Intrinsic Bond Research Articles

Heats of formation on the way from B2H6 to B20H16: thermochemical consequences of multicenter bonding in ab initio and DFT methods.

The objective of this study is to evaluate the effectiveness of various computational methods in reproducing the experimental heats of formation of boron hydrides using the atomization energy approach. The results have demonstrated that the empirical dispersion combined with the BJ damping function provided too large intramolecular dispersion energies, thereby compromising the accuracy of the outcomes produced by the DFT-D3 methods. Additionally, the CCSD(T) method has reproduced the experimental values only when combined with a basis set optimized for an accurate description of the core-valence correlation effect. Furthermore, the number of multicenter bonds present in the molecules under examination has also reflected their stability, as indicated by the heats of formation. Finally, a five-center two-electron (5c-2e) bond has emerged in B5H9, by applying the intrinsic bond orbital (IBO) method.

Facile synthesis and bonding of 4-ferrocenyl-1,2,4-triazol-5-ylidene complexes.

Ferrocene-substituted carbenes have emerged as attractive, redox-active ligands. However, among the compounds studied to date, ferrocenylated 1,2,4-triazol-5-ylidenes, which are closely related to the archetypal imidazol-2-ylidenes, are still unknown. Here, we demonstrate that the triazolium salt [CHN(Me)NCHN(Fc)]I (2; Fc = ferrocenyl), obtained by alkylation of 4-ferrocenyl-4H-1,2,4-triazole (1) with MeI, reacts selectively with metal alkoxide/hydroxide precursors [(cod)Rh(OMe)]2 and [(IPr)Au(OH)] (cod = cycloocta-1,5-diene, IPr = 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene) to produce the ferrocene-substituted 1,2,4-triazol-5-ylidene complexes [(cod)RhI{CN(Me)NCHN(Fc)}] and [(IPr)Au{CN(Me)NCHN(Fc)}]I in good yields. The complexes were characterised by NMR and IR spectroscopy, mass spectrometry, cyclic voltammetry, and single-crystal X-ray diffraction analysis. Density function theory (DFT) calculations were used to rationalise the electrochemical behaviour of the carbene complexes and to elucidate the bonding situation in these compounds. An analysis using intrinsic bond orbitals (IBOs) revealed that the 1,2,4-triazol-5-ylidene ligand exerted a strong trans influence and showed a synergistic stabilisation by the negative inductive and positive π-donor effects of the nitrogen atoms adjacent to the carbene carbon atom; these effects were enhanced by conjugation with the CHN bond at the exterior, similar to that in imidazol-2-ylidenes.

Multinuclear beryllium amide and imide complexes: structure, properties and bonding.

The beryllium amide and imide complexes [Be(HNMes)2]3, [(py)2Be(HNMes)2], [Be(HNDipp)2]2, [Be(NPh2)(μ2-HNDipp)]2 and [Be(NCPh2)2]3 have been prepared and characterised with NMR and IR spectroscopy as well as single crystal X-ray diffraction. Analysis of the localised molecular orbitals (LMOs) and intrinsic atomic orbital (IAO) atomic charges in the framework of the intrinsic bond orbital (IBO) localization method revealed a covalent bonding network consisting of 2-electron-2-centre and 2-electron-3-centre σ bonds, in which one electron pair of the anionic N-donor ligands is involved. The electron deficiency at the beryllium atoms is partially compensated through additional electron donation from the lone pair at the nitrogen atoms.

Revealing the nature of covalently tethered distonic radical anions in the generation of heteroatom-centered radicals: evidence for the polarity-matching PCET pathway.

