Preferred conformers in n-propanol: A PCILO study

Preferred conformers around the central C-C and C-O bonds in n-propanol have been determined using the quantum-mechanical PCILO method and compared with those observed experimentally by microwave spectroscopy. The agreement between theory and experiment is excellent, thus minimizing time consuming searches for microwave transitions corresponding to the preferred conformers.     

Conformation of nucleoside antibiotics

Minor modifications or substitutions in the sugar or in the base part of pyrimidine and purine nucleosides have a profound effect on their biological activity. These modified nucleosides usually become antiviral, antibacterial, or cancerostatic agents and they are collectively called nucleoside antibiotics. The conformational properties of some of these nucleoside antibiotics have been studied by the PCILO method. The results obtained from such study indicate that the conformational preferences of these nucleoside antibiotics are very similar to those of their parent nucleosides and especially so in the situations that occur in aqueous solutions. The important biological significance of these results is that these nucleoside antibiotics can easily get incorporated into growing chains of DNA and RNA by mimicking their parent nucleosides and can interfere with the protein synthesis of RNA or DNA synthesis.     

Differential Expression Analysis of Single-Cell RNA-Seq Data: Current Statistical Approaches and Outstanding Challenges

With the advent of single-cell RNA-sequencing (scRNA-seq), it is possible to measure the expression dynamics of genes at the single-cell level. Through scRNA-seq, a huge amount of expression data for several thousand(s) of genes over million(s) of cells are generated in a single experiment. Differential expression analysis is the primary downstream analysis of such data to identify gene markers for cell type detection and also provide inputs to other secondary analyses. Many statistical approaches for differential expression analysis have been reported in the literature. Therefore, we critically discuss the underlying statistical principles of the approaches and distinctly divide them into six major classes, i.e., generalized linear, generalized additive, Hurdle, mixture models, two-class parametric, and non-parametric approaches. We also succinctly discuss the limitations that are specific to each class of approaches, and how they are addressed by other subsequent classes of approach. A number of challenges are identified in this study that must be addressed to develop the next class of innovative approaches. Furthermore, we also emphasize the methodological challenges involved in differential expression analysis of scRNA-seq data that researchers must address to draw maximum benefit from this recent single-cell technology. This study will serve as a guide to genome researchers and experimental biologists to objectively select options for their analysis.     

One Way Traffic: Base-to-Backbone Hole Transfer in Nucleoside Phosphorodithioate

The directionality of the hole-transfer processes between DNA backbone and base was investigated by using phosphorodithioate [P(S⁻)=S] components. ESR spectroscopy in homogeneous frozen aqueous solutions and pulse radiolysis in aqueous solution at ambient temperature confirmed initial formation of G^.+-P(S⁻)=S. The ionization potential of G-P(S⁻)=S was calculated to be slightly lower than that of guanine in 5′-dGMP. Subsequent thermally activated hole transfer from G^.+ to P(S⁻)=S led to dithiyl radical (P-2S^.) formation on the μs timescale. In parallel, ESR spectroscopy, pulse radiolysis, and density functional theory (DFT) calculations confirmed P-2S^. formation in an abasic phosphorodithioate model compound. ESR investigations at low temperatures and higher G-P(S⁻)=S concentrations showed a bimolecular conversion of P-2S^. to the σ²-σ*¹-bonded dimer anion radical [-P-2S 2S-P-]⁻ [ΔG (150 K, DFT)=−7.2 kcal mol⁻¹]. However, [-P-2S 2S-P-]⁻ formation was not observed by pulse radiolysis [ΔG° (298 K, DFT)=−1.4 kcal mol⁻¹]. Neither P-2S^. nor [-P-2S 2S-P-]⁻ oxidized guanine base; only base-to-backbone hole transfer occurs in phosphorodithioate.     

Designing a safer process for the reaction of TFA with sodium borohydride in THF by calorimetric technique

Reaction of TFA with sodium borohydride in THF is a loss of thermal control involving the evolution of Hydrogen gas. The investigation of the process by RC1e and ARSST showed that the criticality class of the reaction is dependant on the addition of TFA. Heat of reaction (Q _r), adiabatic temperature rise (ΔT _ad), and MTSR data are obtained from RC1e experiment. Exothermic onset temperature, Pressure rise, and self heat rate data are obtained from ARSST experiments. The correlation of these data was utilized to define the criticality class of the reaction under different conditions. The reaction with uncontrolled addition of TFA falls in the undesirable criticality class 5. Vent size data are obtained from the adiabatic calorimeter for undesirable reaction. The criticality class can be changed to class 2 with controlled addition. Accordingly, interlock system to control the undesired reaction and appropriate vent relief system are provided.     

Oxone as a Mild,Inexpensive, and Environmentally Benign Oxidant for the α-Thiocyanation of Ketones

An efficient and direct approach for the α-thiocyanation of ketones with α-hydrogens has been developed using ammonium thiocyanate as a thiocyanating agent and oxone as an oxidant in methanol.     

Synthesis and Antimicrobial Activity of 1‐[(Substituted Carbamoyl)Amino]‐1H,3H‐1λ5‐[1,3,2]oxazaphospholo[3,4‐a]benzimidazol‐1‐ones

1‐[(Substituted carbamoyl)amino]‐1H,3H‐1λ⁵‐[1,3,2]oxazaphospholo[3,4‐a]benzimidazol‐1‐ones were synthesized by reacting benzimidazole 2‐methanol (4) with different chlorides of carbamidophosphoric acids (3) in the presence of triethylamine at 40–45°C. Their ¹H, ¹³C, and ³¹P NMR spectral data were discussed. The title compounds were tested for their activity against the fungi Aspergillus niger and Fusarium solani and bacteria Staphylococcus aureus and Escherichia coli. These compounds showed moderate antibacterial activity when compared with antifungal activity.     

In memory of Professor Ali H. Nayfeh

Nonlinear Dynamics - In this paper, we propose and numerically study a nonlinear, asymmetric, passive metamaterial that achieves giant non-reciprocity with (i) broadband frequency operation and...