Transition Orbitals Research Articles

Experimental and TD-DFT Study of Optical Absorption of Six Explosive Molecules: RDX, HMX, PETN, TNT, TATP, and HMTD

Time dependent density function theory (TD-DFT) has been utilized to calculate the excitation energies and oscillator strengths of six common explosives: RDX (1,3,5-trinitroperhydro-1,3,5-triazine), β-HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine), TATP (triacetone triperoxide), HMTD (hexamethylene triperoxide diamine), TNT (2,4,6-trinitrotoluene), and PETN (pentaerythritol tetranitrate). The results were compared to experimental UV-vis absorption spectra collected in acetonitrile. Four computational methods were tested including: B3LYP, CAM-B3LYP, ωB97XD, and PBE0. PBE0 outperforms the other methods tested. Basis set effects on the electronic energies and oscillator strengths were evaluated with 6-31G(d), 6-31+G(d), 6-31+G(d,p), and 6-311+G(d,p). The minimal basis set required was 6-31+G(d); however, additional calculations were performed with 6-311+G(d,p). For each molecule studied, the natural transition orbitals (NTOs) were reported for the most prominent singlet excitations. The TD-DFT results have been combined with the IPv calculated by CBS-QB3 to construct energy level diagrams for the six compounds. The results suggest optimization approaches for fluorescence based detection methods for these explosives by guiding materials selections for optimal band alignment between fluorescent probe and explosive analyte. Also, the role of the TNT Meisenheimer complex formation and the resulting electronic structure thereof on of the quenching mechanism of II-VI semiconductors is discussed.

Computational study of porphyrin-based dyes with better performance

Using density functional theory (DFT) and time-dependent DFT in different levels, we have systematically studied new porphyrin-based dyes with A-π-D structures focusing on optical absorption, light harvest efficiency, ground state oxidation potential, excited state oxidation potential, and natural transition orbitals. Compared with existing dyes, we find that these new dyes have wide absorption regions (400-1000 nm) with high molar extinction coefficients, and display good energy level alignment for efficient injection of electrons and fast regeneration of the oxidized dyes.

Theoretical Study of the Absorption Spectrum of a Photoisomerizable Iron Complex

We report the time-dependent density functional theory study of the absorption spectrum of an iron complex exhibiting photoisomerization properties. The role of the exchange-correlation functionals and, in particular, the effects of the inclusion of long-range corrections have been considered. The vertical transitions have been analyzed in terms of natural transition orbitals and have shown that the spectrum is dominated by ligand-to-metal charge-transfer transitions, an occurrence that could be promising for future applications of these complexes.

Numerical study of the three-dimensional transit orbits in the circular restricted three-body problem

Transit orbits are defined as the trajectories that can pass through the neck region of the zero velocity surface in the circular restricted three-body problem (CR3BP). The low-energy transfers in the CR3BP or between two CR3BPs are always through the instrumentality of the transit orbits. In this paper, the distribution of the transit orbits in the six-dimensional phase space is explored by using numerical methods. The necessary and sufficient condition of transition is introduced, which defines the distribution of the transit orbits by using the manifolds of the vertical and horizontal Lyapunov orbits and the transit cones. The relationship between the manifolds of the libration point orbits and the boundary of the transit orbits is discovered. By using this relationship, a fast algorithm for detecting the boundary of the transit orbits is developed. Moreover, this boundary is parametrized by using Fourier series, which makes easy to use the conclusions of this paper in future trajectory optimization and mission design. All the analyses in this paper are based on the Sun–Earth CR3BP, but the methods introduced here can be extended to any CR3BPs.

Ground and Excited State Properties of New Porphyrin Based Dyads: A Combined Theoretical and Experimental Study.

The properties of the ground and excited states of several porphyrins appended with external chelates coordinated to ruthenium-bisbipyridine units are reported. The important modification of the absorption spectrum upon coordination with the ruthenium complex showed that a significant electronic communication between the two subunits was present in the ground state. Experimental results were compared with quantum chemistry calculations performed at density functional theory and time-dependent density functional theory level. The influence of the exchange-correlation functional on the quality of the computed absorption spectrum is shown, and the better behavior of hybrid functionals over long-range corrected ones was rationalized. The excited states topology analysis, performed using natural transition orbitals, gave a more evident confirmation of the communication between the subunits and showed that these new compounds can be promising as dyes in dye-sensitized solar cells.

