Hybrid Density Functional Method Research Articles

Models of molecular structures of macrocyclic metal chelates in the ternary 4d M(II) ion–ethanedithioamide–ethanedial systems according to quantum-chemical DFT calculations

The thermodynamic and geometric parameters of the molecular structures of macrotricyclic Tc(II), Ru(II), Rh(II), Pd(II), Ag(II), and Cd(II) complexes with the (NSSN)-coordination of the ligand donor sites formed by complexation of the corresponding M(II) ions with ethanedithioamide H2N–C(=S)–C(=S)–NH2 and ethanedial HC(=O)–CH(=O) have been calculated by the OPBE/TZVPQZP hybrid density functional theory method with the use of the Gaussian09 program package. The bond lengths and bond angles in these complexes have been reported, and it has been stated that the Rh(II) and Ag(II) complexes are nearly planar, the Tc(II), Pd(II), and Cd(II) complexes are slightly nonplanar, while the Ru(II) complex exhibits a rather considerable deviation from coplanarity. The additional five-membered chelate ring resulting from template cross-linking is either strictly planar (in the Tc(II), Rh(II), Pd(II), and Ag(II) complexes) or nearly planar (in the Ru(II) and Cd(II) complexes).

Simulation of structure and stability of carbon nanoribbons

Results of carbon nanoribbons and nanotubes simulation by means of hybrid density functional method and using empirical potentials have been compared. Energy of the nanoribbons formation and their citting from graphene sheet as well as energy of the nanotubes folding from graphene and nanoribbons have been determined. The REBO force field satisfactorily reflects the result of quantum chemical simulations; however, it cannot reproduce the formation of triple bonds between the edge atoms of the nanoribbons in the armchair conformation and thus leads to underestimated stability of the latter. Energy of the nanotubes folding from the nanoribbons is linear with the nanotube diameter.

Structure and mode of action of organophosphate pesticides: A computational study

Six organophosphate pesticides of high to moderate toxicity (dichlorvos (DCV), dicrotophos (DTP), ethoprophos (EPP), methamidophos (MAP), mevinphos (MVP) and omethoate (OMT)) are computationally studied to determine their structure and up to 12 different mechanisms of reaction with methanol. Methanol is chosen as a surrogate molecule to represent the serine residue and imidazole to represent histidine in the active site of acetylcholinesterase, the target enzyme in the central nervous system of organisms. Transition states (first order saddle points) and intermediates along several plausible reaction pathways are computed, along with activation enthalpies, entropies, and free energies. Pathways for different leaving groups are also analyzed. All geometry optimizations of products, reactants, intermediate complexes, and saddle points were performed using hybrid density functional theory method mPW1B95-44 in conjunction with the 6-31+G(d,p) basis set, with and without a polarized continuum model of implicit solvation. Composite rate constants were calculated using a steady-state analysis for mechanisms with more than one activation barrier. Mechanisms explored fall into two main categories, direct and indirect, all involving proton transfer from the methanol hydroxyl group to the oxygen or sulfur of the leaving group. The indirect proton-transfer mechanism is a Wright-type mechanism (Wright and White, 1998) which relays the proton through the phosphinyl oxygen, and the leaving group is positioned on the opposite side to the incoming hydroxyl nucleophile in a distorted trigonal bipyramidal transition state. We explored mechanisms in which one or two water molecules and/or an imidazole molecule assisted in the proton transfer. Generally speaking, whether direct or indirect, the lowest activation energies were obtained for mechanisms in which the phosphinyl oxygen plays a role in transfer, and additionally water assistance (ubiquitous in the enzyme active site) lowers activation barriers.

