Time-dependent Density Function Research Articles

Ratiometric sensing of fluoride and acetate anions based on a BODIPY-azaindole platform and its application to living cell imaging

A new BODIPY-azaindole based fluorescent sensor 1 was designed and synthesized as a new colorimetric and ratiometric fluorescent chemosensor for fluoride. The binding and sensing abilities of sensor 1 towards various anions were studied by absorption, emission and (1)H NMR titration spectroscopies. The spectral responses of 1 to fluoride in acetonitrile-water were studied: an approximately 69 nm red shift in absorption and ratiometric fluorescent response was observed. The striking light yellow to deep brown color change in ambient light and green to blue emission color change are thought to be due to the deprotonation of the indole moiety of the azaindole fluorophore. From the changes in the absorption, fluorescence, and (1)H NMR titration spectra, proton-transfer mechanisms were deduced. Density function theory and time-dependent density function theory calculations were conducted to rationalize the optical response of the sensor. Results were supported by confocal fluorescence imaging and MTT assay of live cells.

Dithizone as novel and efficient chromogenic probe for cyanide detection in aqueous media through nucleophilic addition into diazenylthione moiety

A new selective chemodosimeter probe was developed by the introduction of dithizone (DTZ) as a simple and available dye for detection of cyanide in aqueous media which enables recognition of cyanide over other competing anions such as acetate, dihydrogen phosphate, fluoride and benzoate through covalent bonding. The sensing properties of DTZ were investigated in DMSO/H2O (1:9) and have demonstrated a very high selectivity toward the cyanide anions. A reasonable recognition mechanism was suggested using UV–Vis, 1H NMR and FTIR spectroscopy techniques. Time dependent density function theory (TDDFT) computations of UV–Vis excitation for DTZ2-CN adduct agreed well with our experimental findings. The detection limit of the new chromogenic probe was measured to be 0.48μmolL−1 which is much lower than most recently reported chromogenic probes for cyanide determination. The analytical utility of the method for the analysis of cyanide ions in electroplating wastewater (EPWW), human serum, tap and mineral water samples was demonstrated and the results were compared successfully with the conventional reference method. The short time response and the detection by the naked eye make the method available for the detection and quantitative determination of cyanide in a variety of real samples.

New sesterterpenoids from Salvia mirzayanii - stereochemical characterization by computational electronic circular dichroism

Sesterterpenes are rare in nature and have been reported mostly from marine sponges and algae. Among terrestrial plants, Salvia species are a good source for these compounds. They exhibit diverse biological properties, such as anti-inflammatory, cytotoxic, anti-biofilm, antimicrobial, and anticancer activities. In a project directed at novel bioactive metabolites from endemic Iranian Lamiaceae, we studied Salvia mirzayanii. We isolated five new sesterterpenoids, whose structures were secured by means of extensive NMR (1D and 2D) and MS spectroscopy. Structure elucidation revealed that compounds 1-3 only differ in their configurations at C-13 and C-14. Assignment of relative and absolute configurations was challenging due to free rotation around the C-13/C-14, but could be achieved by comparison of experimental and simulated ECD spectra of all possible stereoisomers by using time dependent density function theory TDDFT/CAM-B3LYP/6 – 31G** in the MeOH using the “self-consistent reaction field” method (SCRF) with the conductor-like polarizable calculation model (CPCM). [1 – 2] Absolute configuration of 4 and 5 were established in a similar manner.

