Improved definition of bond orders for correlated wave functions

The oxidation state in low-valent beryllium and magnesium compounds

Low-valent group 2 (E = Be and Mg) stabilized compounds have been long synthetically pursued. Here we discuss the electronic structure of a series of Lewis base-stabilized Be and Mg compounds. Despite the accepted zero(0) oxidation state nature of the group 2 elements of some recent experimentally accomplished species, the analysis of multireference wavefunctions provides compelling evidence for a strong diradical character with an oxidation state of +2. Thus, we elaborate on the distinction between a description as a donor-acceptor interaction L(0) ⇆ E(0) ⇄ L(0) and the internally oxidized situation, better interpreted as a diradical L(-1) → E(+2) ← L(-1) species. The experimentally accomplished examples rely on the strengthened bonds by increasing the π-acidity of the ligand; avoiding this interaction could lead to an unprecedented low-oxidation state.

DFT Study for Adsorbing of Bromine Monochloride onto BNNT (5,5), BNNT (7,0), BC2NNT (5,5), and BC2NNT (7,0)

The study of intermolecular interactions is of great importance. This study attempted to quantitatively examine the interactions between bromine monochloride (BrCl) with pristine boron nitride nanotube (BNNT) armchair (5,5) and zigzag (7,0) as well as armchair (5,5) BC2NNT and zigzag (7,0) BC2NNT in vacuum. Quantum mechanical studies of such systems are possible in the density functional theory (DFT) framework. For this purpose, various functionals, such as B3LYP-D3, [Formula: see text]B97XD, and M062X, have been used. One of the most suitable basis functionals for the systems studied in this research is 6-311G (d), which has been used in both optimization calculations and calculations related to wave function analyses. The main part of this work is the study of various analyses that reveal the nature of the intermolecular interactions between the two components introduced above. The results of conceptual DFT, natural bond orbital, non-covalent interactions, and quantum theory of atoms in molecules (QTAIM) were consistent and in favor of physical adsorption in all systems. Gallium had more adsorption energy than other dopants. The HOMO–LUMO energy gaps were as follows: BNNT (5,5): 10.296, BNNT (7,0): 9.015, BC2NNT (5,5): 7.022, and BC2NNT (7,0): 5.979[Formula: see text]eV at B3LYP-D3/6-311G (d) model chemistry. The strongest interaction is related to the BC2NNT (7,0)/BrCl cluster: [Formula: see text][Formula: see text]eV. The results of QTAIM and NCI analysis identified the intermolecular interactions of the type of strong van der Waals interaction for these nanotubes. The sensitivity of the adsorption increased when a gas molecule interacted with carbon-doped BNNT, and the change in the frontier orbital gap could be used to design nanosensors to detect BrCl gas.

Non-covalent interactions of cysteine onto C60, C59Si, and C59Ge: a DFT study

The study of intermolecular interactions is of great importance. This study attempted to quantitatively examine the interactions between cysteine (C₃H₇NO₂S) and fullerene nanocages, C₆₀, in vacuum. As the frequent introduction of elements as impurities into the structure of nanomaterials can increase the intensity of intermolecular interactions, nanocages doped with silicon and germanium have also been studied as adsorbents, C₅₉Si and C₅₉Ge. Quantum mechanical studies of such systems are possible in the density functional theory (DFT) framework. For this purpose, various functionals, such as B3LYP-D3, ωB97XD, and M062X, have been used. One of the most suitable basis functionals for the systems studied in this research is 6-311G (d), which has been used in both optimization calculations and calculations related to wave function analyses. The main part of this work is the study of various analyses that reveal the nature of the intermolecular interactions between the two components introduced above. The results of conceptual DFT, natural bond orbital, non-covalent interactions, and quantum theory of atoms in molecules were consistent and in favor of physical adsorption in all systems. Germanium had more adsorption energy than other dopants. The HOMO-LUMO energy gaps were as follows: C₆₀: 5.996, C₅₉Si: 5.309, and C59Ge: 5.188 eV at B3LYP-D3/6-311 G (d) model chemistry. The sensitivity of the adsorption increased when an amino acid molecule interacted with doped C₆₀, and this capability could be used to design nanocarrier to carry cysteine amino acid.

