The effect of hetero-atoms on spin exchange coupling pathways (ECPs): a computational investigation.

The effect of heteroatoms on exchange coupling pathways and the presence of more than one coupling paths are investigated. The lone pairs of sp2-hybridized heteroatoms contribute to aromaticity but do not play any pivotal role in the spin coupling between two spin centers. A conceptual model to describe this behavior of heteroatoms has been introduced, and we name it as the hetero-atom blocking effect. With the occurrence of two π-orbital exchange coupling pathways (ECPs) via bridgehead heteroatoms (B-, N-, O-, or S-), the magnetic exchange coupling constants (J) can be viewed as a signed sum of different individual pathways. The effect of σ-electron coupling is also investigated in this work.

Diborane Concatenation Leads to New Planar Boron Chemistry.

Diborane has long been realized to be analogous to ethylene in terms of its bonding MOs, both as to symmetries and splitting patterns. This naturally suggests an investigation to see whether other similar conjugated hydrocarbons manifest a similar boron-substituted and H2 supplemented borane. That is, for a conjugated hydrocarbon structure with a neighbor-paired resonance pattern, we propose to look at boranes where each carbon atom is replaced by a boron atom, and an H-atom pair is added to each double bond of the resonance structure, with one H above the molecular plane and one below. This construction of concatenated diboranes is uniformly different than that for the previously known stable boranes of 4 or more B atoms. We find from quantum-chemical computations that our so constructed polyboranes are stable. All this suggests a possible novel new chapter in borane chemistry - a chapter with some promise of understandings related to that for (alternant) conjugated hydrocarbons.

Toward Molecular Magnets of Organic Origin via Anion-π Interaction Involving m-Aminyl Diradical: A Theoretical Study.

Here we study a set of novel magnetic organic molecular species with different halide ions (fluoride, chloride, bromide) absorbed ∼2 Å above or below the center of an aromatic π-ring in an m-aminyl diradical. Focus is on the nature of anion-π interaction and its impact on magnetic properties, specifically on magnetic anisotropy and on intramolecular magnetic exchange coupling. In the development of single molecule magnets, magnetic anisotropy is considered to be the most influential factor. A new insight regarding the magnetic anisotropy that determines the barrier height for relaxation of magnetization of m-aminyl diradical-derived anionic complexes is obtained from calculations of the axial zero-field-splitting (ZFS) parameter D. The noncovalent anion-π interaction strongly influences magnetic anisotropy in m-aminyl-halide diradical complexes. In particular, the change of D values from positive (for the m-aminyl diradical, m-aminyl diradical/fluoride, and m-aminyl diradical/chloride complexes) to negative D-values in m-aminyl diradical complexes containing bromide signals a change from oblate to prolate type of spin-density distribution. Furthermore, the noncovalent halide-π interactions lead to large values of intramolecular magnetic exchange coupling coefficients J exhibiting a ferromagnetic sign. The magnitude of J steadily increases going from anionic complexes containing fluoride to chloride and then to bromide. Relations are sought between the magnetic exchange coupling coefficients J and aromaticity, namely structural HOMA (harmonic oscillator model of aromaticity) and magnetic NICS (nucleus independent chemical shift) aromaticity indices, in particular, the NICSzz(+1) component. Finally, possible numerical checks on the conditions relating to validity of the well-known Yamaguchi's formula for calculating the exchange coupling coefficient J in diradical systems are discussed.

A high-spin organic diradical as a spin filter.

Here, in this work we have designed a molecular bridge structure which can be used as a spin filter where the prototypical highly ferromagnetic m-phenylene connected bis(aminoxyl) diradical is used as a bridging fragment between two semi-infinitely widened gold (Au) electrodes along the [100] direction. A state-of-the-art non-equilibrium Green function's (NEGF) method coupled with the density functional theory (DFT) was carried out on this two-probe molecular bridge system to understand its electrical spin transport characteristics. The spin current at various bias voltages from 0.00 V to 4.00 V at intervals of 0.20 V for this Au-diradical-Au molecular junction is evaluated. We also quantify the bias-dependent spin injection coefficients (BDSIC) at different bias voltages and also the spin-filter efficiency at equilibrium, i.e., at zero bias voltage. Also plots of BDSIC vs. voltage, the up- and down-spin current vs. voltage (I-V) curves, and density of states (DOS) at zero bias voltage are evaluated.

Borazine: spin blocker or not?

