Density Functional Theory Computational Results Research Articles

CO2 effect on the fatigue crack growth of X80 pipeline steel in hydrogen-enriched natural gas: Experiment vs DFT

Utilizing the existing natural gas grid presents a promising method for transporting hydrogen on a large scale. However, the effects of natural gas and its impurities on hydrogen-assisted cracking in pipeline steel have not been adequately studied. This study aims to investigate the fatigue performance of X80 pipeline steel in hydrogen-enriched natural gas (HENG) environments and in mixtures containing the impurity CO2. This is achieved through fatigue crack growth rate (FCGR) tests and density functional theory (DFT) calculations. The experimental results show that the FCGR in H2 is slightly faster than that in HENG, whereas it is slower than that in the N2/CO2/H2 mixtures. The enhanced FCGR by CO2 further increases with the increasing CO2 content. DFT computational results indicate that the adsorbed CO2 on the iron surface significantly accelerates the migration of H atoms from surface to subsurface. This promotes the entry of hydrogen into the steel.

Scope and Mechanistic Studies on the Ruthenium-Catalyzed Multicomponent Deaminative C–H Coupling Reaction of Phenols with Aldehydes and Enamines for the Formation of Xanthene and Dioxacyclic Derivatives

The in situ generated catalytic system from the tetranuclear Ru–H complex [(PCy3)(CO)RuH]4(O)(OH)2 (1) with 3,4,5,6-tetrachloro-1,2-benzoquinone (L1) has been found to mediate a multicomponent deaminative coupling reaction of phenols with aldehydes and enamines to form xanthene products. The multicomponent C–H coupling reaction of phenols with 2-hydroxybenzaldehydes and cyclic enamines efficiently installed the tricyclic 1,3-dioxacin derivatives, while the analogous coupling reaction of phenols with 2-hydroxybenzaldehydes and triethylamine selectively formed bicyclic 1,5-dioxacyclic derivatives. The density functional theory (DFT) calculations established two energetically viable mechanistic pathways for the formation of xanthene products, in which both pathways identified the C–O bond cleavage step as the turnover limiting step. A Hammett plot from the coupling reaction of 3,5-dimethoxyphenol with an enamine and para-substituted benzaldehydes p-X-C6H4CHO (X = OMe, Me, H, Cl, CF3) showed a negative slope (ρ = −0.98). The calculated energy analysis showed a similar trend (ρ = −0.59) for the mechanism via the C–O cleavage rate-limiting step. The combined experimental and DFT computational results support a mechanistic path that involves the dehydrative C–H coupling of phenol with aldehyde, followed by the deaminative coupling reaction with an enamine in forming the xanthene product.

Density Functional Theory Investigation on the Structural and Electronic Properties of Pristine, Vacancy, and Group IV Doped Zigzag Boron Nitride Nanotubes

In this work, density functional theory (DFT) calculations were conducted to study the structural and electronic properties of pure, vacancy, and group IV [i.e. carbon (C), silicon (Si), and germanium (Ge) atoms] doped boron nitride nanotubes (BNNTs). The DFT computational results obtained agree well with the literature results. The calculated B−N bond distances obtained in this study are about 1.44 Å – 1.47 Å. Among seven BNNTs, the optimized B35GeN36H12 holds the lowest local energy minimum value in this study Moreover, the structure of B35CN36H12 possesses the smallest HOMO−LUMO energy (2.17 eV) among nine BNNT models considered. The boron (B) atoms hold the positive charges, and the negative charges fall on the nitrogen (N) atoms in this work. Similar results are reported to the molecular electrostatic potentials (MEPs) of studied BNNTs. The distributions of positive and negative electrostatic potentials fall on the regions of N− and B−tips of BNNT frameworks, respectively in this report. The DFT calculations reported that the spin densities were mainly concentrated in the regions around group IV elements, such as C, Si, and Ge atoms. Therefore, we believe that these computed results will provide useful information on the adsorption of hydrogen molecules on the BNNT frameworks in the future.

Computational Exploration of Dirhodium Complex-Catalyzed Selective Intermolecular Amination of Tertiary vs. Benzylic C-H Bonds.

