Characterization of acetylated histidine b1-ion structure: A competition between oxazolone and side chain imidazole moiety

2018 ◽  
Vol 24 (3) ◽  
pp. 261-268 ◽  
Author(s):  
Kranthikumar Yadav ◽  
J Laxmikanth Rao ◽  
R Srinivas ◽  
R Nagaraj ◽  
MV Jagannadham
Keyword(s):  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Mass Spectrometric Study ◽  
Research Area ◽  
Side Chain ◽  
Oxazolone Structure ◽  
Post Translational Modifications ◽  
Tandem Mass Spectrometric ◽  
Oxazolone Ring

The detection of post-translational modifications of proteins is an important comprehensive research area. Over the years, proteomic studies involving protein acetylation have attracted a great deal of attention. In the present study, we have focussed on the acetylation of histidine and the intrinsic stability of b1-ion of oxazolone ring and/or with side chain imidazole bicyclic product. The formation of oxazolone structure may occur when an amino moiety undergoes acetylation reaction and when it is present in the vicinity of the side chain imidazole moiety. Tryptic peptides generated from the proteins of Acenitobacter radioresistens MMC5-containing N-terminal histidine were explored in a standard proteomic workflow. Formation of [Formula: see text] ion with an oxazolone ring in these peptides has been supported by a tandem mass spectrometric study of a synthetic peptide and density functional theory calculations. The results obtained from this study have implications in understanding the fragmentation of the peptides generated in the proteomic workflows.

P—N Bond Length Alterations Monitored by Infrared Absorption and Fourier Transform Raman Spectroscopy in Combination with Density Functional Theory Calculations

2003 ◽  
Vol 57 (8) ◽  
pp. 970-976 ◽  
Author(s):  
M. Bolboaca ◽  
T. Stey ◽  
A. Murso ◽  
D. Stalke ◽  
W. Kiefer
Keyword(s):  
Density Functional Theory ◽  
Fourier Transform ◽  
Density Functional ◽  
Structural Parameters ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Fourier Transform Raman Spectroscopy ◽  
Raman And Infrared Spectroscopy ◽  
Fourier Transform Raman

Fourier transform (FT) Raman and infrared spectroscopy in combination with density functional theory calculations have been applied to the vibrational characterization of the dimeric zinc diphenylphosphanyl(trimethylsilyl)amide complex [(Me3Si)2NZnPh2PNSiMe3]2 and the ortho-metallated species [Li( o-C6H4PPh2NSiMe3)]2·Et2O in relation to their parent starting materials diphenylphosphanyl (trimethylsilyl)amine Ph2P–N(H)SiMe3 and iminophosphorane Ph3P=NSiMe3. The spectroscopic changes evidenced in the spectra were correlated with the structural parameters in order to provide insight as to what extent the P–N bond is affected by the coordination to the metal center. The employment of density functional theory (DFT) calculations in addition to these spectroscopic methods offers the possibility of predicting whether the Lewis-basic imido nitrogen atom is involved in coordination not only in the solid state, but also in the gas phase.

scholarly journals Natural selection based on coordination chemistry: computational assessment of [4Fe–4S]-maquettes with non-coded amino acids

2019 ◽  
Vol 9 (6) ◽  
pp. 20190071 ◽  
Author(s):  
Robert K. Szilagyi ◽  
Rebecca Hanscam ◽  
Eric M. Shepard ◽  
Shawn E. McGlynn
Keyword(s):  
Coordination Chemistry ◽  
Natural Selection ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Theoretical Work ◽  
Testable Hypothesis ◽  
Side Chain ◽  
Regulatory Processes ◽  
Secondary Structure Analysis ◽  
Dynamics Simulations

