Probability Of Hydrogen Bond Formation Research Articles

Crocin-Phospholipid Complex: Molecular Docking, Molecular Dynamics Simulation, Preparation, Characterization, and Antioxidant Activity.

Crocin is a water-soluble carotenoid compound present in saffron (Crocus sativus L.), known for its wide range of pharmacological activities, including cardioprotective, hepatoprotective, anti-tumorigenic, anti-atherosclerosis, and anti-inflammatory effects. The instability of crocin, its low miscibility with oils, and poor bioavailability pose challenges for its pharmaceutical applications. This study aimed to design and prepare a crocin-phospholipid complex (CPC) and assess its physicochemical properties. The study investigated the formation of the complex and its binding affinity through molecular docking. Molecular dynamics (MD) simulations were conducted to find the optimal molar ratio of crocin to phospholipid for the complex's preparation. The CPC was produced using the solvent evaporation method. Techniques such as X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), field-emission scanning electron microscopy (FE-SEM), nuclear magnetic resonance (NMR), and solubility studies were utilized to characterize and confirm the formation of CPC. Additionally, the in vitro antioxidant activity of crocin and CPC was evaluated. Molecular dynamic simulations explored molar ratios of 1: 1, 1: 1.5, and 1: 2 for crocin to phospholipid. The ratio of 1: 2 was found to be the most stable, exhibiting the highest probability of hydrogen bond formation. Molecular docking, FTIR, and NMR studies indicated hydrogen bond interactions between crocin and phospholipid, confirming CPC's formation. XRD and FE-SEM analyses showed a decrease in crocin's crystallinity within the phospholipid complex. Furthermore, the solubility of crocin in n-octanol was enhanced post-complexation, indicating an increase in crocin's lipophilic nature. Phospholipid complexation emerges as a promising technique for enhancing the physicochemical characteristics of crocin.

Micellization, acoustic and thermodynamic study of procaine in aqueous solution at different temperatures

Critical micelle concentrations (CMC) of procaine hydrochloride (PHCl) in aqueous solution has been determined from conductivity (κ), density (ρ) and speed of sound (u) measurements using Williams and Philips methods at the temperature range 298.15–318.15 K intervals of 5 K.The CMC values found by these two methods using the speed of sound, density and conductivity data were in good agreement at all temperature. As the applied temperature increases, the CMC increases, owing to the lower probability of hydrogen bond formation at higher temperatures.The obtained values of the standard Gibbs energy of micellization (ΔGmo) and the standard enthalpy of micellization (ΔHmo) are negative at all investigated temperatures. Thus, one can say that the micellization process and the relationship between drug-water interactions and solute-solute interactions occur at different temperatures. Negative ΔGmo values were recorded when the systems become more hydrophobic. The negative increase in ΔHmo by the increased temperatures can be explained by the exothermic nature of the micellization process. The obtained values of the entropy for micellization (ΔSmo) are positive at all temperatures. The ΔSmo values decrease with temperature increase, this result interpreted as micellazation tend to be energy driven at higher temperatures.Apparent molar volume (V∅), apparent molal volumes at ınfinite dilution (V∅0), micellar apparent molal volumes (V∅mic), changes in apparent molal volumes upon aggregation (ΔVm), apparent molar isentropic compressibilities (K∅(S)), isentropic apparent molal adiabatic compressibilities at infinite dilution (K∅(S)0), micellar ısentropic apparent molal adiabatic compressibilities (K∅(S)m) and changes in isentropic apparent molal adiabatic compressibilities (ΔK∅(S)) of procaine in aqueous solution have been calculated by combining the speed of sound and density measurements. ΔVm are estimated and found to be negative except for 0.43 m3mol−1 (maximum value) at 318.15 K. The variations in these parameters were discussed for micellization process and drug-water interactions and solute-solute interactions at different temperatures.

Interaction of Camptothecin with Model Cellular Membranes.

Accurate and efficient prediction of drug partitioning in model membranes is of significant interest to the pharmaceutical industry. Herein, we utilize advanced sampling methods, specifically, the adaptive biasing force methodology to calculate the potential of mean force for a model hydrophobic anticancer drug, camptothecin (CPT), across three model interfaces. We consider an octanol bilayer, a thick octanol/water interface, and a model 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/water interface. We characterize the enthalpic and entropic contributions of the drug to the potential of mean force. We show that the rotational entropy of the drug is inversely related to the probability of hydrogen bond formation of the drug with the POPC membrane. In addition, in long-time microsecond simulations of a high concentration of CPT above the POPC membrane, we show that strong drug-drug aromatic interactions shift the spatial orientation of the drug with the membrane. Stacks of hydrophobic drugs form, allowing penetration of the drug just under the POPC head groups. These results imply that inhomogeneous membrane models need to take into account the effect of drug aggregation on the membrane environment.

