SciFinder-guided rational design of fluorescent carbon dots for ratiometric monitoring intracellular pH fluctuations under heat shock

Intracellular pH plays a significant role in various biological processes, including cell proliferation, apoptosis, metabolism, enzyme activity and homeostasis. In this work, a novel design strategy for the preparation of pH responsive carbon dots (CDs-pH) for ratiometric intracellular imaging was reported. By using SciFinder database, fluorescent CDs-pH with the required pK_a value of 6.84 were rationally designed, which is vital important for precise sensing of intracellular pH. As a result, the synthesized CDs-pH demonstrated robust ability to test pH fluctuations within the physiological range of 5.4-7.4. The CDs-pH was further utilized for fluorescent ratiometric imaging of pH in living HeLa cells, effectively avoided the influence of autofluorescence from native cellular species. Moreover, real-time monitoring of intracellular pH fluctuation under heat shock was successfully realized. This SciFinder-guided design strategy is simple and flexible, which has a great potential to be used for the development of other types of CDs for various applications.     

Sensing the physicochemical nature of he and ne in micropores by adsorption measurements

He and Ne in contact with molecular sieves in the form of crystalline A zeolites and amorphous carbon molecular sieves fibers (CMSF) were studied by adsorption measurements. Classification of the effective enclosure of zeolitic apertures and of graphitic constrictions, as determined by recent temperature-programmed desorption mass spectrometry (TPD-MS) studies of adsorption of He and Ne onto these materials, was utilized in making a prudent choice of samples and experimental conditions. In view of the former TPD information, the behaviors of adsorption and volumetric measurements reported herein are straightforwardly interpreted. The combined TPD, adsorption isotherms, and dead volume data deepen the understanding of the physicochemical nature of adsorbed gas, where gas adsorption in the vicinity of pore constrictions and/or apertures as well as on the inner surface areas of pores and/or cages could be resolved. Previous conclusions that the huge activation energies measured for Ne/CMSF at high temperatures are unlikely to characterize chemical desorption but reflect those required for overcoming the barrier of effectively constricted apertures were confirmed by the volumetric data presented here. At 77 K, considerable He adsorption was observed in the porous solids and found to be responsible for abnormal deduced values of dead volumes. The occurrence of significant adsorption of He onto A zeolites and CMSF at 77 K warrants the realization that in cases concerning porous materials, volumetrically deduced quantities should not be taken for granted, but should be carefully considered and uniquely interpreted in relation to the specific experimental conditions under which they are taken.     

Reactivity of Singlet Oxygen Toward Proteins: The Effect of Structure in Basic Pancreatic Trypsin Inhibitor and in Ribonuclease A

The reactions of singlet oxygen, ¹O₂, with large peptides have been described previously. It was found that even in these systems, which in their native form are generally not supposed to possess a stable structure in solution, the polypeptide does impede the access of ¹O₂ to the amino acids that react readily with ¹O₂. Here we describe the ¹0₂ reaction with two proteins of well-defined structure. The quenching of ¹O₂ by bovine pancreatic trypsin inhibitor (BPTI) and by ribonuclease A (RNase A) was compared to that of a solution at the same concentration as those of its constituent amino acids that react readily with ¹O₂. The proteins were studied in their native form, when partly denatured by splitting their S-S bonds and when fully denatured. It was found that while in the native form the quenching rate constant was seven times lower in BPTI (2.2 vs 15.2 times 10⁷WM^-1 s^-1) and three times lower in RNase A (11.0 vs 32 times 10⁷M^-l s^-1) than in a mixture of its constituent amino acid residues, it increased upon denaturation reaching in the fully denatured state the value of the corresponding amino acid mixture. More striking is the effect of the protein structure when comparing the fraction of the encounters between ¹O₂ and protein, which cause damage to the protein, as reflected in the decrease of its biological activity. This decrease is assumed to be due to the chemical (oxidative) reactions of ¹O₂ in the protein. In the exceptionally stable BPTI the fraction of such encounters was 0.05 and in RNase A it was 0.2, whereas for the amino acid tryptophan in solution, 0.7 of the collisions with ¹O₂ led to a chemical reaction.     

Vectorization of a classical trajectory code on a floating point systems,Inc. Model 164 attached processor

A triatomic classical trajectory code has been modified by extensive vectorization of the algorithms to achieve much improved performance on an FPS 164 attached processor. Extensive timings on both the FPS 164 and a VAX 11/780 with floating point accelerator are presented as a function of the number of trajectories simultaneously run. The timing tests involve a potential energy surface of the LEPS variety and trajectories with 1000 time steps. The results indicate that vectorization results in timing improvements on both the VAX and the FPS. For larger numbers of trajectories run simultaneously, up to a factor of 25 improvement in speed occurs between VAX and FPS vectorized code.     

