Absorption Spectra of Estradiol and Tryptophan Constructed by the Statistical and Elongation Methods

Abstract

The statistical quantum chemical/molecular dynamical method is developed and employed to reproduce optical spectra. This technique includes quantum-mechanical calculations on energy states and photophysical properties of molecular conformers obtained during molecular dynamical simulation. Polycyclic organic molecule estradiol surrounded by solvent particles and protein structure including tryptophan fragment under thermodynamical conditions are considered. A wide absorption spectrum over several excited electronic states of estradiol is constructed. First longwave absorption band of tryptophan-cage mini protein is built involving the elongation method. These statistical spectra reflect the main features of the corresponding experimental ones.

Inheritance of Photochromic Properties of Nitro-Substituted and Halogenated Spiropyrans Containing the Pyrrolidino[60]fullerene

“…The rates of cross-section radiationless transitions 39,40 such as internal conversion 41,42 and intersystem crossing 43,44 as well as fluorescence with the quantum yields of photoprocesses were estimated using spectroscopically oriented semiempirical intermediate neglect of differential overlap (INDO) method in sp-basis (INDO/sp) 45 similar to the ZINDO method 46 where the multicenter many-electron Coulomb and exchange integrals are calibrated to adjust spectroscopic data of several basic organic molecules in nonpolar aprotic solvents at low temperatures to provide correct transition energies between Franck−Condon (FC) states, 45 which was verified by further works for other organic compounds. 39,40,47−57 This approach is implemented as a standalone code and a development version of GAMESS-09 49 in quantum chemistry of organic photonics (QOP) blocks. 48−50 To use as similar as possible MOs in the aldehyde-substituted molecules and in their hybrid compounds with the PF 60 moiety, the following configuration iteration singles (CIS) settings were applied: 20 highest occupied MOs and 25 lowest unoccupied MOs for SPs and MCs and corresponding number of MOs for the hybrid compounds that are the most appropriate to form the same electronic states in the individual molecules and their hybrid compounds.…”

Insight into the fluorescence quenching of Trp214 at HSA by the Dimetridazole ligand from simulation

“…The spectroscopically oriented semi-empirical Intermediate Neglect of Differential Overlap (INDO) method in a sp-basis (INDO/sp), which is similar to the ZINDO method and successfully applied by Callis and coauthors in numerous works for decades [3,34,35], has been adjusted to provide correct transition energies to Franck-Condon states by calibrating multi-center Coulomb and exchange integrals to spectroscopic data for organic compounds. This has been implemented in a standalone code and in a development version of GAMESS-09 [36] as the Quantum Chemistry of Organic Photonics (QOP) blocks [10,22,36]. The parameters were calibrated against experimental data for representative molecules in the ground state geometry in a non-polar aprotic solvent at low temperature, as previously described in Ref.…”

“…An averaged band absorption intensity on a given  bin corresponds to the relative absorptivity ε = pf, where p = N/N is the probability of finding the fluctuating molecule in an excited state in this energy interval, and the averaged oscillator strength f is defined by the oscillator strength of the N conformers in this  interval [10,22,36]. The relative emission intensity is estimated as the product of probabilities I = pkr [10] where = kr/(kr+kst) is the quantum yield.…”

The role of the exchange in the embedding electrostatic potential for the fragment molecular orbital method

“…Recently, a large number of fragment-based methods [1][2][3][4][5][6][7][8][9][10] have been suggested in order to facilitate computing large systems with quantum-mechanical methods. The fragment molecular orbital ͑FMO͒ [11][12][13] method is based on dividing the system into pieces ͑fragments͒ and performing ab initio calculations on fragments, their pairs, and, optionally, triples.…”