Sang Joon Choe

Comparative DFT study for molecular geometries and spectra of methyl pheophorbides-a: test of M06-2X and two other functionals

The recent interest in the application of density functional theory (DFT) has prompted us to test several functions in molecular geometries of methyl pheophorbides-a (MPa), an important starting material in photodynamic therapy (PDT). In this study, we report on tests for three popular DFT methods: M06-2X, B3LYP, and LSDA. Based on the standard deviation and the mean value, and by using the difference between optimized calculated value and experimental value in geometries, we drew the following conclusions: M06-2X/6-311+G(d,p) attained the smallest standard deviation of difference among the tested DFT methods in terms of bond length, whereas the standard deviation of bond angle in LSDA/6-311+G(d,p) was the smallest. In terms of absolute value, the mean value of LSDA/6-311+G(d,p) calculation was larger than that of M06-2X/6-311+G(d,p). We found that M06-2X/6-311+G(d,p) gave the best performance for MPa in the molecular geometries. The UV-visible spectrum was calculated with time-dependent density-functiona...

Comparison of different theory models and basis sets for the calculation of FbC-M10Iso-Bn geometry and geometries of chlorin-imide and chlorin-isoimide isomeric pairs

Various density functional theory (DFT) methods with different basis sets to predict the molecular geometry of FbC-M10Iso-Bn macrocycle, a chlorin-isoimide, are compared in this study. DFT methods, including M06-2X, B3LYP, LSDA, B3PW91, PBEPBE, and BPV86, are examined. Different basis sets, such as 6-31G*, 6-31+G (d, p), 6-311+G (d, p), 6-311++G (d, p), cc-PVDZ, cc-PVTZ, and cc-PVQZ are also considered. The examined hybrid DFT methods are in agreement with the geometry of X-ray crystallography available for comparison. B3LYP/cc-PVDZ level is particularly consistent with available X-ray crystallography in terms of predicting the geometries of FbC-M10Iso-Bn. Geometries of chlorin-imide and chlorin-isoimide isomeric pairs are described through B3LYP/cc-PVDZ method. The bond lengths of chlorin-isoimide, specifically C13–C14, C14–C15, and C2–C3, increase as bond overlap index decreases because of charge transfer. β-β bond lengths (C2–C3 bond lengths) with a three-substituent benzylcarbamoyl group also increase as bond overlap index decreases compared with other molecules. The bond lengths of chlorin-imide are smaller than those of chlorin-isoimide. Angles with β-β bond lengths, specifically C2–C3–C4 in ring A, also decrease with a three-substituent benzylcarbamoyl group; however, the angles in C1–C2–C3 increase. Potential energy on the surfaces of the chlorin-imide and chlorin-isoimide isomeric pairs is optimized by calculating the total and relative energies at B3LYP/cc-PVDZ level. Results indicate that chlorin-imides are more stable than chlorin-isoimides. Normal-coordinate structural decomposition shows that chlorin-imides exhibit greater deformation than chlorin-isoimides except for FbC-M10Iso-Ph.

Molecular geometries and spectra of methyl pyropheophorbide-a pyrazole derivatives: a density functional theory study

Density functional theory (DFT) electronic structure calculations were performed to predict the geometries of the chlorin macrocycle core in methyl pyropheophorbide-a pyrazole derivatives (e.g. HPMPPa and PPMPPa). These compounds are new photosensitizer materials that possess the dual function activity in photodynamic therapy. We found that the geometries of the two compounds were nearly the same, and that substitution of the pyrazole moieties at C31-position of methyl pyropheophorbide-a did not have significant effects on the geometries of the chlorin macrocycle core. Excitation energies and oscillator strengths were computed by time-dependent DFT. The time-dependent DFT spectrum of HPMPPa and PPMPPa were not affected by the pyrazole substituent. To determine the hydrophilic effect of photosensitizers, we calculated the interaction energy between photosensitizer and water, and observed that the interaction energy of HPMPPa was higher than that of PPMPPa. We found that the interaction energy with specific wavelength (Q-bands) is an important factor to consider in the development of photodynamic therapy.