Program Fullerene: A software package for constructing and analyzing structures of regular fullerenes

Electron-vibrational renormalization in fullerenes through ab initio and machine learning methods

The effect of nuclear vibrations on the electronic eigenvalues and the HOMO-LUMO gap is known for several kinds of carbon-based materials, like diamond, diamondoids, carbon nanoclusters, carbon nanotubes and others, like hydrogen-terminated oligoynes and polyyne. However, it has not been widely analysed in another remarkable kind which presents both theoretical and technological interest: fullerenes. In this article we present the study of the HOMO, LUMO and gap renormalizations due to zero-point motion of a relatively large number (163) of fullerenes and fullerene derivatives. We have calculated this renormalization using density-functional theory with the frozen-phonon method, finding that it is non-negligible (above 0.1 eV) for systems with relevant technological applications in photovoltaics and that the strength of the renormalization increases with the size of the gap. In addition, we have applied machine learning methods for classification and regression of the renormalizations, finding that they can be approximately predicted using the output of a computationally cheap ground state calculation. Our conclusions are supported by recent research in other systems.

Energy Decomposition Scheme for Rectangular Graphene Flakes

We show-to our own surprise-that total electronic energies for a family of m × n rectangular graphene flakes can be very accurately represented by a simple function of the structural parameters m and n with errors not exceeding 1 kcal/mol. The energies of these flakes, usually referred to as multiple zigzag chains Z(m,n), are computed for m, n < 21 at their optimized geometries using the DFTB3 methodology. We have discovered that the structural parameters m and n (and their simple algebraic functions) provide a much better basis for the energy decomposition scheme than the various topological invariants usually used in this context. Most terms appearing in our energy decomposition scheme seem to have simple chemical interpretations. Our observation goes against the well-established knowledge stating that many-body energies are complicated functions of molecular parameters. Our observations might have far-reaching consequences for building accurate machine learning models.

Gas-phase C60Hn+q (n = 0-4, q = 0,1) fullerenes and fulleranes: spectroscopic simulations shed light on cosmic molecular structures

The discovery of C60, C60+, and C70 in the interstellar medium has ignited a profound interest in the astrochemistry of fullerene and related systems. In particular, the presence of diffuse interstellar bands and their association with C60+ has led to the hypothesis that hydrogenated derivatives, known as fulleranes, may also exist in the interstellar medium and contribute to these bands. In this study, we systematically investigated the structural and spectroscopic properties of C60Hn+q (n = 0-4, q = 0,1) using an automated global minimum search and density functional theory calculations. Our results revealed novel global minimum structures for C60H2 and C60H4, distinct from previous reports. Notably, all hydrogenated fullerenes exhibited lower ionization potentials and higher proton affinities compared to C60. From an astrochemical perspective, our results exposed the challenges in establishing definitive spectroscopic criteria for detecting fulleranes using mid-infrared and UV-Vis spectroscopies. However, we successfully identified distinct electronic transitions in the near-infrared range that serve as distinctive signatures of cationic fulleranes. We strongly advocate for further high-resolution experimental studies to fully explore the potential of these transitions for the interstellar detection of fulleranes.

Engineering magic number Au19 and Au20 cage structures using electron withdrawing atoms

Gold cages are a subset of gold nanoparticles and these structures are of major interest due to their favourable physiochemical properties. In order for these structures to be useful in applications, they must be chemically stable. The objective of this research is to transform non-magic number cage structures into magic number cage structures by the addition of electron-withdrawing groups on the cages. The electronic properties for Au₁₉X and Au₂₀X₂ (X = F, Cl, Br, I) are calculated and observed. It is expected that the electron-withdrawing groups will remove the electron density from the gold cages and leave them positively charged. We first optimize the geometries of the initial gold cages and verify the structures are a local minima. From there, we attach our halogens to the gold cages and optimize the structures to determine the NICS values and HOMO-LUMO gaps. NICS values were found to be more negative when a more electronegative halogen was used. Calculations have found that Au₁₉F and Au₂₀F₂ have the most negative NICS values, indicating greater spherical aromaticity. Iodine, being the least electronegative atom, had the most positive NICS value and smallest HOMO-LUMO gap. All calculations are compared to the magic cluster Au₁₈ which satisfies Hirsh's 2(N + 1)² rule for n = 2.