The mechanism and origins of site-selectivity of Rh2(S-tfpttl)4-catalyzed C(sp3)-H bond aminations were studied using density functional theory (DFT) calculations. The synergistic combination of the dirhodium complex Rh2(S-tfpttl)4 with tert-butylphenol sulfamate TBPhsNH2 composes a pocket that can access both tertiary and benzylic C-H bonds. The nonactivated tertiary C-H bond was selectively aminated in the presence of an electronically activated benzylic C-H bond. Both singlet and triplet energy surfaces were investigated in this study. The computational results suggest that the triplet stepwise pathway is more favorable than the singlet concerted pathway. In the hydrogen atom abstraction by Rh-nitrene species, which is the rate- and site-selectivity-determining step, there is an attractive π-π stacking interaction between the phenyl group of the substrate and the phthalimido group of the ligand in the tertiary C-H activation transition structure. By contrast, such attractive interaction is absent in the benzylic C-H amination transition structure. Therefore, the DFT computational results clearly demonstrate how the synergistic combination of the dirhodium complex with sulfamate overrides the intrinsic preference for benzylic C-H amination to achieve the amination of the nonactivated tertiary C-H bond.

Manipulating Excited State Properties of Iridium Phenylpyridine Complexes with "Push-Pull" Substituents.

We have prepared a series of complexes of the type [IrIII(ppy)2(L]n+ complexes (1-4), where ppy is a substituted 2-phenylpyridine and L is a chelating phosphine thioether ligand. The parent complex (1) comprises an unsubstituted phenylpyridine ligand, whereas complex 2 contains a nitro substituent on the pyridine ring, complex 3 features a diphenylamine group on the phenyl ring, and 4 has both nitro and diphenylamine groups. Crystallographic, 1H NMR, and elemental analysis data are consistent with each of the chemical formulae. DFT (density functional theory) computational results show a complicated electronic structure with contributions from Ir, ppy, and the PS ligand. Ultrafast pump-probe data show strong contributions from the phenylpyridine moieties as well as strong panchromatic excited state absorption transitions. The data show that nitro and/or diphenylamine substituents dominate the spectroscopy of this series of compounds.

B/C-doped MoS2 as promising materials for nitrogen removal from natural gas: A first-principles computational study

N2 removal is of great significance to the industrial production and usage of natural gas. It is necessary to find new methods and materials for separating nitrogen (N2) from methane (CH4) with high selectivity and efficiency. Molybdenum disulfide (MoS2) is a promising two-dimensional material. In this work, density functional theory (DFT) was applied to study the influences of non-mental (B, C, N, O and P) doping in 1H- or 1T'-MoS2 monolayer on the adsorption behaviors of N2 and CH4. The result shows that the interaction between either gas and pristine MoS2 is very weak, but that between N2 and MoS2 can be significantly improved by doping B or C. Nevertheless, the adsorption of CH4 is insensitive to such doping. The DFT computational results indicate that doping of B or C in MoS2 is a selective and efficient method to separate N2 from CH4. This study provides valuable information for designing novel approaches and advanced materials for N2 removal from natural gas with high efficiency.

Computational Studies on the Mechanism and Origin of the Different Regioselectivities of Manganese Porphyrin-Catalyzed C-H Bond Hydroxylation and Amidation of Equilenin Acetate.

The manganese porphyrin-catalyzed C-H bond hydroxylation and amidation of equilenin acetate developed by Breslow and his co-worker have been investigated with density functional theory (DFT) calculations. The hydroxylation of C(sp2)-H bond of equilenin acetate leading to the 6-hydroxylated product is more favorable than the hydroxylation of C(sp3)-H bond of equilenin acetate, leading to the 11β-hydroxylation product. The computational results suggest that the C(sp2)-H bond hydroxylation of equilenin acetate undergoes an oxygen-atom-transfer mechanism, which is more favorable than the C(sp3)-H bond hydroxylation undergoing the hydrogen-atom-abstraction/oxygen-rebound (HAA/OR) mechanism by 1.6 kcal/mol. That is why, the 6-hydroxylated product is the major product and the 11β-hydroxylated product is the minor product. In contrast, the 11β-amidated product is the only observed product in manganese porphyrin-catalyzed amidation reaction. The benzylic amidation undergoes a hydrogen-atom-abstraction/nitrogen-rebound (HAA/NR) mechanism, in which hydrogen atom abstraction is followed by nitrogen rebound, leading to the 11β-amidated product. The benzylic C(sp3)-H bond amidation at the C-11 position is more favorable than aromatic amidation at the C-6 position by 4.9 kcal/mol. Therefore, the DFT computational results are consistent with the experiments that manganese porphyrin-catalyzed C-H bond hydroxylation and amidation of equilenin acetate have different regioselectivities.