Трехпараметрическая модель межмолекулярных взаимодействий как основа для классификации и выбора неподвижных фаз для газовой хроматографии

Описан метод трехпараметрической характеристики селективности газохроматографических неподвижных фаз, который базируется на представлении энергии межмолекулярного взаимодействия вкладами неполярных, полярных сил и водородных связей. Все параметры, используемые в математических выражениях, имеют физический смысл, переносимы и не требуют проведения дополнительных экспериментов. Характеристики неподвижных фаз могут быть рассчитаны как из экспериментальных данных по хроматографическому удерживанию, так и a priori, по известной структурной формуле фазы. Описаны оба способа и проведен расчет параметров для ряда веществ. Полученные разными способами характеристики селективности неподвижных фаз согласуются между собой. Рассматривается также основанная на трехпараметрической модели концепция выбора неподвижной фазы для разделения близких веществ.

Biodistribution of Tc-99m Labeled Isoniazid Solid Lipid Nanoparticles in Wistar Rats.

In this study Isoniazid (INH) as one of the first line drugs in treatment of Tuberculosis was investigated to be loaded in Solid Lipid Nanoparticles (SLNs) for reducing hepatotoxicity as well as prolonging drug release. High shear homogenization method was performed to prepare INH SLNs. To compare biodistribution of INH before and after loading in SLNs, INH was labeled by Technetium 99 (Tc99) after derivatization. The particle size of the prepared SLNs was 167 and 200 nm before and after lyophilization, respectively. Loading efficiency was calculated using the reverse method and release study was performed by using the dialysis sack method. Loading efficiency was 98%, and more than 85% of the loaded drug released in 3 h. Differential Scanning calorimeter (DSC) studies were performed for evaluating of the probability of happening hydrogen bonds or other chemical interactions between cholesterol as carrier and isoniazid as active pharmaceutical ingredient. The results could support the probability of hydrogen bond formation between cholesterol and INH. Gamma Scintigraphy studies showed that after administering INH SLNs, longer drug retention in the body was obtained compared to free INH. Quantitative gamma counting showed that the concentration of INH in the liver and intestines could be decreased by using nanotechnology.

Determination of Critical Micelle Concentration and Thermodynamic Evaluations of Micellization of GMS

The uncontrolled distribution of surfactants which are commonly used as household and industrial products like soaps, lubricants and detergents in the global market have provoked this study. The determination of critical micelle concentration (CMC) of glycerol monostearate surfactant (GMS) was evaluated using Conductivity and UV-Visible Spectroscopic techniques respectively. The effect of solubility was quantified and the Krafft temperature was obtained. The thermodynamic feasibility parameters were evaluated using Erying and Vant Hoff’s equations. The CMC values were taken from the sharp breaks in the plots of absorbance versus surfactant concentrations and conductivity versus surfactant concentration respectively. The result showed that as the temperature increases, the CMC initially decreases and then followed by slight increase owing to the smaller probability of hydrogen bond formation at higher temperatures. The result showed that the critical micelle concentration of GMS obtained using Conductivity and UV-Visible techniques were 4.50 × 10-2 and 2.40 × 10-2 moldm-3 respectively and the Krafft temperature (KT) was obtained at 50°C. The Gibbs free energy change of micellization (ΔG° CMC) was found to decrease as temperature increases over the whole temperature range. The entropy change of micellization (ΔS° (CMC)) showed positive values throughout the temperature range tested while the large enthalpy change, ΔH° (CMC) means that in the micellization process, the attractive interaction among hydrophobic chains was opposed by the strong interaction of the oxyethylene chains of glycerol monostearate with water molecules. The study revealed that the use of UV-Visible Spectroscopy technique was a very good and easy way of determining the critical micelle concentration of GMS. This study is also a valuable industrial tool for the production of soap related products and its applications in domestic and industrial processes.

Stochastic Adhesion of Hydroxylated Atomic Force Microscopy Tips to Supported Lipid Bilayers

This work reports results of an atomic force microscopy (AFM) study of adhesion force between hydroxylated AFM tips and supported lipid bilayers (SLBs) of phosphatidylcholine in phosphate buffer saline solution at neutral pH. Silicon nitride AFM probes were hydroxylated by treatment in water vapor plasma and used in force spectroscopy measurements of adhesion force on SLBs with control of contact loading force and residence time. The measurements showed a stochastic behavior of adhesion force that was attributed to stochastic formation of hydrogen bonds between the hydroxyl groups on the AFM tip and oxygen atoms from the phosphate groups of the phosphatidylcholine molecules. Analysis of a large number of force curves revealed a very low probability of hydrogen bond formation, a probability that increased with the increase of contact loading force and residence time. The variance and mean values of adhesion force showed a linear dependence on each other, which indicated that hydrogen bond formation obeyed the Poisson distribution of probability. This allowed for the quantitative determination of the rupture force per hydrogen bond of about 40 pN and showed the absence of other nonspecific interaction forces.

