Effect Of Molecular Size Research Articles

Rejection of Commonly Used Electrolytes in Asymmetric Flow Field Flow Fractionation: Effects of Membrane Molecular Weight Cutoff Size, Fluid Dynamics, and Valence of Electrolytes.

Asymmetric flow field flow fractionation (AF4) is an efficient size-based separation technique for the characterization of submicron size particulates. In AF4, membranes having various molecular weight cutoff sizes are used as a barrier to retain particles while allowing the carrier fluid containing electrolytes to permeate. Here, we have hypothesized that electrolyte rejection by the barrier membrane leads to the accumulation of electrolytes in the channel during operation. Electrolyte accumulation can cause various adverse effects that can lead to membrane fouling. An instrument setup containing a conductivity detector was assembled, and the rejection of commonly used carrier electrolytes such as trisodium citrate, ethylenediaminetetraacetic acid, sodium chloride, and ammonium carbonate was evaluated by varying the concentration, cross-flow rate, focusing flow rate, membrane material type, and cutoff sizes. The results showed that electrolyte rejection increased with a decrease in the electrolyte concentration and the molecular weight cutoff size (pore size) or with an increase in the charge state of the anion in the carrier electrolytes. We proposed an electrostatic repulsion-based rejection mechanism and verified it with the measurement of the rejection rate while varying the electrolyte concentration in the running media.

Cascade engineered synthesis of 2-ethyl-1-hexanol from n-butanal and 2-methyl-1-pentanol from n-propanal using combustion synthesized Cu/Mg/Al mixed metal oxide trifunctional catalyst

2-Ethyl-1-hexanol (2-EH) is a commercially important chemical that requires cost effective catalytic processes for synthesis. The cascade engineered synthesis of 2-EH was done in a single pot from n-butanal using solventless conditions with trifunctional mixed metal oxide containing 5% Cu and Mg/Al ratio of 3. This trifunctional catalyst was made by combustion synthesis technique which resulted in a porous network with narrow pore size distribution. The catalyst was characterized before and after reuse by FTIR, XRD, SEM, TEM, CO2-TPD, NH3-TPD, TPR, TGA and nitrogen BET analysis. The kinetics of reaction and selectivity profile of 2-EH are reported. The work was extended to one pot cascade engineered synthesis of 2-methyl-1-pentanol (2-MP) from n-propanal using the same catalyst. There was a significant effect of molecular size on rate of reaction and selectivity of the product. This is the first ever report on the one pot synthesis of 2-MP from n-propanal.

Simulation study on the effects of chemical structure and molecular size on the acceptor strength in poly(3-hexylthiophene)-based copolymer with alternating donor and acceptor for photovoltaic applications

This research assessed the effects of various chemical structures and molecular sizes on the simulated geometric parameters, electron structures, and spectroscopic properties of single-chain complex alternating donor–acceptor (D–A) monomers and copolymers that are intended for use as photoactive layer in a polymer solar cell by using Kohn–Sham density functional theory with B3LYP exchange-correlation functional. The 3-hexylthiophene (3HT) was selected for electron donor, while eight chemicals, namely thiazole (Z), thiadiazole (D), thienopyrazine (TP), thienothiadiazole (TD), benzothiadiazole (BT), thiadiazolothieno-pyrazine (TPD), oxadiazole (OXD) and 5-diphenyl-1,2,4-triazole (TAZ), were employed as electron acceptor functional groups. The torsional angle, bridge bond length, intramolecular charge transfer, energy levels, and molecular orbitals were analyzed. The simulation results reveal that the geometry and electron structure of donor–acceptor monomer and copolymer are significantly impacted by heterocyclic rings, heteroatoms, fused rings, degree of steric hindrance and coplanarity of the acceptor molecular structure. Planar conformation was obtained from the D copolymer, and a pseudo-planar structure with the TD copolymer. The TAZ acceptor exhibited strong steric hindrance due to its bulky structure and non-planarity of its structure. An analysis of the electron structures indicated that the degree of intramolecular electron-withdrawing capability had the rank order TAZ < Z < D < TPD < OXD < TP < BT < TD. The TD is indicated as the most effective acceptor among those that were simulated. However, the small energy gaps of TD as well as TPD copolymer indicate that these two copolymers can be used in transparent conducting materials. The copolymer based on BT acceptor exhibited good intramolecular charge transfer and absorbed at 656 nm wavelength which is close to the maximum flux of solar spectrum. Hence, the BT acceptor functional group provides a compromise in the characteristics of a donor–acceptor copolymer, useful in a polymeric candidate material for the photoactive layer in a polymer solar cell.

