Density Functional Theoretical Methods Research Articles

Energetics of the OH radical H-abstraction reactions from simple aldehydes and their geminal diol forms.

Carbonyl compounds, especially aldehydes, emitted to the atmosphere, may suffer hydration in aerosols or water droplets in clouds. At the same time, they can react with hydroxyl radicals which may add or abstract hydrogen atoms from these species. The interplay between hydration and hydrogen abstraction is studied using density functional and quantum composite theoretical methods, both in the gas phase and in simulated bulk water. The H-abstraction from the aldehydic and geminal diol forms of formaldehyde, acetaldehyde, glycolaldehyde, glyoxal, methylglyoxal, and acrolein is studied to determine whether the substituent has any noticeable effect in the preference for the abstraction of one form or another. It is found that abstraction of the H-atom adjacent to the carbonyl group gives a more stable radical than same abstraction from the geminal diol in the case of formaldehyde, acetaldehyde, and glycolaldehyde. The presence of a delocalizing group in the Cα (a carbonyl group in glyoxal and methylglyoxal, and a vinyl group in acrolein), reverts this trend, and now the abstraction of the H-atom from the geminal diol gives more stable radicals. A further study was conducted abstracting hydrogen atoms from the other different positions in the species considered, both in the aldehydic and geminal diol forms. Only in the case of glycolaldehyde, the radical formed by H-abstraction from the -CH2OH group is more stable than any of the other radical species. Abstraction of the hydrogen atom in one of the hydroxyl groups in the geminal diol is equivalent to the addition of the •OH radical to the aldehyde. It leads, in some cases, to decomposition into a smaller radical and a neutral molecule. In these cases, some interesting theoretical differences are observed between the results in gas phase and (simulated) bulk solvent, as well as with respect to the method of calculation chosen. DFT (M06-2X, B2PLYP, PW6B95), CCSD(T), and composite (CBS-QB3, jun-ChS, SCVECV-f12) methods using Dunning basis sets and extrapolation to the CBS limit were used to study the energetics of closed shell aldehydes in their keto and geminal-diol forms, as well as the radical derived from them by hydrogen abstraction. Both gas phase and simulated bulk solvent calculations were performed, in the last case using the Polarizable Continuum Model.

Ozone oxidation of nitric oxide: Promoting effect of phosphorus and inhibitory effect of phosphoric acid

AbstractThis work presents experimental and density functional theory theoretical methods to carry out the catalytic role and reaction mechanism of phosphorus (P4) for liquid phase catalytic oxidation nitric oxide. Meanwhile, it carries out the promoting effect of phosphorus and inhibitory effect of phosphoric acid in the ozone oxidation of nitric oxide. The work reveals the significant involvement of P4 in facilitating the NO catalytic oxidation process by generating O3. Meanwhile, the presence of phosphoric acid (H3PO4) hindered the NO catalytic removal process. The calculation results highlight that P4 promoted the formation of O3 and favoured the oxidation pathway (oxidation‐hydration, NO ➔ NO2 ➔ HNO3). During the liquid‐phase NO catalytic removal process, O2 and NO dissolved into the solution, where O2 exhibited preferential adsorbed on P4, promoting the O3 formation. Subsequently, O3 first oxidized NO to NO2. Then, HNO2 and HNO3 were generated under the hydration reaction of NO2 and H2O. Next, O3 further oxidized the generated HNO2 to HNO3, realizing the complete oxidation of NO. The hydration step of NO2 was identified as the key step in the O3 oxidation processes. Furthermore, the generation of H3PO4 led to the consumption of P4 and inhibited the NO removal process. O3 played the crucial role in liquid phase NO oxidation.

Tuning the Electronic and Optical Properties of Phenoxaborin Based Thermally Activated Delayed Fluorescent Materials: A DFT Study.

The electronic and optoelectronic properties of molecules constituted by benzene as linker, phenoxaborin as acceptor coupled with different types of donor moieties are investigated using the density functional theoretical method. The energy gap between the first excited singlet and triplet states (ΔEST) of the designed molecules (1-9) is found to be less than 0.5eV suggesting them as ideal candidates for thermally activated delayed fluorescence (TADF) emitters. The analysis of frontier molecular orbitals of the molecules revealed a minimum spatial overlap between highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) in favor of the small values of ΔEST. Among the molecules studied, the one in which dihydrophenazine acts as the donor has the lowest value of ΔEST. All designed molecules are good electron transporters. The non-linear optical properties of the molecules are also examined.

