Critical assessment of interactions between ct-DNA and choline-based magnetic ionic liquids: evidences of compaction.

Ionic liquids (ILs) have become an alternative green solvent for storage and for stability of DNA. However, an in-depth understanding of binding and molecular interactions between ILs and DNA is needed. In this respect, magnetic ILs (MILs) are promising due to their tunable physicochemical properties. Various spectroscopic techniques and molecular simulations have been employed to unravel the critical factors of the strength and binding mechanism of MILs with DNA. UV-vis spectra unravel the multimodal binding of MILs with DNA, and the intrusion of IL molecules into the minor groove of DNA has been observed from dye displacement studies. Fluorescence correlation spectroscopic studies and scanning electron microscopy confirm the compaction of the DNA. ITC and molecular docking studies estimate the binding affinity of DNA with MILs, of ∼7 kcal mol-1. The 1 µs long-MD simulations give insight into the structural changes in the DNA in the MIL environment. Due to strong interaction with choline ions in the close vicinity, DNA helixes bend or squeeze in length and dilate in diameter (elliptical → spherical), leading to compaction. The post-MD parameters suggest a stronger interaction with [Ch]2[Mn] IL than with [Ch][Fe] IL; hence, the former induces DNA compaction to a more significant extent. Furthermore, decompaction is observed with the addition of sodium salts and is characterized using spectroscopic methods.

Critical assessment of selenourea as an efficient small molecule fluorescence quenching probe to monitor protein dynamics.

Organoselenium compounds have recently been the experimentalists' delight due to their broad applications in organic synthesis, medicinal chemistry, and materials science. Selenium atom replacement of the carbonyl oxygen of the urea moiety dramatically reduces the HOMO-LUMO gap and oxidation potential, which completely changes the physicochemical properties of selenocarbonyl compounds. To our surprise, the photophysics and utility of a simple molecule such as selenourea (SeU) have not been explored in detail, which persuaded us to investigate its role in excited state processes. The steady-state emission, temperature-dependent time-correlated single photon counting, and femtosecond fluorescence upconversion experimental results confirmed that SeU significantly enhances the fluorescence quenching through a photoinduced electron transfer (PET) mechanism with an ∼10 ps ultrafast intrinsic PET lifetime component which is mostly absent in thiourea (TU). A wide range of fluorophores, based on their different redox abilities and fluorescence lifetimes covering a broad spectral window (λex: 390-590 nm and λem: 490-690 nm), were chosen to validate the proof of the concept. It was extended to tetramethylrhodamine (TMR)-5-maleimide labeled lysozyme protein, where we observed significant fluorescence quenching in the presence of SeU. The present work emphasizes that the high quenching efficiency with an ultrafast PET process, reduced orbital energy gap, and higher negative free energy change of the electron transfer reaction are the representative characteristics of selenourea or selenoamides to enable them as potential surrogates of thioamides or oxoamides quenching probes to monitor protein conformational changes and dynamics.

Thiolumazines as Heavy-Atom-Free Photosensitizers for Applications in Daylight Photodynamic Therapy: Insights from Ultrafast Excited-State Dynamics.

Finding appropriate photosensitizers (PSs) for daylight photodynamic therapy (dPDT) applications is extremely challenging, even though heavy-atom-free photosensitizers (HAFPSs) such as thiocarbonyl-modified nucleobases have shown a ray of hope. Few attempts have been made to find alternative natural products for dPDT applications. Pteridine heterocycles consisting of a pyrazine ring and a pyrimidine ring, such as lumazine, which exhibit many structural similarities to the alloxazine ring of the flavin molecule, could be an option for HAFPSs. The photophysical and quantum mechanical studies of the thio-modified lumazines revealed that sequential thiomodifications in lumazine result in a bathochromic shift. Additionally, higher tissue penetration depths were observed for thiolumazines. The fluorescence quenching in the case of thiomodified lumazines was explained using triplet state formation, whereas the contribution from the photoinduced electron transfer process cannot be ignored. It was also noticed that a strong one-photon absorption influenced the two-photon absorption (TPA) process, leading to a self-focusing effect in the visible spectral region. The higher tissue penetration and larger TPA cross section are the hallmark characteristics of the thiolumazines to be considered as potential HAFPSs for dPDT applications.

Hydrogen bonding with polonium.

