Application Of Density Functional Theory Research Articles

Understanding the Structure-Activity Relationship through Density Functional Theory: A Simple Method Predicts Relative Binding Free Energies of Metalloenzyme Fragment-like Inhibitors.

Despite being involved in several human diseases, metalloenzymes are targeted by a small percentage of FDA-approved drugs. Development of novel and efficient inhibitors is required, as the chemical space of metal binding groups (MBGs) is currently limited to four main classes. The use of computational chemistry methods in drug discovery has gained momentum thanks to accurate estimates of binding modes and binding free energies of ligands to receptors. However, exact predictions of binding free energies in metalloenzymes are challenging due to the occurrence of nonclassical phenomena and interactions that common force field-based methods are unable to correctly describe. In this regard, we applied density functional theory (DFT) to predict the binding free energies and to understand the structure-activity relationship of metalloenzyme fragment-like inhibitors. We tested this method on a set of small-molecule inhibitors with different electronic properties and coordinating two Mn2+ ions in the binding site of the influenza RNA polymerase PAN endonuclease. We modeled the binding site using only atoms from the first coordination shell, hence reducing the computational cost. Thanks to the explicit treatment of electrons by DFT, we highlighted the main contributions to the binding free energies and the electronic features differentiating strong and weak inhibitors, achieving good qualitative correlation with the experimentally determined affinities. By introducing automated docking, we explored alternative ways to coordinate the metal centers and we identified 70% of the highest affinity inhibitors. This methodology provides a fast and predictive tool for the identification of key features of metalloenzyme MBGs, which can be useful for the design of new and efficient drugs targeting these ubiquitous proteins.

Halogenation effect on physicochemical properties of Ti3C2 MXenes

Halogenated MXenes have been experimentally demonstrated to be promising two-dimensional materials for a wide range of applicability. However, their physicochemical properties are largely unknown at the atomic level. In this study, we applied density functional theory (DFT) to theoretically investigate the halogenation effects on the structural, electronic, and mechanical characteristics of Ti3C2, which is the most studied MXene material. Three atomic configurations with different adsorption sites for four kinds of halogen terminals (fluorine, chlorine, bromine, and iodine) were considered. Our DFT results reveal that the adsorption site of terminals has a considerable impact on the properties of MXene. This can be ascribed to the different coordination environments of the surface Ti atoms, which change d-orbital splitting configurations of surface Ti atoms and the stabilities of systems. According to the density of states, crystal orbital Hamilton population, and charge analyses, all the considered halogenated MXenes are metallic. The electronic and mechanical properties of the halogenated MXenes are strongly dependent on the electronegativity of the halogen terminal group. The Ti–F bond has more ionic characteristics, which causes Ti3C2F2 mechanically behave in a more ductile manner. Our DFT results, therefore, suggest that the physicochemical properties of MXenes can be tuned for practical applications by selecting specific halogen terminal groups.

Impact of M atomic species on physical properties of M2TlC (M = Ti, Zr, Hf): A first principles calculation

We characterize the physical feature of M2TlC (M = Ti, Zr, and Hf) MAX phase ternary carbides applying density functional theory. Along with previously calculated structural, elastic, and electrical properties, Vickers hardness, dynamical stability, and optical feature of the phases are also calculated. The Pugh ratio and Poisson’s ratio show the compounds’ brittleness in conjunction with their potent directional covalent bonds and combination of ionic contributions. The metallic character of the phases is supported by the Fermi level overlap of the conduction band and valence band. The examined materials have moderate hardness, according to the Vickers hardness, with the Hf2TlC combination having the highest value of 2.60 GPa. A number of well-known phenomena are used to compute and thoroughly analyze the optical characteristics. Notably, all investigated compounds show reflectivity above 44% up to 12.0 eV energy, which is encompassed by the infrared and visible regions. The compounds could therefore be used, in practice, as a coating material to lessen solar heating.

