Stable structures and absorption spectra for SixOy molecular clusters using density functional theory

Structural Chemistry - Calculations are presented of vibrational absorption spectra for energy minimized structures of SixOy molecular clusters using density functional theory (DFT). The size of...     

The effect of conjugated spacer on novel carbazole derivatives for dye‐sensitized solar cells: Density functional theory/time‐dependent density functional theory study

The ground‐state structure and frontier molecular orbital of D‐π‐A organic dyes, CFT1A, CFT2A, and CFT1PA were theoretically investigated using density functional theory (DFT) on B3LYP functional with 6‐31G(d,p) basis set. The vertical excitation energies and absorption spectra were obtained using time‐dependent DFT (TD‐DFT). The adsorptions of these dyes on TiO₂ anatase (101) were carried out by using a 38[TiO₂] cluster model using Perdew–Burke–Ernzerhof functional with the double numerical basis set with polarization (DNP). The results showed that the introduction of thiophene–thiophene unit (T–T) as conjugated spacer in CFT2A could affect the performance of intramolecular charge transfer significantly due to the inter‐ring torsion of T–T being decreased compared with phenylene–phenylene (P–P) spacer of CFP2A in the researhcers' previous report. It was also found that increasing the number of π‐conjugated unit gradually enhanced charge separation between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of these dyes, leading to a high‐efficiency photocurrent generation. The HOMO–LUMO energy gaps were calculated to be 2.51, 2.37, and 2.50 eV for CFT1A, CFT2A, and CFT1PA respectively. Moreover, the calculated adsorption energies of these dyes on TiO₂ cluster were ～14 kcal/mol, implying that these dyes strongly bind to TiO₂ surface. Furthermore, the electronic HOMO and LUMO shapes of all dye–TiO₂ complexes exhibited injection mechanism of electron via intermolecular charge‐transfer transition. © 2012 Wiley Periodicals, Inc.     

Fluorine substituent effect on organic dyes for sensitized solar cells

Two sets of organic dyes containing a stilbene backbone with fluorine substituents were designed for a study on the quantum efficiency of dye-sensitized solar cells (DSSCs). The results revealed that adding a fluorine substituent on the phenyl group ortho to the cyanoacrylate can enhance the light-harvesting performance in comparison with the unsubstituted one. However, when the two ortho-positions were both substituted by fluorine atoms, the performance of DSSCs was substantially reduced. The reason was mainly ascribed to a distortion from a planar geometry caused by steric hindrance. The π-conjugation was therefore disturbed, and the result led to a substantial reduction of the short-circuit photocurrent density (J_sc). Another effect was found that the open-circuit photovoltage (V_oc) of the doubly substituted derivative was lower than that of the mono-substituted one. The more flexible conformation of the difluoro-substituted dyes induced an undesired nonradiative decay, therefore led to a reduction of open-circuit photovoltage. The phenomenon can be verified by electrochemical impendence spectrum. The non-planar geometry was realized by a computation using the density function theory (DFT) model. The slight blue shift of absorption band was also consistent with the calculated transition energy by a time dependent DFT model.     

Y-shaped dyes based on triphenylamine for efficient dye-sensitized solar cells

Three new triphenylamine-based dyes with Y-shaped conformation bearing triphenylamino-vinyl, 10-octyl-10H-phenothiazine-vinyl and 9-octyl-9H-carbazole-vinyl as arms (TT, TP, and TC) have been synthesized. From electrochemical investigations it is found that they can be employed in DSSCs due to the balanced HOMO and LUMO energy levels. Notably, the photo-to-electrical conversion efficiency of the DSSCs sensitized with branched TT, TP, and TC reach 5.12%, 4.84%, and 3.63%, which are higher than that sensitized with T (2.79%), and the DSSC sensitized with TT shows higher IPCE response and better photovoltaic performances (J_sc=12.37 mA/cm², V_oc=0.72 V and ff=0.58) than others. These results reveal that the introduction of branched Y-shaped extended π-conjugated donors to D-π-A dyes cannot only enlarge the spectral response range, but also suppress the molecular aggregation on TiO₂ films to a certain extent, which would enhance the performance of DSSCs.     