What roles do the residue Asp229 and the coordination variation of calcium play of the reaction mechanism of the diisopropyl-fluorophosphatase? A DFT investigation

Phosphotriesterase enzyme diisopropyl-fluorophosphatase (DFPase) from Loligo vulgaris utilizes one Ca2+ ion to efficiently catalyze the hydrolysis of the substrate diisopropyl fluorophosphate and a wide range of organophosphorus nerve agents, including soman, sarin, and tabun. In the present work, the catalytic mechanism of DFPase is investigated using the hybrid density functional theory method B3LYP with a large quantum chemical model of the active site abstracted from the X-ray crystal structure. For the first step, two different pathways were considered: (1) residue Asp229 as a nucleophile in-line attacks on the phosphorus center and (2) an activated water molecule as the nucleophile attacks on the phosphorus center. Both the Asp229 and the activated water molecule are capable of proceeding nucleophilic attack on the substrate in the presence of Ca2+ ion with the associated barriers 14.8 and 6.0 kcal/mol, respectively. The latter is much easier to perform the nucleophile attack. From the phosphoenzyme intermediate with the hexa-coordinated Ca2+, the uncoordinated Glu21 functions as a general base activated an additional water molecule to attack the carbon center of Asp229 and make the phosphate release. Residues Asn120 and Asn175 promote the elimination of the fluoride via donating strong hydrogen bonds. Residue Asp229 plays a dual role during the hydrolysis reaction process, either as a nucleophile or as a general base to activate the water nucleophile. The role of the calcium ion is providing a necessary conformation of the active site, facilitating the nucleophile formation and substrate orientation. Our calculated results shed further light on the organophosphate hydrolysis mechanism and guiding for structure-based protein engineering to modify hydrolysis rates and substrate specific.

Spectroscopy and quantum-chemical calculations of nitro-bis-bipyridyl complexes of ruthenium(II) with 4-substituted pyridine ligands

The luminescence, absorption, and luminescence excitation spectra of complexes cis-[Ru(bpy)2(L)(NO2)]+ [bpy = 2,2′-bipyridyl, L = pyridine, 4-aminopyridine, 4-dimethylaminopyridine, 4-picoline, isonicotinamide, or 4,4′-bipyridyl] in alcoholic (4 : 1 EtOH–MeOH) solutions are studied at 77 K. A linear correlation is established between the energy of the lowest electronically excited metal-toligand charge transfer state d π(Ru) → π*(bpy) of the complexes and the pKa parameter of the free 4-substituted pyridines used as ligands L. The B3LYP/[6-31G(d)+LanL2DZ(Ru)] hybrid density functional method is used to optimize the geometry of complexes and calculate their electronic structure and the charge distribution on the atoms of the nearest environment of ruthenium(II) ions. It is shown that there exists a mutually unambiguous correspondence between the charge on the nitrogen atom of ligands L coordinated in the complex and the pK a parameter of ligands. The calculated energies of the electronically excited metal-to-ligand charge transfer states of complexes linearly (correlation coefficient 0.99) depend on the charge on the nitrogen atom of ligands L, which completely agrees with the experimental data.

Quantum mechanical study on the different fluxional mechanisms in a [Pd(η2-olefin) complex

In this work, using quantum mechanics, different fluxional mechanisms in a Pd(η2-olefin) complex including sulfur inversion, olefin pseudo rotation, Pd–olefin bond dissociation, propeller-like olefin rotation and a bimolecular process have been investigated theoretically in a solvent environment using the polarisable continuum model (PCM). The activation energy, activation enthalpy and activation Gibbs free energy of the different pathways have been calculated and compared with each other and with experimental results. These activation energies for olefin pseudo rotation, Pd–olefin bond dissociation and propeller-like olefin rotation are greater in comparison with those for the sulfur inversion and bimolecular process, which demonstrates that these latter mechanisms are the dominating paths and make the main contributions in the reaction. The computed activation enthalpies of the sulfur inversion and bimolecular process pathways are in good agreement with the experimental values. All of the calculations have been performed using a hybrid density functional method (B3LYP) in the solution phase.

Mechanism of covalent adsorption of benzenesulfonamide onto COOH– and COCl– functionalised carbon nanotubes

Using density functional theory, two mechanisms of covalent adsorption of benzenesulfonamide in water in the presence of functionalised carbon nanotubes were investigated. COOH– and COCl–functionalised carbon nanotubes can bond to the benzenesulfonamide via OH (OH pathway) and Cl (Cl pathway) groups, respectively. The activation energy and activation Gibbs free energy of the two pathways have been calculated and compared with each other. It was found that the OH pathway has an energy barrier higher than the Cl pathway and, in contrast to the Cl pathway, product formation is endothermic and non-spontaneous, being thus the reason for the dominance of the Cl pathway. All the calculations were performed using a hybrid density functional method (B3LYP) in the solution phase (polarised continuum model or PCM).

