How hot? Systematic convergence of the replica exchange method using multiple reservoirs

We have devised a systematic approach to converge a replica exchange molecular dynamics simulation by dividing the full temperature range into a series of higher temperature reservoirs and a finite number of lower temperature subreplicas. A defined highest temperature reservoir of equilibrium conformations is used to help converge a lower but still hot temperature subreplica, which in turn serves as the high‐temperature reservoir for the next set of lower temperature subreplicas. The process is continued until an optimal temperature reservoir is reached to converge the simulation at the target temperature. This gradual convergence of subreplicas allows for better and faster convergence at the temperature of interest and all intermediate temperatures for thermodynamic analysis, as well as optimizing the use of multiple processors. We illustrate the overall effectiveness of our multiple reservoir replica exchange strategy by comparing sampling and computational efficiency with respect to replica exchange, as well as comparing methods when converging the structural ensemble of the disordered Aβ_21‐30 peptide simulated with explicit water by comparing calculated Rotating Overhauser Effect Spectroscopy intensities to experimentally measured values. © 2009 Wiley Periodicals, Inc. J Comput Chem 31: 620–627, 2010     

Kinetics study of norbixin’s first stage thermal decomposition,using dynamic method

Cis-norbixin isomer obtained by hydrolysis of cis-bixin and isolated by solvent extraction from annatto seeds. The thermal decomposition data of the cis-norbixin samples were analyzed by thermogravimetric analysis at different heating rates in the 25–900°C temperature range. DSC curves showed that thermal decomposition reactions for cis-norbixin occurred in the solid phase. The kinetic parameters, such as activation energy and pre-exponential factor were determined using integral and approximate methods: Coats–Redfern, Madhusudanan, Horowitz–Metzger and Van Krevelen. F1 mechanism describes well the first stage of the thermal decomposition.     

Efficient α-chlorination of carbonyl containing compounds under basic conditions using methyl chlorosulfate

An efficient method for the α-chlorination of ketones under basic conditions is described using methyl chlorosulfate. Its applicability for the chlorination of other functional groups has also been studied and it is equally useful for the synthesis of α-chloroesters and amides. Methyl chlorosulfate is described for the first time as a positive chlorine source. Some aldol reactions which occur during the chlorination of some substrates are also reported.     

Synthesis and properties of new triazole methanofullerenes under the “click-chemistry” conditions

The “click-chemistry” methods were used for the first time to synthesize new 1,2,3-triazole derivatives of fullerene, promising for the study of their biological activity, as well as for the preparation of new fullerene-containing materials on their basis. The purity and composition of the compounds synthesized were confirmed by MALDI-TOF mass spectrometry and HPLC, their structures were confirmed by a combination of 2D NMR homo- and heteronuclear correlation.     

Approximate series solution of fourth-order boundary value problems using decomposition method with Green’s function

This paper proposes a new efficient approach for obtaining approximate series solutions to fourth-order two-point boundary value problems. The proposed approach depends on constructing Green’s function and Adomian decomposition method (ADM). Unlike existing methods like ADM or modified ADM, the proposed approach avoids solving a sequence of nonlinear equations for the undetermined coefficients. In fact, the proposed method gives a direct recursive scheme for obtaining approximations of the solution with easily computable components. We also discuss the convergence and error analysis of the proposed scheme. Moreover, several numerical examples are included to demonstrate the accuracy, applicability, and generality of the proposed approach. The numerical results reveal that the proposed method is very effective and simple.     

