l-Arabinose Conformers Adsorption on Ruthenium Surfaces: A DFT Study

Abstract

Adsorption of 5 L-arabinose tautomers – one acyclic and four cyclic (α and β, pyranose and furanose) species – on a ruthenium surface was studied as a precursor-process of the, nowadays more and more, industrially important sugar catalytic hydrogenation on metal surfaces in water medium. The study was mostly referred to a 37-atom metal catalyst fragment, even though border-effects on the adsorption processes were also checked employing a 61-atom metal fragment. In order to figure out conformational effects on the title process the tautomer flexibility was, at first, investigated by the genetic-algorithm based code Balloon, considering the conformational spaces of the different aquo tautomers. On the whole, 30 L-arabinose conformers, representing the complete conformational set (of a “realistic” water solution), were isolated by the genetic-algorithm based code Balloon. These were further refined at DFT level and then analyzed when interacting with a ruthenium surface, always at DFT level, by SIESTA. It was found that i) cyclic L-arabinose tautomers give rise to less strong adsorption than the acyclic tautomeric form; ii) L-arabinose molecules preferentially adsorb perpendicularly to the metallic surface; iii) one among the α-pyranose and one among the β-furanose derivatives are largely the most abundant adsorbed species; iv) the dominant L-arabinopyranose and\ud L-arabinofuranose surface configurations are clearly related to corresponding not-adsorbed species that preserve both conformations and intramolecular hydrogen bonds during their the adsorption. The consideration of the points above allowed us to pick out significant properties, characterizing L-arabinose adsorption on ruthenium

α-d-Glucopyranose Adsorption on a Pd30 Cluster Supported on Boron Nitride Nanotube

“…The first affects the interaction geometry of the two surface binding modes, the second conversely rules the occurrence of single or multiple adsorption on the two metallic planes. It is interesting to note that along the adsorption process, the conformation of a-D-glucopyranose is retained, irrespective of the implicated binding modes [7]. Very similar geometries and interaction energies are found if the a-D-glucopyranose adsorbs on the unsupported Pd 30 .…”

“…While early results showed that more than 700 conformations are possible [9], the D-glucose in water is found almost exclusively in the a closed pyranose form. Even considering that the conformational ensemble of the a-D-glucopyranose could be small if adsorbed on a metal surface as, for example, already found for similar sugars adsorbed on ruthenium [7], the number of different conformations to take into account in a systematic investigation would be prohibitively high. For this reason, in the present study we used only the most stable a-D-glucopyranose conformation obtained in gas phase by Corchado et al [6] through a combined molecular dynamics and DFT study.…”

Rational modifications on champion porphyrin dye SM315 using different electron-withdrawing moieties toward high performance dye-sensitized solar cells

“…The optimization of dye/(TiO 2 ) 38 systems was performed using the SIESTA ab initio package, [43][44][45] the reliability of which has been proved by lots of related investigations and could give a good balance between accuracy and computational cost. [46][47][48][49][50][51][52][53] The computational details about SIESTA are given in the ESI. † Based on the optimized geometries, the partial density of states (PDOS) profiles on TiO 2 were evaluated at the PCM-M06/SVP level of theory through single point calculations using the Gaussian code.…”

Conformation Analysis of Environmentally Friendly Insulating Gas C5-PFK

“…The molecule energy and structure of different conformers of C5-PFK molecule differ, which lead to the difference of required energy for decomposition during discharge or heating, and may also affect the transition state and decomposition pathway to some extent [20]- [22]. When C5-PFK molecule participates in the adsorption or chemical reactions on solid (metal materials or organic insulating material) surfaces, the C5-PFK conformers have different range of molecular frontier orbitals or adsorption site, which may influence the reaction mechanism between the gas-solid interface [23]- [25]. Therefore, conformation analysis of C5-PFK molecule has certain guiding significance for its further study.…”