Molecular Orbital Research Articles

DFT, Molecular Docking, Bioactivity and ADME Analyses of Vic-dioxim Ligand Containing Hydrazone Group and its Zn(II) Complex.

Cancer is one of the diseases affecting a large population worldwide and resulting in death. Finding new anti-cancer drugs that are target-focused and have low toxicity is of great importance. This study aimed to investigate the effects of vic-dioxime derivatives carrying hydrazone group and its Zn(II) complex on cancer using molecular docking, bioactivity and quantum chemical calculations. Molecular docking studies were performed on epidermal growth factor receptor and vascular endothelial growth factor receptor 2 target proteins. Furthermore, molecular geometry was performed, and the frontier molecular orbitals, Mulliken charges and molecular electron density distribution were evaluated using density functional theory. Also, the bioactivity parameters of the compounds were evaluated, and ADME analysis was performed using web-based tools. Higher binding affinity was observed for Zn(II) complex with target proteins vascular endothelial growth factor receptor 2 and against epidermal growth factor receptor when compared with LH2. Only the Zn(II) complex against the epidermal growth factor receptor had ligand efficiency and fit quality in the valid range. Furthermore, LH2 has the most potent electrophilic ability (acceptor) among other compounds. Moreover, both LH2 and Zn(II) complexes strongly satisfy Lipinski's rule of five. In conclusion, these novel compounds, especially Zn(II) complex, can be new candidates for anticancer drug development studies which are target-focused and have low toxicity.

MBE-CASSCF Approach for the Accurate Treatment of Large Active Spaces.

We present a novel implementation of the complete active space self-consistent field (CASSCF) method that makes use of the many-body expanded full configuration interaction (MBE-FCI) method to incrementally approximate electronic structures within large active spaces. On the basis of a hybrid first-order algorithm employing both Super-CI and quasi-Newton strategies for the optimization of molecular orbitals, we demonstrate both computational efficacy and high accuracy of the resulting MBE-CASSCF method. We assess the performance of our implementation on a set of established numerical tests before applying MBE-CASSCF in the investigation of the triplet-quintet spin gap of iron(II) porphyrin with active spaces as large as 50 electrons in 50 orbitals.

High‐Energy Nitrogen Rings Stabilized by Superatomic Properties

AbstractHow to stabilize nitrogen‐rich high‐energy‐density molecules under conventional conditions is particularly important for the energy storage and conversion of such systems and has attracted extensive attention. In this work, the theoretical study shows for the first time that the stabilization mechanism of the nitrogen ring conforms to the superatomic properties at the atomic level. This result occurs because the stabilized anionic nitrogen rings generally exhibit planar high symmetry and the injected electrons occupy the superatomic molecular orbitals (SAMOs) of the nitrogen rings. According to these results, the typical stabilized anionic nitrogen ring structures N64−, N5−, and N42− are identified, which possess delocalized molecular orbitals with the same symmetry as the atomic orbitals and electron arrangement consistent with the electron shell arrangement of the atom. On this basis, a pathway is further designed to stabilize nitrogen rings by introducing metal atoms as electron donors to form neutral ThN6, LiN5, and MgN4 structures, thereby replacing the anionization of systems. This study highlights the importance of developing nitrogen‐rich energetic materials from the perspective of superatoms.

Beyond Single-Reference Fixed-Node Approximation in Ab Initio Diffusion Monte Carlo Using Antisymmetrized Geminal Power Applied to Systems with Hundreds of Electrons.

Diffusion Monte Carlo (DMC) is an exact technique to project out the ground state (GS) of a Hamiltonian. Since the GS is always bosonic, in Fermionic systems, the projection needs to be carried out while imposing antisymmetric constraints, which is a nondeterministic polynomial hard problem. In practice, therefore, the application of DMC on electronic structure problems is made by employing the fixed-node (FN) approximation, consisting of performing DMC with the constraint of having a fixed, predefined nodal surface. How do we get the nodal surface? The typical approach, applied in systems having up to hundreds or even thousands of electrons, is to obtain the nodal surface from a preliminary mean-field approach (typically, a density functional theory calculation) used to obtain a single Slater determinant. This is known as single reference. In this paper, we propose a new approach, applicable to systems as large as the C60 fullerene, which improves the nodes by going beyond the single reference. In practice, we employ an implicitly multireference ansatz (antisymmetrized geminal power wave function constraint with molecular orbitals), initialized on the preliminary mean-field approach, which is relaxed by optimizing a few parameters of the wave function determining the nodal surface by minimizing the FN-DMC energy. We highlight the improvements of the proposed approach over the standard single-reference method on several examples and, where feasible, the computational gain over the standard multireference ansatz, which makes the methods applicable to large systems. We also show that physical properties relying on relative energies, such as binding energies, are affordable and reliable within the proposed scheme.

