Axial H-Bonding Solvent Controls Inhomogeneous Spectral Broadening, While Peripheral H-Bonding Solvent Controls Vibronic Broadening: Cresyl Violet in Methanol.

The dynamics of the nuclei of both a chromophore and its condensed-phase environment control many spectral features, including the vibronic and inhomogeneous broadening present in spectral line shapes. For the cresyl violet chromophore in methanol, we here analyze and isolate the effect of specific chromophore-solvent interactions on simulated spectral densities, reorganization energies, and linear absorption spectra. Employing both chromophore and its condensed-phase environment control many spectral features, including the vibronic and inhomogeneous broadening present in spectral line shapes. For the cresyl violet chromophore in methanol, we here analyze and isolate the effect of specific chromophore-solvent interactions on simulated spectral densities, reorganization energies, and linear absorption spectra. Employing both force field and ab initio molecular dynamics trajectories along with the inclusion of only certain solvent molecules in the excited-state calculations, we determine that the methanol molecules axial to the chromophore are responsible for the majority of inhomogeneous broadening, with a single methanol molecule that forms an axial hydrogen bond dominating the response. The strong peripheral hydrogen bonds do not contribute to spectral broadening, as they are very stable throughout the dynamics and do not lead to increased energy-gap fluctuations. We also find that treating the strong peripheral hydrogen bonds as molecular mechanical point charges during the molecular dynamics simulation underestimates the vibronic coupling. Including these peripheral hydrogen bonding methanol molecules in the quantum-mechanical region in a geometry optimization increases the vibronic coupling, suggesting that a more advanced treatment of these strongly interacting solvent molecules during the molecular dynamics trajectory may be necessary to capture the full vibronic spectral broadening.

Comparison of Linear Response Theory, Projected Initial Maximum Overlap Method, and Molecular Dynamics-Based Vibronic Spectra: The Case of Methylene Blue.

The simulation of optical spectra is essential to molecular characterization and, in many cases, critical for interpreting experimental spectra. The most common method for simulating vibronic absorption spectra relies on the geometry optimization and computation of normal modes for ground and excited electronic states. In this report, we show that the utilization of such a procedure within an adiabatic linear response (LR) theory framework may lead to state mixings and a breakdown of the Born-Oppenheimer approximation, resulting in a poor description of absorption spectra. In contrast, computing excited states via a self-consistent field method in conjunction with a maximum overlap model produces states that are not subject to such mixings. We show that this latter method produces vibronic spectra much more aligned with vertical gradient and molecular dynamics (MD) trajectory-based approaches. For the methylene blue chromophore, we compare vibronic absorption spectra computed with the following: an adiabatic Hessian approach with LR theory-optimized structures and normal modes, a vertical gradient procedure, the Hessian and normal modes of maximum overlap method-optimized structures, and excitation energy time-correlation functions generated from an MD trajectory. Because of mixing between the bright S1 and dark S2 surfaces near the S1 minimum, computing the adiabatic Hessian with LR theory and time-dependent density functional theory with the B3LYP density functional predicts a large vibronic shoulder for the absorption spectrum that is not present for any of the other methods. Spectral densities are analyzed and we compare the behavior of the key normal mode that in LR theory strongly couples to the optical excitation while showing S1/S2 state mixings. Overall, our study provides a note of caution in computing vibronic spectra using the excited-state adiabatic Hessian of LR theory-optimized structures and also showcases three alternatives that are less sensitive to adiabatic state mixing effects.

The Influence of Electronic Polarization on Nonlinear Optical Spectroscopy.

The environment surrounding a chromophore can dramatically affect the energy absorption and relaxation process, as manifested in optical spectra. Simulations of nonlinear optical spectroscopy, such as two-dimensional electronic spectroscopy (2DES) and transient absorption (TA), will be influenced by the computational model of the environment. We here compare a fixed point charge molecular mechanics model and a quantum mechanical (QM) model of the environment in computed 2DES and TA spectra of Nile red in water and the chromophore of photoactive yellow protein (PYP) in water and protein environments. In addition to simulating these nonlinear optical spectra, we directly juxtapose the computed excitation energy correlation function to the dynamic Stokes shift function often used to analyze environment dynamics. Overall, we find that for the three systems studied here the mutual electronic polarization provided by the QM environment manifests in broader 2DES signals, as well as a larger reorganization energy and a larger static Stokes shift due to stronger coupling between the chromophore and the environment.

Vibronic and Environmental Effects in Simulations of Optical Spectroscopy.

