Single-layer MoS2 is proving to be a versatile material for a wide variety of electronic, optical, and chemical applications. Sulfur depletion, without destabilization of the single layer, is ...considered a prudent way for making the basal plane of the layer catalytically active. Based on the results of our density-functional-theory examination of vacancy structures on one side of an MoS2 layer, we show that the formation energy per sulfur vacancy is the lowest (energetically favorable) when the vacancies form a row and that the longer the row, the lower the formation energy. In addition, we find that the lowest energy barrier for the diffusion of sulfur vacancy at the row structures through the exchange of a vacancy with a nearby sulfur atom is 0.79 eV and that this barrier increases as the row elongates. We also evaluate the propensity for catalytic activity of an MoS2 layer with two types of sulfur-vacancy structures (row and patch) and find the energetics for alcohol synthesis from syngas to be more favorable for the layer with a sulfur-vacancy patch.
The relation between lignin sequence and its 3D structure Rawal, Takat B.; Zahran, Mai; Dhital, Brittiny ...
Biochimica et biophysica acta. G, General subjects/Biochimica et biophysica acta. General subjects (Online),
20/May , Letnik:
1864, Številka:
5
Journal Article
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Lignin, the second most abundant biopolymer on earth, plays a major structural role in plants, conferring mechanical strength and regulating water conduction. Understanding the three-dimensional ...structure of lignin is important for fundamental reasons as well as engineering plants towards lignin valorization. Lignin lacks a specific primary sequence, making its average chemical composition the focus of most recent studies. However, it remains unclear whether the 3D structure of lignin molecules depends on their sequence.
We performed all-atom molecular dynamics simulation of three S/G-lignin molecules with the same average composition but different sequence.
A detailed statistical analysis of the radius of gyration and relative shape anisotropy reveals that the lignin sequence has no statistically significant effect on the global three-dimensional structure. We found however, that homopolymers of C-lignin with the same molecular weight have smaller radii of gyration than S/G-lignin. We attribute this to lower hydroxyl content of C-lignin, which makes it more compact and rigid.
The 3D structure of lignin is influenced by the overall content of monomeric units and interunit linkages and not by its precise primary sequence.
Lignin is assumed to not have a well-defined primary structure. The results presented here demonstrate there are no significant differences in the global 3D structure of lignin molecules with the same average composition but different primary sequence.
•Lignin does not have a well-defined primary structure or sequence.•The radii of gyration of models of lignin with different sequence but the same average composition are statistically similar.•C-lignin, because of its lower hydroxyl content, has smaller size than S/G-lignin with the same molecular weight.
Single-layer, defect-laden hexagonal boron nitride (
dh
-BN) is attracting a great deal of attention for its diverse applications: catalysis on the one hand, and single photon emission on the other. ...As possible probes for identifying some common defects in single-layer h-BN, we present results of
ab initio
calculations for the adsorption and vibrational characteristics of syngas molecules (H
2
, CO, CO
2
) on
dh
-BN containing one of four types of defects: nitrogen vacancy (V
N
), boron vacancy (V
B
), Stone-Wales defect (SW), and nitrogen substituted by boron (B
N
). Through a comparative examination of adsorption features, charge transfer, electronic structure, and vibrational spectrum, we obtain a deep understanding of the interaction of these molecules with
dh
-BN and the role of the defect states. We find that while CO, CO
2
and atomic hydrogen chemisorb, molecular H
2
physisorbs on
dh
-BN with the four considered defect types. V
N
and V
B
show strong affinity for CO and CO
2
since the defect states induced by them lie close to the Fermi level. SW does not favor adsorption of these small molecules, as the process for each is endothermic. In the case of B
N
, CO adsorbs strongly but CO
2
only weakly. Vibrational frequencies of notable modes localized at the adsorbed molecules are analyzed and suggested as measures for identification of the defect type. Through a simple comparison of adsorption characteristics of the molecules on these defects, we propose
dh
-BN with V
N
to be a good catalyst candidate for CO
2
hydrogenation.
