Recent Progress in Density Functional Methodology for Biomolecular Modeling

Multiscale molecular modelling: from electronic structure to dynamics of nanosystems and beyond

Important contemporary biological and materials problems often depend on interactions that span orders of magnitude differences in spatial and temporal dimensions. This Tutorial Review attempts to provide an introduction to such fascinating problems through a series of case studies, aimed at beginning researchers, graduate students, postdocs and more senior colleagues who are changing direction to focus on multiscale aspects of their research. The choice of specific examples is highly personal, with examples either chosen from our own work or outstanding multiscale efforts from the literature. I start with various embedding schemes, as exemplified by polarizable continuum models, 3-D RISM, molecular DFT and frozen-density embedding. Next, QM/MM (quantum mechanical/molecular mechanical) techniques are the workhorse of pm-to-nm/ps-to-ns simulations; examples are drawn from enzymes and from nanocatalysis for oil-sands upgrading. Using polarizable force-fields in the QM/MM framework represents a burgeoning subfield; with examples from ion channels and electron dynamics in molecules subject to strong external fields, probing the atto-second dynamics of the electrons with RT-TDDFT (real-time - time-dependent density functional theory) eventually coupled with nuclear motion through the Ehrenfest approximation. This is followed by a section on coarse graining, bridging dimensions from atoms to cells. The penultimate chapter gives a quick overview of multiscale approaches that extend into the meso- and macro-scales, building on atomistic and coarse-grained techniques to enter the world of materials engineering, on the one hand, and cell biology, on the other. A final chapter gives just a glimpse of the burgeoning impact of machine learning on the structure-dynamics front. I aim to capture the excitement of contemporary leading-edge breakthroughs in the description of physico-chemical systems and processes in complex environments, with only enough historical content to provide context and aid the next generation of methodological development. While I aim also for a clear description of the essence of methodological breakthroughs, equations are kept to a minimum and detailed formalism and implementation details are left to the references. My approach is very selective (case studies) rather than exhaustive. I think that these case studies should provide fodder to build as complete a reference tree on multiscale modelling as the reader may wish, through forward and backward citation analysis. I hope that my choices of cases will excite interest in newcomers and help to fuel the growth of multiscale modelling in general.

Discovery and design of soft polymeric bio-inspired materials with multiscale simulations and artificial intelligence

Establishing the “Materials 4.0” paradigm requires intimate knowledge of the virtual space in materials design.

Chemical feasibility of the general acid/base mechanism of glmS ribozyme self-cleavage

In numerous Gram-positive bacteria, the glmS ribozyme or catalytic riboswitch regulates the expression of glucosamine-6-phosphate (GlcN6P) synthase via site-specific cleavage of its sugar-phosphate backbone in response to GlcN6P ligand binding. Biochemical data have suggested a crucial catalytic role for an active site guanine (G40 in Thermoanaerobacter tengcongensis, G33 in Bacillus anthracis). We used hybrid quantum chemical/molecular mechanical (QM/MM) calculations to probe the mechanism where G40 is deprotonated and acts as a general base. The calculations suggest that the deprotonated guanine G40(-) is sufficiently reactive to overcome the thermodynamic penalty arising from its rare protonation state, and thus is able to activate the A-1(2'-OH) group toward nucleophilic attack on the adjacent backbone. Furthermore, deprotonation of A-1(2'-OH) and nucleophilic attack are predicted to occur as separate steps, where activation of A-1(2'-OH) precedes nucleophilic attack. Conversely, the transition state associated with the rate-determining step corresponds to concurrent nucleophilic attack and protonation of the G1(O5') leaving group by the ammonium moiety of the GlcN6P cofactor. Overall, our calculations help to explain the crucial roles of G40 (as a general base) and GlcN6P (as a general acid) during glmS ribozyme self-cleavage. In addition, we show that the QM/MM description of the glmS ribozyme self-cleavage reaction is significantly more sensitive to the size of the QM region and the quality of the QM-MM coupling than that of other small ribozymes.

Theoretical Research into Anticancer Activity of Diterpenes Isolated from the Paraiban Flora

Many studies of the scientific literature discuss the anticancer activity of diterpenes inhibiting the Akt/IKK/NF-κB pro-survival signaling cascade, mainly by the activation of serine/threonine phosphatase PP2A. The aim of this work was to evaluate and compare the anticancer potential of three atisane, three kaurane and three trachylobane diterpenes extracted from the roots of Xylopia langsdorffiana. Thus, we investigated the reactivity (H-LGAP parameter), HOMO atmosphere favorable to neutralize the radical reactivity, and the docking of compounds with PP2A. With all approaches, this theoretical study showed that atisane diterpenes have favorable characteristics for antitumor activity, like electron donating ability and greater hydrophilic interactions with the enzyme, by inhibition of Akt/IKK/NF-κB, and activation of PP2A.