Plasmonic Circular Dichroism Study of DNA–Gold Nanoparticles Bioconjugates

Plasmonic circular dichroism (CD) responses of hybrid nanostructures containing noble metal nanoparticles and chiral molecules have received increasing interest with various applications in nanophotonics. Chiral biomolecules show strong CD signals typically found in the ultraviolet region, whereas, in the visible range, they produce a weak signal. Strengthening the CD signal in the visible region is of high importance, which could be achieved through fabrication of novel hybrid nanostructures. Herein, gold nanoparticles (GNPs) have been assembled via DNA linker to investigate the possibility of enhancing plasmonic CD signal in the visible range. DNA-linked assemblies with pre- and postannealed conditions were characterized by ultraviolet–visible spectroscopy, dynamic light scattering (DLS), and CD spectropolarimetry. In the presence of DNA linker with sticky ends, the aggregation phenomenon was traced by red shifts of surface plasmon resonance of nanoparticles. Time-dependent hybridization of single-stranded “sticky ends” with DNA-conjugated GNPs and increased probability of hydrogen bond formation lead to enhancement of CD signals in the ultraviolet region. Complexation of biomolecule and nanoparticle assemblies induced enhanced CD signals in the visible range, which was noticed both before and after purification. DLS characterization of the assemblies also confirmed the difference in the size of aggregates, which could be controlled by the linker molecules. This investigation encourages possibility of utilizing plasmonic CD technique as a tool for tracing fabricated nanostructure assemblies with enhanced characterization possibility.

Modeling of Dielectric Properties of Complex Fluids with an Equation of State

The static permittivity is a key property for describing solutions containing polar and hydrogen bonding compounds. However, the precise relationship between the molecular and dielectric properties is not well-established. Here we show that the relative permittivity at zero frequency (static permittivity) can be modeled simultaneously with thermodynamic properties. The static permittivity is calculated from an extension of the framework developed by Onsager, Kirkwood, and Fröhlich to associating mixtures. The thermodynamic properties are calculated from the cubic-plus-association (CPA) equation of state that includes the Wertheim association model as formulated in the statistical associating fluid theory (SAFT) to account for hydrogen bonding molecules. We show that, by using a simple description of the geometry of the association, we may calculate the Kirkwood g-factor as a function of the probability of hydrogen bond formation. The results show that it is possible to predict the static permittivity of complex mixtures over wide temperature and pressure ranges from simple extensions of well-established theories simultaneously with the calculation of thermodynamic properties.

Structural parameters of glycine zwitterion hydration from the data of the integral equation method in the RISM approach

The structural parameters of glycine zwitterion in water were studied by means of the integral equation method in the framework of the RISM approximation. According to calculations, five water molecules are located in the nearest environment of the -NH3+ group, and two of them are the H-bonded with this group. At the same time, six water molecules are located in the nearest environment of the −COO− group, and three of them are the H-bonded with this group. The average number of water molecules in the first hydration shell of −CH2 group is four. It has been shown that the probability of hydrogen bond formation between water molecules and the hydrogen atom H1 of the −NH3+ group is low, and there is no H-bonding between water molecules and the nitrogen atom the −NH3+ group.

A Single Amino Acid of Human Immunodeficiency Virus Type 2 Capsid Protein Affects Conformation of Two External Loops and Viral Sensitivity to TRIM5α

We previously reported that human immunodeficiency virus type 2 (HIV-2) carrying alanine or glutamine but not proline at position 120 of the capsid protein (CA) could grow in the presence of anti-viral factor TRIM5α of cynomolgus monkey (CM). To elucidate details of the interaction between the CA and TRIM5α, we generated mutant HIV-2 viruses, each carrying one of the remaining 17 possible amino acid residues, and examined their sensitivity to CM TRIM5α-mediated restriction. Results showed that hydrophobic residues or those with ring structures were associated with sensitivity, while those with small side chains or amide groups conferred resistance. Molecular dynamics simulation study revealed a structural basis for the differential TRIM5α sensitivities. The mutations at position 120 in the loop between helices 6 and 7 (L6/7) affected conformation of the neighboring loop between helices 4 and 5 (L4/5), and sensitive viruses had a common L4/5 conformation. In addition, the common L4/5 structures of the sensitive viruses were associated with a decreased probability of hydrogen bond formation between the 97th aspartic acid in L4/5 and the 119th arginine in L6/7. When we introduced aspartic acid-to-alanine substitution at position 97 (D97A) of the resistant virus carrying glutamine at position 120 to disrupt hydrogen bond formation, the resultant virus became moderately sensitive. Interestingly, the virus carrying glutamic acid at position 120 showed resistance, while its predicted L4/5 conformation was similar to those of sensitive viruses. The D97A substitution failed to alter the resistance of this particular virus, indicating that the 120th amino acid residue itself is also involved in sensitivity regardless of the L4/5 conformation. These results suggested that a hydrogen bond between the L4/5 and L6/7 modulates the overall structure of the exposed surface of the CA, but the amino acid residue at position 120 is also directly involved in CM TRIM5α recognition.