A comprehensive investigation of the intermolecular interactions between CH2N2 and X12Y12 (X = B, Al, Ga; Y = N, P, As) nanocages

In this paper, we have theoretically determined the possibility of adsorption of the gaseous CH2N2 molecule on the surface of X12Y12 nanocages, where X = B, Al, Ga and Y = N, P, As. The electronic structure calculations have been performed by density functional theory (DFT) using four functionals (i.e., B3LYP-D3, M06-2X, ωB97XD, and CAM-B3LYP), together with the 6-311G(d) basis function. We find that the adsorption of CH2N2 on top of the X–Y bond of the nanocage is the most preferred site for adsorption. The adsorption process is accompanied by a charge-transfer phenomenon, which results in a strong bond between the terminal N atom of diazomethane and the X atom of the nanocage. This gives rise to significant changes in the highest and lowest occupied molecular orbital (HOMO and LUMO, respectively) energies and thus attribute properties to the nanocages that enable them to act as building blocks of CH2N2 sensing materials.

Comparison of DAFH and FALDI-like approaches

Two complementary methodologies for extracting useful insights into electronic structure and bonding from contemporary wavefunctions are compared. The first of these, known as the analysis of domain-averaged Fermi holes (DAFH), mostly provides visually appealing descriptions of the role and the extent of electron sharing in chemical bonding. The second one, known as the fragment, atom, localized, delocalized and interatomic (FALDI) charge density decomposition scheme, uses the partitioning of certain localization and delocalization indices to focus on highly visual contributions associated with individual domains and with pairs of domains, respectively. Four variants of a FALDI-like approach are investigated here in some detail, mostly to establish which of them are the most reliable and the most informative. In addition to ‘full’ calculations that use the correlated pair density, the consequences for the DAFH and FALDI-like procedures of using instead a popular one-electron approximation are explored. Additionally, the geometry dependence of the degree of acceptability of the errors that this introduces for delocalization indices is assessed for different formal bond multiplicities. The familiar molecular test systems employed for these various linked investigations are the breaking of the bonds in H2 and in N2, as well as the nature of the bonding in B2H6, as a simple example of multicenter bonding. One of the key outcomes of this study is a clear understanding of how DAFH analysis and a particular variant of FALDI-like analysis could be most profitably deployed to extract complementary insights into more complex and/or controversial bonding situations.

An Ultimate Investigation on the Adsorption of Amantadine on Pristine and Decorated Fullerenes C59X (X=Si, Ge, B, Al, Ga, N, P, and As): A DFT, NBO, and QTAIM Study

In this investigation, the feasibility of detecting the amantadine (AMD) molecule onto the outer surface of pristine fullerene (C[Formula: see text]), as well as C[Formula: see text]X ([Formula: see text], Ge, B, Al, Ga, N, P, and As) decorated structures, was carefully evaluated. For achieving this goal, a density functional theory level of study using the HSEH1PBE functional together with a 6-311G(d) basis set has been used. Subsequently, the B3LYP-D3, wB97XD and M062X functionals with a 6-311G(d) basis set were also employed to consider the single point energies. Natural bond orbital (NBO) and the quantum theory of atoms in molecules (QTAIM) were implemented using the B3LYP-D3/6-311G(d) method and the results were compatible with the electronic properties. In this regard, the total density of states (TDOSs), the Wiberg bond index (WBI), natural charge, natural electron configuration, donor–acceptor NBO interactions, and the second-order perturbation energies are performed to explore the nature of the intermolecular interactions. All of the energy calculations and population analyses denote that by adsorbing of the AMD molecule onto the surface of the considered nanostructures, the intermolecular interactions are of the type of strong physical adsorption. Among the doped fullerenes, Ge-doped structure has very high adsorption energy compared to other elements. Generally, it was revealed that the sensitivity of the adsorption will be increased when the AMD molecule interacts with the decorated fullerenes and decrease the HOMO–LUMO band gap; therefore, the change of electronic properties can be used to design suitable nanocarrier.

The adsorption of chlorofluoromethane on pristine, and Al- and Ga-doped boron nitride nanosheets: a DFT, NBO, and QTAIM study

In the present investigation, the feasibility of detecting the chlorofluoromethane (CFM) gas molecule onto the outer surface of pristine single layer boron nitride nanosheet (BNNS), as well as its aluminum (Al)- and gallium (Ga)-doped structures, was carefully evaluated. For achieving this goal, a density functional theory level of study using the Perdew, Burke, and Ernzerhof exchange-correlation (PBEPBE) functional together with a 6-311G(d) basis set has been used. Subsequently, the B3LYP, CAM-B3LYP, wB97XD, and M062X functionals with a 6-311G(d) basis set were also employed to consider the single-point energies. Natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) were implemented by using the B3LYP-D3/6-311G(d) method, and the results were compatible with the electronic properties. In this regard, the total density of states (TDOSs), the Wiberg bond index (WBI), natural charge, natural electron configuration, donor-acceptor natural bond orbital interactions, and the second-order perturbation energies are performed to explore the nature of the intermolecular interactions. All of the energy calculations and population analyses denote that by adsorbing of the gas molecule onto the surface of the considered nanostructures, the intermolecular interactions are of the type of strong chemical adsorption. Among the doped nanosheets, Ga-doped nanosheet has very high adsorption energy compared with other elements (i.e., Ga-doped > Al-doped > pristine). Generally, it was revealed that the sensitivity of the adsorption will be increased when the gas molecule interacts with decorated nanosheets and decrease the HOMO-LUMO band gap; therefore, the change of electronic properties can be used to design suitable nanosensors to detect CFM gas. Graphical abstract.

