Modeling of solvent flow effects in enzyme catalysis under physiological conditions

A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with absorbing boundaries are combined with densities obtained from explicit simulation to obtain the overall probability density for the total reaction cycle time of the enzymatic system. The method is used to investigate the catalytic transfer of a phosphoryl group in a phosphoglycerate kinase-ADP-bis phosphoglycerate system, one of the steps of glycolysis. The direct simulation of the enzyme-substrate binding and reaction is carried out using an elastic network model for the protein, and the solvent motions are described by multiparticle collision dynamics which incorporates hydrodynamic flow effects. Systems where solvent-enzyme coupling occurs through explicit intermolecular interactions, as well as systems where this coupling is taken into account by including the protein and substrate in the multiparticle collision step, are investigated and compared with simulations where hydrodynamic coupling is absent. It is demonstrated that the flow of solvent particles around the enzyme facilitates the large-scale hinge motion of the enzyme with bound substrates, and has a significant impact on the shape of the probability densities and average time scales of substrate binding for substrates near the enzyme, the closure of the enzyme after binding, and the overall time of completion of the cycle.     

Biginelli reaction under microwave irradiation conditions without a solvent

Russian Journal of General Chemistry -     

Air sampling of organophosphate triesters using SPME under non-equilibrium conditions

Solid phase micro-extraction (SPME) was used to collect air samples of semi-volatile organophosphate triesters, a group of compounds that are commonly used as flame retardants/plasticisers and have therefore become ubiquitous indoor air pollutants. SPME is a simple sampling technique with several major advantages, including time-efficiency and low solvent consumption. Analyte losses also tend to be relatively low. In quantitative SPME, measurements are normally taken after the analyte has reached partitioning equilibrium between the fibre and the sample matrix. However, equilibrium sampling of semi-volatile compounds in air with SPME often takes several hours. Clearly, time-weighted average (TWA) sampling using SPME under non-equilibrium conditions could be considerably faster. So, in this study, the possibility of sampling organophosphate triesters under non-equilibrium conditions was tested. The most important variables proved to be the fibre coating and the air velocity during sampling. The highest uptake rate was obtained with polydimethylsiloxane (PDMS, 100 m). The rate for this fibre was 150-fold higher than obtained with PDMS/DVB and Carbowax/DVB, both 65 m. Contrary to theoretical expectations, the uptake rate appeared to be constant for all tested air velocities over the fibre surface >7 cm/s. These findings suggest that the uptake rate for non-equilibrium SPME sampling is independent of the sampling flow above this flow rate, which would considerably enhance the robustness and flexibility of the method. Applying this method for TWA sampling, with sampling periods of 1 h, detection limits lower than 2 ng/m³ for individual organophosphate esters were obtained.     

Synthesis of aurones under neutral conditions using a deep eutectic solvent

Aurones are an interesting, but little studied member of the flavanoid family of natural products. Of the various methods available for their synthesis, the simplest involves the condensation of a coumaranone with an aldehyde. This reaction can be performed under acidic or basic conditions. We have recently discovered an effectively neutral set of conditions that employ the deep eutectic solvent comprised of choline chloride and urea as both solvent and catalyst. Modest to good yields can be achieved for a range of aldehydes, thereby facilitating further study of aurones from both a biological as well as a spectroscopic perspective.     

Simulation and theory of flexible equilibrium polymers under poor solvent conditions

Grand canonical Monte Carlo simulation and simple statistical thermodynamic theory are used to model the aggregation and phase separation of systems of reversibly polymerizing monomers, capable of forming chains with or without the ability to cyclize into rings, with isotropic square-well attractions between nonbonded pairs of monomers. The general trend observed in simulation of chain-only systems, as predicted in a number of published theoretical works, is that the critical temperature for phase separation increases and the critical monomer density decreases with rising polymer bond strength. Introduction of the equilibrium between chains and rings into the theory lowers the predicted critical temperature and increases the predicted critical density. While the chain-only theories predict a vanishing critical density in the limit of complete polymerization, when ring formation is taken into account the predicted critical density in the same limit approaches the density of the onset of the ring-chain transition. The theoretically predicted effect of cyclization on chemical potential is in good qualitative agreement with a subset of simulation results in which chain-only systems were compared with equilibrium mixtures of rings and chains. The influence of attractions on the aggregation number and radius of gyration of chains and rings observed in simulations is also discussed.     

