Electronic propensity of Cu(II) versus Cu(I) sites in zeolites to activate NO — Spin- and orbital-resolved Cu–NO electron transfer

2013 ◽  
Vol 91 (7) ◽  
pp. 538-543 ◽  
Author(s):  
Mariusz Radoń ◽  
Paweł Kozyra ◽  
Adam Stępniewski ◽  
Jerzy Datka ◽  
Ewa Broclawik
Keyword(s):  
Electron Transfer ◽  
Density Functional ◽  
Lone Pair ◽  
Blue Shift ◽  
Open Shell ◽  
Minor Importance ◽  
Antibonding Orbital ◽  
Spin Manifolds ◽  
Copper Center ◽  
Nitrogen Lone Pair

Electronic factors responsible for the notable decline of NO activation by Cu(II) with respect to Cu(I) sites in zeolites are investigated within spin-resolved analysis of electron transfer channels between the copper center and the substrate. The results of natural orbitals for chemical valence (NOCV) charge transfer analysis for a minimal model of Cu(II) sites in zeolite ZSM-5 ({T1Cu}+ NO) are compared with those for Cu(I)–NO and referenced to an interaction of NO with bare Cu+ cations. The bonding of NO, which is an open-shell and non-innocent ligand, gives rise to a noticeable nondynamical correlation in the adduct with Cu(II) (reflected in a broken-symmetry solution obtained at the density functional theory (DFT) level). Four distinct components of electron transfer between the copper and NO are identified: (i) donation of an unpaired electron from the NO π∥* antibonding orbital to the Cu species, (ii) backdonation from copper d⊥ to the NO antibonding orbital, (iii) “covalent” donation from NO π∥ and Cu d∥ orbitals to the bonding region, and (iv) donation from the nitrogen lone pair to Cus,d. Large variations in channel identity and significance may be noted among studied systems and between spin manifolds: channel i is effective only in the bonding of NO with either a naked Cu+ cation or Cu(II) site. Channel ii comes into prominence only for the model of the Cu(I) site: it strongly activates the NO bond by populating antibonding π*, which weakens the N–O bond, in contrast to channel i depopulating the antibonding orbital and strengthening the N–O bond. Channels iii and iv, however, may contribute to the strength of the bonding between NO and copper, and are of minor importance for the activation of the NO bond. This picture perfectly matches the IR experiment: interaction with either Cu(II) sites or a naked Cu+ cation imposes a comparable blue-shift of NO stretching frequency, while the frequency becomes strongly red-shifted for a Cu(I) site in ZSM-5 due to enhanced π* backdonation.

scholarly journals Investigation of the position of the radical in z3-ions resulting from electron transfer dissociation using infrared ion spectroscopy

2019 ◽  
Vol 217 ◽  
pp. 434-452 ◽  
Author(s):  
Lisanne J. M. Kempkes ◽  
Jonathan Martens ◽  
Giel Berden ◽  
Kas J. Houthuijs ◽  
Jos Oomens
Keyword(s):  
Mass Spectrometry ◽  
Density Functional Theory ◽  
Electron Transfer ◽  
Density Functional ◽  
Electron Transfer Dissociation ◽  
Open Shell ◽  
Molecular Structures ◽  
Functional Theory ◽  
Ion Spectroscopy ◽  
Molecular Dynamics Calculations

The molecular structures of six open-shell z3-ions resulting from electron transfer dissociation mass spectrometry (ETD MS) were investigated using infrared ion spectroscopy in combination with density functional theory and molecular mechanics/molecular dynamics calculations.

scholarly journals Conversions of Localized Excess Electrons and Spin States under External Electric Field: Inter-Cage Electron-transfer Isomer (C20F20)3&K2

2020 ◽  
Author(s):  
Jia-Min Tang ◽  
Yin-Feng Wang ◽  
Tian Qin ◽  
Xue-Xia Liu ◽  
Zhijun Wang ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Electric Field ◽  
External Electric Field ◽  
Singlet State ◽  
Lone Pair ◽  
Open Shell ◽  
Spin States ◽  
New Members ◽  
Excess Electrons ◽  
State 1

