Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics.

RNA hairpins capped by 5'-GNRA-3' or 5'-UNCG-3' tetraloops (TLs) are prominent RNA structural motifs. Despite their small size, a wealth of experimental data, and recent progress in theoretical simulations of their structural dynamics and folding, our understanding of the folding and unfolding processes of these small RNA elements is still limited. Theoretical description of the folding and unfolding processes requires robust sampling, which can be achieved by either an exhaustive time scale in standard molecular dynamics simulations or sophisticated enhanced sampling methods, using temperature acceleration or biasing potentials.

QM/MM calculations with deMon2k.

The density functional code deMon2k employs a fitted density throughout (Auxiliary Density Functional Theory), which offers a great speed advantage without sacrificing necessary accuracy. Powerful Quantum Mechanical/Molecular Mechanical (QM/MM) approaches are reviewed. Following an overview of the basic features of deMon2k that make it efficient while retaining accuracy, three QM/MM implementations are compared and contrasted.

Kinetic and structural characterization of an alternatively spliced variant of human mitochondrial 5'(3')-deoxyribonucleotidase.

Human mitochondrial 5'(3')-deoxyribonucleotidase (mdN) catalyzes dephosphorylation of nucleoside monophosphates, and thus helps maintain homeostasis of deoxynucleosides required for mitochondrial DNA synthesis. Mature mdN is a 23-kDa dimeric protein with highest expression levels in the heart, brain and skeletal muscle. We have identified an alternative splice variant of the mdN gene containing an 18-nucleotide insertion encoding 6 amino acids (GKWPAT) at the 3'-end of the penultimate exon 4.

The Semiempirical Quantum Mechanical Scoring Function for In Silico Drug Design.

This Minireview discusses the latest developments in modern quantum mechanics (QM)-based computer-aided drug design, especially using semiempirical QM (SQM) methods. It first tackles biochemical and biophysical quantities and the approaches to their measurements. Protein-ligand affinities are determined mostly by noncovalent interactions.

Modulation of aldose reductase inhibition by halogen bond tuning.

In this paper, we studied a designed series of aldose reductase (AR) inhibitors. The series was derived from a known AR binder, which had previously been shown to form a halogen bond between its bromine atom and the oxygen atom of the Thr-113 side chain of AR. In the series, the strength of the halogen bond was modulated by two factors, namely bromine-iodine substitution and the fluorination of the aromatic ring in several positions.

Multiparametric characterization of nonelectroactive self-assembled monolayers during their formation.

The formation of nonelectroactive self-assembled monolayers (SAMs) at the electrode/electrolyte interface was characterized with simultaneous impedance, gravimetric, and direct current measurements. In the presence of specifically adsorbing inorganic ions, this provides key information about the formation of SAMs. Gravimetric measurements allow an estimation of the adsorbate surface coverage; and completion of the assembly process can then be monitored in real-time.

Assessing the accuracy and performance of implicit solvent models for drug molecules: conformational ensemble approaches.

The accuracy and performance of implicit solvent methods for solvation free energy calculations were assessed on a set of 20 neutral drug molecules. Molecular dynamics (MD) provided ensembles of conformations in water and water-saturated octanol. The solvation free energies were calculated by popular implicit solvent models based on quantum mechanical (QM) electronic densities (COSMO-RS, MST, SMD) as well as on molecular mechanical (MM) point-charge models (GB, PB).

Plugging the explicit σ-holes in molecular docking.

A novel approach in molecular docking was successfully used to reproduce protein-ligand experimental geometries. When dealing with halogenated compounds the correct description of halogen bonds between the ligand and the protein is shown to be essential. Applying a simple molecular mechanistic model for halogen bonds improved the protein-ligand geometries as well as halogen bond features, which makes it a promising tool for future computer-aided drug development.

The formate channel FocA exports the products of mixed-acid fermentation.

Formate is a major metabolite in the anaerobic fermentation of glucose by many enterobacteria. It is translocated across cellular membranes by the pentameric ion channel/transporter FocA that, together with the nitrite channel NirC, forms the formate/nitrite transporter (FNT) family of membrane transport proteins. Here we have carried out an electrophysiological analysis of FocA from Salmonella typhimurium to characterize the channel properties and assess its specificity toward formate and other possible permeating ions.

On Extension of the Current Biomolecular Empirical Force Field for the Description of Halogen Bonds.

Until recently, the description of halogen bonding by standard molecular mechanics has been poor, owing to the lack of the so-called σ hole localized at the halogen. This region of positive electrostatic potential located on top of a halogen atom explains the counterintuitive attraction of halogenated compounds interacting with Lewis bases. In molecular mechanics, the σ hole is modeled by a massless point charge attached to the halogen atom and referred to as an explicit σ hole (ESH).

Brine rejection from freezing salt solutions: a molecular dynamics study.

The atmospherically and technologically very important process of brine rejection from freezing salt solutions is investigated with atomic resolution using molecular dynamics simulations. The present calculations allow us to follow the motion of each water molecule and salt ion and to propose a microscopic mechanism of brine rejection, in which a fluctuation (reduction) of the ion density in the vicinity of the ice front is followed by the growth of a new ice layer. The presence of salt slows down the freezing process, which leads to the formation of an almost neat ice next to a disordered brine layer.

On differences between hydrogen bonding and improper blue-shifting hydrogen bonding.

Twenty two hydrogen-bonded and improper blue-shifting hydrogen-bonded complexes were studied by means of the HF, MP2 and B3LYP methods using the 6-31G(d,p) and 6--311 ++G(d,p) basis sets. In contrast to the standard H bonding, the origin of the improper blue-shifting H bonding is still not fully understood. Contrary to a frequently presented idea, the electric field of the proton acceptor cannot solely explain the different behavior of the H-bonded and improper blue-shifting H-bonded complexes.

Synthesis of [5]-, [6]-, and [7]helicene via Ni(0)- or Co(I)-catalyzed isomerization of aromatic cis,cis-dienetriynes.

An original approach to helicene frameworks exploiting atom economic isomerization of appropriate energy-rich aromatic cis,cis-dienetriynes has been developed. The new paradigm provides nonphotochemical syntheses of helicenes based on the easy, convergent, and modular assembly of key cis,cis-dienetriynes and their nickel(0)-catalyzed [2+2+2] cycloisomerization. The potential of the methodology is underlined by the syntheses of the parent [5]helicene (2), 7,8-dibutyl[5]helicene (23), [6]helicene (24), and [7]helicene (25).

Prediction of an inverse heavy-atom effect in H-C-CH(2)Br: bromine substituent as a pi acceptor.

A comparison of spin-orbit coupling calculated [CASSCF(6,6)/(cc-pVDZ on C,H and VDZ+P on Br] for bromomethylcarbene and methylcarbene predicts a highly unusual inverse heavy-atom effect by the Br substituent, particularly at geometries near the syn conformation. This behavior is due to a vacant 4d orbital on the Br atom acting as a weak pi-electron acceptor and overwhelming the even weaker effect of the pi-symmetry lone pair donor 4p orbital, which in itself would cause a small normal heavy-atom effect.