Chemically modified titanium oxide nanostructures for dye-sensitized solar cells

We report a simple and yet powerful method to improve the performance of TiO2-based N3 dye-sensitized solar cells (DSSCs) by hydrogen-treatment of TiO2 nanostructures as photoelectrodes. The solar conversion efficiency of DSSC based on TiO2 rutile nanowires was increased from 0.28% to 0.45% after the nanowire electrode was annealed at 350°C in a pure hydrogen atmosphere. The enhanced conversion efficiency was attributed to improved charge transport as a result of increased electron density by three orders of magnitude upon hydrogenation. While the conversion efficiency was improved by 61%, the overall efficiency was still low, possibly due to the limited loading of N3 dye molecules on TiO2 nanowires. To improve dye loading, a similar study of hydrogen-treated Degussa P25 nanoparticles (H-P25) electrodes was conducted in which the conversion efficiency was enhanced by 13% compared to untreated P25. The DSSC based on H-P25 achieved a very high photocurrent, 20.81mA/cm2, and solar conversion efficiency, 9.30%, under 1sun illumination. The donor density of H-P25 was found to increase by 1.5 times compared to P25, consistent with the relatively small enhancement in overall conversion efficiency. To gain new physical insight into the dye sensitization process, ultrafast transient absorption (TA) spectroscopy was applied to probe the excited dynamics of N3 dye in ethanol solution as well as adsorbed on H-P25, P25 and ZrO2. The TA spectrum of H-P25 and P25 was dominated by N3+ generated following electron injection, which occurs in <150fs. In addition, time dependent density function theory (TDDFT) calculations of N3 and N3+ provided further insight into the origin of TA spectra as well as the related dynamic processes. The results demonstrate that hydrogenation of TiO2 electrodes can be a low cost and effective way to enhance performance of DSSC by rationally introducing bandgap states that enhanced the donor density and thereby charge transport.

TDDFT study of excitation of water molecules with short laser pulses

We explore the excitation of water molecules subject to short and intense laser pulses in the frame of time-dependent density function theory (TDDFT) at the level of the time-dependent local-density approximation (TDLDA), applied to valence electrons, coupled non-adiabatically to molecular dynamics (MD) of ions. We first study the optical absorption spectra of the water molecule as an observable in the “linear" domain and results are in good agreement with experiments. We then explore the influence of the laser frequency on the excitation. It is found that when the laser frequency is off-resonant or highly above the resonant region, the excitations are weak whereas for the resonant frequency case, the ionization is enhanced and bond lengths are enlarged. Furthermore, a direct coupling of ions with the laser pulse with the off-resonant frequency is found when investigating the OH bond lengths. We finally study the effect of laser intensity on the excitation of H2O and it is found that ionization increases when the laser intensity varies from low to high and we observe stable vibrations to Coulomb fragmentation when the ionization is up to typically two more charge units.

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.

Lowest triplet (n, π*) electronic state of acrolein: Determination of structural parameters by cavity ringdown spectroscopy and quantum-chemical methods

The cavity ringdown absorption spectrum of acrolein (propenal, CH(2)=CH-CH=O) was recorded near 412 nm, under bulk-gas conditions at room temperature and in a free-jet expansion. The measured spectral region includes the 0(0)(0) band of the T(1)(n, π*) ← S(0) system. We analyzed the 0(0)(0) rotational contour by using the STROTA computer program [R. H. Judge et al., J. Chem. Phys. 103, 5343 (1995)], which incorporates an asymmetric rotor Hamiltonian for simulating and fitting singlet-triplet spectra. We used the program to fit T(1)(n, π*) inertial constants to the room-temperature contour. The determined values (cm(-1)), with 2σ confidence intervals, are A = 1.662 ± 0.003, B = 0.1485 ± 0.0006, C = 0.1363 ± 0.0004. Linewidth analysis of the jet-cooled spectrum yielded a value of 14 ± 2 ps for the lifetime of isolated acrolein molecules in the T(1)(n, π*), v = 0 state. We discuss the observed lifetime in the context of previous computational work on acrolein photochemistry. The spectroscopically derived inertial constants for the T(1)(n, π*) state were used to benchmark a variety of computational methods. One focus was on complete active space methods, such as complete active space self-consistent field (CASSCF) and second-order perturbation theory with a CASSCF reference function (CASPT2), which are applicable to excited states. We also examined the equation-of-motion coupled-cluster and time-dependent density function theory excited-state methods, and finally unrestricted ground-state techniques, including unrestricted density functional theory and unrestricted coupled-cluster theory with single and double and perturbative triple excitations. For each of the above methods, we or others [O. S. Bokareva et al., Int. J. Quantum Chem. 108, 2719 (2008)] used a triple zeta-quality basis set to optimize the T(1)(n, π*) geometry of acrolein. We find that the multiconfigurational methods provide the best agreement with fitted inertial constants, while the economical unrestricted Perdew-Burke-Ernzerhof exchange-correlation hybrid functional (UPBE0) technique performs nearly as well.