Controlling O2 Reactivity in Synthetic Analogues of [NiFeS]- and [NiFeSe]-Hydrogenase Active Sites.

Strategies for limiting, or reversing, the degradation of air-sensitive, base metal catalysts for the hydrogen evolution/oxidation reaction on contact with adventitious O2 are guided by nature's design of hydrogenase active sites. The affinity of oxygen for sulfur and selenium, in [NiFeS]- and [NiFeSe]-H2ase, yields oxygenated chalcogens under aerobic conditions, and delays irreversible oxygen damage at the metals by maintaining the NiFe core structures. To identify the controlling features of S-site oxygen uptake, related Ni(μ-EPhX)(μ-S'N2)Fe (E = S or Se, Fe = (η5-C5H5)FeII(CO)) complexes were electronically tuned by the para-substituent on μ-EPhX (X = CF3, Cl, H, OMe, NMe2) and compared in aspects of communication between Ni and Fe. Both single and double O atom uptake at the chalcogens led to the conversion of the four-membered ringcore, Ni(μ-EPhX)(μ-S'N2)Fe, to a five-membered ringNi-O-E-Fe-S', where an O atom inserts between E and Ni. In the E = S, X = NMe2 case, the two-oxygen uptake complex was isolated and characterized as the sulfinato species with the second O of the O2SPh-NMe2 unit pointing out of the five-membered Ni-O-S-Fe-S' ring. Qualitative rates of reaction and ratios of oxygen-uptake products correlate with Hammett parameters of the X substituent on EPhX. Density functional theory computational results support the observed remote effects on the NiFe core reactivity; the more electron-rich sulfurs are more O2 responsive in the SPhX series; the selenium analogues were even more reactive with O2. Mass spectral analysis of the sulfinato products using a mixture of 18O2/16O2 suggests a concerted mechanism in O2 addition. Deoxygenation, by reduction or O atom abstraction reagents, occurs for the 1-O addition complexes, while the 2-O, sulfinato, analogues are inert. The abstraction of oxygen from the 1-O, sulfenato species, is related to oxygen repair in soluble, NAD+-reducing [NiFe]-H2ase (Horch, M.; Lauterbach, L.; et al. J. Am. Chem. Soc. 2015, 137, 2555-2564).

Differences in self-assembly of spherical C60 and planar PTCDA on rippled graphene surfaces

It was recently recognized that two-dimensional (2D) graphene exhibits nonplanar aberrations such as a rippled surface. Understanding the self-assembly of organic semiconductor molecules on monolayer 2D curved graphene surfaces is a paramount issue for ultimate application in semiconductor and optoelectronic devices. Herein, we report on the preparation of fullerene, C60 and perylenetetracarboxylic dianhydride (PTCDA) molecules adsorbed on a rippled graphene surface. We find that the spherical C60 molecules form a quasi-hexagonal close packed (hcp) structure, while the planar PTCDA molecules form a disordered herringbone structure. These 2D layer systems have been characterized by experimental scanning tunneling microscope (STM) imaging and computational density functional theory (DFT) approaches. The DFT computational results exhibit interaction energies for adsorbed molecule/rippled graphene complexes located in the 2D graphene valley sites that are significantly larger in comparison with adsorbed idealized planar/molecule graphene 2D complexes. In addition, we report that the adsorbed PTCDA molecules prefer different orientations when the rippled graphene peak regions are compared to the valley regions. This difference in orientations causes the PTCDA molecules to form a disordered herringbone structure on the rippled graphene surface. The results of this study clearly illustrate significant differences in C60 and PTCDA molecular packing on rippled graphene surfaces.

Enantioselective permeations of amino acids through L-proline-modified gold nanochannel membrane: an experimental and theoretical study.

