Solid state NMR studies and density functional theory (DFT) calculations of conformers of quercetin

This work presents the first comparative analysis of two crystallographic modifications of quercetin (3,3',4',5,7-penta-hydroxyflavone). The existence of dihydrate and unhydrated forms of quercetin in the solid state is confirmed by several experimental techniques e.g. X-ray diffraction of powders, DSC, TGA, and NMR. Our studies allow an understanding of the complexity of quercetin samples obtained from different sources. A PASS-2D experiment is employed to establish principal values of 13C chemical shift tensors for both modifications. Solid state NMR spectroscopy and DFT GIAO calculations provide unique information about NMR shielding and electron density distribution for different conformers. It has been concluded that changes of conformation and hydrogen bonding pattern have great influence on bond order parameters of quercetin. Theoretical calculations and experimental data do not exclude the existence of the syn conformer of quercetin, which so far was not considered in the condensed phase.     

四唑互变异构反应的密度泛函理论(DFT)研究

运用11种密度泛函理论方法对四唑互变异构反应进行了计算研究。结果表明,B3LYP-DFT法与从头算的优化几何和能量最为吻合;在6-31^*基组下B3LYP计算的IR频率与MP2/6-311G^*^*计算结果相差很小;用未经校正的B3LYP计算频率求得的产物(2H-四唑)的热力学性质与实测结果也完全一致;由此推荐B3LYP-DFT法适合于对四唑化合物作系统研究。     

The use of the hybrid density functional theory (DFT) approach for calculation of vibrational spectra: nitromethane

The molecular geometry of nitromethane was optimized and its force field and vibrational spectrum were calculated by the BECKE3LYP method. The accuracy of optimization of the geometry of MeNO₂ obtained by this method using the 6–311G(d,p) and 6–311++G(d,p) basis sets is not poorer than that obtained at the second-order Møller-Plesset level of perturbation theory (MP2). The vibrational frequencies of nitromethane and its d₁, d₂, and d₃ isotopomers obtained by the BECKE3LYP method are in much better agreement with the experimental data than those calculated at the MP2 level using the same basis set. The average absolute error of calculations performed without the use of any scaling factors is ～2% for frequencies; the maximum deviation is ～4%.     

DOPA醌在Cu(100)表面吸附的密度泛函理论研究

采用广义梯度密度泛函理论(GGA)的BLYP方法结合周期性平板模型,以原子簇Cu41为模拟表面,对DOPA醌分子在Cu(100)表面不同位置的吸附模型进行了构型优化、能量计算以及Mulliken布居分析,结果表明通过相邻的羰基垂直吸附在表面的桥位是其最佳吸附方式,吸附能为247.2310kJ/mol;其次为顶位、顶位R45和穴位,吸附能分别为227.7162kJ/mol、220.7305kJ/mol和217.8456kJ/mol。Mulliken布居分析结果表明整个吸附体系发生了由Cu原子向DOPA醌分子的电荷转移。     

DFT quantum-chemical calculations of nitrogen oxide chemisorption and reactivity on the Cu(100) surface

A DFT quantum-chemical study of NO adsorption and reactivity on the Cu₂₀ and Cu₁₆ metal clusters showed that only the molecular form of NO is stabilized on the copper surface. The heat of monomolecular adsorption was calculated to be ΔH _m = ?49.9 kJ/mol, while dissociative adsorption of NO is energetically unfavorable, ΔH _d = + 15.7 kJ/mol, and dissociation demands a very high activation energy, E _a = + 125.4 kJ/mol. Because of the absence of NO dissociation on the copper surface, the formation mechanism of the reduction products, N₂ and N₂O, is debatable since the surface reaction ultimately leads to N-O bond cleavage. As the reaction occurs with a very low activation energy, E _a = 7.3 kJ/mol, interpretation of the NO direct reduction mechanism is both an important and intriguing problem because the binding energy in the NO molecule is high (630 kJ/mol) and the experimental studies revealed only physically adsorbed forms on the copper surface. It was found that the formation mechanism of the N₂ and N₂O reduction products involves formation (on the copper surface) of the (O_adN-NO_ad) dimer intermediate that is chemisorbed via the oxygen atoms and characterized by a stable N-N bond (r _N-N ～1.3 Å). The N-N binding between the adsorbed NO molecules occurs through electron-accepting interaction between the oxygen atoms in NO and the metal atoms on the “defective” copper surface. The electronic structure of the (O_adN-NO_ad) surface dimer is characterized by excess electron density (ON-NO)^δ? and high reactivity in N-O_ad bond dissociation. The calculated activation energy of the destruction of the chemisorbed intermediate (O_adN-NO_ad) is very low (E _a = 5–10 kJ/mol), which shows that it is kinetically unstable against the instantaneous release of the N₂ and N₂O reduction products into the gas phase and cannot be identified by modern experimental methods of metal surface studies. At the same time, on the MgO surface and in the individual (Ph₃P)₂Pt(O₂N₂) complex, a stable (O_adN-NO_ad) dimer was revealed experimentally.     