COMPENSATION OF INTRA-SPEAKER VARIABILITY IN SPEAKER DIARIZATION

A method, system, and computer program product compensation of intra-speaker variability in speaker diarization are provided. The method includes: dividing a speech session into segments of duration less than an average duration between speaker change; parameterizing each segment by a time dependent probability density function supervector, for example, using a Gaussian Mixture Model; computing a difference between successive segment supervectors; and computing a scatter measure such as a covariance matrix of the difference as an estimate of intra-speaker variability. The method further includes compensating the speech session for intra-speaker variability using the estimate of intra-speaker variability.

Calculations of flow-induced orientation distributions for analysis of linear dichroism spectroscopy

Spectroscopic techniques involving flow-oriented samples and polarised light, such as linear dichroism (LD), are becoming increasingly useful to probe biomacromolecular assemblies. However, the magnitude of the signal and in some cases the shape of the spectrum are dependent on the distribution of the orientations of the molecules in the sample. Despite great progress in the modelling of dilute and semi-dilute suspension mechanics, these theories have had remarkably little impact on the community practising LD. We perform calculations with a model combining Brownian effects and rotations in a steady shear flow of a dilute suspension of rigid, rodlike particles. We calculate the time-dependent probability density functions for the orientation distributions of three biomolecular assemblies: M13 bacteriophage, DNA molecules of well-defined length, and FtsZ protofilaments. Our calculations allow us to compute directly (rather than infer from experiment) the LD orientation parameter, S, for such assemblies. The results from the model are consistent with experiment for M13 bacteriophage and allow us to estimate S empirically for reasonably short DNA molecules. In analysing the particle size distribution for the process of FtsZ polymerisation, we find that results from the model aid our understanding of the process.

TDDFT studies of electronic spectra and excited states of the triphenylamine-based organic sensitizers and organic sensitizer–titanium dioxide cluster complexes

The absorption spectra and excited states of four triphenylamine-based organic dye molecules (TC1, TC2, TC3 and TC4) for dye sensitized solar cells (DSSC) have been theoretically investigated with density function theory (DFT) and time-dependent density function theory (TDDFT). In order to simulate the optical properties of the real DSSCs, sensitizer/titanium dioxide cluster interface systems TC4-(TiO2)n (n = 1–8) are also modeled. It is found that different adsorption sites and sizes of the clusters will exert critical effects on the molecular orbital energy levels of the complexes, and ultimately on their light-harvesting capabilities. In all the tested sensitizer/titanium dioxide cluster interface systems, the binding of the organic dye molecule to the 3-fold-coordinated titanium of the cluster (TiO2)6 could most benefit the widening of the spectrum response region and the interactions between the sensitizer and the cluster. From the intuitive physical pictures given by the three-dimensional (3D) real-space analysis methods of transition and charge difference densities, one reveals the photo-induced charge transfer microcosmic process of the sampled organic sensitizer/titanium dioxide cluster system TC4-(TiO2)6.

A dual-channel probe for selective fluoride determination and application in live cell imaging

Abstract A dual-channel fluoride anions probe has been synthesized from 4-hydroxy-1,8-Naphthalimide and t-butyldiphenylsilyl derivative. The probe presents selective coloration for fluoride anion that can be recognized by naked-eye. And it can quantitatively determine fluoride anion in aqueous and organic media. In MeCN/H 2 O ( v / v , 50:50), the detection limit of the probe is found to be 0.35 mg L −1 which satisfied EPA's requirements. While density function theory and time-dependent density function theory calculations were conducted to rationalize the optical response of the probe. Furthermore, the biological application shows that it could be successfully employed as a selective fluoride probe in the fluorescence imaging of living cells.

Tuning photophysical properties of triphenylamine and aromatic cyano conjugate-based wavelength-shifting compounds by manipulating intramolecular charge transfer strength

Abstract A series of triphenylamine-based aromatic cyano compounds have been synthesized as red-emitting fluorophores with large Stokes shifts in both solution (>100 nm in CHCl3) and solid state (>150 nm in film). Intramolecular charge transfer (ICT) properties of the synthesized compounds are examined using UV–Vis absorptions, photoluminescence measurements and solvatochromic studies. Our studies suggest that Stokes shifts of these compounds can be fine-tuned by manipulating the ICT strength between donor and acceptor with various electronic donating groups, and the largest Stokes shifts are typically associated with compounds that have the strong ICT characters. The observed spectroscopic properties of the compounds are consistent with theoretical calculations using density function theory (DFT) or time-dependent density function theory (TD-DFT). The calculations suggest that the ICT occurs from localized HOMO to localized LUMO with magnitudes of 60–80%. The relative quantum yields of these fluorophores in solution are various and highly solvent dependent. In solid state, the quantum yields of the compounds are significantly increased and some can reach to 0.40.

