Strength Of Transition Dipole Moments Research Articles

Aqueous Contact Ion Pairs of Phosphate Groups with Na+, Ca2+ and Mg2+ – Structural Discrimination by Femtosecond Infrared Spectroscopy and Molecular Dynamics Simulations

Abstract The extent of contact and solvent shared ion pairs of phosphate groups with Na+, Ca2+ and Mg2+ ions in aqueous environment and their relevance for the stability of polyanionic DNA and RNA structures is highly debated. Employing the asymmetric phosphate stretching vibration of dimethyl phosphate (DMP), a model system of the sugar-phosphate backbone of DNA and RNA, we present linear infrared, femtosecond infrared pump-probe and absorptive 2D-IR spectra that report on contact ion pair formation via the presence of blue shifted spectral signatures. Compared to the linear infrared spectra, the nonlinear spectra reveal contact ion pairs with increased sensitivity because the spectra accentuate differences in peak frequency, transition dipole moment strength, and excited state lifetime. The experimental results are corroborated by long time scale MD simulations, benchmarked by density functional simulations on phosphate-ion-water clusters. The microscopic interpretation reveals subtle structural differences of ion pairs formed by the phosphate group and the ions Na+, Ca2+ and Mg2+. Intricate properties of the solvation shell around the phosphate group and the ion are essential to explain the experimental observations. The present work addresses a challenging to probe topic with the help of a model system and establishes new experimental data of contact ion pair formation, thereby underlining the potential of nonlinear 2D-IR spectroscopy as an analytical probe of phosphate-ion interactions in complex biological systems.

THEORETICAL STUDY ON PHOTOINDUCED INTRAMOLECULAR CHARGE TRANSFER IN A NOVEL ORGANIC SENSITIZER C201

A new organic dye (C201) composed of triarylamine unit as electron donor and anchoring unit as electron acceptor, was theoretically investigated by quantum chemical methods. We optimized the geometry of C201 with density functional theory (DFT) at B3LYP/6-311G (d) level. Densities of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO), as well as the energies are listed. The excited states of the dye molecules C201 were calculated by time dependent-DFT (TD-DFT) method. Two main visible bands at 572 nm and 407 nm were mainly attributed to the electronic transition from HOMO→LUMO and HOMO-1→LUMO, respectively. 3D cube representations including transition density (TD) and charge difference density (CDD) directly visualized the character of intramolecular charge transfer of C201. The orientation and strength of transition dipole moment were showed visually using TD. Furthermore, we illustrate the orientation and results of the intramolecular charge transfer by CDD.

Transition Dipole, Charge Transfer, and Electron-hole Coherence in Two-photon Absorption: Visualizations with Two Dimensional Site and Three Dimensional Cube Representations

The developed visualization methods of two dimensional (2D) site and three dimensional (3D) cube representations have been performed to show the orientation of transition dipole, charge transfer, and electron-hole coherence in two-photon absorption (TPA). The 3D cube representations of transition density can reveal visually the orientation and strength of transition dipole moment, and charge different density show the orientation of charge transfer in TPA. The 2D site representation can reveal visually the electron-hole coherence in TPA. The combination of 2D site and 3D cube representations provide clearly inspect into the charge transfer process and the contribution of excited molecular segments for TPA.

Optical Properties of Neutral and Charged Low Band Gap Alternating Copolyfluorenes: TD-DFT Investigation

Electronic structure and optical properties of neutral and charged low band gap alternating copolyfluorenes (Green 1, which is based on alternating repeating units consisting of alkyl-substituted fluorene and a thiophene-[1,2,5]thiadiazolo-[3,4]quinoxaline-thiophene (T-TDQ-T) unit were investigated theoretically with time-dependent density functional theory (TD-DFT) method, and their excited state properties were further analyzed with 2D site and 3D cube representations. For neutral Green 1, the band gap, binding energy, exciton binding energy, and nuclear relaxation energy were obtained. The transition dipole moments of neutral and charged Green 1 are compared using 3D transition density, which reveals the orientation and strength of transition dipole moments. The charge redistribution of neutral and charged Green 1 upon excitation are displayed and compared with 3D charge difference density. The electron-hole coherences of neutral and charged Green 1 upon excitation are investigated with 2D site representation (transition density matrix). The excited state properties of neutral Green 1 calculated with TD-DFT method are compared with that calculated with ZINDO method, which reveals the importance of electron-electron interaction (in TD-DFT) in the excited state properties.

