scholarly journals Accurate Prediction of Absorption Spectral Shifts of Proteorhodopsin Using a Fragment-Based Quantum Mechanical Method

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4486
Author(s):  
Chenfei Shen ◽  
Xinsheng Jin ◽  
William J. Glover ◽  
Xiao He
Keyword(s):  
Electric Fields ◽  
Electrostatic Interactions ◽  
Spectral Shift ◽  
Mechanical Method ◽  
Excitation Energies ◽  
Color Tuning ◽  
Spectral Shifts ◽  
Quantum Mechanical Method ◽  
Experimental Values ◽  
Molecular Fractionation

Many experiments have been carried out to display different colors of Proteorhodopsin (PR) and its mutants, but the mechanism of color tuning of PR was not fully elucidated. In this study, we applied the Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps (EE-GMFCC) method to the prediction of excitation energies of PRs. Excitation energies of 10 variants of Blue Proteorhodopsin (BPR-PR105Q) in residue 105GLN were calculated with the EE-GMFCC method at the TD-B3LYP/6-31G* level. The calculated results show good correlation with the experimental values of absorption wavelengths, although the experimental wavelength range among these systems is less than 50 nm. The ensemble-averaged electric fields along the polyene chain of retinal correlated well with EE-GMFCC calculated excitation energies for these 10 PRs, suggesting that electrostatic interactions from nearby residues are responsible for the color tuning. We also utilized the GMFCC method to decompose the excitation energy contribution per residue surrounding the chromophore. Our results show that residues ASP97 and ASP227 have the largest contribution to the absorption spectral shift of PR among the nearby residues of retinal. This work demonstrates that the EE-GMFCC method can be applied to accurately predict the absorption spectral shifts for biomacromolecules.

Systematic calculations of energy levels and transitions rates in Mo XXVIII

2020 ◽  
Vol 75 (8) ◽  
pp. 739-747
Author(s):  
Feng Hu ◽  
Yan Sun ◽  
Maofei Mei
Keyword(s):  
Energy Levels ◽  
Oscillator Strengths ◽  
Atomic Data ◽  
Data Sets ◽  
Electron Systems ◽  
Excitation Energies ◽  
Experimental Values ◽  
Qed Effects ◽  
Hyperfine Structures ◽  
Good Agreement

AbstractComplete and consistent atomic data, including excitation energies, lifetimes, wavelengths, hyperfine structures, Landé gJ-factors and E1, E2, M1, and M2 line strengths, oscillator strengths, transitions rates are reported for the low-lying 41 levels of Mo XXVIII, belonging to the n = 3 states (1s22s22p6)3s23p3, 3s3p4, and 3s23p23d. High-accuracy calculations have been performed as benchmarks in the request for accurate treatments of relativity, electron correlation, and quantum electrodynamic (QED) effects in multi-valence-electron systems. Comparisons are made between the present two data sets, as well as with the experimental results and the experimentally compiled energy values of the National Institute for Standards and Technology wherever available. The calculated values including core-valence correction are found to be in a good agreement with other theoretical and experimental values. The present results are accurate enough for identification and deblending of emission lines involving the n = 3 levels, and are also useful for modeling and diagnosing plasmas.

Experimental and Theoretical Studies of 2- (naphthalen-1-yl (piperidin-1-yl) methyl)phenol Compound

2020 ◽  
Vol 42 (6) ◽  
pp. 818-818
Author(s):  
Yeliz Ula Yeliz Ula
Keyword(s):  
Molecular Orbital ◽  
Theoretical Data ◽  
Biologically Active ◽  
Oscillator Strengths ◽  
Excitation Energies ◽  
Petasis Reaction ◽  
Vis Spectroscopy ◽  
Phenol Compound ◽  
Lowest Unoccupied Molecular Orbital ◽  
Experimental Values

The 2- (naphthalen-1-yl (piperidin-1-yl) methyl) phenol compound is an alkylaminophenol compound and has been experimentally synthesized by the Petasis reaction. In this study Structural analysis was carried out by FT-IR, NMR, UV-Vis spectroscopy. The high antioxidant value of the compound showed that it could be a potential biologically active drug. Theoretical data support all experimental analysis of the new compound. Comparisons were made by double method. For this purpose, DFT (B3LYP) and HF methods have been used with 6-311G ++ (d, p) set. Also, the compoundand#39;s electronic and structural properties (bond lengths, bond angles and dihedral angles), the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies, electrostatic potential (MEP), vibrational frequencies, Mulliken atomic charges, excitation energies, and oscillator strengths were calculated. As a result; the theoretical and experimental values were found to be compatible.