Environmental Effects on the Norbornadiene-quadricyclane Photoswitch for Molecular Solar Thermal Energy Storage

Today’s need for renewable energy combined with modern societies' reliability on on-demand power leads us to find solutions that can store excess or produce directly to storage for later use. A MOlecular Solar Thermal (MOST) based on norbornadiene/quadricyclane(NBD/QC) does the latter with an isomeric photoswitching molecule pair. The theoretical studies of molecular solar thermals (MOST) provide a needed understanding of potential synthetic candidates. We have investigated an array of more complex solvation models for the norbornadiene/quadricycle (NBD/QC) photoswitch and the impacts of the models on the first absorption energy. Our results have been obtained with various density functional theoretical methods and basis sets.

Structure and stability of different triplets involving artificial nucleobases: clues for the formation of semisynthetic triple helical DNA

A triple helical DNA can control gene expression, help in homologous recombination, induce mutations to facilitate DNA repair mechanisms, suppress oncogene formations, etc. However, the structure and function of semisynthetic triple helical DNA are not known. To understand this, various triplets formed between eight artificial nucleobases (P, Z, J, V, B, S, X, and K) and four natural DNA bases (G, C, A, and T) are studied herein by employing a reliable density functional theoretic (DFT) method. Initially, the triple helix-forming artificial nucleobases interacted with the duplex DNA containing GC and AT base pairs, and subsequently, triple helix-forming natural bases (G and C) interacted with artificial duplex DNA containing PZ, JV, BS, and XK base pairs. Among the different triplets formed in the first category, the C-JV triplet is found to be the most stable with a binding energy of about − 31 kcal/mol. Similarly, among the second category of triplets, the Z-GC and V-GC triplets are the most stable. Interestingly, Z-GC and V-GC are found to be isoenergetic with a binding energy of about − 30 kcal/mol. The C-JV, and Z-GC or V-GC triplets are about 12–14 kcal/mol more stable than the JV and GC base pairs respectively. Microsolvation of these triplets in 5 explicit water molecules further enhanced their stability by 16–21 kcal/mol. These results along with the consecutive stacking of the C-JV triplet (C-JV/C-JV) data indicate that the synthetic nucleobases can form stable semisynthetic triple helical DNA. However, consideration of a full-length DNA containing one or more semisynthetic bases or base pairs is necessary to understand the formation of semisynthetic DNA in living cells.

Layered bimetallic oxide composite film: A highly efficient and reusable photocatalytic film for removal of tetracycline antibiotics

To fabricate novel photocatalytic materials is critical to the removal of emerging pharmaceutical pollutants from water samples. However, the photocatalytic materials still face the challenges of degradation performance and reusability. Here, layered bimetallic oxide (LBMO) composites were constructed by using hydrothermal synthesis method of layered double hydroxides (LDH) as precursors, and the LBMO films were prepared by dispersing the LBMO composites in poly(acrylonitrile-co-maleic acid) (PANCMA) solution. The obtained LBMO/PANCMA films exhibited high removal efficiency and good reusability for tetracycline (TC) degradation. Under the optimal conditions, the removal rate of LBMO/PANCMA composite film (20 mg) for TC (20 μg/mL) was 99.34 % within 40 min of light exposure, and retain above 85 % of removal rate even after 10 consecutive uses. Moreover, the possible TC degradation pathways were deduced by analyzing the TC degradation intermediates with LC-MS method, and the toxicity evolution of the TC degradation products was appraised by using density functional theoretical (DFT) method. This study provides a simple and feasible synthesis strategy for membrane-based photocatalytical materials to remove environmental pollutions.

Tuning of the Singlet-Triplet Energy Gap of Donor-Linker-Acceptor Based Thermally Activated Delayed Fluorescent Emitters.

