Molecular design based on polyribonucleotides fixed in the structure of liquid-crystalline dispersion and cross-linked via polymeric chelate bridges

A method of molecular design based on cross-linking of polyribonucleotide molecules with polymeric chelate bridges (anthracycline-Cu²⁺-…-Cu²⁺-anthracycline) was developed. The formation of polymeric chelate cross-bridges between neighboring polyribonucleotide molecules in the particles of liquid-crystalline dispersions was shown to require the formation of external complex (anthracycline-polyribonucleotide). The properties (shape, size, optical activity, etc.) of molecular constructions composed of different polyribonucleotides were studied and compared. Molecular constructions on the basis of polyribonucleotides could be used as sensing elements with adjustable properties in biosensor technology, nanobiotechnology, and molecular pharmacology.     

Structure and interactions of aggrecans: statistical thermodynamic approach

Weak polyelectrolytes tethered to cylindrical surfaces are investigated using a molecular theory. These polymers form a model system to describe the properties of aggrecan molecules, which is one of the main components of cartilage. We have studied the structural and thermodynamical properties of two interacting aggrecans with a molecular density functional theory that incorporates the acid-base equilibrium as well as the molecular properties: including conformations, size, shape, and charge distribution of all molecular species. The effect of acidity and salt concentration on the behavior is explored in detail. The repulsive interactions between two cylindrical-shaped aggrecans are strongly influenced by both the salt concentration and the pH. With increasing acidity, the polyelectrolytes of the aggrecan acquire charge and with decreasing salt concentration those charges become less screened. Consequently the interactions increase in size and range with increasing acidity and decreasing salt concentration. The size and range of the forces offers a possible explanation to the aggregation behavior of aggrecans and for their ability to resist compressive forces in cartilage. Likewise, the interdigitation of two aggrecan molecules is strongly affected by the salt concentration as well as the pH. With increasing pH, the number of charges increases, causing the repulsions between the polymers to increase, leading to a lower interdigitation of the two cylindrical polymer layers of the aggrecan molecules. The low interdigitation in charged polyelectrolytes layers provides an explanation for the good lubrication properties of polyelectrolyte layers in general and cartilage in particular.     

The beauty of molecular surfaces as revealed by self-organizing neural networks

The Kohonen neural network is a self-organizing network that can be used for the projection of the surface properties of molecules. This allows one to view properties on a molecular surface, like the electrostatic potential in a single picture. These maps are useful for the comparison of molecules and provide a new definition of molecular similarity.     

Mechanical Properties of Mammalian and Fish Gelatins as a Function of the Contents of α-Chain, β-Chain,and Low and High Molecular Weight Fractions

Small-strain oscillatory measurements and size-exclusion chromatography coupled to multiangle laser light scattering were used to study the mechanical properties and the molecular weight distribution, respectively, of acid porcine skin gelatins (type A), lime bovine bone gelatins (type B), and cold water fish gelatins, while principal component analysis (PCA) and partial least squares regression were used to relate the mechanical properties with the molecular weight distribution. The present study suggests a linear relationship between the mechanical properties and the fractions of low molecular weight (LMW) molecules, α-chains, β-chains, and high molecular weight (HMW) molecules. The Bloom value for mammalian gelatin was positively correlated with the fractions of α-chains, β-chains, and HMW molecules and negatively correlated with the fraction of LMW molecules. The dynamic storage modulus for cold water fish gelatin was positively correlated with the fractions of β-chains and HMW molecules and negatively correlated with the fractions of LMW molecules and α-chains.     

Investigations of Nematic-Isotropic Transition by Means of Constant Pressure Molecular Dynamics Simulations

Abstract

Constant pressure molecular dynamics simulations, which secure the system to be under hydrostatic pressure, are used to simulate the behavior of liquid crystals consisting of anisotropic molecules with both translational and orientational freedom. In order to investigate to what extent can the properties known to real liquid crystalline phases be explained by the anisotropy of the shape of the molecules alone, the molecular dynamic (MD) simulation uses purely repulsive short-range pair potentials representing soft spherocylinders. A clear change in the microscopic as well as the macroscopic physical properties are observed near the phase transition from nematic liquid crystal to isotropic liquid.     