A close inspection of the charge-transfer excitation by TDDFT with various functionals: An application of orbital- and density-based analyses

In order to clarify the origin of the excited state properties gained by time-dependent density functional theory (TDDFT) with various functionals, we investigate them in terms of the orbital- and density-based properties: natural transition orbitals (NTO), transition density (TD), and charge difference density (CDD). We focus on the spectra of N-phenylpyrrole: a molecule in which the charge transfer (CT) excitations are included in its excited states. As a reference, we also analyze the spectra of naphthalene: a molecule whose excited states are characterized with local excitations (LE). Throughout the analyses with NTO, TD and CDD, we clarify the distinguished nature of the CT spectra and its origin gained by the long range corrected (LC) TDDFT.

Electronic Spectroscopy and Computational Studies of Glutathionylco(III)balamin

We have studied glutathionylcobalamin (GS-Cbl) by optical spectroscopy and with density functional theory (DFT) and time-dependent DFT (TD-DFT) electronic structure methods of truncated geometric models. We examined the geometric structure of the models by comparison of DFT calculations with recent high-resolution experimental X-ray structure data ( Hannibal, L. et al. Inorg. Chem. 2010, 49, 9921) for GS-Cbl, and we examined the TD-DFT excitation simulations by comparison of the models with measured optical spectra. The calculations employed the B3LYP hybrid functional and the nonhybrid BP86 functional in both vacuum and water (conductor polarized continuum model (cpcm)) with the 6-311G(d,p) basis set. The optimized geometric structure calculations for six truncated models were made by varying the chemical structure, solvent model, and the two DFT functionals. All showed similar geometry. Charge decomposition analysis (CDA) and extended charge decomposition analysis (ECDA), especially with BP86 shows the similar charge transfer nature of the Co-S bond in GS-Cbl and the Co-C bond in CH(3)Cbl. Mayer and Wiberg bond orders illustrate the similar covalent nature of the two bonds. Finally, absolute optical spectral simulation calculations were compared with the experimental UV-visible extinction spectrum and the electronic circular dichroism (ECD) differential extinction spectrum. The BP86 method shows more spectral features, and the best fit was found for a GS-Cbl model with 5,6-dimethylbenzimidazole at the BP86/6-311G(d,p) level with a water cpcm solvent model. The excited state transitions were investigated with Martin's natural transition orbitals (NTOs). The BP86 calculations also showed π bonding interactions between Co and the axial S of the GS- ligand in the molecular orbitals (MOs) and NTOs.

Effects of mutations on the absorption spectra of copper proteins: a QM/MM study

The ground and excited state properties of copper proteins are studied and analyzed using hybrid quantum mechanics/molecular mechanics technique. Wild-type plastocyanin, characterized by an intense blue color, and wild-type nitrosocyanin, a red protein, are considered. These proteins differ from some ligands of the copper containing chromophore; we also studied the effects of selective mutations of one of the active site residue in plastocyanin. It is shown that this mutation is able to strongly modify the UV/VIS spectrum continuously modifying the absorption spectrum of the protein that from blue becomes red. Electrostatic and polarization effects of the macromolecular environment on the chromophore are taken into account using original techniques. Principal transitions are analyzed by mean of natural transition orbitals.

Improved Treatment of Surrounding Effects: UV/vis Absorption Properties of a Solvated Ru(II) Complex.

The UV/vis and circular-dichroism spectra of a bis-bipyridinyl ruthenium complex are computed at the density functional theory level and the time dependent density functional level of theory. The effects of the solvent, here water, have been taken into account, by polarizable continuum methods and by a hybrid quantum-mechanics/molecular-mechanics approach combined with molecular dynamics. The effects of the solvent have been decomposed in geometric, electrostatic, and polarization of the environment. The principal transitions have been analyzed by means of natural transition orbitals.

