Chemical promenades: Exploring potential-energy surfaces with immersive virtual reality

The virtual-reality framework AVATAR (Advanced Virtual Approach to Topological Analysis of Reactivity) for the immersive exploration of potential-energy landscapes is presented. AVATAR is based on modern consumer-grade virtual-reality technology and builds on two key concepts: (a) the reduction of the dimensionality of the potential-energy surface to two process-tailored, physically meaningful generalized coordinates, and (b) the analogy between the evolution of a chemical process and a pathway through valleys (potential wells) and mountain passes (saddle points) of the associated potential energy landscape. Examples including the discovery of competitive reaction paths in simple A + BC collisional systems and the interconversion between conformers in ring-puckering motions of flexible rings highlight the innovation potential that augmented and virtual reality convey for teaching, training, and supporting research in chemistry.     

Kinetic Isotope Effect as a Tool To Investigate the Oxygen Reduction Reaction on Pt-based Electrocatalysts – Part II: Effect of Platinum Dispersion

We investigated the oxygen reduction reaction (ORR) mechanism on Pt nanoparticles (NPs) dispersed on several carbon blacks with various physicochemical properties (i. e. specific surface ranging from 80 to 900 m² g⁻¹, different graphitization degree, etc.). Using the kinetic isotope effect (KIE) along with various electrochemical characterizations, we determined that the rate determining step (RDS) of the ORR is a proton-independent step when the density of Pt NPs on the surface of the carbon support is high. Upon decrease of the density of Pt NPs on the surface, the RDS of the ORR starts involving a proton, as denoted by an increase of the KIE >1. This underlined the critical role played by the carbon support in the oxygen reduction reaction electrocatalysis by Pt supported on high surface area carbon.     

Optimization of the HPLC enantioseparation of 3,3′‐dibromo‐5,5′‐disubstituted‐4,4′‐bipyridines using immobilized polysaccharide‐based chiral stationary phases

The HPLC enantioseparation of nine atropisomeric 3,3′,5,5′‐tetrasubstituted‐4,4′‐bipyridines was performed in normal and polar organic (PO) phase modes using two immobilized polysaccharide‐based chiral columns, namely, Chiralpak IA and Chiralpak IC. The separation of all racemic analytes, the effect of the chiral selector, and mobile phase (MP) composition on enantioseparation and the enantiomer elution order (EEO) were studied. The beneficial effect of nonstandard solvents, such as tetrahydrofuran (THF), dichloromethane (DCM), and methyl t‐butyl ether on enantioseparation was investigated. All selected 4,4′‐bipyridines were successfully enantioseparated on Chiralpak IA under normal or PO MPs with separation factors from 1.14 to 1.70 and resolutions from 1.3 to 6.5. Two bipyridines were enantioseparated at the multimilligram level on Chiralpak IA. Differently, Chiralpak IC was less versatile toward the considered class of compounds and only five bipyridines out of nine could be efficiently separated. In particular, on these columns, the ternary mixture n‐heptane/THF/DCM (90:5:5) as MP had a positive effect on enantioseparation. An interesting phenomenon of reversal of the EEO depending on the composition of the MP for the 3,3′‐dibromo‐5,5′‐bis‐(E)‐phenylethenyl‐4,4′‐bipyridine along with an exceptional enantioseparation for the 3,3′‐dibromo‐5,5′‐bis‐ferrocenylethynyl‐4,4′‐bipyridine (α = 8.33, R_s = 30.6) were observed on Chiralpak IC.     

Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines

A mixed parallel scheme that combines message passing interface (MPI) and multithreading was implemented in the AutoDock Vina molecular docking program. The resulting program, named VinaLC, was tested on the petascale high performance computing (HPC) machines at Lawrence Livermore National Laboratory. To exploit the typical cluster‐type supercomputers, thousands of docking calculations were dispatched by the master process to run simultaneously on thousands of slave processes, where each docking calculation takes one slave process on one node, and within the node each docking calculation runs via multithreading on multiple CPU cores and shared memory. Input and output of the program and the data handling within the program were carefully designed to deal with large databases and ultimately achieve HPC on a large number of CPU cores. Parallel performance analysis of the VinaLC program shows that the code scales up to more than 15K CPUs with a very low overhead cost of 3.94%. One million flexible compound docking calculations took only 1.4 h to finish on about 15K CPUs. The docking accuracy of VinaLC has been validated against the DUD data set by the re‐docking of X‐ray ligands and an enrichment study, 64.4% of the top scoring poses have RMSD values under 2.0 Å. The program has been demonstrated to have good enrichment performance on 70% of the targets in the DUD data set. An analysis of the enrichment factors calculated at various percentages of the screening database indicates VinaLC has very good early recovery of actives. © 2013 Wiley Periodicals, Inc.     