Effect of Molecular Size of Modifying Agents on the Properties of Gelatin films

Effect of Molecular Size of Modifying Agents on the Properties of Gelatin films

Expansion characteristics of expandable styrene/methyl methacrylate copolymer particles: The effects of copolymer molecular weight and particle size

Spherical foamable particles were synthesized by suspension polymerization of methyl methacrylate and styrene in the presence of a blowing agent. When the surrounding temperature was high enough to vaporize the blowing agent and soften the polymer shell, the particles were expanded due to pressure difference across the shell. The effects of initiator and crosslinker concentration on the particle size, average molecular weight, and molecular weight distribution of synthesized copolymer, pentane content and expansion properties (density, residual pentane, and dimensional stability of pre-expanded beads) of expandable particles were investigated. The results showed that the expansion behavior of the particles was dependent on molecular weight of the matrix polymer and size of the synthesized particles. In a constant copolymer molecular weight, the pre-expanded bead density decreased with increasing of particle size whereas it increased with molecular weight in a constant particle size. Moreover, the crosslinker improved dimensional stability of the pre-expanded beads.

Crystal Structures and Phase Sequences of Metallocenium Salts with Fluorinated Anions: Effects of Molecular Size and Symmetry on Phase Transitions to Ionic Plastic Crystals.

Sandwich compounds often exhibit various phase transitions, including those to plastic phases. To elucidate the general features of the phase transitions in metallocenium salts, the thermal properties and crystal structures of [Fe(C5 Me5 )2 ]X ([1]X), [Co(C5 Me5 )2 ]X ([2]X), and [Fe(C5 Me4 H)2 ]X ([3]X) have been investigated, where the counter anions (X) are Tf2 N (=(CF3 SO2 )2 N- ), OTf (=CF3 SO3- ), PF6 , and BF4 . The Tf2 N salts commonly undergo phase transitions from an ordered phase at low temperatures to an anion-disordered phase, followed by a plastic phase and finally melt at high temperatures. All these salts exhibit a phase transition to a plastic phase, and the transition temperature generally decreases with decreasing cation size and increasing anion size. The crystal structures of these salts comprise an alternating arrangement of cations and anions. About half of these salts exhibit phase transitions at low temperatures, which are mostly correlated with the order-disorder of the anion.

Site-specific Isopeptide Bridge Tethering of Chimeric gp41 N-terminal Heptad Repeat Helical Trimers for the Treatment of HIV-1 Infection.

Peptides derived from the N-terminal heptad repeat (NHR) of HIV-1 gp41 can be potent inhibitors against viral entry when presented in a nonaggregating trimeric coiled-coil conformation via the introduction of exogenous trimerization motifs and intermolecular disulfide bonds. We recently discovered that crosslinking isopeptide bridges within the de novo helical trimers added exceptional resistance to unfolding. Herein, we attempted to optimize (CCIZN17)3, a representative disulfide bond-stabilized chimeric NHR-trimer, by incorporating site-specific interhelical isopeptide bonds as the redox-sensitive disulfide surrogate. In this process, we systematically examined the effect of isopeptide bond position and molecular sizes of auxiliary trimeric coiled-coil motif and NHR fragments on the antiviral potency of these NHR-trimers. Pleasingly, (IZ14N24N)3 possessed promising inhibitory activity against HIV-1 infection and markedly increased proteolytic stability relative to its disulfide-tethered counterpart, suggesting good potential for further development as an effective antiviral agent for treatment of HIV-1 infection.

Stagnation pressure effect on Prandtl Meyer function for air

When the stagnation pressure of a perfect gas increases, the specific heat and their ratio do not remain constant anymore and start to vary with this pressure. The gas does not stay perfect. Its state equation change and it becomes for a real gas. In this case, the effects of molecular size and intermolecular attraction forces intervene to correct the state equation, the thermodynamic parameters and the value of Prandtl Meyer function. The aim of this work is developing a new form of Prandtl Meyer function based on those assumptions; and determining the effect of stagnation pressure on this function. With the assumptions that Berthelot’s state equation accounts for molecular size and intermolecular force effects, expressions are developed for analysing the supersonic flow for thermally and calorically imperfect gas lower than the dissociation molecules threshold. The supersonic parameters depend directly on the stagnation parameters of the combustion chamber. The application is for air. A computation of error was made in this case to give a limit of the perfect gas and the high temperature models compared to the real gas model.