Properties of transit trajectory in the restricted three and four-body problem

In the restricted three-body problem if the Jacobi constant is just below the value corresponding to Lagrangian point only a little neck exists around the equilibrium point and capture trajectories are indicated as low-energy. Capture properties depend on the dynamics around these critical points and qualitative results can be obtained using linearized systems. In this paper, to study transit trajectory properties in the restricted three and four-body problem, the Earth–Moon–Sun–Satellite system is considered as example and studied using different models. In the circular restricted three-body problem (Earth–Moon–Satellite), transit, non transit and asymptotic trajectories, are easily identified by using the principal reference frame. Dynamics around Lagrangian point are then studied introducing the Moon eccentricity into the elliptical restricted three-body model. A preferential region for transit orbit is individuated and studied as a function of eigenvalue properties. To introduce the Sun effect, the bi-circular four-body model is considered and dynamics around Lagrangian points studied as a function of angular distance between Earth–Sun and Earth–Moon line. Finally, results obtained in the elliptical three-body model and bi-circular four-body model, are compared with numerical simulations using real Sun–Moon–Earth ephemeris.

Planet Hunters: the first two planet candidates identified by the public using the Kepler public archive data★

Planet Hunters is a new citizen science project, designed to engage the public in an exoplanet search using NASA Kepler public release data. In the first month after launch, users identified two new planet candidates which survived our checks for false- positives. The follow-up effort included analysis of Keck HIRES spectra of the host stars, analysis of pixel centroid offsets in the Kepler data and adaptive optics imaging at Keck using NIRC2. Spectral synthesis modeling coupled with stellar evolutionary models yields a stellar density distribution, which is used to model the transit orbit. The orbital periods of the planet candidates are 9.8844 \pm0.0087 days (KIC 10905746) and 49.7696 \pm0.00039 (KIC 6185331) days and the modeled planet radii are 2.65 and 8.05 R\oplus. The involvement of citizen scientists as part of Planet Hunters is therefore shown to be a valuable and reliable tool in exoplanet detection.

A QM/MM study on the spinach plastocyanin: Redox properties and absorption spectra

The absorption spectrum of spinach plastocyanin protein is studied at time dependent density functional theory level. The reversible copper I–copper II oxido-reduction is also taken into account and the role of the protein is considered. The effects of the macromolecule environment are taken into account by a hybrid quantum mechanics/molecular mechanics method. The electrostatic interactions between the active site and the rest of the molecule have been shown to modify greatly the properties of the system and non-equilibrium polarization response of the protein environment to the transition has been considered in our model by the inclusion of a dielectric constant in the molecular mechanical part. The geometrical effects have also been considered by comparing results in the protein with simple isolated model systems. Particular attention is devoted to the intense 600nm absorption band, and both oxidized (copper II) and reduced (copper I) systems have been studied. The nature of the excited states has been analyzed by using natural transition orbitals formalism. The redox properties of the protein have been analyzed by comparison of oxidized and reduced system, and the easy electron transfer is explained by the fact that the coordination geometry of the copper ion is constrained by the protein structure.

Simulations of light induced processes in water based on ab initio path integrals molecular dynamics. I. Photoabsorption

We have performed large-scale simulations of UV absorption spectra of water clusters (monomer to octamer) using a combination of ab initio path-integral molecular dynamics with reflection principle. The aim of the present work is four-fold: (1) To explore the transition from isolated molecules to bulk water from the perspective of UV photoabsorption. (2) To investigate quantum nuclear and thermal effects on the shape of the water UV spectra. (3) To make an assessment of the density functional theory functionals to be used for water excited states. (4) To check the applicability of the QM/MM schemes for a description of the UV absorption. Within the path integral molecular dynamics (PIMD)/reflection principle approach both the thermal and quantum vibrational effects including anharmonicities are accounted for. We demonstrate that shape of the spectra is primarily controlled by the nuclear quantum effects. The excited states and transition characteristics of the water clusters were calculated with the time-dependent density functional theory and equation-of-motion coupled clusters singles and doubles methods. Based on our benchmark calculations considering the whole UV spectrum we argue that the BHandHLYP method performs best among the 6 functionals tested (B3LYP, BHandHLYP, BNL, CAM-B3LYP, LC-ωPBE, and M06HF). We observe a gradual blueshift of the maximum of the first absorption peak with the increasing cluster size. The UV absorption spectrum for the finite size clusters (i.e., the peak centers, peak widths, and photoabsorption cross section) essentially converges into the corresponding bulk water spectrum. The effect of distant molecules accounted for within the polarizable continuum model is shown to be almost negligible. Using the natural transition orbitals we demonstrate that the first absorption band is formed by localized excitations while the second band includes delocalized excited states. Consequently, the QM/MM electrostatic embedding scheme can only be used for the modeling of the low energy part of the spectrum.