The spin blocker capacity of borazine is investigated. Specifically, meta-B-B, meta-N-N and para-B-N connected borazines are used as spin-blocker couplers comprised of a pair of radicals: two iminonitroxides (IN); IN and tetrathiafulvalene radical cations (TTF); or two TTFs. Density functional theory (DFT) is used to elucidate the spin blocker capacity of the linkage-specific (meta or para) borazine-coupler and elaborate the role of the lowest unoccupied molecular orbital (LUMO) in magnetic-exchange. Furthermore, a qualitative relation between different magnetic aromaticity indices is made using both nuclear-independent chemical shift (NICS) and the harmonic oscillator model of aromaticity (HOMA). The NICS values are calculated at the centre of the borazine spacer fragment of these diradical species and then also at 0.5 Å increments of the virtual probe from this centre position up to an orthogonal distance of 2.0 Å from the centre. The HOMA values are calculated for the borazine ring fragment in these diradicals. Based on the HOMA and NICS values, it is evident that the borazine exhibits less aromatic character than benzene itself - due to the polar nature of B-N π-bonding. The LUMO mediated spin-exchange between the two consecutive singly occupied molecular orbitals (SOMOs) is explicitly discussed and confirmed to play a pivotal role. The parity of the coupler pathways, i.e. even or odd number of bonds along a selected pathway, between radical moieties is an important factor in predicting the nature and extent of magnetic exchange for these diradicals. Surprisingly, borazine does not always act as a spin-coupling blocker - rather in some cases the coupling is enhanced as compared to a homoatomic (carbon-based) benzene coupler.

Clar theory extended for polyacenes and beyond.

An extension of Clar's classical sextet ideas is presented to allow resonance-based weak-pairing long bonds. As the prototypic illustration, the theory is developed in the context of polyacenes, where this extension is needed to properly understand what goes on in this sort of polymer, whose radicality increases with chain length. A quantification of these novel Clar-sextic ideas is made, and detailed computational results are reported for the polyacenes even to the limit of arbitrary long chains. Resonance energies, bond lengths, and local (ring) aromaticity indices are addressed. It is emphasized that weak pairing is not at all unique to the polyacenes, but also applies whenever there are suitable boundaries (say of the "zig-zag" type) on general grapheneic structures--thereby readily explaining novel features of different boundaries.

Flow network QSAR for the prediction of physicochemical properties by mapping an electrical resistance network onto a chemical reaction poset.

Usual quantitative structure-activity relationship (QSAR) models are computed from unstructured input data, by using a vector of molecular descriptors for each chemical in the dataset. Another alternative is to consider the structural relationships between the chemical structures, such as molecular similarity, presence of certain substructures, or chemical transformations between compounds. We defined a class of network-QSAR models based on molecular networks induced by a sequence of substitution reactions on a chemical structure that generates a partially ordered set (or poset) oriented graph that may be used to predict various molecular properties with quantitative superstructure-activity relationships (QSSAR). The network-QSAR interpolation models defined on poset graphs, namely average poset, cluster expansion, and spline poset, were tested with success for the prediction of several physicochemical properties for diverse chemicals. We introduce the flow network QSAR, a new poset regression model in which the dataset of chemicals, represented as a reaction poset, is transformed into an oriented network of electrical resistances in which the current flow results in a potential at each node. The molecular property considered in the QSSAR model is represented as the electrical potential, and the value of this potential at a particular node is determined by the electrical resistances assigned to each edge and by a system of batteries. Each node with a known value for the molecular property is attached to a battery that sets the potential on that node to the value of the respective molecular property, and no external battery is attached to nodes from the prediction set, representing chemicals for which the values of the molecular property are not known or are intended to be predicted. The flow network QSAR algorithm determines the values of the molecular property for the prediction set of molecules by applying Ohm's law and Kirchhoff's current law to the poset network of electrical resistances. Several applications of the flow network QSAR are demonstrated.

Partially ordered sets: ranking and prediction of substances' properties.

There are at least two significant applications of partial order theory in chemistry: Ranking methods and substances' properties prediction. In both cases, a set of objects is endowed with a partial order relation e.g. "more polluting than", "can be obtained from", "more reactive than" etc. The couple of set and partial order relation is known in mathematics as a partially ordered set (poset). Ranking methods, such as the Hasse diagram technique, lead to a partial order where several incomparabilities (lack of order) appear between pairs of objects. This phenomenon is quite common in ranking studies, and it often is circumvented by a combination of object features leading to a total order. However, such a combination introduces subjectivities and bias in the ranking process. Here a step-by-step procedure is shown to turn incomparabilities into comparabilities taking into account all the possible bias by a linear combination of features. In such a manner, it is possible to predict how probable it is to obtain a particular total order from a given poset. Similarly, it is possible to calculate the needed bias over certain attributes to obtain a particular total order. An example application is shown where substances are ranked according to their bioconcentration factor and biodegradation potential. Another application of partial order theory to chemistry has to do with the prediction of properties for a set of substances related in a (preferably systematic) chemical fashion. A customary relation is "can be obtained from"; if such a relation is set up for a given molecular structure e.g. benzene, and all its substituted derivatives (say chlorinated ones) are considered, then the set of benzene and its chlorinated derivatives are partially ordered. Taking advantage of the poset generated, different methods can be applied to predict properties of the substances considered in the poset. Such methods include the poset-average, cluster expansion, and splinoid methods. In this paper we discuss each one of these methods, its advantages and disadvantages and we outline its applicability to estimate cooperative free energies of hemoglobins with different degree of oxygenation.