Nonlinear Optical Materials: Predicting the First-Order Molecular Hyperpolarizability of Organic Molecular Structures

Experimental nonlinear optics (NLO) is usually expensive due to the high-end photonics and electronic devices needed to perform experiments such as incoherent second harmonic generation in liquid phase, multi-photon absorption, and excitation. Nevertheless, exploring NLO responses of organic and inorganic compounds has already opened a world of new possibilities. For example, NLO switches, NLO frequency converters, and a new way to obtain biological images through the incoherent second harmonic generation (SHG) originate from first-order molecular hyperpolarizability (β). The microscopic effect of the coherent or incoherent SHG is, in fact, the β. Therefore, estimating β without using expensive photonic facilities will optimize time- and cost-efficiency to predict if a specific molecular structure can generate light with double its incident frequency. In this work, we have simulated the β values of 27 organic compounds applying density functional theory (PBE0, TPSSh, wB97XD, B3LYP, CAM-B3LYP, and M06-2X) and Hartree–Fock methods using the Gaussian software package. The predicted β was compared with the experimental analogs obtained by the well-known Hyper–Rayleigh Scattering (HRS) technique. The most reliable functionals were CAM-B3LYP and M06-2X, with an unsigned average error of around 25%. Moreover, we have developed post-processing software—Hyper-QCC, providing an effortless, fast, and reliable way to analyze the Gaussian output files.

Structural, electronic and thermoelectric properties of PbS, PbSe and their ternary alloy PbSe1−xSx

Solid-state thermoelectric devices offer the possibility of exploiting waste heat from engines and power plants and converting it into electrical energy. One of the greatest challenges in the development of thermoelectric material systems is to find new thermoelectric materials with high thermoelectric figures of merit ZT. In this work, the structural, electronic and thermoelectric properties of PbSe[Formula: see text]S[Formula: see text] ([Formula: see text], 0.25, 0.50, 0.75 and 1) semiconductors are investigated by applying density functional theory in a full potential linearized augmented plane wave method (FP-LAPW). Calculations of structural properties were completed using the generalized gradient approximation GGA of Perdew Burke and Ernzerhof PBE to get reliable lattice constant results with experimental values. The obtained electronic results show that the PbSe[Formula: see text]S[Formula: see text] material is a narrow band gap semiconductor. In addition, the thermoelectric properties are studied on the basis of the fully iterative solution of the Boltzmann transport equation. PbSe[Formula: see text]S[Formula: see text] had a high figure of merit indicating that our materials are promising candidates in thermoelectric applications.

First-Principles Examination of Multiple Criteria of Organic Solvent Oxidative Stability in Batteries

Oxidative instability of the liquid electrolyte at or near battery cathode oxide surfaces has significant detrimental effects on batteries. Organic solvent molecules are often the fuel and precursors of such degradation processes, releasing electrons and protons that react with cathode oxides and electrolyte anions. These reactions contribute to cathode–electrolyte interphase (CEI) film formation, transition-metal ion dissolution, and phase transformation of the surface regions of the cathode. Here we apply density functional theory calculations to examine four criteria of oxidative stability (oxidation potential, hydrogen removal energies, and initial reactivity on two types of oxide facets) using four different solvent/additive molecules (ethylene carbonate, fluoroethylene carbonate, 1,3-dioxolane, and dimethyl ether). The ranking of molecular stability differs with each criterion. Surprisingly, the all-oxygen-terminated basal planes of layered oxides exhibit lower reaction barriers than spinel surface facets with exposed transition-metal cations, especially for ether solvents; the calculations also suggest basal planes contribute to the dissolution of transition-metal ions. The structure–degradation relation complexity underscores the challenge of understanding the function of the CEI but also offers a guide to future degradation-mitigation strategies including facet engineering. Our predictions and models help establish a framework for future studies relevant to high-voltage conditions.

