The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP

In drug discovery, protonation states and tautomerization are easily overlooked. Through a Merck–Rutgers collaboration, this paper re-examined the initial settings and preparations for the Thermodynamic Integration (TI) calculation in AMBER Free-Energy Workflows, demonstrating the value of careful consideration of ligand protonation and tautomer state. Finally, promising results comparing AMBER TI and Schrödinger FEP+ are shown that should encourage others to explore the value of TI in routine Structure-based Drug Design.     

Nucleic acid reactivity: Challenges for next‐generation semiempirical quantum models

Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical (QM)/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity to quantify their limitations and guide the development of next‐generation quantum models with improved accuracy. Neglect of diatomic differential overlap and self‐consistent density‐functional tight‐binding semiempirical models are evaluated against high‐level QM benchmark calculations for seven biologically important datasets. The datasets include: proton affinities, polarizabilities, nucleobase dimer interactions, dimethyl phosphate anion, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions. As an additional baseline, comparisons are made with several commonly used density‐functional models, including M062X and B3LYP (in some cases with dispersion corrections). The results show that, among the semiempirical models examined, the AM1/d‐PhoT model is the most robust at predicting proton affinities. AM1/d‐PhoT and DFTB3‐3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well. Further, a recently developed linear‐scaling “modified divide‐and‐conquer” model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers. The semiempirical models considered here are shown to underestimate the isotropic polarizabilities of neutral molecules by approximately 30%. The semiempirical models also fail to adequately describe torsion profiles for the dimethyl phosphate anion, the nucleoside sugar ring puckers, and the rotations about the nucleoside glycosidic bond. The modeling of pentavalent phosphorus, particularly with thio substitutions often used experimentally as mechanistic probes, was problematic for all of the models considered. Analysis of the strengths and weakness of the models suggests that the creation of robust next‐generation models should emphasize the improvement of relative conformational energies and barriers, and nonbonded interactions. © 2015 Wiley Periodicals, Inc.     

Comparison of structural,thermodynamic, kinetic and mass transport properties of Mg2+ ion models commonly used in biomolecular simulations

The prevalence of Mg²⁺ ions in biology and their essential role in nucleic acid structure and function has motivated the development of various Mg²⁺ ion models for use in molecular simulations. Currently, the most widely used models in biomolecular simulations represent a nonbonded metal ion as an ion‐centered point charge surrounded by a nonelectrostatic pairwise potential that takes into account dispersion interactions and exchange effects that give rise to the ion's excluded volume. One strategy toward developing improved models for biomolecular simulations is to first identify a Mg²⁺ model that is consistent with the simulation force fields that closely reproduces a range of properties in aqueous solution, and then, in a second step, balance the ion–water and ion–solute interactions by tuning parameters in a pairwise fashion where necessary. The present work addresses the first step in which we compare 17 different nonbonded single‐site Mg²⁺ ion models with respect to their ability to simultaneously reproduce structural, thermodynamic, kinetic and mass transport properties in aqueous solution. None of the models based on a 12‐6 nonelectrostatic nonbonded potential was able to reproduce the experimental radial distribution function, solvation free energy, exchange barrier and diffusion constant. The models based on a 12‐6‐4 potential offered improvement, and one model in particular, in conjunction with the SPC/E water model, performed exceptionally well for all properties. The results reported here establish useful benchmark calculations for Mg²⁺ ion models that provide insight into the origin of the behavior in aqueous solution, and may aid in the development of next‐generation models that target specific binding sites in biomolecules. © 2015 Wiley Periodicals, Inc.     

Determination of the Failure Stresses for Fluid-filled Microcapsules that Rupture Near the Elastic Regime

The encapsulation of liquids within an external wall or shell is an important technology often utilized in the production of many commercial products. The mechanical characterization of such microcapsules is paramount in order to fully understand their performance in their target environment. Some microcapsules, with wall materials such as inorganic based compounds, rupture at small deformations, commonly near the elastic regime. The study herein presents a general methodology that enables calculation of the failure stresses leading to the elastic-like rupture of microcapsules under parallel compression testing. Two scenarios of failure, brittle and ductile, were considered. Analyses of the critical stresses present within the microcapsule wall during different degrees of fractional deformation were obtained using finite element modelling, resulting in similar values for both the brittle and ductile scenarios. The correlations presented were used to determine the failure stresses of tetraethoxyorthosilane-methyltrimethoxysilane (TEOS-MTMS) microcapsules with a model core oil, which are 11?C14?±?10?MPa. The data were further analyzed using Weibull distributions.     