By doping two potassium atoms among three CF cages, peanut-shaped single molecular solvated dielectron (CF)&K was theoretically presented. The triplet structures with two excess electrons individually inside left and middle cages (isomers I or II) are thermodynamically more stable than both open-shell (OS) and close-shell (CS) singlet ones with lone pair of excess electrons inside middle cage. Applying an oriented external electric field (OEEF) of -20 × 10 au (-0.1018 V/Å) or a larger one can result in both left-to-right transfers of the two excess electrons, and then releasing the OEEF can form new kind of inter-cage electron-transfer isomers (III or IV). Each triplet I ~ IV with three redox sits may be new members of mixed-valent compounds, namely, Robin-Day Class II. For electrified I of (CF)&K , the following spin states are ground state: 1) triplet state in field ranges of -120 × 10 < F < -30 × 10 au and 30 × 10 < F < 111 × 10 au; 2) CS singlet state in range of F ≥ 111 × 10 and ≤ -120 × 10 au; 3) OS singlet state in ranges of -30 × 10 ≤ F ≤ -5 × 10 au and 5 × 10 ≤ F ≤ 30 × 10 au.

scholarly journals Structural Changes of the Trinuclear Copper Center in Bilirubin Oxidase upon Reduction

Molecules ◽  
2018 ◽  
Vol 24 (1) ◽  
pp. 76 ◽  
Author(s):  
Takaki Tokiwa ◽  
Mitsuo Shoji ◽  
Vladimir Sladek ◽  
Naoki Shibata ◽  
Yoshiki Higuchi ◽  
...  
Keyword(s):  
Structural Change ◽  
Density Functional ◽  
Structural Changes ◽  
Open Shell ◽  
Type I ◽  
Bilirubin Oxidase ◽  
Shell System ◽  
Structure Changes ◽  
Copper Center ◽  
Electron Reduction

Geometric and electronic structure changes in the copper (Cu) centers in bilirubin oxidase (BOD) upon a four-electron reduction were investigated by quantum mechanics/molecular mechanics (QM/MM) calculations. For the QM region, the unrestricted density functional theory (UDFT) method was adopted for the open-shell system. We found new candidates of the native intermediate (NI, intermediate II) and the resting oxidized (RO) states, i.e., NIH+ and RO0. Elongations of the Cu-Cu atomic distances for the trinuclear Cu center (TNC) and very small structural changes around the type I Cu (T1Cu) were calculated as the results of a four-electron reduction. The QM/MM optimized structures are in good agreement with recent high-resolution X-ray structures. As the structural change in the TNC upon reduction was revealed to be the change in the size of the triangle spanned by the three Cu atoms of TNC, we introduced a new index (l) to characterize the specific structural change. Not only the wild-type, but also the M467Q, which mutates the amino acid residue coordinating T1Cu, were precisely analyzed in terms of their molecular orbital levels, and the optimized redox potential of T1Cu was theoretically reconfirmed.

Electronic spectrum of bibenzimidazole homologue: effects of solvents and acid concentration

1989 ◽  
Vol 67 (7) ◽  
pp. 1200-1205 ◽  
Author(s):  
Awadesh Kumar ◽  
Hemant K. Sinha ◽  
Sneh K. Dogra
Keyword(s):  
Spectral Characteristics ◽  
Solvent Molecule ◽  
Lone Pair ◽  
Direct Interaction ◽  
Blue Shift ◽  
Intramolecular Hydrogen Bonding ◽  
Wavelength Absorption ◽  
Nitrogen Lone Pair ◽  
Intramolecular Hydrogen ◽  
Different Characteristics

The absorption and fluorescence spectra of bibenzimidazole (BBI), N, N′-dimethylbibenzimidazole (MBBI), and methylene, 2,2′-bibenzimidazole (MtBBI) have been recorded in six solvents of different characteristics and at various acid concentrations. This study indicates the presence of intramolecular hydrogen bonding in BBI in both S0 and S1 states, leading to large conjugation of two benzimidazole (BI) rings. The geometry of BBI is the same in the S0 and S1 states. The spectral characteristics of BBI are insensitive to the solvents. The interaction of solvent molecule attached to the nitrogen lone pair and methyl group rotates the benzimidazolyl ring in MBBI around the single bond. This leads to a blue shift in the long wavelength absorption band maximum and a decrease in the intensity of this band. The two MBI rings are coplanar in the S1 state. Presence of methylene group inhibits the direct interaction between the BI groups and these rings behave almost independently, i.e., the spectral characteristics of this molecule nearly resemble those of benzimidazole. Keywords: absorption spectrum, fluorescence spectrum, pKa, bibenzimidazoles, excited state pKa.