Including both environmental and vibronic effects is important for accurate simulation of optical spectra, but combining these effects remains computationally challenging. We outline two approaches that consider both the explicit atomistic environment and the vibronic transitions. Both phenomena are responsible for spectral shapes in linear spectroscopy and the electronic evolution measured in nonlinear spectroscopy. The first approach utilizes snapshots of chromophore-environment configurations for which chromophore normal modes are determined. We outline various approximations for this static approach that assumes harmonic potentials and ignores dynamic system-environment coupling. The second approach obtains excitation energies for a series of time-correlated snapshots. This dynamic approach relies on the accurate truncation of the cumulant expansion but treats the dynamics of the chromophore and the environment on equal footing. Both approaches show significant potential for making strides toward more accurate optical spectroscopy simulations of complex condensed phase systems.

Virtual Screening of Hole Transport, Electron Transport, and Host Layers for Effective OLED Design.

The alignment of energy levels within an OLED device is paramount for high efficiency performance. In this study, the emissive, electron transport, and hole transport layers are consecutively evolved under the constraint of fixed electrode potentials. This materials development strategy takes into consideration the full multilayer OLED device, rather than just individual components. In addition to introducing this protocol, an evolutionary method, a genetic algorithm (GA), is evaluated in detail to increase its efficiency in searching through a library of 30 million organic compounds. On the basis of the optimization of the variety of GA parameters and selection methods, an exponential ranking selection protocol with a high mutation rate is found to be the preferred method for quickly identifying the top-performing molecules within the large chemical space. This search through OLED materials space shows that the pyridine-based central core with acridine-based fragments are good target host molecules for common electrode materials. Additionally, weak electron-donating groups, such as naphthalene- and xylene-based fragments, appear often in the optimal electron-transport layer materials. Triphenylamine- and acridine-based fragments, due to their strong electron-donating character, were found to be good candidates for the hole-transport layer.

Temperature effects on adsorption and diffusion dynamics of CH3CH2(ads) and H3C-C≡C(ads) on Ag(111) surface and their self-coupling reactions: ab initio molecular dynamics approach.

Density functional theory (DFT)-based molecular dynamics (DFTMD) simulations in combination with a Fourier transform of dipole moment autocorrelation function are performed to investigate the adsorption dynamics and the reaction mechanisms of self-coupling reactions of both acetylide (H3C-C(ß)≡C(α) (ads)) and ethyl (H3C(ß)-C(α)H2(ads)) with I(ads) coadsorbed on the Ag(111) surface at various temperatures. In addition, the calculated infrared spectra of H3C-C(ß)≡C(α)(ads) and I coadsorbed on the Ag(111) surface indicate that the active peaks of -C(ß)≡C(α)- stretching are gradually merged into one peak as a result of the dominant motion of the stand-up -C-C(ß)≡C(α)- axis as the temperature increases from 200 K to 400 K. However, the calculated infrared spectra of H3C(ß)-C(α)H2(ads) and I coadsorbed on the Ag(111) surface indicate that all the active peaks are not altered as the temperature increases from 100 K to 150 K because only one orientation of H3C(ß)-C(α)H2(ads) adsorbed on the Ag(111) surface has been observed. These calculated IR spectra are in a good agreement with experimental reflection absorption infrared spectroscopy results. Furthermore, the dynamics behaviors of H3C-C(ß)≡C(α)(ads) and I coadsorbed on the Ag(111) surface point out the less diffusive ability of H3C-C(ß)≡C(α)(ads) due to the increasing s-character of Cα leading to the stronger Ag-Cα bond in comparison with that of H3C(ß)-C(α)H2(ads) and I coadsorbed on the same surface. Finally, these DFTMD simulation results allow us to predict the energetically more favourable reaction pathways for self-coupling of both H3C-C(ß)≡C(α)(ads) and H3C(ß)-C(α)H2(ads) adsorbed on the Ag(111) surface to form 2,4-hexadiyne (H3C-C≡C-C≡C-CH3(g)) and butane (CH3-CH2-CH2-CH3(g)), respectively. The calculated reaction energy barriers for both H3C-C≡C-C≡C-CH3(g) (1.34 eV) and CH3-CH2-CH2-CH3(g) (0.60 eV) are further employed with the Redhead analysis to estimate the desorption temperatures approximately at 510 K and 230 K, respectively, which are in a good agreement with the experimental low-coverage temperature programmed reaction spectroscopy measurements.

A Taiwanese Propolis Derivative Induces Apoptosis through Inducing Endoplasmic Reticular Stress and Activating Transcription Factor-3 in Human Hepatoma Cells.