Protein scaffold-based molecular probes for cancer molecular imaging

Protein scaffold molecules are powerful reagents for targeting various cell signal receptors, enzymes, cytokines and other cancer-related molecules. They belong to the peptide and small protein platform with distinct properties. For the purpose of development of new generation molecular probes, various protein scaffold molecules have been labeled with imaging moieties and evaluated both in vitro and in vivo. Among the evaluated probes Affibody molecules and analogs, cystine knot peptides, and nanobodies have shown especially good characteristics as protein scaffold platforms for development of in vivo molecular probes. Quantitative data obtained from positron emission tomography, single photon emission computed tomography/CT, and optical imaging together with biodistribution studies have shown high tumor uptakes and high tumor-to-blood ratios for these probes. High tumor contrast imaging has been obtained within 1 h after injection. The success of those molecular probes demonstrates the adequacy of protein scaffold strategy as a general approach in molecular probe development.     

Theoretical study of two-photon absorption properties and up-conversion efficiency of new symmetric organic π-conjugated molecules for photovoltaic devices

Organic material with high intensity of two-photon absorption (TPA) induced fluorescence can be used as the frequency up-converter materials for improving efficiency of the solar cells. In this work, the organic molecular structures were designed by symmetrically grafting two elongated conjugated linkers on a conjugated core and then adding donor groups at both terminals. Fluorene derivatives as a core acceptor, phenylethynyl as the conjugated linker and diphenylamino or methyl-9H-carbozole as the donor end groups were selected. Quantum mechanical modeling techniques were applied to investigate the molecular electronic structure and properties. Absorption properties of these novel π-conjugated organic molecules were studied. The TPA cross-sections of these derivatives were calculated using few-states models, respectively. The effects of donor and acceptor groups on the TPA behaviors of these designed molecules were investigated. The up-conversion efficiency of designed molecules was also calculated.     

Evolution of opsins and phototransduction

Opsins are the universal photoreceptor molecules of all visual systems in the animal kingdom. They can change their conformation from a resting state to a signalling state upon light absorption, which activates the G protein, thereby resulting in a signalling cascade that produces physiological responses. This process of capturing a photon and transforming it into a physiological response is known as phototransduction. Recent cloning techniques have revealed the rich and diverse nature of these molecules, found in organisms ranging from jellyfish to humans, functioning in visual and non-visual phototransduction systems and photoisomerases. Here we describe the diversity of these proteins and their role in phototransduction. Then we explore the molecular properties of opsins, by analysing site-directed mutants, strategically designed by phylogenetic comparison. This site-directed mutant approach led us to identify many key features in the evolution of the photoreceptor molecules. In particular, we will discuss the evolution of the counterion, the reduction of agonist binding to the receptor, and the molecular properties that characterize rod opsins apart from cone opsins. We will show how the advances in molecular biology and biophysics have given us insights into how evolution works at the molecular level.     

The electronic transport properties of B<Subscript>40</Subscript> fullerenes with chalcogens as anchor atoms

Fullerenes are the most popular molecules to use in applications related to molecular electronics because of their superconductive nature. These molecules show a diverse range of properties, including optical, electronic, and structural characteristics. In this work, we focused on the electronic transport properties of molecular devices consisting of the fullerene B₄₀ or B₄₀ with different anchor atoms between two gold electrodes in a two-probe configuration. The elements used as anchor atoms in the B₄₀ molecules were oxygen, selenium, and sulfur, i.e., chalcogens. The current characteristics of these fullerene-based molecular devices were calculated and analyzed. The analysis highlighted the superior electrical conductivity of the pure B₄₀ device compared to the devices based on its chalcogen-anchored variants. The conductivities of the molecular devices were ranked as follows: pure B₄₀?>?selenium-anchored > sulfur-anchored > oxygen-anchored B₄₀. It was also noted that the devices based on B₄₀ and its chalcogen-anchored variants gave nonzero conductance values at zero bias. These results pave the way for the application of these molecules in future nanodevices utilizing extremely small bias voltages.     

The effect of storage and active ingredient properties on the drug release profile of poly(ethylene oxide) matrix tablets

Different molecular weight forms of poly(ethylene oxide) can be used successfully in controlled release drug delivery due to their excellent matrix forming properties. Drug release of these materials follows nearly zero order kinetics, and is mainly governed by polymer swelling and erosion and diffusion of drug molecules. Because of its partly amorphous structure, poly(ethylene oxide) undergoes structural changes caused by elevated temperature and relative humidity of the storage medium resulting in an increased drug release. This physical process can be highly influenced by the structure of different drug molecules, such as polymer-binding ability and hydration tendency. These properties of two basic drugs embedded into poly(ethylene oxide) matrices were characterized by molecular modelling and an attempt was made to reveal their effect on the change of drug release stability, a prerequisite of the marketing authorization of dosage forms. The findings suggest that both the hydration properties of the active ingredient and the molecular weight of the polymer influence the effect of physical ageing of poly(ethylene oxide) on the drug release properties of the matrix.     