Combinatorics of reaction-network posets.

Reaction networks are viewed as derived from ordinary molecular structures related in reactant-product pairs so as to manifest a chemical super-structure. Such super-structures then are candidates for applications in a general combinatoric chemistry. Notable additional characterization of a reaction super-structure occurs when such reaction graphs are directed, as for example when there is progressive substitution (or addition) on a fixed molecular skeleton. Such a set of partially ordered entities is in mathematics termed a poset, which further manifests a number of special properties, as then might be utilized in different applications. Focus on the overall "super-structural" poset goes beyond ordinary molecular structure in attending to how a structure fits into a (reaction) network, and thereby brings an extra "dimension" to conventional stereochemical theory. The possibility that different molecular properties vary smoothly along chains of interconnections in such a super-structure is a natural assumption for a novel approach to molecular property and bioactivity correlations. Different manners to interpolate/extrapolate on a poset network yield quantitative super-structure/activity relationships (QSSARs), with some numerical fits, e.g., for properties of polychlorinated biphenyls (PCBs) seemingly being quite reasonable. There seems to be promise for combinatoric posetic ideas.

What Electronic Structures and Geometries of Carborane Mono- and ortho-, meta-, and para-Diradicals are Preferred?

Structures, relative stabilities, singlet-triplet gaps, and the ground-state character of mono- and diradicals derived from the three icosahedral carborane cage isomers have been computed by unrestricted broken-symmetry DFT and by CASPT2 methods. Whereas the bond dissociation energies (BDE) leading to the carborane monoradicals are close to the benzene BDE, the most stable carborane radicals are derived from dissociations of hydrogens farthest away from the carbon atoms. All the monomeric carborane diradicals are determined to have singlet ground states. However, the energetic accessibility of triplet states in some of the species offers the potential of building diradical multidimensional carborane network architectures with interesting magnetic properties.

What Is the Limit of Atom Encapsulation for Icosahedral Carboranes?

The stability of endohedral carboranes X@{1,n-C2B10H12} (X = Li(+), Be(2+); n = 2, 7, 12) and X@{CB11H12(-)} (X = Li(+), Be(2+)) is studied using electronic structure calculations with the B3LYP/6-311+G(d,p) model. Our calculations suggest that all endohedral compounds are local energy minima; for the exohedral complexes X···cage, the global energy minimum always corresponds to the X atom above a triangular face of the icosahedron. In the latter the X atom is furthest apart from the carbon atoms of the cage. As opposite to exohedral {Be(2+)···cage} complexes, no global energy minima were found for exohedral complexes {Li(+)···cage} whereby a carbon atom is present in the triangular face of the icosahedron below the Li(+) cation.

Modeling the bioconcentration factors and bioaccumulation factors of polychlorinated biphenyls with posetic quantitative super-structure/activity relationships (QSSAR).

During bioconcentration, chemical pollutants from water are absorbed by aquatic animals via the skin or a respiratory surface, while the entry routes of chemicals during bioaccumulation are both directly from the environment (skin or a respiratory surface) and indirectly from food. The bioconcentration factor (BCF) and the bioaccumulation factor (BAF) for a particular chemical compound are defined as the ratio of the concentration of a chemical inside an organism to the concentration in the surrounding environment. Because the experimental determination of BAF and BCF is time-consuming and expensive, it is efficacious to develop models to provide reliable activity predictions for a large number of chemical compounds. Polychlorinated biphenyls (PCBs) released from industrial activities are persistent pollutants of the environment that produce widespread contamination of water and soil. PCBs can bioaccumulate in the food chain, constituting a potential source of exposure for the general population. To predict the bioconcentration and bioaccumulation factors for PCBs we make use of the biphenyl substitution-reaction network for the sequential substitution of H-atoms by Cl-atoms. Each PCB structure then occurs as a node of this reaction network, which is some sort of super-structure, turning out mathematically to be a partially ordered set (poset). Rather than dealing with the molecular structure via ordinary QSAR we use only this poset, making different quantitative super-structure/activity relationships (QSSAR). Thence we developed cluster expansion and splinoid QSSARs for PCB bioconcentration and bioaccumulation factors. The predictive ability of the BAF and BCF models generated for 20 data sets (representing different conditions and fish species) was evaluated with the leave-one-out cross-validation, which shows that the splinoid QSSAR (r between 0.903 and 0.935) are better than models computed with the cluster expansion (r between 0.745 and 0.887). The splinoid QSSAR models for BAF and BCF yield predictions for the missing PCBs in the investigated data sets.

