Mutual influence of tetrel and halogen bonds between XCN (X=Cl,Br) and 4-TF3-pyridine (T=C,Si, Ge)

Journal of Molecular Modeling - In this work, we explore the possibility of using computationally inexpensive electronic structure methods, such as semiempirical and DFTB calculations, for the...     

Electronic recording of plant penetration by the cereal aphids Rhopalosiphum padi and Metopolophium dirhodum on resistant and susceptible wheat seedlings

Plant penetration by the aphids Rhopalosiphum padi and Metopolophium dirhodum was monitored using an electronic recording method. Recordings over 3 h showed that phloem ingestion was reduced on resistant wheat, when compared with a more susceptible species, but this trend was reversed when results from longer (12 h) experiments were used. Plant penetration by M. dirhodum was reduced by attachment to the electronic system, but the behaviour of R. padi was relatively unaffected. The results are discussed in relation to prospects for using electronic methods as a screening procedure.     

Investigation of the UV-Vis absorption of bis(N-methylthiosemicarbazonato) zinc Zn[ATSM]

The electronic structure and absorption spectra of Zn[ATSM] 2 has been modelled using ZINDO and TD-DFT methods. The calculations reproduce both the physical and electronic structure of the complex, and provided good agreement with the X-ray crystal structure and UV-Vis absorption spectrum. The calculated electronic structure was used to generate a qualitative picture of the changes in electron distribution that occur during the absorption of light. The calculated shifts in electron density after absorption of a photon suggest a new synthetic direction for this project.     

Exciton interactions in synthetic porphyrin dimers

The Soret absorption spectra of six synthetic rigid porphyrin dimers whose crystal structures have been determined are simulated using simple exciton theory. The objective is to test the validity of the point dipole and associated approximations; the electronic interaction parameters are thus calculated using data obtained from the monomer spectra, with no adjustable parameters. Satisfactory agreement between theory and experiment is obtained for one class of dimers but not for a second. This poses a challenge for semiempirical electronic structure methods as to whether improvements over the point dipole calculations can be obtained.     

电子鼻技术在快速检测小麦矮腥黑穗病菌中的应用

由小麦矮腥黑穗病菌(TCK)引起的小麦矮腥黑穗病是我国重要的检疫性病害,为明确电子鼻技术在快速检测小麦矮腥黑穗病菌方面的可行性,利用电子鼻对含有TCK和小麦光腥黑穗病菌(TFL)不同冬孢子数(50g小麦种子中冬孢子数分别为0、100、101、102、103、104、105)的小麦进行了检测,采用主成分分析法(PCA)和线性判别法(LDA)进行数据分析。结果发现,这2种分析方法均可将不含TCK冬孢子的小麦和含TCK冬孢子的小麦区分开来,而且通过LDA分析,可将TCK冬孢子含量为100、101、102及103以上的处理区分开来。另外,通过PCA分析,可将TCK与TFL区分开来。此结果为电子鼻技术在快速检测小麦矮腥黑穗病菌中的应用奠定了基础。     

“电子”cDNA文库筛选指导基因的全长cDNA克隆

“电子”ｃＤＮＡ库筛选主要是指通过采用生物信息学的方法延伸表达序列标签（ＥＳＴ）序列,以获得基因的部分及至全长ｃＤＮＡ序列,避免或部分避免构建与筛选ｃＤＮＡ库等烦琐的实验室工作。该方法具体体现了ＥＳＴ数据库的迅速扩张已导致识别与克隆新基因的策略发生革命性的变化。ＥＳＴ序列ＺＡ７３为本实验室克隆到的可能参与辐射致气管上皮细胞恶性转化过程的基因片段,本研究采用“电子”ｃＤＮＡ库筛选的方法对其可能     

Magnetophoresis and ferromagnetic resonance of magnetically labeled cells

We develop in this paper two methods, based on different physical concepts, to quantify the uptake of magnetic nanoparticles in biological cells. The first one, magnetophoresis, is based on the measurement of the velocity of magnetically labeled cells submitted to a magnetic field gradient. The second one quantitates the particles' electronic spin using an electron paramagnetic resonance experiment. We show a quantitative agreement between both methods for macrophagic cells. The uptake kinetics and uptake capacity are discussed for macrophagic cells and other cell lines.     