A molecular theory of recognition and activation at a 5-HT receptor based on a quantum chemical approach to structure activity relationships

The study of structure activity relationships (SAR) is based on the delineation of the causal relationships between the properties of molecules and the observed responses evoked by the interaction of these molecules with biological systems. The methods of theoretical and quantum chemistry describe accurately the molecular properties that are determined by molecular structure and provide a rigorous link between structure and activity. We study the molecular events in the pharmacological mechanism of drugs interacting with the receptor of 5-hydroxytryptamine (5-HT, serotonin) by defining the elements of recognition and by analyzing the changes induced in a molecular model for the receptor. These steps define the relationship between the properties of the drugs and their ability to be recognized and cause the activation of the receptors. Consequently, our quantum chemical studies of drug-receptor interactions explain the selectivity of receptors and the molecular determinants for agonism and antagonism on the 5-HT receptor.     

CNS Drug Design Based on Principles of Blood-Brain Barrier Transport

Abstract: Lipid-soluble small molecules with a molecular mass under a 400–600-Da threshold are transported readily through the blood-brain barrier in vivo owing to lipid-mediated transport. However, other small molecules lacking these particular molecular properties, antisense drugs, and peptide-based pharmaceuticals generally undergo negligible transport through the blood-brain barrier in pharmacologically significant amounts. Therefore, if present day CNS drug discovery programs are to avoid termination caused by negligible blood-brain barrier transport, it is important to merge CNS drug discovery and CNS drug delivery as early as possible in the overall CNS drug development process. Strategies for special formulation that enable drug transport through the blood-brain barrier arise from knowledge of the molecular and cellular biology of blood-brain barrier transport processes.     

Atomistic simulation studies of cholesteryl oleates: model for the core of lipoprotein particles

We have conducted molecular dynamics simulations to gain insight into the atomic-scale properties of an isotropic system of cholesteryl oleate (CO) molecules. Cholesteryl esters are major constituents of low density lipoprotein particles, the key players in the formation of atherosclerosis, as well as the storage form of cholesterol. Here the aim is to clarify structural and dynamical properties of CO molecules under conditions, which are suggestive of those in the core of low density lipoprotein particles. The simulations in the fluid phase indicate that the system of CO molecules is characterized by an absence of translational order, as expected, while the orientational order between distinct CO molecules is significant at short distances, persisting over a molecular size. As for intramolecular properties, the bonds along the oleate chain are observed to be weakly ordered with respect to the sterol structure, unlike the bonds along the short hydrocarbon chain of cholesterol where the ordering is significant. The orientational distribution of the oleate chain as a whole with respect to the sterol moiety is of broad nature, having a major amount of extended and a less considerable proportion of bended structures. Distinct transient peaks at specific angles also appear. The diffusion of CO molecules is found to be a slow process and characterized by a diffusion coefficient of the order of 2x10(-9) cm2/s. This is considerably slower than diffusion, e.g., in ordered domains of lipid membranes rich in sphingomyelin and cholesterol. Analysis of the rotational diffusion rates and trans-to-gauche transition rates yield results consistent with experiments.     

Protein Molecular Surface Mapped at Different Geometrical Resolutions

Many areas of biochemistry and molecular biology, both fundamental and applications-orientated, require an accurate construction, representation and understanding of the protein molecular surface and its interaction with other, usually small, molecules. There are however many situations when the protein molecular surface gets in physical contact with larger objects, either biological, such as membranes, or artificial, such as nanoparticles. The contribution presents a methodology for describing and quantifying the molecular properties of proteins, by geometrical and physico-chemical mapping of the molecular surfaces, with several analytical relationships being proposed for molecular surface properties. The relevance of the molecular surface-derived properties has been demonstrated through the calculation of the statistical strength of the prediction of protein adsorption. It is expected that the extension of this methodology to other phenomena involving proteins near solid surfaces, in particular the protein interaction with nanoparticles, will result in important benefits in the understanding and design of protein-specific solid surfaces.     