Elucidating the Magnitude of Internal Reorganization Energy of Molecular Excited States from the Perspective of Transition Density

Quantifying vibronic couplings in molecular excited states is crucial for the elucidation of a broad range of photophysical phenomena. In this study, we compare different theoretical approaches for the calculation of reorganization energy, a measure of vibronic coupling strength, and provide a rigorous derivation to show that molecular transition density characterizing electron-hole excitation could be used to quantify the magnitude of reorganization energy. The theory enables a descriptor based on molecular-orbital coefficients and atomic transition densities to quantify the magnitude of reorganization energies in molecular excited states. Applying the approach to low-lying excited states of polyacenes, we demonstrate that transition density distribution explains the difference in the magnitude of the reorganization energy of different excited states. Furthermore, to clarify the applicability of the transition density descriptor in molecular design for small-reorganization energy molecules, we investigate a broad range of molecular chromophores to show the effectiveness of the proposed theory. With this perspective on the relationship between reorganization energy and transition density, we successfully provide a quantitative rule to identify π-conjugated systems with small reorganization energy in the excited state, which should be useful for the development of novel optoelectronic materials.

Proof of concept for poor inhibitor binding and efficient formation of covalent adducts of KRASG12C and ARS compounds

The use of selective covalent inhibitors with low binding affinity and high reactivity with the target enzyme is a promising way to solve a long-standing problem of the "undruggable" RAS-like proteins. Specifically, compounds of the ARS family that prevent the activation of the GDP-bound G12C mutant of Kirsten RAS (KRAS) are in the focus of recent experimental research. We report the first computational characterization of the entire reaction mechanism of the covalent binding of ARS-853 to the KRASG12C·GDP complex. The application of molecular dynamics, molecular docking and quantum mechanics/molecular mechanics approaches allowed us to model the inhibitor binding to the protein and the chemical reaction of ARS-853 with Cys12 in the enzyme binding site. We estimated a full set of kinetic constants and carried out numerical kinetic analysis of the process. Thus, we were able to compare directly the physicochemical parameters of the reaction obtained in silico and the macroscopic parameters observed in experimental studies. From our computational results, we explain the observed unusual dependence of the rate constant of covalent complex formation, kobs, on the ARS concentration. The latter depends both on the non-covalent binding step with the equilibrium constant, Ki, and on the rate constant of covalent adduct formation, kinact. The calculated ratio kinact/Ki = 213 M-1 s-1 reproduces the corresponding experimental value of 250 ± 30 M-1 s-1 for the interaction of ARS-853 with KRASG12C. Electron density analysis in the reactive region demonstrates that covalent bond formation occurs efficiently according to the Michael addition mechanism, which assumes the activation of the C[double bond, length as m-dash]C bond of ARS-853 by a water molecule and Lys16 in the binding site of KRASG12C. We also refine the kinact and Ki constants of the ARS-107 compound, which shares common features with ARS-853, and show that the decrease in the kinact/Ki ratio in the case of ARS-107 is explained by changes in both Ki and kinact constants.

Cobalt/Lewis Acid Catalysis for Hydrocarbofunctionalization of Alkynes via Cooperative C-H Activation

A catalytic system comprising a cobalt-diphosphine complex and a Lewis acid (LA) such as AlMe₃ has been found to promote hydrocarbofunctionalization reactions of alkynes with Lewis basic and electron-deficient substrates such as formamides, pyridones, pyridines and related azines, imidazo[1,2-a]pyridines, and azole derivatives through site-selective C-H activation. Compared with known Ni/LA catalytic systems for analogous transformations, the present catalytic systems not only feature convenient setup using inexpensive and bench-stable precatalyst and ligand such as Co(acac)₃ and 1,3-bis(diphenylphosphino)propane (dppp) but also display distinct site-selectivity toward C-H activation of pyridone and pyridine derivatives. In particular, a completely C4-selective alkenylation of pyridine has been achieved for the first time. Meanwhile, the present catalytic system proved to promote exclusively C5-selective alkenylation of imidazo[1,2-a]pyridine derivatives. Mechanistic studies including DFT calculations on the Co/Al-catalyzed addition of formamide to alkyne have suggested that the reaction involves cleavage of the carbamoyl C-H bond as the rate-limiting step, which proceeds through a ligand-to-ligand hydrogen transfer (LLHT) mechanism leading to an alkenyl(carbamoyl)cobalt intermediate.