Synthesis and characterization of low-dimensional N-heterocyclic carbene lattices.

The covalent interaction of N-heterocyclic carbenes (NHCs) with transition metal atoms gives rise to distinctive frontier molecular orbitals (FMOs). These emergent electronic states have spurred the widespread adoption of NHC ligands in chemical catalysis and functional materials. Although formation of carbene-metal complexes in self-assembled monolayers on surfaces has been explored, design and electronic structure characterization of extended low-dimensional NHC-metal lattices remains elusive. Here we demonstrate a modular approach to engineering one-dimensional (1D) metal-organic chains and two-dimensional (2D) Kagome lattices using the FMOs of NHC-Au-NHC junctions to create low-dimensional molecular networks exhibiting intrinsic metallicity. Scanning tunneling spectroscopy and first-principles density functional theory reveal the contribution of C-Au-C π-bonding states to dispersive bands that imbue 1D- and 2D-NHC lattices with exceptionally small work functions.

Benzotrifuran based organic molecules for optoelectronic and charge transport properties for organic electronic devices

AbstractThe key motive of the current work is the detailed study of charge transport and optoelectronic properties of Benzotrifuran based organic molecules for organic electronic device applications. Density functional theory (DFT) and time dependent‐DFT simulations were executed on studied organic molecules. The absorption characteristics are ascertained and the results are compared with corresponding known experimental results. Frontier molecular orbitals, that is; highest occupied molecular orbital and lowest unoccupied molecular orbital, electron extraction potential, electron affinities, ionization potentials, reorganization energies (Z), and hole extraction potential of all the studied molecules are explored. In contrast, all of the examined organic compounds are with low hole (Zh) and electron (Ze) reorganization energies, making them suitable for use in organic electrical devices.

Cation-Stacking Approach Enabling Interconversion between Bis(xanthylium) and its Reduced Species.

Cyclophane-type dications with two units of xanthylium were designed, with the expectation that intramolecular interaction between cation units could induce changes in absorption and redox behavior. The desired dications were synthesized via the macrocyclic diketone as a key intermediate, which was efficiently obtained by a stepwise etherification. X-ray and UV/Vis measurements revealed that the cyclophane-type dications adopt a stacking structure in both the crystal and solution. Due to the intramolecular interaction caused by π-π stacking of the xanthylium units, a considerable blue shift compared to the corresponding monocations and a two-stage one-electron reduction process were observed in the dications. Furthermore, upon electrochemical reduction of dications, the formation of biradicals via radical cation species was demonstrated by UV/Vis spectroscopy with several isosbestic points at both stages. Therefore, the cation-stacking approach is a promising way to provide novel properties due to perturbation of their molecular orbitals and to stabilize the reduced species even though they have open-shell characters.

Tetraborated Intrinsically Axial Chiral Multi‐resonance Thermally Activated Delayed Fluorescence Materials

Chiral multi‐resonance thermally activated delayed fluorescence (CP‐MR‐TADF) materials hold promise for circularly polarized organic light‐emitting diode (CP‐OLED) and 3D display. Herein, we present two pairs of tetraborated intrinsically axial CP‐MR‐TADF materials, R/S‐BDBF‐BOH and R/S‐BDBT‐BOH, with conjugation‐extended bidibenzo[b,d]furan and bidibenzo[b,d]thiophene as chiral sources, which effectively participate in the distribution of frontier molecular orbitals. Due to the heavy‐atom effect, sulfur atoms are introduced to accelerate the reverse intersystem crossing process and increase efficiency of molecules. R/S‐BDBF‐BOH and R/S‐BDBT‐BOH manifest ultra‐pure blue emission peaking at 458/459 nm with full width at half maximum of 27 nm (0.16 eV), photoluminescence quantum yields of 90%/91% and dissymmetry factors (|gPL|) of 6.8 × 10‐4/8.5 × 10‐4, respectively. Correspondingly, the CP‐OLEDs exhibit good performances with external quantum efficiency of 30.1% and |gEL| factors of 1.2 × 10‐3.