Block-localized wavefunction (BLW) method at the density functional theory (DFT) level

The block-localized wavefunction (BLW) approach is an ab initio valence bond (VB) method incorporating the efficiency of molecular orbital (MO) theory. It can generate the wavefunction for a resonance structure or diabatic state self-consistently by partitioning the overall electrons and primitive orbitals into several subgroups and expanding each block-localized molecular orbital in only one subspace. Although block-localized molecular orbitals in the same subspace are constrained to be orthogonal (a feature of MO theory), orbitals between different subspaces are generally nonorthogonal (a feature of VB theory). The BLW method is particularly useful in the quantification of the electron delocalization (resonance) effect within a molecule and the charge-transfer effect between molecules. In this paper, we extend the BLW method to the density functional theory (DFT) level and implement the BLW-DFT method to the quantum mechanical software GAMESS. Test applications to the pi conjugation in the planar allyl radical and ions with the basis sets of 6-31G(d), 6-31+G(d), 6-311+G(d,p), and cc-pVTZ show that the basis set dependency is insignificant. In addition, the BLW-DFT method can also be used to elucidate the nature of intermolecular interactions. Examples of pi-cation interactions and solute-solvent interactions will be presented and discussed. By expressing each diabatic state with one BLW, the BLW method can be further used to study chemical reactions and electron-transfer processes whose potential energy surfaces are typically described by two or more diabatic states.     

Molecular structure and vibrational assignment of melaminium phthalate by density functional theory (DFT) and ab initio Hartree-Fock (HF) calculations

The molecular geometry, the normal mode frequencies and corresponding vibrational assignment of melaminium phthalate (C₃H₇N₆⁺·C₈H₅O₄⁻) in the ground state were performed by HF and B3LYP levels of theory using the 6-31G(d) basis set. The optimized bond length numbers with bond angles are in good agreement with the X-ray data. The vibrational spectra of melaminium phthalate which is calculated by HF and B3LYP methods, reproduces vibrational wave numbers with an accuracy which allows reliable vibrational assignments. The title compound has been studied in the 4000–100 cm⁻¹ region where the theoretical evaluation and assignment of all observed bands were made.     

Adsorption of transition metal atoms on the NiO(100) surface and on NiO/Ag(100) thin films

We have studied the adsorption of Au, Pd, and Pt atoms on the NiO(100) surface and on NiO/Ag(100) thin films using plane wave DFT+U calculations. The scope of this work is to compare the adsorption properties of NiO, a reducible transition metal oxide, with those of MgO, a simple binary oxide with the same crystal structure and similar lattice parameter. At the same time, we are interested in the adsorption characteristics of NiO ultra-thin films (three atomic layers) deposited on Ag(100) single crystals. Also in this case the scope is to compare NiO/Ag(100) with the corresponding MgO/Ag(100) films which show unusual properties for the case of Au adsorption. The results show that the transition metal atoms bind in a similar way on NiO(100) and NiO/Ag(100) films, with Pt, Pd, and Au forming bonds of decreasing strength in this order. No charging effects occur for Au adsorbed on NiO/Ag(100) films, at variance with MgO/Ag(100). The reasons are analyzed in terms of work function of the metal/oxide interface. Possible ways to modify this property by growing alternate layers of MgO and NiO are discussed.     

