Bond Topology Research Articles

Cooperative Large-Hysteresis Spin-Crossover Transition in the Iron(II) Triazolate [Fe(ta)2] Metal-Organic Framework.

The metal-organic framework [Fe(ta)2] (Hta = 1H-1,2,3-triazole) containing Fe(II) ions and 1,2,3-triazolate ligands shows a reversible phase transition while retaining the cubic crystal symmetry and space group Fd3m (no. 227). The phase transition between room temperature (RT-[Fe(ta)2]; a = 16.6315(2) Å, V = 4600.39(8) Å3) and high temperature (HT-[Fe(ta)2]; a = 17.7566(4) Å, V = 5598.6(1) Å3) phases occurs at a temperature above 290 °C, whereas the phase transition between HT- and RT-[Fe(ta)2] starts at a temperature below 210 °C. Both [Fe(ta)2] polymorphs have identical bond topologies, but they differ by a large increase of the unit cell's volume of 22% for HT-[Fe(ta)2]. The compounds are characterized by powder X-ray diffraction, differential scanning calorimetry, and thermogravimetric analyses. Additionally, Mössbauer spectroscopy, magnetic studies, and the electronic structure of both phases are discussed in detail with respect to the spin-crossover transition from the low-spin (RT-[Fe(ta)2]) to the high-spin phase (HT-[Fe(ta)2]).

Reactive elements dependence of elastic properties and stacking fault energies of γ-Ni, γ′-Ni3Al and β-NiAl

Abstract The reactive element effects (REEs) have been proven to improve the thermal oxidation resistance of β-NiAl. However, their effects on mechanical properties, which are significant implications for the Ni-based superalloys substrate and β-NiAl bond coat of thermal barrier coatings (TBCs), have not been well understood so far. In this work, the basic elastic properties, ideal strengths, and stacking fault energies of reactive elements (REs: Hf, Zr, Dy, Y, La) doping γ-Ni, γ′-Ni3Al, β-NiAl systems have been calculated using the first-principles method. The elastic properties results suggest that all five REs can enhance the ductilities of γ-Ni, β-NiAl, and γ′-Ni3Al, of which La performs best. More interesting, the complicated stacking fault (CSF) and anti-phase boundary (APB) energies of γ-Ni and β-NiAl decrease with the addition of REs in order of La > Y(Dy)>Zr > Hf, showing a totally opposite trend to that of commonly accepted the REEs on oxidation. The significant charge density redistributions could explain the physical origin of the improvement of plastic deformation ability for β-NiAl. This work gives insight into the mechanism of RE effects on the ductility and strength of γ-Ni, γ′-Ni3Al, β-NiAl materials, providing theoretical guidance for Ni-based superalloys design via a combinational analysis of bond topology and electronic structure.

Experimental and Quantum Mechanical Characterization of an Oxygen-Bridged Plutonium(IV) Dimer.

We report the synthesis and characterization of K4 {[PuCl2 (NO3 )3 ]2 (μ2 -O)}⋅H2 O, which contains the first known μ2 -oxo bridge between two PuIV metal centers. Adding to its uniqueness is the Pu-(μ2 -O) bond length of 2.04 Å, which is the shortest of other analogous compounds. The Pu-(μ2 -O)-Pu bridge is characterized by the mixing of s-, d-, and p-orbitals from Pu with the p-orbitals of O; the 5f-orbitals do not participate in bonding. Natural bond orbital analysis indicates that Pu and O interact through one 3c-2e σPu-O-Pu and two 3c-2e πPu-O-Pu bonding orbitals and that the electron density is highly polarized on the μ2 -O. Bond topology properties analysis indicates that the Pu-(μ2 -O) bond shares both ionic and covalent character. Quantum mechanical calculations also show that the dimer has multiconfigurational ground states, where the nonet, septet, quintet, triplet, and singlet are close in energy. This work demonstrates the interplay between experimental and computational efforts that is required to understand the chemical bonding of Pu compounds.

EGF-like and Other Disulfide-rich Microdomains as Therapeutic Scaffolds.

