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opencc-zeroJan 2020View details →

Data from: Fullerene-like structures of Cretaceous crinoids reveal topologically limited skeletal possibilities

In general there are few cases where numbers or types of possible phenotypes are known, although vast state spaces have been postulated. Rarely applied in this context, graph theory and topology enable enumeration of possible phenotypes and evolutionary transitions. Here, we generate polyhedral calyx graphs for the Late Cretaceous, stemless crinoids Marsupites testudinarius and Uintacrinus socialis (Uintacrinoidea Zittel 1879) revealing structural similarities to carbon fullerenes and fulleroids (respectively). The Uintacrinus calyx incorporates numerous plates (e.g. |V| ≥ 197), which are small, light, low-density and have 4 to 8 sides. Therefore, the corresponding number of possible plate arrangements, given by the number of polyhedral graphs, is large (>> 〖1×10〗^14). Graph vertices representing plates with sides > 6 introduce negative Gaussian curvature and topological instability. However, observed Uintacrinus graph cardinalities (|V|) do not allow more stable pentaradial configurations. In contrast, the Marsupites calyx dual graph has 17 faces that are pentagonal or hexagonal. Therefore, it is structurally identical to a carbon fullerene, specifically C30-D5h. Corresponding graph restrictions result in radical constraint to only three structural options. Further restriction to pentaradial symmetry allows only one possibility: the Marsupites phenotype. This robust, stable topology is consistent with adaptation to the predation pressures of the Mesozoic marine revolution. Consequently, the most plausible evolutionary pathway between unitacrinoid phenotypes was a mixed heterochronic trade-off to fewer, larger calyx plates. Therefore, topological limitations radically constrained uintacrinoid skeletal possibilities but thereby aided evolution of a novel adaptive phenotype.

opencc-zeroApr 2022View details →

DFT investigation on the application of pure and doped X12N12 (X = B and Al) fullerene-like nano-cages towards the adsorption of temozolomide

The sensitivity of pure and doped X12 N12 (X = B and Al) fullerene-like nano-cages (FLNs) toward the anticancer drug temozolomide (TMZ) is probed herein at DFT/M06-2X-D3/6-311G(d,p) theoretical level in both gas phase and water. A noticeable affinity of the FLNs toward TMZ was observed along with the negative gas-phase adsorption energies -1.37 and -2.09 eV for the most stable configurations of pure B12N12 and Al12N12 pristines, respectively. Considerable charge transfer from TMZ to the FLNs was also revealed via NBO analysis and the Hirshfeld atomic charges, making the dipole moment vector of the molecular complexes to be oriented from the nano-cages to the TMZ moiety. Furthermore, a percentage decrease in the HOMO-LUMO energy gap (ΔEg) of 38.09 and 17.72 % was obtained for the B12N12 and Al12N12 nano-cages, respectively. The percentage change in ΔEg was found to be reduced upon doping and solvation of the FLNs. Finally, a recovery time in vacuum ultraviolet light of 1.06 s is found for the complex with pure B12N12, which in addition to the above-mentioned parameters make this boron nitride cage the best sensor for TMZ, among the FLNs considered in the present work.

zenodo36/100

NEP potential training and testing files for monolayer quasi-hexagonal-phase fullerene (qHPF)

This dataset contains the force-field parameter files and reference dataset described in the manuscript "Atomistic insights into the mechanical anisotropy and fragility of monolayer fullerene networks using quantum mechanical calculations and machine-learning molecular dynamics simulations" (to be published). The format of nep.in file is compatible with the GPUMD 3.3.1 (https://github.com/brucefan1983/GPUMD/releases/tag/v3.3.1).

opencc-by-4.0Mar 2023View details →

zenodo36/100

Dataset: The Largest Fullerene

Dataset containing optimized structures of isolated, icosahedral fullerenes, multi-layer fullerene "onions", and stacked graphene layers, organized in folders after types. Graphene structures are also organized after numbers of stacked layers. Optimized using the AIREBO force field in LAMMPS. The file names contain the number of atoms in each structure, the allotrope type, and the force field used (AIREBO). Data consists of standard xyz-structure files with the following structure: <ul> <li>Line 1: Number of atoms in the file.</li> <li>Line 2: Comment line containing the potential energy of the optimized structure with the AIREBO force field together with the author list.</li> <li>Line 3 to end of file: Atomic symbol followed by Cartesian coordinates in units of Ångström (Å, 10-10 m).</li> </ul>

publicApr 2022View details →

DFT investigation on the application of pure and doped X12N12 (X = B and Al) fullerene-like nano-cages towards the adsorption of temozolomide

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publicFeb 2020View details →

Data from: Fullerene-like structures of Cretaceous crinoids reveal topologically limited skeletal possibilities

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NEP potential training and testing files for quasi-hexagonal-phase fullerene (QHPF) and face-centered-cubic bulk-phase fullerene (BPF)

This dataset contains the force-field parameter files and reference dataset described in the manuscript "Anisotropic and high thermal conductivity in monolayer quasi-hexagonal fullerene: A comparative study against bulk phase fullerene" (to be published). The format of nep.in file is compatible with the GPUMD 3.3.1 (https://github.com/brucefan1983/GPUMD/releases/tag/v3.3.1).

Interfaces of fullerene derivatives and additives with MAPbI3

The coordinates of interface models obtained and used for the analysis presented in this article(1) are available. Fullerene Derivatives are; the 2,5-(dimethyl ester) fulleropyrrolidine C60 (DMEC60) and the C70 isomer (DMEC70), and the [6,6]-phenyl-C61-butyric acid methyl ester (PCBMC60), and the C70 isomer (PCBMC70). Additives are; chlorobenzene (CB), methylammonium chloride (MACl), and sulfamic acid (SA). Each interface is the conformation of a minimum of the studied potential energy surface. (1) Montero-Alejo, A. L.; Barría-Cáceres, F.; Lodeiro, L.; Menéndez-Proupin, E. Effective Interfaces between Fullerene Derivatives and CH3NH3PbI3 to Improve Perovskite Solar Cell Performance. J. Phys. Chem. C 2023, 127 (1), 41–51. https://doi.org/10.1021/acs.jpcc.2c06499 .

Atomic structures derived from high-temperature and -pressure transformations from C60 fullerenes

These are XYZ files containing the atomic structures depicted in the high-temperature and high-pressure C60 phase diagram (figure 7) of this publication: <blockquote> Machine learning force fields based on local parametrization of dispersion interactions: Application to the phase diagram of C60 Heikki Muhli, Xi Chen, Albert P. Bartók, Patricia Hernández-León, Gábor Csányi, Tapio Ala-Nissila, and Miguel A. Caro Phys. Rev. B 104, 054106 (2021) <a href="https://doi.org/10.1103/PhysRevB.104.054106">https://doi.org/10.1103/PhysRevB.104.054106</a> </blockquote> The structures were generated with a general-purpose Gaussian approximation potential (GAP)  for carbon whose training database included a large number of C60 structures. Refer to the publication listed above for the details of the simulation and an analysis of the structures.