In situ degradation of fluoroquinolone antibiotics in groundwater by CoFe2O4 nanoparticle-activated peroxymonosulfate: Performance, activation mechanism, degradation pathway

For fluoroquinolone antibiotics, which are widely present in groundwater in China and extremely hazardous, highly dispersed CoFe2O4 nanoparticles (NPs) that can efficiently activate peroxymonosulfate (PMS) and rapidly degrade three fluoroquinolone antibiotics, were successfully prepared by the sol-gel method. The presence of Cl− and HCO3− reduced the degradation efficiency of CoFe2O4/PMS system for NOF, while H2PO4− showed a positive effect. The pH range for efficient degradation of fluoroquinolone antibiotics in the CoFe2O4/PMS oxidation system was between 3 and 9. Two reactive radicals, SO4−• and HO•, played an important role in the degradation process. The ability of the catalyst to degrade the antibiotics decreased from the initial 97.12%–88.72% after five repeated uses. The application of density-functional theory (DFT) indicated the chemical bonds in NOF that are vulnerable to free radicals (N13, C5, F19, and O20). Three degradation pathways of NOF were summarized in combination with the LC-MS results. The potential of the CoFe2O4 NPs for practical applications in in situ remediation was verified by testing the migration ability and in situ degradation of NOF in two column experiments. Overall, this paper provides a theoretical basis for the practical application of nanomaterial-activated PMS in ISCO for groundwater remediation.

Seed-mediated synthesis of a modified micro-mesoporous MIL-101(Cr) for improved benzene and toluene adsorption at room conditions

The modification of metal-organic frameworks (MOFs) for enhanced volatile organic compounds (VOCs) removal is a huge challenge. Therefore, it is of great importance to find a proper strategy to tune the porosity of MOFs and their VOCs removal performance. In this study, we report a novel seed-mediated synthesis strategy using a low-cost and heteroatom-rich carbon structure (MIC-COOH) to prepare hierarchical micro-mesoporous MIL-101(Cr). Different amounts of MIC-COOH were applied to investigate the efficiency of seed concentration on the fundamental specification of the created hierarchical MIL-101(Cr) and its benzene and toluene uptake. The results showed that the increase of MIC-COOH significantly enhanced the mesoporous volume in the MOF structure, resulting in the creation of large surface area (up to 2971.5 m2/g) and high pore volume (up to 2.21 cm3/g). MIL@MIC-4% nanostructure exhibited 235.3 ± 0.05 and 291.6 ± 0.04 wt% adsorption efficiency for benzene and toluene, respectively, which are ⁓3.0 and 4.1 times greater than those of pristine MIL-101(Cr). It also exhibited higher cyclic adsorption efficiency than that of the pristine MIL-101(Cr) after five consecutive adsorption-desorption cycles. The uptake behavior of benzene and toluene on the modified MIL@MIC structure was also perused by applying density functional theory (DFT) calculations. According to the findings, it was revealed that the cooperative charge transfers between MIL-101(Cr) and MIC-COOH through the structure can play an efficient role in the enhanced uptake of benzene and toluene molecules.

A unique triple–channel fluorescent probe for discriminative detection of cyanide, hydrazine, and hypochlorite

Herein, the first triple-channel fluorescent probe, TTB, excited at the same wavelength (λex = 360 nm) in the same sensing medium for the detection and discrimination of cyanide, hydrazine, and hypochlorite, is disclosed. While a fluorescent white color appeared (λem = 470 nm) with the addition of cyanide ion into the probe solution, upon addition of hydrazine and hypochlorite, green (λem = 503 nm) and orange (λem = 585 nm) fluorescent colors, respectively, were observed. A naked-eye detection for the three ions was documented. With the appearance of orange color, a mega Stokes shift of 175 nm was observed. The probe exhibited excellent selectivity and lower detection limits of 0.24 μM, 4.1 nM and 0.27 μM, and dynamic ranges of 0.0–2.0 μM, 0.0–0.05 μM and 0.0–2.0 μM for cyanide, hydrazine and hypochlorite, respectively. The sensing mechanism was investigated through computational studies before and after the addition of cyanide, hypochlorite, and hydrazine, applying density functional theory (DFT), along with the calculation of optical properties by time-dependent DFT (TD-DFT) method. The results were found to be in good agreement with the experimental values. Remarkably, the probe, TTB, successfully detected cyanide, hydrazine, and hypochlorite in complex water samples. Moreover, the detection of cyanide was successfully performed in apricot kernels, as well as hypochlorite in fruits and vegetables.