Thermally activated delayed fluorescent emitters based on carbazole donor, benzonitrile acceptor with the linkers biphenyl, bipyridine and naphthalene are investigated using the density functional theoretical method. The molecule in which bipyridine acts as the linker with the least ΔEST is further selected for the designing of a series of D-L-A framework TADF molecules. Remarkably, the ΔEST is decreased successively by attaching the additional cyano groups at the acceptor site which is further reduced when the electron donating methoxy groups are attached at the donor site. To know the effect of substituents on ΔEST, the acceptor moiety of the D-L-A framework is modified with -F, -Cl and -CF3 substituents. The studies showed a relatively less decrement in the value of ΔEST compared to the cyano substituted molecules. However, ΔEST significantly reduced further on attaching methoxy groups at the donor site.

High-level studies of the singlet states of quadricyclane, including analysis of a new experimental vacuum ultraviolet absorption spectrum by configuration interaction and density functional calculations.

A synchrotron-based vacuum ultraviolet absorption spectrum (VUV) of quadricyclane (QC) is reported with energies up to 10.8eV. Extensive vibrational structure has been extracted from the broad maxima by fitting short energy ranges of the VUV spectrum to high level polynomial functions and processing the regular residuals. Comparison of these data with our recent high-resolution photoelectron spectral of QC showed that this structure must be attributed to Rydberg states (RS). Several of these appear before the valence states at higher energies. Both types of states have been calculated by configuration interaction, including symmetry-adapted cluster studies (SAC-CI) and time dependent density functional theoretical methods (TDDFT). There is a close correlation between the SAC-CI vertical excitation energies (VEE) and both Becke 3-parameter hybrid functional (B3LYP), especially Coulomb-attenuating method-B3LYP determined ones. The VEE for several low-lying s-, p, d-, and f-RS have been determined by SAC-CI and adiabatic excitation energies by TDDFT methods. Searches for equilibrium structures for 11,3A2 and 11B1 states for QC led to rearrangement to a norbornadiene structure. Determination of the experimental 00 band positions, which show extremely low cross-sections, has been assisted by matching features in the spectra with Franck-Condon (FC) fits. Herzberg-Teller (HT) vibrational profiles for the RS are more intense than the FC ones, but only at high energy, and are attributed to up to ten quanta. The vibrational fine structure of the RS calculated by both FC and HT procedures gives an easy route to generating HT profiles for ionic states, which usually require non-standard procedures.

Complementary base pair interactions between different rare tautomers of the second-generation artificial genetic alphabets

The functionality of a semisynthetic DNA in the biological environment will depend on the base pair nature of its complementary base pairs. To understand this, base pair interactions between complementary bases of recently proposed eight second-generation artificial nucleobases are studied herein by considering their rare tautomeric conformations and a dispersion-corrected density functional theoretic method. It is found that the binding energies of two hydrogen-bonded complementary base pairs are more negative than those of the three hydrogen-bonded base pairs. However, as the former base pairs are endothermic, the semisynthetic duplex DNA would involve the latter base pairs.

The excited states of azulene: A study of the vibrational energy levels for the lower ππ*-valence states by configuration interaction and density functional calculations, and theoretical studies of the Rydberg states.

A new vacuum ultraviolet absorption (VUV) spectrum of azulene vapor has been obtained by using a synchrotron radiation source. The onset of the ultraviolet spectrum, previously reported by Sidman et al., has been analyzed in detail by Franck-Condon (FC) and Herzberg-Teller (HT) methods. The photoelectron spectral profile identifies the 3px-Rydberg state 00 band to be 131cm-1 from the VUV maximum. Excited state energy levels were calculated by three independent methods: the wide scan VUV spectrum was correlated with symmetry adapted cluster configuration interaction calculations. The low energy portion of the spectrum was studied by both time dependent density functional theoretical methods (TDDFT) and multi-reference multi-root CI (MRD-CI). Equilibrium structures were determined for valence states at the TDDFT level. Rydberg states were determined by both TDDFT and MRD-CI. The FC + HT analyses were performed on the TDDFT wave-functions. The HT intensity profiles are generally low in intensity, relative to the FC ones; however, HT is dominant in the second singlet state (S2, 11A1). As a result, numerous non-symmetric modes, their overtones, and combination bands show considerable intensity in that band. Energies obtained from use of extremely diffuse s-, p-, d-, or f-character functions enabled realistic extrapolation to the IE1 for many Rydberg states (RS). The lowest RS (3b13s) based on IE2 lies at 4.804eV with a quantum defect of 0.714. Differentiation between valence and RS is readily made using the second moments of the charge distribution.

