrogen bonding distributions along the interface. For the water−graphite interface, we investigate these same structural features at a contact angle of 90° at 300 K. Specifically, we focus on comparing the results obtained from the three association functionals and six PC-SAFT water parameter sets from literature with experimental data and molecular simulation results. We find that the three association functionals exhibit qualitatively similar behavior in the calculation of surface tension, and it is more influenced by the parameter set rather than the association functional. The optimal functional or parameter set for the calculation of density profile of the vapor − liquid interface remains inconclusive, whereas preferable parameter sets and functionals have been identified for the water−graphite interface. Furthermore, the three functionals demonstrate a remarkably similar and qualitatively accurate depiction of the hydrogen bonding structures at both interfaces when compared with molecular simulation results. The level of quantitative accuracy, however, relies on whether the parameter set accurately reproduces the average number of hydrogen bonds of bulk water as observed in this particular set of molecular simulation results. The results of the present work offer valuable guidance for further investigation into the adsorption and wetting behavior of water on graphite-like surface, as well as the properties of water confined at the nanoscale.

Density functional theory and molecular dynamics simulation of water molecules confined between parallel graphene oxide surfaces using new interaction potentials

In this study, the interaction potential of water molecule with a graphene oxide (GO) plate containing OH and O groups has been calculated using the M06-2X/6-31g(d,p) level of theory at different orientations and intermolecular distances and fitted to the Born-Huggins-Meyer (BHM) model. There are good agreements between the calculated and the OPLS-AA and Dreiding models, especially for the GO(O)-H2O interactions. To examine the new computed models, we have used the closer potentials to the OPLS-AA and Dreiding models in the molecular dynamics (MD) simulations. We have calculated several properties using the different obtained interaction potentials including average number of hydrogen bonds per water molecule (〈HB〉) between confined water molecules and between water and GO-surfaces, radial distribution function (RDF), self-diffusion coefficient, and angle distribution function of the confined water molecules between the GO plates. Our results showed good agreements between the OPLS-AA and Dreiding models and some calculated potentials. However, some calculated models showed completely different behavior which discussed in details. According to the results, we concluded that the OH-2 and O1-OH2 models show totally better agreement with the famous force fields than the other calculated potentials. This work provides a simple method for the development of new force fields specifically for these types of systems which are in good agreement with the well-known force fields.

Dielectric relaxation and hydrogen bonding studies of 1-iodobutane 1,4-dioxane mixture using TDR technique

Complex dielectric measurements by using the Time Domain Reflectometry technique between the frequency range 10 MHz to 30 GHz have been accomplished for different concentrations of 1-iodobutane (IDB) and 1, 4-Dioxane (DX) binary mixtures at 5 °C to 25 °C temperatures. Debye model was used to fit the complex permittivity spectra of IDB-DX binary mixture. The Luzar model is applied to calculate the average number of hydrogen bonds in IDB-IDB and IDB-DX molecules. The measured value of hydrogen bond density is found to be maximum for this binary mixture at dioxane concentration VDX ≈ 0.7. To study the dielectric behavior and to observe the modification in the strength of hydrogen bond in the presence of other nonpolar molecule is the main aim of the proposed work. Measurement of Kirkwood correlation factor and Bruggeman factor provide the valuable information regarding the formation of hydrogen bonded molecular multimers and intermolecular interaction in the binary mixture. Information on the molecular interactions in binary mixtures is also provided by the study.

Chilling alcohol on the computer: isothermal compressibility and the formation of hydrogen-bond clusters in liquid propan-1-ol

Molecular dynamics simulations have been performed to compute the isothermal compressibility κT\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\kappa _T$$\\end{document} of liquid propan-1-ol in the temperature range 200≤T≤300\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$200 \\le T\\le 300$$\\end{document} K. A change in behaviour, from normal (high T) to anomalous (low T), has been identified for κT\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\kappa _T$$\\end{document} at 210<T<230\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$210<T<230$$\\end{document} K. The average number of hydrogen bonds (H–bond) per molecule turns to saturation in the same temperature interval, suggesting the formation of a relatively rigid network. Indeed, simulation results show a strong tendency to form H–bond clusters with distinct boundaries, with the average largest size and width of the size distribution growing upon decreasing temperature, in agreement with previous theoretical and experimental studies. These results also emphasise a connection between the behaviour of κT\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\kappa _T$$\\end{document} and the formation of nanometric structures.Graphic

Exploring Fullerenol-C60(OH)24 interactions with lipid bilayers: Molecular dynamics study of agglomeration and surface deposition