Disulfide bonds typically introduce conformational constraints into peptides and proteins, conferring improved biopharmaceutical properties and greater therapeutic potential. In our opinion, disulfide-rich microdomains from proteins are potentially a rich and under-explored source of drug leads. A survey of the UniProt protein database shows that these domains are widely distributed throughout the plant and animal kingdoms, with the EGF-like domain being the most abundant of these domains. EGF-like domains exhibit large diversity in their disulfide bond topologies and calcium binding modes, which we classify in detail here. We found that many EGF-like domains are associated with disease phenotypes, and the interactions they mediate are potential therapeutic targets. Indeed, EGF-based therapeutic leads have been identified, and we further propose that these domains can be optimized to expand their therapeutic potential using chemical design strategies. This Review highlights the potential of disulfide-rich microdomains as future peptide therapeutics.

Syntheses and electron density distribution studies in two new imidazole derivatives

Imidazole derivatives find wide scale and diverse applications. In this work two new imidazole based compounds have been synthesized. Their structures were confirmed using NMR, Mass Spectrometry and IR techniques. In addition, three dimensional structures were elucidated using single crystal X-rays diffraction analysis. The structures were refined using the classical independent atom model and the aspherical pseudo-atom model from an electron density database. The electrostatic properties and the topology of covalent bonds and intermolecular interactions of both the molecules were quantified on the basis of transferred electron density parameters. This study encourages the use of transferability principle for routine structure analysis as it gives better refinement statistics and reliable estimation of chemical reactivity through the study of electrostatic properties.

Fifty years of fragility: A view from the cheap seats

Recent advances in understanding the origins of glass-forming fragility in terms of fundamental bonding structure in network-forming glasses (NFGs) includes a proposition that the fragility index is uniquely defined by a single mean field parameter, a coarse-grained variant of the average bond density, 〈nCG〉. This finding resonates with much earlier speculations, first voiced by Nemilov in an under-appreciated paper (Nemilov, 1966), that the fragility in oxide glasses is roughly correlated to the average bridging oxygen per network-forming polyhedron. Here, we provide an abbreviated look at the history of the fragility concept and its correlations with other glass properties as well as its association to the bond topology in network-forming glasses. While we acknowledge the precedence of Nemilov's work in this area (Nemilov, 1966, 1992, 2006, 2007), we also clarify important differences between his qualitative correlation and the more quantitative findings of recent work by ourselves and others.

Enhanced Deep-Learning Prediction of Molecular Properties via Augmentation of Bond Topology.

Deep learning has made great strides in tackling chemical problems, but still lacks full-fledged representations for three-dimensional (3D) molecular structures for its inner working. For example, the molecular graph, commonly used in chemistry and recently adapted to the graph convolutional network (GCN), is inherently a 2D representation of 3D molecules. Herein we propose an advanced version of the GCN, called 3DGCN, which receives 3D molecular information from a molecular graph augmented by information on bond direction. While outperforming state-of-the-art deep-learning models in the prediction of chemical and biological properties, 3DGCN has the ability to both generalize and distinguish molecular rotations in 3D, beyond 2D, which has great impact on drug discovery and development, not to mention the design of chemical reactions.

Single crystal, spectral and electronic transition studies on (E)-N-(3-methoxy-4-hydroxybenzylidene)-4-nitrobenzohydrazide monohydrate