scholarly journals Separation of water–ethanol solutions with carbon nanotubes and electric fields

2016 ◽  
Vol 18 (48) ◽  
pp. 33310-33319 ◽  
Author(s):  
Winarto Winarto ◽  
Daisuke Takaiwa ◽  
Eiji Yamamoto ◽  
Kenji Yasuoka
Keyword(s):  
Carbon Nanotubes ◽  
Electric Field ◽  
Electric Fields ◽  
Electrostatic Interactions ◽  
Water Molecules ◽  
Ordered Structure

Under an electric field, water prefers to fill CNTs over ethanol, and electrostatic interactions within the ordered structure of the water molecules determine the separation effects.

scholarly journals On the electromagnetic fields due to variable electric charges and the intensities of spectrum lines according to the quantum theory

1935 ◽  
Vol 150 (870) ◽  
pp. 416-421 ◽  
Keyword(s):  
Quantum Theory ◽  
Wave Functions ◽  
Spectral Lines ◽  
Quantum Mechanical ◽  
Final States ◽  
Electric Moment ◽  
Mechanical Method ◽  
Quantum Mechanical Method ◽  
Consistent Method ◽  
Time Average

In a recent paper Schott has criticized the quantum mechanical method of finding the intensities of spectral lines, and in particular the assumption that the intensity may be derived by treating the atom as a dipole, radiating classically. The electric moment of this dipole is taken as p = e -2 πivt ∫ Ψ* f rΨ i d τ + Conjugate complex, (1A) where Ψ i and Ψ f are the wave functions of the initial and final states of the atom respectively, and in the Quantum Theory the usual assumption is that the energy radiated per unit time is given by R = 2 |p¨ ¯ | 2 /3 c 2 , (1B) where p¨ ¯ is the time average of p¨. A more consistent method is suggested in which the electric density ρ and the current j, corresponding to the transition, are found, and the electromagnetic field due to these two is examined.

Modification of the porphyrin chromophore by ring fusion: identifying trends due to annelation of the porphyrin nucleus

2001 ◽  
Vol 05 (03) ◽  
pp. 267-288 ◽  
Author(s):  
TIMOTHY D. LASH
Keyword(s):  
Soret Band ◽  
Spectral Shift ◽  
Aromatic Rings ◽  
Ring Fusion ◽  
Spectral Shifts ◽  
Hyper Spectral ◽  
Two Factors ◽  
Porphyrin Analogues ◽  
Soret Absorption ◽  
Soret Region

The effects exerted by fused aromatic rings on the UV-vis spectra of porphyrins are surveyed. Modified porphyrin chromophores with fused benzene, 1,2-naphthalene, 9,10-phenanthrene or phenanthroline rings are surprisingly little affected even when a maximum number of ring fusions are incorporated. Linearly annealed naphtho- or anthraporphyrins show large red shifts to the Q bands but the Soret absorptions are weakened and undergo only minor bathochromic shifts. Fluoranthoporphyrins give multiple bands in the Soret region, but the Q band region is virtually unaffected by this tetracyclic ring system. On the other hand, metal chelates of fluoranthoporphyrins show surprisingly strong bands near 600 nm. Benzothiadiazole rings split and weaken the Soret band, but the Q bands region is unexceptional. However, metal coordination again produces relatively intense bands near 600 nm. The most significant results were obtained for porphyrins with fused acenaphthylene rings. Monoacenaphthoporphyrins (41) have three Soret bands at 387, 431 and 454 nm, and the longest wavelength Q band is shifted to 658 nm. opp-Diacenaphthoporphyrin (43) further shifts these bands with two Soret absorbances at 443 and 470 nm, and an additional strong peak is observed at 692 nm. The metal complexes of these systems also show strong bands between 602 and 656 nm. Still larger effects are produced by tetraacenaphthoporphyrin (47), the dication for which in trifluoroacetic acid (TFA)–chloroform has a Soret absorption at 528 nm. Tetraaryltetraacenaphthoporphyrins (48) are even more red shifted, showing Soret bands between 556 and 570 nm for the free bases and 565 to 588 nm for the related dications. The lead(II) chelate for tetraphenylporphyrin (48a) shows an additional 'hyper' spectral shift that brings the Soret band to 604 nm, and this effect can also be achieved by introducing four meso-phenylethynyl substituents onto the tetraacenaphthoporphyrin nucleus (49). In addition, by combining these two factors for the lead(II) chelate of 49, a record-breaking value for the Soret band of 642 nm can be achieved. Spectral shifts due to ring annelation in porphyrin analogues are also discussed, including those for oxybenziporphyrins, oxypyriporphyrins, carbaporphyrins and sapphyrins.

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