In this work, the physical–chemical properties of lipid membranes interacting with Fullerenol-C60(OH)24 molecules immersed in an aqueous solution were studied using Molecular Dynamics (MD) simulations. In order to analyze the role played by the concentration of Fullerene-C60(OH)24 in the interaction with lipid membranes, we carried out simulations with variations in the number (n = 1, 2, 4, 8, 12, 16 or 20) of Fullerene-C60(OH)24 molecules present in the solution in which the lipid membrane was immersed. The lipid membrane simulated was composed of DOPC (dipalmitoylphosphatidylcholine) with 30% of cholesterol molecules (DOPC/CHOL(30%)). The average behavior of the Coulomb and vdW interaction energy shows that as the Fullerenol-C60(OH)24 molecules concentration increases, insertion of Fullerenol in the lipid bilayer becomes energetically unfavorable since they tend to interact with each other, leading to the formation of clusters. From the mass density, we confirmed that there is a decrease in the insertion of Fullerenol-C60(OH)24 molecules in the bilayer as n increases. We noticed that Fullerenol molecules get closer to each other and are deposited on the surface of the lipid bilayers but do not penetrate them. The diffusion coefficient (MSD) reveals a decrease in the mobility of Fullerenol molecules as n increases. This observation confirms the agglomeration of Fullerenol on the lipid membrane’s surface. A detailed analysis of hydrogen bonds (HB) involving Fullerenol–Fullerenol, Fullerenol–DOPC, and Fullerenol–Water pairs provides insight into this phenomenon. While the average number of HBs in the Fullerenol–Water pair remains relatively constant as n increases, there is a significant increase in HB interactions for the Fullerenol–Fullerenol pair. In contrast, the Fullerenol–DOPC pair experiences a decrease in HBs, underscoring the preference of Fullerenol to agglomerate and deposit onto the lipid membrane's surface.

Conformation and hydration property of low-acetyl gellan gum under microwave irradiation: Experiments and molecular dynamics simulations

The effect of microwave irradiation on the conformation and hydration properties of low-acetyl gellan gum was investigated to reveal the mechanism using experimental methods and molecular dynamics (MD) simulations. The experimental data showed that cross-sectional radius of gyration of the gellan chain treated by microwave or water bath were identical and microwave treatment could improve the water holding capability and restrict water mobility. On the other hand, results of root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) showed that microwave irradiation had little impact on the structural conformation of the low-acetyl gellan molecule. The analysis of radial distribution function and interaction energy demonstrated that microwaves modified the gellan-water molecules structure by energy transfer, making hydration shells of the gellan molecule become more structured. In addition, there was an enhancement of the average hydrogen bond number and lifetime under microwave irradiation due to rearrangement and reorient of molecules. These findings can explain the mechanism of microwave-promoted gellan gum gelation to some extent, which enhance industrial applications of low-acetyl gellan.

Molecular dynamics simulation of desalination process using polyoxometalate ionic liquid confined in carbon nanotubes

In this work, the effect of positioning of [Keggin][emim]3 ionic liquid (IL) into carbon nanotubes (CNTs) with different concentrations has been examined in the desalination process at different external pressures using molecular dynamics (MD) simulations. Another membrane was also modelled composed of four similar CNTs with almost equal space from each other. Using of only Keggin anions into the charged CNT was also studied in the desalination process. To study the mechanism of the water and ions fluxes, the potential of mean force, average number of hydrogen bonds, and self-diffusion coefficient have been also computed and discussed. The results showed that the placing of [Keggin][emim]3 IL into a CNT decreases the water flux (Nwaterns=74at150MPa) relative to the empty CNT (Nwaterns=834). However, the four CNTs configuration shows increase in the water flux (Nwaterns=183at150MPa) than the one CNT system. The placing of one polyoxometallate IL into the CNT increases the salt rejection 10 to 20 times than the empty-CNT system at low and high pressures, respectively. Moreover, positioning of the two ILs results in the complete salt rejection at all pressures. These results indicate that the use of polyoxometalate ILs into the CNT efficiently increases the salt rejection. The self-diffusion of confined water molecules in the single IL-CNT composite (D = 0.73 × 10-9 m2/s) is also smaller than the empty CNT at 150 MPa (D = 1.89 × 10-9 m2/s). The results also indicated that using of the Keggin anions into the charged CNT leads to the more water flux (Nwaterns=250at150MPa) and complete salt rejection relative to the fixing of [Keggin][emim]3 IL into the uncharged CNT. The effects of CNT charge distributions, temperature, and CNT chirality have been also examined on the desalination process.