Electronic and vibrational contributions to the reorganization energy of photosynthetic pigments

Charge transport is dependent on properties such as reorganization energy (λ) and free energy. These quantities are typically estimated applying density functional theory (DFT) to optimized geometries. However, most pigments in photosynthesis are conjugated, making delocalization and vibrational effects relevant. Here, we calculated reorganization energies of 15 molecules relevant to photosynthesis using a reliable DFT-based approach. Tuning the functional’s long-range parameter prevents over-delocalization of orbitals, while molecular vibrations are accounted for via an ensemble method. Results show that functional tuning decreases λ, but vibrational effects produce distributions of λ, affecting charge transfer rates in up to one order of magnitude.

Surface Curvature Effect on Dual-Atom Site Oxygen Electrocatalysis.

Improved oxygen electrocatalysis is crucial for the ever-growing energy demand. Metal-nitrogen-carbon (M-N-C) materials are promising candidates for catalysts. Their activity is tunable via varying electronic and geometric properties, such as porosity. Because of the difficulty in modeling porosity, M-N-Cs with variable surface curvature remained largely unexplored. In this work, we developed a realistic in-pore dual-atom site M-N-C model and applied density functional theory to investigate the surface curvature effect on oxygen reduction and evolution reactions. We show that surface curving tailors both scaling relations and energy barriers. Thus, we predict that adjusting the surface curvature can improve the catalytic activity toward mono- and bifunctional oxygen electrocatalysis.

Substitutional effects on the Na-involved electrochemical properties of isomeric benzoquinones

The possibility of the isomeric benzoquinones, 1,2-benzoquinone (1,2-BQ) and 1,4-benzoquinone (1,4-BQ) with electron withdrawing functional groups (-PO3H2, –COOH, –NO2 and –CN), as prospective cathodes in sodium ion batteries is explored applying Density Functional Theory (DFT) approach. In order to investigate the redox behavior of the first and second discharged states, the sodiation of the considered derivatives with one and two number of sodium ions are made. The obtained redox potentials (ΔEred) of bare quinones are in good agreement with the experimental ΔEred. A linear correlation fit with R2>∼0.95 is found to exist between the obtained LUMO (lowest unoccupied molecular orbital) energies and ΔEred. In general, higher ΔEred of ∼ 4.2 V with charge capacities of 186mAh/g and 258mAh/g is observed for NO2 and CN containing BQ derivatives. Unexpected deviation in ΔEred of phosphonate derivatives emphasizes the role of intramolecular hydrogen bonds, conformational changes and steric hindrance on the redox properties.

Discovery and Computational Studies of Potent Covalent Kinase Inhibitors with α-Substituent Electrophiles Targeting Cysteine.

Both reversible noncovalent inhibitors and irreversible covalent inhibitors targeting tyrosine kinases have their disadvantages. The reversible covalent inhibitors with electrophilic group cyanoacrylamide as warheads reacting with cysteine residues could solve the dilemmas. However, there are still several unresolved issues regarding the electrophilic groups. In this manuscript, a series of EGFR inhibitors with double electron-withdrawing substituents introduced into the Cα position on the olefin bond were designed and synthesized. The binding structures and characteristics of inhibitors with the kinase in both the first noncovalent binding phase and the second covalent binding step were explored and combined with molecular docking and molecular dynamics simulations. Then, the reverse β-elimination reactions of the thiol-Michael adducts were investigated by applying density functional theory calculations. In addition, the effects of different electrophilic substituents of Cα on the binding between the inhibitors and kinase were elucidated. The results suggested that the electrophilicity and size of the electron-withdrawing groups play an important role in the specific interactions during the reaction. The compounds with the electron-withdrawing groups that had medium electrostatic and steric complementarity to the kinase active site could cooperatively stabilize the complexes and showed relatively good potent activities in the kinase assay experiment. The mechanical and structural information in this study could enhance our understanding of the functioning of the electron-withdrawing groups in the covalent inhibitors. The results might help to design efficient cysteine targeting inhibitors in the future.

