High-resolution electron spectroscopy and molecular structures of Cu–(2,2′-bipyridine) and Cu-(4,4′-bipyridine)

2013 ◽  
Vol 91 (7) ◽  
pp. 613-620 ◽  
Author(s):  
Xu Wang ◽  
Jung Sup Lee ◽  
Dong-Sheng Yang

Copper complexes of 2,2′-bipyridine (22BIPY) and 4,4′-bipyridine (44BIPY) were prepared in a laser-vaporization supersonic molecular beam source and identified by laser photoionization time-of-flight mass spectrometry. Electronic spectra and molecular structures were studied with pulsed-field ionization zero electron kinetic energy (ZEKE) electron spectroscopy, density functional theory (DFT) and second-order Møller–Plesset perturbation (MP2) calculations, and spectral simulations. Adiabatic ionization energies and metal–ligand and ligand-based vibrational frequencies of Cu–22BIPY and Cu–44BIPY were measured from the ZEKE spectra. Ground electronic states and molecular structures of the two complexes were determined by comparing the spectroscopic measurements with the theoretical calculations. The ground state of Cu–22BIPY ( 2 B1, C2v) has a planar bidentate structure with Cu binding to two nitrogen atoms and two pyridine molecules in the cis configuration. The ground state of Cu–44BIPY ( 2 A, C2) has a monodentate structure with Cu binding to one nitrogen and two pyridines in a twisted configuration. The ionization energy of Cu–22BIPY is considerably lower and its bond energy is much higher than that of Cu–44BIPY. The different ionization and dissociation energies are attributed to the distinct metal binding modes of the two complexes. It has been found that the DFT calculations yield the correct structures for the Cu–22BIPY complex, whereas the MP2 calculations produce the best structures for the Cu–44BIPY complex.

2009 ◽  
Vol 87 (1) ◽  
pp. 297-306 ◽  
Author(s):  
Xu Wang ◽  
Dong-Sheng Yang

Copper complexes of x-aminopyridine (x = 2, 3, 4) were prepared in a laser vaporization supersonic molecular beam source and identified using laser photoionization time-of-flight mass spectrometry. These complexes were studied by pulsed-field ionization zero electron kinetic energy (ZEKE) spectroscopy and second-order Møller-Plesset perturbation theory. Three structures formed by Cu binding to the pyridine nitrogen (σα), the amino nitrogen (σβ), and the pyridine ring (π) were considered by the theoretical calculations, but only the σα structures with Cu binding to the pyridine nitrogen were confirmed by the spectroscopic measurements. Adiabatic ionization energies and metal-ligand and ligand-based vibrational frequencies of the σα complexes were measured from the ZEKE spectra, and the metal-ligand bond energies of the neutral and ionized complexes were predicted by the theory. The ionization energies of the Cu complexes are about 20 000 cm–1 lower than that of bare Cu atom. This ionization energy shift is the result of the stronger Cu+-ligand bonding because of the additional charge-dipole interaction in the ion. Although the three complexes are formed by Cu coordination to the pyridine nitrogen atom, the position of the amino group affects the metal-ligand bonding strengths in both neutral and ionized species. These effects include the structural resonance and hydrogen bonding in the neutral complexes and the electric dipole moment and bidentate bonding in the ions.Key words: photoelectron, PFI-ZEKE, ab initio, copper aminopyridine.


Crystals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1044
Author(s):  
Ayman A. Zaki ◽  
Mohamed Hagar ◽  
Rua B. Alnoman ◽  
Mariusz Jaremko ◽  
Abdul-Hamid Emwas ◽  
...  

A new liquid crystalline, optical material-based Schiff base core with a near to room-temperature mesophase, (4-methoxybenzylideneamino)phenyl oleate (I), was prepared from a natural fatty acid derivative, and its physical and chemical properties investigated by experimental and theoretical approaches. The molecular structure was confirmed by elemental analysis, FT-IR (Fourier-Transform-Infrared Spectroscopy) and NMR (nuclear magnetic resonance) spectroscopy. Optical and mesomorphic activities were characterized by differential scanning calorimetry (DSC) and polarized optical microscopy (POM). The results show that compound (I) exhibits an enantiotropic monomorphic phase comprising a smectic A phase within the near to room-temperature range. Ordinary and extraordinary refractive indices as well as birefringence with changeable temperatures were analyzed. Microscopic and macroscopic order parameters were also calculated. Theoretical density functional theory (DFT) calculations were carried out to estimate the geometrical molecular structures of the prepared compounds, and the DFT results were used to illustrate the mesomorphic results and optical characteristics in terms of their predicted data. Three geometrical isomers of the prepared compound were investigated to predict the most stable isomer. Many parameters were affected by the geometrical isomerism such as aspect ratio, planarity, and dipole moment. Thermal parameters of the theoretical calculations revealed that the highest co-planar aromatic core is the most stable conformer.


