Monitoring of yeast fermentation by ion mobility spectrometry measurement and data visualisation with Self-Organizing Maps

Ion mobility spectrometry (IMS) measurement combined with unsupervised neurocomputing is considered as a new potential method for on-line monitoring of fermentation and other processes producing volatile compounds that involve micro-organisms. This was demonstrated in a model system in which a strain of brewer’s yeast (Saccharomyces cerevisiae) was cultivated in a bench-top fermenter. Five phases of yeast growth could be detected from measurements of the exhaust gases from the fermenter, as indicated by the changes in ion mobility spectra analysed by computational methods.The data were first processed using the Self-Organizing Map (SOM) algorithm, the results showing that the phases of fermentation can be detected and identified. The cultivations were also shown by Sammon’s mapping to be comparable to a certain level of accuracy. Contaminated cultivation could be detected by its distinctive ion mobility spectrometry profile.     

Multi-turn time-of-flight mass spectrometers with electrostatic sectors

The mass resolution of a time-of-flight (TOF) mass spectrometer is directly proportional to its total flight pathlength. Multi-turn or multi-passage ion optical geometries are necessary to obtain fight distances of sufficient length within reasonable size limitations. We have investigated ion optics for a multi-turn TOF mass spectrometer with electrostatic sectors. The concept of 'perfect' focusing conditions is introduced. Furthermore, a new type of multi-turn TOF mass spectrometer, the MULTUM Linear plus, was developed. It consists of four cylindrical electric sectors and 28 electric quadrupole lenses. It has a vacuum chamber 60 x 70 x 20 cm in size. Mass resolution is demonstrated to increase according to the number of ion cycles. A mass resolution of 350 000 (m/z = 28, FWHM) was achieved after 501.5 cycles. The MULTUM Linear plus analyzer is not simple, however; 28 electric quadrupole lenses are used. In order to reduce the number of ion optical parts, an improved multi-turn TOF mass spectrometer, the MULTUM II, consisting of only four toroidal electric sectors, was also developed. The possibility of tandem mass spectrometric applications using multi-turn TOF mass spectrometers is also discussed.     

A coincidence transmission electron microscope with digital waveform measuring system for analytical microscopy

We have been developing a new analytical transmission electron microscope (TEM), called a coincidence TEM, which in principle enables elemental mapping images to be observed at a high signal‐to‐noise (S/N) ratio under very low dose radiation conditions. In this paper, we report the development of a coincidence TEM with a digital waveform measuring system for obtaining a coincidence elemental mapping image. In this system, analog signals detected by a Si(Li) detector and a multianode, position‐sensitive photomultiplier (PSPM) are continuously converted into 12‐bit digital waveform data at a rate of 100 MHz, and transferred to a PC. From the transferred digital waveform data, information on X‐ray photon energy, electron incident position, and detection times of both X rays and electrons are calculated by digital waveform measurement, which lead to the observation of a successful coincidence elemental mapping image. Copyright © 2005 John Wiley & Sons, Ltd.     

X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists

We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X-ray crystallography to reveal the binding mode of an antagonist series to the A_2A adenosine receptor (AR). Eight A_2AAR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A_2AAR were experimentally determined and investigated through a cycle of ligand-FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X-ray crystallography of the A_2AAR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A_2AAR, an emerging target in immuno-oncology.     

Synthesis and characterization of dimeric μ-oxidovanadium complexes as the functional model of vanadium bromoperoxidase

Two vanadium (IV) complexes [V^IVO(Haeae-sal)(MeOH)]⁺ ( 1 ) and [V^IVO(Haeae-hyap)(MeOH)]⁺ ( 2 ) were prepared by reacting [VO(acac)₂] with ligands [H₂aeae-sal] ( I ) and [H₂aeae-hyap] ( II ) respectively. Condensation of 2-(2-aminoethylamino)ethanol with salicylaldehyde and 2-hydroxyacetophenone produces the ligands ( I ) and ( II ) respectively. Both vanadium complexes 1 and 2 are sensitive towards aerial oxygen in solution and rapidly convert into vanadium(V) dioxido species. Vanadium(V) dioxido species crystalizes as the dimeric form in the solid-state. Single-crystal XRD analysis suggests octahedral geometry around each vanadium center in the solid-state. To access the benefits of heterogeneous catalysis, vanadium(V) dioxido complexes were anchored into the polymeric chain of chloromethylated polystyrene. All the synthesized neat and supported vanadium complexes have been studied by a number of techniques to confirm their structural and functional properties. Bromoperoxidase activity of the synthesized vanadium(V) dioxido complexes 3 and 4 was examined by carrying out oxidative bromination of salicylaldehyde and oxidation of thioanisole. In the presence of hydrogen peroxide, 3 shows 94.4% conversion ( TOF value of 2.739 × 10² h⁻¹) and 4 exhibits 79.0% conversion (TOF value of 2.403 × 10² h⁻¹) for the oxidative bromination of salicylaldehyde where 5-bromosalicylaldehyde appears as the major product. Catalysts 3 and 4 also efficiently catalyze the oxidation of thioanisole in the presence of hydrogen peroxide where sulfoxide is observed as the major product. Covalent attachment of neat catalysts 3 and 4 into the polymer chain enhances substrate conversion (%) and their catalytic efficiency increases many folds, both in the oxidative bromination and oxidation of thioether. Polymer supported catalysts 5 displayed 98.8% conversion with a TOF value of 1.127 × 10⁴ h⁻¹ whereas catalyst 6 showed 95.7% conversion with a TOF value of 4.675 × 10³ h⁻¹ for the oxidative bromination of salicylaldehyde. These TOF values are the highest among the supported vanadium catalysts available in the literature for the oxidative bromination of salicylaldehyde.     