On the electronic structure of the primary electron donor in bacterial photosynthesis – the bacteriochlorophyll dimer as viewed by EPR/ENDOR methods

The primary electron donor (D) plays a prominent role in electron transfer reactions in the primary processes of photosynthesis. In purple photosynthetic bacteria D is a dimer of bacteriochlorophyll molecules. Investigations on its electronic structure using EPR and ENDOR (electron nuclear double resonance) methods are summarized, focussing on results obtained in the last six years. These encompass studies on the cation radical (D+·) of mutants in which the immediate environment of D is modified through mutagenesis, particularly hydrogen bond and heterodimer mutants. Models using these results to describe the electronic interaction of the dimer halves are discussed. Also, High-Field (95 GHz) EPR to obtain the G-tensor of D+· is addressed. Furthermore, ENDOR on the photoexcited triplet state of D (DT), which in some aspects could serve as a model for the excited singlet state, are discussed. Different approaches towards correlating the electronic structure with function, in particular with the rates of electron transfer reactions, are described.     

Electronic microarray analysis of 16S rDNA amplicons for bacterial detection

Electronic microarray technology is a potential alternative in bacterial detection and identification. However, conditions for bacterial detection by electronic microarray need optimization. Using the NanoChip electronic microarray, we investigated eight marine bacterial species. Based on the 16S rDNA sequences of these species, we constructed primers, reporter probes, and species-specific capture probes. We carried out two separate analyses for longer (533 bp) and shorter (350 and 200 bp) amplified products (amplicons). To detect simultaneously the hybridization signals for the 350- and 200-bp amplicons, we designed a common reporter probe from an overlapping sequence within both fragments. We developed methods to optimize detection of hybridization signals for processing the DNA chips. A matrix analysis was performed for different bacterial species and complementary capture probes on electronic microarrays. Results showed that, when using the longer amplicon, not all bacterial targets hybridized with the complementary capture probes, which was characterized by the presence of false-positive signals. However, with the shorter amplicons, all bacterial species were correctly and completely detected using the constructed complementary capture probes.     

The use of gas-sensor arrays to diagnose urinary tract infections

Sensorial analysis based on the utilisation of human senses, is one of the most important and straightforward investigation methods in food and chemical analysis. An electronic nose has been used to detect in vivo Urinary Tract Infections from 45 suspected cases that were sent for analysis in a UK Health Laboratory environment. These samples were analysed by incubation in a volatile generation test tube system for 4-5 h. The volatile production patterns were then analysed using an electronic nose system with 14 conducting polymer sensors. An intelligent model consisting of an odour generation mechanism, rapid volatile delivery and recovery system, and a classifier system based on learning techniques has been considered. The implementation of an Extended Normalised Radial Basis Function network with advanced features for determining its size and parameters and the concept of fusion of multiple classifiers dedicated to specific feature parameters has been also adopted in this study. The proposed scheme achieved a very high classification rate of the testing dataset, demonstrating in this way the efficiency of the proposed scheme compared with other approaches. This study has shown the potential for early detection of microbial contaminants in urine samples using electronic nose technology.     

Physiologically Motivated Monitoring of Fermentation Processes by Means of an Electronic Nose

An on‐line approach of non‐invasive monitoring of the physiological changes in fermentation processes is presented. In yeast batch and bacterial fed‐batch fermentations it is shown that metabolic state changes can be revealed using an electronic nose. The transient responses of the gas sensors to the changes in the composition of the volatiles emitted from the cell cultures during fermentation are used to retrieve a semi‐quantitative representation of the physiological state of the cultures. With the sensor responses of the electronic nose it is shown that physiological variables such as rates of growth, substrate uptake and product formation can be depicted. The non‐invasive method thus seems as a pertinent alternative to conventional bioreactor monitoring methods.     

A new type of semi-empirical molecular orbital method for large molecules.

A new type of molecular orbital method is proposed. It is applicable to large molecules containing large conjugated substructures. Only π-electrons in the conjugated part, but all-valence electrons in the non-conjugated part of a molecule, are taken into account explicitly. The Fock matrix elements are evaluated from the semi-empirical values employed in the existing all-valence-electron methods. The examples presented here suggest that the new type of MO method predicts electronic structures which are quite similar to those obtained by complete semi-empirical MO calculations. This new method may make it possible to reasonably well describe the electronic structure of, and interaction between, large molecules using considerably less computation time and core storage than the complete calculation analogs.     

Stereoelectronic features of the cinchona alkaloids determine their differential antimalarial activity.

