Enantioselective organocatalytic Diels-Alder reactions: a density functional theory and kinetic isotope effects study

The mechanism and enantioselectivity of the organocatalytic Diels-Alder reaction were computationally investigated by density functional theory at the B3LYP/6-31G(d) level of theory. The uncatalyzed Diels-Alder reaction was also studied to explore the effect of the organocatalyst on this reaction in terms of energetics, selectivity, and mechanism. The catalyzed reaction showed improved endo/exo selectivity, and the free energy of activation was significantly lowered in the presence of the catalyst. Both uncatalyzed and catalyzed reactions exhibited concerted asynchronous reaction mechanism with the degree of asynchronicity being more evident in the presence of the catalyst. The Corey's experimentally derived predictive selection rules for the outcome of the organocatalytic Diels-Alder reaction were also theoretically analyzed, and an excellent agreement was found between experiment and theory.     

Magnetic effects of disulfide bridges: a density functional and semiempirical study

Density functional chemical shielding calculations are reported for methane and hydrogen disulfide dimers. The calculations show that the contributions of disulfide bridges to the chemical shielding of neighboring protons is sizable at distances that are frequently sampled in protein structures. A semiempirical model of the quantum chemical data is developed. It is shown that magnetic anisotropy effects of disulfide are poorly described by the McConnell equation, both qualitatively and quantitatively. In particular, the ratio of magnetic anisotropy contributions to shielding along and perpendicular to the magnetic anisotropy principal axis do not conform to the predictions of the McConnell equation, and magnetic anisotropy effects are not null along the magic angle axis. A sulfur-based model of the magnetic anisotropy of the disulfide is developed and shown to give much better agreement with the quantum chemical data.     

Thermodynamic and kinetic study of ibuprofen with hydroxyl radical: A density functional theory approach

Ibuprofen, a frequently detected pharmaceutical in natural and engineered waters, was studied in both neutral and anionic forms using density functional theory at the B3LYP/6‐311++G**//B3LYP/6‐31G* level of theory in its reaction with hydroxyl radical ( ? OH). The reaction pathways included ? OH addition to aromatic ring, abstraction of a H‐atom, and nucleophilic attack on the carbonyl group. The results showed that H‐atom abstraction pathways are the most favorable. The free energy change for H‐atom abstraction reaction ranges from ?37.8 to ?15.9 kcal/mol; for ? OH addition ranges from ?3.85 to ?1.23 kcal/mol; and for nucleophilic attack on the carbonyl group is 13.9 kcal/mol. The calculated rate constant between neutral ibuprofen and ? OH, 6.72 × 10⁹ M^?1s^?1, is consistent with the experimental value, 6.5 ± 0.2 × 10⁹ M^?1s^?1. Our results provide direct evidence for byproduct formation and identification on the molecular level. © 2013 Wiley Periodicals, Inc.     

Mechanisms of difluoroethylene ozonolysis: a density functional theory study

We present a density functional theory (DFT) study on the mechanisms of gas-phase ozonolysis of three isomers of difluoroethylene, namely, cis-1,2-difluoroethylene, trans-1,2-difluoroethylene, and 1,1-difluoroethylene. MPW1K/cc-pVDZ and BHandHLYP/cc-pVDZ methods are employed to optimize the geometries of stationary points as well as the points on the minimum energy path (MEP). The energies of all the points were further refined at the QCISD(T)/cc-pVDZ and QCISD(T)/6-31+G(df,p) levels of theory with zero-point energy (ZPE) corrections. The ozone-cis-1,2-difluoroethylene reaction is predicted to be slower than the ozone-trans-1,2-difluoroethylene reaction. The enhanced reactivity of trans-1,2-difluoroethylene relative to the cis isomer is similar to the reactions of ozone with cis- and trans-dichloroethylene. The ozone-1,1-difluoroethylene reaction is predicted to be slower than the ozone-trans-1,2-difluoroethylene reaction. These results are in agreement with experimental studies. The calculated mechanisms indicate that in ozone-difluoroethylene reactions the yields of OH might be trivial, which is different from the reactions of ozone with unsaturated hydrocarbons.     

Hydroxyl radical and hydroxide ion in liquid water: a comparative electron density functional theory study

Ab initio density functional theory molecular dynamics simulations of the solvated states of the hydroxyl radical and hydroxide ion are performed using the Becke-Lee-Yang-Parr (BLYP) exchange-correlation functional (Becke, A. D. Phys. Rev. A 1988, 38, 3098. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785). The structures of the solvation shells of the two species are examined. It is found that the OH radical forms a relatively well-defined solvation complex with four neighboring water molecules. Three of these molecules are hydrogen bonded to the OH, while the fourth is hemibonded via a three-electron two-centered bond between the oxygen atoms of the OH and water. The activity and the diffusion mechanism of the OH radical in water is discussed in comparison with the OH- ion. Although the results are partially influenced by the tendency of the BLYP density functional to overestimate hemibonded structure, the present simulations suggest that the widely accepted picture of rapid diffusion of OH radical in water through hydrogen exchange reaction may need to be reconsidered.     