L-Proline-modified gold nanochannel membrane (L-Pro-GNM) was prepared and applied for the enantioselective permeations of amino acid enantiomers including tyrosine (Tyr), tryptophan (Trp) and phenylalanine (Phe). Experimental results show that L-Pro-GNM has enantioselectivities for Tyr and Phe enantiomers. Furthermore, the chiral recognition mechanism was studied by density functional theory (DFT) and reduced density gradient (RDG). DFT computational results illustrate that the fundamental chiral recognition system contains two chiral selectors and one selectand, which can be used to evaluate the enantioselective efficiencies of other chiral compounds and the enantioselective ability of other potential amino acid-modified GNM. Finally, graphs obtained by RDG using Multiwfn show helpful visual interactions between the chiral selector and selectand. Results indicate that the electrostatic interaction and hydrogen bonding are responsible for the binding of the chiral selector and selectand, and the larger binding energy shows larger van der Waals interactions.

Effect of ligands in TiCl3(OAr) catalysts for ethylene polymerization: Computational and experimental studies

Ethylene insertion into the TiC bond at the TiCl3(OAr) catalysts in ethylene polymerization was investigated with density functional theory (DFT), in order to explore the effect of different Ar- ligands, such as C6H5-, 2,6-Me2C6H3- or 2,6-iPr2C6H3-. The computational results showed the activation energy and reaction heat of the insertion of ethylene monomer into the TiC bond in the [TiClOArCH2CH3]+ active center were between those in the [TiClCpCH2CH3]+ and [TiCl2CH2CH3]+ active centers, due to that the aryloxy group could slightly change the chemical environment of the active titanium cation. Moreover, the ethylene polymerization was carried out using these TiCl3(OAr) catalysts supported by MgCl2 (TiCl3(OAr)/MgCl2), and polyethylene (PE) was obtained with higher molecular weight and relatively narrow molecular weight distribution, like the polymerization using metallocene catalysts. The experimental results were consist with the DFT computational results, indicating that the ethylene polymerization could be controlled by adjusting the Ar- ligand in the TiCl3(OAr) catalysts.

Influence of Rotator Design on the Speed of Self-Assembled Four-Component Nanorotors: Coordinative Versus Dispersive Interactions.

Four-component nanorotors are prepared by the self-assembly of stator [Cu4(4)]4+ with its four copper(I)-loaded phenanthroline stations and various rotators carrying one, two, or three pyridine terminals. The fourth component, 1,4-diazabicyclo[2.2.2]octane, serves as a connecting axle between rotator and stator. Capitalizing on the heteroleptic pyridyl and phenanthroline metal complexes concept, the rotator's pyridine terminals are connected to the copper(I)-loaded phenanthroline stations (Npy → [Cu(phen)]+) in the STOP state and disconnected in the transition state of rotation. As the barrier of the thermally activated rotation, measured by variable-temperature 1H NMR, is mainly governed by attractive forces between stator stations and rotator terminals, it increases along the series Ea (monopyridine rotator) < Ea (dipyridine rotator) < Ea (tripyridine rotator). However, there are even distinct differences in rate between rotors with equal number of rotator terminals. The change from the 5,10-dipyridyl (cis) to 5,15-dipyridyl (trans) zinc porphyrin rotator enhances the rotational frequency by almost 1000-fold. Density functional theory computational results suggest that not only coordinative Npy → [Cu(phen)]+ interactions but also dispersive attraction influence the barrier of rotation.

Roles of Zeolite Confinement and Cu–O–Cu Angle on the Direct Conversion of Methane to Methanol by [Cu2(μ-O)]2+-Exchanged AEI, CHA, AFX, and MFI Zeolites