Stability and migration of large oxygen clusters in UO(2+x): density functional theory calculations

Using ab initio molecular dynamics simulations and nudged elastic band calculations we examine the finite temperature stability, transition pathways, and migration mechanisms of large oxygen clusters in UO(2+x). Here we specifically consider the recently proposed split quad-interstitial and cuboctahedral oxygen clusters. It is shown that isolated cuboctahedral clusters may transform into more stable configurations that are closely linked to the split quad-interstitial. The split quad-interstitial is stable with respect to single interstitials occupying the empty octahedral holes of the UO(2) lattice. In order to better understand discrepancies between theory and experiments, the simulated atomic pair distribution functions for the split quad-interstitial structures are analyzed with respect to the distribution function for U(4)O(9) previously obtained from neutron diffraction data. Our nudged elastic band calculations suggest that the split quad-interstitial may migrate by translating one of its constituent di-interstitial clusters via a barrier that is lower than the corresponding barrier for individual interstitials, but higher than the barrier for the most stable di-interstitial cluster.     

Chemisorption of OCN on Cu (100) surface: a density functional study

The chemisorption of cyanato radial (OCN) on Cu (100) surface is studied by using density functional theory (DFT) and the cluster model method. Cu₁₄ cluster is used to simulate the surface. Vertical bonding geometries with the nitrogen or oxygen atom down, and a parallel bonding geometry are considered, respectively. The present calculations show that cyanato-N species absorbed on the surface is more favorable than the other configurations. It indicates that OCN species is linearly bonded to the Cu (100) surface via the nitrogen atom, and is in good agreement with the experimental result. The cyanato-N species at the bridge site is most stable. For cyanato-N, the calculated symmetric and asymmetric OCN stretch frequencies are all blue-shifted compared with the calculated gaseous values, which is consistent with the experiment result. The charge transfer from the surface to OCN causes a work function increase on the surface. Bonding of OCN to the metal surface is largely ionic.     

A density functional theory (DFT) and time-dependent density functional theory (TDDFT) study on optical transitions in oligo(p-phenylenevinylene)-fullerene dyads and the applicability to resonant energy transfer

The optical transitions of three different size oligo(p-phenylenevinylene)-fullerene dyads (OPV(n)-MPC(60); n = 2-4) and of the corresponding separate molecules are studied using density functional theory (DFT) and time-dependent density functional theory. The DFT is used to determine the geometries and the electronic structures of the ground states. Transition energies and excited-state structures are obtained from the TDDFT calculations. Resonant energy transfer from OPV(n) to MPC(60) is also studied and the Fermi golden rule is used, along with two simple models to describe the electronic coupling to calculate the energy transfer rates. The hybrid-type PBE0 functional is used with a split-valence basis set augmented with a polarization function (SV(P)) in calculations and the calculated results are compared to the corresponding experimental results. The calculated PBE0 spectra of the OPV(n)-MPC(60) dyads correspond to the experimental spectra very well and are approximately sums of the absorption spectra of the separate OPV(n) and MPC(60) molecules. Also, the absorption energies of OPV(n) and MPC(60) and the emission energies of OPV(n) are predicted well with the PBE0 functional. The PBE0 calculated resonant energy transfer rates are in a good agreement with the experimental rates and show the existence of many possible pathways for energy transfer from the first excited singlet states of the OPV(n) molecules to the MPC(60) molecule.     

Density functional theory (DFT)-based modified embedded atom method potentials: Bridging the gap between nanoscale theoretical simulations and DFT calculations

A density functional theory (DFT)-calculation scheme for constructing the modified embedded atom method (MEAM) potentials for face-centered cubic (fcc) metals is presented. The input quantities are carefully selected and a more reliable DFT approach for surface energy determination is introduced in the parameterization scheme, enabling MEAM to precisely predict the surface and nanoscale properties of metallic materials. Molecular dynamics simulations on Pt and Au crystals show that the parameterization empl...     