Vibrational Spectra and Quantum Calculations of Ethylbenzene

Normal vibrations of ethylbenzene in the first excited state have been studied using resonant two-photon ionization spectroscopy. The band origin of ethylbenzene of S1←S0 transition appeared at 37586 cm−1. A vibrational spectrum of 2000 cm−1 above the band origin in the first excited state has been obtained. Several chain torsions and normal vibrations are obtained in the spectrum. The energies of the first excited state are calculated by the time-dependent density function theory and configuration interaction singles (CIS) methods with various basis sets. The optimized structures and vibrational frequencies of the S0 and S1 states are calculated using Hartree-Fock and CIS methods with 6-311++G(2d,2p) basis set. The calculated geometric structures in the S0 and S1 states are gauche conformations that the symmetric plane of ethyl group is perpendicular to the ring plane. All the observed spectral bands have been successfully assigned with the help of our calculations.

Bisabololoxide derivatives from Artemisia persica, and determination of their absolute configurations by ECD

Five antiplasmodial bisabololoxide sesquiterpene diesters were isolated from an EtOAc extract of the aerial parts of Artemisia persica following an HPLC-time-based activity profiling of the extract. Structure elucidation was achieved by 1D and 2D NMR experiments. Relative configurations of cyclohexenone/cyclohexene and tetrahydropyran moieties of 1–5 were established on the basis of 3JH–H coupling constants and NOE difference spectra. Stereochemical correlation of the two rings, and assignment of absolute configuration of 1–5 were achieved by comparison of experimental ECD spectra with simulated ECD data for possible stereoisomers, by using time dependent density function theory (TDDFT). Bisaboloids 1–4 exhibited in vitro antimalarial activity against Plasmodium falciparum, with IC50 values ranging from 2.8 to 20.1μM, and selectivity indices (SI) in L-6 cells of 3.7–11.9.

Bisabololoxide derivatives from Artemisia persica, and determination of their absolute configurations by ECD

Five new antiplasmodial bisabololoxide sesquiterpene diesters were isolated from an EtOAc extract of the aerial parts of Artemisia persica following an HPLC-time-based activity profiling of the extract. Structure elucidation was achieved by 1D and 2D NMR experiments. Relative configurations of cyclohexenone/cyclohexene and tetrahydropyran moieties of 1–5 were established on the basis of 3 J H-H coupling constants and NOE difference spectra. Stereochemical correlation of the two rings, and assignment of absolute configuration of 1–5 were achieved by comparison of experimental ECD spectra with simulated ECD data for possible stereoisomers, by using time dependent density function theory (TDDFT). Bisaboloids 1-4 exhibited in vitro antimalarial activity against Plasmodium falciparum, with IC50 values ranging from 2.8 to 20.1µM, and selectivity indices (SI) in L-6 cells of 3.7 to 11.9.

Absolute configuration of natural products through quantum chemical calculation of CD spectra-selected examples

Chiroptical methods such as electronic circular dichroism (ECD) has been used for assignment of absolute configuration since several decades, but were limited in their applicability. Recent progress in the areas of conformational analysis and time dependent density function theory (TDTDF) calculation allows prediction of CD spectra by quantum chemical calculations. This is especially valuable for the analysis of new molecular entities when chemical synthesis of the reference compound is not an alternative. We successfully applied this methodology to establish the absolute configuration of structurally diverse and conformationally rigid or flexible molecules including monoterpenes, sesquiterpene coumarins, bisabolol sesquiterpenes, and complex isoprenoids with novel scaffolds. With a series of bisabolol oxide esters we demonstrate the assignment of absolute configuration by ECD calculation for compounds in which relative stereochemistry of two discrete parts of the molecule but not of its entirety could be established by NMR.