Cage-size effects on the encapsulation of P2 by fullerenes

The classic pnictogen dichotomy stands for the great contrast between triply bonding very stable N₂ molecules and its heavier congeners, which appear as dimers or oligomers. A banner example involves phosphorus as it occurs in nature as P₄ instead of P₂ , given its weak π-bonds or strong σ-bonds. The P₂ synthetic value has brought Lewis bases and metal coordination stabilization strategies. Herein, we discuss the unrealized encapsulation alternative using the well-known fullerenes' capability to form endohedral and stabilize otherwise unstable molecules. We chose the most stable fullerene structures from C_n (n = 50, 60, 70, 80) and experimentally relevant from C_n (n = 90 and 100) to computationally study the thermodynamics and the geometrical consequences of encapsulating P₂ inside the fullerene cages. Given the size differences between P₂ and P₄ , we show that the fullerenes C₇₀ -C₁₀₀ are suitable cages to side exclude P₄ and host only one molecule of P₂ with an intact triple bond. The thermodynamic analysis indicates that the process is favorable, overcoming the dimerization energy. Additionally, we have evaluated the host-guest interaction to explain the origins of their stability using energy decomposition analysis.

Efficient and accurate density-based prediction of macromolecular polarizabilities

Accurately and efficiently predicting macromolecules' polarizabilities is an open problem. In this work, we employ a few simple density-based quantities from the information-theoretic approach (ITA) to predict polarizability of proteins. We first build quantitative structure/property relationships between molecular polarizabilities and ITA quantities. We then verify the broad applicability of ITA quantities for polarizability prediction for inorganic, organic, and biological systems with both localized and delocalized electronic structure. As a proof-of-concept application, we predict the molecular polarizabilities of complex proteins. Based on the linear regression equations for 20 natural amino acid residues, 400 dipeptides, and 8000 tripeptides, one then predicts the molecular polarizability of a larger peptide or even a protein once the molecular wavefunction is obtained. Because it is extremely costly to determine the wavefunction for a macromolecule like a protein, we propose to combine the ITA with the linear-scaling generalized energy-based fragmentation (GEBF) method to predict the macromolecular polarizability. In GEBF, the total molecular polarizability is obtained as a linear combination of the corresponding quantities from a series of small subsystems. We can predict them based on the subsystem wavefunction and linear regression equations rather than compute them from the nearly-intractable coupled-perturbed Hartree-Fock or Kohn-Sham equations for the whole macromolecule. Computational results showcase that the GEBF-ITA protocol should be an inexpensive yet accurate theoretical tool for predicting macromolecular polarizabilities.

Magnetically Induced Current Densities in π-Conjugated Porphyrin Nanoballs

Magnetically induced current densities (MICDs) of Zn-porphyrinoid nanostructures have been studied at the density functional theory level using the B3LYP functional and the def2-SVP basis set. Six of the studied Zn-porphyrinoid nanostructures consist of two crossing porphyrinoid belts, and one is a porphyrinoid nanoball belonging to the octahedral (O) point group. The Zn-porphyrin units are connected to each other via butadiyne linkers as in a recently synthesized porphyrinoid structure resembling two crossed belts. The MICDs are calculated using the gauge-including magnetically induced current method. Current-density pathways and their strengths were determined by numerically integrating the MICD passing through selected planes that cross chemical bonds or molecular rings. The current-density calculations show that the studied neutral molecules are globally nonaromatic but locally aromatic sustaining ring currents only in the individual porphyrin rings or around two neighboring porphyrins. The ring-current strengths of the individual porphyrin rings are 20% weaker than in Zn-porphyrin, whereas oxidation leads to globally aromatic cations sustaining ring currents that are somewhat stronger than for Zn-porphyrin.

