scholarly journals Ultrafast proton release reaction and primary photochemistry of phycocyanobilin in solution observed with fs-time-resolved mid-IR and UV/Vis spectroscopy

2021 ◽  
Author(s):  
Maximilian Theiß ◽  
Merten Grupe ◽  
Tilman Lamparter ◽  
Maria Andrea Mroginski ◽  
Rolf Diller
Keyword(s):  
Density Functional ◽  
Transient Absorption ◽  
Vibrational Analysis ◽  
Density Functional Theory Calculations ◽  
Chem Phys ◽  
Molecular Structures ◽  
Ir Absorption ◽  
Time Resolved ◽  
Time Constants ◽  
Vis Spectroscopy

AbstractDeactivation processes of photoexcited (λex = 580 nm) phycocyanobilin (PCB) in methanol were investigated by means of UV/Vis and mid-IR femtosecond (fs) transient absorption (TA) as well as static fluorescence spectroscopy, supported by density-functional-theory calculations of three relevant ground state conformers, PCBA, PCBB and PCBC, their relative electronic state energies and normal mode vibrational analysis. UV/Vis fs-TA reveals time constants of 2.0, 18 and 67 ps, describing decay of PCBB*, of PCBA* and thermal re-equilibration of PCBA, PCBB and PCBC, respectively, in line with the model by Dietzek et al. (Chem Phys Lett 515:163, 2011) and predecessors. Significant substantiation and extension of this model is achieved first via mid-IR fs-TA, i.e. identification of molecular structures and their dynamics, with time constants of 2.6, 21 and 40 ps, respectively. Second, transient IR continuum absorption (CA) is observed in the region above 1755 cm−1 (CA1) and between 1550 and 1450 cm−1 (CA2), indicative for the IR absorption of highly polarizable protons in hydrogen bonding networks (X–H…Y). This allows to characterize chromophore protonation/deprotonation processes, associated with the electronic and structural dynamics, on a molecular level. The PCB photocycle is suggested to be closed via a long living (> 1 ns), PCBC-like (i.e. deprotonated), fluorescent species.

The role of the metal ion in the photophysical behavior of Co(II), Ni(II), and Cu(II) octabutoxynaphthalocyanines: insights from ultra-fast time-resolved spectroscopy and DFT/TDDFT calculations

2010 ◽  
Vol 14 (08) ◽  
pp. 689-700 ◽  
Author(s):  
Giampaolo Ricciardi ◽  
Alexandra V. Soldatova ◽  
Angela Rosa
Keyword(s):  
Density Functional Theory ◽  
Metal Ion ◽  
Density Functional ◽  
Transient Absorption ◽  
Density Functional Theory Calculations ◽  
Fast Time ◽  
Central Metal ◽  
Functional Theory ◽  
Time Resolved ◽  
Deactivation Mechanism

The photo-deactivation mechanism of the MNc(OBu)8 (M = Co, Ni, Cu) series of complexes is reviewed, with special emphasis on the role played by the central metal. Ultra-fast transient absorption experiments and Density Functional Theory and time-dependent Density Functional Theory calculations consistently show that the central metal modifies the photo-deactivation mechanism of the investigated complexes by inducing substantial changes in the nature and energy of the excited states lying between the photo-generated state and the ground state.

Computational Investigation of the Asymmetry in Photosynthetic Reaction Center Models from First Principles

2020 ◽  
Author(s):  
Denis Artiukhin ◽  
Patrick Eschenbach ◽  
Johannes Neugebauer
Keyword(s):  
Spin Density ◽  
Reaction Center ◽  
Density Functional ◽  
Photosynthetic Reaction Center ◽  
Chem Phys ◽  
Molecular Structures ◽  
Error Characteristic ◽  
Molecular Systems ◽  
Density Distributions ◽  
The Asymmetry