Effect of confinement on the electronic and optical properties of azobenzene: cucurbituril as a means of confinement

The host–guest complexes of cucurbituril and azobenzene are investigated using dispersion corrected density functional theoretical methods. Different orientations of the guest azobenzene inside cucurbiturils of different sizes are examined. The host–guest interaction and the alteration of the physical properties of constituent units are studied. Among different orientations of azobenzene inside cucurbituril, the horizontally oriented cis complex is found to be the most stable. The maximum absorption wavelength (λmax) of trans isomer undergoes red shift due to the confinement inside the cucurbituril cage whereas that of the cis isomer exhibits a blue shift when aligned horizontally inside the cucurbituril cage. The transfer of electron density and the non-linear optical properties of these complexes are also discussed.

Clustering of auro-acetylenes via C-Au⋯π interactions: Gold-hydrogen analogy

The structure, stability, electronic and thermochemical properties of small clusters of auro-acetylenes (C2Au2) are investigated using dispersion-corrected density functional theoretical (DFT) method. The studies showed that auro-acetylene clusters are connected mainly via C-Au⋯π interactions analogous to C-H⋯π interactions in acetylene clusters. In the most stable structures of trimer and tetramer, each of the constituent unit acts both as a C-Au⋯π donor and as a C-Au⋯π acceptor forming cyclic structures akin to acetylene clusters. The studies also revealed that the C-Au⋯π interactions are stronger than the aurophilic interactions forming the clusters.

Insights into the effect of distal histidine and water hydrogen bonding on NO ligation to ferrous and ferric heme: a DFT study.

The effect of distal histidine on ligation of NO to ferrous and ferric-heme, has been investigated with the high-level density functional theoretical (DFT) method. It has been predicted that the distal histidine significantly stabilizes the interaction of NO ferrous-heme (by −2.70 kcal mol−1). Also, water hydrogen bonding is quite effective in strengthening the Fe–NO bond in ferrous heme. In contrast in ferric heme, due to the large distance between the H2O and O(NO) and lack of hydrogen bonding, the distal histidine exhibits only a slight effect on the binding of NO to the ferric analogue. Concerning the bond nature of FeII–NO and FeIII–NO in heme, a QTAIM analysis predicts a partially covalent and ionic bond nature in both systems.

DFT/TD-DFT study of electronic and phosphorescent properties in cycloplatinated complexes: implications for OLEDs.

High level density functional and time-dependent density functional (DFT, TD-DFT) theoretical methods have been employed to investigate the photophysical properties of 5 inorganic compounds resulting from Pt(ii) and ppy (2-phenyl-pyridine) ligands. This study is intended to provide insight into the capability of the selected systems to be used in OLED devices. In addition to an exploration of their ground and excited state geometry and electronic structures, the electronic transitions responsible for their absorption and spectra, as well as other photophysical properties, have been analyzed. To this end, their charge transfer parameters, the triplet exciton generation, phosphorescence quantum yield, and radiative decay rates have been studied. Overall, the results confirm that the selected systems are promising candidates to be used in OLED devices. Moreover, the results of this study assist in understanding the photophysical properties of Pt(ii) complexes with ppy ligands.

Synthesis, growth, spectral and computational studies on aminomethylpyridinium trichloroacetate single crystal

The molecular compounds 2-amino-6-methylpyridine and trichloroacetic acid were synthesized in the ratio 1:1 and a single crystal aminomethylpyridinium trichloroacetate (AMPTA) was grown with the base compound 2-amino-6-methylpyridine (2AMP) as a donor and the acid compound trichloroacetic acid (TA) functions as an acceptor. The modes of vibration with the functional group was investigated from the analysis of FTIR spectroscopy. The existence of proton was prognosticated by 1H NMR spectral analysis. The π→π∗ transition shifted to wavelength 310 nm in UV–vis-NIR spectra confirms the emergence of the AMPTA crystal. The percentage of transmittance spectrum showed the suitability of the compound for non-linear optical applications. TG-DTA analysis was done to study the thermal stability and the melting point of AMPTA crystal was assessed through thermogravimetry (TG) and differential thermal analysis (DTA). The density functional theoretical method (DFT) was carried out with the help of the B3LYP/3-21G(d,p) basis set, and the results were compared with the experimental values.