Recognition of the intermediacy and regulation of reactivity patterns of radical intermediates in radical chemistry have profound impacts on harnessing and developing the full potential of open-shell species in synthetic settings. In this work, the possibility of in situ formation of O/N-X intermediates from Brønsted base covalently tethered carbonyl hypohalites (BCTCs) for the generation of heteroatom-centered radicals has certainly been excluded by NMR experiments and density functional theory calculations. Instead, the spectroscopic analyses reveal that the BCTCs serve as precursors of tether-tunable distonic radical anions (TDRAs) which have been unequivocally substantiated to be involved in the direct cleavage of O/N-H bonds to generate the corresponding heteroatom-centered radicals. Meanwhile, a deep insight into the properties and reactivities of the resulting TDRAs indicates that the introduction of a tethered Brønsted base on the parent open-shell species reinforces their stabilities and leads to a reversal of electrophilicity. Moreover, the dual descriptor values and electrophilicity indices are calculated based on eleven reported radical reactions involving various electrophilic/nucleophilic radical species, further confirming their validity in the prediction of the polar effect and the polarity-matching consistency between nucleophilic TDRAs and protic O/N-H bonds. The additional halogen-free experiments mediated by the combination of phthaloyl peroxide and TEMPO also prove the feasibility of the TDRA-assisted philicity-regulation approach. Lastly, detailed intrinsic bond orbital (IBO) and Hirschfeld spin population analyses are employed to elucidate that the H-atom abstraction processes are the polarity-matching proton-coupled electron transfer (PCET) pathways, with a degree of oxidative asynchronicity.

Orbital and free energy landscape expedition towards the unexplored catalytic realm of aromatically modified FLPs for CO2 sequestration.

The emergence of frustrated Lewis pairs (FLPs) has created a whole new dimension in the development of metal free catalysts for CO2 sequestration. Efforts have been made to enhance the catalytic activity of the FLPs. The aromatic modulation of the catalytic sites has been successfully demonstrated to enhance the activity towards CO2. Although various aromatically modified geminal FLPs have been investigated for CO2 capture, the catalytic space of these FLPs has not been fully resolved yet. Thus, to fulfil the knowledge gap in the understanding of the catalytic behaviour and to extend the concept of aromatically enhanced FLPs, in the present study all the possible combinations of aromatic and antiaromatic modulations of the acidic and basic sites have been proposed and examined using density functional theory based orbital analysis. Further to verify the results obtained from the orbital analysis and to fully explore the catalytic space of the proposed systems, free energy landscapes have been examined using metadynamics simulations. The detailed intrinsic bond orbital (IBO) and principal interacting orbital (PIO) analyses capture crucial details of the reactions. Furthermore, evolution of anisotropy of induced current density (AICD) along the reaction justifies the effect of aromatic/antiaromatic modulation on the catalytic sites. The results show that highly asynchronous mechanisms have been found due to the aromatic/antiaromatic modulations. The simultaneous favourable aromatic/antiaromatic modification on the acidic and basic sites may greatly reduce the CO2 activation barrier. The enhancement of the acidic character of the B atom in the intramolecular FLPs (IFLPs) leads to a thermodynamically more feasible reaction with stable CO2 adducts. The acidic site has been found to play a major role in controlling the kinetics and thermodynamics of the reaction. This study provides valuable insights into the catalytic realm of the aromatically modified FLPs, which can be utilized to design more efficient and specific next-generation FLPs.

A unified strength criterion for two-dimensional materials via bond failure analysis

The family of two-dimensional (2D) materials, including graphene, hexagonal boron nitride, transition metal dichalcogenides, and others, exhibits a wide range of lattice structures and defect configurations, leading to complex deformation mechanisms and mechanical failure behaviors. However, there is currently no universally accepted criterion that accurately describes the mechanical failures of these materials. In this study, we aim to address this issue by introducing the concept of intrinsic bond strength, which is solely dependent on the local chemical environment of the bond and is independent of loading states, defect types, and fracture bonds. We demonstrate the existence of this intrinsic bond strength and propose a unified strength criterion that considers the balance between the intrinsic bond strength and local stress state for any 2D material. By employing this unified strength criterion, we are able to accurately predict the failure of various 2D materials with different types of defects, including voids, cracks, grain boundaries, and hydrogenation. This work resolves a longstanding issue in predicting the mechanical failure of 2D materials via bond failure analysis, and carries important implications for the design and development of 2D materials with enhanced mechanical properties.

