TY  - JOUR
A1  - Titov, Evgenii
T1  - On the low-lying electronically excited states of azobenzene dimers
BT  - Transition density matrix analysis
JF  - Molecules : a journal of synthetic chemistry and natural product chemistry / Molecular Diversity Preservation International
N2  - Azobenzene-containing molecules may associate with each other in systems such as self-assembled monolayers or micelles. The interaction between azobenzene units leads to a formation of exciton states in these molecular assemblies. Apart from local excitations of monomers, the electronic transitions to the exciton states may involve charge transfer excitations. Here, we perform quantum chemical calculations and apply transition density matrix analysis to quantify local and charge transfer contributions to the lowest electronic transitions in azobenzene dimers of various arrangements. We find that the transitions to the lowest exciton states of the considered dimers are dominated by local excitations, but charge transfer contributions become sizable for some of the lowest pi pi* electronic transitions in stacked and slip-stacked dimers at short intermolecular distances. In addition, we assess different ways to partition the transition density matrix between fragments. In particular, we find that the inclusion of the atomic orbital overlap has a pronounced effect on quantifying charge transfer contributions if a large basis set is used.
KW  - azobenzene
KW  - dimer
KW  - transition density matrix
KW  - exciton
KW  - charge transfer
KW  - excited states
KW  - TD-DFT
KW  - ADC(2)
Y1  - 2021
U6  - https://doi.org/10.3390/molecules26144245
SN  - 1420-3049
VL  - 26
IS  - 14
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Mayer, Dennis
A1  - Picconi, David
A1  - Robinson, Matthew S.
A1  - Gühr, Markus
T1  - Experimental and theoretical gas-phase absorption spectra of thionated uracils
JF  - Chemical physics : a journal devoted to experimental and theoretical research involving problems of both a chemical and physical nature
N2  - We present a comparative study of the gas-phase UV spectra of uracil and its thionated counterparts (2-thiouracil, 4-thiouracil and 2,4-dithiouracil), closely supported by time-dependent density functional theory calculations to assign the transitions observed. We systematically discuss pure gas-phase spectra for the (thio)uracils in the range of 200-400 nm (similar to 3.2-6.4 eV), and examine the spectra of all four species with a single theoretical approach. We note that specific vibrational modelling is needed to accurately determine the spectra across the examined wavelength range, and systematically model the transitions that appear at wavelengths shorter than 250 nm. Additionally, we find in the cases of 2-thiouracil and 2,4-dithiouracil, that the gas-phase spectra deviate significantly from some previously published solution-phase spectra, especially those collected in basic environments.
KW  - Thiouracil
KW  - Uracil
KW  - UV-VIS Spectroscopy
KW  - Excited-state calculations;
KW  - TD-DFT
KW  - Gas phase
Y1  - 2022
U6  - https://doi.org/10.1016/j.chemphys.2022.111500
SN  - 0301-0104
VL  - 558
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Goetze, Jan P.
A1  - Greco, Claudio
A1  - Mitric, Roland
A1  - Bonacic-Koutecky, Vlasta
A1  - Saalfrank, Peter
T1  - BLUF Hydrogen network dynamics and UV/Vis spectra: A combined molecular
 dynamics and quantum chemical study
JF  - JOURNAL OF COMPUTATIONAL CHEMISTRY
N2  - Blue light sensing using flavin (BLUF) protein photoreceptor domains change their hydrogen bond network after photoexcitation. To explore this phenomenon, BLUF domains from R. sphaeroides were simulated using Amber99 molecular dynamics (MD). Five starting configurations were considered, to study different BLUF proteins (AppA/BlrB), Trp conformations (Win/Wout), structure determination (X-ray/NMR), and finally, His protonation states. We found dependencies of the hydrogen bonds on almost all parameters. Our data show an especially strong correlation of the Trp position and hydrogen bonds involving Gln63. The latter is in some contradiction to earlier results (Obanayama et al., Photochem. Photobiol. 2008, 84 10031010). Possible origins and implications are discussed. Our calculations support conjectures that Gln63 is more flexible with Trp104 in Win position. Using snapshots from MD and time-dependent density functional theory, UV/vis spectra for the chromophore were determined, which account for molecular motion of the protein under ambient conditions. In accord with experiment, it is found that the UV/vis spectra of BLUF bound flavin are red-shifted and thermally broadened for all calculated p ? p* transitions, relative to gas phase flavin at T = 0 K. However, differences in the spectra between the various BLUF configurations cannot be resolved with the present approach. (c) 2012 Wiley Periodicals, Inc.
KW  - blue-light sensor
KW  - flavin
KW  - molecular dynamics
KW  - TD-DFT
KW  - BLUF domains
Y1  - 2012
U6  - https://doi.org/10.1002/jcc.23056
SN  - 0192-8651
VL  - 33
IS  - 28
SP  - 2233
EP  - 2242
PB  - WILEY-BLACKWELL
CY  - HOBOKEN
ER  -