Substituent effects on benzdiyne: a density functional theory study

Density functional theory (DFT) studies were performed to investigate the effect of substituents on the properties of benzdiyne derivatives. Twelve substituted benzdiynes-C(6)X(2), where X = F, Cl, Br, Me, CF(3), CN, OH, NO(2), NH(2), OMe, NMe(2), and Ph-were considered along with the unsubstituted 1,4-benzdiyne. The structures, vibrational frequencies, and IR intensities of these benzdiynes were studied with a popular three-parameter hybrid density functional (B3LYP) combined with the split-valence 6-31G(d) basis set and Dunning's correlation-consistent polarized triple-zeta (cc-pVTZ) basis set. The relative stabilities of the substituted benzdiynes were studied with the help of reaction energies of isodesmic reactions, which showed that the electron-withdrawing groups destabilized the benzdiynes more than they did the corresponding benzenes, whereas the electron-donating groups stabilized the benzdiynes more than they did their benzene counterparts. Correlation analyses revealed that field/inductive effects played a more important role than did resonance effects. The changes in atomic charges and spin populations due to the substituents were also studied. The asymmetric nu(Ctbd1;C) stretching modes obtained were close to the 1500-cm(-)(1) mark. Reinvestigation of the experimental results supported these results; a weak IR band at 1486 cm(-)(1) was assigned to this asymmetric stretching mode in C(6)(CF(3))(2) F. Some other benzdiynes also had large IR intensity values for their asymmetric nu(Ctbd1;C) vibrational modes due to the coupling with other vibrational modes. Heats of formation for the substituted benzdiynes were obtained from the reaction energies calculated at the B3LYP/cc-pVTZ level of theory.     

Atomistic kinetic Monte Carlo study of atomic layer deposition derived from density functional theory

To describe the atomic layer deposition (ALD) reactions of HfO₂ from Hf(N(CH₃)₂)₄ and H₂O, a three‐dimensional on‐lattice kinetic Monte‐Carlo model is developed. In this model, all atomistic reaction pathways in density functional theory (DFT) are implemented as reaction events on the lattice. This contains all steps, from the early stage of adsorption of each ALD precursor, kinetics of the surface protons, interaction between the remaining precursors (steric effect), influence of remaining fragments on adsorption sites (blocking), densification of each ALD precursor, migration of each ALD precursors, and cooperation between the remaining precursors to adsorb H₂O (cooperative effect). The essential chemistry of the ALD reactions depends on the local environment at the surface. The coordination number and a neighbor list are used to implement the dependencies. The validity and necessity of the proposed reaction pathways are statistically established at the mesoscale. The formation of one monolayer of precursor fragments is shown at the end of the metal pulse. Adsorption and dissociation of the H₂O precursor onto that layer is described, leading to the delivery of oxygen and protons to the surface during the H₂O pulse. Through these processes, the remaining precursor fragments desorb from the surface, leaving the surface with bulk‐like and OH‐terminated HfO₂, ready for the next cycle. The migration of the low coordinated remaining precursor fragments is also proposed. This process introduces a slow reordering motion (crawling) at the mesoscale, leading to the smooth and conformal thin film that is characteristic of ALD. © 2013 Wiley Periodicals, Inc.     

Formation mechanism of methane during coal evolution:A density functional theory study

The formation mechanism of methane （CH4） during coal evolution has been investigated by density functional theory （DFT） of quantum chemistry. Thermogenic gas, which is generated during the thermal evolution of medium rank coal, is the main source of coalbed methane （CBM）. Ethylbenzene （A） and 6,7-dimethyl-5,6,7,8-tetrahydro-1-hydroxynaphthalene （B） have been used as model compounds to study the pyrolysis mechanism of highly volatile bituminous coal （R）, according to the similarity of bond orders and bond lengths. All possible paths are designed for each model. It can be concluded that the activation energies for H-assisted paths are lower than others in the process of methane formation; an H radical attacking on β-C to yield CH4 is the dominant path for the formation of CH4 from highly volatile bituminous coal. In addition, the calculated results also reveal that the positions on which H radical attacks and to which intramolecular H migrates have effects on methyl cleavage.     