On the importance of unconventional Cu⋯π interaction in tetrachloro-bis(1,10-phenanthroline)-dicopper(II) complex: Insights from experiment and theory

A copper-phenanthroline complex, namely [bis(μ2‑chloro)-dichloro-bis(1,10-phenanthroline)-di-copper(II)] has been synthesized and structurally characterized by single-crystal X-ray diffraction. The X-ray structure of the complex is stabilized through the hydrogen bond, π⋯π, and Cu⋯π interactions. The Cu⋯π interactions of the title complex along with two other complexes (retrieved from CSD) are analyzed in great detail through various theoretical calculations. Hirshfeld surface analysis and fingerprint plot quantify the non-covalent interactions. The interaction energies associated with intermolecular interactions have been calculated based on QTAIM (Quantum Theory of atoms in molecule). The analysis of topological parameters of charge density at (3, −1) bond critical points characterize the interactions as “closed-shell” interactions. The non-covalent interactions are further characterized by the Non-Covalent Interaction (NCI) plot index, Independent Gradient Module based on Hirshfeld partition of molecular density (IGMH), and Intrinsic Bond Strength Index for Weak interaction (IBSIW).

Unprecedented Activation of CO2 by α-Amino Boronic Acids.

Efficient and environmentally benign transformation of carbon dioxide (CO2) into valuable chemicals is mainly obstructed by the lack of suitable catalysts. To date, various catalysts have already been investigated for the conversion of CO2 molecules, but still finding metal-free, simple, and environment-friendly catalysts is a topic of utmost interest among researchers. Thus, in this regard, the present work projects α-amino boronic acids (AABs) as a metal-free and simple catalyst for CO2 activation. The density functional theory (DFT)-based calculations have been carried out to explore the catalytic potential of AABs. The detailed electronic structure analysis of the considered AABs unveils the catalytic similarities with frustrated Lewis pairs (FLPs) in a gas phase. Interestingly, a peculiar catalytic action of AABs has been observed in the presence of solvents. The contrasting catalytic behavior of AABs in solvents has been extensively investigated by employing principal interacting orbital (PIO), intrinsic bond orbital (IBO), and natural bond orbital (NBO) analyses along the reaction paths. The results of the orbital studies provide concrete ground for the observed reaction mechanism. Further, the energetic analysis of the reaction of CO2 with AABs reveals that <5 kcal/mol energy is required for activation in a solvent phase, and the formed adducts are readily active. These observations show that AABs can be considered as an efficient catalyst for CO2 activation.

Mechanistic Study of Reduction of Nitrite to NO by the Copper(II) Complex: Different Concerted Proton-Electron Transfer Reactivity between Nitrite and Nitro Complexes.

The literature contains numerous reports of copper complexes for nitrite (NO2-) reduction. However, details of how protons and electrons arrive and how nitric oxide (NO) is released remain unknown. The influence of the coordination mode of nitrite on reactivity is also under debate. Kundu and co-workers have reported nitrite reduction by a copper(II) complex [J. Am. Chem. Soc. 2020, 142, 1726-1730]. In their report, the copper(II) complex reduced nitrite using a phenol derivative as a reductant, resulting in NO, a hydroxyl copper(II) complex, and the corresponding biphenol. Also, the involvement of proton-coupled electron transfer was proposed by mechanistic studies. Herein, density functional theory calculations were performed to determine a mechanism for reduction of nitrite by a copper(II) complex. As a result of geometry optimization of an initial complex, two possible structures were obtained: Cu-ONO and Cu-NO2. Two possible reaction pathways initiated from Cu-ONO or Cu-NO2 were then considered. The calculation results indicated that the Cu-ONO pathway is energetically favorable. When changes in the electronic structure were considered, both pathways were found to involve concerted proton-electron transfer (CPET). In addition, an intrinsic reaction coordinate analysis revealed that the two pathways were achieved by different types of CPET. Furthermore, an intrinsic bond orbital analysis clearly indicated that, in the Cu-ONO pathway, the chemical events involved proceeded concertedly yet asynchronously.

(μ3 -F)(BrF5 )3 ]- - An Unprecedented Molecular Fluoridobromate(V) Anion in Cs[Br3 F16

The reaction of Cs[BrF6 ] with BrF5 gave the compound Cs[Br3 F16 ] with the unprecedented propeller-shaped, C3 -symmetric [(μ3 -F)(BrF5 )3 ]- anion. All other currently known fluoridobromates(V) contain only octahedral [BrF6 ]- anions, which, unlike the related [IF6 ]- anions, never exhibited stereochemical activity of the lone pair on the Br atoms. Despite the same coordination number of six for the Br atom in the [BrF6 ]- and [(μ3 -F)(BrF5 )3 ]- anions, the longer μ3 -F-Br bonds provide additional space, allowing the lone pairs on the Br atoms to become stereochemically active. Cs[Br3 F16 ] was characterized by single-crystal X-ray diffraction, Raman spectroscopy, and quantum-chemical calculations for both the solid-state compound and the isolated anion at 0 K. Intrinsic bond orbital calculations show that the μ3 -F-Br bond is essentially ionic in nature and also underpin the stereochemical activity of the lone pairs of the Br(V) atoms.