Nuclear Quantum Effects in H+ and OH– Diffusion along Confined Water Wires

The diffusion of protons and hydroxide ions along water wires provides an efficient mechanism for charge transport that is exploited by biological membrane channels and shows promise for technological applications such as fuel cells. However, what is lacking for a better control and design of these systems is a thorough theoretical understanding of the diffusion process at the atomic scale. Here we focus on two aspects of this process that are often disregarded because of their high computational cost: the use of first-principles potential energy surfaces and the treatment of the nuclei as quantum particles. We consider proton and hydroxide ions in finite water wires using density functional theory augmented with an apolar cylindrical confining potential. We employ machine learning techniques to identify the charged species, thus obtaining an agnostic definition that takes explicitly into account the delocalization of the charge in the Grotthus-like mechanism. We include nuclear quantum effects (NQEs) through the thermostated ring polymer molecular dynamics method and model finite system size effects by considering Langevin dynamics on the potential of mean force of the charged species, allowing us to extract the same "universal" diffusion coefficient from simulations with different wire sizes. In the classical case, diffusion coefficients depend significantly on the potential energy surface, in particular on how dispersion forces modulate water-water distances. NQEs, however, make the diffusion less sensitive to the underlying potential and geometry of the wire.

Evaluation of mesoporous silicate nanoparticles for the sustained release of the anticancer drugs: 5-fluorouracil and 7-hydroxycoumarin

In this study, effects of chemical structure and molecular size of the anticancer drugs 5-fluorouracil and 7-hydroxycoumarin on their release from MCM-48 nanoparticles were investigated. Nanoparticles of the mesoporous silicate material, MCM-48, were prepared and characterized by XRD, SEM and FTIR. Loading of 5-fluorouracil and 7-hydroxycoumarin onto the nanoparticles was confirmed by FTIR and TGA measurements, and loading capacities of about 24 and 14 % were achieved, respectively. Release experiments for 5-fluorouracil were conducted in buffer solutions at pH = 7.4 and 5.2. However, due to the instability of 7-hydroxycoumarin in basic media, release experiments were conducted only in acidic buffer solution at pH = 5.2. The release of 5-fluorouracil was slightly affected by the pH of the release medium, and it was almost complete in about 2 h. However, the release of 7-hydroxycoumarin which has a larger size and higher acidity followed a prolonged release mode over a period of 12 h. The prolonged release of 7-hydroxycoumarin from MCM-48 nanoparticles points out to the potential use of this system as sustained release delivery carrier.

Effects of molecular size and chemical factor on plasma gene transfection

In order to clarify the mechanism of plasma gene transfection, the relationship between transfection efficiency and transferred molecular size was investigated. Molecules with low molecular mass (less than 50 kDa; dye or dye-labeled oligonucleotide) and high molecular mass (more than 1 MDa; plasmid DNA or fragment of plasmid DNA) were transferred to L-929 cells. It was found that the transfection efficiency decreases with increasing in transferred molecular size and also depends on the tertiary structure of transferred molecules. Moreover, it was suggested the transfection mechanism is different between the molecules with low (less than 50 kDa) and high molecular mass (higher than 1 MDa). For the amount of gene transfection after plasma irradiation, which is comparable to that during plasma irradiation, it is shown that H2O2 molecules are the main contributor. The transfection efficiency decreased to 0.40 ± 0.22 upon scavenging the H2O2 generated by plasma irradiation using the catalase. On the other hand, when the H2O2 solution is dropped into the cell suspension without plasma irradiation, the transfection efficiency is almost 0%. In these results, it is also suggested that there is a synergetic effect of H2O2 with electrical factors or other reactive species generated by plasma irradiation.

Molecular dynamics study on polymer filling into nano-cavity by injection molding

Injection molding is one of the cost-effective technologies to produce polymer items towards mass production. In nano-injection molding, the final replication quality of nanostructures is strongly dependent on the filling quality in nano-cavities. In this paper, simulation models for polymer filling into nano-cavities were constructed to investigate the effects of molecular weight and cavity size. The glass transition temperature of isotactic PMMA with different molecular weights was calculated. Characteristics of configuration and snapshots during the filling process were analyzed. Density distribution, velocity profiles and mean-square gyration radius were proposed to investigate the filling quality and the flow behavior. Simulation results showed that the calculated glass transition temperature was higher than the experimental result and increased with the molecular weight. The filling behavior and final replication quality were highly depended on the molecular weight and the cavity size. A higher density distribution was observed in the edges along the nano-cavity by the nonbonding interactions. During the filling process, the gyration radius was firstly decreased rapidly, and then went up to approach the initial value. Atoms in central area exhibited the highest flow velocity, while the velocities of atoms were gradually decreased with the distance from the center.

