Quantum Chemical Studies Of Nucleic Acids Can We Construct A Bridge To The Rna Structural Biology And Bioinformatics Communities?

In this feature article we provide a side-by-side introduction for two research fields quantum chemical calculations of molecular interaction in nucleic acids and RNA structural bioinformatics Our main aim is to demonstrate that these research areas while largely separated in contemporary literature have substantial potential to complement each other that could significantly contribute to our understanding of the exciting world of nucleic acids We identify research questions amenable to the combined application of modern ab initio methods and bioinformatics analysis of experimental structures while also assessing the limitations of these approaches The ultimate aim is to attain valuable physicochemical insights regarding the nature of the fundamental molecular interactions and how they shape RNA structures, dynamics, function, and evolution

Comparative Analysis of Credit Risk Models in Relation to SME Segment

The importance of credit risk management is well known and was deeply investigated by the banking industry. There is a pressure on financial institutions to still improve their credit risk management systems, so the credit risk of a bank is an unflagging object of discussion. The aim of this article to compare the predicting abilities of several bankruptcy models to the SME segment in the Czech Republic and its subsegments - medium sized, small and micro enterprises. We have focused on small and medium sized enterprises (SMEs) considering their fundamental role played in the Czech economy and the considerable attention placed on SMEs. We have chosen popular bankruptcy models that are often applied, namely the Altman Z-score, Altman model developed especially for SMEs in 2007, the Ohlson O-score, the Zmijewski’s model, the Taffler’s model, and the IN05 model. The basic form of the models was used as proposed by their authors. The results were compared using the contingency table and ROC curve. We have found that the best prediction models are Zmijewski´s and Ohlson´s models which use probit and logit methodologies and according to our analysis, their prediction ability is better than that of models based on discriminant analysis. Surprisingly, model IN05 designed for Czech companies provides average results only. One of the worst performing models is Altman 2007, which was created specifically for SMEs, but according to our analysis it only provides subordinates results

Noncanonical Hydrogen Bonding In Nucleic Acids. Benchmark Evaluation Of Key Base-phosphate Interactions In Folded Rna Molecules Using Quantum-chemical Calculations And Molecular Dynamics Simulations

RNA molecules are stabilized by a wide range of non canonical interactions that are not present in DNA. Among them, the recently classified base phosphate (BPh) interactions belong to the most important ones. Twelve percent of nucleotides in the ribosomal crystal structures are involved in BPh interactions. BPh interactions are highly conserved and provide major constraints on RNA sequence evolution. Here we provide assessment of the energetics of BPh interactions using MP2 computations extrapolated to the complete basis set of atomic orbitals and corrected for higher-order electron correlation effects. The reference computations are compared with DFT-D and DFT-D3 approaches, the SAPT method, and the molecular mechanics force field. The computations, besides providing the basic benchmark for the BPh interactions, allow some refinements of the original classification, including identification of some potential doubly bonded BPh patterns. The reference computations are followed by analysis of some larger RNA fragments that consider the context of the BPh interactions. The computations demonstrate the complexity of interaction patterns utilizing the BPh interactions in real RNA structures. The BPh interactions are often involved in intricate interaction networks. We studied BPh interactions of protonated adenine that can contribute to catalysis of hairpin ribozyme, the key BPh interaction in the S-turn motif of the sarcin ricin loop, which may predetermine the S-turn topology and complex BPh patterns-from the glmS riboswitch. Finally, the structural stability of BPh interactions in explicit solvent molecular dynamics simulations is assessed. The simulations well preserve key BPh interactions and allow dissection of structurally/functionally important water-meditated BPh bridges, which could not be considered in earlier bioinformatics classification of BPh interactions

Catalyst-Free Hydrogen Synthesis from Liquid Ethanol: An ab Initio Molecular Dynamics Study

This is the author accepted manuscript. The final version is available from American Chemical Society via the DOI in this record.The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jpcc.9b01037.Hydrogen is the simplest, oldest, and most widespread molecule in nature. Nevertheless, the vast majority of the hydrogen industrial production stems from steam reforming of methane performed at high temperatures or pressures. Albeit other chemical routes to the hydrogen synthesis, involving, for example, water electrolysis and novel photocatalysts, have recently been explored, no catalyst-free reaction pathways have been identified, seriously limiting the large-scale deployment of hydrogen. On the basis of state-of-the-art ab initio molecular dynamics simulations, here, we present a study revealing a novel synthesis route to hydrogen from neat liquid ethanol, which has been achieved at room temperature and in the absence of any catalyst, upon electric field exposure. This result paves the way to the unprecedented catalyst-free experimental synthesis of hydrogen from liquid ethanol by exploiting a commonly employed field emitter tip apparatus

Effect of genome sequence on the force-induced unzipping of a DNA molecule

We considered a dsDNA polymer in which distribution of bases are random at the base pair level but ordered at a length of 18 base pairs and calculated its force elongation behaviour in the constant extension ensemble. The unzipping force $F(y)$ vs. extension $y$ is found to have a series of maxima and minima. By changing base pairs at selected places in the molecule we calculated the change in $F(y)$ curve and found that the change in the value of force is of the order of few pN and the range of the effect depending on the temperature, can spread over several base pairs. We have also discussed briefly how to calculate in the constant force ensemble a pause or a jump in the extension-time curve from the knowledge of $F(y)$