Tetraborated Intrinsically Axial Chiral Multi-resonance Thermally Activated Delayed Fluorescence Materials.

Chiral multi-resonance thermally activated delayed fluorescence (CP-MR-TADF) materials hold promise for circularly polarized organic light-emitting diode (CP-OLED) and 3D display. Herein, we present two pairs of tetraborated intrinsically axial CP-MR-TADF materials, R/S-BDBF-BOH and R/S-BDBT-BOH, with conjugation-extended bidibenzo[b,d]furan and bidibenzo[b,d]thiophene as chiral sources, which effectively participate in the distribution of frontier molecular orbitals. Due to the heavy-atom effect, sulfur atoms are introduced to accelerate the reverse intersystem crossing process and increase efficiency of molecules. R/S-BDBF-BOH and R/S-BDBT-BOH manifest ultra-pure blue emission peaking at 458/459 nm with full width at half maximum of 27 nm (0.16 eV), photoluminescence quantum yields of 90%/91% and dissymmetry factors (|gPL|) of 6.8 × 10-4/8.5 × 10-4, respectively. Correspondingly, the CP-OLEDs exhibit good performances with external quantum efficiency of 30.1% and |gEL| factors of 1.2 × 10-3.

Tandem four-component reaction to access fused polycycles exhibiting aggregation-enhanced through-space charge transfer emission.

Rapid construction of new fluorescence emitters is essential in advancing synthetic luminescent materials. This study illustrated a piperidine-promoted reaction of chiral dialdehyde with benzoylacetonitrile and malonitrile, leading to the formation of the 6/6/7 fused cyclic product in good yield. The proposed reaction mechanism involves a dual condensation/cyclization process, achieving the formation of up to six bonds for fused polycycles. The single crystal structure analysis revealed that the fused cyclic skeleton contains face-to-face naphthyl and cyanoalkenyl motifs, which act as the electronic donor and acceptor, respectively, potentially resulting in through-space charge transfer (TSCT) emission. While the TSCT emissions were weak in solution, a notable increase in luminescence intensity was observed upon aggregation, indicating bright fluorescent light. A series of theoretical analyses further supported the possibility of spatial electronic communication based on frontier molecular orbitals, the distance of charge transfer, and reduced density gradient analysis. This work not only provides guidance for the one-step synthesis of complex polycycles, but also offers valuable insights into the design of aggregation-enhanced TSCT emission materials.

Unraveling redox pathways of the disulfide bond in dimethyl disulfide: Ab initio modeling.

In cellular environments, the reduction of disulfide bonds is pivotal for protein folding and synthesis. However, the intricate enzymatic mechanisms governing this process remain poorly understood. This study addresses this gap by investigating a disulfide bridge reduction reaction, serving as a model for comprehending electron and proton transfer in biological systems. Six potential mechanisms for reducing the dimethyl disulfide (DMDS) bridge through electron and proton capture were explored. Thermodynamic and kinetic analyses elucidated the sequence of proton and electron addition. MD-PMM, a method that combines molecular dynamics simulations and quantum-chemical calculations, was employed to compute the redox potential of the mechanism. This research provides valuable insights into the mechanisms and redox potentials involved in disulfide bridge reduction within proteins, offering an understanding of phenomena that are challenging to explore experimentally. All calculations used the Gaussian 09 software package at the MP2/6-311 + g(d,p) theory level. Visualization of the molecular orbitals and electron densities was conducted using Gaussview6. Molecular dynamics simulations were performed using GROMACS with the CHARMM36 force field. The PyMM program (Python Program for QM/MM Simulations Based on the Perturbed Matrix Method) is used to apply the Perturbed Matrix Method to MD simulations.