Stagnation pressure effect on the supersonic flow parameters with application for air in nozzles

ABSTRACTWhen the stagnation pressure of a perfect gas increases, the specific heat and their ratio do not remain constant anymore and start to vary with this pressure. The gas doesn't stay perfect. Its state equation changes and it becomes a real gas. In this case, the effects of molecular size and intermolecular attraction forces intervene to correct the state equation. The aim of this work is to determine the effect of stagnation pressure on the thermodynamic, physical and geometrical supersonic flow parameters in order to find a general form for real gas. With the assumptions that Berthelot's state equation accounts for molecular size and intermolecular force effects, expressions are developed for analysing the supersonic flow for thermally and calorically imperfect gas lower than the dissociation molecules threshold. The design parameters of the supersonic nozzle-like thrust coefficient depend directly on the stagnation parameters of the combustion chamber. The application made for air. A computation of error was made in this case to give a limit of the perfect gas model compared to the real gas model.

Preparation of chitosan nanoparticles by TPP ionic gelation combined with spray drying, and the antibacterial activity of chitosan nanoparticles and a chitosan nanoparticle–amoxicillin complex

Chitosan nanoparticles were prepared from chitosan with various molecular weights by tripolyphosphate (TPP) ionic gelation combined with a spray drying method. The morphologies and characteristics of chitosan nanoparticles were determined by TEM, FE-SEM and from their mean sizes and zeta potentials. The effect of chitosan molecular weight (130, 276, 760 and 1200 cPs) and size of spray dryer nozzle (4.0, 5.5 and 7.0 µm) on mean size, size distribution and zeta potential values of chitosan nanoparticles was investigated. The results showed that the mean size of chitosan nanoparticles was in the range of 166–1230 nm and the zeta potential value ranged from 34.9 to 59 mV, depending on the molecular weight of chitosan and size of the spray dryer nozzles. The lower the molecular weight of chitosan, the smaller the size of the chitosan nanoparticles and the higher the zeta potential. A test for the antibacterial activity of chitosan nanoparticles (only) and a chitosan nanoparticle–amoxicillin complex against Streptococcus pneumoniae was also conducted. The results indicated that a smaller chitosan nanoparticle and higher zeta potential showed higher antibacterial activity. The chitosan nanoparticle–amoxicillin complex resulted in improved antibacterial activity as compared to amoxicillin and chitosan nanopaticles alone. Using a chitosan nanoparticle–amoxicillin complex could reduce by three times the dosage of amoxicillin while still completely inhibiting S. pneumoniae.

Molecular transport in collagenous tissues measured by gel electrophoresis

Molecular transport in tissues is important for drug delivery, nutrient supply, waste removal, cell signaling, and detecting tissue degeneration. Therefore, the objective of this study was to investigate gel electrophoresis as a simple method to measure molecular transport in collagenous tissues. The electrophoretic mobility of charged molecules in tissue samples was measured from relative differences in the velocity of a cationic dye passing through an agarose gel in the absence and presence of a tissue section embedded within the gel. Differences in electrophoretic mobility were measured for the transport of a molecule through different tissues and tissue anisotropy, or the transport of different sized molecules through the same tissue. Tissue samples included tendon and fibrocartilage from the proximal (tensile) and distal (compressive) regions of the bovine flexor tendon, respectively, and bovine articular cartilage. The measured electrophoretic mobility was greatest in the compressive region of the tendon (fibrocartilage), followed by the tensile region of tendon, and lowest in articular cartilage, reflecting differences in the composition and organization of the tissues. The anisotropy of tendon was measured by greater electrophoretic mobility parallel compared with perpendicular to the predominate collagen fiber orientation. Electrophoretic mobility also decreased with increased molecular size, as expected. Therefore, the results of this study suggest that gel electrophoresis may be a useful method to measure differences in molecular transport within various tissues, including the effects of tissue type, tissue anisotropy, and molecular size.