Organocatalysed three-component domino synthesis of 1,4-dihydropyridines under solvent free conditions

An organocatalysed protocol for one-pot synthesis of 1,4-dihydropyridines via three-component coupling of cinnamaldehyde, aniline and β-keto esters under solvent free conditions at ambient temperature is reported. The reaction is generally very fast and the products are obtained in high yield. The catalytic activity of small organic molecules like amino acids (acidic, basic and neutral), ephedrine and cinchona alkaloids was studied.     

Palladium-catalyzed addition of disulfides and diselenides to alkynes under solvent free conditions

An efficient methodology was developed for performing palladium-catalyzed E-E (E = S, Se) bond addition to alkynes under solvent free conditions. Compared to reaction in solvent significant enhancement of reaction rate, improved efficiency and remarkable catalyst stability were observed under solvent free conditions. The addition reactions were carried out with high stereoselectivity and yields in a short reaction time.     

Ion products of water in 1m NaCl under hydrothermal conditions

The apparent ion product of water Q _w has been determined potentiometrically at pressure up to 96.7 MPa and temperatures up to 246°C in solutions of ionic strength 1.019m (NaCl). A concentration cell employing hydrogen electrodes was used. It was found that-logQ _w varies from 13.64 at 4.1 MPa and 20°C to 9.98 at 96.7 MPa and 230°C.     

Grafted polymer layers under variable solvent conditions: A Monte Carlo simulation

Polymer chains anchored with one end at a hard wall under variable solvent conditions are investigated by Monte Carlo simulations using the bond- fluctuation model. Detail information on the structural properties are obtained above, at, and below the Θ-point and discussed in terms of the appropriate theories. In particular, the scaling of the brush thickness is formulated and verified by the simulation data. For the dynamics at the Θ-point, both the relaxation time of the chain configuration and the mean-square time displacement are studied. At temperatures distinctly below the Θ-point, we find that the layer develops considerable lateral inhomogeneity in its density, which has not been predicted by previous theories.     

Synthesis of 4-aryl substituted 3,4-dihydropyrimidinones using silica-chloride under solvent free conditions

This paper describes an improved procedure for the efficient and facile synthesis of 4-aryl substituted 3, 4-dihydropyrimidinones under mild reaction conditions with excellent yields using inexpensive silica chloride under solvent free conditions.     

Synthesis and cytotoxic activity of some novel benzocoumarin derivatives under solvent free conditions

In the present study, a rapid, less expensive, clean and environmental friendly route to synthesis new pyrazoles, pyrazolopyridazines and condensed pyrimidines was developed via grinding of 2-(3-(dimethylamino)acryloyl)-3H-benzo[f]chromen-3-one (1) with different reagents. All the new compounds were characterized and established using elemental analysis and spectral data. Eight compounds were selected for in vitro antiproliferative against different human cancer cell lines entitled melanoma, cancers of the lung, leukemia, breast, brain, colon, prostate, ovary and kidney by the USA NCI.     