Magnetically Induced Current Densities in Zinc Porphyrin Nanoshells

The molecular structures of porphyrinoid cages were obtained by constructing small polyhedral graphs whose vertices have degree-4. The initial structures were then fully optimized at the density functional theory (DFT) level using the generalized gradient approximation. Some of polyhedral vertices were replaced with Zn–porphyrin units and their edges were replaced with ethyne or butadiyne bridges or connected by fusing two neighboring Zn–porphyrin units. Molecule 1 is an ethyne-bridge porphyrinoid nanotube, whose ends are sealed with a Zn–porphyrin. Molecule 2 is the corresponding open porphyrinoid nanotube. Molecule 3 is a clam-like porphyrinoid cage, whose shells consist of fused Zn–porphyrins, and the two halves are connected via butadiyne bridges. Molecule 4 is a cross-belt of fused Zn–porphyrins, and molecule 5 is a cross-belt of Zn–porphyrins connected with butadiyne bridges. The magnetically induced current density of the optimized porphyrinoid cages was calculated for determining the aromatic character, the degree of aromaticity and the current-density pathways. The current-density calculations were performed at the DFT level with the gauge—including magnetically induced currents (GIMIC) method using the B3LYP hybrid functional and def2-SVP basis sets. Calculations of the current densities show that molecule 2 sustains a paratropic ring current around the nanotube, whereas sealing the ends as in molecule 1 leads to an almost nonaromatic nanotube. Fusing porphyrinoids as in molecules 3 and 4 results in complicated current-density pathways that differ from the ones usually appearing in porphyrinoids. The aromatic character of molecules 4 and 5 changes upon oxidation. The neutral molecule 4 is antiaromatic, whereas the dication is nonaromatic. Molecule 5 is nonaromatic, and its dication is aromatic.

Simulating fullerene polyhedral formation from planar precursors

The synthesis path of the C₆₀-Buckyball fullerene from a planar precursor developed by Scott et al. [Science, 2002, 295, 5559] is investigated with density functional theory (DFT) methods. Various theoretically possible closing paths are analysed with respect to structural and energetic properties. The initial geometries were obtained by geometric interpolation of a cardboard-like model comprising rigid rings connected by hinges, which were then fully optimized with a selection of DFT-functionals. Analysis of the fully optimised geometries shows remarkable stability of face planarity, bond lengths and bond angles for all studied geometries, indicating soundness of the "cardboard with hinges"-model for approximating reaction paths for molecules of this type. This raises hope for development of a force field description of fullerene precursor molecules that can aid in discovery and analysis of good precursor candidates for rational synthesis of new fullerenes.

Thermochemical stabilities of giant fullerenes using density functional tight binding theory and isodesmic-type reactions

We present a systematic assessment of the density functional tight binding (DFTB) method for calculating heats of formation of fullerenes with isodesmic-type reaction schemes. We show that DFTB3-D/3ob can accurately predict Δ_f H values of the 1812 structural isomers of C₆₀ , reproduce subtle trends in Δ_f H values for 24 isolated pentagon rule (IPR) isomers of C₈₄ , and predict Δ_f H values of giant fullerenes that are in effectively exact agreement with benchmark DSD-PBEP86/def2-QZVPP calculations. For fullerenes up to C₃₂₀ , DFTB Δ_f H values are within 1.0 kJ mol^-1 of DSD-PBEP86/def2-QZVPP values per carbon atom, and on a per carbon atom basis DFTB3-D/3ob yields exactly the same numerical trend of (Δ_f H [per carbon] = 722n^-0.72  + 5.2 kJ mol^-1 ). DFTB3-D/3ob is therefore an accurate replacement for high-level DHDFT and composite thermochemical methods in predicting of thermochemical stabilities of giant fullerenes and analogous nanocarbon architectures.

On correlation of hyperbolic volumes of fullerenes with their properties

We observe that fullerene graphs are one-skeletons of polyhedra, which can be realized with all dihedral angles equal to π /2 in a hyperbolic 3-dimensional space. One of the most important invariants of such a polyhedron is its volume. We are referring this volume as a hyperbolic volume of a fullerene. It is known that some topological indices of graphs of chemical compounds serve as strong descriptors and correlate with chemical properties. We demonstrate that hyperbolic volume of fullerenes correlates with few important topological indices and so, hyperbolic volume can serve as a chemical descriptor too. The correlation between hyperbolic volume of fullerene and its Wiener index suggested few conjectures on volumes of hyperbolic polyhedra. These conjectures are confirmed for the initial list of fullerenes.