Through insights from first-principles calculations, we predict defect-laden
h
-BN, particularly with N vacancy, to have good propensity toward CO and CO
2
hydrogenation. Vibrational frequencies of CO and CO
2
are proposed as identifiers of defect type.
The interaction of xylan, an abundant plant polysaccharide, with cellulose microfibrils is essential for secondary cell wall strength. A deeper understanding of these interactions is crucial both to ...improve our understanding of plant cell wall architecture and to design alternate strategies to overcome cellulose recalcitrance for the production of biofuels and sustainable biomaterials. Naturally occurring acetate or glucuronic acid substitutions on xylan have been shown to influence xylan-cellulose interactions. Here, we use unrestrained molecular dynamics simulations to determine the interactions with the (110) hydrophilic face of cellulose fibers of four different xylans. In the absence of cellulose, all xylans, independent of the substitution pattern, adopt a highly flexible threefold helical screw conformation. However, when xylan is spatially close to a cellulose surface 1,2 linked acetyl xylans (2AcX) adopt rigid twofold helical screw conformations. The 2AcX conformations are primarily stabilized by interactions between the acetylated oxygen and the glycosidic linkage with C-O6 of cellulose. In contrast, the glycosidic oxygens and acetyl decorations for 1,3 linked acetyl groups (3AcX) are oriented away from the cellulose surface and the 3AcX xylans maintain threefold helical screw conformations on the cellulose surface. Our results show that evenly spaced chemical functionalization (with acetyl groups) and the position of substitution (1,2) on xylan backbone play key roles in tuning the xylan-cellulose interactions to stabilize the twofold helical screw conformations of xylan on the cellulose surface. A comparison with previous experimental findings further suggests that 1,2 substitutions induce twofold helical screw conformations of xylan on the cellulose surface irrespective of the chemical nature of the substituent, while 1,3 substitutions primarily bind lignin in threefold helical screw conformations rather than cellulose in plant cell walls.
We present results of ab initio density functional theory (DFT) based calculations of the geometry, electronic structure, and reactivity of subnanometer-sized (29-atom) transition metal nanoparticles ...(NPs) (Cu29, Ag29, and Au29) supported on single-layer MoS2. As compared to its pristine form, defect-laden MoS2 (with a S vacancy row) has relatively larger effect on the above properties of the NPs. The NPs bind more strongly on defect-laden than on pristine MoS2 (in the order Cu29 > Ag29 > Au29), confirming the important role of vacancies in stabilizing the NPs on the support. The presence of vacancies also leads to an increase in charge transfer from the NPs to MoS2 (with the same elemental trend as for their binding energy) and to a shift of the d-band center of the NPs further toward the Fermi level, in turn influencing their propensity toward chemical activity. We examine the adsorption and dissociation of O2 as the prototype reactions and find that there is no barrier for O2 to adsorb on top of an atom at the NP apex, where the frontier orbitals are localized, and that the dissociation channel proceeds through a chemisorbed state. The presence of the support leads to increase in the number of sites at which O2 can adsorb with similar binding energy (<0.1 eV difference). Interestingly, energy barriers for both dissociation and recombination of O2, when adsorbing at the NP apex, increase in the presence of the MoS2 support. However, since the increase in the barrier for recombination is much larger than for dissociation, the latter should be more favored. In particular, for defect-laden MoS2 supported Au29 the recombination faces a barrier of 1.36 eV whereas the dissociation does 0.5 eV, implying that the defect-laden support may significantly improve the catalytic performance of Au29 toward oxidation reaction.
