Klaudia Mrazikova

• Doctor of Philosophy
• J. Heyrovsky Institute of Physical Chemistry ASCR

Hydrogen bonds (H-bonds) are pivotal in various chemical and biological systems and exhibit complex behavior under external perturbations. This study investigates the structural, vibrational, and energetic properties of prototypical H-bonded dimers – water (H2O)2, hydrogen fluoride (HF)2, hydrogen sulfide (H2S)2, and ammonia (NH3)2 – and the respec...

Hydrogen bonds (H-bonds) are pivotal in various chemical and biological systems and exhibit complex behavior under external perturbations. This study investigates the structural, vibrational, and energetic properties of prototypical H-bonded dimers – water (H2O)2, hydrogen fluoride (HF)2, hydrogen sulfide (H2S)2, and ammonia (NH3)2 – and the respec...

Recent ground-based observations of Venus have detected a single spectral feature consistent with phosphine (PH3) in the middle atmosphere, a gas which has been suggested as a biosignature on rocky planets. The presence of PH3 in the oxidized atmosphere of Venus has not yet been explained by any abiotic process. However, state-of-the-art experiment...

Phosphate···π, also called anion···π, contacts occur between nucleobases and anionic phosphate oxygens (OP2) in r(GNRA) and r(UNNN) U-turn motifs (N = A,G,C,U; R = A,G). These contacts were investigated using state-of-the-art quantum-chemical methods (QM) to characterize their physicochemical properties and to serve as a reference to evaluate AMBER...

Phosphate…π, also called anion…π, contacts occur between nucleobases and phosphate OP oxygens in r(GNRA) and r(UNNN) U-turn motifs (N = A,G,C,U; R = A,G). We investigated these contacts in detail by using state-of-the-art quantum chemical methods (QM) to characterize some of their physico-chemical properties and to evaluate the ability of the AMBER...

Influx of matter from impacting meteoroids and hydrothermal crater weathering are important factors modifying the rock and mineral inventory of young planets undergoing heavy bombardment. These processes may have influenced not only the geochemical environment of, e.g. , early Mars and other planets, but also the peculiar prebiotic chemistry on ear...

The lone-pair…π (lp…π) (deoxy)ribose…nucleobase stacking is a recurring structural motif in Z DNA and RNAs that is characterized by sub-van der Waals lp…π contacts (<3.0 Å). It is part of the structural signature of the CpG Z-steps in Z-DNA and r(UNCG) tetraloops. These nucleic acid structures are poorly behaving in molecular dynamics (MD) simulati...

The lone-pair…π (lp…π) (deoxy)ribose…nucleobase stacking is a recurring structural motif in Z DNA and RNAs that is characterized by sub-van der Waals lp…π contacts (<3.0 Å). It is part of the structural signature of the CpG Z-steps in Z-DNA and r(UNCG) tetraloops. These nucleic acid structures are poorly behaving in molecular dynamics (MD) simulati...

Synthesis of RNA nucleobases from formamide is one of the recurring topics of prebiotic chemistry research. Earlier reports suggest that thymine, the substitute for uracil in DNA, may also be synthesized from formamide in the presence of catalysts enabling conversion of formamide to formaldehyde. In the current paper, we show that to a lesser exten...

Phosphorothioates (PTs) are important chemical modifications of the RNA backbone where a single nonbridging oxygen of the phosphate is replaced with a sulfur atom. PT can stabilize RNAs by protecting them from hydrolysis and is commonly used as a tool to explore their function. It is, however, unclear what basic physical effects PT has on RNA stabi...

Explicit solvent atomistic molecular dynamics (MD) simulations represent an established technique to study structural dynamics of RNA molecules and an important complement for diverse experimental methods. However, performance of molecular mechanical (MM) force fields (ff's) remains far from satisfactory even after decades of development, as appare...

Phosphorothioates (PTs) are important chemical modifications of the RNA backbone where a single non-bridging oxygen of the phosphate is replaced with a sulphur atom. PT can stabilize RNAs by protecting them from hydrolysis and is commonly used as tool to explore their function. It is, however, unclear what basic physical effects PT has on RNA stabi...

Formation and structural modification of oxygenated polycyclic aromatic hydrocarbons (oxyPAHs) by UV irradiation on minerals have recently been proposed as a possible channel of PAH transformation in astrochemical and prebiotic scenarios of possible relevance for the origin of life. Herein, it is demonstrated that high‐energy proton‐beam irradiatio...

Explicit solvent atomistic molecular dynamics (MD) simulations represent an established technique to study structural dynamics of RNA molecules and an important complement for diverse experimental methods. However, performance of molecular mechanical (MM) force fields (ffs) remains far from satisfactory even after decades of development, as apparen...

Current interest in lone‐pair⋅⋅⋅π (lp⋅⋅⋅π) interactions is gaining momentum in biochemistry and (supramolecular) chemistry. However, the physicochemical origin of the exceptionally short (ca. 2.8 Å) oxygen‐to‐nucleobase plane distances observed in prototypical Z‐DNA CpG steps remains unclear. High‐level quantum mechanical calculations, including SA...

Current interest for lone‐pair…π (lp…π) non‐covalent interactions is gaining momentum in biochemistry and (supramolecular)chemistry. However, the physico‐chemical origin of the exceptionally short (≈2.8 Å) oxygen to nucleobase plane distances observed in prototypical Z‐DNA CpG steps remains unclear. Accurate quantum mechanical calculations includin...