Halogen atom-doped graphene/MoSe2 heterojunction Schottky barrier height modulation

Achieving lower Schottky barrier heights in logic devices remains a formidable challenge. In this paper, the effect of halogen atoms doping on the type and height of graphene/MoSe2 Schottky is investigated using density functional theory. For monolayer MoSe2, the doping of halogen atoms introduces impurity energy levels in the energy band and leads to a change in the position of the Fermi energy level. Graphene and MoSe2 bonding retains their respective intrinsic electrochemical properties and bond with weak van der Waals forces to form n-type Schottky contacts. The doping of halogen atoms effectively changes the Schottky type and height of graphene/MoSe2. The Schottky type of heterojunctions doped with F, Cl, and Br atoms changes from n-type contacts to ohmic contacts. I and At atoms effectively reduce the Schottky barrier height of graphene/MoSe2. The disparity charge density indicates that the electrons in graphene are transferred to MoSe2, forming a built-in electric field pointing from graphene to MoSe2. After the doping of halogen atoms, the interlayer charge transfer between graphene and MoSe2 is significantly reduced, and the Fermi energy level appears to be shifted downward, which eventually leads to the reduction of the Schottky barrier height.

σ‐Cyclopropyl to π‐Allyl Rearrangement at AuIII

AbstractThe possibility for AuIII σ‐cyclopropyl complexes to undergo ring‐opening and give π‐allyl complexes was interrogated. The transformation was first evidenced within (P,C)‐cyclometalated complexes, it occurs within hours at −50 °C. It was then generalized to other ancillary ligands. With (N,C)‐cyclometalated complexes, the rearrangement occurs at room temperature while it proceeds already at −80 °C with a dicationic (P,N)‐chelated complex. Density Functional Theory (DFT) calculations shed light on the mechanism of the transformation, a disrotatory electrocyclic ring‐opening. Intrinsic Bond Orbital (IBO) analysis along the reaction profile shows the cleavage of the distal σ(CC) bond to give a π‐bonded allyl moiety. Careful inspection of the structure and bonding of cationic σ‐cyclopropyl complexes support the possible existence of C−C agostic interactions at AuIII.

σ-Cyclopropyl to π-Allyl Rearrangement at AuIII.

The possibility for AuIII σ-cyclopropyl complexes to undergo ring-opening and give π-allyl complexes was interrogated. The transformation was first evidenced within (P,C)-cyclometalated complexes, it occurs within hours at -50 °C. It was then generalized to other ancillary ligands. With (N,C)-cyclometalated complexes, the rearrangement occurs at room temperature while it proceeds already at -80 °C with a dicationic (P,N)-chelated complex. Density Functional Theory (DFT) calculations shed light on the mechanism of the transformation, a disrotatory electrocyclic ring-opening. Intrinsic Bond Orbital (IBO) analysis along the reaction profile shows the cleavage of the distal σ(CC) bond to give a π-bonded allyl moiety. Careful inspection of the structure and bonding of cationic σ-cyclopropyl complexes support the possible existence of C-C agostic interactions at AuIII .

The Telluraboranes closo-TeB5Cl5 and closo-TeB11Cl11 with Exceptionally Long Body Diagonals: Syntheticand Bonding Motifs for Innovative Octahedral and Icosahedral Geometries.

Six-vertex closo-TeB5Cl5 (1) and twelve-vertex closo-TeB11Cl11 (2) telluraboranes have been prepared via co-pyrolysis of B2Cl4 with TeCl4in vacuo at temperatures between 360ºC and 400°C. Both compounds are sublimable, off-white solids, and they have been characterized by one- and two-dimensional 11B-NMR and high-resolution mass spectroscopy. Both ab initio/GIAO/NMR and DFT/ZORA/NMR computations support octahedral and icosahedral geometries for 1 and 2, respectively, as expected due to their closo-electron counts. The octahedral structure of 1 has been confirmed by single-crystal X-ray diffraction on an incommensurately modulated crystal. The corresponding bonding properties have been analyzed in terms of the intrinsic bond orbital (IBO) approach. 1 is the first example of a polyhedral telluraborane with a cluster size smaller than 11 vertices.