For most potent antimalarial activity, the cinchona alkaloids appear to require certain electronic features, particularly a sufficiently acidic hydroxyl proton and an electric field direction pointing from the aliphatic nitrogen atom towards the quinoline ring. These observations are the result of an analysis of molecular electronic properties of eight cinchona alkaloids and an in vivo metabolite calculated using ab initio 3-21G quantum chemical methods in relation to their in vitro IC50 values against chloroquine-sensitive and chloroquine-resistant Plasmodium falciparum parasites. The purpose is to provide a profile of the electronic characteristics necessary for potent antimalarial activity for use in the design of new antimalarial agents and to gain insight into the mechanistic path for antimalarial activity. Distinguishing features of the weakly active epiquinine and epiquinidine include a higher dipole moment, a different direction of the electric field, a greater intrinsic nucleophilicity, lower acidity of the hydroxyl proton, a lesser electron affinity of the lowest unoccupied molecular orbitals, and a higher proton affinity than the active cinchona alkaloids. A moderately potent quinine metabolite possesses some, but not all, of the same electronic features as the most potent cinchona alkaloids. Both the positioning of the hydroxyl and aliphatic amine groups and their electronic features appear to play a crucial role for antimalarial potency of the cinchona alkaloids, most likely by controlling the ability of these groups to form effective intermolecular hydrogen bonds.     

Biological structures as photonic objects

Samples of the material of mollusks bowls, peacock wing elements, and human horn skin have been investigated using the methods of spectroscopy, atomic-force microscopy, X-ray diffraction analysis, and thermoconductance. Ordered superstructures were revealed in these objects. Evidence for effective interactions of both electromagnetic and electronic waves with these structures was obtained. It was shown that the interaction with electromagnetic waves reveals photonic properties and the interaction with electronic waves, the semiconducting properties of biological objects.     

Electronic thrombocyte count from total blood]

Platelets were simultaneously counted in 52 persons by the conventional method of Cronkite and Brecher and with a new electronic cell volume analyser. The platelet counts estimated by the electronic analyser were 10% lower than that measured with the conventional method. This difference decreased to 1.5% when the same diluent was used for both methods. The described electronic counting method of platelets in whole blood is a simple procedure, which gives well reproducible and exact results.     

Computer-aided analysis of the interactions of glutamine synthetase with its inhibitors

Mechanism of inhibition of glutamine synthetase (EC 6.3.1.2; GS) by phosphinothricin and its analogues was studied in some detail using molecular modeling methods. Among three possible conformations of phosphinothricin in the active site of GS, this compatible with binding mode of methionine sulfoximine, determined recently by crystallography, was found to be energetically favored. Basing on these results eleven inhibitors of GS were docked into its active site. Taking into consideration that phosphinothricin acts as suicide inhibitor, which is due to phosphorylation by the enzyme, seven of studied analogues were additionally analyzed in their phosphorylated forms. All the inhibitor-enzyme complexes were evaluated quantitatively by using eight scoring functions implemented in Insight and Sybyl program packages and significant correlation between the obtained scores and experimental pK(i) values was achieved. Computed surface charge distribution for five selected inhibitors in both free and phosphorylated forms and their comparison with electronic structure of enzymatic reaction transition state allowed us to determine important electronic features required to construct potent inhibitors of glutamine synthetase.     

In vivo dosimetry for lung radiotherapy including SBRT

SBRT for lung cancer is being rapidly adopted as a treatment option in modern radiotherapy centres. This treatment is one of the most complex in common clinical use, requiring significant expertise and resources. It delivers a high dose per fraction (typically ∼6–30 Gy/fraction) over few fractions. The complexity and high dose delivered in only a few fractions make powerful arguments for the application of in vivo dosimetry methods for these treatments to enhance patient safety. In vivo dosimetry is a group of techniques with a common objective – to estimate the dose delivered to the patient through a direct measurement of the treatment beam(s). In particular, methods employing an electronic portal imaging device have been intensely investigated over the past two decades. Treatment verification using in vivo dosimetry approaches has been shown to identify errors that would have been missed with other common quality assurance methods. With the addition of in vivo dosimetry to verify treatments, medical physicists and clinicians have a higher degree of confidence that the dose has been delivered to the patient as intended.In this review, the technical aspects and challenges of in vivo dosimetry for lung SBRT will be presented, focusing on transit dosimetry applications using electronic portal imaging devices (EPIDs). Currently available solutions will be discussed and published clinical experiences, which are very limited to date, will be highlighted.