New Hexazirconium Clusters Containing Hydrogen Atoms

Reduction of ZrBr₄ with HSnBu₃ yielded a blue solid. When this blue solid was treated with PMe₃, a hexanuelear cluster [Zr₆Br₁₄H₄( PMe₃)₄] (2) was isolated. Reaction of the blue solid with [PPh₄]Br in CH₂Cl₂ resulted in the formation of a paramagnetic and unstable cluster anion, [Zr₆Br₁₈H₅]^2– (3), which disproportionated to form a new cluster anion, [Zr₆Br₁₈H₅]^3– (4) and some Zr(IV) species. Compounds containing 4 can also be obtained from reaction of the blue solid with Br^– in MeCN. Reduction of ZrCl₄ with HsnBu₃ gave a red–brown solid, and [Zr₆Cl₁₄H₄(AsMe₃)₄] (9) and [Zr₅Cl₁₂H₄(AsMe₃)₅](8) were obtained by reaction of the red–brown solid with AsMe₃. No cluster compounds containing amine ligands were obtained in the reaction of the red–brown solid with amines; only compounds containing the [Zr₆Cl₁₈ H₅]^3– anion and ammonium cations were isolated. Altogether ten products were characterized by single crystal X-ray diffraction and where possible, by ¹H NMR studies.     

New membrane materials for potassium-selective ion-sensitive field-effect transistors

Several polymeric materials were studied as membrane materials for potassium-selective ion-sensitive field-effect transistors (ISFETs) to overcome the problems related with the use of conventional plasticized poly(vinyl chloride) membranes casted on ISFET gate surfaces. Several acrylate materials, such as ACE, Epocryl and derivatives, showed no reproducible results. Three room-temperature vulcanizing (RTV)-type silicone rubbers were tested. The addition-type RTV-2 silicone rubber was not suitable as a membrane material, but the condensation-type RTV-1 and especially the RTV-2 silicone rubber showed good results. ISFETs with a Silopren membrane showed a durability of at least 2 months.     

Regioselective cyclomanganation of Schiff bases. An unexpected effect of chloro substituents

In this paper we describe the synthesis of new metallacycles by the cyclomanganation reaction of benzyl-benzylidene-amines by using [MnMe(CO)₅] as metallating agent. These ligands can undergo metallation on different aromatic carbon atoms but no important differences have been found in the regioselectivity of the process, that can be related to the electronic effect of the substituents, and in all the cases studied the endo-cyclomanganated complexes of para-substituted imines have been obtained. The corresponding exo-metallacycles were obtained by reaction of [MnMe(CO)₅] on the imine 2,6-Cl₂C₆H₃CHNCH₂Ph and 2,4,6-Me₃C₆H₂CHNCH₂Ph, derived from 2,6-dichlorobenzaldehyde and 2,4,6-trimethylbenzaldehyde, respectively.The results described suggest that the mechanism of the cyclomanganation is similar to that of cyclopalladation and it can be proposed that cyclomanganation takes place by the formation of a four-centered transition state, involving the C-H and Mn-C_acetyl bonds, in the acetyl coordination complex formed in the first step of the reaction.     

Recent liquid chromatographic-(tandem) mass spectrometric applications in proteomics

Conventional proteomics makes use of two-dimensional gel electrophoresis followed by mass spectrometric analysis of tryptic fragments derived from in-gel digestion of proteins. Although being a very strong technique capable of separating and visualizing hundreds of proteins, 2D-gel electrophoresis has some well-documented disadvantages as well. More recently, liquid chromatographic-(tandem) mass spectrometric techniques have been developed to overcome some of the shortcomings of 2D-gel electrophoresis. In this review we have described several recent applications of liquid chromatography-(tandem) mass spectrometry in the field of proteomics and especially in the field of membrane proteomics, quantitative proteomics and in the analysis of post-translational modifications.     

A new method for the preparation of 2-thio substituted furans by methylsulfanylation of gamma-dithiane carbonyl compounds

Several related methods for the preparation of differentially substituted 2-thiofurans are described. The general procedure involves the formation of a thionium ion from a gamma-dithianyl substituted carbonyl compound followed by cyclization of this reactive intermediate onto the tethered carbonyl group. Two methods for thionium ion generation were explored. One of these involved an acid-catalyzed reaction of beta-ketenedithioacetals, prepared from the condensation of 2,2-bis(methylsulfanyl)acetaldehyde with a variety of ketones. Cyclization followed by loss of methane thiol gave 2-thiofurans 17, 18 and 23, 24 in 70-90% yield. Attempts to prepare 5-heteroatom substituted 2-thiofurans from the corresponding beta-ketenedithioacetal amides or esters were unsuccessful, leading to 1,2-thio rearranged products. A more successful route involved the reaction of beta-acetoxy-gamma-thianyl carbonyl compounds with dimethyl(methylthio)sulfonium tetrafluoroborate (DMTSF). Treatment of the dithiane with this reagent resulted in the smooth generation of a thionium ion. Cyclization followed by loss of acetic acid afforded thiofurans 17, 18, 23, 47-49, 51, and 61-64 in 40-100% yield. The N-butenyl substituted thioamido furan furnished a rearranged hexahydropyrroloquinolin-2-one in high yield when heated at 110 degrees C.     

Theoretical Definition of a Functional Group and the Molecular Orbital Paradigm

It is the purpose of this review to demonstrate that the empirical classification of the observations of chemistry in terms of the properties assigned to functional groups is a consequence of and is predicted by physics. This is accomplished by showing that the atoms and functional groups of chemistry can be identified with bounded space-filling objects whose properties are defined by quantum mechanics. The quantum mechanical definition of a group is combined with a new pictorial representation of its form to obtain a unified picture which should make it eminently recognizable to chemists. This picture, when combined with the demonstrated ability of these groups to recover the measured properties of atoms in molecules, is offered as one which meets the expectations a chemist associates with the concept of a functional group. The manner in which this physical definition of a group differs fundamentally from models of functional groups based upon molecular orbital theory is discussed.