Dual-Self-Restricted GFP Chromophore Analogues with Significantly Enhanced Emission

The tremendous gap of fluorescence emission of synthetic green fluorescent protein (GFP) chromophore to the protein itself makes it impossible to use for applications in molecular and cellular imaging. Here, we developed an efficient methodology to enhance the photoluminescence response of synthetic GFP chromophore analogues by constructing dual-self-restricted chromophores. Single self-restricted chromophores were first generated with 2,5-dimethoxy substitution on the aromatic ring, which were further modified with phenyl or 2,5-dimethoxy phenyl to form dual-self-restricted chromophores. These two chromophores showed an obvious solvatofluorochromic color palette across blue to yellow with a maximum emission Stokes shift of 95 nm and dramatically enhanced fluorescence emission in various aprotic solvents, especially in hexane, where the QY reached around 0.6. Importantly, in acetonitrile and dimethyl sulfoxide, the fluorescence QYs of both chromophores were over 0.22, which were the highest reported so far in high polar organic solvents. Meanwhile, the fluorescence lifetimes also improved obviously with the maximum of around 4.5 ns. Theoretical calculations revealed a more favorable Mülliken atomic charge translocation over the double-bond bridge and illustrated much higher energy barriers for the Z/E photoisomerization together with larger bond orders compared with the GFP core chromophore, p-HBDI. Our work significantly improved the fluorescence emission of synthetic GFP chromophore analogues in polar solvents while reserved the multicolor emitting function, providing a solid molecular motif for engineering high-performance fluorescent probes.

Deductive molecular mechanics of four-coordinated carbon allotropes

We propose a semi-quantitative quantum-chemical model ranging the energies of four-coordinated carbon allotropes on the energy scale and providing efficient and precise estimates of their structure and elastic properties (hardness).

The influence of external electric fields on charge reorganization energy in organic semiconductors

Charge reorganization energies (λ) of inter-ring carbon–carbon (IRCC) bond connected conjugated polycyclics are shown to exhibit an electric-field-driven anisotropic character.

The influence of correlation on (de)localization indices from a valence bond perspective

When going beyond the Hartree-Fock level to correlated methods, one observes a significant reduction in the delocalization index. This is commonly interpreted as a weakening of electron sharing due to electron correlation, although this is rather counter-intuitive to the concomitant energy lowering. In this study, we use an analytical valence bond model and full CI calculations to show that this reduction in the delocalization index actually goes hand in hand with increased covalent contributions at the expense of ionic contributions. This suggests that we should be careful in formulating interpretations of these results in (de)localization indices. Graphical Abstract Variation of the localization Δ(Ω_A, Ω_A) and delocalization index Δ(Ω_A, Ω_B) as a function of the parameter ω. By adjusting this parameter ω from [Formula: see text] to 0, we can gradually change the underlying wave function from a Hartree-Fock to a Heitler-London description.

Theoretical investigations of the chemical bonding in MM'O2 clusters (M, M' = Be, Mg, Ca)

Motivated by the known stability of the somewhat unusual Be₂O₂ rhombus, which features a short Be-Be distance but no direct metal-metal bonding, we investigate the nature of the bonding interactions in the analogous clusters MM'O₂ (M, M' = Be, Mg, Ca). CCSD/cc-pVTZ and CCSD(T)/cc-pVQZ calculations, amongst others, are used to determine optimized geometries and the dissociation energies for splitting the MM'O₂ clusters into metal oxide monomers. The primary tools used to investigate the chemical bonding are the analysis of domain-averaged Fermi holes, including the generation of localized natural orbitals, and the calculation of appropriate two- and three-center bond indices. Insights emerging from these various analyses concur with earlier studies of M₂O₂ rhombic clusters in that direct metal-metal bonding was not observed in the MM'O₂ rings whereas weak three-center (3c) bonding was detected in the MOM' moieties. In general terms, these mixed MM'O₂ clusters exhibit features that are intermediate between those of M₂O₂ and M'₂O₂, and the differences between the M and M' atoms appear to have little impact on the overall degree of 3c MOM' bonding. Graphical abstract Bonding situation in MM'O₂ clusters (M, M' = Be, Mg, Ca).