Formation mechanism of methane during coal evolution: A density functional theory study

The formation mechanism of methane (CH₄) during coal evolution has been investigated by density functional theory (DFT) of quantum chemistry. Thermogenic gas, which is generated during the thermal evolution of medium rank coal, is the main source of coalbed methane (CBM). Ethylbenzene (A) and 6,7-dimethyl-5,6,7,8-tetrahydro-1-hydroxynaphthalene (B) have been used as model compounds to study the pyrolysis mechanism of highly volatile bituminous coal (R), according to the similarity of bond orders and bond lengths. All possible paths are designed for each model. It can be concluded that the activation energies for H-assisted paths are lower than others in the process of methane formation; an H radical attacking on β-C to yield CH₄ is the dominant path for the formation of CH₄ from highly volatile bituminous coal. In addition, the calculated results also reveal that the positions on which H radical attacks and to which intramolecular H migrates have effects on methyl cleavage.     

Atmospheric oxidation mechanism of p-xylene: a density functional theory study

We report an investigation of the mechanistic features of OH-initiated oxidation reactions of p-xylene using density function theory (DFT). Reaction energies for the formation of the aromatic intermediate radicals have been obtained to determine their relative stability and reversibility, and their activation barriers have been analyzed to assess the energetically favorable pathways to propagate the p-xylene oxidation. OH addition is predicted to occur dominantly at the ortho position, with branching ratios of 0.8 and 0.2 for ortho and ipso additions, respectively, and the calculated overall rate constant is in agreement with available experimental studies. Under atmospheric conditions, the p-xylene peroxy radicals arising from initial OH and subsequent O(2) additions to the ring are shown to cyclize to form bicyclic radicals, rather than to react with NO to lead to ozone formation. With relatively low barriers, isomerization of the p-xylene bicyclic radicals to more stable epoxide radicals likely occurs, competing with O(2) addition to form bicyclic peroxy radicals. The study provides thermochemical and kinetic data for assessment of the photochemical production potential of ozone and formation of toxic products and secondary organic aerosol from p-xylene oxidation.     

Laser ionization of solid RDX: a density functional theory study

Structural Chemistry - Structural changes induced via ionization in an RDX lattice have been studied by using optimized [(RDX)2]0 conformers comprising eight combinations of four RDX isomers using...     

烯丙醇与臭氧反应机理的密度泛函理论研究

应用密度泛函理论的MPW1K,BHandHLYP和MPWB1K方法,结合6-31+G(d,p)基组优化了烯丙醇与臭氧反应势能面上各驻点的几何构型,通过同一水平的振动频率分析确认了中间体和过渡态.反应路径上的驻点都在HL理论水平下进行单点能量校正,并进行了MPW1K/6-31+G(d,p)水平下的零点振动能校正(ZPE).对反应机理的详尽分析表明臭氧抽取烯丙醇羟基基团中H的通道的反应势垒比臭氧加合烯丙醇双键基团通道的反应势垒高,臭氧与烯丙醇双键加合生成臭氧化物为最可几反应路径.在加合反应历程中,氢迁移通道需经过氢迁移和离解等复杂过程,最终要产生少量的OH自由基,与烃烯类臭氧化反应产生大量OH自由基的结果相反.     

Electronic structure of copper phthalocyanine: a comparative density functional theory study

We present a systematic density functional theory study of the electronic structure of copper phthalocyanine (CuPc) using several different (semi)local and hybrid functionals and compare the results to experimental photoemission data. We show that semilocal functionals fail qualitatively for CuPc primarily because of underbinding of localized orbitals due to self-interaction errors. We discuss an appropriate choice of functional for studies of CuPc/metal interfaces and suggest the Heyd-Scuseria-Ernzerhof screened hybrid functional as a suitable compromise functional.     

Adsorption of atoms on cu surfaces: a density functional theory study

The chemisorption of atoms (H, N, S, O, and C) on Cu surfaces has been systematically studied by the density functional theory generalized gradient approximation method with the slab model. Our calculated results indicate that the orders of the adsorption energy are H < N < S < O < C on Cu(111) and H < N < O < S < C on Cu(110) and Cu(100). Furthermore, the adsorption energies of the given atoms on Cu(100) are larger than those on Cu(111) and Cu(110). The preferred adsorption sites are a 3-fold hollow site on Cu(111) and a 4-fold hollow site on Cu(100), but the preferred adsorption sites on Cu(110) are different for different adatoms. The energy, as well as the geometry, is in good agreement with the experimental and other theoretical data. In addition, this study focuses on the electronic and geometric properties of the metal-atom (M-A) bond to explain the difference in adsorption energies among adatoms. A detailed investigation of the density of states curves explains the nature of the most stable site. Finally, we test the effect of the coverage and find that the surface coverage has no influence on the preferred adsorption sites of the given adatoms on Cu(110) with the exception of hydrogen and oxygen, but has much influence on the value of the adsorption energy.     