Cis–trans isomerisation and absorption properties of the ring-extended azobenzene

A series of azobenzene derivatives which differ in the number of rings attached to benzene is investigated using dispersion-corrected density-functional theoretical methods. The studies on the effect of extended rings on the energy of cis and trans isomers (ΔE cis–trans) of the derivatives revealed that ΔE cis–trans is increased from azobenzene to azoanthracene, however, decreased when the rings are extended in two dimensions. The time-dependent density-functional theoretical studies showed that the extension of rings in two-dimension shifts absorption maximum from ultraviolet to visible region. The investigations on fluorine and amino-substituted derivatives of azocoronene showed its cis isomer as lower in energy than trans isomer.

The vacuum ultraviolet absorption spectrum of norbornadiene: Vibrational analysis of the singlet and triplet valence states of norbornadiene by configuration interaction and density functional calculations.

A synchrotron-based vacuum ultraviolet (VUV) absorption spectrum of norbornadiene (NBD) is reported, and the extensive vibrational structure obtained has been analyzed. The previously known 5b13s-Rydberg state has been reinterpreted by comparison with our recent high-resolution photoelectron spectral analysis of the X2B1 ionic state. Additional vibrational details in the region of this Rydberg state are observed in its VUV spectrum when compared with the photoelectron 2B1 ionic state; this is attributed to the underlying valence state structure in the VUV. Valence and Rydberg state energies have been obtained by configuration interaction and time-dependent density functional theoretical methods. Several low-lying singlet valence states, especially those that arise from ππ* excitations, conventionally termed NV1 to NV4, have been examined in detail. Their Franck-Condon (FC) and Herzberg-Teller (HT) profiles have been investigated and fitted to the VUV spectrum. Estimates of the experimental 00 band positions have been made from these fits. The anomaly of the observed UV absorption by the 1A2 state of NBD is attributed to HT effects. Generally, the HT components are less than 10% of the FC terms. The calculated 5b13s lowest Rydberg state also shows a low level of HT components. The observed electron impact spectra of NBD have been analyzed in detail in terms of triplet states.

Stacked dimers of Fe-porphyrin with hydrazine and pyrazine as linkers

Stacking of iron-porphyrin dimers of different spin states is investigated using the dispersion corrected density functional theoretical methods. The studies showed that the dimer adopts a face centered and a slipped parallel stacking in its singlet and nonet spin states, respectively. The effect of linker on stacking revealed that hydrazine linked stacked dimer acquires an open jaw-like geometry, whereas pyrazine linked dimer leads to a symmetrical arrangement with mean planes of two rings parallel. Relative to the monomer, the absorption band of the dimer undergoes blue and red shifts in singlet and nonet spin states, respectively.

Density functional studies of the catalytic oxidation of CO using small aurocarbons

The catalytic activity of small aurocarbons C4H3Au and C4Au4 for the transformation of CO to CO2 is investigated using the dispersion corrected density functional theoretical method. The activation energy barrier 1.54 eV for the reaction in presence of C4H3Au is reduced to 1.38 eV on substituting all the hydrogen atoms by gold atoms. Effect of pre-occupation of CO and O2 on the mechanism and energetics of the reaction is examined. The study revealed that the pre-adsorption of CO at all the gold sites of C4Au4 significantly reduces the energy barrier for the reaction.

Clustering of carbon dioxide around zinc oxide cluster

The clustering and energetics of adsorption of CO2 on zinc oxide cage are investigated using dispersion corrected density functional theoretical method. The gas molecules are adsorbed over the cage by van der Waals interaction. The interaction energy is increased uniformly until the adsorption of twenty-five molecules of CO2 which belongs to the first coordination shell of the cage. A correlation between stabilization energy and the molecular electrostatic potential minimum (Vmin) indicating that less electron rich nature of oxygens of the cage promotes adsorption of CO2. Quantum theory of atoms in molecules analysis substantiated weak interactions between the adsorbed CO2 molecules.