Quasi-degenerate extension of local N-electron valence state perturbation theory with pair-natural orbital method based on localized virtual molecular orbitals.

Chemical phenomena involving near-degenerate electronic states, such as conical intersections or avoided crossing, can be properly described using quasi-degenerate perturbation theory. This study proposed a highly scalable quasi-degenerate second-order N-electron valence state perturbation theory (QD-NEVPT2) using the local pair-natural orbital (PNO) method. Our recent study showed an efficient implementation of the PNO-based state-specific NEVPT2 method using orthonormal localized virtual molecular orbitals (LVMOs) as an intermediate local basis. This study derived the state-coupling (or off-diagonal) terms to implement QD-NEVPT2 in an alternative manner to enhance efficiency based on the internally contracted basis and PNO overlap matrices between different references. To facilitate further acceleration, a local resolution-of-the-identity (RI) three-index integral generation algorithm was developed using LMOs and LVMOs. Although the NEVPT2 theory is considered to be less susceptible to the intruder-state problem (ISP), this study revealed that it can easily suffer from ISP when calculating high-lying excited states. We ameliorated this instability using the imaginary level shift technique. The PNO-QD-NEVPT2 calculations were performed on small organic molecules for the 30 lowest-lying states, as well as photoisomerization involving the conical intersection of 1,1-dimethyldibenzo[b,f] silepin with a cis-stilbene skeleton. These calculations revealed that the PNO-QD-NEVPT2 method yielded negligible errors compared to the canonical QD-NEVPT2 results. Furthermore, we tested its applicability to a large photoisomerization system using the green fluorescent protein model and the ten-state calculation of the large transition metal complex, showcasing that off-diagonal elements can be evaluated at a relatively low cost.

Investigation of Anticancer Properties of 2-benzylidene-1-indanone and Its Derivatives by DFT and Molecular Docking

In this study, 2-benzylidene-1-indanone and its derivatives, which is a chalcone compound and contains indanone in its structure, were examined. Quantum chemical parameters for these compounds were calculated with the B3LYP method and the 6-31G(d) basis set and evaluated for their biological activity. The effect of different functional groups (F, Cl, Br, CF3, CH3 and OCH3) attached to the 2-benzylidene-1-indanone compound on biological activity was investigated. Some quantum chemical parameters such as highest energy filled molecule orbital energy (EHOMO), lowest non-bonding empty molecule orbital energy (ELUMO), energy gap (ΔE), hardness (η), softness (σ), global molecular electrophilicity (ω) index, global molecular nucleophilicity (ɛ) index, electron-accepting (ω+) and electron-donating (ω-) electrophilicity index were calculated for the biological activities of the compounds. Frontier molecular orbitals and molecular electrostatic potential (MEP) maps were interpreted. The biological activities of 2-benzylidine-1-indanone and some of its derivatives bearing the 1-indanone skeleton were evaluated by performing molecular docking studies with the target protein PDB ID = 1HJD corresponding to the melanoma cell line. The activity ranking obtained with quantum chemical parameters was found to be compatible with the binding energies obtained from docking results.

The electronic, structural and nonlinear optical properties of licochalcone L in the aqueous solution and gaseous phase: A DFT study

In the present article, various conformers of licochalcone L, a chalcone derivative extracted from the G. inflata root, have been analyzed in the aqueous solution and gaseous phase using calculation based on density functional theory (DFT). Nonlinear optical parameters such as dipole moment (μ), mean polarizability (α), polarizability anisotropy (Δα) and the first order hyperpolarizability (β) have been estimated to examine the NLO properties of the title molecule. These parameters were found to be significantly higher than those of standard molecules, indicating the potential NLO applications of licochalcone L. The analysis of natural bond orbitals (NBO) has been carried out to characterize various intramolecular interactions. The nucleus-independent chemical shift (NICS) technique has been used to investigate the aromaticity. Further, the pKa values have been computed for each hydroxyl group, revealing that the neutral form predominates at physiological pH, while the monoanionic form becomes predominant at pH greater than 9. The impact of solvation on the molecular electrostatic potentials and frontier molecular orbitals has been investigated for the neutral as well as monoanionic form of licochalcone L. A variety of global chemical reactivity descriptors have been calculated to highlight the structure-activity relationship.