The single crystal of (E)-N-(3-Methoxy-4-hydroxybenzylidene)-4-nitrobenzohydrazide monohydrate (MHBNB) was grown by a slow evaporation method. The crystal structure was determined by single crystal X-ray diffraction method. The electron density, Hirshfeld surface and fingerprint analysis reveals that the crystal packing is governed by several weak OH⋯C, OH⋯O and OH⋯N intermolecular interactions. The analysis of bond critical points (BCP) and topology of the crystalline form of MHBNB were done. The intrusion of H2O molecule does not affect the aromaticity of the pheyl rings but marginally disturbs the aromaticity of hydrazide link. The FT-IR (4000-400 cm−1) and FT-Raman (3500-50 cm−1) spectra were recorded to study the vibrational behavior of MHBNB molecule. To explore the electronic transition of MHBNB, the UV absorbance spectrum was recorded in the range of 200–800 nm. Furthermore, the Density functional theory (DFT) and Time-dependent DFT (TD-DFT) calculations were performed to investigate the molecular geometry, vibrational behavior, electronic excitation and inter-intramolecular charge transfers within the molecule. The singlet (S) and Triplet (T) electronic excited states (n state = 6) of MHBNB were examined, in which, the electron spin density (s), excitation energy (ΔE1-6), oscillator strength (f) and electric dipole moment (μ) were examined. The frontier molecular orbitals (FMOs) were studied to find the band gap of FMOs. The natural atomic orbitals (NAO) and natural localized molecular orbitals (NLMO) of MHBNB were analyzed. The density of states (DOS) and Total density of states (TDOS) of functional groups in MHBNB molecule were also evaluated. This compound has very good first order hyperpolarizability (β0) coefficient.

A priori bond-valence and bond-length calculations in rock-forming minerals

Within the framework of the bond-valence model, one may write equations describing the valence-sum rule and the loop rule in terms of the constituent bond valences. These are collectively called the network equations, and can be solved for a specific bond topology to calculate its a priori bond valences. A priori bond valences are the ideal values of bond strengths intrinsic to a given bond topology that depend strictly on the formal valences of the ion at each site in the structure, and the bond-topological characteristics of the structure (i.e. the ion connectivity). The a priori bond valences are calculated for selected rock-forming minerals, beginning with a simple example (magnesiochromite, = 1.379 bits per atom) and progressing through a series of gradually more complex minerals (grossular, diopside, forsterite, fluoro-phlogopite, phlogopite, fluoro-tremolite, tremolite, albite) to finish with epidote (= 4.187 bits per atom). The effects of weak bonds (hydrogen bonds, long Na+—O2− bonds) on the calculation of a priori bond valences and bond lengths are examined. For the selected set of minerals, a priori and observed bond valences and bond lengths scatter closely about the 1:1 line with an average deviation of 0.04 v.u. and 0.048 Å and maximum deviations of 0.16 v.u. and 0.620 Å. The scatter of the corresponding a priori and observed bond lengths is strongly a function of the Lewis acidity of the constituent cation. For cations of high Lewis acidity, the range of differences between the a priori and observed bond lengths is small, whereas for cations of low Lewis acidity, the range of differences between the a priori and observed bond lengths is large. These calculations allow assessment of the strain in a crystal structure and provide a way to examine the effect of bond topology on variation in observed bond lengths for the same ion-pair in different bond topologies.

Tailoring Bond Topologies in Open-Shell Graphene Nanostructures.

Polycyclic aromatic hydrocarbons exhibit a rich spectrum of physicochemical properties depending on the size and, more critically, on the edge and bond topologies. Among them, open-shell systems-molecules hosting unpaired electron densities-represent an important class of materials for organic electronic, spintronic, and optoelectronic devices, but remain challenging to synthesize in solution. We report the on-surface synthesis and scanning tunneling microscopy- and spectroscopy-based study of two ultralow-gap open-shell molecules, namely peri-tetracene, a benzenoid graphene fragment with zigzag edge topology, and dibenzo[ a, m]dicyclohepta[ bcde, nopq]rubicene, a nonbenzenoid nonalternant structural isomer of peri-tetracene with two embedded azulene units. Our results provide an understanding of the ramifications of altered bond topologies at the single-molecule scale, with the prospect of designing functionalities in carbon-based nanostructures via engineering of bond topology.