Square ice formation in CrOCl and graphene confinement

The structure and thermodynamic properties of water in nanoscale confinement environment are greatly involved in the research field of material science and nanotechnology. However, a complete picture of the ordered structure formation and thermodynamics behavior of the confined water inside two parallel nanosheets with different surface atomic arrangement is still lacking. In this paper, by using molecular dynamics (MD) simulations, we study the structural variation and thermodynamics behavior for water molecules confined between two parallel CrOCl with a square surface atomic arrangement and two parallel graphene nanosheets with a hexagonal surface atomic arrangement. Square ice, with a lattice constant 2.1 and 2.0 Å, is observed inside the two parallel CrOCl and graphene nanosheets, respectively. By calculating the configuration entropy of the molecular dipoles St , it is found that, in the CrOCl confinement, St reaches a peak value and then is greatly reduced due to the square ice formation. On the other hand, in the graphene confinement, St continues to grow after the square ice formation and is then reduced after reaching its peak value. Interestingly, it is found that the square ice could be stable at a higher entropy state under the external pressure than the bulk water at ambient condition. By calculating the orientational order parameters M, it shows that the conventional tetrahedral geometry of hydrogen bonding between water molecules breaks due to the square ice formation. By analyzing the average number of hydrogen bonds of water molecules Nh , it is found that the hydrogen bond interaction of the square ice relies on the confinement environment, where Nh is reduced in the CrOCl confinement and increased in the graphene confinement. Probability distribution functions of the dipole orientation angles between the x- or z-axis and the projection of the oxygen atoms of the water molecules are also calculated. It is observed that the square ice structure is paralleled with the x-axis (unit cell axis) in the CrOCl confinement and tilted with the x-axis (the zigzag direction of graphene) at an angle 30° in the graphene confinement. Furthermore, the square ice formation is found to be insensitive to temperature. Our result reveals the peculiar ordered structure and thermodynamics behavior of water in different nanoscale confinement environments.

Molecular Dynamics Simulation to Evaluate the Stability of Tetra-n-butyl Ammonium/Phosphonium Bromide Semiclathrate Hydrates in the Presence and Absence of Methane, Carbon Dioxide, Methanol, and Ethanol Molecules

Stability of tetra-n-butyl ammonium bromide (TBAB) and tetra-n-butyl phosphonium bromide (TBPB) semiclathrate hydrates with a hydration number of 38 is studied by the molecular dynamics (MD) simulation in the absence and presence of methane, carbon dioxide, methanol, and ethanol molecules. All of the simulation runs are performed under NVT (constant number of atoms, volume, and temperature) and NPT (constant number of atoms, pressure, and temperature) conditions using optimized potentials for liquid simulations-all-atom (OPLS-AA) force field with nonpolarizable water models (including SPC, TIP3P, TIP4P, and TIP4P/Ice), where the operating conditions include a temperature range of 250–350 K and pressures of 0.1 and 50 MPa. The potential energy and structural analysis, mean square displacement (MSD), diffusion coefficient, radial distribution function (RDF), lattice parameter, and the average number of hydrogen bonds between water–water molecules are evaluated by employing MD strategy. According to the potential energy results, the order for the water models in both TBAB and TBPB hydrate stabilities is as follows: TIP4P/Ice > TIP4P ≈ SPC > TIP3P. This order agrees well with the previous studies of gas hydrates and ices. In the absence and presence of methane and carbon dioxide guest molecules, the height of the peaks in the RDF of oxygen–oxygen atoms decreases with lowering pressure and increasing temperature; greater MSD, diffusion coefficient, and lattice parameter values are also achieved. Thus, in the absence and/or presence of guest gas molecules, the stability of TBAB and TBPB hydrate cages decreases with increasing temperature and reducing pressure. A good match is noticed between the results of MD simulation and previous experimental and theoretical studies, confirming the accuracy and validation of the simulation method. Reduction of the hydrogen bond balance between water molecules and formation of new hydrogen bonds between the water and the hydroxyl groups of methanol and/or ethanol molecules in the cages indicate that methanol and ethanol molecules have an inhibitory effect on TBAB and TBPB hydrates. Due to different hydrophilic versus hydrophobic behaviors of alcohols, the extent of disruption of hydrogen bonds between water–water molecules of TBAB and TBPB hydrates in the presence of methanol is larger than that in the presence of ethanol, which is consistent with the MD simulation results of clathrate hydrate. This study can help to further understand the semiclathrate hydrate stability or dissociation conditions at a molecular scale for better design and operation of corresponding processes.