Cysteine is the only coded amino acid in biology that contains a thiol functional group. Deprotonated thiolate is essential for anchoring iron–sulfur ([Fe–S]) clusters, as prosthetic groups to the protein matrix. [Fe–S] metalloproteins and metalloenzymes are involved in biological electron transfer, radical chemistry, small molecule activation and signalling. These are key metabolic and regulatory processes that would likely have been present in the earliest organisms. In the context of emergence of life theories, the selection and evolution of the cysteine-specific R–CH 2 –SH side chain is a fascinating question to confront. We undertook a computational [4Fe–4S]-maquette modelling approach to evaluate how side chain length can influence [Fe–S] cluster binding and stability in short 7-mer and long 16-mer peptides, which contained either thioglycine, cysteine or homocysteine. Force field-based molecular dynamics simulations for [4Fe–4S] cluster nest formation were supplemented with density functional theory calculations of a ligand-exchange reaction between a preassembled cluster and the peptide. Secondary structure analysis revealed that peptides with cysteine are found with greater frequency nested to bind preformed [4Fe–4S] clusters. Additionally, the presence of the single methylene group in cysteine ligands mitigates the steric bulk, maintains the H-bonding and dipole network, and provides covalent Fe–S(thiolate) bonds that together create the optimal electronic and geometric structural conditions for [4Fe–4S] cluster binding compared to thioglycine or homocysteine ligands. Our theoretical work forms an experimentally testable hypothesis of the natural selection of cysteine through coordination chemistry.

scholarly journals A theoretical investigation on the isomerism and the NMR properties of thiosemicarbazones

2007 ◽  
Vol 5 (2) ◽  
pp. 396-419 ◽  
Author(s):  
N. Nuwan De Silva ◽  
Titus Albu
Keyword(s):  
Density Functional ◽  
Chemical Shifts ◽  
Intermolecular Hydrogen Bond ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
1H And 13C Nmr ◽  
Nmr Characterization ◽  
Hybrid Density Functional ◽  
Nmr Properties

AbstractHybrid density functional theory calculations at the mPW1PW91/6-31+G(d,p) level of theory have been used to investigate the optimized structures and other molecular properties of five different series of thiosemicarbazones. The investigated compounds were obtained from acenaphthenequinone, isatin and its derivatives, and alloxan. The focus of the study is the isomerism and the NMR characterization of these thiosemicarbazones. It was found that only one isomer is expected for thiosemicarbazones and methylthiosemicarbazones, while for dimethylthiosemicarbazones, two isomers are possible. All investigated thiosemicarbazones exhibit a hydrazinic proton that is highly deshielded and resonates far downfield in the proton NMR spectra. This proton is a part of a characteristic sixmembered ring, and its NMR properties are a result of its strong, intermolecular hydrogen bond. The relationships between the calculated 1H and 13C NMR chemical shifts and various geometric parameters are reported.

Formation and Direct Detection of Non-Conjugated Triplet 1,2-Biradical from β,γ-Vinylarylketone

2015 ◽  
Vol 68 (11) ◽  
pp. 1707 ◽  
Author(s):  
H. Dushanee M. Sriyarathne ◽  
Kosala R. S. Thenna-Hewa ◽  
Tianeka Scott ◽  
Anna D. Gudmundsdottir
Keyword(s):  
Rate Constant ◽  
Density Functional ◽  
Flash Photolysis ◽  
Laser Flash Photolysis ◽  
Direct Detection ◽  
Density Functional Theory Calculations ◽  
Laser Flash ◽  
Triplet Excited State ◽  
Functional Theory

Laser flash photolysis of 2-methyl-1-phenylbut-3-en-1-one (1) conducted at irradiation wavelengths of 266 and 308 nm results in the formation of triplet 1,2-biradical 2 that has λmax at 370 and 480 nm. Biradical 2 is formed with a rate constant of 1.1 × 107 s–1 and decays with a rate constant of 2.3 × 105 s–1. Isoprene-quenching studies support the notion that biradical 2 is formed by energy transfer from the triplet-excited state of the ketone chromophore of 1. Density functional theory calculations were used to verify the characterization of triplet biradical 2 and validate the mechanism for its formation. Thus, it has been demonstrated that intramolecular sensitization of simple alkenes can be used to form triplet 1,2-biradicals with the two radical centres localized on the adjacent carbon atoms.