Two‐Terminal Molecular Memory through Reversible Switching of Quantum Interference Features in Tunneling Junctions

AbstractLarge‐area molecular tunneling junctions comprising self‐assembled monolayers of redox‐active molecules are described that exhibit two‐terminal bias switching. The as‐prepared monolayers undergo partial charge transfer to the underlying metal substrate (Au, Pt, or Ag), which converts their cores from a quinoid to a hydroquinoid form. The resulting rearomatization converts the bond topology from a cross‐conjugated to a linearly conjugated π system. The cross‐conjugated form correlates to the appearance of an interference feature in the transmission spectrum that vanishes for the linearly conjugated form. Owing to the presence of electron‐withdrawing nitrile groups, the reduction potential and the interference feature lie close to the work function and Fermi level of the metallic substrate. We exploited the relationship between conjugation patterns and quantum interference to create nonvolatile memory in proto‐devices using eutectic Ga–In as the top contact.

Two-Terminal Molecular Memory through Reversible Switching of Quantum Interference Features in Tunneling Junctions.

Large‐area molecular tunneling junctions comprising self‐assembled monolayers of redox‐active molecules are described that exhibit two‐terminal bias switching. The as‐prepared monolayers undergo partial charge transfer to the underlying metal substrate (Au, Pt, or Ag), which converts their cores from a quinoid to a hydroquinoid form. The resulting rearomatization converts the bond topology from a cross‐conjugated to a linearly conjugated π system. The cross‐conjugated form correlates to the appearance of an interference feature in the transmission spectrum that vanishes for the linearly conjugated form. Owing to the presence of electron‐withdrawing nitrile groups, the reduction potential and the interference feature lie close to the work function and Fermi level of the metallic substrate. We exploited the relationship between conjugation patterns and quantum interference to create nonvolatile memory in proto‐devices using eutectic Ga–In as the top contact.

Bond topology and structural arrangements in inorganic crystals

Bond topology and structural arrangements in inorganic crystals

Exploring rare chemical phenomena using fractional nuclear charges: The cis‐effect in N2F2

AbstractThe so called cis‐effect, in which the cis form of an ethylenic compound is more stable than its trans‐isomer, is a good example of a rare phenomenon described only for a few isomeric pairs. In this work, a novel approach to the study of this rare effect is attempted by changing the nuclear charges of the fluoride and nitrogen in cis‐ and trans‐N2F2. This allowed the survey of a large number of isomeric pairs composed sharing the same molecular topology, while varying the electronegativity of selected atoms. The results show an increasing stabilization of the cis‐isomers when increasing the electronegativity of the fluoride atoms, in line with the accepted zeitgeist linking this effect to the electronegativity of the peripheral groups. However, a similar behavior was also found when varying the nuclear charge of the nitrogen atoms. This prompted a more in‐depth look at the electronic structure of these compounds, gathering descriptors from Bader's Quantum Theory of Atoms in Molecules. A descriptive linear model was derived from these descriptors using a two‐stage stepwise linear regression. Further inspection of the model linked the destabilization of the trans‐isomers with a deviation from the idealized trigonal planar geometry predicted by the Valence Shell Electron Pair Repulsion model. This tendency was explained by an increase in the ionic character of the NF bonds. Furthermore, the current model suggests that the Coulombic repulsion between the two peripheral atoms in the cis‐isomers prevents such large deviations from the idealized geometry, thus, contributing to their relative stabilization. The qualitative rules governing the cis‐effect in N2F2 were further tested on other compounds with a similar bond topology.

Alkyne Origami: Folding Oligoalkynes into Polyaromatics.

