Potential Achilles heels of SARS-CoV-2 are best displayed by the base order-dependent component of RNA folding energy

The base order-dependent component of folding energy has revealed a highly conserved region in HIV-1 genomes that associates with RNA structure. This corresponds to a packaging signal that is recognized by the nucleocapsid domain of the Gag polyprotein. Long viewed as a potential HIV-1 "Achilles heel," the signal can be targeted by a new antiviral compound. Although SARS-CoV-2 differs in many respects from HIV-1, the same technology displays regions with a high base order-dependent folding energy component, which are also highly conserved. This indicates structural invariance (SI) sustained by natural selection. While the regions are often also protein-encoding (e. g. NSP3, ORF3a), we suggest that their nucleic acid level functions can be considered potential "Achilles heels" for SARS-CoV-2, perhaps susceptible to therapies like those envisaged for AIDS. The ribosomal frameshifting element scored well, but higher SI scores were obtained in other regions, including those encoding NSP13 and the nucleocapsid (N) protein.     

The adsorption of endothelin 1 to phospholipids is governed by electrostatic interactions: A monolayer and fluorescence study

In order to elucidate the influence on the lipidic environment on the recognition process of its membrane associated receptor, the interactions of the vasoconstrictor peptide endothelin 1 with various phospholipids have been investigated using different lipidic model membranes: monolayers at constant surface pressure, vesicles and micelles. A monolayer study of ET1 adsorbed onto the water surface has shown that the C-terminus of the peptide points towards the aqueous phase. Penetration measurements into lipidic monolayers indicate that ET1 adsorbs to phospholipids with an orientation similar to that of the air–water interface and fluorescence measurements are in agreement with such an orientation of the peptide. This adsorption is selective for neutral phospholipids and indicates that the nature of the phospholipid headgroups is of major importance for the approach of the membrane associated receptor.     

Negative adsorption due to electrostatic exclusion of micelles

Interactions of surfactants with solid substrates are important in the controlling of processes such as flotation, coating, flocculation and sedimentation. These interactions usually lead to adsorption on solids, but can also result in an exclusion of the reagents with dire consequences. In this work electrostatic exclusion of negatively charged dodecylbenzene sulfonate micelles from quartz/water, Bio-Sil/water and alumina/water interfaces has been investigated as a function of pH and ionic strength. Measurable negative adsorption of these surfactants from similarly charged solid/liquid interface was observed in the micellar region. In the case of porous samples with large surface area, comparison of pore size with the micelle size is necessary to avoid any erroneous conclusions regarding the role of electrostatic exclusion in a given system. A theoretical model for the electrostatic exclusion of micelles is developed and used to calculate the adsorption of negatively charged dodecylbenzene sulfonate on negatively charged quartz (pH 7), silica (Bio-Sil A, pH 3) and alumina (pH 11) in the micellar concentration region. The micellar exclusion values calculated using the model are in excellent agreement with the experimental results.     

亚烷基卡宾与甲醛环加成反应机理的理论研究

用二阶微扰理论研究了单重态亚烷基卡宾与甲醛发生的三种环加成反应的机理 ，采用MP2/6－31G~*方法计算了势能面上各驻点的构型参数、振动频率和能量。根 据能量数据可以预言环加成反应（1）的a途径将是单重态亚烷基卡宾与甲醛环加成 反应的主要反应通道，该反应由两步组成：（I）亚烷基卡宾与甲醛生成了一富能 中间体（INT1a），是一无势垒的放热反应，（II）中间体异构化为产物亚烷基环 乙烷，其势垒为24.1 kJ·mol~(-1)(MP2/6-31G~*)。     

Forward and backward pericyclic photochemical reactions have intermediates in common, yet cyclobutenes break the rules.

Photochemical pericyclic reactions are believed to proceed via a so-called pericyclic minimum on the lowest excited potential surface (S(1)), which is common to both the forward and backward reactions. Such a common intermediate has never been directly detected. The photointerconversion of 1,3-butadiene and cyclobutene is the prevailing prototype for such reactions, yet only diene ring closure proceeds with the stereospecificity that the Woodward-Hoffmann rules predict. This contrast seems to exclude a common intermediate. Using ultrafast spectroscopy, we show that the excited states of two cyclobutene/diene isomeric pairs are linked by not one, but by two common minima, p* and ct*. Starting from the diene side (cyclohepta-1,3-diene and cycloocta-1,3-diene), electrocyclic ring closure passes via the pericyclic minimum p*, whereas ct* is mainly responsible for cis-trans isomerization. Starting from the corresponding cyclobutenes (bicyclo[3.2.0]heptene-6 and bicyclo[4.2.0]octene-7), the forbidden isomer is formed from ct*. The path branches at the first (S(2)/S(1)) conical intersection towards p* and ct*. The fact that the energetically unfavorable ct* path can compete is ascribed to a dynamic effect: the momentum in C=C twist direction, acquired--such as in other olefins--in the Franck-Condon region of the cyclobutenes.     

