Calculation of two-photon absorption spectra of donor-pi-acceptor compounds in solution using quadratic response time-dependent density functional theory

Linear and quadratic response time-dependent density functional theories have been applied to calculate the photophysical properties of donor-pi-acceptor molecules which are known to have large nonlinear absorption. The linear absorption and two-photon absorption spectra predicted using hybrid functionals, including the Coulomb-attenuated model, with continuum solvation models are reported and compared to experiment and to previous theoretical predictions. While the quadratic response with these functionals overestimated the TPA cross sections relative to experiment when a Gaussian linewidth function was used, a fairly good agreement was obtained when a Lorentzian linewidth function was applied. In addition, the comparison of the TPA cross sections calculated by the sum over states with those calculated by the two-state approximation indicates the importance of the higher energy states in TPA, particularly in nondegenerate experiments.     

Time-dependent density functional theory studies of the photoswitching of the two-photon absorption spectra in stilbene, metacyclophenadiene, and diarylethene chromophores

Photochromophores such as cis-stilbene (1a), metacyclophenadiene (2a), and the diarylethene 3a undergo photoinduced conrotatory opening and closing of a central bond and are currently being sought out as potential candidates for media within 3D optical information storage devices. Strong molecular two-photon absorption (inducing the reversible photoisomerization) is a necessary feature for this application due to the need for high 3D spatial resolution. Here, the one- and two-photon absorption (OPA and TPA) characteristics of the open- and closed-ring isomers of 1-3 have been investigated using time-dependent density functional theory. It was determined that the excited states populated by two-photon absorption were nearly 1 eV higher in energy than the lowest energy excited state populated by one-photon absorption. The electronic structures of the TPA and OPA accessed states were then compared utilizing natural transition orbital analysis. There, it was found that states excited by OPA had pipi* character about the C-C framework associated with the bond formation/scission of the central C-C bond. In contrast, the states populated by TPA have pipi* character along the C-C skeletal periphery, including phenyl excitations. It is postulated that these differences in excited state electronic structure may lead to reaction pathways alternative to photoisomerization about the central C-C bond, impacting the utility of these compounds as 3D information storage media.     

Comparative quantum mechanics/molecular mechanics (QM/MM) and density functional theory calculations on the oxo-iron species of taurine/alpha-ketoglutarate dioxygenase

We present here the first quantum mechanical/molecular mechanics (QM/MM) studies of taurine/alpha-ketoglutarate dioxygenase (TauD) enzymes. Our studies are focused on the chemical properties of the oxo-iron species and the effect of the protein environment on its structural and electronic behavior. Although the active site region of TauD is very polar with many key hydrogen bonding interactions and salt bridges, the actual effect of the protein environment on the ordering and relative energies of the possible spin state structures is found to be quite small. Optimized geometries are very close to ones observed with density functional theory models that did not take the protein environment into consideration. The calculations show that protonation of the histidine ligands of iron is essential to reproduce the correct electronic representations of the enzyme. Hydroxylation studies of taurine by the oxo-iron active species predict that it is a very efficient catalyst that reacts with substrates via low reaction barriers.     

Photoisomerization of stilbene: a spin-flip density functional theory approach

The photoisomerization process of 1,2-diphenylethylene (stilbene) is investigated using the spin-flip density functional theory (SFDFT), which has recently been shown to be a promising approach for locating conical intersection (CI) points (Minezawa, N.; Gordon, M. S. J. Phys. Chem. A2009, 113, 12749). The SFDFT method gives valuable insight into twisted stilbene to which the linear response time-dependent DFT approach cannot be applied. In contrast to the previous SFDFT study of ethylene, a distinct twisted minimum is found for stilbene. The optimized structure has a sizable pyramidalization angle and strong ionic character, indicating that a purely twisted geometry is not a true minimum. In addition, the SFDFT approach can successfully locate two CI points: the twisted-pyramidalized CI that is similar to the ethylene counterpart and another CI that possibly lies on the cyclization pathway of cis-stilbene. The mechanisms of the cis--trans isomerization reaction are discussed on the basis of the two-dimensional potential energy surface along the twisting and pyramidalization angles.     

Density functional response theory calculations of three-photon absorption

Three-photon absorption probabilities delta(3PA) have been calculated through application of a recently derived method for cubic response functions within density functional theory (DFT). Calculations are compared with Hartree-Fock (HF) and with a coupled cluster hierarchy of models in a benchmarking procedure. Except for cases having intermediate states near resonance, density functional theory is demonstrated to be in sufficient agreement with the highly correlated methods in order to qualify for predictions of delta(3PA). For the larger systems addressed, a set of acceptor A and donor D substituted pi-conjugated systems formed by trans-stilbene and dithienothiophene (DTT), we find noticeable differences in the magnitude of delta(3PA) between HF and DFT, although similar trends are followed. It is shown that the dipolar structures, TS-AD and DTT-AD, have substantially larger delta(3PA) than other types of modifications which is in accordance with observations for two-photon absorption. This is the first application of density functional theory to three-photon absorption beyond the use of few-state models.     

Prediction of formation constants of metal-ammonia complexes in aqueous solution using density functional theory calculations

Density functional theory calculation of gas-phase Delta G of replacement of a water molecule by NH(3) on [M(H(2)O)(6)](n+)(g) for 19 different metal ions correlates well with Delta G of formation of mono NH(3) complexes of these ions in water, suggesting this approach will permit prediction of formation constants in aqueous solution, and produce insights into theories of metal complex formation reactions.     