Qualitative spectroscopic characterization of the matrix–silane coupling agent interface across metal fibre reinforced ion exchange resin composite membranes

The characterization of novel metal reinforced electro-dialysis ion exchange membranes, for water desalination, by attenuated total reflectance Fourier transform infrared spectroscopy mapping is presented in this paper. The surface of the porous stainless steel fibre meshes was treated in order to enhance the amount of surface oxide groups and increase the material hydrophilicity. Then, the metal membranes were functionalized through a sol–gel reaction with silane coupling agents to enhance the affinity with the ion exchange resins and avoid premature metal oxidation due to redox reactions at the metal–polymer interface. Polished cross sections of the composite membranes embedded into an epoxy resin revealed interfaces between metallic frameworks and the silane layer at the interface with the ion exchange material. The morphology of the metal–polymer interface was investigated with scanning electron microscopy and Fourier transform infrared micro-spectroscopy. Fourier transform infrared mapping of the interfaces was performed using the attenuated total reflectance mode on the polished cross-sections at the Australian Synchrotron. The nature of the interface between the metal framework and the ion exchange resin was shown to be homogeneous and the coating thickness was found to be around 1 μm determined by Fourier transform infrared micro-spectroscopy mapping. The impact of the coating on the properties of the membranes and their potential for water desalination by electro-dialysis are also discussed.     

Site mapping and small molecule blind docking reveal a possible target site on the SARS-CoV-2 main protease dimer interface

The SARS-CoV-2 virus is causing COVID-19 resulting in an ongoing pandemic with serious health, social, and economic implications. Much research is focused in repurposing or identifying new small molecules which may interact with viral or host-cell molecular targets. An important SARS-CoV-2 target is the main protease (M^pro), and the peptidomimetic α-ketoamides represent prototypical experimental inhibitors. The protease is characterised by the dimerization of two monomers each which contains the catalytic dyad defined by Cys¹⁴⁵ and His⁴¹ residues (active site). Dimerization yields the functional homodimer. Here, our aim was to investigate small molecules, including lopinavir and ritonavir, α-ketoamide 13b, and ebselen, for their ability to interact with the M^pro. The sirtuin 1 agonist SRT1720 was also used in our analyses. Blind docking to each monomer individually indicated preferential binding of the ligands in the active site. Site-mapping of the dimeric protease indicated a highly reactive pocket in the dimerization region at the domain III apex. Blind docking consistently indicated a strong preference of ligand binding in domain III, away from the active site. Molecular dynamics simulations indicated that ligands docked both to the active site and in the dimerization region at the apex, formed relatively stable interactions. Overall, our findings do not obviate the superior potency with respect to inhibition of protease activity of covalently-linked inhibitors such as α-ketoamide 13b in the M^pro active site. Nevertheless, along with those from others, our findings highlight the importance of further characterisation of the M^pro active site and any potential allosteric sites.     

Preparation and formation mechanism of CdS nano-films via chemical bath deposition

CdS semiconductor nano-films were grown on ITO glass substrates by means of chemical bath deposition (CBD), with Cd(NO₃)₂ as Cd ion and (NH₂)₂CS as S ion sources. The concentration of Cd ions, deposition temperature, deposition time and post-treatment temperature have an impact on the formation of CdS nano-films. UV-vis absorption spectrum and atomic force microscope (AFM) images indicated that the change of concentration and post-treatment temperature may adjust the band-gap of CdS to obtain stable, homogeneous and compact films. Formation mechanism of the crystal nucleus and CdS film was also discussed. Active sites on the surface of ITO are critical to the formation of the crystal nucleus and a uniform and compact CdS nano-film. The active site and crystal nucleus are formed due to the comprehensive effect of electricity, thermodynamics and chemistry. __________ Translated from Journal of Jilin University (Science Edition), 2007, 45(1): 116–120 [译自: 吉林大学学报(自然科学版)]     

思维导图促进分析化学课堂思政教学的探索——以“酸碱滴定法基本原理”为例

在分析化学课程的教学中,通过充分发掘其中的思政元素,将其与教学内容进行有机结合,达到育人的目的。通过引入思维导图教学法,搭建思政元素与教学内容的桥梁,学生可以快速把握所学知识。通过学生的表现,分析教学效果,存在的问题等,为课堂思政与本科化学教学有机结合提供一定的借鉴。     

RATE OF INTRA-MOLECULAR CONTACT FORMATION IN SHORT TWO-DIMENSIONAL COMPACT POLYMERS CHAINS

It is important to know the rate of intra-molecular contact formation in proteins in order to understand how proteins fold clearly. Here we investigate the rate of intra-molecular contact formation in short two-dimensional compact polymer chains by calculating the probability distribution p(r) of end-to-end distance r using the enumeration calculation method and HP model on two-dimensional square lattice. The probability distribution of end-to-end distance p(r) of short two-dimensional compact polymers chains may consist of two parts, i.e. p(r) = p1(r) p2(r), where p1(r) and p2(r) are different for small r. The rate of contact formation decreases monotonically with the number of bonds N, and the rate approximately conforms to the scaling relation of k(N) ∝ N-α. Here the value of α increases with the contact radius a and it also depends on the percentage of H (hydrophobic) residues in the sequences of compact chains and the energy parameters of εHH, εHP and εPP . Some comparisons of theoretical predictions with experimental results are also made. This investigation may help us to understand the protein folding.