2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Mustafa Karakaya ◽  
Fatih Ucun ◽  
Ahmet Tokatlı

The optimized molecular structures and vibrational frequencies and also gauge including atomic orbital (GIAO)1H and13C NMR shift values of benzoylcholine chloride [(2-benzoyloxyethyl) trimethyl ammonium chloride] have been calculated using density functional theory (B3LYP) method with 6-31++G(d) basis set. The comparison of the experimental and calculated infrared (IR), Raman, and nuclear magnetic resonance (NMR) spectra has indicated that the experimental spectra are formed from the superposition of the spectra of two lowest energy conformers of the compound. So, it was concluded that the compound simultaneously exists in two optimized conformers in the ground state. Also the natural bond orbital (NBO) analysis has supported the simultaneous exiting of two conformers in the ground state. The calculated optimized geometric parameters (bond lengths and bond angles) and vibrational frequencies for both the lowest energy conformers were seen to be in a well agreement with the corresponding experimental data.


2020 ◽  
Vol 85 (8) ◽  
pp. 1021-1032 ◽  
Author(s):  
Branislav Milovanovic ◽  
Milena Petkovic ◽  
Mihajlo Etinski

G-quartets are supra-molecular structures that consist of four guanine molecules connected by eight hydrogen bonds. They are additionally stabilized by metal cations. In this contribution, the excited states of G-quartet and its complexes with lithium, sodium and potassium were studied by employing time-dependent density functional theory. The findings indicate that vertical excitations from the optimized ground state involve transitions from several bases, whereas excitations from the optimized lowest excited state include transitions from one base. The charge-transfer character of these states was analyzed. It was shown that the cations are able to modify positions of the maxima of the fluorescence spectra of the complexes.


Polyhedron ◽  
1997 ◽  
Vol 16 (12) ◽  
pp. 2029-2035 ◽  
Author(s):  
Joseph M. O'Connor ◽  
Kristin Hiibner ◽  
Arnold L. Rheingold ◽  
Louise M. Liable-Sands

2005 ◽  
Vol 19 (11) ◽  
pp. 473-487 ◽  
Author(s):  
HENRIK BOHR ◽  
K. J. JALKANEN ◽  
F. BARY MALIK

An investigation of the physics, underlying the damage caused to DNA by UV radiation and its subsequent repair via a photoreactivation mechanism, is presented in this study. Electronic pathways, starting from the initial damage to the final repair process, are presented. UV radiation is absorbed to create a hole-excited thymine or other pyrimidine that subsequently is responsible for the formation of a dimer. The negative-ion of the cofactor riboflavin, FADH-, formed by the exposure of the photolyase protein to visible light, interacts with the hole-excited electronic orbital of the thymine dimer inducing a photon-less Auger transition, which restores the two thymines to the ground state, thereby detaching the lesion and repairing the DNA. Density functional theoretical calculations supporting the theory are presented. The mechanism involves the least amount of energy dissipation and is charge neutral. It also avoids radiation damage in the repair process. Recent experimental data are compatible with this theory.


2017 ◽  
Vol 200 ◽  
pp. 559-578 ◽  
Author(s):  
Chiara Giorio ◽  
Steven J. Campbell ◽  
Maurizio Bruschi ◽  
Alexander T. Archibald ◽  
Markus Kalberer

Ozonolysis of alkenes is a key reaction in the atmosphere, playing an important role in determining the oxidising capacity of the atmosphere and acting as a source of compounds that can contribute to local photochemical “smog”. The reaction products of the initial step of alkene-ozonolysis are Criegee intermediates (CIs), which have for many decades eluded direct experimental detection because of their very short lifetime. We use an innovative experimental technique, stabilisation of CIs with spin traps and analysis with proton transfer reaction mass spectrometry, to measure the gas phase concentration of a series of CIs formed from the ozonolysis of a range of both biogenic and anthropogenic alkenes in flow tube experiments. Density functional theory (DFT) calculations were used to assess the stability of the CI-spin trap adducts and show that the reaction of the investigated CIs with the spin trap occurs very rapidly except for the large β-pinene CI. Our measurement method was used successfully to measure all the expected CIs, emphasising that this new technique is applicable to a wide range of CIs with different molecular structures that were previously unidentified experimentally. In addition, for the first time it was possible to study CIs simultaneously in an even more complex reaction system consisting of more than one olefinic precursor. Comparison between our new experimental measurements, calculations of stability of the CI-spin trap adducts and results from numerical modelling, using the master chemical mechanism (MCM), shows that our new method can be used for the quantification of CIs produced in situ in laboratory experiments.


2020 ◽  
Author(s):  
Denis Artiukhin ◽  
Patrick Eschenbach ◽  
Johannes Neugebauer

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.


2018 ◽  
Author(s):  
Mihails Arhangelskis ◽  
Athanassis Katsenis ◽  
Novendra Novendra ◽  
Zamirbek Akimbekov ◽  
Dayaker Gandrath ◽  
...  

By combining mechanochemical synthesis and calorimetry with theoretical calculations, we demonstrate that dispersion-corrected periodic density functional theory (DFT) can accurately survey the topological landscape and predict relative energies of polymorphs for a previously inaccessible fluorine-substituted zeolitic imidazolate framework (ZIF). Experimental screening confirmed two out of three theoretically anticipated polymorphs, and the calorimetric measurements provided an excellent match to theoretically calculated energetic difference between them.<br>


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