Photodegradation of EDTA using Fenton’s reagent: a pilot-scale study

The presence of ethylenediaminetetraacetic acid (EDTA) in decontamination wastes can cause complexation of cations resulting in interferences in their removal by various treatment processes, for example chemical precipitation, ion exchange, etc., and can negatively affect the quality of the final form of the waste. Advanced oxidation processes using ozone, H₂O₂, ultrasonics (US), ultraviolet (UV) light, Fenton’s reagent (Fe(II) + H₂O₂), alone or in combination, are regarded as possible methods of clean and ecologically safe remedial treatment for the degradation of organics. In this study, the development of a column photoreactor (15 L) and a shallow-tank photoreactor (100 L) was carried out at the Centralised Waste Management Facility, Kalpakkam, India. Pilot-scale (batch) studies of the photocatalytic degradation of EDTA (20,000 mg/L) using UV + Fenton’s reagent in these reactor geometries were attempted. The effect of the power of the UV radiation on the kinetics of photodegradation of EDTA (20,000 mg/L) was studied using the column photoreactor. The shallow-tank reactor was used to study the photodegradation of EDTA (20,000 mg/L) using UV radiation, visible radiation, and sunlight. The successful use of sunlight as a source of energy and its greater effectiveness than UV radiation in the treatment of EDTA are presented.     

Synthesis of N-formylated β-lactams using nano-sulfated TiO2 as catalyst under solvent-free conditions

An easily accessible catalyst, nano-sulfated titania, efficiently catalyzes the N-formylation of β-lactams and all types of amines (primary, secondary, aromatic, and aliphatic) in solvent-free conditions at room temperature.     

A new tool for the study of polymerization under supercritical conditions – preliminary results

Efficient stirring is needed to realize heat flow analysis with a thermally homogeneous medium. Because dispersion polymerization with supercritical fluids can be destabilized under stirring, a preliminary target has been to find a compromise between synthesis and basic reaction calorimetry requirements. This paper describes the use of poly (dimethylsiloxane) macromonomer with a molecular weight 5000 g/mol as stabilizer for the dispersion polymerization of methyl methacrylate in supercritical carbon dioxide. The effect of stirring speed and stabilizer concentration has been examined. This study has shown that poly (methyl methacrylate) can be produced at high yield and molecular weight using 10 wt% (respect to monomer) poly (dimethylsiloxane) macromonomer at stirring speeds up to 600 rpm. A polymerization enthalpy of −57.6±2 kJ/mol has been calculated being in good agreement with previously reported data. Thus, preliminary results for the heat balance using the newly developed high pressure reaction calorimeter for supercritical fluid applications have shown the important potential of reaction calorimetry to promote supercritical fluid technologies at industrial scale allowing for the determination of kinetics and thermodynamic and safety data, respectively.     

Unusual formation of β-carboline dimers under Bischler-Napieralski reaction conditions: an old reaction with a new direction

l-N-Formyl tryptophan methyl ester (3) underwent a Bischler-Napieralski reaction with POCl₃ at room temperature or under microwave irradiation, resulting in the unusual formation of β-carboline dimers 5 and 6. Most importantly, acetylation using Ac₂O of each of the dimers 5 and 6 separately afforded 1-[3′-carbomethoxy-β-carbolinyl]-3-carbomethoxy-9-acetyl-β-carboline (7) as the only product, the structure of which was confirmed by X-ray crystallography studies.     

Copper-catalyzed trifluoromethylation of terminal alkynes using Umemoto’s reagent

A copper-catalyzed method for trifluoromethylation of terminal alkynes with Umemoto’s reagent has been developed. The reaction is conducted at room temperature and shows good tolerance to a variety of functional groups.     

Determination of Henry’s constant using a photoacoustic sensor

We present a simple method for measuring Henry’s constant k_Hof ethanol using photoacoustic spectroscopy. At T =  298.1 K the measured value fork_H is (0.877  ±  0.039)kPa · kg · mol ^− 1. Our data show that Henry’s law is valid at ethanol molalities between 0.1mol · kg ^− 1 and 1.4 mol · kg ^− 1. The temperature dependence of Henry’s constant was carefully examined by measuring the ethanol vapour pressure of six different aqueous solutions between T =  273.1 K and T =  298.1 K. By analysing the gas phase concentration and applying Henry’s law, an ethanol molality of 0.864 mol · kg ^− 1in the liquid phase can be measured with an error of  ± 0.038mol · kg ^− 1. The detection limit of the photoacoustic sensor is a gaseous ethanol pressure of 10 ^− 3kPa. Ethanol molality changes as low as 1.10 ^− 3mol · kg ^− 1can be measured.     