Development of high refractive index UiO-66 framework derivatives via ligand halogenation.

UiO-66 is a Zr-based metal-organic framework (MOF) with exceptional chemical and thermal stability. The modular design of a MOF allows the tuning of its electronic and optical properties to obtain tailored materials for optical applications. Making use of the halogenation of the 1,4-benzenedicarboxylate (bdc) linker, the well-known monohalogenated UiO-66 derivatives were examined. In addition, a novel diiodo bdc based UiO-66 analogue is introduced. The novel UiO-66-I2 MOF is fully characterized experimentally. By applying density functional theory (DFT), fully relaxed periodic structures of the halogenated UiO-66 derivatives are generated. Subsequently, the HSE06 hybrid DFT functional is used to calculate the electronic structures and optical properties. The obtained band gap energies are validated with UV-Vis measurements to assure a precise description of the optical properties. Finally, the calculated refractive index dispersion curves are evaluated underlining the capabilities to tailor the optical properties of MOFs by linker functionalization.

Impacts of external fields on aromaticity and acidity of benzoic acid: a density functional theory, conceptual density functional theory and information-theoretic approach study.

The impact of external fields on the molecular structure and reactivity properties has been of considerable interest in the recent literature. Benzoic acid as one of the most widely used compounds in medicinal and materials sciences is known for its dual propensity in aromaticity and acidity. In this work, we systematically investigate the impact of a uniform external electric field on these properties. We apply density functional theory, conceptual density functional theory, and an information-theoretic approach to appreciate the change pattern of aromaticity and acidity properties in external fields with different strengths. Our results show that they possess different change patterns under external fields, which can be satisfactorily rationalized by variations in reactivity descriptors and partial charges. The surprising yet novel results from this study should enrich the body of our knowledge about the impact of external fields for different kinds of electronic properties and provide guidance and foundation for future studies of this phenomenon in other molecular systems.

Tuning the optical properties of the metal-organic framework UiO-66 via ligand functionalization.

Metal-organic frameworks (MOFs) are a promising class of materials for optical applications, especially due to their modular design which allows fine-tuning of the relevant properties. The present theoretical study examines the Zr-based UiO-66-MOF and derivatives of it with respect to their optical properties. Starting from the well-known monofunctional amino- and nitro-functionalized UiO-66 derivatives, we introduce novel UiO-66-type MOFs containing bifunctional push-pull 1,4-benzenedicarboxylate (bdc) linkers. The successful synthesis of such a novel UiO-66 derivative is also reported. It was carried out using a para-nitroaniline (PNA)-based bdc-analogue linker. Applying density functional theory (DFT), suitable models for all UiO-66-MOF analogues were generated by assessing different exchange-correlation functionals. Afterwards, HSE06 hybrid functional calculations were performed to obtain the electronic structures and optical properties. The detailed HSE06 electronic structure calculations were validated with UV-Vis measurements to ensure reliable results. Finally, the refractive index dispersion of the seven UiO-66-type materials is compared, showing the possibility to tailor the optical properties by the use of functionalized linker molecules. Specifically, the refractive index can be varied over a wide range from 1.37 to 1.78.

Binding of carboxylate and water to monovalent cations.

The interactions of carboxylate anions with water and cations are important for a wide variety of systems, both biological and synthetic. To gain insight on properties of the local complexes, we apply density functional theory, to treat the complex electrostatic interactions, and investigate mixtures with varied numbers of carboxylate anions (acetate) and waters binding to monovalent cations, Li+, Na+ and K+. The optimal structure with overall lowest free energy contains two acetates and two waters such that the cation is four-fold coordinated, similar to structures found earlier for pure water or pure carboxylate ligands. More generally, the complexes with two acetates have the lowest free energy. In transitioning from the overall optimal state, exchanging an acetate for water has a lower free energy barrier than exchanging water for an acetate. In most cases, the carboxylates are monodentate and in the first solvation shell. As water is added to the system, hydrogen bonding between waters and carboxylate O atoms further stabilizes monodentate structures. These structures, which have strong electrostatic interactions that involve hydrogen bonds of varying strength, are significantly polarized, with ChelpG partial charges that vary substantially as the bonding geometry varies. Overall, these results emphasize the increasing importance of water as a component of binding sites as the number of ligands increases, thus affecting the preferential solvation of specific metal ions and clarifying Hofmeister effects. Finally, structural analysis correlated with free energy analysis supports the idea that binding to more than the preferred number of carboxylates under architectural constraints are a key to ion transport.