Quantum Chemical Insight into La2C96: Metal Carbide Fullerene La2C2@C94 versus Dimetallofullerene La2@C96

A family of dilanthanum-containing endohedral metallofullerene La₂C_2n (n = 46-51) was synthesized recently. In the present work, a systematical investigation on La₂C₉₆ series including the carbide clusterfullerene form La₂C₂@C₉₄ and the conventional dimetallofullerene form La₂@C₉₆ was implemented by density functional theory, combined with statistical mechanics. Three isomers, i.e., La₂@D₂(191838)-C₉₆, La₂C₂@C_s(153479)-C₉₄, and La₂C₂@C₁(153491)-C₉₄ were disclosed to be thermodynamically stable at the temperature region of endohedral metallofullerene formation. La₂@D₂(191838)-C₉₆ is the prevailing isomer at low temperature, while La₂C₂@C_s(153479)-C₉₄ and La₂C₂@C₁(153491)-C₉₄ are the most and second-most abundant isomers at high temperature. Interestingly, the highest occupied molecular orbital (HOMO) of La₂C₂@C₁(153491)-C₉₄ is distributed on one pole of the cage, and the lowest unoccupied molecular orbital (LUMO) of this isomer is mainly located on the equator of the cage, which can facilitate synthesis of regioselective derivatives. This work will provide useful information for further experimental identification and application of La₂C₉₆.

Mechanistic insights on the Pd-catalyzed addition of C-X bonds across alkynes - a combined experimental and computational study

The Pd-catalyzed intramolecular addition of carbamoyl chlorides and aryl halides across alkynes is investigated by means of DFT calculations and mechanistic test experiments. The data suggest a mechanistic pathway that involves oxidative addition, alkyne insertion, cis → trans isomerization and reductive elimination. Our data indicate that oxidative addition is the reactivity limiting step in the addition of aryl chlorides and bromides across alkynes. However, for the corresponding addition of carbamoyl chlorides, alkyne insertion is found to be limiting. Full energetic reaction pathways for the intramolecular additions across alkynes are presented herein and the role of ligands, alkyne substituents and tether moieties are discussed. Notably, the calculations could rationalize a pronounced effect of the alkyne substituent, which accounts for the exceptional reactivity of TIPS-substituted alkynes. In particular, the bulky silyl moiety is shown to significantly destabilize the formed Pd(ii)-intermediates, thus facilitating both cis → trans isomerization and reductive elimination, which overall results in a flatter energetic landscape and a therefore increased catalytic efficiency.

Sc3N@Cs(39715)–C82: a missing isomer linked to Sc3N@C2v(39718)–C82 by a single step Stone–Wales transformation

Density functional theory combined with statistical mechanics calculations indicate that Sc₃N@C_2v(39718)–C₈₂ and Sc₃N@C_s(39715)–C₈₂ linked by a single Stone–Wales transformation can be obtained at the fullerene formation temperature region.

Structure, aromaticity, stability, and energetic performance of the analogues and derivatives of s-heptazine

s-heptazine is one of the most attractive polycyclic C-N precursors for graphitic carbon nitride materials (CNx). In this paper in order to find the relationships between the structure, aromaticity, and stability for this novel compound, its analogues with three conjoint six-membered rings (I∼V) and derivatives with different substituents (VI-1∼VI-5) were investigated using the density functional theory method. Aromaticity was predicted using the magnetic criterion iso-chemical shielding surface in the Z direction (ICSSzz) obtained with the gauge-independent atomic orbital (GIAO) method. Stability was estimated by the band gap and the topological properties obtained from the atoms in molecules theory. Results show that replacement of the CH groups with the nitrogen atoms in the tricyclic core enhances both the aromaticity and the stability. s-heptazine (VI) that has the maximum number of N atoms among analogues I∼VI possesses the largest aromaticity and the best stability. Substitutions of -NH2, -NHNH2, and -N3 groups increase not only the aromaticity but also the stability; -NO2 increases the aromaticity while decreases the stability; -CN decreases both the aromaticity and the stability. Furthermore, the energetic performance of VI-1∼VI-5 was evaluated according to the estimated specific impulse (Is). The obtained Is has the order of VI-5>VI-4>VI-3>VI>VI-1>VI-2. The Is of VI-5 is higher than that of HMX (1, 3, 5, 7-tetranitro-1, 3, 5, 7-tetraazacyclooctane).