scholarly journals Synthesis, DFT Calculations, and In Vitro Antioxidant Study on Novel Carba-Analogs of Vitamin E

Antioxidants ◽  
2019 ◽  
Vol 8 (12) ◽  
pp. 589 ◽  
Author(s):  
Aneta Baj ◽  
Jakub Cedrowski ◽  
Ewa Olchowik-Grabarek ◽  
Artur Ratkiewicz ◽  
Stanislaw Witkowski
Keyword(s):  
Antioxidant Activity ◽  
Electron Transfer ◽  
Vitamin E ◽  
Density Functional ◽  
Lone Pair ◽  
Hydrogen Atom Transfer ◽  
Hydroxyl Group ◽  
Styrene Oxidation ◽  
Chain Breaking

Vitamin E is the most active natural lipophilic antioxidant with a broad spectrum of biological activity. α-Tocopherol (α-T), the main representative of the vitamin E family, is a strong inhibitor of lipid peroxidation as a chain-breaking antioxidant. Antioxidant and antiradical properties of vitamin E result from the presence of a phenolic hydroxyl group at the C-6 position. Due to stereoelectronic effects in the dihydropyranyl ring, the dissociation enthalpy for phenolic O–H bond (BDEOH) is reduced. The high chain-breaking reactivity of α-T is mainly attributed to orbital overlapping of the 2p-type lone pair on the oxygen atom (O1) in para position to the phenolic group, and the aromatic π-electron system. The influence of the O1 atom on the antioxidant activity of vitamin E was estimated quantitatively. The all-rac-1-carba-α-tocopherol was synthesized for the first time. Along with model compounds, 1-carba-analog of Trolox and its methyl ester were screened for their in vitro antioxidant activity by inhibition of styrene oxidation, and for the radical-reducing properties by means of 2,2-diphenyl-1-picrylhydrazyl free radical (DPPH) scavenging assay. To study the antioxidant activity, density functional theory (DFT) was also applied. Reaction enthalpies related to HAT (hydrogen atom transfer), SET–PT (sequential electron transfer—proton transfer), and SPLET (sequential proton loss—electron transfer) mechanisms were calculated.

Computationally Assisted Design of High Signal-to-Noise Photoinduced Electron Transfer-Based Voltage-Sensitive Dyes

2020 ◽  
Author(s):  
Rishikesh Kulkarni ◽  
Anneliese Gest ◽  
Chun Kei Lam ◽  
Benjamin Raliski ◽  
Feroz James ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Dft Calculations ◽  
Photoinduced Electron Transfer ◽  
Density Functional ◽  
Embryonic Stem ◽  
High Sensitivity ◽  
Md Simulations ◽  
High Signal ◽  
Signal To Noise ◽  
Green Fluorescent

<p>High signal-to-noise optical voltage indicators will enable simultaneous interrogation of membrane potential in large ensembles of neurons. However, design principles for voltage sensors with high sensitivity and brightness remain elusive, limiting the applicability of voltage imaging. In this paper, we use molecular dynamics (MD) simulations and density functional theory (DFT) calculations to guide the design of a bright and sensitive green-fluorescent voltage-sensitive fluorophore, or VoltageFluor (VF dye), that uses photoinduced electron transfer (PeT) as a voltage-sensing mechanism. MD simulations predict an 11% increase in sensitivity due to membrane orientation, while DFT calculations predict an increase in fluorescence quantum yield, but a decrease in sensitivity due to a decrease in rate of PeT. We confirm these predictions by synthesizing a new VF dye and demonstrating that it displays the expected improvements by doubling the brightness and retaining similar sensitivity to prior VF dyes. Combining theoretical predictions and experimental validation has resulted in the synthesis of the highest signal-to-noise green VF dye to date. We use this new voltage indicator to monitor the electrophysiological maturation of human embryonic stem cell-derived medium spiny neurons. </p>

scholarly journals Spectral Probe for Electron Transfer and Addition Reactions of Azide Radicals with Substituted Quinoxalin-2-Ones in Aqueous Solutions

2021 ◽  
Vol 22 (2) ◽  
pp. 633
Author(s):  
Konrad Skotnicki ◽  
Slawomir Ostrowski ◽  
Jan Cz. Dobrowolski ◽  
Julio R. De la Fuente ◽  
Alvaro Cañete ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Aqueous Solutions ◽  
Absorption Spectra ◽  
Density Functional ◽  
Reduction Potential ◽  
Biological Significance ◽  
Radical Cations ◽  
Basis Sets ◽  
Double Bonds ◽  
Reduction Potentials