Molecular dynamics simulation of brushes formed by star polyelectrolytes under theta solvent conditions

Using molecular dynamics simulations, we have studied polyelectrolyte brushes formed by partially or fully charged star polymers tethered on a planar surface under theta solvent conditions. The diagram of states for salt‐free solutions differs in the location of osmotic regime (OB) compared with the respective diagram reported by Borisov and Zhulina. In contrast, simulation results dictate that the OB regime appears for values of the ratio F /α ^?1/2 l_B ^?1 much larger than unity, which is the threshold of counterion localization, with F denoting the branch functionality, α the charged units fraction and l_B the Bjerrum length. The simulation results support that the brush height scaling laws H ～ α ² l_B F ^1.049S ³s ^?1 and H ～ α^0.302 F ^0.23S for the charged Pincus Brush (PB) and osmotic (OB) regimes, respectively, where S is the spacer length and s is the grafted area per star chain. The respective theoretical scaling laws are H ～ α ² l_B F ^1.88S ³s ^?1 and H ～ α ^1/2 F ^0.44S . © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55 , 1110–1117     

An efficient synthesis of pyrazole chalcones under solvent free conditions at room temperature

An easy,safe,solvent free and effective method for the synthesis of pyrazole-substituted chalcones has been achieved by grinding pyrazole aldehydes and acetophenones in the presence of activated barium hydroxide(C-200) in high yield within short span of time.All reactions were carried out just by grinding the two reactants in the presence of activated barium hydroxide(C-200). Results are also compared with sodium hydroxide and potassium hydroxide.     

Ion pairs in aqueous electrolyte microdrops under conditions of a flat nanopore

The molecular mechanisms of aqueous solvent penetration into a flat nanopore with hydrophobic structureless walls containing a Na⁺Cl^? ion pair with nonfixed distance between ions is studied by computer simulations. A detailed many-body polycenter model of intermolecular interactions calibrated with respect to experimental data for the free energy of attachment of water vapor molecules and quantum-chemical calculations in clusters is used. The ion pair hydration results in its decomposition. Drawing the molecules into the gap between ions makes easier penetration of solvent and filling of the nanopore with electrolyte. The ion-pair dissociation is accompanied by dramatic changes in the chemical potential of molecules and electric properties of the whole system. The thermodynamic characteristics of decomposition are stable as regards variations in the pore width. The post-decomposition electric polarizability demonstrates strong anisotropy associated with the nanopore flatness.     

Ion pairing of quaternary salts in solvent mixtures

Conductances at 25.00°C are reported for the following systems: tetrabutylammonium bromide in dimethyl sulfoxide-acetone mixtures (Bu₄NBr in Me₂SO–Me₂CO); tetraphenylphosphonium bromide (Ph₄PBr) in water Me₂SO, Me₂CO, and in the mixtures H₂O–Me₂SO, Me₂SO–Me₂CO and Me₂CO–H₂O; Ph₄PCl in Me₂SO, Me₂CO, H₂O–Me₂SO, and Me₂SO–Me₂CO; and tetrapropylammonium bromide (Pr₄NBr) in Me₂SO and Me₂CO. The data were analyzed using the Fuoss 1978 equation which is based on the coupled equilibria: (unpaired ions)(solvent-separated pairs)(contact pairs). The conductimetric pairing constantK _A =K _R(l+K _s) is the product of two factors:K _R, which describes the first (diffusion controlled) equilibrium andK _s=exp(–E _s/kT), which describes the second (system-specific) equilibrium. Ions with overlapping cospheres (of diameterR) are defined as paired: their center-to-center distancer lies in the rangearR; contact pairs (r=a) are ions which have one ion of opposite charge as a nearest neighbor, all other nearest and next nearest neighbors being solvent molecules. The quantityE _s is the difference in free energy between the states defined byr=R andr=a. For the Me₂SO–Me₂CO systems,E _s is positive for solutions in Me₂SO and decreases through zero to negative values as the fraction of the less polarizable acetone increases. For solutions in waterE _s is also positive. On addition of Me₂SO or Me₂CO,E _s initially increases, goes through a maximum, and then decreases to negative values as the fraction of the less polarizable component increases. The decrease is an electrostatic effect, common to all the systems. The initial increase inE _s appears when the small water molecules surrounding solvent-separated pairs are replaced by organic molecules which have greater volumes than water.     