Do not bend the triple bonds! This familiar undergraduate mantra must be disobeyed if the alkyne group is used as a building block in molecular construction. This Account will describe our exploits in "alkyne origami", that is, folding oligoalkynes into new shapes via cyclization cascades. This research stems from a set of guidelines for the cyclizations of alkynes that we suggested in 2011 ( Gilmore Chem. Rev. 2011 , 111 , 6513 ; Alabugin J. Am. Chem. Soc. 2011 , 133 , 12608 ). The guidelines blended critical analysis of ∼40 years of experimental research with computations into the comprehensive predictions of the relative favorability of dig-cyclizations of anions and radicals. In this Account, we will show how this new understanding has been instrumental in building polyaromatics. In particular, we illustrate the utility of these stereoelectronic models by developing a toolbox of practical, selective, and efficient synthetic transformations. The high energy and high carbon content render alkynes the perfect precursors for the preparation of polyaromatic ribbons and other carbon-rich materials with precisely controlled structure and reactivity. Still, the paradox of alkyne reactivity (alkynes store a lot of energy but are protected kinetically by their relatively strong π-bonds) requires precise use of stereoelectronic factors for lowering the activation barriers for alkyne cyclizations. These factors are drastically different in the "all-exo" and the "all-endo" cyclization cascades of oligoynes. This Account will highlight the interplay between the stereoelectronics of bond formation and topology of acyclic precursor "folding" into a polycyclic ribbon. The topology of folding is simpler for the endo cascades, which are compatible with initiation either at the edge or at the center. In contrast, the exo cascades require precise folding of an oligoalkyne ribbon by starting the cascade exactly at the center of the chain. These differences define the key challenges in the design of these two types of alkyne cyclization cascades. For the endo processes, the folding is simple, but these processes require a strategy ("LUMO Umpolung") for inverting the usual stereoelectronic requirements of alkyne cyclizations. We also show how alkenes can be used as alkyne equivalents in cyclizations coupled with fragmentations and how one can make endo cyclization products without ever going through an endo cyclization. In contrast, each elementary step of the exo cascades benefits from the inherent exo preference for the radical attack, but these cascades require precise initiation by starting exactly at the central alkyne unit of the oligoyne. This strict selectivity requirement led to the development of traceless directing groups capable of supramolecular assistance to the initiation step and self-terminating departure at the end of the cascade. With attention to electronic effects that can stop radical cascades, oligoalkynes can be selectively converted into precisely shaped and functionalized polyaromatic products. The generality of these concepts is further illustrated by the development of radical "peri annulations" at the zigzag edge of acenes.

Biotransformation, spectroscopic investigation, crystal structure and electrostatic properties of 3,7α-dihydroxyestra-1,3,5(10)-trien-17-one monohydrate studied using transferred electron-density parameters.

The biologically transformed product of estradiol valerate, namely 3,7α-dihydroxyestra-1,3,5(10)-trien-17-one monohydrate, C18H22O3·H2O, has been investigated using UV-Vis, IR, 1H and 13C NMR spectroscopic techniques, as well as by mass spectrometric analysis. Its crystal structure was determined using single-crystal X-ray diffraction based on data collected at 100 K. The structure was refined using the independent atom model (IAM) and the transferred electron-density parameters from the ELMAM2 database. The structure is stabilized by a network of hydrogen bonds and van der Waals interactions. The topology of the hydrogen bonds has been analyzed by the Bader theory of `Atoms in Molecules' framework. The molecular electrostatic potential for the transferred multipolar atom model reveals an asymmetric character of the charge distribution across the molecule due to a substantial charge delocalization within the molecule. The molecular dipole moment was also calculated, which shows that the molecule has a strongly polar character.

Chemographic exploration of the hyalotekite structure-type

ABSTRACTThe hyalotekite group has been approved by the Commission on New Minerals, Nomenclature and Classification of the International Mineralogical Association (memorandum 57–SM/16). The general formula of the minerals of the hyalotekite group may be written as: A2B2M2[Si8T4O28]W where A = Ba2+, Pb2+ or K+; B = Ba2+, Pb2+ or K+; M = Ca2+, Y3+ or REE3+; T = Si4+, B3+ or Be2+; and W = F– or □ (where REE = rare-earth elements and □ = vacancy).Four minerals are currently known in this group: hyalotekite, Ba4Ca2[Si8B2(SiB)O28]F, triclinic, I$\bar 1$; khvorovite, Pb2+4Ca2[Si8B2(SiB)O28]F, triclinic I$\bar 1$; kapitsaite-(Y), Ba4(YCa)[Si8B2B2O28]F, triclinic, I$\bar 1$; and itsiite Ba4Ca2[Si8B4O28]□, tetragonal, I$\bar 4$2m.We explore the possible end-member compositions within this group by conflating the properties of an end-member with the stoichiometry imposed by the bond topology of the hyalotekite structure-type and the crystal-chemical properties of its known constituents. There are two high-coordination sites in the hyalotekite structure, A and B, and occupancy of each of these sites can be determined only by crystal-structure refinement. If these two sites are considered together, there are 19 end-member compositions of the triclinic structure and six end-member compositions of the tetragonal structure involving A and B = Ba2+, Pb2+, K+; M = Ca2+, Y3+, REE3+; and T = Si4+, B3+, Be2+. There is the possibility for many other hyalotekite-group minerals, and two potential new minerals have been identified from data in the literature.