Activating transcription factor-(ATF-) 3, a stress-inducible transcription factor, is rapidly upregulated under various stress conditions and plays an important role in inducing cancer cell apoptosis. NBM-TP-007-GS-002 (GS-002) is a Taiwanese propolin G (PPG) derivative. In this study, we examined the antitumor effects of GS-002 in human hepatoma Hep3B and HepG2 cells in vitro. First, we found that GS-002 significantly inhibited cell proliferation and induced cell apoptosis in dose-dependent manners. Several main apoptotic indicators were found in GS-002-treated cells, such as the cleaved forms of caspase-3, caspase-9, and poly(ADP-ribose) polymerase (PARP). GS-002 also induced endoplasmic reticular (ER) stress as evidenced by increases in ER stress-responsive proteins including glucose-regulated protein 78 (GRP78), growth arrest- and DNA damage-inducible gene 153 (GADD153), phosphorylated eukaryotic initiation factor 2 α (eIF2 α ), phosphorylated protein endoplasmic-reticular-resident kinase (PERK), and ATF-3. The induction of ATF-3 expression was mediated by mitogen-activated protein kinase (MAPK) signaling pathways in GS-002-treated cells. Furthermore, we found that GS-002 induced more cell apoptosis in ATF-3-overexpressing cells. These results suggest that the induction of apoptosis by the propolis derivative, GS-002, is partially mediated through ER stress and ATF-3-dependent pathways, and GS-002 has the potential for development as an antitumor drug.

Chemical mechanism of surface-enhanced Raman scattering spectrum of pyridine adsorbed on Ag cluster: ab initio molecular dynamics approach.

The surface-enhanced Raman scattering (SERS) spectrum of pyridine adsorbed on Ag20 cluster (pyridine-Ag20 ) at room temperature is calculated by performing ab initio molecular dynamics simulations in connection with a Fourier transform of the polarizability autocorrelation function to investigate the static chemical enhancement behind the SERS spectrum. The five enhanced vibrational modes of pyridine, namely, υ6a, υ1, υ12, υ9a, and υ8a, can be assigned and identified by using a new analytical scheme, namely, single-frequency-pass filter, which is based on a Fourier transform filtering technique. To understand the factors evoking the enhancement in the SERS spectrum, the dynamic properties of molecular structures and charges for both of the free pyridine and adsorbed pyridine are analyzed. The calculated results indicate that the vibrational amplitudes of adsorbed pyridine are enhanced due to both of the electron transfer from pyridine to Ag20 cluster and the softening of pyridine bond. In addition, the N-Ag stretching within pyridine-Ag20 will couple with these five vibrational modes of pyridine. Consequently, the electron transfer between pyridine and Ag20 cluster induced by different molecular vibrational modes prompts the redistribution of electron density of pyridine. These factors collectively cause the noticeable change in polarizability during molecular vibrations and hence result in the enhancement of Raman peaks.

Temperature dependence of vibrational modes of CH3CC(ads) and I(ads) coadsorbed on Ag(111): ab initio molecular dynamics approach.

Ab initio molecular dynamics simulations accompanied by a Fourier transform of the dipole moment (aligned perpendicular to the surface) autocorrelation function are implemented to investigate the temperature-dependent infrared (IR) active vibrational modes of CH3C(ß)C(α)(ads) and I(ads) when coadsorbed on an Ag(111) surface at 200 and 400 K, respectively. The analytic scheme of the Fourier transform of a structural coordinate autocorrelation function is used to identify two distinguishable IR active peaks of C(ß)C(α) stretching, which are characterized by two types of dynamic motion of adsorbed CH3C(ß)C(α)(ads) at 200 K, namely, the motion of the tilted CC(ß)C(α) axis and the motion of the stand-up CC(ß)C(α) axis. These two recognisable IR active peaks of C(ß)C(α) stretching are gradually merged into one peak as a result of the dominant motion of the stand-up CC(ß)C(α) axis as the temperature increases from 200 to 400 K. The calculated intensities of the IR active peaks of the asymmetrical deformation mode of CH3 and the asymmetrical stretching mode of CH3, with their dynamic dipole moments nearly perpendicular to the CC(ß)C(α) axis, become relatively weak; however, the symmetrical deformation mode of CH3 and the symmetrical stretching mode of CH3, with their dynamic dipole moments randomly directed away from the CC(ß)C(α) axis, will not have direct correspondence between the intensities of their IR active peaks and the angle between the Ag(111) surface and the CC(ß)C(α) axis as the temperature increases from 200 to 400 K. Finally, the increased flipping from the motion of the tilted CC(ß)C(α) axis to the motion of the stand-up CC(ß)C(α) axis followed by its diffusion, resulting from the increasing temperature from 200 to 400 K or even higher, seems to be the initial event that initiates the alkyne self-coupling reaction that leads to the final production of H3CCCCCCH3.