QSAR study of the acute toxicity to fathead minnow based on a large dataset

Acute fathead minnow toxicity is an important basis of hazard and risk assessment for compounds in the aquatic environment. In this paper, a large dataset consisting of 963 organic compounds with acute toxicity towards fathead minnow was studied with a QSAR approach. All molecular structures of compounds were optimized by the hybrid density functional theory method. Dragon molecular descriptors and log Kow were selected to describe molecular information. Genetic algorithm and multiple linear regression analysis were combined to develop models. A global prediction model for compounds without known mode of action and two local models for organic compounds that exhibit narcosis toxicity and excess toxicity were developed, respectively. For all developed models, internal validations were performed by cross-validation and external validations were implemented by the setting of validation set. In addition, applicability domains of models were evaluated using a leverage method and outliers were listed and checked using toxicological knowledge.

Structure analysis and spectroscopic characterization of 2-Fluoro-3-Methylpyridine-5-Boronic Acid with experimental (FT-IR, Raman, NMR and XRD) techniques and quantum chemical calculations

Possible stable conformers, geometrical molecular structures, vibrational properties as well as band assignments, nuclear magnetic shielding tensors of 2-Fluoro-3-Methylpyridine-5-Boronic Acid (2F3MP5BA) were studied experimentally and theoretically using FT-IR, Raman, (CP/MAS) NMR and XRD spectroscopic methods. FT-IR and Raman spectra were evaluated in the region of 3500–400 cm−1, and 3200–400 cm−1, respectively. The optimized geometric structures, vibrational wavenumbers and nuclear magnetic shielding tensors were examined using Becke-3–Lee–Yang–Parr (B3LYP) hybrid density functional theory method with 6–311++G(d, p) basis set. 1H, 13C NMR chemical shifts were calculated using the gauge invariant atomic orbital (GIAO) method. 1H, 13C, APT and HETCOR NMR experiments of title molecule were carried out in DMSO solution. 13C CP/MAS NMR measurement was done with 4 mm zirconium rotor and glycine was used as an external standard. Single crystal of 2F3MP5BA was also prepared for XRD measurements. Assignments of vibrational wavenumbers were also strengthened by calculating the total energy distribution (TED) values using scaled quantum mechanical (SQM) method.

Defect calculations in semiconductors through a dielectric-dependent hybrid DFT functional: The case of oxygen vacancies in metal oxides.

We investigate the behavior of oxygen vacancies in three different metal-oxide semiconductors (rutile and anatase TiO2, monoclinic WO3, and tetragonal ZrO2) using a recently proposed hybrid density-functional method in which the fraction of exact exchange is material-dependent but obtained ab initio in a self-consistent scheme. In particular, we calculate charge-transition levels relative to the oxygen-vacancy defect and compare computed optical and thermal excitation/emission energies with the available experimental results, shedding light on the underlying excitation mechanisms and related materials properties. We find that this novel approach is able to reproduce not only ground-state properties and band structures of perfect bulk oxide materials but also provides results consistent with the optical and electrical behavior observed in the corresponding substoichiometric defective systems.

Tensile-strain effect of inducing the indirect-to-direct band-gap transition and reducing the band-gap energy of Ge

By means of a hybrid density-functional method, we investigate the tensile-strain effect of inducing the indirect-to-direct band-gap transition and reducing the band-gap energy of Ge. We consider [001], [111], and [110] uniaxial tensility and (001), (111), and (110) biaxial tensility. Under the condition of no normal stress, we determine both normal compression and internal strain, namely, relative displacement of two atoms in the primitive unit cell, by minimizing the total energy. We identify those strain types which can induce the band-gap transition, and evaluate the critical strain coefficient where the gap transition occurs. Either normal compression or internal strain operates unfavorably to induce the gap transition, which raises the critical strain coefficient or even blocks the transition. We also examine how each type of tensile strain decreases the band-gap energy, depending on its orientation. Our analysis clearly shows that synergistic operation of strain orientation and band anisotropy has a great influence on the gap transition and the gap energy.