The bonding between NO and the NiO(100) surface

Summary The interaction between NO and different possible adsorption sites of the NiO(100) surface is studied. The Ni²⁺ cation gives a bonding to NO in reasonable agreement with experiment, but only if a crystal potential corresponding to less than completely ionic charges is assumed. The computed angle of 43° is also in good agreement with experiment. O^1– sites in both weak and strong crystal potentials also give a strong interaction with NO, 1.3 and 0.5 eV, respectively. In this case the angle is larger or around 70°. The O^2– anion and Ni¹⁺ sites do not give any significant bonding irrespective of assumed crystal potential and can be excluded as adsorption sites. The computed vibrational frequency for the adsorbed NO show shifts of +50, –85 and –200 cm^–1 for adsorption on Ni²⁺ in the weak potential, and O^1– in strong and weak potential, respectively. Only one, downwards shifted, frequency has been observed in the experiment but the most likely candidate for the experimentally observed adsorption site with a binding of 0.5 eV, is still the Ni²⁺ in a weak potential. Nitrogen core level shifts are also computed and discussed and the fully screened core-hole state is obtained for a cluster model, NiF₄O+NO, of Ni²⁺ in NiO with an ionicity lower than the standard ± 2.This work is dedicated to Prof. Inga Fischer-Hjalmars     

Efficient hybrid density functional calculations in solids: assessment of the Heyd-Scuseria-Ernzerhof screened Coulomb hybrid functional

The present work introduces an efficient screening technique to take advantage of the fast spatial decay of the short range Hartree-Fock (HF) exchange used in the Heyd-Scuseria-Ernzerhof (HSE) screened Coulomb hybrid density functional. The screened HF exchange decay properties and screening efficiency are compared with traditional hybrid functional calculations on solids. The HSE functional is then assessed using 21 metallic, semiconducting, and insulating solids. The examined properties include lattice constants, bulk moduli, and band gaps. The results obtained with HSE exhibit significantly smaller errors than pure density functional theory (DFT) calculations. For structural properties, the errors produced by HSE are up to 50% smaller than the errors of the local density approximation, PBE, and TPSS functionals used for comparison. When predicting band gaps of semiconductors, we found smaller errors with HSE, resulting in a mean absolute error of 0.2 eV (1.3 eV error for all pure DFT functionals). In addition, we present timing results which show the computational time requirements of HSE to be only a factor of 2-4 higher than pure DFT functionals. These results make HSE an attractive choice for calculations of all types of solids.     

Designing new donor materials based on functionalized DCCnT with different electron-donating groups: A density functional theory (DFT) and time dependent density functional theory (TDDFT)-based study

Finding a promising donor/acceptor material of organic solar cells is one of the most important ways to improve their power conversion efficiency. Extensive studies have focused on designing and synthesizing new and suitable materials. Small organic molecule materials, different from polymers, have many merits, such as easy synthesis and modification, less by-products, and crystallinity. In the present work, we theoretically design a series of new donor materials based on 1-(1,1-dicyanomethylene)-cyclohex-2-ene-substituted oligothiophenes, that is, DCCnT (n = 1-4) series. Furthermore, we model and predict photoelectric properties of functionalized DCCnT with different electron-donating groups (─CH₃/─CHCH₂/─OCH₃/─NH₂/─OH). The calculated results, based on density functional theory and time-dependent functional theory, show that DCCnT-X (X = OH, NH₂, and OCH₃) series show odd-even effect of dipole moments when n varies from 1 to 4, whereas DCCnT-CH₃ and DCCnT-CHCH₂ do not. Finally, we find that DCC3T-X (X = OH, OCH₃, and NH₂) may be better candidates of donor materials because of their larger dipole moments, stronger electron donating ability, and smaller exciton binding energy with respect to prototype DCCnT molecules.     

Density functional theory for adsorption of HCHO on the FeO（100） surface

The density functional theory (DFT) and periodic slab model were used to get information concerning the adsorption of HCHO on the FeO(100) surface. A preferred η2-(C,O)-di-σ four-membered ring adsorption conformation on the Fe-top site was found to be the most favorable structure with the predicted adsorption energy of 210.7 kJ/mol. The analysis of density of states, Mulliken population, and vibrational frequencies before and after adsorption showed clear weakening of the carbonyl bond, and high sp3 charact...     