Olfactory receptor neuron profiling using sandalwood odorants

The mammalian olfactory system can discriminate between volatile molecules with subtle differences in their molecular structures. Efforts in synthetic chemistry have delivered a myriad of smelling compounds of different qualities as well as many molecules with very similar olfactive properties. One important class of molecules in the fragrance industry are sandalwood odorants. Sandalwood oil and four synthetic sandalwood molecules were selected to study the activation profile of endogenous olfactory receptors when exposed to compounds from the same odorant family. Dissociated rat olfactory receptor neurons were exposed to the sandalwood molecules and the receptor activation studied by monitoring fluxes in the internal calcium concentration. Olfactory receptor neurons were identified that were specifically stimulated by sandalwood compounds. These neurons expressed olfactory receptors that can discriminate between sandalwood odorants with slight differences in their molecular structures. This is the first study in which an important class of perfume compounds was analyzed for its ability to activate endogenous olfactory receptors in olfactory receptor neurons.     

Interactions of anticancer drugs with usual and mismatch base pairs - density functional theory studies

The antitumor activity of a drug is associated with its molecular properties as well as its interactions with target molecules. The molecular structures of usual, mismatch base pairs and their drug (Hydroxyurea and 5-Fluorouracil) interacting complexes were studied using density functional theory methods. The two and three-body interaction energies have been used to analyze the influence of a drug on the stability of base pairs. The sharing of electron density between the interacting molecules is shown through electron density difference maps. The Atoms in Molecules theory and Natural Bond Orbital analysis have been performed to study the hydrogen bonds in the drug interacting complexes.     

Theoretical investigation of auxiliary electronic acceptors in modifying D-D-π-A sensitizers for dye-sensitized solar cells

In light of the performance of the SD2 pigments in DSSC, in order to expand the absorption spectral scope, decrease the energy difference between the highest occupied and the lowest unoccupied molecular orbitals, with SD2 dye molecular electron donor and electron acceptor as the fundamental framework, the indole fragment and thiophene derivative in the prototype dye molecule were replaced by the two π-bridges (labeled PA, PB, respectively) and the four auxiliary electron acceptors (labeled A1, A2, A3, A4, respectively). For the sake of characterizing dye molecules as thoroughly as possible in DSSC, the frontier orbital energy levels, ultraviolet absorption spectra, natural bond orbital analysis, intramolecular charge transfer, charge and hole reorganization energies, parameters influencing the short-circuit current density and the open-circuit photovoltage for these eight individual dye molecules are carried out to try to fully characterize the properties of these dye molecules. According to these computational results of physical quantities and based on the performance of these dye molecules in the above aspects, in this paper, six free molecular models were picked out to combine with titanium dioxide cluster to calculate their geometrical structures, frontier orbital distributions, electron excitation energies, ultraviolet absorption spectra and the composition of the electronic transitions in chloroform solvent with polarizable continuum model. The results of these calculations show that the PA-A2 and PB-A4 dye molecule has better properties in electron transfer and spectral absorption range before and after the adsorption on the titanium dioxide.     

Molecular insights into the irreversible mechanical behavior of sickle hemoglobin

Sickle cell disease is caused by the amino acid substitution of glutamic acid to valine, which leads to the polymerization of deoxygenated sickle hemoglobin (HbS) into long strands. These strands are responsible for the sickling of red blood cells (RBCs), making blood hyper-coagulable leading to an increased chance of vaso-occlusive crisis. The conformational changes in sickled RBCs traveling through narrow blood vessels in a highly viscous fluid are critical in understanding; however, there are few studies that investigate the origins of the molecular mechanical behavior of sickled RBCs. In this work, we investigate the molecular mechanical properties of HbS molecules. A mechanical model was used to estimate the directional stiffness of an HbS molecule and the results were compared to adult human hemoglobin (HbA). The comparison shows a significant difference in strength between HbS and HbA, as well as anisotropic behavior of the hemoglobin molecules. The results also indicated that the HbS molecule experienced more irreversible mechanical behavior than HbA under compression. Further, we have characterized the elastic and compressive properties of a double stranded sickle fiber using six HbS molecules, and it shows that the HbS molecules are bound to each other through strong inter-molecular forces.     

Humic acid as a colloidal surfactant

The Na⁺-humate sol is studied as a surface active substance (surfactant) capable of lowering the surface tension of water, and of spreading on the water surface with observable velocity to form a thin film. Based on these properties, it is concluded that sol should contain molecules of intermediate molecular weight as well as their associates (micelles) whose weight depends on the number of molecules in the micelles.