We perform density functional theory (DFT) calculations of the energetics for several pathways associated with methanol partial oxidation (MPO) reaction on singly distributed Pd on ZnO (Pd1/ZnO) and ...use them in kinetic Monte Carlo (KMC) simulations for elucidating reaction mechanism. We compare these results for Pd1/ZnO with those obtained for the same set of reactions on a 32-atom Pd16Zn16 nanocluster. Our KMC simulations show that Pd1/ZnO offers high, temperature-dependent selectivity (∼93%) for H2 production and a moderate one (∼76%) for CO2, in good agreement with experiment (which reports 90 and 85%, respectively). On the other hand, Pd16Zn16 yields no selectivity for H2 but almost perfect, temperature-independent selectivity (∼100%) for CO2 and H2O, leading to full oxidation of methanol. The high activity of Pd1/ZnO for MPO can be credited to the singly distributed Pd sites and to the Pd-modified geometric and electronic structures of the neighboring Zn sites, and its high H2 selectivity may be related to the abundant supply of H atoms resulting from methanol decomposition on the surface. Pd loading has a decisive impact on adsorption and dissociation of methanol and oxygen. With higher Pd loadings, the activity of the Zn site alters in such a way that it provides weaker binding to methanol and stronger binding to O2, thereby resulting in facile O2 dissociation. Singly distributed Pd atoms not only serve as a more stable binding site for methanol than does Pd in Pd16Zn16 but also induce spontaneous CO2 formation and nearly spontaneous dissociation of H2O. In an alternate but slower pathway for production of CO2 involving HCOO* intermediate on Pd1/ZnO, the rate-limiting step is dissociation of H2COO*, followed by decomposition of HCOO* into CO2* and H*.
Here, we report that a cationic bimetallic site consisting of one Pd and three Zn atoms (Pd1Zn3) supported on ZnO (Pd1Zn3/ZnO) exhibits an extraordinarily high catalytic activity for the generation ...of H2 through methanol partial oxidation (MPO) that is 2–3 orders of magnitude higher than that of a metallic Pd–Zn site on Pd–Zn nanoalloy (Pd–Zn/ZnO). Computational studies uncovered that the positively charged Pd atom of the subnanometer Pd1Zn3 bimetallic site largely decreases the activation barrier for dehydrogenation of methanol as compared to a metallic Pd atom of Pd–Zn alloy, thus switching the rate-determining step of MPO from methanol dehydrogenation over a Pd–Zn alloy with high barrier to the O2 dissociation step on a cationic Pd1Zn3 site with a low barrier, which is supported by our kinetics studies. The significantly higher catalytic activity and selectivity for H2 production over a cationic bimetallic site suggest a new approach to design bimetallic catalysts.
A particularly promising approach to deconstructing and fractionating lignocellulosic biomass to produce green renewable fuels and high-value chemicals pretreats the biomass with organic solvents in ...aqueous solution. Here, neutron scattering and molecular-dynamics simulations reveal the temperature-dependent morphological changes in poplar wood biomass during tetrahydrofuran (THF):water pretreatment and provide a mechanism by which the solvent components drive efficient biomass breakdown. Whereas lignin dissociates over a wide temperature range (>25 °C) cellulose disruption occurs only above 150 °C. Neutron scattering with contrast variation provides direct evidence for the formation of THF-rich nanoclusters (Rg ∼ 0.5 nm) on the nonpolar cellulose surfaces and on hydrophobic lignin, and equivalent waterrich nanoclusters on polar cellulose surfaces. The disassembly of the amphiphilic biomass is thus enabled through the local demixing of highly functional cosolvents, THF and water, which preferentially solvate specific biomass surfaces so as to match the local solute polarity. A multiscale description of the efficiency of THF:water pretreatment is provided: matching polarity at the atomic scale prevents lignin aggregation and disrupts cellulose, leading to improvements in deconstruction at the macroscopic scale.
The detection of intermediate species and the correlation of their ultrafast dynamics with the morphology and electronic structure of a surface is crucial to fully understand and control ...heterogeneous photoinduced and photocatalytic reactions. In this work, the ultrafast photodissociation dynamics of CH3Br molecules adsorbed on variable-size Au clusters on MgO/Mo(100) is investigated by monitoring the CH3 + transient evolution using a pump–probe technique in conjunction with surface mass spectrometry. Furthermore, extreme-UV photoemission spectroscopy in combination with theoretical calculations is employed to study the electronic structure of the Au clusters on MgO/Mo(100). Changes in the ultrafast dynamics of the CH3 + fragment are correlated with the electronic structure of Au as it evolves from monomers to small nonmetallic clusters to larger nanoparticles with a metallic character. This work provides a new avenue to a detailed understanding of how surface-photoinduced chemical reactions are influenced by the composition and electronic structure of the surface.
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