Methanol oxidation on the PtPd(111) alloy surface: A density functional theory study

The mechanisms of methanol (CH₃OH) oxidation on the PtPd(111) alloy surface were systematically investigated by using density functional theory calculations. The energies of all the involved species were analyzed. The results indicated that with the removal of H atoms from adsorbates on PtPd(111) surface, the adsorption energies of (i) CH₃OH, CH₂OH, CHOH, and COH increased linearly, while those of (ii) CH₃OH, CH₃O, CH₂O, CHO, and CO exhibited odd‐even oscillation. On PtPd(111) surface, CH₃OH underwent the preferred initial C H bond scission followed by successive dehydrogenation and then CHO oxidation, that is, CH₃OH → CH₂OH → CHOH → CHO → CHOOH → COOH → CO₂. Importantly, the rate‐determining step of CH₃OH oxidation was found to switch from CO → CO₂ on Pt(111) to COOH → CO₂ + H on PtPd(111) with a lower energy barrier of 0.96 eV. Moreover, water also decomposed into OH more easily on PtPd(111) than on Pt(111). The calculated results indicate that alloying Pt with Pd could efficiently improve its catalytic performance for CH₃OH oxidation through altering the primary pathways from the CO path on pure Pt to the non‐CO path on PtPd(111).     

Theoretical investigation of nitro derivatives of tetrazole with density functional theory (DFT)

The B3LYP of density function theory (DFT) method was employed to calculate seven nitrotetrazoles. The optimized geometries, IR spectra and thermodynamic properties at 6-31G* level are obtained. Their heats of formation were computed accurately using the designed isodemic and isogyric reactions. The calculated total energies and heats of formation consistently show that C-nitrotetrazoles are more stable than the N-isomers.     

In vivo monitoring an important plant immune signaling molecule salicylic acid by rhodamine-engineered probes and their density functional theory (DFT) calculations

Monitoring the dynamic fluctuations of plant immune signaling molecules is particularly meaningful and challenging in crop protection. Herein, four rhodamine-functionalized probes (F₁-F₄) were designed and synthesized to attempt to selectively detect a plant hormone salicylic acid (SA). Screening results revealed that probe F₁ bearing a 4,5-dimethoxy-2-nitrobenzyl carbamate moiety was extremely sensitive and selective towards SA along with a conspicuous fluorescence “turn-on” manner. The Job’s plot experiment disclosed a 1:1 binding mode together with a binding constant of 1.34 × 10⁴ M^?1, indicating that an appreciable hydrogen bonding interaction happened between probe F₁ and SA, thereby leading to the spirolactam ring breakage and the succeeding fluorescence generation. Concentration-dependent titration assays offered an available linear relationship for quantifying SA (15–70 μM) and the detection limit of probe F₁ to SA was 1 μM. Density functional theory (DFT) calculations displayed that a smaller energy gap (ΔE_F1-Ⅱ = 498.89 kJ/mol) was obtained between its lowest unoccupied molecular orbital (LUMO) and highest occupied molecular orbital (HOMO), manifesting that probe F₁ was more reactive and sensitive than those of probes F₂-F₄ (ΔE = 567.07 ～ 601.74 kJ/mol) after adsorption with salicylic acid. Meanwhile, the possible monitoring mechanism was elucidated by ¹H NMR titration experiments, probe-SA DFT calculations, and HRMS. Finally, in vivo confocal imaging results found that probe F₁ could delicately and selectively monitor SA on the roots of cucumber. This study can motivate the intensive exploration of multitudinous fluorescent probes for direct SA monitoring in vivo.     

The (010) surface of alpha-MoO3, a DFT + U study

We apply periodic density functional theory to alpha-MoO3 and its (010) surface. The formation energy and structure of defects in the form of surface oxygen vacancies are found to depend critically on the treatment of electron localisation which is achieved in the periodic model using the DFT + U method. Calculated vibrational states for the defect free surface are found to agree well with surface science experimental data and we show that the molybdenyl stretching mode is shifted to a lower frequency in the neighbourhood of a terminal oxygen vacancy. Adsorption of molecular oxygen at the defect site can result in O2, O2(-) or O2(2-) surface species depending on the geometry of adsorption.