Effect of Temperature on the Critical Micelle Concentration and Micellization Thermodynamic of Nonionic Surfactants: Polyoxyethylene Sorbitan Fatty Acid Esters

In this study, non‐ionic surfactants, polyoxyethylene sorbitan fatty acid esters (polysorbate) are chosen to examine the temperature effect on the CMC over a wide temperature range. The enthalpy and entropy of micelle formation are evaluated according to the phase separation model. The surface tension of solutions was determined by means of Du Nöuys ring. The CMC values were taken from the sharp breaks in the surface tension vs. logarithms of surfactant concentration plots. As the surfactants′ chain length increases the CMC at a constant temperature decreases, which is directly related to the decrease of hydrophilicity of the molecules. For each surfactant, as the system temperature increases, the CMC initially decreases and then increases, owing to the smaller probability of hydrogen bond formation at higher temperatures. The onset of micellization tends to occur at higher concentrations as the temperature increases. To evaluate the enthalpy of micellization, the CMCs are first correlated by a polynomial equation. It is found that ∆Gºm decreases monotonically as the temperature increases over the whole temperature range. Both ∆Hºm and ∆Sºm appear to be decrease monotonically with an increase in temperature. The compensation temperature was found to be 42 ºC by linear regression over the whole temperature range and for all three surfactant systems together.

Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds.

We study atomic models of the thermodynamics of the structural transition of peptides that form alpha-helices. The effect of sequence variation on alpha-helix formation for alanine-rich peptides, Ac-Ala21-methyl amide (A21) and Ac-A5 (AAARA)3A-methyl amide (Fs peptide), is investigated by atomic simulation studies of the thermodynamics of the helix-coil transition in explicit water. The simulations show that the guanidinium group in the Arg side chains in the Fs peptide interacts with the carbonyl group four amino acids upstream in the chain and desolvates backbone hydrogen bonds. This desolvation can be directly correlated with a higher probability of hydrogen bond formation. We find that Fs has higher helical content than A21 at all temperatures. A small modification in the amber force field reproduces the experimental helical content and helix-coil transition temperatures for the Fs peptide.

Properties of the network of the hydrogen bonds of water

Networks of the hydrogen bonds and those consisting of lines connecting nearby molecules were constructed using configurations of water molecules obtained by the Monte-Carlo method. The concentrations of closed cycles of hydrogen bonds were established to be determined only by the probability of hydrogen bond formation. Characteristics of a model ideal water network were determined. Topological properties of the Polk model and those of the network of nearest neighbors substantially differ from the properties of the ideal network. The totality of the hydrogen bonds in pure water was proposed to be considered as a hierarchical system. Three topologically different structures of water associates were determined.

1H NMR study of water relaxation and self-diffusion in human serum albumin aqueous solutions

Water proton spin-lattice relaxation and self-diffusion in aqueous solutions of human serum albumin have been studied by1H NMR as a function of the protein concentration. Spin-lattice relaxation data, which display a nonlinear behaviour with the protein concentration, could be fitted with a two-phase model taking into account the experimentally determined hydration («bound») water values. Despite a similar trend is registered for the water self-diffusion coefficient, such a model has been found unable to explain the related experimental data taken as a function of the biomolecule concentration. On the other hand, the solute-induced proton self-diffusion decrease could be satisfactorily interpreted by postulating an enhanced probability of hydrogen-bond formation occurring within the «vicinal» water surrounding the biomolecules for several hydration shells. The consistency within the two models is discussed in connection with the magnetic interactions occurring within the solute-solvent systems.

Water proton self-diffusion and hydrogen bonding in aqueous human albumin solutions

The self-diffusion coefficient, D, of water has been determined by the NMR static field gradient method as a function of the serum albumin weight dissolved in water. A non-linear behaviour of D was found with increasing protein concentration. The data that could not be interpreted by taking into account the measured fraction of bound water have been satisfactorily explained in terms of a solute-induced enhancement of the probability of hydrogen bond formation.