Quantitative Analogue Simulation of Planar Molecules.

Synthetic quantum systems provide a pathway for exploring the physics of complex quantum matter in a programmable fashion. This approach becomes particularly advantageous when it comes to systems that are thermodynamically unfavorable. By sculpting the potential landscape of Cu(111) surfaces with carbon monoxide quantum corrals in a cryogenic scanning tunneling microscope, we created analogue simulators of planar organic molecules, including antiaromatic and non-Kekulé species that are generally reactive or unstable. Spectroscopic imaging of such synthetic molecules reveals close replications of molecular orbitals obtained from ab initio calculations of the organic molecules. We further illustrate the quantitative nature of such analogue simulators by faithful extraction of bond orders and global aromaticity indices, which are otherwise technically daunting using real molecules. Our approach therefore sets the stage for new research frontiers pertaining to the quantum physics and chemistry of designer nanostructures.

Ultrafast fragmentation of highly-excited doubly-ionized deoxyribose: role of the liquid water environment.

Ab initio molecular dynamics simulations are used to investigate the fragmentation dynamics following the double ionization of 2-deoxy-D-ribose (DR), a major component in the DNA chain. Different ionization scenarios are considered to provide a complete picture. First focusing on isolated DR2+, fragmentation patterns are determined for the ground electronic state, adding randomly distributed excitation energy to the nuclei. These patterns differ for the two isomers studied. To compare thermal and electronic excitation effects, Ehrenfest dynamics are also performed, allowing to remove the two electrons from selected molecular orbitals. Two intermediate-energy orbitals, localized on the carbon chain, were selected. The dissociation pattern corresponds to the most frequent pattern obtained when adding thermal excitation. On the contrary, targeting the four deepest orbitals, localized on the oxygen atoms, leads to selective ultrafast C-O and/or O-H bond dissociation. To probe the role of environment, a system consisting of a DR molecule embedded in liquid water is then studied. The two electrons are removed from either the DR or the water molecules directly linked to the sugar through hydrogen bonds. Although the dynamics onset is similar to that of isolated DR when removing the same deep orbitals localized on the sugar oxygen atoms, the subsequent fragmentation patterns differ. Sugar damage also occurs following the Coulomb explosion of neighboring H2O2+ molecules due to interaction with the emitted O or H atoms.

Unconventional Band Structure via Combined Molecular Orbital and Lattice Symmetries in a Surface-Confined Metallated Graphdiyne Sheet.

Graphyne (GY) and graphdiyne (GDY)-based monolayers represent the next generation two-dimensional (2D) carbon-rich materials with tunable structures and properties surpassing those of graphene. However, the detection of band formation in atomically thin GY/GDY analogues has been challenging, as both long-range order and atomic precision have to be fulfilled in the system. Here, we report direct evidence of band formation in on-surface synthesized metallated Ag-GDY sheets with mesoscopic (∼1µm) regularity. Employing scanning tunneling and angle-resolved photoemission spectroscopies, energy-dependent transitions of real-space electronic states above the Fermi level and formation of the valence band are respectively observed. Furthermore, density functional theory (DFT) calculations corroborate our observations and reveal that doubly degenerate frontier molecular orbitals on a honeycomb lattice give rise to flat, Dirac and Kagome bands close to the Fermi level. DFT modeling also indicates an intrinsic band gap for the pristine sheet material, which is retained for a bilayer with h-BN, whereas adsorption-induced in-gap electronic states evolve at the synthesis platform with Ag-GDY decorating the (111) facet of silver. These results illustrate the tremendous potential for engineering novel band structures via molecular orbital and lattice symmetries in atomically precise 2D carbon materials. This article is protected by copyright. All rights reserved.

