Syntheses with nitriles,XCV: Deamination of cytosine derivatives

Summary Treatment of 2-formyl-3-dimethylamino-propenenitrile (1a) and 2-ethoxycarbonyl-3-dimethylamino-propenenitrile (1b), resp., with substituted ureas led to the 2-cyano-3-ureidoacrylates2, which can be cyclized under alkaline conditions to give 5-formyl-5-cyano-, and 5-alkoxycarbonyl-2-oxopyrimidine derivatives3,6, and7. Reaction of3 with isopentylnitrite gave a mixture of the deaminated and oxidized product4 and the oxo derivative5, which was acetalized during the separation step. Similar reaction with the alkoxycarbonyl derivatives7 led to the formation of 1-alkyl-5-alkoxycarbonyl-pyrimidine-2,6-diones8a–d.

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Synthesen mit Nitrilen, 95. Mitt.: Deaminierung von Cytosinderivaten

Zusammenfassung Die Reaktion von 2-Formyl-3-dimethylamino-propennitril (1a) und 2-Ethoxycarbonyl-3-dimethylamino-propennitril (1b) mit substituierten Harnstoffen führte zur Bildung der 2-Cyan-3-ureidoacrlate2, welche unter alkalischen Bedingungen zu den 5-Formyl-, 5-Cyan- oder 5-Alkoxycarbonyl-2-oxopyrimidinen3,6 bzw.7 cyclisiert werden konnten. Reaktion von3 mit Isopentylnitrit ergab eine Mischung aus deaminiertem und zugleich oxidiertem Produkt4 sowie dem Oxoderivat5, welches während der Säulentrennung auf Kieselgel zusätzlich acetalisiert worden war. Die ähnliche Reaktion mit den Alkoxycarbonyl-Derivativen7 führte zur Bildung der 1-Alkyl-5-alkoxycarbonyl-pyrimidin-2,6-dione8a–d.

     

Potential of metal–fullerene hybrids as strong nanocarriers for cytosine and guanine nucleobases: A detailed DFT study

In this article, the adsorption of cytosine and guanine molecules on the surface of Cr-doped C20 fullerene (C19Cr) and Ni-doped C20 fullerene (C19Ni) are studied using first-principles density functional theory (DFT) calculations. In order to thoroughly comprehend the influences of the molecules on the metal-fullerene complexes, the geometric parameters, the binding energies, transferred charges, the magnitude of dipole moments, thermochemical parameters, frontier molecular orbitals, and the global indices of activities are calculated. The results highlighted that the interactions of both cytosine and guanine molecules with metal-fullerene complexes are highly exothermic, suggesting that these molecules might be chemisorbed on their adsorbents. The C19Cr exhibits a better adsorption behavior toward the molecules compared to C19Ni, and cytosine has the higher binding energies with metal-fullerene complexes in comparison with guanine. Further analyses showed that the C19Cr experiences significant changes in its electronic properties upon adsorption of the cytosine molecule. However, the small variations in the electronic properties of C19Ni after complexation with guanine indicate that this complex is not sensitive to the guanine. Furthermore, the results of frontier molecular orbital reveal the strong (moderate) interactions between the C19Cr with the cytosine (guanine) molecule and moderate (weak) interactions between the C19Ni with the cytosine (guanine) molecule. Therefore, the C19Cr and C19Ni have moderate sensitivities to cytosine and guanine molecules. More excitingly, our findings divulge promising potential of the Cr-fullerene complex as a biochemical adsorbent for cytosine.     

The SI Unit Candela

The history of photometry, the measurement of light—and thus also the root of the basic unit for the luminous intensity, goes back to the seventeenth century. The theoretical foundations are provided by Johann H. Lambert in his treatise on photometry around 1760. With industrialization in the nineteenth century, there is an increasing demand for stable reference light sources for the measurement of light and for an reliable definition of the unit for light. But it is not until the middle of the twentieth century that the basic prerequisites had been created to use a common, internationally recognized unit, the Candela, as a measure of the visible light. The following article describes the basics and the boundary conditions that arise for the unit candela from the revision of the SI.     

A quantitative model of error accumulation during PCR amplification

The amplification of target DNA by the polymerase chain reaction (PCR) produces copies which may contain errors. Two sources of errors are associated with the PCR process: (1) editing errors that occur during DNA polymerase-catalyzed enzymatic copying and (2) errors due to DNA thermal damage. In this study a quantitative model of error frequencies is proposed and the role of reaction conditions is investigated. The errors which are ascribed to the polymerase depend on the efficiency of its editing function as well as the reaction conditions; specifically the temperature and the dNTP pool composition. Thermally induced errors stem mostly from three sources: A+G depurination, oxidative damage of guanine to 8-oxoG and cytosine deamination to uracil. The post-PCR modifications of sequences are primarily due to exposure of nucleic acids to elevated temperatures, especially if the DNA is in a single-stranded form. The proposed quantitative model predicts the accumulation of errors over the course of a PCR cycle. Thermal damage contributes significantly to the total errors; therefore consideration must be given to thermal management of the PCR process.     

