Themed collection Theoretical chemical physics of biological systems

Computational methods offer an unparalleled opportunity to dissect in minute detail enzymatic reaction mechanisms.

Toward a multifrequency virtual spectrometer: status and perspectives.

A review of the basic ingredients of developing coarse-grained models and conditions to be satisfied for preserving the correct physical mechanisms.

The chemical structure of hypericin and the crystal structure of SERCA1A with the identified binding pockets that were subject to docking in the present study.

The physicochemical characterization of the several 5-HT₃-R interfaces allows the prediction, on atomistic bases, of the role played by the extracellular moieties of the A–E subunits in the formation of functional or non-functional receptors.

We show severe convergence problems for QM/MM free-energy perturbations even if based on tailored force fields or semiempirical calculations.

Computational methods for accurately calculating the binding affinity of a ligand for a protein play a pivotal role in rational drug design.

Towards elucidating the role of base stacking in the conformational preference of tandem GA base pairs in RNA.

The picture shows the enzyme renin, whose catalytic mechanism was studied in atomistic detail. The enzyme is coloured grey, the substrate is coloured orange, and the cleavage point (Leu10-Val11), the catalytic aspartic dyad and the water molecule are coloured by element, and depicted in ball and stick representation.

The color variation of computationally designed rhodopsin mutants is investigated using a multiconfigurational quantum chemistry based QM/MM method.

Voltage-gated potassium channels exposed to fullerene.

MD simulations of E2 enzymes were carried out and analyzed to provide a quantitative description of their functional dynamics. The functionally relevant differences between the closed and open conformations were unravelled, and critical residues involved in long-range communication paths were detected.

In this work we describe a computationally efficient algorithm to determine minimum energy paths in complex systems.

There is evidence that the interaction of the α-ketol group of the Doxorubicin and Epirubicin anti-cancer drugs with Fe(III) generates hydroxyl radicals under aerobic conditions, which may cause cardiotoxicity in patients.

In this study interaction between glycine and cisplatin is explored.

The UV/Visible absorption properties of a polypyridyl ruthenium complex upon intercalation on DNA are studied at the mixed quantum mechanics molecular mechanics level of theory.

Deprotonation of ground-state deoxyguanosine sites in one-electron-oxidized DNA has been investigated, including both the purine and the sugar moieties. A new mechanistic proposal is provided supporting the formation of C centered radicals under physiological conditions.

XYG3 and XYGJ-OS functionals provide an overall good agreement with reference values for the S22, S22x5 and JSCH-2005 benchmark sets.

Investigation on the structure and acidity of citric acid upon its complexation to Al(III).

Excellent antioxidants in aqueous solution, at physiological pH, via a single electron transfer mechanism from the phenoxide anions.

This multi-scale theoretical study provides new insights into the cisplatin biological activity. The induced rare tautomeric form of the guanine–cytosine base pair in the A context emerges as a well-suited candidate to promote its in vivo cytotoxicity.

Extensive, unbiased simulations of a 10-residue β-hairpin disclose a turn-directed folding process and show that hydrophobic cross-strand side-chain interactions may cause packing frustration that could nucleate aggregative events.

We provide a physical basis for the opposite ion selectivity in Na_v and Ca_v channels with the EEEE motif.