Two halogenated coplanar Schiff base complexes: Insights into the impact of halogen substitution on intermolecular interactions via theoretical calculations

The manipulation of intermolecular interaction intensities significantly influences a wide range of domains in material science, attracting widespread attention from researchers. In this study, we used a strategy distinct from the adjustment of molecular skeletons, through the introduction of different halogenated ligands, two new coplanar halogenated Schiff base complexes with large conjugate structure [CuII(3,5-Cl-Salphmen)]·DMF(CuL3,5-Cl) and [CuII(3Br-5Cl-Salphmen)]·DMF(CuL3Br5Cl), where 3,5-Cl-Salphmen(H2L3,5-Cl) = N,N′-bis(3,5-dichlorosalicylidene)- diamine, 3Br-5Cl-Salphmen(H2L3,5-Br) = N,N′-bis(3‑bromo-5-chlorosalicylidene)- diamine were obtained. The effects of different substituted atoms on molecular orbitals, energy levels, intermolecular interstrength are analyzed in detail by DFT theory calculations, and compared with CuII-3,5-Br-Salphmen(CuL3,5-Br) and non-halogenated analogues CuII-Salphmen(CuLH). Analysis results show that the strategy of increasing molecular conjugation by the substitution of different halogen atoms can not only effectively modulate the charge distribution on the benzene ring but also can precisely control the binding energy as well as strength of intermolecular interactions.

First-Principles Study of Discharge Products and Their Stability for Lithium-Nitrogen Batteries.

Li-N2 batteries present a relatively novel approach to N2 immobilization, and an advanced N2/Li3N cycling method is introduced in this study. The low operating overpotential of metal-air batteries is quite favorable to their stable cycling performance, providing a prospect for the development of a new type of battery with extreme voltage. The battery system of Li-N2 uses N2 as the positive electrode, lithium metal as the negative electrode, and a conductive medium containing soluble lithium salts as the electrolyte. In accordance with its voltage-distribution trend, a variety of lithium-nitrogen molecule intermediates are produced during the discharge process. There is a lack of theoretical description of material changes at the microscopic level during the discharge process. In this paper, the first-principles approach is used to simulate and analyze possible material changes during the discharge process of Li-N2 batteries. The discharge process is simulated on a 4N-graphene anode substrate model, and simulations of its electrostatic potential, Density of States (DOS), HOMO (Highest Occupied Molecular Orbital) and LUMO (Lowest Unoccupied Molecular Orbital) aspects confirm that the experimentally found Li3N becomes the final stabilized product of the Li-N2 battery. It can also be seen in the density of states that graphene with adsorption of 4N transforms from semiconducting to metallic properties. In addition, the differential charge also indicates that the Li-N2 material has a strong adsorption effect on the substrate, which can play the dual role of electricity storage and nitrogen fixation.

Exploring the effects of mono-bromination on hole-electron transport and distribution in dibenzofuran and dibenzothiophene isomers: a first-principles study.

This study delves into hole-electron transport and distribution properties inherent in mono-brominated dibenzofuran (DBF) and dibenzothiophene (DBT) isomers. As determined by frontier molecular orbitals, all brominated structures have narrower bandgaps than their primary structures. The TD-DFT calculation showed that 2BDBT had the highest absorption wavelength of all molecules at 315.35nm. Notably, the study unveils remarkably low electron and hole reorganization energies due to bromine substitution in DBF and DBT molecules. Specifically, the 4BDBF has the lowest hole reorganization energy of all DBF configurations, 0.229eV. In addition, 3BDBF has 0.226eV less electron reorganization energy than all other molecules. Compared to DBT, 3BDBT has the lowest electron reorganization energy of 0.254eV. Overall, this research sheds significant light on the fundamental electronic and hole transport characteristics of bromine-substituted DBF and DBT isomers, highlighting their promising role in polymer design as donors/acceptors for advanced organic electronic applications. Molecular structures were optimized using Density Functional Theory (DFT) B3LYP/6-311 + + G (d, p) level of theory, and the study further elucidates these molecules' energy levels and absorption spectra through Time-Dependent Density Functional Theory TD-DFT; these calculations were performed using Gaussian 09W software package. The key parameters such as reorganization energies, Electron Localization Function map, Laplacian Bond Order, and NCI-RDG were meticulously examined for the molecules with the results of DFT calculations were analyzed and displayed by utilizing the software packages VMD 1.9.4 and Multiwfn 3.8, aiming to comprehend their charge transport and distribution properties.