The quantified NTO analysis for the electronic excitations of molecular many-body systems

We show that the origin of electronic transitions of molecular many-body systems can be investigated by a quantified natural transition orbitals (QNTO) analysis and the electronic excitations of the total system can be mapped onto a standard orbitals set of a reference system. We further illustrate QNTO on molecular systems by studying the origin of electronic transitions of DNA moiety, thymine and thymidine. This QNTO analysis also allows us to assess the performance of various functionals used in time-dependent density functional response theory.

Topology of lunar capture orbits: a numerical study

This paper is concerned with the topological study of low-energy trajectories to the Moon, with emphasis to long-term lunar capture orbits, in the context of the classical circular restricted three-body problem. An original cylindrical representation of the phase space, associated with the third body dynamics, is proposed. Periodic orbits, transit orbits, and trajectories asymptotic to the periodic orbit around the Lagrange point 1 L are mapped through this cylindrical representation. Conley's theorem on the topology of lunar capture trajectories is employed to locate the initial conditions of potential interest, i.e. those generating long-term capture lunar orbits. This approach allows finding a number of long-term capture trajectories. One of these trajectories exhibits special features, in terms both of capture duration and of geometric distribution. A simple strategy - that nevertheless minimizes propellant consumption - to transform low-energy trajectories into the final (supposedly desired) circular orbit around the Moon is then proposed.

Ground and excited state properties of photoactive platinum(iv) diazido complexes: Theoretical considerations

Recently synthesized by the group of Sadler, the platinum(IV) diazido complexes [Pt(N(3))(2)(OH)(2)(L')(L'')] (L' and L'' are N-donor ligands) have potential to be used as photoactivatable metallodrugs in cancer chemotherapy. In the present study optimized structures and UV-Vis electronic spectra of trans,trans,trans- and cis,trans,cis-[Pt(N(3))(2)(OH)(2)(NH(3))(2)] (1t and 1c, respectively) as well as cis,trans,cis-[Pt(N(3))(2)(OH)(2)(L)(2)] (L = NH(3), NH(2)CH(3), NF(3), PH(3), PF(3), H(2)O, CO, OH(-), CN(-), py, imid; 2c-11c) and cis,trans-[Pt(N(3))(2)(OH)(2)(bpy)] (12c) complexes were predicted using density functional theory (DFT). The ground state electronic structures of all complexes were analyzed with the help of the natural bond orbital analysis (NBO). The electronic spectra of 1c and 1t were computed using time-dependent density functional theory (TDDFT) with five different density functionals and the ab initio CASSCF/CASPT2 method (for the five lowest energy transitions). The best agreement with available experiments was found in the case of the long-range corrected ωB97X functional. The electronic transitions were characterized by the analysis of the natural transition orbitals (NTO). The low-lying excited singlet states of 1t and 1c have significant azide-to-platinum(IV) charge-transfer character (LMCT). Geometry optimization of the three lowest singlet excited states performed using TDDFT results in the simultaneous dissociation of two azide ligands with the formation of the azidyl radicals N(3)˙ and photoreduction of Pt(IV) to Pt(II). Variation of the ligand L does not strongly affect the nature and the relative energies of the low-lying states. It is shown that the replacement of the OH(-) groups in 1c by OPh(-) ligands results in the red shift of the intense N(3)(-)→Pt LMCT band and the appearance of transitions with significant intensity in the visible region of the spectrum. The dissociative nature of the low-lying unoccupied orbitals remains unaffected. These theoretical results may suggest new experimental routes for the improvement of the photochemical activity of Pt(IV) diazido complexes.