Exploring odd-even effects of simple oligomer-like DRCNnT series: a study based on density functional theory/time-dependent density functional theory calculations

Odd-even effects of short-circuit current density and power conversion efficiency (PCE) are an interesting phenomenon in some organic solar cells. Although some explanations have been given, why they behave in such a way is still an open question. In the present work, we investigate a set of acceptor-donor-acceptor simple oligomer-like small molecules, named the DRCNnT (n = 5-9) series, to give an insight into this phenomenon because the solar cells based on them have high PCE (up to 10.08%) and show strong odd-even effects in experiments. By modeling the DRCNnT series and using density functional theory, we have studied the ground-state electronic structures of the DRCNnT (n = 5-9) series in condensed phase. The calculated results reproduce the experimental trends well. Furthermore, we find that the exciton-binding energies of the DRCNnT series may be one of the key parameters to explain this phenomenon because they also show odd-even effects. In addition, by studying the effects of alkyl branch and terminal group on odd-even effects of dipole moment, we find that eliminating one or two alkyl branches does not break the odd-even effects of dipole moments, but eliminating one or two terminal groups does. Finally, we conclude that removing one alkyl branch close to the terminal group of DRCN5T can decrease highest occupied molecular orbital (HOMO) energy (thus increasing open circuit voltage) and increase dipole moment (thus enhancing charge separation and short-circuit current). This could be a new and simple method to increase the PCE of DRCN5T-based solar cells.     

Structure, spectroscopy, and reactivity properties of porphyrin pincers: a conceptual density functional theory and time-dependent density functional theory study

Porphyrin and pincer complexes are both important categories of compounds in biological and catalytic systems. The idea to combine them is computationally investigated in this work. By employment of density functional theory (DFT), conceptual DFT, and time-dependent DFT approaches, structure, spectroscopy, and reactivity properties of porphyrin pincers are systematically studied for a selection of divalent metal ions. We found that the porphyrin pincers are structurally and spectroscopically different from their precursors and are more reactive in electrophilic and nucleophilic reactions. A few quantitative linear/exponential relationships have been discovered between bonding interactions, charge distributions, and DFT chemical reactivity indices. These results are implicative in chemical modification of hemoproteins and understanding chemical reactivity in heme-containing and other biologically important complexes and cofactors.     

Stochastic theory of interfacial enzyme kinetics: A kinetic Monte Carlo study

In the spirit of Gillespie’s stochastic approach we have formulated a theory to explore the advancement of the interfacial enzyme kinetics at the single enzyme level which is ultimately utilized to obtain the ensemble average macroscopic feature, lag-burst kinetics. We have provided a theory of the transition from the lag phase to the burst phase kinetics by considering the gradual development of electrostatic interaction among the positively charged enzyme and negatively charged product molecules deposited on the phospholipid surface. It is shown that the different diffusion time scales of the enzyme over the fluid and product regions are responsible for the memory effect in the correlation of successive turnover events of the hopping mode in the single trajectory analysis which again is reflected on the non-Gaussian distribution of turnover times on the macroscopic kinetics in the lag phase unlike the burst phase kinetics.     

Fluorene-based oligomers as red light-emitting materials: a density functional theory study

The electronic structures, charge injection and transport, absorption and emission spectra, properties of two series of fluorene-based oligomers {2-[2-{2-[5-(9H-Fluoren-3-yl)-thiophen-2-yl]-vinyl}-6-(2-thiophen-2-yl-vinyl)-pyran- 4-ylidene]-malononitrile} _n (FTPM) _n and {2-{2-{2-[5-(9H-Fluoren-2-yl)-2-hydroxy- 3-methoxy-phenyl]-vinyl}-6-[2-(2-hydroxy-3-methoxy-phenyl)-vinyl]-pyran-4- ylidene}-malononitrile} _n (FOOPM) _n (n = 1–4) have been investigated by the density functional theory (DFT) approach. The ground-state geometries of (FTPM)₄ and (FOOPM)₄ optimized at B3LYP/6-31G(d) level exhibited zigzag arrangements. The energies of HOMO and LUMO, HOMO–LUMO energy gaps (ΔE _H–L ) of (FTPM) _n and (FOOPM) _n (n = ∞) were obtained by linear extrapolation method. Moreover, the calculations of ionization potential (IP), electronic affinity (EA), and reorganization energy (λ) were used to evaluate the charge injection and transport abilities. For (FTPM)₄ and (FOOPM)₄, the TDDFT calculations revealed that the absorption peaks can be characterized as π–π* transition and couple with the location of electron density distribution changes in different repeat units. All the earlier theoretical investigations are intended to establish the structure–property relationships, which can provide guidance to design the organic light-emitting diodes (OLEDs) with high performance.