Mechanistic Insights into RNA Transphosphorylation from Kinetic Isotope Effects and Linear Free Energy Relationships of Model Reactions

Phosphoryl transfer reactions are ubiquitous in biology and the understanding of the mechanisms whereby these reactions are catalyzed by protein and RNA enzymes is central to reveal design principles for new therapeutics. Two of the most powerful experimental probes of chemical mechanism involve the analysis of linear free energy relations (LFERs) and the measurement of kinetic isotope effects (KIEs). These experimental data report directly on differences in bonding between the ground state and the rate‐controlling transition state, which is the most critical point along the reaction free energy pathway. However, interpretation of LFER and KIE data in terms of transition‐state structure and bonding optimally requires the use of theoretical models. In this work, we apply density‐functional calculations to determine KIEs for a series of phosphoryl transfer reactions of direct relevance to the 2′‐O‐transphosphorylation that leads to cleavage of the phosphodiester backbone of RNA. We first examine a well‐studied series of phosphate and phosphorothioate mono‐, di‐ and triesters that are useful as mechanistic probes and for which KIEs have been measured. Close agreement is demonstrated between the calculated and measured KIEs, establishing the reliability of our quantum model calculations. Next, we examine a series of RNA transesterification model reactions with a wide range of leaving groups in order to provide a direct connection between observed Brønsted coefficients and KIEs with the structure and bonding in the transition state. These relations can be used for prediction or to aid in the interpretation of experimental data for similar non‐enzymatic and enzymatic reactions. Finally, we apply these relations to RNA phosphoryl transfer catalyzed by ribonuclease A, and demonstrate the reaction coordinate–KIE correlation is reasonably preserved. A prediction of the secondary deuterium KIE in this reaction is also provided. These results demonstrate the utility of building up knowledge of mechanism through the systematic study of model systems to provide insight into more complex biological systems such as phosphoryl transfer enzymes and ribozymes.     

A continuous-flow synthesis of annulated and polysubstituted furans from the reaction of ketones and α-haloketones

A synthesis of di-, tri- and tetra-substituted furans from reaction of the corresponding ketones and α-haloketones with LiHMDS is reported. Reaction under continuous-flow conditions gave increased yields and removed the need for external cooling when compared to the unoptimised batch conditions.     

Reagent concentration effects in the REM resin solid phase synthesis of tertiary amines

The use of reagent concentration has resulted in increased rates for all stages of the REM resin synthesis of tertiary amines. These increases in rate translate into faster reaction times, higher yields and lower reagent consumption. Of the methods examined, the most successful was the use of perfluorous solvents, either alone or with a small amount of organic co-solvent.     

Investigations of alkali doped Fe2O3--V2O5 catalysts by transmission and conversion electron Mössbauer spectroscopy

Fe₂O₃--V₂O₅ catalysts doped with Cs₂SO₄ (molar ratio: V:Fe:Cs=1:0.74:0.06) were found to be a rather inhomogeneous mixture of various crystalline and amorphous iron vanadate phases. After calcination in air the catalyst was divided into three different parts which were analyzed separately revealing the formation of FeVO₄ in the top and bottom fraction of the crucible and Fe₂V₄O₁₃ in the middle fraction. As compared to the well crystallized FeVO₄ reference sample, the quadrupole splittings of FeVO₄ in the Cs-doped catalysts were larger pointing to more distorted iron sites which were assumed to be responsible for high catalytic selectivities. In contrast, the quadrupole splittings of FeVO₄ in the less selective K- and Rb-doped Fe₂O₃--V₂O₅ catalysts were smaller. Additional components in the bottom fraction were also α-Fe₂O₃ and Fe_1-xS. As indicated by the CEMS spectra the latter is located preferentially on the surface of the catalyst particles. This revised version was published online in August 2006 with corrections to the Cover Date.     

Reactivity of 3-alkyl-4-arylazomethylene-3,4-dihydro-1,2,3-benzotriazines in protic solvents: 1,4-Addition reactions and dimroth rearrangement

3-Alkyl-4-arylazomethylene-3,4-dihydro-1,2,3-benzotriazines 5a and 5b undergo facile 1,4-addition of methanol or ethanol to afford stable crystalline hydrazones, 6 and 8 which have been characterised by spectroscopic analysis. In particular, the nmr spectrum of 8 shows novel features due to the diastereotopic nature of the CH₂ protons in the two O-ethyl groups. Compound 5b shows a property unique to the compounds in this series; refluxing this arylazomethylenetriazine in ethanol affords a rearranged product, characterised as the 1-aryl-2-cinnolinylhydrazine ( 9 ). The formation of 9 is rationalised as a ring opening-ring closure process analogous to the Dimroth rearrangement. The cinnoline 9 displays some novel chemistry arising from the facility of the arylhydrazino substituent to react with acid to give a fragmentation product, 3-methylindazole ( 7 ).     

QSO metal-line absorbers: The key to large-scale structure?

A study of the spatial autocorrelation of heavy-element-containing absorption systems in QSOs has shown strong clustering. Based on this correlation, it is proposed that more data may facilitate study of large-scale structure at larger scales and earlier epochs than previously possible. It may be possible to measure the slope of the primordial power spectrum, and set a new lower bound on the mass density of the universe in nonrelativistic species, including the unknown dark matter, whether or not it is baryonic.