Recent interest in Cu-exchanged zeolite catalysts for methane hydroxylation has been broadened to small-pore Cu-zeolites such as Cu-SSZ-13 (Cu-CHA), Cu-SSZ-16 (Cu-AFX), and Cu-SSZ-39 (Cu-AEI), which were reported to produce more methanol per copper atom than the medium-pore Cu-ZSM-5 (Cu-MFI) and large-pore Cu-mordenite (Cu-MOR) zeolites do. To elucidate the nature of such fascinating catalytic activities, theoretical investigations based on density functional theory (DFT) were performed on the direct conversion of methane to methanol by [Cu2(μ-O)]2+-exchanged AEI, CHA, AFX, and MFI zeolites in periodic systems. DFT computational results show that the important activation energies for C–H bond dissociation by [Cu2(μ-O)]2+-AEI, -CHA, and -AFX zeolites are lower than those for [Cu2(μ-O)]2+-MFI zeolite. Moreover, the rate-determining methanol desorption and N2O decomposition by [2Cu]2+-AEI zeolite are also found to require low barriers, which renders [Cu2(μ-O)]2+-AEI zeolite highly active for the direct conve...

Polarizability Effects Dominate the Chromatographic Retention Behavior of Spheroidal and Elipsoidal Metallofullerene Nanospheres

The chromatographic retention behavior of spherical and elipsodial metallofullerenes provides a unique class for studying subtle intermolecular dispersive (London effect) and inductive (Debye effect) solution-state/solid-phase interactions. The known trimetallic nitride endohedral metallofullerene A3N@C80 isomers are nearly spherical A3N@C80-Ih and ellipsoidal A3N@C80-D5h. These metallofullerene isomers are readily available with group IIIB and lanthanide trimetallic nitride clusters (A3N)6+. In the current study, chromatographic HPLC retention behavior is monitored for two different HPLC stationary phases, pentabromobenzyl and pyrenylethyl and augmented by density functional theory computational results. Although dipole moments, lanthanide contraction, and charge transfer from the internal cluster (A3N)6+ are important factors controlling chromatographic retention, our results suggest that the fullerene cage polarizability is the dominant factor controlling chromatographic separation of A3N@C80-Ih and el...

Hydrogen Sulfide Oxidation by Myoglobin.

Enzymes in the sulfur network generate the signaling molecule, hydrogen sulfide (H2S), from the amino acids cysteine and homocysteine. Since it is toxic at elevated concentrations, cells are equipped to clear H2S. A canonical sulfide oxidation pathway operates in mitochondria, converting H2S to thiosulfate and sulfate. We have recently discovered the ability of ferric hemoglobin to oxidize sulfide to thiosulfate and iron-bound hydropolysulfides. In this study, we report that myoglobin exhibits a similar capacity for sulfide oxidation. We have trapped and characterized iron-bound sulfur intermediates using cryo-mass spectrometry and X-ray absorption spectroscopy. Further support for the postulated intermediates in the chemically challenging conversion of H2S to thiosulfate and iron-bound catenated sulfur products is provided by EPR and resonance Raman spectroscopy in addition to density functional theory computational results. We speculate that the unusual sensitivity of skeletal muscle cytochrome c oxidase to sulfide poisoning in ethylmalonic encephalopathy, resulting from the deficiency in a mitochondrial sulfide oxidation enzyme, might be due to the concentration of H2S by myoglobin in this tissue.

Co(salophen)-Catalyzed Aerobic Oxidation of p-Hydroquinone: Mechanism and Implications for Aerobic Oxidation Catalysis.

Macrocyclic metal complexes and p-benzoquinones are commonly used as co-catalytic redox mediators in aerobic oxidation reactions. In an effort to gain insight into the mechanism and energetic efficiency of these reactions, we investigated Co(salophen)-catalyzed aerobic oxidation of p-hydroquinone. Kinetic and spectroscopic data suggest that the catalyst resting-state consists of an equilibrium between a Co(II)(salophen) complex, a Co(III)-superoxide adduct, and a hydrogen-bonded adduct between the hydroquinone and the Co(III)-O2 species. The kinetic data, together with density functional theory computational results, reveal that the turnover-limiting step involves proton-coupled electron transfer from a semi-hydroquinone species and a Co(III)-hydroperoxide intermediate. Additional experimental and computational data suggest that a coordinated H2O2 intermediate oxidizes a second equivalent of hydroquinone. Collectively, the results show how Co(salophen) and p-hydroquinone operate synergistically to mediate O2 reduction and generate the reactive p-benzoquinone co-catalyst.