Structural characterization, solvent effects on nuclear magnetic shielding tensors, experimental and theoretical DFT studies on the vibrational and NMR spectra of 3-(acrylamido)phenylboronic acid

Structural elucidation of 3-(acrylamido)phenylboronic acid (C9H10BNO3) was carried out with 1H, 13C and HETCOR NMR techniques. Solvent effects on nuclear magnetic shielding tensors were examined with deuterated dimethyl sulfoxide, acetone, methanol and water solvents. The correct order of appearance of carbon and hydrogen atoms on NMR scale from highest magnetic field region to the lowest one were investigated using different types of theoretical levels and the details of the levels were presented in this study. Stable structural conformers and vibrational band analysis of the title molecule (C9H10BNO3) were studied both experimental and theoretical viewpoints using FT-IR, Raman spectroscopic methods and density functional theory (DFT). FT-IR and Raman spectra were obtained in the region of 4000–400 cm−1, and 3700–10 cm−1, respectively. Becke-3-Lee-Yang-Parr (B3LYP) hybrid density functional theory method with 6-31++G(d, p) basis set was included in the search for optimized structures and vibrational wavenumbers. Experimental and theoretical results show that after application of a suitable scaling factor density functional B3LYP method resulted in acceptable results for predicting vibrational wavenumbers except OH and NH stretching modes which is most likely arising from increasing unharmonicity in the high wave number region and possible intra and inter molecular interaction at OH edges those of which are not fully taken into consideration in theoretical processes. To make a more quantitative vibrational assignments, potential energy distribution (PED) values were calculated using VEDA 4 (Vibrational Energy Distribution Analysis) program.

π-Hole interaction: a theoretical insight into the mechanism of SO2 captured by [Et 2NEMim][Tetz] ionic liquids.

The mechanism of SO2 capture by 1-(2-diethylaminoethyl)-3-methylimidazolium tetrazolate ([Et2NEMim][Tetz]) was investigated using B3LYP hybrid density functional methods at 6-31 + G(d,p) level. In order to find the origin of the high capacity of the subjected ionic liquids (IL) for SO2 capture, the 1: n (n = 1-5) complexes formed between [Et2NEMim][Tetz] and 1-5 SO2 molecules were optimized. Two interaction modes (π-hole interaction and hydrogen bond) were found in each 1: n (n = 1-5) complex; the second order perturbation stabilization energies, E(2)s, confirmed that the main interaction mode was a π-hole interaction. The calculated interaction energies indicated that the first SO2 absorption should be chemical absorption. The capture of the second and third SO2 should fall between chemical and physical interaction, and the fourth and fifth SO2 are incorporated by physical absorption. Thermodynamic analyses indicated that SO2 capture favors lower temperature and higher pressure. Owing to the interactions between SO2 and the [Tetz] anion or the [Et2NEMim] cation, the SOO asymmetric stretching frequency exhibits an obviously red shift in the complex. The strong absorptions of SOO asymmetric stretching in complex (1:5) appear at 1295 cm(-1) (interaction between SO2 and the [Tetz](-) anion) and 1247 cm(-1) (interaction between SO2 and the tertiary nitrogen on the cation). Graphical Abstract Geometric structures of the most stable [ET 2 NEMim][Tetz]ionic liquid (IL; left), and most stable SO2 complex (n = 1-5; right) optimized at the B3LYP/6-31+G (d,p) level (distances in angstroms).