Low solvent consumption gel permeation chromatography method

This study presents the possibility of reducing the volume of solvent necessary for gel permeation chromatography analysis by up to 20 times when using two 2.1-mm internal diameter (ID) columns instead of the traditional three 7.5-mm ID columns. The low solvent consumption method was optimized by evaluating the number of theoretical plates at different flow rates. By injecting a broad polystyrene standard 16 times, good reproducibility and accuracy of weight average molecular weights (M_w) and peak surface areas were obtained for the optimized method.     

Iridium catalysed alkylation of tert-butyl cyanoacetate with alcohols under solvent free conditions

Ir-catalysed alkylation of tert-butyl cyanoacetate with a range of substituted benzyl and heteroaryl alcohols under solvent free conditions afforded the corresponding monoalkylated products in moderate to high yields.     

Microwave-assisted synthesis of α-aminophosphinic acids from hypophosphorus acid salts under solvent free conditions

A simple, efficient, and general method has been developed for the synthesis of α-aminophosphinic acids from hypophosphorus salts under solvent-free conditions using microwave irradiation. α-Aminophosphinic acids were obtained in high yield under mild conditions by reaction of the amine salts of hypophosphorus acid with aldehydes in the presence of microwave irradiation.     

Impact of solvent conditions on separation and detection of basic drugs by micro liquid chromatography-mass spectrometry under overloading conditions

In this study the impact of solvent conditions on the performance of μLC/MS for the analysis of basic drugs was investigated. Our aim was to find experimental conditions that enable high-performance chromatographic separation particularly at overloading conditions paired with a minimal loss of mass spectrometric detection sensitivity. A focus was put on the evaluation of the usability of different kinds of acidic modifiers (acetic acid (HOAc), formic acid (FA), methansulfonic acid (CH₃SO₃H), trifluoroacetic acid (TFA), pentafluoropropionic acid (PFPA), and heptafluorobutyric acid (HFBA)). The test mixture consisted of eleven compounds (bunitrolol, caffeine, cocaine, codeine, diazepam, doxepin, haloperidol, 3,4-methylendioxyamphetamine, morphine, nicotine, and zolpidem). Best chromatographic performance was obtained with the perfluorinated acids. Particularly, 0.010–0.050% HFBA (v/v) was found to represent a good compromise in terms of chromatographic performance and mass spectrometric detection sensitivity. Compared to HOAc, on average a 50% reduction of the peak widths was observed. The use of HFBA was particularly advantageous for polar compounds such as nicotine; only with such a hydrophobic ion-pairing reagent chromatographic retention of nicotine was observed. Best mass spectrometric performance was obtained with HOAc and FA. Loss of detection sensitivity induced by HFBA, however, was moderate and ranged from 0 to 40%, which clearly demonstrates that improved chromatographic performance is able to compensate to a large extent the negative effect of reduced ionization efficiency on detection sensitivity. Applications of μLC/MS for the qualitative and quantitative analysis of clinical and forensic toxicological samples are presented.     

Effects of solvent on TEOS hydrolysis kinetics and silica particle size under basic conditions

In-situ liquid-state ²⁹Si nuclear magnetic resonance was used to investigate the temporal concentration changes during ammonia-catalyzed initial hydrolysis of tetraethyl orthosilicate in different solvents (methanol, ethanol, n-propanol, iso-propanol and n-butanol). Dynamic light scattering was employed to monitor simultaneous changes in the average diameter of silica particles and atomic force microscopy was used to image the particles within this time frame. Solvent effects on initial hydrolysis kinetics, size and polydispersity of silica particles were discussed in terms of polarity and hydrogen-bonding characteristics of the solvents. Initial hydrolysis rate and average particle size increased with molecular weight of the primary alcohols. In comparison, lower hydrolysis rate and larger particle size were obtained in the secondary alcohol. Exceptionally, reactions in methanol exhibited the highest hydrolysis rate and the smallest particle size. Ultimately, our investigation elaborated, and hence confirmed, the influences of chemical structure and nature of the solvent on the formation and growth of the silica particles under applied conditions.