A DFT-based study of surface chemistries of rutile TiO2 and SnO2(110) toward formaldehyde and formic acid

Rutile TiO2 and SnO2 are two structurally similar metal oxides found applications in catalysis and solid-state sensory devices as well as optics and electronics. In present work, we studied the adsorption and conversion of formaldehyde and formic acid on the (110) surfaces of rutile TiO2 and SnO2 based on density functional theory computational results. As oxygen vacancy is one of the most important and common defects on these metal oxides, the effect of the oxygen vacancy on adsorption and transformation were also examined. The results show that the adsorption of formaldehyde and formic acid resulted in similar adsorption configurations on SnO2(110) and TiO2(110). On the stoichiometric surface, SnO2 exhibits a stronger binding toward the adsorbates than TiO2. On the other hand, TiO2(110) with one bridge-bonded oxygen vacancy shows a stronger binding toward the adsorbates than SnO2(110) with the same type of defects. The bridge-bonded oxygen vacancy played important roles in adsorption and conversion and the Vo-bidentate formate species is the key intermediate in the oxidation of formaldehyde to formic acid. TiO2(110) has a higher activity than SnO2(110) for the reactions examined herein.

Mechanistic Information from Nonstationary Points.

The thermal cyclization of enyne-carbodiimides substituted at both the alkyne and carbodiimide terminus showed two curved Hammett correlations (log k/k0 against σp) that were fully reproduced by DFT (density functional theory) computational results. The latter suggest a concerted mechanism, but the transition state (TS) analysis failed to reveal any mechanistic insight about the reason for a curved Hammett correlation. Instead a preTS inspection, i.e., examination of the electronic and steric details on route between reactant and TS, furnished a detailed picture of the mechanism.

Synthesis, characterization and solvatochromism study of mixed-chelate copper(II) complexes: A combined experimental and density functional theoretical study

The mixed-chelate copper(II) complexes [Cu(Ph-acac)(diamine)]X, where Ph-acac is 1-phenyl-1,3-butanedione, diamine is N,N-dimethyl,N′-benzyl-1,2-diaminoethane and X=ClO4−, PF6− and BF4−) have been synthesized and characterized spectroscopically (by IR and UV–Vis) and structurally (by single-crystal X-ray diffraction). The X-ray structure of [Cu(Ph-acac)(diamine)]ClO4 demonstrated that the central copper atom is placed in a square planar geometry made by Ph-acac and diamine chelates. Solvatochromism behavior of the compounds was studied in 14 organic solvents, which showed a positive trend with increasing donor power of the solvents. Multi-parametric equation has been utilized to explain the solvent effect on the d–d transition of the complexes using SPSS/PC software. The stepwise multiple linear regression (SMLR) method demonstrated that the donor power of the solvent plays the most important role in the solvatochromism of the compounds. To study the electronic structure of the complex and to confirm the mechanism of the observed solvatochromism, a computation analysis was accomplished on [Cu(Ph-acac)(diamine)]+ by the density functional theory (DFT) and time-dependent DFT calculations. DFT computational results buttressed the experimental observations and indicated that the solvatochromism phenomenon is due to coordination of the solvent molecules on the above and below of the molecular plane, which causes change in geometry of the complex from square planer to octahedron. In this process the d–d transition band of the complex moves to the red with increasing the DN of the solvent.

Influence of solvent on crystal nucleation of risperidone.

Over 2100 induction time experiments were carried out for the medium-sized, antipsychotic drug molecule, risperidone in seven different organic solvents. To reach the same induction time the required driving force increases in the order: cumene, toluene, acetone, ethyl acetate, methanol, propanol, and butanol, which reasonably well correlates to the interfacial energies as determined within classical nucleation theory. FTIR spectroscopy has been used to investigate any shifts in the spectra and to estimate the interaction of solute and solvent at the corresponding site. The solution condition has also been investigated by Density Functional Theory (DFT) calculations over (1 : 1) solvent-solute binding interactions at 8 different sites on the risperidone molecule. The DFT computational results agree with the spectroscopic data suggesting that these methods do capture the binding strength of solvent molecules to the risperidone molecule. The difficulty of nucleation correlates reasonably to the DFT computations and the spectroscopic measurements. The results of the different measurements suggest that the stronger the solvent binds to the risperidone molecule in solution, the slower the nucleation becomes.