A Density Functional Study of the Nonlinear Optical Properties of Edge-Functionalized Nonplanar Nanographenes.

The atomically precise edge chlorination of nanographenes has recently been reported as a crucial technology of functionalization through which the planar structure and optical properties of nanographenes can be significantly changed. To check the effects of molecular size, geometrical symmetry and edge functionalization of nanographenes on their optical properties, a series of nanographenes is studied in the framework of density functional theory with the B3LYP functional. Our results indicate that edge functionalization remarkably changes the nonlinear optical properties and increases the anisotropy of nanographenes compared to the effects of the molecular size and system geometric symmetry. Furthermore, the nonlinear optical properties of nanographenes can be tuned by precise edge functionalization, which opens a new avenue for using nanographenes as nonlinear optical materials.

Attosecond time delay in the valence photoionization of C240 versus C60

SynopsisWe investigate effects of electron correlations on the attosecond time delay of the photoionization from HOMO and HOMO-1 electrons in C240. A comparison with earlier C60 results assesses the molecular size effect.

Effect of molecular diameters on state-to-state transport properties: The shear viscosity coefficient

Shear viscosity coefficient is calculated for both equilibrium and strongly non-equilibrium state-to-state vibrational distributions taking into account increasing diameters of vibrationally excited molecules. Under conditions of local thermal equilibrium, the effect of vibrational excitation on the shear viscosity coefficient is found to be negligible for temperatures below 5000K. For T>10000K, the contribution of excited states becomes important. Under non-equilibrium conditions characteristic for shock heated and supersonic expanding flows vibrational level populations deviate strongly from the Boltzmann distribution. Nevertheless, estimated coupled effect of molecular size and non-Boltzmann distributions on the shear viscosity coefficient is negligible.

Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations?

BackgroundCheminformaticians are equipped with a very rich toolbox when carrying out molecular similarity calculations. A large number of molecular representations exist, and there are several methods (similarity and distance metrics) to quantify the similarity of molecular representations. In this work, eight well-known similarity/distance metrics are compared on a large dataset of molecular fingerprints with sum of ranking differences (SRD) and ANOVA analysis. The effects of molecular size, selection methods and data pretreatment methods on the outcome of the comparison are also assessed.ResultsA supplier database (https://mcule.com/) was used as the source of compounds for the similarity calculations in this study. A large number of datasets, each consisting of one hundred compounds, were compiled, molecular fingerprints were generated and similarity values between a randomly chosen reference compound and the rest were calculated for each dataset. Similarity metrics were compared based on their ranking of the compounds within one experiment (one dataset) using sum of ranking differences (SRD), while the results of the entire set of experiments were summarized on box and whisker plots. Finally, the effects of various factors (data pretreatment, molecule size, selection method) were evaluated with analysis of variance (ANOVA).ConclusionsThis study complements previous efforts to examine and rank various metrics for molecular similarity calculations. Here, however, an entirely general approach was taken to neglect any a priori knowledge on the compounds involved, as well as any bias introduced by examining only one or a few specific scenarios. The Tanimoto index, Dice index, Cosine coefficient and Soergel distance were identified to be the best (and in some sense equivalent) metrics for similarity calculations, i.e. these metrics could produce the rankings closest to the composite (average) ranking of the eight metrics. The similarity metrics derived from Euclidean and Manhattan distances are not recommended on their own, although their variability and diversity from other similarity metrics might be advantageous in certain cases (e.g. for data fusion). Conclusions are also drawn regarding the effects of molecule size, selection method and data pretreatment on the ranking behavior of the studied metrics.Graphical A visual summary of the comparison of similarity metrics with sum of ranking differences (SRD).Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-015-0069-3) contains supplementary material, which is available to authorized users.

Density-functional errors in ionization potential with increasing system size.

This work investigates the effects of molecular size on the accuracy of density-functional ionization potentials for a set of 28 hydrocarbons, including series of alkanes, alkenes, and oligoacenes. As the system size increases, delocalization error introduces a systematic underestimation of the ionization potential, which is rationalized by considering the fractional-charge behavior of the electronic energies. The computation of the ionization potential with many density-functional approximations is not size-extensive due to excessive delocalization of the incipient positive charge. While inclusion of exact exchange reduces the observed errors, system-specific tuning of long-range corrected functionals does not generally improve accuracy. These results emphasize that good performance of a functional for small molecules is not necessarily transferable to larger systems.