Combined use of three forms of chiroptical spectroscopies in the study of the absolute configuration and conformational properties of 3-phenylcyclopentanone, 3-phenylcyclohexanone,and 3-phenylcycloheptanone

Three forms of chiroptical spectroscopies, electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and optical rotatory dispersion (ORD) have been employed to study the configuration and conformational properties of the three molecules: (S)-3-phenylcyclopentanone, (S)-3-phenylcyclohexanone, and (S)-3-phenylcycloheptanone (including (S)-3-phenylcyclopentanone-2,2,5,5-d₄ and (S)-3-phenylcyclohexanone-2,2,6,6-d₄). ECD and VCD spectra in the mid-IR for the three molecular systems are marginally dependent on fine conformational details, as interpreted in terms of standard DFT computational methods, with common spectroscopic features to the three systems clearly identified. Accounting for vibronic coupling mechanisms reproduces the structuring of ECD n→π^∗ band. The ORD curves are quite similar for the three types of molecules, but their interpretation highlights a crucial role played by conformations of the cycloalkanone ring in the case of (S)-3-phenylcycloheptanone. The same conclusions are reached by considering the VCD spectra in the CH-stretching region.     

Enzymatically synthesized polyaniline film deposition studied by simultaneous open circuit potential and electrochemical quartz crystal microbalance measurements

The chemical and enzymatic deposition of polyaniline (PANI) films by in situ polymerization was studied and the resulting films were characterized. The film formation and polymerization processes were simultaneously monitored by the evolution of the open circuit potential and quartz-crystal microbalance measurements. Different substrates, such as Indium-Tin oxide electrodes and gold-coated quartz-crystal electrodes were used as substrates for PANI deposition. Electroactive PANI films were successfully deposited by in situ enzymatic polymerization at low oxidation potential. The electrogravimetric response of the enzymatically deposited PANI film was studied by cyclic voltammetry in monomer-free acidic medium. The morphology of the films was observed by scanning electron microscopy, revealing a granular structure in enzymatically deposited PANI. The PANI films were also characterized by thermogravimetric analysis, electrochemical impedance spectroscopy, and X-ray photoelectron and Fourier-transformed infrared spectroscopy. The simultaneous use of quartz crystal microbalance and open circuit potential is presented as a very useful technique to monitor enzymatic reactions involving oxidoreductases.     

Mass spectrometric characterization of two novel inflammatory peptides from the venom of the social wasp Polybia paulista

The social wasp P. paulista is relatively common in southeast Brazil causing many medically important stinging incidents. The seriousness of these incidents is dependent on the amount of venom inoculated by the wasps into the victims, and the characteristic envenomation symptoms are strongly dependent on the types of peptides present in the venom. In order to identify some of these naturally occurring peptides available in very low amounts, an analytical protocol was developed that uses a combination of reversed-phase and normal-phase high-performance liquid chromatography (HPLC) of wasp venom for peptide purification, with matrix-assisted laser desorption/ionization time-of-flight post-source decay mass spectrometry (MALDI-Tof-PSD-MS) and low-energy collision-induced dissociation (CID) in a quadrupole time-of-flight tandem mass spectrometry (QTof-MS/MS) instrument for peptide sequencing at the sub-picomole level. The distinction between Leu and Ile was achieved both by observing d-type fragment ions obtained under CID conditions and by comparison of retention times of the natural peptides and their synthetic counterparts (with different combinations of I and/or L at N- and C-terminal positions). To distinguish the isobaric residues K and Q, acetylation of peptides was followed by Q-Tof-MS analysis. The primary sequences obtained were INWLKLGKMVIDAL-NH(2) (MW 1611.98 Da) and IDWLKLGKMVMDVL-NH(2) (MW 1658.98 Da). Micro-scale bioassay protocols characterized both peptides as presenting potent hemolytic action, mast cell degranulation, and chemotaxis of polymorphonucleated leukocyte (PMNL) cells. The primary sequences and the bioassay results suggest that these toxins constitute members of a new sub-class of mastoparan toxins, directly involved in the occurrence of inflammatory processes after wasp stinging.     