Lewis Acid-Assisted C(sp3)-C(sp3) Reductive Elimination at Gold.

The phosphine-borane iPr2P(o-C6H4)BFxyl2 (Fxyl = 3,5-(F3C)2C6H3) 1-Fxyl was found to promote the reductive elimination of ethane from [AuMe2(μ-Cl)]2. Nuclear magnetic resonance monitoring revealed the intermediate formation of the (1-Fxyl)AuMe2Cl complex. Density functional theory calculations identified a zwitterionic path as the lowest energy profile, with an overall activation barrier more than 10 kcal/mol lower than without borane assistance. The Lewis acid moiety first abstracts the chloride to generate a zwitterionic Au(III) complex, which then readily undergoes C(sp3)-C(sp3) coupling. The chloride is finally transferred back from boron to gold. The electronic features of this Lewis-assisted reductive elimination at gold have been deciphered by intrinsic bond orbital analyses. Sufficient Lewis acidity of boron is required for the ambiphilic ligand to trigger the C(sp3)-C(sp3) coupling, as shown by complementary studies with two other phosphine-boranes, and the addition of chlorides slows down the reductive elimination of ethane.

Crystal structure, bond characteristics and microwave dielectric properties of Ce2[Zr1-x(Sr1/3B2/3)x]3(MoO4)9 (B = Ta, Sb) solid solutions

A series of Ce2[Zr1-x(A)x]3(MoO4)9 (A = Sr1/3Ta2/3, Sr1/3Sb2/3; x = 0.02, 0.04, 0.06, 0.08 and 0.10) (abbreviated as CZ1-xTx and CZ1-xSx) microwave dielectric ceramics were studied systematically with respect to microstructures, sintering behaviors, crystal structures, microwave dielectric properties and infrared vibrational modes. Density measurements and scanning electron microscopy (SEM) reveal the dense and homogeneous microstructures. X-ray diffraction (XRD) results confirm the formation of solid solutions belonging to the hexagonal system with a R3‾c space group, and the lattice volume increases with raising the doping content. Furthermore, the complex chemical bond theory was used to calculate the intrinsic bond parameters, and the correlations between the microwave dielectric properties and intrinsic bond parameters were established. Finally, far infrared (FIR) spectra reveal that the main polarization contribution stems from the absorptions of the phonon oscillations in these two groups of ceramics. Typically, the optimum microwave dielectric properties are achieved for CZ0.9T0.1 and CZ0.94S0.06 ceramics with εr = 10.24, Q × f = 92,009 GHz (at 9.70 GHz), τf = −8.84 ppm °C−1 and εr = 10.40, Q × f = 82,696 GHz (at 9.69 GHz) and τf = −8.04 ppm °C−1, respectively. Interestingly, the CZ0.9T0.1 ceramic exhibits the maximum Q × f value in the ion doped Ce2Zr3(MoO4)9 ceramics while retaining a good τf = −8.84 ppm °C−1.

Bond formation insights into the Diels-Alder reaction: A bond perception and self-interaction perspective.

The behavior of electrons during bond formation and breaking cannot commonly be accessed from experiments. Thus, bond perception is often based on chemical intuition or rule-based algorithms. Utilizing computational chemistry methods, we present intrinsic bond descriptors for the Diels-Alder reaction, allowing for an automatic bond perception. We show that these bond descriptors are available from localized orbitals and self-interaction correction calculations, e.g., from Fermi-orbital descriptors. The proposed descriptors allow a sparse, simple, and educational inspection of the Diels-Alder reaction from an electronic perspective. We demonstrate that bond descriptors deliver a simple visual representation of the concerted bond formation and bond breaking, which agrees with Lewis' theory of bonding.