The azide radical (N3●) is one of the most important one-electron oxidants used extensively in radiation chemistry studies involving molecules of biological significance. Generally, it was assumed that N3● reacts in aqueous solutions only by electron transfer. However, there were several reports indicating the possibility of N3● addition in aqueous solutions to organic compounds containing double bonds. The main purpose of this study was to find an experimental approach that allows a clear assignment of the nature of obtained products either to its one-electron oxidation or its addition products. Radiolysis of water provides a convenient source of one-electron oxidizing radicals characterized by a very broad range of reduction potentials. Two inorganic radicals (SO4●−, CO3●−) and Tl2+ ions with the reduction potentials higher, and one radical (SCN)2●− with the reduction potential slightly lower than the reduction potential of N3● were selected as dominant electron-acceptors. Transient absorption spectra formed in their reactions with a series of quinoxalin-2-one derivatives were confronted with absorption spectra formed from reactions of N3● with the same series of compounds. Cases, in which the absorption spectra formed in reactions involving N3● differ from the absorption spectra formed in the reactions involving other one-electron oxidants, strongly indicate that N3● is involved in the other reaction channel such as addition to double bonds. Moreover, it was shown that high-rate constants of reactions of N3● with quinoxalin-2-ones do not ultimately prove that they are electron transfer reactions. The optimized structures of the radical cations (7-R-3-MeQ)●+, radicals (7-R-3-MeQ)● and N3● adducts at the C2 carbon atom in pyrazine moiety and their absorption spectra are reasonably well reproduced by density functional theory quantum mechanics calculations employing the ωB97XD functional combined with the Dunning’s aug-cc-pVTZ correlation-consistent polarized basis sets augmented with diffuse functions.

scholarly journals Research on Molecular Structure and Electronic Properties of Ln3+ (Ce3+, Tb3+, Pr3+)/Li+ and Eu2+ Co-Doped Sr2Si5N8 via DFT Calculation

Molecules ◽  
2021 ◽  
Vol 26 (7) ◽  
pp. 1849
Author(s):  
Ziqian Yin ◽  
Meijuan Li ◽  
Jianwen Zhang ◽  
Qiang Shen
Keyword(s):  
Molecular Structure ◽  
Energy Level ◽  
Density Functional ◽  
Formation Energy ◽  
Electronic Band Structure ◽  
Blue Shift ◽  
Lanthanide Ions ◽  
Partial Replacement ◽  
Electronic Band ◽  
Charge Imbalance

We use density functional theory (DFT) to study the molecular structure and electronic band structure of Sr2Si5N8:Eu2+ doped with trivalent lanthanides (Ln3+ = Ce3+, Tb3+, Pr3+). Li+ was used as a charge compensator for the charge imbalance caused by the partial replacement of Sr2+ by Ln3+. The doping of Ln lanthanide atom causes the structure of Sr2Si5N8 lattice to shrink due to the smaller atomic radius of Ln3+ and Li+ compared to Sr2+. The doped structure’s formation energy indicates that the formation energy of Li+, which is used to compensate for the charge imbalance, is the lowest when the Sr2 site is doped. Thus, a suitable Li+ doping site for double-doped lanthanide ions can be provided. In Sr2Si5N8:Eu2+, the doped Ce3+ can occupy partly the site of Sr12+ ([SrN8]), while Eu2+ accounts for Sr12+ and Sr22+ ([SrN10]). When the Pr3+ ion is selected as the dopant in Sr2Si5N8:Eu2+, Pr3+ and Eu2+ would replace Sr22+ simultaneously. In this theoretical model, the replacement of Sr2+ by Tb3+ cannot exist reasonably. For the electronic structure, the energy level of Sr2Si5N8:Eu2+/Li+ doped with Ce3+ and Pr3+ appears at the bottom of the conduction band or in the forbidden band, which reduces the energy bandgap of Sr2Si5N8. We use DFT+U to adjust the lanthanide ion 4f energy level. The adjusted 4f-CBM of CeSr1LiSr1-Sr2Si5N8 is from 2.42 to 2.85 eV. The energy range of 4f-CBM in PrSr1LiSr1-Sr2Si5N8 is 2.75–2.99 eV and its peak is 2.90 eV; the addition of Ce3+ in EuSr1CeSr1LiSr1 made the 4f energy level of Eu2+ blue shift. The addition of Pr3+ in EuSr2PrSr2LiSr1 makes part of the Eu2+ 4f energy level blue shift. Eu2+ 4f energy level in EuSr2CeSr1LiSr1 is not in the forbidden band, so Eu2+ is not used as the emission center.