We present a computational analysis of the asymmetry in reaction center models of photosystem I, photosystem II, and bacteria from <i>Synechococcus elongatus</i>, <i>Thermococcus vulcanus</i>, and <i>Rhodobacter sphaeroides</i>, respectively. The recently developed FDE-diab methodology [J. Chem. Phys., 148 (2018), 214104] allowed us to effectively avoid the spin-density overdelocalization error characteristic for standard Kohn–Sham Density Functional Theory and to reliably calculate spin-density distributions and electronic couplings for a number of molecular systems ranging from dimeric models in vacuum to large protein including up to about 2000 atoms. The calculated spin densities showed a good agreement with available experimental results and were used to validate reaction center models reported in the literature. We demonstrated that the applied theoretical approach is very sensitive to changes in molecular structures and relative orientation of molecules. This makes FDE-diab a valuable tool for electronic structure calculations of large photosynthetic models effectively complementing the existing experimental techniques.

scholarly journals Ground- and excited-state characteristics in photovoltaic polymer N2200

RSC Advances ◽  
2021 ◽  
Author(s):  
Guanzhao Wen ◽  
Xianshao Zou ◽  
Rong Hu ◽  
Jun Peng ◽  
Zhifeng Chen ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Excited State ◽  
Steady State ◽  
Excited States ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Time Dependent ◽  
Functional Theory ◽  
Time Resolved ◽  
Dependent Density

Ground- and excited-states properties of N2200 have been studied by steady-state and time-resolved spectroscopies as well as time-dependent density functional theory calculations.

scholarly journals Elucidating the Drug Release from Metal-Organic Framework Nanocomposites via in Situ Synchrotron Microspectroscopy and Theoretical Modelling

2019 ◽  
Author(s):  
Barbara Souza ◽  
Lorenzo Dona ◽  
Kirill Titov ◽  
Paolo Bruzzese ◽  
Zhixin Zeng ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Drug Release ◽  
Density Functional ◽  
Metal Organic Framework ◽  
Density Functional Theory Calculations ◽  
Theoretical Modelling ◽  
Time Resolved ◽  
Drug Molecules ◽  
Metal Organic

Nanocomposites comprising metal-organic frameworks (MOFs) embedded in a polymeric matrix are promising carriers for drug delivery applications. While understanding the chemical and physical transformations of MOFs during the release of confined drug molecules is challenging, this is central to devising better ways for controlled release of therapeutic agents. Herein we demonstrate the efficacy of synchrotron microspectroscopy to track the in situ release of 5-fluorouracil (5-FU) anticancer drug molecules from a drug@MOF/polymer composite (5-FU@HKUST-1/polyurethane). Using experimental time-resolved infrared spectra jointly with newly developed density functional theory calculations, we reveal the detailed dynamics of vibrational motions underpinning the dissociation of 5-FU bound to the framework of HKUST-1 upon water exposure. We discover that HKUST-1 creates hydrophilic channels within the hydrophobic polyurethane matrix hence helping to tune drug release rate. The synergy between a hydrophilic MOF with a hydrophobic polymer can be harnessed to engineer a tunable nanocomposite that alleviates the unwanted burst effect commonly encountered in drug delivery.<br>

scholarly journals Elucidating the Drug Release from Metal-Organic Framework Nanocomposites via in Situ Synchrotron Microspectroscopy and Theoretical Modelling

2019 ◽  
Author(s):  
Barbara Souza ◽  
Lorenzo Dona ◽  
Kirill Titov ◽  
Paolo Bruzzese ◽  
Zhixin Zeng ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Drug Release ◽  
Density Functional ◽  
Metal Organic Framework ◽  
Density Functional Theory Calculations ◽  
Theoretical Modelling ◽  
Time Resolved ◽  
Drug Molecules ◽  
Metal Organic

Nanocomposites comprising metal-organic frameworks (MOFs) embedded in a polymeric matrix are promising carriers for drug delivery applications. While understanding the chemical and physical transformations of MOFs during the release of confined drug molecules is challenging, this is central to devising better ways for controlled release of therapeutic agents. Herein we demonstrate the efficacy of synchrotron microspectroscopy to track the in situ release of 5-fluorouracil (5-FU) anticancer drug molecules from a drug@MOF/polymer composite (5-FU@HKUST-1/polyurethane). Using experimental time-resolved infrared spectra jointly with newly developed density functional theory calculations, we reveal the detailed dynamics of vibrational motions underpinning the dissociation of 5-FU bound to the framework of HKUST-1 upon water exposure. We discover that HKUST-1 creates hydrophilic channels within the hydrophobic polyurethane matrix hence helping to tune drug release rate. The synergy between a hydrophilic MOF with a hydrophobic polymer can be harnessed to engineer a tunable nanocomposite that alleviates the unwanted burst effect commonly encountered in drug delivery.<br>

scholarly journals 1,3,4-Thiadiazole-Containing Azo Dyes: Synthesis, Spectroscopic Properties and Molecular Structure