All-Nitrogen Cages and Molecular Crystals: Topological Rules, Stability, and Pyrolysis Paths

We combined ab initio molecular dynamics with the intrinsic reaction coordinate in order to investigate the mechanisms of stability and pyrolysis of N4 ÷ N120 fullerene-like nitrogen cages. The stability of the cages was evaluated in terms of the activation barriers and the activation Gibbs energies of their thermal-induced breaking. We found that binding energies, bond lengths, and quantum-mechanical descriptors failed to predict the stability of the cages. However, we derived a simple topological rule that adjacent hexagons on the cage surface resulted in its instability. For this reason, the number of stable nitrogen cages is significantly restricted in comparison with their carbon counterparts. As a rule, smaller clusters are more stable, whereas the earlier proposed large cages collapse at room temperature. The most stable all-nitrogen cages are the N4 and N6 clusters, which can form the van der Waals crystals with densities of 1.23 and 1.36 g/cm3, respectively. The examination of their band structures and densities of electronic states shows that they are both insulators. Their power and sensitivity are not inferior to the modern advanced high-energy nanosystems.

ZZ Polynomials for Isomers of (5,6)-Fullerenes Cn with n = 20–50

A compilation of ZZ polynomials (aka Zhang–Zhang polynomials or Clar covering polynomials) for all isomers of small (5,6)-fullerenes Cn with n = 20–50 is presented. The ZZ polynomials concisely summarize the most important topological invariants of the fullerene isomers: the number of Kekulé structures K, the Clar number Cl, the first Herndon number h1, the total number of Clar covers C, and the number of Clar structures. The presented results should be useful as benchmark data for designing algorithms and computer programs aiming at topological analysis of fullerenes and at generation of resonance structures for valence-bond quantum-chemical calculations.

Fullerene Thermochemical Stability: Accurate Heats of Formation for Small Fullerenes, the Importance of Structural Deformation on Reactivity, and the Special Stability of C60

We have used quantum chemistry computations, in conjunction with isodesmic-type reactions, to obtain accurate heats of formation (HoFs) for the small fullerenes C₂₀ (2358.2 ± 8.0 kJ mol^-1), C₂₄ (2566.2 ± 7.6), and the lowest-energy isomers of C₃₂ (2461.1 ± 15.4), C₄₂ (2629.0 ± 20.5), and C₅₄ (2686.2 ± 25.3). As part of this endeavor, we have also obtained accurate HoFs for several medium-sized molecules, namely 216.6 ± 1.4 for fulvene, 375.5 ± 1.5 for pentalene, 670.8 ± 2.9 for acepentalene, and 262.7 ± 2.5 for acenaphthylene. We combine the energies of the small fullerenes and previously obtained energies for larger fullerenes (from C₆₀ to C₆₀₀₀) into a full picture of fullerene thermochemical stability. In general, the per-carbon energies can be reasonably approximated by the "R+D" model that we have previously developed [Chan et al. J. Chem. Theory Comput. 2019, 15, 1255-1264], which takes into account Resonance and structural Deformation factors. In a case study on C₅₄, we find that most of the high-deformation-energy atoms correspond to the sites of the C-Cl bond in the experimentally captured C₅₄Cl₈. In another case study, we find that C₆₀ has the lowest value for the maximum local-deformation energy when compared with similar-sized fullerenes, which is consistent with its "special stability". These results are indicative of structural deformation playing an important role in the reactivity of fullerenes.

Bootstrap Embedding For Large Molecular Systems

Recent developments in quantum embedding theories have provided attractive approaches to correlated calculations for large systems. In this work, we extend our previous work [J. Chem. Theory Comput. 2019, 15, 4497-4506; J. Phys. Chem. Lett. 2019, 10, 6368-6374] on bootstrap embedding (BE) to enable correlated ab initio calculations at the coupled cluster with singles and doubles (CCSD) level for large molecules. We introduce several new algorithmic developments that significantly reduce the computational cost of BE, while maintaining its accuracy. The resulting implementation scales as O(N³) for the integral transform and O(N) for the CCSD calculation. Numerical results on a series of conjugated molecules suggest that BE with reasonably sized fragments can recover more than 99.5% of the total correlation energy of a full CCSD calculation, while the required computational resources (time and storage) compare favorably to one popular local correlation scheme: domain localized pair natural orbital (DLPNO). The largest BE calculation in this work involves ∼2900 basis functions and can be performed on a single node with 16 CPU cores and 64 GB of memory in a few days. We anticipate that these developments represent an important step toward the application of BE to solve practical problems.