Benchmark density functional theory calculations for nanoscale conductance

We present a set of benchmark calculations for the Kohn-Sham elastic transmission function of five representative single-molecule junctions. The transmission functions are calculated using two different density functional theory methods, namely an ultrasoft pseudopotential plane-wave code in combination with maximally localized Wannier functions and the norm-conserving pseudopotential code SIESTA which applies an atomic orbital basis set. All calculations have been converged with respect to the supercell size and the number of k|| points in the surface plane. For all systems we find that the SIESTA transmission functions converge toward the plane-wave result as the SIESTA basis is enlarged. Overall, we find that an atomic basis with double zeta and polarization is sufficient (and in some cases, even necessary) to ensure quantitative agreement with the plane-wave calculation. We observe a systematic downshift of the SIESTA transmission functions relative to the plane-wave results. The effect diminishes as the atomic orbital basis is enlarged; however, the convergence can be rather slow.     

Conjugate spacer effect on molecular structures and absorption spectra of triphenylamine dyes for sensitized solar cells: density functional theory calculations

The molecular structures and absorption spectra of triphenylamine dyes containing variable thiophene units as the spacers (TPA1-TPA3) were investigated by density functional theory (DFT) and time-dependent DFT. The calculated results indicate that the strong conjugation is formed in the dyes and the length of conjugate bridge increases gradually with the increased thiophene spacers. The interfacial charge transfer between the TiO2 electrode and TPA1-TPA3 are electron injection processes from the excited dyes to the semiconductor conduction band. The simulated absorption bands are assigned to π→π* transitions, which exhibit appreciable red-shift with respect to the experimental bands due to the lack of direct solute-solvent interaction and the inherent approximations in TD-DFT. The effect of thiophene spacers on the molecular structures, absorption spectra and photovoltaic performance were comparatively discussed and points out that the choice of appropriate conjugate bridge is very important for the design of new dyes with improved performance.     

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...     

Recent applications of density functional theory calculations to biomolecules

The purpose of this overview is to highlight the broad scope and utility of current applications of density functional theory (DFT) methods for the study of the properties and reactions of biomolecules. This is illustrated using examples selected from research carried out within our research group and in collaboration with others. The examples include the hyperfine coupling constants of amino acid radicals, the use of an amino acid as a chiral catalyst for the formation of carbon–carbon bonds in the aldol reaction, hydrogen-bond mediated catalysis of an aminolysis reaction, radiation-induced protein–DNA cross-links, and the mechanism by which an antitumor drug cleaves DNA. We demonstrate that DFT-based methods can be applied successfully to a broad range of problems that remain beyond the scope of conventional electron-correlation methods. Furthermore, we show that contemporary computational quantum chemistry complements experiment in the study of biological systems. Received: 19 December 2001 / Accepted: 8 April 2002 / Published online: 4 July 2002     

Methylation of zebularine investigated using density functional theory calculations

Deoxyribonucleic acid (DNA) methylation is an epigenetic phenomenon, which adds methyl groups into DNA. This study reveals methylation of a nucleoside antibiotic drug 1‐(β‐D ‐ribofuranosyl)‐2‐pyrimidinone (zebularine or zeb) with respect to its methylated analog, 1‐(β‐D ‐ribofuranosyl)‐5‐methyl‐2‐pyrimidinone (d5) using density functional theory calculations in valence electronic space. Very similar infrared spectra suggest that zeb and d5 do not differ by types of the chemical bonds, but distinctly different Raman spectra of the nucleoside pair reveal that the impact caused by methylation of zeb can be significant. Further valence orbital‐based information details on valence electronic structural changes caused by methylation of zebularine. Frontier orbitals in momentum space and position space of the molecules respond differently to methylation. Based on the additional methyl electron density concentration in d5, orbitals affected by the methyl moiety are classified into primary and secondary contributors. Primary methyl contributions include MO8 (57a), MO18 (47a), and MO37 (28a) of d5, which concentrates on methyl and the base moieties, suggest certain connection to their Frontier orbitals. The primary and secondary methyl affected orbitals provide useful information on chemical bonding mechanism of the methylation in zebularine. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Lattice density functional theory of molecular diffusion

A density functional theory of diffusion is developed for lattice fluids with molecular flux as a functional of the density distribution. The formalism coincides exactly with the generalized Ono-Kondo density functional theory when there is no gradient of chemical potential, i.e., at equilibrium. Away from equilibrium, it gives Fick's first law in the absence of a potential energy gradient, and it departs from Fickian behavior consistently with the Maxwell-Stefan formulation. The theory is applied to model a nanopore, predicting nonequilibrium phase transitions and the role of surface diffusion in the transport of capillary condensate.     

Studies of iridium nanoparticles using density functional theory calculations

The energetics and the electronic and magnetic properties of iridium nanoparticles in the range of 2-64 atoms were investigated using density functional theory calculations. A variety of different geometric configurations were studied, including planar, three-dimensional, nanowire, and single-walled nanotube. The binding energy per atom increases with size and dimensionality from 2.53 eV/atom for the iridium dimer to 6.09 eV/atom for the 64-atom cluster. The most stable geometry is planar until four atoms are reached and three-dimensional thereafter. The simple cubic structure is the most stable geometric building block until a strikingly large 48-atom cluster, when the most stable geometry transitions to face-centered cubic, as found in the bulk metal. The strong preference for cubic structure among small clusters demonstrates their rigidity. This result indicates that iridium nanoparticles intrinsically do not favor the coalescence process. Nanowires formed from linear atomic chains of up to 4-atom rings were studied, and the wires formed from 4-atom rings were extremely stable. Single-walled nanotubes were also studied. These nanotubes were formed by stacking 5- and 6-atom rings to form a tube. The ring stacking with each atom directly above the previous atom is more stable than if the alternate rings are rotated.