Theoretical study on the N-demethylation mechanism of theobromine catalyzed by P450 isoenzyme 1A2

Theobromine, a widely consumed pharmacological active substance, can cause undesirable muscle stiffness, nausea and anorexia in high doses ingestion. The main N-demethylation metabolic mechanism of theobromine catalyzed by P450 isoenzyme 1A2 (CYP1A2) has been explored in this work using the unrestricted hybrid density functional method UB3LYP in conjunction with the LACVP(Fe)/6-31G (H, C, N, O, S, Cl) basis set. Single-point calculations including empirical dispersion corrections were carried out at the higher 6-311++G** basis set. Two N-demethylation pathways were characterized, i.e., 3-N and 7-N demethylations, which involve the initial N-methyl hydroxylation to form carbinolamines and the subsequent carbinolamines decomposition to yield monomethylxanthines and formaldehydes. Our results have shown that the rate-limiting N-methyl hydroxylation occurs via a hydrogen atom transfer (HAT) mechanism, which proceeds in a spin-selective mechanism (SSM) in the gas phase. The carbinolamines generated are prone to decomposition via the contiguous heteroatom-assisted proton-transfer. Strikingly, 3-N demethylation is more favorable than 7-N demethylation due to its lower free energy barrier and 7-methylxanthine therefore is the optimum product reported for the demethylation of theobromine catalyzed by CYP1A2, which are in good agreement with the experimental observation. This work has first revealed the detail N-demethylation mechanisms of theobromine at the theoretical level. It can offer more significant information for the metabolism of purine alkaloid.

NMR, FT-IR, Raman and UV–Vis spectroscopic investigation and DFT study of 6-Bromo-3-Pyridinyl Boronic Acid

Possible stable conformers and geometrical molecular structures of 6-Bromo-3-Pyridinyl Boronic acid (6B3PBA; C5H5BBrNO2) were studied experimentally and theoretically using FT-IR and Raman spectroscopic methods. FT-IR and Raman spectra were recorded in the region of 4000–400 cm−1 and 3700–400 cm−1, respectively. The structural properties were investigated further, using 1H, 13C, 1H coupled 13C, HETCOR, COSY and APT NMR techniques. The optimized geometric structures were searched by Becke-3–Lee–Yang–Parr (B3LYP) hybrid density functional theory method with 6-311++G(d, p) basis set. Vibrational wavenumbers of 6B3PBA were calculated whereby B3LYP density functional methods including 6-311++G(d, p), 6-311G(d, p), 6-311G(d), 6-31G(d, p) and 6-31G(d) basis sets. The comparison of the experimentally and theoretically obtained results using mean absolute error and experimental versus calculated correlation coefficients for the vibrational wavenumbers indicates that B3LYP method with 6-311++G(d, p) gives more satisfactory results for predicting vibrational wavenumbers when compared to the 6-311G(d, p), 6-311G(d), 6-31G(d, p) and 6-31G(d) basis sets. However, this method and none of the mentioned methods here seem suitable for the calculations of OH stretching modes, most likely because increasing unharmonicity in the high wave number region and possible intra and inter molecular interactions at OH edges lead some deviations between experimental and theoretical results. Moreover, reliable vibrational assignments were made on the basis of total energy distribution (TED) calculated using scaled quantum mechanical (SQM) method.

Computational discovery of ferromagnetic semiconducting single-layerCrSnTe3

Despite many single-layer materials being reported in the past decade, few of them exhibit magnetism. Here we perform first-principles calculations using accurate hybrid density functional methods (HSE06) to predict that single-layer ${\mathrm{CrSnTe}}_{3}$ (CST) is a ferromagnetic semiconductor, with band gaps of 0.9 and 1.2 eV for the majority and minority spin channels, respectively. We determine the Curie temperature as 170 K, significantly higher than that of single-layer ${\mathrm{CrSiTe}}_{3}$ (90 K) and ${\mathrm{CrGeTe}}_{3}$ (130 K). This is due to the enhanced ionicity of the Sn-Te bond, which in turn increases the superexchange coupling between the magnetic Cr atoms. We further explore the mechanical and dynamical stability and strain response of this single-layer material for possible epitaxial growth. Our study provides an intuitive approach to understand and design single-layer magnetic semiconductors for a wide range of spintronics and energy applications.