Excitation spectra of nitro-diphenylaniline: accurate time-dependent density functional theory predictions for charge-transfer dyes

Using time-dependent density functional theory (TD-DFT) and the polarizable continuum model (PCM), we have computed the absorption spectra of nitro-diphenylamine dyes. It turns out that the 6-311+G(2d,p) and 6-311G(d,p) basis sets provide, respectively, almost perfectly converged excitation spectra and geometries. Using the PBE0 hybrid functional, we obtain a valuable correlation between PCM-TD-DFT and experimental lambdamax with mean signed/absolute deviations of -4 nm (0.03 eV)8 nm (0.06 eV) and relatively small extreme discrepancies, although the excitations responsible for the color of this class of dyes present a charge-transfer character. The changes in the electron density upon absorption are analyzed through an orbital picture. In addition, a relationship between the light fastness and a well-identified vibrational frequency is proposed.     

Matrix infrared spectra and density functional theory calculations of molybdenum hydrides

Laser-ablated Mo atoms react with H2 upon condensation in excess argon, neon, and hydrogen. The molybdenum hydrides MoH, MoH2, MoH4, and MoH6 are identified by isotopic substitution (H2, D2, HD, H2 + D2) and by comparison with vibrational frequencies calculated by density functional theory. The MoH2 molecule is bent, MoH4 is tetrahedral, and MoH6 appears to have the distorted trigonal prism structure.     

Analysis of vibrational spectra of L-alanylglycine based on density functional theory calculations

FT Raman and IR spectra of the crystallized biologically active molecule, L-alanylglycine (L-Ala-Gly) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies of L-Ala-Gly have been investigated with the help of B3LYP density functional theory (DFT) method. The calculated molecular geometry has been compared with the experimental data. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). The optimized geometry shows the non-planarity of the peptide group of the molecule. Potential energy surface (PES) scan studies has also been carried out by ab initio calculations with B3LYP/6-311+G** basis set. The red shifting of NH3+ stretching wavenumber indicates the formation of N-H...O hydrogen bonding. The change in electron density (ED) in the sigma* antibonding orbitals and E2 energies have been calculated by natural bond orbital analysis (NBO) using DFT method. The NBO analysis confirms the occurrence of strong intermolecular hydrogen bonding in the molecule.     

Density functional theory calculations on the molecular structures and vibration spectra of platinum(II) antitumor drugs

A comparison of six density functional theory (DFT) methods and six basis sets for predicting the molecular structures and vibration spectra of cisplatin is reported. The theoretical results are discussed and compared with the experimental data. It is remarkable that LSDA/SDD level is clearly superior to all the remaining density functional methods (including mPW1PW) in predicting the structures of cisplatin. Mean deviation between the calculated harmonic and observed fundamental vibration frequencies for each method is also calculated. The results indicate that PBE1PBE/SDD is the best method to predict all frequencies on average for cisplatin molecule in DFT methods.     

Origin of substituent effects in the absorption spectra of peroxy radicals: time dependent density functional theory calculations.

We investigate the assignment of electronic transitions in alkyl peroxy radicals. Past experimental work has shown that the phenyl peroxy radical exhibits a transition in the visible region; however, previous high level calculations have not reproduced this observed absorption. We use time dependent density functional theory (TDDFT) to characterize the electronic excitations of the phenyl peroxy radical as well as other hydrocarbon substituted peroxy radicals. TDDFT calculations of the phenyl peroxy radical support an excitation in the visible spectrum. Further, we investigate the nature of this visible absorption using electron attachment/detachment density diagrams of the peroxy radicals and present a qualitative picture of the origin of the visible absorption based on molecular orbital perturbations. The peroxy radical substituent is also compared against isoelectronic radical groups. The visible absorption is determined to be dependent on mixing of the alkyl and radical substituent orbitals.     

Hybrid density functional theory/molecular mechanics calculations of two-photon absorption of dimethylamino nitro stilbene in solution

The dimethylamino nitro stilbene (DANS) molecule is studied for exploring solvent effects on two-photon absorption using the quantum mechanical/molecular mechanical (QM/MM) response theory approach, where the quantum part is represented by density functional theory. We have explored the role of geometrical change of the chromophore in solution, the importance of taking a dynamical average over the sampled structures and the role of a granular representation of the polarization and electrostatic interactions with the classically described medium. The line shape function was simulated by the QM/MM technique thereby allowing for non-empirical prediction of the absolute two-photon cross section. We report a maximum in the TPA cross section for a medium of intermediate solvent polarity (i.e. in chloroform) and provide the grounds for an explanation of this effect which recently has been experimentally observed for a series of charge transfer species in solvents of different polarity. The calculations of absorption energies reproduce well the positive solvatochromic behavior of DANS and are in good agreement with experimental spectra available for the chloroform and DMSO solvents. In line with recent development of the QM/MM response technique for color modeling, we find this methodology to offer a versatile tool to predict and analyze two-photon absorption phenomena taking place within a medium.     