scholarly journals Green One-Pot Synthesis of Coumarin-Hydroxybenzohydrazide Hybrids and Their Antioxidant Potency

Antioxidants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1106
Author(s):  
Marko R. Antonijević ◽  
Dušica M. Simijonović ◽  
Edina H. Avdović ◽  
Andrija Ćirić ◽  
Zorica D. Petrović ◽  
...  
Keyword(s):  
Antioxidant Activity ◽  
Electron Transfer ◽  
Density Functional ◽  
Electron Transfer Reaction ◽  
Hydrogen Atom Transfer ◽  
Special Importance ◽  
Theory Approach ◽  
One Pot ◽  
Antioxidant Potency

Compounds from the plant world that possess antioxidant abilities are of special importance for the food and pharmaceutical industry. Coumarins are a large, widely distributed group of natural compounds, usually found in plants, often with good antioxidant capacity. The coumarin-hydroxybenzohydrazide derivatives were synthesized using a green, one-pot protocol. This procedure includes the use of an environmentally benign mixture (vinegar and ethanol) as a catalyst and solvent, as well as very easy isolation of the desired products. The obtained compounds were structurally characterized by IR and NMR spectroscopy. The purity of all compounds was determined by HPLC and by elemental microanalysis. In addition, these compounds were evaluated for their in vitro antioxidant activity. Mechanisms of antioxidative activity were theoretically investigated by the density functional theory approach and the calculated values of various thermodynamic parameters, such as bond dissociation enthalpy, proton affinity, frontier molecular orbitals, and ionization potential. In silico calculations indicated that hydrogen atom transfer and sequential proton loss–electron transfer reaction mechanisms are probable, in non-polar and polar solvents respectively. Additionally, it was found that the single-electron transfer followed by proton transfer was not an operative mechanism in either solvent. The conducted tests indicate the excellent antioxidant activity, as well as the low potential toxicity, of the investigated compounds, which makes them good candidates for potential use in food chemistry.

scholarly journals Spectroscopic evidence for direct flavin-flavin contact in a bifurcating electron transfer flavoprotein

2020 ◽  
Vol 295 (36) ◽  
pp. 12618-12634
Author(s):  
H. Diessel Duan ◽  
Nishya Mohamed-Raseek ◽  
Anne-Frances Miller
Keyword(s):  
Electron Transfer ◽  
Density Functional ◽  
Protein Denaturation ◽  
Rhodopseudomonas Palustris ◽  
Density Functional Theory Calculations ◽  
Site Directed Mutagenesis ◽  
Functional Theory ◽  
Electron Transfer Flavoprotein ◽  
Midpoint Potential ◽  
Ct Complex

A remarkable charge transfer (CT) band is described in the bifurcating electron transfer flavoprotein (Bf-ETF) from Rhodopseudomonas palustris (RpaETF). RpaETF contains two FADs that play contrasting roles in electron bifurcation. The Bf-FAD accepts electrons pairwise from NADH, directs one to a lower-reduction midpoint potential (E°) carrier, and the other to the higher-E° electron transfer FAD (ET-FAD). Previous work noted that a CT band at 726 nm formed when ET-FAD was reduced and Bf-FAD was oxidized, suggesting that both flavins participate. However, existing crystal structures place them too far apart to interact directly. We present biochemical experiments addressing this conundrum and elucidating the nature of this CT species. We observed that RpaETF missing either FAD lacked the 726 nm band. Site-directed mutagenesis near either FAD produced altered yields of the CT species, supporting involvement of both flavins. The residue substitutions did not alter the absorption maximum of the signal, ruling out contributions from residue orbitals. Instead, we propose that the residue identities modulate the population of a protein conformation that brings the ET-flavin and Bf-flavin into direct contact, explaining the 726 nm band based on a CT complex of reduced ET-FAD and oxidized Bf-FAD. This is corroborated by persistence of the 726 nm species during gentle protein denaturation and simple density functional theory calculations of flavin dimers. Although such a CT complex has been demonstrated for free flavins, this is the first observation of such, to our knowledge, in an enzyme. Thus, Bf-ETFs may optimize electron transfer efficiency by enabling direct flavin-flavin contact.

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