How to Stabilize a Heptagon-Containing C80 Cage by Endohedral Derivation

Nonclassical fullerene is a new member of the fullerene family. In the present work, a systematic investigation on La_xSc_3-xN@C₈₀ (x = 0-3) covering both classical and nonclassical C₈₀ cages was performed utilizing density functional theory combined with statistical mechanics. At absolute zero, LaSc₂N@Hept(6)-C_s(2)-C₈₀ with a heptagon-containing nonclassical carbon is the second most stable isomer, whereas at the temperature range of endohedral metallofullerene (EMF) formation, due to the large vibrational frequencies, LaSc₂N@Hept(6)-C_s(2)-C₈₀ is the third most abundant isomer, and its mole fraction is very low, accounting for the low experimental yield of LaSc₂N@Hept(6)-C_s(2)-C₈₀; La₂ScN@Hept(6)-C_s(2)-C₈₀, and La₃N@Hept(6)-C_s(2)-C₈₀ are the overwhelming isomers of the corresponding series, but compared with the cases of Sc₃N@C₈₀ and LaSc₂N@C₈₀, La₂ScN and La₃N clusters suffer much larger constraints from the C₈₀ cages, perhaps preventing the synthesis of La₂ScN@C₈₀ and La₃N@C₈₀ species. Because of the large mole fractions and large electron donation and back-donation of La₂ScN@Hept(6)-C_s(2)-C₈₀ and La₃N@Hept(6)-C_s(2)-C₈₀, it can be inferred that La₂ScN and La₃N clusters may be used to stabilize some other larger nonclassical fullerene cages. This work will provide useful insights into the origins of stabilization of nonclassical fullerene cages by endohedral derivation and guidelines for synthesis EMF with nonclassical cages.

The Eigenproblem Translated for Alignment of Molecules

Molecular conformation as a subproblem of the geometrical shaping of the molecules is essential for the expression of biological activity. It is well known that from the series of all possible sugars, those that are most naturally occurring and usable by living organisms as a source of energy—because they can be phosphorylated by hexokinase, the first enzyme in the glycolysis pathway—are D-sugars (from the Latin dextro). Furthermore, the most naturally occurring amino acids in living cells are L-sugars (from the Latin laevo). However, a problem arises in dealing with the comparison of their conformers. One alternative way to compare sugars is via their molecular alignment. Here, a solution to the eigenproblem of molecular alignment is communicated. The Cartesian system is rotated, and eventually translated and reflected until the molecule arrives in a position characterized by the highest absolute values of the eigenvalues observed on the Cartesian coordinates. The rotation alone can provide eight alternate positions relative to the reflexes of each coordinate.

A Simple Model for Relative Energies of All Fullerenes Reveals the Interplay between Intrinsic Resonance and Structural Deformation Effects in Medium-Sized Fullerenes

Fullerenes are sheets of sp² carbon atoms wrapped around to form spheres. With this simple consideration, we have in the present study devised and (with over 3600 DFT data points) successfully validated a simple model, termed R+D, for estimating the relative energies of fullerenes. This model contains a resonance component to account for the intrinsic differences between the π-energies of different fullerenes, and a deformation component for treating the distortions from planarity. Notably, we find that both terms (and they alone) are required to obtain good relative energies, which lends support to the formulation of the R+D model. An interesting finding is that for some medium-sized IPR fullerenes, their isomers show similar variations in the two components. We deduce that these fullerenes may represent a good opportunity for tuning molecular properties for practical applications. We hope that the promising results of the present study will encourage further investigations into fullerenes from a fundamental perspective.

Aromaticity, Coulomb repulsion, π delocalization or strain: who is who in endohedral metallofullerene stability?

Three different models for endohedral metallofullerene structure prediction are compared, revealing the physical origin of the stability of these compounds.