Prediction of iron K-edge absorption spectra using time-dependent density functional theory

Iron K-edge X-ray absorption pre-edge features have been calculated using a time-dependent density functional approach. The influence of functional, solvation, and relativistic effects on the calculated energies and intensities has been examined by correlation of the calculated parameters to experimental data on a series of 10 iron model complexes, which span a range of high-spin and low-spin ferrous and ferric complexes in O(h) to T(d) geometries. Both quadrupole and dipole contributions to the spectra have been calculated. We find that good agreement between theory and experiment is obtained by using the BP86 functional with the CP(PPP) basis set on the Fe and TZVP one of the remaining atoms. Inclusion of solvation yields a small improvement in the calculated energies. However, the inclusion of scalar relativistic effects did not yield any improved correlation with experiment. The use of these methods to uniquely assign individual spectral transitions and to examine experimental contributions to backbonding is discussed.     

Analysis of vibrational spectra of 5,6-dimethyl benzimidazole based on density functional theory calculations

The vibrational spectra of 5,6-dimethyl benzimidazole (5,6DBZ) have been computed using the standard B3LYP/6-311G** method and basis set combinations. The solid phase FT-IR and FT-Raman spectra were recorded in the region 4000-400 and 3500-100 cm(-1), respectively. A close agreement was achieved between the observed and calculated frequencies by employing normal coordinate calculations. The observed and simulated spectra were found to be well comparable.     

Analysis of vibrational spectra of 2 and 3-methylpiperidine based on density functional theory calculations

The experimental and theoretical vibrational spectra of 2 and 3-methylpiperidine (abbreviated as 2-MP and 3-MP) were studied. The FT-Infrared spectra of 2-MP and 3-MP molecules were recorded in the liquid phase. The structural and spectroscopic analysis of the title molecules were made by using density functional harmonic calculations. For the title molecules, only one form was found most stable structure by using B3LYP level with the 6-311G (d,p) basis set. Selected experimental bands were assigned and characterized based on the scaled theoretical wave numbers by their total energy distribution (TED).     

Panchromatic push-pull chromophores based on triphenylamine as donors for molecular solar cells

Two new push-pull chromophores based on triphenylamine as donor and 2-carboxymethyl-2-cyanomethylenethiazole as acceptor have been synthesized. Both exhibit strong light absorption covering from 300 to 800 nm. Electrochemical studies show HOMO-LUMO gaps of 2.01 and 1.54 eV, making, together with the panchromatic absorption, these systems promising materials in the field of molecular photovoltaic devices.     

Time-dependent density functional theory benchmarking for the calculations of atomic spectra: efficiency of exc-ETDZ basis set

We present a time-dependent density functional theory (TD-DFT) benchmarking of recently constructed basis set, namely exc-ETDZ (Guevara et al. in J Chem Phys 131: 064104, 2009) for predicting the atomic spectra of the first-row atoms. A systematic testing with 31 density functional methods has been performed to see whether convincing performance of this basis set carries over the TD-DFT formalism. The efficiency of exc-ETDZ basis set for reproducing atomic spectra has been compared with Pople- and Dunning-style basis sets. We focused on the atomic low-lying valence excited states with single excitation character for our benchmarking, and the calculated excitation energies were compared to experimental data. On average, the functionals providing the best match with exc-ETDZ basis are BMK, BH&HLYP and ωB97. Moreover, on the basis of comparison between the results of these superior functionals with CIS(D) estimates, it turned out that TD-DFT and CIS(D) errors are of the same order of magnitude, once the exc-ETDZ basis set is used. Finally, the results of present study indicate that different functionals show results that are highly dependent on the atomic configuration as well as the basis set.     