Thermoresponsive hydrogels from symmetrical triblock copolymers poly(styrene-block-(methoxy diethylene glycol acrylate)-block-styrene)

A series of symmetrical, thermo-responsive triblock copolymers was prepared by reversible addition-fragmentation chain transfer (RAFT) polymerization, and studied in aqueous solution with respect to their ability to form hydrogels. Triblock copolymers were composed of two identical, permanently hydrophobic outer blocks, made of low molar mass polystyrene, and of a hydrophilic inner block of variable length, consisting of poly(methoxy diethylene glycol acrylate) PMDEGA. The polymers exhibited a LCST-type phase transition in the range of 20-40 °C, which markedly depended on molar mass and concentration. Accordingly, the triblock copolymers behaved as amphiphiles at low temperatures, but became water-insoluble at high temperatures. The temperature dependent self-assembly of the amphiphilic block copolymers in aqueous solution was studied by turbidimetry and rheology at concentrations up to 30 wt %, to elucidate the impact of the inner thermoresponsive block on the gel properties. Additionally, small-angle X-ray scattering (SAXS) was performed to access the structural changes in the gel with temperature. For all polymers a gel phase was obtained at low temperatures, which underwent a gel-sol transition at intermediate temperatures, well below the cloud point where phase separation occurred. With increasing length of the PMDEGA inner block, the gel-sol transition shifts to markedly lower concentrations, as well as to higher transition temperatures. For the longest PMDEGA block studied (DP(n) about 450), gels had already formed at 3.5 wt % at low temperatures. The gel-sol transition of the hydrogels and the LCST-type phase transition of the hydrophilic inner block were found to be independent of each other.     

Influence of nanodispersed boehmite on polypropylene photooxidation

Nanocomposites containing pure or organically modified nanoboehmites of different sizes were prepared by melt compounding with polypropylene. The samples were UV light irradiated in artificial accelerated conditions representative of solar irradiation (λ > 300 nm) at 60 °C in air. The chemical modifications resulting from photooxidation were followed by IR and UV-visible spectroscopies. The presence of pristine nanoboehmites was shown to change the rate of oxidation of polypropylene by reducing the oxidation induction period due to the presence of residual processing antioxidant. The differences of the oxidation induction periods between the nanocomposites and the pristine polymer disappear after solvent extraction of the antioxidant. The inefficiency of traditional antioxidant in retarding the photooxidation of polypropylene containing nanodispersed boehmite is proved. Antioxidant migration to the boehmite surface induced by the preferential interaction with the polar filler is proposed as an explanation. The oxidative behaviour of the organically modified boehmites was shown to depend on the type of organic substituent. p-Toluenesulfonate reduces the adsorption of antioxidants while the presence of a long-chain alkyl benzensulfonate increased the oxidation rate by generation of radical initiators.     

Chiral enrichment of serine via formation,dissociation, and soft-landing of octameric cluster ions

Chiral enrichment of serine is achieved in experiments that involve formation of serine octamers starting from non-racemic serine solutions. Serine octamers were generated by means of electrospray and sonic spray ionization of aqueous solutions of d(3)-L-serine (108 Da) and D-serine (105 Da) having different molar ratios of enantiomers. A cyclic process involving the formation of chirally-enriched octameric cluster ions and their dissociation, viz. Ser(1) --> Ser(8) --> Ser(1), allows serine monomers to be regenerated with increased enantiomeric excess as shown in two types of experiments: (1) Chiral enrichment in serine was observed in MS/MS/MS experiments in a quadrupole ion trap in which the entire distribution of serine octamers formed from non-racemic solutions was isolated, collisionally activated, and fragmented. Monomeric serine was regenerated with increased enantiomeric excess upon dissociation of octamers when compared with the enantiomeric composition of the original solution. (2) Chiral enrichment was observed in the products of soft-landing of mass-selected protonated serine octamers. These ions were generated by means of electrospray or sonic spray ionization, mass selected, and collected on a gold surface using ion soft-landing. Chiral enrichment of the soft-landed serine was established by redissolving the recovered material and comparing the intensities of protonated molecular ions of d(3)-L-serine and D-serine after APCI-MS analysis. Both of these experiments showed comparable results, suggesting that formation of serine octamers depends only on the enantiomeric composition of the serine solution and that the magnitude of the chiral preference is intrinsic to octamers formed from solutions of given chiral composition.