Intramolecular charge transfer in the dye molecules containing bis-dimethylfluoreneaniline

Two novel metal-free organic dyes (JK-1, JK-2), composed of bis-dimethylfluoreneaniline moiety as the electron donor and cyanoacrylic acid moiety as the electron acceptor, are theoretically investigated with quantum chemical methods. The energies and densities of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO), as well as the binding energies, are compared between the two dyes. The HOMO → LUMO electronic transition describes their lowest singlet excited states. The orientation and strength of transition dipole moment are revealed visually with transition density. We also show the orientation and results of the intramolecular charge transfer with charge difference density. Transition density matrices provide information about the electron–hole coherence and excitation delocalization. Theoretical results reveal that exciton size and transition dipole moment increase with the expansion of the π conjugation and the charge transfer occurs from donor unit across the π bridge to the acceptor unit.

Do coupling exciton and oscillation of electron-hole pair exist in neutral and charged π-dimeric quinquethiophenes?

Optical physical properties of neutral and charged quinquethiophene monomer, and neutral and cationic pi-dimeric quinquethiophenes were investigated with density functional theory as well as the two dimensional (2D) site (transition density matrix) and three dimensional (3D) cube (transition density and charge difference density) representations, stimulated by the recent experimental report [T. Sakai et al., J. Am. Chem. Soc. 127, 8082 (2005)]. Transition density shows the orientation and strength of the transition dipole moment of neutral and charged quinquethiophene monomer, and charge difference density reveals the orientation and result of the charge transfer in neutral and charged quinquethiophene monomer. To study if coupling exciton and oscillation of electron-hole pair exist in neutral and cationic pi-dimeric quinquethiophenes, the coupling constants J (coupling exciton of electron-hole pair) and K (coupling oscillation of electron-hole pair) were introduced to the exciton coordinate and momentum operators, respectively, and the 2D and 3D analysis methods were further developed by extending our previous theoretical methods [M. T. Sun, J. Chem. Phys. 124, 054903 (2006)]. With the new developed 2D and 3D analysis methods, we investigated the excited state properties of neutral and cationic pi-dimeric quinquethiophenes, especially on the coupling exciton and oscillation of electron-hole pair between monomers. The 2D results show that there is neither coupling exciton (J=0) nor oscillation (K=0) of electron-hole pair in neutral pi-dimeric quinquethiophenes. For some excited states of cationic pi-dimeric quinquethiophenes, there is no coupling exciton (J=0), but there is coupling oscillation (K not equal0); while for some excited states, there are both coupling exciton and coupling oscillator simultaneously (J not equal0 and K not equal0). The strength of transition dipole moments of pi-dimeric quinquethiophenes were interpreted with 3D transition density, which reveals the orientations of their two subtransition dipole moments. The 3D charge transition density reveals the orientation and result of intermonomer and/or intramonomer charge transfer. The calculated results reveal that excited state properties of neutral pi-dimeric quinquethiophene are significantly different from those of the cationic pi-dimeric quinquethiophenes.

CHARGE AND ENERGY TRANSFER IN BINAPHTHALENE MOLECULE WITH TWO SPIROPYRAN UNITS USED FOR CHIRAL MOLECULAR SWITCHES AND LOGIC GATES

A new binaphthalene molecule with two spiropyran units used for chiral molecular switches and logic gates was synthesized and characterized.12 In this paper, charge and energy transfer in binaphthalene molecule with two spiropyran units are theoretically investigated with quantum chemistry method, as well as 2D and 3D real space analysis methods, since molecule construction with photoinduced electron transfer or charge transfer is one of the most frequently used pathways for building useful sensors and molecular machines. The orientation and strength of transition dipole moment in absorption spectra are obtained by 3D transition density. The orientation and results of intramolecular charge transfer on the excitation are obtained with 3D charge difference densities. The electron-hole coherence and excitation delocalization in absorption spectra are investigated with 2D contour plots of transition density matrix. Overall, the computed results remain in good agreement with the relevant experimental data, and the theoretical results reveal the relationship between the function of sensor and the excited state properties of the structure and transformation of the compound, upon addition of acid and base in absorption spectra.