Prediction of high-valent iron K-edge absorption spectra by time-dependent density functional theory

In recent years, a number of high-valent iron intermediates have been identified as reactive species in iron-containing metalloproteins. Inspired by the interest in these highly reactive species, chemists have synthesized Fe(IV) and Fe(V) model complexes with terminal oxo or nitrido groups, as well as a rare example of an Fe(VI)-nitrido species. In all these cases, X-ray absorption spectroscopy has played a key role in the identification and characterization of these species, with both the energy and intensity of the pre-edge features providing spectroscopic signatures for both the oxidation state and the local site geometry. Here we build on a time-dependent DFT methodology for the prediction of Fe K- pre-edge features, previously applied to ferrous and ferric complexes, and extend it to a range of Fe(IV), Fe(V) and Fe(VI) complexes. The contributions of oxidation state, coordination environment and spin state to the spectral features are discussed. These methods are then extended to calculate the spectra of the heme active site of P450 Compound II and the non-heme active site of TauD. The potential for using these methods in a predictive manner is highlighted.     

Toward panchromatic organic functional molecules: density functional theory study on the electronic absorption spectra of substituted tetraanthracenylporphyrins

To achieve full solar spectrum absorption of organic dyes for organic solar cells and organic solar antenna collectors, a series of tetraanthracenylporphyrin derivatives including H(2)(TAnP), H(2)(α-F(4)TAnP), H(2)(β,β'-F(8)TAnP), H(2)(γ,γ'-F(8)TAnP), H(2)(δ,δ'-F(8)TAnP), H(2)[α-(NH(2))(4)TAnP], H(2)[β,β'-(NH(2))(8)TAnP], H(2)[γ,γ'-(NH(2))(8)TAnP], and H(2)[δ,δ'-(NH(2))(8)TAnP] was designed and their electronic absorption spectra were systematically studied on the basis of TDDFT calculations. The nature of the broad and intense electronic absorptions of H(2)(TAnP) in the range of 500-1700 nm is clearly revealed, and different types of π → π* electronic transitions associated with different absorption bands are revealed to correspond to different electron density moving direction between peripherally fused 14-electron-π-conjugated anthracene units and the central 18-electron-π-conjugated porphyrin core. Introduction of electron-donating groups onto the periphery of the H(2)(TAnP) macrocycle is revealed to be able to lead to novel NIR dyes such as H(2)[α-(NH(2))(4)TAnP] and H(2)[δ,δ'-(NH(2))(8)TAnP] with regulated UV-vis-NIR absorption bands covering the full solar spectrum in the range of 300-2400 nm.     

Negative effect on molecular planarity to achieve organic ternary memory: triphenylamine as the spacer

Adjusting the spacers between the electron-acceptor and the elector-donor is important to design organic ternary memory material but rarely reported. In this paper, two small molecules, ZIPGA and ZIPCAD with benzene ring or triphenylamine as the spacers, were designed and synthesized to fabricate memory devices. The Al/ZIPGA/indium-tin oxide (ITO) device showed ternary characteristics, whereas Al/ZIPCAD/ITO had no obvious memory characteristics. Density functional theory calculation, X-ray diffraction (XRD) and atomic force microscopy (AFM) were employed to interpret the different memory properties. ZIPGA thin film has the closer intermolecular packing and flatter surface morphology than ZIPCAD film, which was favorable to the electron migration. This work demonstrates the importance of spacers and reveals that triphenylamine may be not a good spacer in design of new memory material.     

Effect of beta-ring rotation on the structures and vibrational spectra of beta-carotene: density functional theory analysis

The effect of beta-ring rotation on the structures and vibrational spectroscopic characteristics of beta-carotene, including infrared (IR) intensities and Raman activities, is analyzed using density functional theory. Two stable isomers having Ci symmetry are obtained. The reversion of bond lengths is ascribed to the hyperconjugation effect. The natural bond orbital (NBO) charge analysis suggests that the NBO charges of C5 can be used to estimate the degree of pi-electron delocalization. These structural variations are used to analyze and assign the vibrational spectra. It is concluded that (a) the similar rotational angle dependencies of nu1 and nu2 frequencies justify the contribution of C=C stretch vibrations to the nu2 mode and explain the same conjugation length dependencies of nu1 and nu2 frequencies in polyenes, (b) the nu1 mode can be assigned to the C=C stretching in the central part of polyene chain, whereas beta-rings play an important role in nu2 and IR1 bands, especially for the all-trans isomer, and (c) the transition dipole moment of the calculated IR1 absorption band is relevant to the conjugation degree and the crossing angle between the eigenvectors of the polyene chain and the C5=C6 stretching vibration. This theoretical analysis, together with our previous Raman spectral experiments, suggests that the C6-C7 bond is easier to be twisted than other parts of beta-carotene molecule and so provides an insight into the structures of carotenoids and the properties of binding sites in carotenoproteins.