The eight classes of positive-curvature graphitic nanocones.

The eight different classes of single-wall positive-curvature graphitic nanocones are emphasized, characterized, and illustrated. Local transformations among different possible apex-region structures within a common class are investigated, it being noted that there is no short sequence of such transformations which convert from any one of these eight classes to another. Attention is directed to class identification and to nanocone codes, especially for "buckycones" comprised solely from pentagonal and hexagonal rings.

Posetic quantitative superstructure/activity relationships (QSSARs) for chlorobenzenes.

As a result of the widespread industrial use of polychlorinated hydrocarbons, they have accumulated in nearly all types of environmental compartments, especially in aquatic systems. Particularly, chloroaromatics are among the most undesirable industrial effluents because of their persistence and toxicity. To predict chlorobenzene (CB) toxicities, we make use of a novel scheme that looks beyond simple molecular structure to the manner in which such a structure embeds in an overall reaction network. Thence, a resultant modeling gives a quantitative superstructure/activity relationship (QSSAR) with the (chloro-substitution) reaction network viewed mathematically as a partially ordered set (or poset). Different numerical fittings to the overall poset lead to different QSSAR models, of which we investigate three: average poset, cluster expansion, and splinoid poset QSSAR models for the CBs' toxicities against various species (Poecilia reticulata,Pimephales promelas, Daphnia magna, Rana japonica, etc). Excellent results are obtained for all QSSAR toxicity models. On the basis of the poset reaction diagram, all three of these QSSAR models reflect, in distinct ways, the topology of the network that describes the interconversion of chemical species. Although in the majority of investigated datasets all poset QSSAR models give very good predictions, in some cases, they complement each other. These differences show that more reliable predictions can be obtained by using a consensus prediction that combines data from the three posetic models.

Molecules-in-molecule estimation of the extent of localization of Kekuléan substructures in polycyclic aromatic hydrocarbons.

This article first revises graph-theoretical (local aromaticity and overall molecular) indices, introduced by M. Randic in 1975, for benzenoid hydrocarbons and somewhat improves them for computer enumeration. This goes beyond total Kekulé structure enumeration, yielding an index calculation useful for the quantitative estimation of localization of different Kekuléan substructures (including ethylene-, benzene-, annulene-, and radialene-units). This may be viewed as a "molecules-in molecule" approach to polycyclic aromatic hydrocarbons within the context of graph theoretical partitioning.

Random walks and chemical graph theory.

Simple random walks probabilistically grown step by step on a graph are distinguished from walk enumerations and associated equipoise random walks. Substructure characteristics and graph invariants correspondingly defined for the two types of random walks are then also distinct, though there often are analogous relations. It is noted that the connectivity index as well as some resistance-distance-related invariants make natural appearances among the invariants defined from the simple random walks.

Computing wiener-type indices for virtual combinatorial libraries generated from heteroatom-containing building blocks.

The expensive and time-consuming process of drug lead discovery is significantly accelerated by efficiently screening molecular libraries with a high structural diversity and selecting subsets of molecules according to their similarity toward specific collections of active compounds. To characterize the molecular similarity/diversity or to quantify the drug-like character of compounds the process of screening virtual and synthetic combinatorial libraries uses various classes of structural descriptors, such as structure keys, fingerprints, graph invariants, and various topological indices computed from atomic connectivities or graph distances. In this paper we present efficient algorithms for the computation of several distance-based topological indices of a molecular graph from the distance invariants of its subgraphs. The procedures utilize vertex- and edge-weighted molecular graphs representing organic compounds containing heteroatoms and multiple bonds. These equations offer an effective way to compute for weighted molecular graphs the Wiener index, even/odd Wiener index, and resistance-distance index. The proposed algorithms are especially efficient in computing distance-based structural descriptors in combinatorial libraries without actually generating the compounds, because only distance-based indices of the building blocks are needed to generate the topological indices of any compound assembled from the building blocks.