The effect of temperature and sulfolane concentration on aqueous electrolyte with molecular crowding: A molecular dynamics simulation study

Molecular crowding agents can significantly suppress water activity by affecting hydrogen bonds. Here, we performed molecular dynamics simulation to study the effect of temperature and concentration of sulfolane, a crowding agent, on aqueous electrolytes. The mean square displacement, diffusion coefficient, coordination number, number density distribution, and average number of intermolecular hydrogen bonds were calculated and discussed. Due to the molecular crowding, the effect of temperature and sulfolane concentration on the average number of hydrogen bonds between water molecules is very interesting. When the concentration of sulfolane is low, the average number of hydrogen bonds between water molecules decreases monotonically with increasing temperature. However, when the concentration of sulfolane reaches a certain value, the average number of hydrogen bonds between water molecules no longer monotonically decreases but first increases and then decreases. When the concentration of sulfolane continues to increase, the average number of hydrogen bonds between water molecules tended to an abnormal monotonic increase. This work provides a deep study of the molecular crowding at the molecular level under wide ranges of temperature and concentration for designing aqueous electrolytes.

Correlation between chemical denaturation and the unfolding energetics of Acanthamoeba actophorin

The actin filament network is in part remodeled by the action of a family of filament severing proteins that are responsible for modulating the ratio between monomeric and filamentous actin. Recent work on the protein actophorin from the amoeba Acanthamoeba castellani identified a series of site-directed mutations that increase the thermal stability of the protein by 22°C. Here, we expand this observation by showing that the mutant protein is also significantly stable to both equilibrium and kinetic chemical denaturation, and employ computer simulations to account for the increase in thermal or chemical stability through an accounting of atomic-level interactions. Specifically, the potential of mean force (PMF) can be obtained from steered molecular dynamics (SMD) simulations in which a protein is unfolded. However, SMD can be inefficient for large proteins as they require large solvent boxes, and computationally expensive as they require increasingly many SMD trajectories to converge the PMF. Adaptive steered molecular dynamics (ASMD) overcomes the second of these limitations by steering the particle in stages, which allows for convergence of the PMF using fewer trajectories compared with SMD. Use of the telescoping water scheme within ASMD partially overcomes the first of these limitations by reducing the number of waters at each stage to only those needed to solvate the structure within a given stage. In the PMFs obtained from ASMD, the work of unfolding Acto-2 was found to be higher than the Acto-WT by approximately 120 kCal/mol and reflects the increased stability seen in the chemical denaturation experiments. The evolution of the average number of hydrogen bonds and number of salt bridges during the pulling process provides a mechanistic view of the structural changes of the actophorin protein as it is unfolded, and how it is affected by the mutation in concert with the energetics reported through the PMF.

Evaluating the behavior and principle of deep eutectic solvent on ephedrine-type alkaloid extraction from Ephedrae Herba.

In this study, deep eutectic solvent (DES), as a new green solvent, was used to extract bioactive alkaloids from Ephedrae Herba using supersonic extraction. In a variety of tested hydrophilic and hydrophobic DESs, DES composed of choline chloride and xylitol was proved to be the most efficient solvent. Factors affecting extraction efficiency, including the mole ratio of hydrogen bond acceptor/hydrogen bond donor, water contention, and solid/liquid ratio, were optimized individually. Under optimal conditions, the yield of ephedrine (EP) and pseudoephedrine obtained using this new method was 14.24 and 4.32 mg/g, respectively, which was higher than that using the traditional solvent (acidified water and methanol). Furthermore, the extraction mechanism of DES and EP was investigated using molecular dynamics simulation study. Structural properties such as radial distribution functions and average number of hydrogen bonds were then computed. The results showed that hydrogen bonds and van der Waals forces are important driving forces of extraction; in addition, the hydrogen bonds between the Cl atom of choline chloride and N atom of EP played a dominant part in the extraction process. Based on the extraction principle, the extraction method using choline chloride as extraction solvent was also discussed.

Designing of Peptide Based Multi-Epitope Vaccine Construct against Gallbladder Cancer Using Immunoinformatics and Computational Approaches.

Gallbladder cancer (GBC) is an aggressive and difficult to treat biliary tract carcinoma with a poor survival rate. The aim of this study was to design a peptide-based multi-epitope vaccine construct against GBC using immunoinformatics approaches. Three proteins implicated in the progression of GBC were selected for B and T cell epitope prediction and the designing of the potential vaccine construct. Seven CTL, four HTL and six Bcell epitopes along with a suitable adjuvant were selected and connected using linkers for designing the vaccine construct. The secondary and tertiary models of the designed vaccine were generated and satisfactorily validated. A Ramachandran plot of the final 3D model showed more than 90% of the residues in allowed regions and only 0.4% in disallowed regions. The binding affinity of a vaccine construct with TLR 2, 3 and 4 receptors was assessed through molecular docking and simulation. The average numbers of hydrogen bonds for vaccine-TLR 2, 3 and 4 complexes in the simulation were 15.36, 16.45, and 11.98, respectively, and remained consistent over a 100 ns simulation period, which is critical for their function. The results of this study provide a strong basis for further evaluation through in vitro/in vivo experimental validation of the safety and efficacy of the designed vaccine construct.