Determination of the gas-phase acidity of methylthioacetic acid using the Cooks’ kinetic method

We determined the gas-phase acidity of methylthioacetic acid (MTA) in a triple-quadrupole mass spectrometer using the Cooks’ kinetic method with the consideration of entropy effects. The negatively charged proton-bound dimers were generated by electrospray ionization. Collision-induced dissociation was applied to the dimer ions and the product ion ratios were measured at four different collision energies. The gas-phase acidity (ΔH _acid) of MTA was determined to be 340.0±1.7 kcal/mol using the extended kinetic method and 339.8±1.7 kcal/mol using the standard kinetic method. The entropy term is insignificant in this case and can be ignored. The standard kinetic method yielded a free energy of deprotonation of MTA (ΔG _acid) of 333.0±1.7 kcal/mol. The entropy of the acid dissociation, ΔS _acid, was estimated to be 22.8 cal/mol K. Theoretical prediction at the B3LYP/6-31+G* level of theory gives a similar value for ΔH _acid of 338. 9 kcal/mol. In the gas-phase, MTA is a stronger acid than methoxyacetic acid, although in solution, MTA is a weaker one.     

A new method for introduction ω-side chain of prostanoid using Barton radical reaction

A new method for introductionω-/side chain of prostanoid was described in this note.Starting from acid chloride(3),via Barton radical reaction,a transα,β-unsaturated ketone sython was introduced.     

Optimizing the hydrothermal performance of helically corrugated coiled tube heat exchangers using Taguchi’s empirical method: energy and exergy analysis

Journal of Thermal Analysis and Calorimetry - In this work, a three-dimensional study of shell and helically corrugated coiled tube heat exchanger with considering exergy loss is investigated....     

Synthesis of bioactive heterocycles using reusable heterogeneous catalyst HClO4–SiO2 under solvent-free conditions

We are reporting a simple, efficient and green protocol for the synthesis of chromenes and dihydropyrimidines (products of Knoevenagel and Biginelli reaction, respectively) by the use of silica-supported perchloric acid (HClO₄–SiO₂) as an effective heterogeneous catalyst. Short reaction times, high product yields, simple procedure and reusability of the catalyst are the superior characteristics of this protocol.     

Rescoring of docking poses under Occam’s Razor: are there simpler solutions?

Ligand affinity prediction from docking simulations is usually performed by means of highly empirical and diverse protocols. These protocols often involve the re-scoring of poses generated by a force field (FF) based Hamiltonian to provide either estimated binding affinities—or alternatively, some empirical goodness score. Re-scoring is performed by so-called scoring functions—typically, a reweighted sum of FF terms augmented by additional terms (e.g., desolvation/entropic penalty, hydrophobicity, aromatic interactions etc.). Sometimes, the scoring function actually drives ligand positioning, but often it only operates on the best scoring poses ranked top by the initial ligand positioning tool. In either of these rather intricate scenarios, scoring functions are docking-specific models, and most require machine-learning-based calibration. Therefore, docking simulations are less straightforward when compared to “standard” molecular simulations in which the FF Hamiltonian defines the energy, and affinity emerges as an ensemble average property over pools of representative conformers (i.e., the trajectory). Paraphrasing on Occam’s Razor principle, additional model complexity is only acceptable if demonstrated to bring a significant improvement of prediction quality. In this work we therefore examined whether the complexity inherent to scoring functions is indeed justified. For this purpose we compared sampler for multiple protein–ligand entities, a general purpose conformation sampler based on the AMBER/GAFF FF, complemented with continuum solvation terms, with several state of the art docking tools that rely on calibrated scoring functions (Glide, Gold, Autodock-Vina) in terms of its ability to top-rank the actives from large and diverse ligand series associated with various proteins. There is no clear winner of this study, where each program performed well on most of the targets, but also failed with respect to at least one of them. Therefore, a well-parameterized force field with a simple, energy-based ligand ranking protocol appears to be an as effective docking protocol as intricate rescoring strategies based on scoring functions. A tool that can sample the conformational space of the free ligand, the bound ligand and the protein binding site using the same force field may avoid many of the approximations common to contemporary docking protocols and allow e.g., for docking into highly flexible active sites, when current scoring functions are not well suited to estimate receptor strain energies.     