Hydrogen bonding (H-bonding) with heavier chalcogens such as polonium and tellurium is almost unexplored owing to their lower electronegativities, providing us an opportunity to delve into the uncharted territory of X-H⋯Po/Te H-bonds (X-H, X = O, N, C). Employing high-level quantum mechanical calculations that include dispersion correction and the relativistic effect and considering dimethyl polonium (Me2Po) as the model H-bond donor, we have provided evidence of the X-H⋯Po H-bonds for the first time. The H-bond energies can be as much as 30 kJ mol-1, which is energetically comparable to any conventional H-bonds. It is counterintuitive from the perspective of low electronegativity of polonium but possible if one considers the contributions from polarizability, dispersion, and the relativistic effect. We strongly believe that these fundamental studies are expected to impact polonium chemistry, such as in marine science, as dimethyl polonium is one of the major chemicals produced by aerobic marine microorganisms and tracer applications of polonium for environmental carbon cycles.

Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking.

Understanding the noncovalent interactions (NCIs) among the residues of proteins and nucleic acids, and between drugs and proteins/nucleic acids, etc., has extraordinary relevance in biomolecular structure and function. It helps in interpreting the dynamics of complex biological systems and enzymatic activity, which is esential for new drug design and efficient drug delivery. NCIs like hydrogen bonding (H-bonding) and π-stacking have been researchers' delight for a long time. Prominent among the recently discovered NCIs are halogen, chalcogen, pnictogen, tetrel, carbo-hydrogen, and spodium bonding, and n → π* interaction. These NCIs have caught the imaginations of various research groups in recent years while explaining several chemical and biological processes. At this stage, a holistic view of these new ideas and findings lying scattered can undoubtedly trigger our minds to explore more. The present review attempts to address NCIs beyond H-bonding and π-stacking, which are mainly n → σ*, n → π* and σ → σ* type interactions. Five of the seven NCIs mentioned earlier are linked to five non-inert end groups of the modern periodic table. Halogen (group-17) bonding is one of the oldest and most explored NCIs, which finds its relevance in biomolecules due to the phase correction and inhibitory properties of halogens. Chalcogen (group 16) bonding serves as a redox-active functional group of different active sites of enzymes and acts as a nucleophile in proteases and phosphates. Pnictogen (group 15), tetrel (group 14), triel (group 13) and spodium (group 12) bonding does exist in biomolecules. The n → π* interactions are linked to backbone carbonyl groups and protein side chains. Thus, they are crucial in determining the conformational stability of the secondary structures in proteins. In addition, a more recently discovered to and fro σ → σ* type interaction, namely carbo-hydrogen bonding, is also present in protein-ligand systems. This review summarizes these grand epiphanies routinely used to elucidate the structure and dynamics of biomolecules, their enzymatic activities, and their application in drug discovery. It also briefs about the future perspectives and challenges posed to the spectroscopists and theoreticians.

Structural Dynamics of RNA in the Presence of Choline Amino Acid Based Ionic Liquid: A Spectroscopic and Computational Outlook.

Ribonucleic acid (RNA) is exceedingly sensitive to degradation compared to DNA. The current protocol for storage of purified RNA requires freezing conditions below -20 °C. Recent advancements in biological chemistry have identified amino acid-based ionic liquids as suitable preservation media for RNA, even in the presence of degrading enzymes. However, the mechanistic insight into the interaction between ILs and RNA is unclear. To the best of our knowledge, no attempts are made so far to provide a molecular view. This work aims to establish a detailed understanding of how ILs enable structural stability to RNA sourced from Torula yeast. Herein, we manifest the hypothesis of multimodal binding of IL and its minimal perturbation to the macromolecular structure, with several spectroscopic techniques such as time-resolved fluorescence and fluorescence correlation spectroscopy (FCS) aided with molecular dynamics at microsecond time scales. Relevant structural and thermodynamic details from biophysical experiments confirm that even long-term RNA preservation with ILs is a possible alternative devoid of any structural deformation. These results establish a unifying mechanism of how ILs are maintaining conformational integrity and thermal stability. The atomistic insights are transferable for their potential applications in drug delivery and biomaterials by considering the advantages of having maximum structural retention and minimum toxicity.

Doubling Förster Resonance Energy Transfer Efficiency in Proteins with Extrinsic Thioamide Probes: Implications for Thiomodified Nucleobases.

Designing a potential protein-ligand pair is pivotal, not only to track the protein structure dynamics, but also to assist in an atomistic understanding of drug delivery. Herein, the potential of a small model thioamide probe being used to study albumin proteins is reported. By monitoring the Förster resonance energy transfer (FRET) dynamics with the help of fluorescence spectroscopic techniques, a twofold enhancement in the FRET efficiency of 2-thiopyridone (2TPY), relative to that of its amide analogue, is observed. Molecular dynamics simulations depict the relative position of the free energy minimum to be quite stable in the case of 2TPY through noncovalent interactions with sulfur, which help to enhance the FRET efficiency. Finally, its application is shown by pairing thiouracils with protein. It is found that the site-selective sulfur atom substitution approach and noncovalent interactions with sulfur can substantially enhance the FRET efficiency, which could be a potential avenue to explore in the design of FRET probes to study the structure and dynamics of biomolecules.