Position Isomerism on One and Two Photon Absorption in Multibranched Chromophores: A TDDFT Investigation

Recently, branching and click chemistry strategies have been combined to design a series of optically active chromophores built from triazole moieties. These triazole-based multipolar chromophores have been shown to be promising candidates for two-photon absorption (TPA) transparency optimization in perspective of optical limiting in the visible region. In this work, the nature of one- and two-photon absorption properties in a family of triazole-based chromophores has been investigated using hybrid time-dependent density functional theory (TD-DFT). We use recent extensions of TD-DFT to determine nonlinear optical responses and natural transition orbitals to analyze the underlying electronic processes. Our results are also interpreted in the framework of the Frenkel exciton model. In agreement with experimental data, we found that introducing a triazole moiety into multibranched chromophores substantially modifies their optical behavior due to changes in electronic delocalization and charge-transfer properties between donating end groups and the branching center that can be controlled by the triazole ring. Structural conformations via modulation of the torsion between phenyl and triazole rings significantly alter the excited state electronic structure. Moreover, isomer positioning also greatly influences both linear and nonlinear optical responses such as TPA. Our theoretical findings allow elucidation of these differences and contribute to the general understanding of structure-property relations. Consequently, the interplay of donor/acceptor strength, triazole regioisomerism, and branching are shown to provide flexible means allowing for precise tuning of both linear and nonlinear optical responses, thus opening new perspectives toward synergic TPA architectures.

Effect of deprotonation on absorption and emission spectra of Ru(ii)-bpy complexes functionalized with carboxyl groups

Changes in the ground and excited state electronic structure of the [Ru(bpy)(3)](2+) (bpy = 2,2'-bipyridine) complex induced by functionalization of bpy ligands with carboxyl and methyl groups in their protonated and deprotonated forms are studied experimentally using absorption and emission spectroscopy and theoretically using density functional theory (DFT) and time dependent DFT (TDDFT). The introduction of the carboxyl groups shifts the metal-to-ligand-charge-transfer (MLCT) absorption and emission bands to lower energies in functionalized complexes. Our calculations show that this red-shift is due to the stabilization of the lowest unoccupied orbitals localized on the substituted ligands, while the energies of the highest occupied orbitals localized on the Ru-center are not significantly affected. Consistent with previously observed trends in optical spectra of related Ru(II) complexes, deprotonation of the carboxyl groups results in a blue shift in the absorption and phosphorescence spectra. The effect originates from interplay of positive and negative solvatochromism in the protonated and deprotonated complexes, respectively. This results in more delocalized character of the electron transition orbitals in the deprotonated species and a strong destabilization of the three lowest unoccupied orbitals localized on the substituted and unsubstituted ligands, all of which contribute to the lowest-energy optical transitions. We also found that owing to the complexity of the excited state potential energy surfaces, the calculated lowest triplet excited state can be either weakly optically allowed (3)MLCT or optically forbidden Ru (3)d-d transition depending on the initial wavefunction guess used in TDDFT calculations.

Natural transition orbitals and rowe's equations of motion

Natural transition orbitals and rowe's equations of motion

A generalization of the hartree-fock one-particle potential

By making the assumption that the addition (subtraction) of an electron from a many-body wave function may be represented by a single spin orbital, variationally determined, two distinct one-particle potentials are derived. They represent, respectively, the effective interaction of the (N - 1)-electron system with the Nth electron, and the effective interaction of the N-electron system with the (N + 1)th electron. Nonlocal exchange arises because of the indistinguishability of electrons. The “core” electrons are allowed to be correlated with each other and to be polarized by the electron in question. Eigenvalues to these potentials represent, respectively, ionization potentials and electron affinities, and the eigenfunctions are variationally determined spin orbitals (“standing-wave solutions”), termed the “natural transition orbitals.” The two-body density matrix of a reference state approximating an eigenfunction of the many-body Hamiltonian is required as input to the theory. Given this input, the method is linear, requiring no interations. In the limit of no correlation in the reference N-body state (provided the occupied orbitals span the Hartree-Fock space), the two potentials reduce to the unrestricted Hartree-Fock potential for occupied and virtual orbitals.