Application of Elimination Voltammetry to the Resolution of Adenine and Cytosine Signals in Oligonucleotides. I. Homo‐oligodeoxynucleotides dA9 and dC9

Elimination voltammetry with linear scan (EVLS) has been applied to the resolution of reduction signals of adenine and cytosine in short synthetic homo‐oligodeoxynucleotides (dA₉ and dC₉). In comparison with the common electrochemical methods (linear sweep, differential pulse, and square‐wave voltammetry) EVLS enables one to resolve the overlapped signals by using the function which eliminates the charging and kinetic currents (I_c, I_k) and conserves the diffusion current (I_d). For the adsorbed electroactive substance, this elimination function gives a good readable peak‐counterpeak which has successfully been utilized to the analysis of overlapped reduction signals of adenine and cytosine on hanging mercury drop electrode (HMDE). The height and potential of signals studied were affected by the dC₉/dA₉ ratio, the time of accumulation, the stirring speed during the adsorption, and pH. Our results showed that EVLS in connection with the adsorption procedure is a useful tool for qualitative and quantitative studies of short oligonucleotides.     

Λ-、Δ-[Rh(bpy)2chrysi]3+对含C:T错配的DNA序列识别作用的分子模拟研究

通过分子模拟方法研究了手性金属配合物[Rh(bpy)2Chrysi]3 (bpy=2,2’- bipyridine;Chrysi=5,6-chrysenequinonediimine)对包含C:T错配碱基对的B-DNA序列的识别作用。结合类似的针对含G:A错配的和正常的B-DNA序列的识别作用研究,发现配合物[Rh(bpy)2Chrysi]3 可以对错配B-DNA序列进行序列特异性的识别．能量对比计算结果表明,该经典插入识别作用倾向于在错配碱基对附近进行,其中Δ-[Rh(bpy)2charysi]3 比其手性异构体更占优势．这同Barton教授工作组的实验结果是一致的。另外插入作用倾向于在错配序列中的正常双碱基对C3A4／G374(错配碱基对附近)中从小沟进行．与该配合物对含G:A错配的和正常的B-DNA序列的识别作用不同的是,对包含C:T错配碱基对的B-DNA序列的识别作用倾向于从小沟进行．这一点可能源于C:T碱基对结构的不同．     

Λ-及Δ-[Ru(phen)2dppz]n+对错配DNA的识别作用的分子模拟

本文通过在ESFF(Extensible Systematic Force Field)力场下对其作用中的体系势能进行分子力学计算，分析了手性金属配合物Λ－及Δ-[Ru(phen)2dppz]^n 对错配DNA d(CCGAATGAGG)2的识别机理，并在分子水平上对其做了详细解释。     

光聚物材料中布喇格偏移的动态分析

对光致聚合全息存储材料光化学反应过程和引起布喇格偏移的因素进行了分析,通过理论推导,得到了曝光时间与布喇格偏移量的关系.实验曲线表明,材料的布喇格偏移先是随着曝光量的增加而增加,最后达到饱和值.实验的结果与理论分析进行比较,两者符合较好,说明对于布喇格偏移随时间变化动态过程的分析比较合理.     

Molecular beam epitaxy of Ca1−xRxF2+x (R=Nd, Er) layers: study of RHEED pattern and lattice mismatch

Ca_1−xNd_xF_2+x and Ca_1−xEr_xF_2+x layers were grown on CaF₂(1 1 1) substrates at 600 and 550°C, respectively, by molecular beam epitaxy. Reflection high-energy electron diffraction (RHEED) investigation revealed that Ca_1−xNd_xF_2+x layers have two types of surface structure, namely (1×1) and ( )R30⁰ with hexagonal symmetry, depending on Nd mole fraction, while Ca_1−xEr_xF_2+x layers have three types of surface structure, namely (1×1) and (2×2) with hexagonal symmetry, and a triple rotated domain structure based on a rectangular cell depending on Er mole fraction. The lattice mismatch of the epilayers and substrate, which is important for applications involving buffer layers, was measured by X-ray rocking curve (XRC) analysis.     

考虑不同脉冲形状时群速失配效应在二次谐波自相关法中的影响

本文讨论了在考虑不同脉冲形状时群速失配效应对二次谐波自相关法测量超短光脉冲宽度的影响.结果表明了脉冲形状不同时,群速失配效应对干涉自相关法和强度自相关法的影响不同.