Noncovalent chemistry of xenon opens the door for anesthetic xenon recovery using Bio-MOFs.

Designing an inexpensive and highly efficient recovery process for xenon (Xe) is gaining importance in the development of sustainable applications. Using metal organic frameworks (MOFs) for separating Xe from anesthetic gas mixtures has been a recent topic studied rarely and superficially in the literature. We theoretically investigated Xe recovery performances of 43 biological MOFs (Bio-MOFs) formed by biocompatible metal cations and biological endogenous linkers. Xe uptakes and Xe permeabilities in its binary mixtures with CO2, O2, and N2 were investigated by applying Grand Canonical Monte Carlo and Molecular Dynamics simulations. Materials with metalloporphyrin, hexacarboxylate, triazine, or pyrazole ligands, dimetallic paddlewheel units, relatively large pore sizes (PLD > 5 Å and LCD > 10 Å), large void fractions (≈0.8), and large surface areas (>2900 m2 g-1) have been determined as top performing Bio-MOFs for Xe recovery. By applying Density Functional Theory simulations and generating electron density difference maps, we determined that Xe-host interactions in the top performing Bio-MOFs are maximized mainly due to noncovalent interactions of Xe, such as charge-induced dipole and aerogen-π interactions. Polarized Xe atoms in the vicinity of cations/anions as well as π systems are fingerprints of enhanced guest-host interactions. Our results show examples of rarely studied aerogen interactions that play a critical role in selective adsorption of Xe in nanoporous materials.

Anisotropic Carrier Mobility and Spectral Fingerprints of Two-Dimensional γ-Phosphorus Carbide with Antisite Defects.

We apply density functional theory to study carrier mobility in a γ-phosphorus carbide monolayer. Although previous calculations predicted high and anisotropic mobility in this material, we show that the mobility can be significantly influenced by common antisite defects. We demonstrate that at equilibrium concentrations defects do not inhibit carrier mobility up to temperatures of 1000 K. However, defects can change the mobility at high nonequilibrium concentrations of about 10-4 to 10-2 defects per atom. At the low end of this concentration range, defects act as traps for charge carriers and inhibit their mobility. At the high end of this range, defects change the effective carrier masses and deformation potentials, and they can lead to both an increase and a decrease in mobility. We also report the Raman and IR spectra associated with antisite defects. We predict new vibrational modes and shifts of the existing modes due to the defects.

The encapsulation of atomically-thin MgB2-based superconductors in two-dimensional material bilayers

Two-dimensional (2D) superconductors are a class of materials with unique properties that can potentially exhibit novel superconductivity at a reduced dimensionality, as well as pave the way for miniaturizing superconducting devices at the atomic limit. However, such materials are highly sensitive to interaction with their substrates and the environment, and therefore it is necessary to find potential methods for chemically isolating them. We address this problem by examining the possibility of isolating the medium-temperature 2D MgB2-based superconductors. We examine two possible structures: the monolayer stoichiometric MgB2 and the B-caged Mg3B8 structure. By solving the anisotropic Eliashberg equations, we predict that the latter possesses K upon application of a small lateral (3% tensile) strain, with an electron–phonon coupling of 0.88. To investigate protecting the superconductivity of these two layers, we apply density functional theory calculations to examine their encapsulation in a graphene bilayer or a hexagonal boron nitride bilayer. We find that both have high potential as encapsulation systems to protect the superconductivity of the 2D MgB2-based superconductors, in particular B-caged (B–Mg) n systems.