Liquid chromatography–tandem mass spectrometry method for the detection of marine lipophilic toxins under alkaline conditions

A new LC–MS/MS method for the separation and detection of the most prominent marine lipophilic toxin groups comprising okadaic acid, dinophysistoxins, yessotoxins, azaspiracids, pectenotoxins, spirolides and some okadaic acid fatty acid esters has been developed. With this method 28 different marine lipophilic biotoxins can be analysed in a single run. Separation was achieved with an acetonitrile/water gradient containing ammonium hydroxide (pH 11). All toxins were stable under these basic conditions. Compared to chromatography using an acidic gradient, the limit of detection (LODs) for okadaic acid, yessotoxin, gymnodimine and 13-desmethyl spirolide C were improved two- to three-fold, mainly due to better peak shapes. The azaspiracids and pectenotoxins-2 showed comparable LODs under acidic and basic conditions. A major advantage of the developed method is that toxins can be clustered in retention time windows separated for positively and negatively ionized molecular ions. Therefore, there is no need for rapid polarity switching or two separate runs for one sample. The new method showed good repeatability and reproducibility and is an important step in the development of alternatives to the animal tests currently in use for shellfish toxin analysis.     

Synthesis of new chiral keto alcohols by baker’s yeast

Fourteen chiral α- and β-keto alcohols 2a–2r were synthesized by the asymmetric reduction of their corresponding diketones 1a–1r via baker’s yeast. In addition, ten corresponding racemic α-keto alcohols were synthesized by the benzoin condensation of their corresponding aldehydes, which were used for the determination of the ee values through their chiral resolution on chiral HPLC. Amongst the 15 diketones, 1j and chiral α-keto alcohols 2i, 2j and chiral β-keto alcohol 2r are novel compounds. Six keto alcohols 2b, 2c, 2d, 2f, 2h and 2p were synthesized by baker’s yeast for the first time. There are some studies in the literature where baker’s yeast was applied to the diketones 1a, 1g, 1e, 1k and 1n under various conditions different to those reported herein. The yields and the ee values of these studies were not as high as ours. All of the keto alcohols synthesized were characterized by IR, NMR (¹H and ¹³C), and MS. The relationship between the structure of the diketone and the yield, diastereoselectivity and enantiomeric excess is also discussed.     

The prospect of the dalton in the new SI: an educator’s point of view

If the definitions of the kilogram and the mole, based on exact values of the Planck and Avogadro constants, respectively, are accepted within the framework of the new SI, then the current definition of the dalton cannot be retained. Acceptance implies redefinition of the dalton exactly in terms of the kilogram. The redefined, exact dalton is useless in mass spectrometry, and hence, a new quantity for the carbon-12 reference mass would have to be established—against the principle of Ockham’s razor. In order to remove the roots of this awkward concept, the kilogram based on the Planck constant, and the mole, consisting of a particular number of entities equal to the inexactly determined numerical value of gram-to-dalton mass ratio, should be included in the new SI system. Some controversies related to the concept of mole have been also briefly outlined.     

Highly efficient synthesis of β-amino esters via Mannich-type reaction under solvent-free conditions using ZnCl_2 catalyst

β-Amino esters were synthesized via ZnCl_2-catalyzed Mannich-type reaction of imines and malonate esters under solvent-free conditions in 6 min.Theβ-amino ester was converted into the corresponding aspartic acid derivatives.