HSCCS自由基势能面的理论研究

在CCSD(T)/6-311G(d,f)//MP2/6-311G(d,f) ZPE水平下,计算得到含有8个异构体和11个过渡态的HSCCS自由基体系势能面,讨论了异构体的结构与稳定性及异构体之间的异构化过程.结果表明异构体m1的能量最低,除m1以外,异构体m2和m3的能量也比较低,在MP2水平上,过渡态TS1的能量比异构体m2仅高3.9kJ/mol,而在CCSD(T)水平上,TS1的能量比m2低14.6 kJ/mol,这说明异构体m2可以迅速转化为能量更低的m1.异构体m3的能量比异构体m1高49.99 kJ/mol,可以推断,在合适的实验条件下可以观测到异构体m1.     

Studies on controlled potential coulometric determination of gallium in sodium perchlorate and sodium thiocyanate

Controlled potential coulometric (CPC) studies were carried out for developing a method to determine gallium at milligram levels, in the mixed supporting electrolyte medium (4 M NaClO₄ + 0.5 M NaSCN), employing stirring mercury as a working electrode. Investigations for optimization of working electrode potentials, quantity of charge, level of background current and electrolysis time for achieving quantitative reduction of Ga(III) to Ga and its oxidation back to Ga(III), were undertaken. Effect of gallium content and interference of zinc in of gallium determination were also studied. The developed methodology was employed for the determination of gallium in pure Ga as well as in synthetic U + Ga mixture solutions. Accuracy and precision values of better than 0.5% were obtained at 1-2 mg levels.     

密度泛函理论和从头算方法对富勒烯分子静电势的比较研究

分别在Hartree-Fock和密度泛函B3LYP理论下,用6-31G*基组研究了C60和C70分子的静电势,比较了这方法计算得到上述分子静电势值的大小,静电势图形和静电势差值曲线,分析了富勒烯的电子相关效应.     

Isomers of C20: an energy profile III

Semiempirical calculations, at the PM3 level provided within the Winmopac v2.0 software package, are used to geometrically optimize and determine the absolute energies (heats of formation) of a variety of C(20) isomers that are predicted to exist in and around the ring and cage isomers. Using the optimized Cartesian coordinates for the ring and the cage isomers, a saddle-point calculation was performed. The resulting energy profile, consisting of a series of peaks and valleys, is used as a starting point for the identification and location of fifteen additional isomers of C(20) that are predicted to be energetically stable, both via geometry optimizations and force constant analysis. These additional isomers were subsequently determined to lie adjacent to one another on the potential surface and establish a step-wise transformation between the ring and the cage. Transition-state optimization of the Cartesian coordinates at the saddle point between adjacent isomers was performed to quantify the energy of the transition state. The step-wise process from one isomer to another, which extends out over the three-dimensional surface, is predicted to require approximately 15% less energy than that of the direct, two-dimensional transformation predicted in the bowl-cage profile. However, the net atomic rearrangement for the step-wise process is about four times greater than that of the direct process. Although less in energy, the amount of atomic rearrangement in the step-wise process would make the occurrence of such a route prohibitive. Utilizing the direct distance separating the three primary isomers (ring, bowl, cage), the method of triangulation is performed to quantitatively position other C(20) structures on the potential surface, relative to the ring, bowl, and cage isomers.     

N-取代吩噻嗪和DDQ的电荷转移络合作用

具有盼嘤酸化学结构的化合物有广泛的用途I‘－＼其中吩嘤埃衍生物在医学上用作抗精神病药物特别受到药理学家们的注意，发现其药理作用与其分子提供电子的能力有关卜‘」但是我们应该注意到，作为抗精神病药物的吩嚷嚷衍生物，其吩座爆分子的氮原子都连有一个叔胺基链问，例如氯丙障（I）和奋乃静（11）．而我们知道，胺类特别是叔胺类有强的提供电子的能力＊；在上述的药物分子中是主要的提供电子因素，因此以这类化合物作为给体研究其供电子能力，是不能实际反映吩嘤嗓分子本身的给电子能力的．吩嘤噪类属于二苯并杂环化合物，分子中既…