Exploring the energy landscapes of cyclic tetrapeptides with discrete path sampling

[Image: see text] Cyclic tetrapeptides are an important class of biologically active molecules that exhibit interesting conformational dynamics, with slow interconversion of several different structures. We present calculations on their energy landscapes using discrete path sampling. In acyclic peptides and large cyclic peptides, isomers containing cis-peptide groups are much less stable than the all-trans isomers and separated from them by large barriers. Strain in small cyclic peptides causes the cis and trans isomers to be closer in energy and separated by much lower barriers. If d-amino acids or proline residues are introduced, isomers containing cis-peptides become more stable than the all-trans structures. We also show that changing the polarity of the solvent has a significant effect on the energy landscapes of cyclic tetrapeptides, causing changes in the orientations of the peptide groups and in the degree of intramolecular hydrogen bonding

Visualizing energy landscapes with metric disconnectivity graphs

The visualization of multidimensional energy landscapes is important, providing insight into the kinetics and thermodynamics of a system, as well the range of structures a system can adopt. It is, however, highly nontrivial, with the number of dimensions required for a faithful reproduction of the landscape far higher than can be represented in two or three dimensions. Metric disconnectivity graphs provide a possible solution, incorporating the landscape connectivity information present in disconnectivity graphs with structural information in the form of a metric. In this study, we present a new software package, PyConnect, which is capable of producing both disconnectivity graphs and metric disconnectivity graphs in two or three dimensions. We present as a test case the analysis of the 69-bead BLN coarse-grained model protein and show that, by choosing appropriate order parameters, metric disconnectivity graphs can resolve correlations between structural features on the energy landscape with the landscapes energetic and kinetic properties

Anionic cobalt-platinum-ethynyl (CoPt–C₂H) metal-organic subnanoparticles:a DFT modeling study

Anionic CoPt-ethynyl metal-organic clusters have been investigated comprehensively. The lowest energetic of anionic ConPtm(ethynyl) clusters have been generally found as 3D structure but with low symmetrical point groups. Our results indicate that the most preferred dissociation channel of the studied clusters is Co atom ejection and the favorable dissociation channel is independent of cluster size. The anionic Pt5C2H cluster shows the highest chemical stability according to the HOMO-LUMO Gap analysis. The C2H generally prefers to bind on a bridge site with a few exceptions. The Co4−5 nanoparticles have a lengthening effect on the C≡C bond of the ethynyl molecule, which may be valuable for C≡C bond activation. In addition, the lowest and the highest vibrational frequencies are reported to guide further experimental studies

Pentameric PdAu and PdPt nanoparticles on the MgO(1 0 0) surface and their CO and O₂ adsorption properties

The surface mode of the Birmingham Cluster Genetic Algorithm (S-BCGA), which performs an unbiased global optimisation search for clusters adsorbed on a surface, has been employed for the global optimisation of noble metal pentamers on an MgO(1 0 0) substrate. The effect of element identity and alloying in surface-bound neutral subnanometre particles is calculated by energetic analysis of all compositions of supported 5-atom PdAu and PdPt clusters. Our results show that the binding strengths of the component elements to the surface are in the order Pt > Pd > Au. In addition, alloying Pd with Au and Pt is favorable for this size since excess energy calculations show a preference for bimetallic clusters for both cases. Furthermore, the electronic behaviour, which is intermediate between molecular systems and bulk metals allows tuning of the characteristics of particles in the subnanometre size range. The adsorption of CO and O2 probe molecules are also modelled and it is found that CO and O2 adsorption leads to a weakening of the cluster–surface interaction

O2 dissociation on M@Pt core-shell particles for 3d, 4d and 5d transition metals

Density functional theory calculations are performed to investigate oxygen dissociation on 38-atom truncated octahedron platinum-based particles. This study progresses our previous work (Jennings et al. Nanoscale, 2014, 6, 1153), where it was shown that flexibility of the outer Pt shell played a crucial role in facilitating fast oxygen dissociation. In this study, the effect of forming M@Pt (M core, Pt shell) particles for a range of metal cores (M = 3d, 4d, and 5d transition metals) is considered, with respect to O2 dissociation on the Pt(111) facets. We show that forming M@Pt particles with late transition metal cores results in favorable shell flexibility for very low O2 dissociation barriers. Conversely, alloying with early transition metals results in a more rigid Pt shell because of dominant M-Pt interactions, which prevent lowering of the dissociation barriers

State and regional performance of wheat varieties, Oklahoma 1979-83

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Bifunctional Electrocatalysts for Oxygen Reduction and Borohydride Oxidation Reactions Using Ag3Sn Nanointermetallic for the Ensemble Effect

2017-2018 > Academic research: refereed > Publication in refereed journal201805 bcrcAccepted ManuscriptOthersNational Natural Science Foundation of China; the Research Fund of State Key Laboratory of Solidification Processing in China; the Aeronautic Science Foundation Program of China; the Science and Technology Innovation Fund of Western Metal Materials; the Doctoral Fund of Ministry of Education of ChinaPublishe