Resonant response in nonequilibrium steady states

The time-dependent probability density function of the order parameter of a system evolving toward a stationary state exhibits an oscillatory behavior if the eigenvalues of the corresponding evolution operator are complex. The frequencies ωn, with which the system reaches its stationary state, correspond to the imaginary part of such eigenvalues. If the system (at the stationary state) is further driven by a small and oscillating perturbation with a given frequency ω, we formally prove that the linear response to the probability density function is enhanced when ω=ωn for n∈N. We prove that the occurrence of this phenomenon is characteristic of systems that are in a nonequilibrium stationary state. In particular, we obtain an explicit formula for the frequency-dependent mobility in terms of the relaxation to the stationary state of the (unperturbed) probability current. We test all these predictions by means of numerical simulations considering an ensemble of noninteracting overdamped particles on a tilted periodic potential.

A stochastic surrogate model approach applied to calibration of unstable fluid flow experiments

We propose a stochastic approach for calibration of mixing zone lengths in shock tube experiments. The methodology relies on taking into account uncertain initial data propagated through the basic multifluid Euler equations. In this work, the initial interface position is supposed uncertain, modeled by a stochastic process. The size of the mixing zone is then defined as the support of the probability density function of the stochastic process. This time dependent probability density function is estimated with non-intrusive generalized Polynomial Chaos, its support being in this case cheaply evaluated. This methodology relies on the application of an ergodic principle (Wiener, 1938) and generalizes linear perturbations analysis. It is applied in this Note to the calibration of several experimental results.

Commutative Prospect Theory and Confident Behaviour Under Risk and Uncertainty in Psychological Space

This paper contributes to the literature on decision making under risk and uncertainty by attaching a weighted probability space to outcome space. Thereby inducing a commutative map of behavior on prospect theory's function space. We endow that space with a psychological metric space, and a time dependent probability density function with kurtosis controlled by a subject's strength of preference. Several new results are derived on that behavioral topological apparatus. First, we prove that gambles are random fields over outcome space. In which case, an uncertain prospect or act is akin to an unobserved configuration of a random field. Second, we introduce a priority heuristic result by proving that a subject's confidence evolves like a stopped behavioral stochastic process depicted by behavior mimicking epsilon-homotopy of a fair gamble, i.e. a martingale. There, we use Dudley-Talagrand metric to characterize large deviation probabilities for the stopped process. Third, we introduce an impossibility theorem for equivalent martingale measures on psychological space -- which explains why subjects gamble with over or under confidence almost surely. We use that to construct a confidence index, and a term structure of confidence'' from simulated probability distributions. Fourth, we show that even when subjects have Von Neuman Morgenstern preferences, and know ex-ante that the gamble is fair, they still exhibit confident behavior due to the common consequence of probability leakage arising from measurement error -- a de facto priority heuristic. Fifth, our model mitigates critique of constructive choice models which allege that expected-utility models, and prospect theory, are unable to explain anomalous results that deviate from actuarially fair gambles.

Synthesis and characterizations of benzothiadiazole-based fluorophores as potential wavelength-shifting materials

► The benzothiadiazole-based fluorophores were synthesized as wavelength-shifting materials for improving the efficiency of man-made solar cells. ► They show specific spectral properties with absorbance from UV to 600 nm and strong emission around 700 nm. ► Their large Stokes shifts were due to the strong intramolecular charge transfer effect during excitation. ► More planar geometry in their excitation states gave them higher quantum yields. The synthesized benzothiadiazole-based series fluorophores as potential wavelength-shifting materials exhibit large Stokes shifts (>160 nm) with multiple broad absorbance bands from UV region to 600 nm and a strong fluorescence peak around 700 nm (in CHCl 3 ). Intramolecular charge transfer (ICT) characters of the synthesized compounds are examined using UV–vis and photoluminescence solvatochromic shift measurements. Among the synthesized compounds, the fluorophores with asymmetrical structures exhibit larger Stokes shifts than those with symmetrical structures due to large dipole moment changes upon excitation. The fluorophores with electron-donating methoxyl groups attached to the triphenylamine donors are found to have strong ICT properties. Photophysical experimental results are supported by theoretical calculations using Density Function Theory (DFT) and Time Dependent Density Function Theory (TD-DFT) methods. Calculated frontier molecular orbitals (MOs) of ground states on these fluorophores showed an increase in ICT character up to 50% from HOMO to LUMO. Geometric optimization calculations of the excited state reveal that these fluorophores show a more planar structure for the excited state than the ground state, which allows more π–π* overlap and leads to larger Stokes shifts and higher quantum yields.