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2822
Author(s):  
Agnieszka Kudelko ◽  
Monika Olesiejuk ◽  
Marcin Luczynski ◽  
Marcin Swiatkowski ◽  
Tomasz Sieranski ◽  
...  
Keyword(s):  
Azo Dyes ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Spectroscopic Properties ◽  
Radiation Absorption ◽  
Functional Theory ◽  
Chemical Structures ◽  
Vis Spectroscopy ◽  
High Yields

Three series of azo dyes derived from 2-amino-5-aryl-1,3,4-thiadiazoles and aniline, N,N-dimethylaniline and phenol were synthesized in high yields by a conventional diazotization-coupling sequence. The chemical structures of the prepared compounds were confirmed by 1H-NMR, 13C-NMR, IR, UV-Vis spectroscopy, mass spectrometry and elemental analysis. In addition, the X-ray single crystal structure of a representative azo dye was presented. For explicit determination of the influence of a substituent on radiation absorption in UV-Vis range, time-dependent density functional theory calculations were performed.

scholarly journals Including dispersion interactions in the ONETEP program for linear-scaling density functional theory calculations

2008 ◽  
Vol 465 (2103) ◽  
pp. 669-683 ◽  
Author(s):  
Quintin Hill ◽  
Chris-Kriton Skylaris
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Computational Cost ◽  
Density Functional Theory Calculations ◽  
Binding Energies ◽  
Molecular Structures ◽  
Dispersion Interactions ◽  
Biomolecular Systems ◽  
Functional Theory ◽  
High Level

While density functional theory (DFT) allows accurate quantum mechanical simulations from first principles in molecules and solids, commonly used exchange-correlation density functionals provide a very incomplete description of dispersion interactions. One way to include such interactions is to augment the DFT energy expression by damped London energy expressions. Several variants of this have been developed for this task, which we discuss and compare in this paper. We have implemented these schemes in the ONETEP program, which is capable of DFT calculations with computational cost that increases linearly with the number of atoms. We have optimized all the parameters involved in our implementation of the dispersion correction, with the aim of simulating biomolecular systems. Our tests show that in cases where dispersion interactions are important this approach produces binding energies and molecular structures of a quality comparable with high-level wavefunction-based approaches.

scholarly journals Physicochemical Insight into Coordination Systems Obtained from Copper(II) Bromoacetate and 1,10-Phenanthroline

Molecules ◽  
2020 ◽  
Vol 25 (22) ◽  
pp. 5324
Author(s):  
Ewelina Krejner ◽  
Tomasz Sierański ◽  
Marcin Świątkowski ◽  
Marta Bogdan ◽  
Rafał Kruszyński
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Building Blocks ◽  
Radiation Absorption ◽  
Ir Absorption ◽  
Bromoacetic Acid ◽  
Functional Theory ◽  
Hirshfeld Analysis ◽  
Coordination Systems

Two different coordination compounds of copper were synthesized from the same building blocks (1,10-phenanthroline, bromoacetate anions, and copper cations). The synthesis parameters were carefully designed and evaluated to allow the change of the resulting compounds molecular structure, i.e., formation of mononuclear (bromoacetato-O,O’)(bromoacetato-O)aqua(1,10-phenanthroline-N,N’)copper(II) and dinuclear (μ-bromido-1:2κ2)bis(μ-bromoacetato-1κO,2κO’)bis(1,10-phenanthroline-N,N’)dicopper(II) bromoacetate bromoacetic acid solvate. The crystal, molecular and supramolecular structures of the studied compounds were determined and evaluated in Hirshfeld analysis. The UV-Vis-IR absorption and thermal properties were studied and discussed. For the explicit determination of the influence of compounds structure on radiation absorption in UV-Vis range, density functional theory and time-dependent density functional theory calculations were performed.

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