[Analysis of growth dynamics of Curcuma wenyujin].

OBJECTIVE: To study the accumulation of matter and dynamic of chemical compositions in rhizoma of Curcuma wenyujin for its cultivation. METHODS: The weight of various parts and chemical composition content of rhizoma were determined at regular time. RESULTS: The growth of Curcuma wenyujin could be divided into the seedling period, the rhizoma growing period and dry matter accumulating period. In seedling period, the aerial parts were the center of organism, the matter accumulated mainly in leaves; In rhizoma growing period, the organic center were gradually transformed from the aerial parts to the underground parts. The tendency of total chemical composition quantity in rhizome presented rises at first but gradually dropped at last. CONCLUSIONS: The growth of Curcuma wenyujin has two organic centers, the seedling period and the rhizoma vegetal and weighted period. The total chemical composition quantity in Curcuma wenyujin rhizome reaches the maximum value from the last third part of October to mid-November.

Density functional study of the interfacial electron transfer pathway for monolayer-adsorbed InN on the TiO(2) anatase (101) surface.

Density functional theory (DFT) in connection with ultrasoft pseudopotential (USP) and generalized gradient spin-polarized approximations (GGSA) is applied to calculate the adsorption energies and structures of monolayer-adsorbed InN on the TiO(2) anatase (101) surface and the corresponding electronic properties, that is, partial density of states (PDOS) for surface and bulk layers of the TiO(2) anatase (101) surface and monolayer-adsorbed InN, to shed light on the possible structural modes for initial photoexcitation within the UV/vis adsorption region followed by fast electron injection through the InN/TiO(2) interface for an InN/TiO(2)-based solar cell design. Our calculated adsorption energies found that the two most probable stable structural modes of monolayer-adsorbed InN on the TiO(2) anatase (101) surface are (1) an end-on structure with an adsorption energy of 2.52 eV through N binding to surface 2-fold coordinated O (O(cn2)), that is, InN-O(cn2), and (2) a side-on structure with an adsorption energy of 3.05 eV through both N binding to surface 5-fold coordinated Ti (Ti(cn5)) and In bridging two surface O(cn2), that is, (O(cn2))(2)-InN-Ti(cn5). Our calculated band gaps for both InN-O(cn2) and (O(cn2))2-InN-Ti(cn5) (including a 1.0-eV correction using a scissor operator) of monolayer-adsorbed InN on the TiO(2) anatase (101) surface are red-shifted to 1.7 eV (730 nm) and 2.3 eV (540 nm), respectively, which are within the UV/vis adsorption region similar to Gratzel's black dye solar cell. Our analyses of calculated PDOS for both surface and bulk layers of the TiO(2) anatase (101) surface and monolayer-adsorbed InN on the TiO(2) anatase (101) surface suggest that the (O(cn2))(2)-InN-Ti(n5) configuration of monolayer-adsorbed InN on the TiO(2) anatase (101) surface would provide a more feasible structural mode for the electron injection through the InN/TiO(2) interface. This is due to the presence of both occupied and unoccupied electronic states for monolayer-adsorbed InN within the band gap TiO(2) anatase (101) surface, which will allow the photoexcitation within the UV/vis adsorption region to take place effectively, and subsequently the photoexcited electronic states will overlap with the unoccupied electronic states around the lowest conduction band of the TiO(2) anatase (101) surface, which will ensure the electron injection through the InN/TiO(2) interface. Finally, another thing worth our attention is our preliminary study of double-layer-adsorbed InN on the TiO(2) anatase (101) surface, that is, (O(cn2))(2)-(InN)(2)-Ti(cn5), with a calculated band gap red-shifted to 2.6 eV (477 nm) and a different overlap of electronic states between double-layer-adsorbed InN and the TiO(2) anatase (101) surface qualitatively indicated that there is an effect of the thickness of adsorbed InN on the TiO(2) anatase (101) surface on both photoexcitation and electron injection processes involved in the photoinduced interfacial electron transfer through InN/TiO(2). A more thorough and comprehensive study of different layers of InN adsorbed in all possible different orientations on the TiO(2) anatase (101) surface is presently in progress.