Non-conventional Hydrogen Bonding and Aromaticity: A Systematic Study on Model Nucleobases and Their Solvated Clusters.

The conceptual development of aromaticity is essential to rationalize and understand the structure and behavior of aromatic heterocycles. This work addresses for the first time, the interconnection between aromaticity and sulfur/selenium centered hydrogen bonds (S/SeCHBs) involved in representative heterocycle models of canonical nucleobases (2-Pyridone; 2PY) and its sulfur (2-Thiopyridone; 2TPY) and selenium (2-Selenopyridone; 2SePY) analogs. The nucleus-independent chemical shift (NICS) and gauge induced magnetic current density (GIMIC) values suggested significant reduction of aromaticity upon replacement of exocyclic carbonyl oxygen with sulfur and selenium. However, we observed two-fold (57 %) and three-fold (80 %) enhancement in the aromaticity for 2TPY dimer, and 2SePY dimer, respectively which are connected through S/SeCHBs. Aromaticity enhancement was also noticed in 1 : 1 H-bonded complexes (heterodimers), micro hydrated clusters and for bulk hydration. It is expected that exocyclic S and Se incorporation into heterocycles without compromising aromatic loss would definitely reinforce to design new supramolecular building blocks via S/SeCH-bonded complexes.

Non-covalent interactions with inverted carbon: a carbo-hydrogen bond or a new type of hydrogen bond?

In contrast to the conventional and non-conventional non-covalent interactions (NCIs) such as hydrogen bond and carbon bond, a bidirectional NCI without π- and/or lone pair(s) of electrons has never been reckoned until the present report, which confirms that this type of NCI can be possible with the involvement of mostly σ-electrons. This newly discovered NCI can be coined as carbo-hydrogen bond (CH-bond) based on its resemblances with both carbon bond (C-bond) and hydrogen bond (H-bond) or Ci:::H interaction. A detailed crystal structure analysis of 5-cyano-1,3-dehydroadamantane, which contains inverted carbon atoms (Ci) and Ci-Ci σ-bond, gave us the opportunity to unveil the very first existence of the Ci:::H interaction. With the aid of several quantum chemical calculations, we came to the conclusion that molecules carrying Ci-Ci σ-bonds are capable of forming CH-bonds with main group hydrides through the σCi-Ci → σ*X-H (H-bond) and σX-H → σ*Ci-Ci (C-bond) orbital interactions. The interaction energy can be as much as -31.27 kJ mol-1, which is comparable to that of the water dimer and it is also one of the prominent attractive forces that hold the molecules together in the crystal structure, can be responsible for the enzymatic activity of cytochrome P411-E10 and the formation of non-covalent organic framework (NCOF) with trigonal and tetragonal CH-bond connectors.

Amino-Acid-Based Ionic Liquids for the Improvement in Stability and Activity of Cytochrome c: A Combined Experimental and Molecular Dynamics Study.

The demand for long-term storage and stability of proteins has increased substantially in the pharmaceutical industries, yet the sensitivity of proteins toward the environment has become a cardinal task for researchers. To deal with this, we have selected a multifunctional enzyme Cytochrome-c (Cyt-c) involved in many chemical and biochemical reactions as model protein, which is very sensitive and loses structural integrity on exposure to the environment. The remarkable features of ionic liquids (ILs) have entitled them as alternatives to aqueous and organic solvents for solubility, storage, and surrogate reaction medium. Hence, we have adapted the biocompatible and nontoxic cation and anion based amino acid ILs (CAAAILs) as potential solvents for storage and stability of Cyt-c. Herein, we report the molecular insights and thermodynamics of interaction between CAAAILs and Cyt-c with the help of isothermal titration calorimetry (ITC), transmission electron microscopy (TEM), UV-vis, CD, and fluorescence spectroscopy as well as molecular docking and molecular dynamics (MD) simulations. The structure and stability of Cyt-c remain unchanged in the presence of CAAAILs. Both electrostatic and hydrophobic interactions are accountable for the binding of CAAAILs in the region between terminal helices and the loop of Cyt-c through nonspecific multiple binding sites, which can be exploited for storage and stability of proteins and will be helpful in designing new biobased ILs for biochemical applications.