Theoretical study of lithium oxide clusters adsorbed on anatase TiO2 surface

The search for materials that have broad applicability as photocatalysts is growing interest. Titanium dioxide (TiO2) is a semiconductor with demonstrated photocatalytic properties, and its improvement with lithium oxide (LO) adsorption (LO-TiO2) is investigated using density functional theory (DFT). The modeling of the electronic structure of three types of LO as lithium oxide (Li2O)n, lithium peroxide (Li2O2)n, and lithium superoxide radical (LiO2)n (n = 1,2,3) adsorbed on anatase TiO2 shows an increase in their reactivities. The bandgap energy decreases in the range of 3.07–0.33 eV compared to TiO2 (3.2 eV) and conducting states from LO and 2p orbital of O(TiO2) towards 3d orbital of titanium (TiO2) are generated. The Independent Gradient Model and the intrinsic bond strength index are applied to gain insight into the intermolecular interactions between LO and TiO2. These results are coherent with that predicted by the interaction energy of LO-TiO2, which suggests that the more stable systems are (Li2O)2 and (Li2O2)3. Optical properties calculated with TD-DFT show a visible shift of the main absorption band compared to TiO2. The theoretical results show that the adsorption of lithium oxide onto a TiO2 surface would be an excellent strategy to produce a material as a visible light-activated photocatalyst.

Thermostability enhancement of Escherichia coli phytase by error-prone polymerase chain reaction (epPCR) and site-directed mutagenesis.

Phytase efficiently hydrolyzes phytate to phosphate; thus, it is widely used to increase phosphorus availability in animal feeds and reduce phosphorus pollution through excretion. Phytase is easily inactivated during feed pelleting at high temperature, and sufficient thermostability of phytase is essential for industrial applications. In this study, directed evolution was performed to enhance phytase thermostability. Variants were initially expressed in Escherichia coli BL21 for screening, then in Pichia pastoris for characterization. Over 19,000 clones were generated from an error-prone Polymerase Chain Reaction (epPCR) library; 5 mutants (G10, D7, E3, F8, and F9) were obtained with approximately 9.6%, 10.6%, 11.5%, 11.6%, and 12.2% higher residual activities than the parent after treatment at 99°C for 60min. Three of these mutants, D7, E3, and F8, exhibited 79.8%, 73.2%, and 92.6% increases in catalytic efficiency (kcat/Km), respectively. In addition, the specific activities of D7, E3, and F8 were 2.33-, 1.98-, and 2.02-fold higher than parental phytase; they were also higher than the activities of all known thermostable phytases. Sequence analysis revealed that all mutants were substituted at residue 75 and was confirmed that the substitution of cysteine at position 75 was the main contribution to the improvement of thermostability of mutants by saturation mutagenesis, indicating that this amino acid is crucial for the stability and catalytic efficiency of phytase. Docking structure analysis revealed that substitution of the C75 residue allowed the mutants to form additional hydrogen bonds in the active pocket, thereby facilitating binding to the substrate. In addition, we confirmed that the intrinsic C77-C108 disulfide bond in E. coli phytase is detrimental to its stability.

Novel Bis-1,3,4-Thiadiazoles Derivatives: Synthesis, Spectroscopic Characterization, DFT Calculations and Evaluation of their Antimicrobial and Antioxidant Activities

Two new, bis-1,3,4-thiadiazoles derivatives (I and II), were prepared by cyclization reaction of oxalic acid with N-alkyl/allyl thiosemicarbazides and phosphorous oxychloride (POCl3). Then the newly prepared products screened for their antimicrobial and antioxidant activities. The biological activity results shown that tested compounds exhibited effective antibacterial activity against six different bacteria. However, the compound II demonstrated greater ABTS˙+ scavenging ability. The characterization of the synthesized molecules was done by FT-IR, 1H NMR, 13C NMR spectroscopic methods and elemental analysis. Moreover, the experimental FT-IR and NMR spectra of the molecules were compared with the results calculated at the cc-pvtz, 6-311g(2d,2p), and 6-311++g(2d,2p) levels of theory. The effect of substituted groups on the spectral and electronic properties of the compounds was investigated. NCI and QTAIM analyses were performed to examine the effects of allyl group and intramolecular interactions on σ and π bonds. How the N-H bonds of the substituted groups affect the bond degrees was investigated using Fuzzy, Laplacian and Mayer approaches, and the relationship of the data with the antioxidant properties of the compounds was examined. In addition, the relationship between bond stretching force constant and intrinsic bond strength index, electron density, and delocalization index for some bonds was revealed.