Classification of self-assembling protein nanoparticle architectures for applications in vaccine design

We introduce here a mathematical procedure for the structural classification of a specific class of self-assembling protein nanoparticles (SAPNs) that are used as a platform for repetitive antigen display systems. These SAPNs have distinctive geometries as a consequence of the fact that their peptide building blocks are formed from two linked coiled coils that are designed to assemble into trimeric and pentameric clusters. This allows a mathematical description of particle architectures in terms of bipartite (3,5)-regular graphs. Exploiting the relation with fullerene graphs, we provide a complete atlas of SAPN morphologies. The classification enables a detailed understanding of the spectrum of possible particle geometries that can arise in the self-assembly process. Moreover, it provides a toolkit for a systematic exploitation of SAPNs in bioengineering in the context of vaccine design, predicting the density of B-cell epitopes on the SAPN surface, which is critical for a strong humoral immune response.

Cracking the barcode of fullerene-like cortical microcolumns

Artificial neural systems and nervous graph theoretical analysis rely upon the stance that the neural code is embodied in logic circuits, e.g., spatio-temporal sequences of ON/OFF spiking neurons. Nevertheless, this assumption does not fully explain complex brain functions. Here we show how nervous activity, other than logic circuits, could instead depend on topological transformations and symmetry constraints occurring at the micro-level of the cortical microcolumn, i.e., the embryological, anatomical and functional basic unit of the brain. Tubular microcolumns can be flattened in fullerene-like two-dimensional lattices, equipped with about 80 nodes standing for pyramidal neurons where neural computations take place. We show how the countless possible combinations of activated neurons embedded in the lattice resemble a barcode. Despite the fact that further experimental verification is required in order to validate our claim, different assemblies of firing neurons might have the appearance of diverse codes, each one responsible for a single mental activity. A two-dimensional fullerene-like lattice, grounded on simple topological changes standing for pyramidal neurons' activation, not just displays analogies with the real microcolumn's microcircuitry and the neural connectome, but also the potential for the manufacture of plastic, robust and fast artificial networks in robotic forms of full-fledged neural systems.

Comprehensive theoretical study of all 1812 C60 isomers

All 1812 C₆₀ isomers are investigated with high-level quantum chemical methods to benchmark semiempirical approaches and find appropriate stability criteria.

A Comparison of the Elastic Properties of Graphene- and Fullerene-Reinforced Polymer Composites: The Role of Filler Morphology and Size

Nanoscale carbon-based fillers are known to significantly alter the mechanical and electrical properties of polymers even at relatively low loadings. We report results from extensive molecular-dynamics simulations of mechanical testing of model polymer (high-density polyethylene) nanocomposites reinforced by nanocarbon fillers consisting of graphene flakes and fullerenes. By systematically varying filler concentration, morphology, and size, we identify clear trends in composite stiffness with reinforcement. To within statistical error, spherical fullerenes provide a nearly size-independent level of reinforcement. In contrast, two-dimensional graphene flakes induce a strongly size-dependent response: we find that flakes with radii in the 2–4 nm range provide appreciable enhancement in stiffness, which scales linearly with flake radius. Thus, with flakes approaching typical experimental sizes (~0.1–1 μm), we expect graphene fillers to provide substantial reinforcement, which also is much greater than what could be achieved with fullerene fillers. We identify the atomic-scale features responsible for this size- and morphology-dependent response, notably, ordering and densification of polymer chains at the filler–matrix interface, thereby providing insights into avenues for further control and enhancement of the mechanical properties of polymer nanocomposites.

Novel hollow all-carbon structures

A new family of cavernous all-carbon structures is proposed. These molecular cage structures are constructed by edge subdivisions and leapfrog transformations from cubic polyhedra or their duals. The obtained structures were then optimized at the density functional level. These hollow carbon structures represent a new class of carbon allotropes which could lead to many interesting applications.

Highly Symmetric and Congruently Tiled Meshes for Shells and Domes

We describe the generation of all possible shell and dome shapes that can be uniquely meshed (tiled) using a single type of mesh face (tile), and following a single meshing (tiling) rule that governs the mesh (tile) arrangement with maximal vertex, edge and face symmetries. Such tiling arrangements or congruently tiled meshed shapes, are frequently found in chemical forms (fullerenes or Bucky balls, crystals, quasi-crystals, virus nano shells or capsids), and synthetic shapes (cages, sports domes, modern architectural facades). Congruently tiled meshes are both aesthetic and complete, as they support maximal mesh symmetries with minimal complexity and possess simple generation rules. Here, we generate congruent tilings and meshed shape layouts that satisfy these optimality conditions. Further, the congruent meshes are uniquely mappable to an almost regular 3D polyhedron (or its dual polyhedron) and which exhibits face-transitive (and edge-transitive) congruency with at most two types of vertices (each type transitive to the other). The family of all such congruently meshed polyhedra create a new class of meshed shapes, beyond the well-studied regular, semi-regular and quasi-regular classes, and their duals (platonic, Catalan and Johnson). While our new mesh class is infinite, we prove that there exists a unique mesh parametrization, where each member of the class can be represented by two integer lattice variables, and moreover efficiently constructable.