Controlling destructive quantum interference in tunneling junctions comprising self-assembled monolayers via bond topology and functional groups.

Quantum interference effects (QI) are of interest in nano-scale devices based on molecular tunneling junctions because they can affect conductance exponentially through minor structural changes. However, their utilization requires the prediction and deterministic control over the position and magnitude of QI features, which remains a significant challenge. In this context, we designed and synthesized three benzodithiophenes based molecular wires; one linearly-conjugated, one cross-conjugated and one cross-conjugated quinone. Using eutectic Ga-In (EGaIn) and CP-AFM, we compared them to a well-known anthraquinone in molecular junctions comprising self-assembled monolayers (SAMs). By combining density functional theory and transition voltage spectroscopy, we show that the presence of an interference feature and its position can be controlled independently by manipulating bond topology and electronegativity. This is the first study to separate these two parameters experimentally, demonstrating that the conductance of a tunneling junction depends on the position and depth of a QI feature, both of which can be controlled synthetically.

Ortho-Substituent Effects on Diphenylurea Packing Motifs

Hydrogen bonding between urea groups is a widely used motif in crystal engineering and supramolecular chemistry studies. In an effort to discern how the steric and electronic properties of substituents affect the molecular conformation and crystal packing of ortho-substituted N,N′-diphenylureas (oPUs), herein we report the synthesis, characterization, and polymorph screening of eight members of this family. Of the 16 total oPU structures known (including nine structures from this study and seven previously reported), only two are isostructural. These 16 structures are sorted into three general architecture types based on their hydrogen bond topologies. In Type I, urea molecules related by translation form linear one-dimensional (1D) hydrogen bonded chains. In Type II, urea molecules rotate about a 1D hydrogen bond axis forming twisted chains. Urea groups do not hydrogen bond to one another in Type III. Energy calculations performed at the B3LYP/6-31G(d,p) level show a higher rotational barrier about the amide bond in oPUs compared to meta-substituted diphenylureas (mPUs), which may explain the smaller range of torsion angles observed in oPUs compared to mPUs. Although ortho-substitution does not seem to limit the hydrogen bonding between urea groups in most cases, a notably higher percentage of oPU phases are polar compared to PUs with other substitution patterns. This suggests restricted conformations might offer some advantage in achieving acentric materials.

Prediction of hypervalent molecules: investigation on MnC (M = Li, Na, K, Rb and Cs; n = 1-8) clusters.

New hypervalent molecules have emerged from a systematic exploration of the structure and bonding of MnC (M = Li, Na, K, Rb and Cs; n = 1-8) clusters via an unbiased CALYPSO structure investigation combined with density functional theory. The global minimum structures are obtained at the B3LYP/6-311+G* and CCSD(T)/6-311+G* levels of theory. The observed growth behavior clearly indicates that the ground state of MnC (M = Li, Na, K, Rb and Cs; n = 1-8) is transformed from a planar to a three-dimensional (3D) structure at n = 4. A maximum of six alkali atoms can be bound atomically to a carbon atom. The determination of the averaged binding energies Eb(n), fragmentation energies ΔE(n) and HOMO-LUMO energy gaps unambiguously supports the stability of M6C. This indicated conclusively that 6 is a magic Li-coordination number for C. The nature of bonding is further investigated by an insightful analysis of the highest occupied molecular orbital (HOMO) and the topology of chemical bonds for the most stable clusters. In the final step, electron localization functions (ELF) and density of states (DOS) are determined in order to consolidate the acquired information on the studied electronic structures.