Comparative hydrogen adsorption on the pure Al and mixed Al–Si nano clusters: A first principle DFT study

Hydrogen adsorption on the pure Aln and mixed AlnSim (n=5–7, n+m=5–7) nano clusters were investigated using B3LYP hybrid density functional method. The large negative values of adsorption energy show that adsorption is exothermic and chemisorption type. Adsorption energies vary not only with cluster size but also with cluster composition. Adsorption of hydrogen on the Si atom is energetically more favorable than adsorption on the Al atom in almost all of clusters. The positive values of distortion energy for all clusters indicate structural destabilization of the clusters as a result of hydrogen adsorption. The stability and reactivity of hydrogenated clusters were also discussed using binding energy per atom and chemical hardness. Our results reveal that all AlnSimH2 clusters are more stable than corresponding AlnH2 clusters and stability of AlnSimH2 clusters increases with atomic percentage of Si.

Gaussian-based cutoff scheme on Hartree–Fock exchange term of dielectric-dependent potential

A Gaussian-based cutoff scheme in the dielectric-dependent Hartree–Fock (HF) exchange potential under periodic boundary conditions is discussed. The scheme is applied to HF and hybrid density functional theory methods. For comparison, we examine short-range potentials based on the complementary error function. To investigate the behaviors of these short-range exchange potentials, we study several polymers, such as polyethylene and polytetrafluoroethylene.

Band Gap Reduction in ZnO and ZnS by Creating Layered ZnO/ZnS Heterostructures.

Wurtzite-type zinc oxide (ZnO) and zinc sulfide (ZnS) have electronic band gaps that are too large for light-harvesting applications. Using screened hybrid density-functional methods, we show that the band gaps of ZnO and ZnS can be dramatically reduced by creating layered ZnO/ZnS bulk heterostructures in which m contiguous monolayers of ZnO alternate with n contiguous monolayers of ZnS. In particular, the band gap decreases by roughly 40% upon substitution of every tenth monolayer of ZnS with a monolayer of ZnO (and vice versa) and becomes as low as 1.5 eV for heterostructures with m = 3 to m = 9 contiguous monolayers of ZnO alternating with n = 10 - m monolayers of ZnS. The predicted band gaps of layered ZnO/ZnS heterostructures span the entire visible spectrum, which makes these materials suitable for photovoltaic device engineering.

Theoretical and experimental study on the interaction between 1-butyl-3-methylimidazolium acetate and CO2

Recently, CO2 had been applied for regeneration of biomass polymers from acetate based ionic liquids (AcILs). To explore the interaction mechanisms between the AcILs and CO2, the reaction of [CO2]n (n=1–4) with 1-butyl-3-methylimidazolium acetate ([Bmim]OAc) has been investigated using the B3LYP hybrid density functional methods at 6-311++G(d,p) level. The complexes formed by [Bmim]OAc and CO2 were optimized and the most stable structure of the complexes was chosen to form [Bmim]OAc+2CO2, [Bmim]OAc+3CO2 and [Bmim]OAc+4CO2 systems. Results show that strong hydrogen bonds exist between the O atom in CO2 and the H atom in [Bmim]+ in each complex. Along with the increase of the number of CO2, the ability of [Bmim]OAc interacts with CO2 and the strength of the hydrogen bonds between cation and anion can be reduced continuously. Compared with other complexes, the interaction energy of [Bmim]OAc+4CO2 system is so small that this complex is easy to dissociate into [Bmim]OAc+3CO2 system and CO2. In addition, the vibrational frequencies of the complexes are analyzed. Owing to the interaction between CO2 and [Bmim]OAc, the OC–O asymmetrical stretching frequency appears an obviously red shift in the complex. Furthermore, for natural bond orbital (NBO) analysis, the second order perturbation stabilization energies (E(2)) that denotes the intensity of the interactions between [Bmim]OAc and CO2 indicates the interaction of [Bmim]OAc with CO2 plays an important role in the H-bonding properties of [Bmim]OAc. Atoms in molecules (AIM) analysis shows the bonding properties of these complexes. These results show that the strength of hydrogen bonds between [Bmim]OAc and CO2 is strong, which means that the interactions between [Bmim]OAc and CO2 affect the initial hydrogen bonds in IL due to the formation of new hydrogen bonds in the complexes. All the calculation data provide the interaction mechanism on the dissolution of CO2, and help to develop the precipitation of biomass from ionic liquid solutions by compressed CO2.