The topology of fullerenes

Fullerenes are carbon molecules that form polyhedral cages. Their bond structures are exactly the planar cubic graphs that have only pentagon and hexagon faces. Strikingly, a number of chemical properties of a fullerene can be derived from its graph structure. A rich mathematics of cubic planar graphs and fullerene graphs has grown since they were studied by Goldberg, Coxeter, and others in the early 20th century, and many mathematical properties of fullerenes have found simple and beautiful solutions. Yet many interesting chemical and mathematical problems in the field remain open. In this paper, we present a general overview of recent topological and graph theoretical developments in fullerene research over the past two decades, describing both solved and open problems. WIREs Comput Mol Sci 2015, 5:96-145. doi: 10.1002/wcms.1207 Conflict of interest: The authors have declared no conflicts of interest for this article. For further resources related to this article, please visit the WIREs website.

Efficient ring perception for the Chemistry Development Kit

BACKGROUND

The Chemistry Development Kit (CDK) is an open source Java library for manipulating and processing chemical information. A key aspect in handling chemical structures is the determination of the chemical rings. The rings of a structure are used areas including descriptors, stereochemistry, similarity, screening and atom typing. The CDK includes multiple algorithms for determining the rings of a structure on demand. Non-unique descriptions of rings were often used due to the slower performance of the unique alternatives.

RESULTS

Efficient algorithms for handling chemical ring perception have been implemented and optimised in the CDK. The algorithms provide much faster computation of new and existing types of rings. Several optimisation and implementation considerations are discussed which improve real case usage. The performance is measured on several publicly available data sets and in several cases the new implementations were found to be more than an order of magnitude faster.

CONCLUSIONS

Algorithmic improvements allow handling of much larger datasets in reasonable time. Faster computation allows more appropriate rings to be utilised in procedures such as aromaticity. Several areas that require ring perception have also seen a noticeable improvement. The time taken to compute the unique rings is now comparable allowing a correct usage throughout the toolkit. All source code is open source and freely available.

Structural, electronic and energetic properties of giant icosahedral fullerenes up to C6000: insights from an ab initio hybrid DFT study

An accurate and detailed electronic structure study of giant carbon fullerenes, benefitting from improved symmetry exploitation in the CRYSTAL14 code.

Structure and properties of the nonface-spiral fullerenes T-C₃₈₀, D₃-C₃₈₄, D₃-C₄₄₀, and D₃-C₆₇₂ and their halma and leapfrog transforms

The structure and properties of the three smallest nonface-spiral (NS) fullerenes NS-T-C₃₈₀, NS-D₃-C₃₈₄, NS-D₃-C₄₄₀, and the first isolated pentagon NS-fullerene, NS-D₃-C₆₇₂, are investigated in detail. They are constructed by either a generalized face-spiral algorithm or by vertex insertions followed by a force-field optimization using the recently introduced program Fullerene. The obtained structures were then further optimized at the density functional level of theory and their stability analyzed with reference to Ih-C₆₀. The large number of hexagons results in a higher stability of the NS-fullerenes compared to C60, but, as expected, in a lower stability than most stable isomers. None of the many investigated halma transforms on nonspiral fullerenes, NS-T-C₃₈₀, NS-D₃-C₃₈₄, NS-D₃-C₄₄₀, and NS-D₃-C₆₇₂, admit any spirals, and we conjecture that all halma transforms of NS-fullerenes belong to the class of NS-fullerenes. A similar result was found to not hold for the related leapfrog transformation. We also show that the first known NS-fullerene with isolated pentagons, NS-D₃-C₆₇₂, is a halma transform of D3-C₁₆₈.