Communication of molecular fluorophores with other photoluminescence centres in carbon dots

The establishment of structure-photoluminescence (PL) relationships remains an ultimate challenge in the field of carbon dots (CDs). It is now commonly understood that various structural domains may evolve during the preparation of CDs; nonetheless, we are still far from capturing the specific features that determine the overall PL of CDs. Although the core, surface and molecular states are usually considered the three main sources of PL, it is not known to which extent they interact and/or affect one another. Expectedly, the communication between the different PL centres depends on the mutual arrangement and the type of linking. To gain insights into such a communication, time-dependent density functional theory (TD-DFT) calculations were performed for several (N-doped/O-functionalized) polyaromatic hydrocarbons (PAHs) as representative models for the core/surfaces PL states and the prototypical molecular fluorophore (MF) 5-oxo-1,2,3,5-tetrahydroimidazo-[1,2-α]-pyridine-7-carboxylic acid (IPCA), considering different interaction modes, namely hydrogen bonded and stacked complexes as well as covalently bonded and fused structures. Our results revealed that each of the studied arrangements in some way supported the communication between the PL centres. The deactivation pathways typically involve multiple charge and energy transfer events that can promote the formation of charge separated states and/or lead to the activation of other PL centres in CDs. Depending on the arrangement, the doping pattern and surface functionalization, both the CD core and the MF can act as an electron donor or acceptor, which could help to design CDs with desirable hole–electron surface/core characteristics.Web of Science1584032402

Carbon-Based Materials at Nanoscale

[No abstract available

Stabilizing and Modulating Color by Copigmentation: Insights from Theory and Experiment

Natural anthocyanin pigments/dyes and phenolic copigments/co-dyes form noncovalent complexes, which stabilize and modulate (in particular blue, violet, and red) colors in flowers, berries, and food products derived from them (including wines, jams, purees, and syrups). This noncovalent association and their electronic and optical implications constitute the copigmentation phenomenon. Over the past decade, experimental and theoretical studies have enabled a molecular understanding of copigmentation. This review revisits this phenomenon to provide a comprehensive description of the nature of binding (the dispersion and electrostatic components of π–π stacking, the hydrophobic effect, and possible hydrogen-bonding between pigment and copigment) and of spectral modifications occurring in copigmentation complexes, in which charge transfer plays an important role. Particular attention is paid to applications of copigmentation in food chemistry.P.T. thanks the “Conseil Régional du Limousin” for financial support and CALI (CAlcul en LImousin). Financial support from the Czech Science Foundation (P208/12/G016), the Ministry of Education, Youth and Sports of the Czech Republic (project LO1305), and the Operational Program Education for Competitiveness-European Social Fund (project CZ.1.07/2.3.00/20.0058 of the Ministry of Education, Youth and Sports of the Czech Republic) is also gratefully acknowledged. The work at IMDEA was supported by the Spanish Ministerio de Economía y Competitividad (MINECO; project CTQ2014-58801)

ChannelsDB: database of biomacromolecular tunnels and pores

ChannelsDB (http://ncbr.muni.cz/ChannelsDB) is a database providing information about the positions, geometry and physicochemical properties of channels (pores and tunnels) found within biomacromolecular structures deposited in the Protein Data Bank. Channels were deposited from two sources; from literature using manual deposition and from a software tool automatically detecting tunnels leading to the enzymatic active sites and selected cofactors, and transmembrane pores. The database stores information about geometrical features (e.g. length and radius profile along a channel) and physicochemical properties involving polarity, hydrophobicity, hydropathy, charge and mutability. The stored data are interlinked with available UniProt annotation data mapping known mutation effects to channel-lining residues. All structures with channels are displayed in a clear interactive manner, further facilitating data manipulation and interpretation. As such, ChannelsDB provides an invaluable resource for research related to deciphering the biological function of biomacromolecular channels

Sensitivity of the RNA structure to ion conditions as probed by molecular dynamics simulations of common canonical RNA duplexes

RNA molecules play a key role in countless biochemical processes. RNA interactions, which are of highly diverse nature, are determined by the fact that RNA is a highly negatively charged polyelectrolyte, which leads to intimate interactions with an ion atmosphere. Although RNA molecules are formally single stranded, canonical (Watson−Crick) duplexes are key components of folded RNAs. A double-stranded (ds) RNA is also important for the design of RNA-based nanostructures and assemblies. Despite the fact that the description of canonical dsRNA is considered the least problematic part of RNA modeling, the imperfect shape and flexibility of dsRNA can lead to imbalances in the simulations of larger RNAs and RNA-containing assemblies. We present a comprehensive set of molecular dynamics (MD) simulations of four canonical A-RNA duplexes. Our focus was directed toward the characterization of the influence of varying ion concentrations and of the size of the solvation box. We compared several water models and four RNA force fields. The simulations showed that the A-RNA shape was most sensitive to the RNA force field, with some force fields leading to a reduced inclination of the A-RNA duplexes. The ions and water models played a minor role. The effect of the box size was negligible, and even boxes with a small fraction of the bulk solvent outside the RNA hydration sphere were sufficient for the simulation of the dsRNA.Web of Science6372146213

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