scholarly journals Bottom-up Fabrication and Atomic-scale Characterization of Triply-linked, Laterally π-Extended Porphyrin Nanotapes

2021 ◽  
Author(s):  
Qiang Sun ◽  
Luis M. Mateos ◽  
Roberto Robles ◽  
Nicolas Lorente ◽  
Pascal Ruffieux ◽  
...  
Keyword(s):  
Electronic Properties ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Molecular Wires ◽  
Atomic Scale ◽  
Functional Theory ◽  
Structural And Electronic Properties ◽  
Scale Characterization ◽  
Low Solubility

<p>Porphyrin nanotapes (Por NTs) have attracted vast interest as potential molecular wires thanks to their exceptional electronic properties. Recently, Por NTs have been synthesized by solution-based methods, demonstrating high versatility and great potential for technological applications. However, their synthesis is tedious and their characterization limited by low solubility and stability. Here, we report the first example of meso-meso triply-fused Por NTs, which are prepared from a readily available Por precursor through a two-step synthesis on Au(111). The structural and electronic properties of individual Por NTs are addressed, both on Au(111) and on a thin insulating NaCl layer, by high-resolution scanning probe microscopy/spectroscopy complemented by density functional theory calculations.<br></p>

scholarly journals Cage effects control the mechanism of methane hydroxylation in zeolites

Science ◽  
2021 ◽  
Vol 373 (6552) ◽  
pp. 327-331
Author(s):  
Benjamin E. R. Snyder ◽  
Max L. Bols ◽  
Hannah M. Rhoda ◽  
Dieter Plessers ◽  
Robert A. Schoonheydt ◽  
...  
Keyword(s):  
Active Sites ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Spectroscopic Characterization ◽  
Single Turnover ◽  
Small Pore ◽  
Conversion Of Methane ◽  
Hindered Diffusion ◽  
Cage Effects

Catalytic conversion of methane to methanol remains an economically tantalizing but fundamentally challenging goal. Current technologies based on zeolites deactivate too rapidly for practical application. We found that similar active sites hosted in different zeolite lattices can exhibit markedly different reactivity with methane, depending on the size of the zeolite pore apertures. Whereas zeolite with large pore apertures deactivates completely after a single turnover, 40% of active sites in zeolite with small pore apertures are regenerated, enabling a catalytic cycle. Detailed spectroscopic characterization of reaction intermediates and density functional theory calculations show that hindered diffusion through small pore apertures disfavors premature release of CH3 radicals from the active site after C-H activation, thereby promoting radical recombination to form methanol rather than deactivated Fe-OCH3 centers elsewhere in the lattice.

scholarly journals Structural characterization of a non-heme iron active site in zeolites that hydroxylates methane

2018 ◽  
Vol 115 (18) ◽  
pp. 4565-4570 ◽  
Author(s):  
Benjamin E. R. Snyder ◽  
Lars H. Böttger ◽  
Max L. Bols ◽  
James J. Yan ◽  
Hannah M. Rhoda ◽  
...  
Keyword(s):  
Active Site ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Heme Iron ◽  
Zeolite Lattice ◽  
Non Heme Iron ◽  
Bonding Interaction ◽  
Lattice Density ◽  
X Ray Absorption

Iron-containing zeolites exhibit unprecedented reactivity in the low-temperature hydroxylation of methane to form methanol. Reactivity occurs at a mononuclear ferrous active site, α-Fe(II), that is activated by N2O to form the reactive intermediate α-O. This has been defined as an Fe(IV)=O species. Using nuclear resonance vibrational spectroscopy coupled to X-ray absorption spectroscopy, we probe the bonding interaction between the iron center, its zeolite lattice-derived ligands, and the reactive oxygen. α-O is found to contain an unusually strong Fe(IV)=O bond resulting from a constrained coordination geometry enforced by the zeolite lattice. Density functional theory calculations clarify how the experimentally determined geometric structure of the active site leads to an electronic structure that is highly activated to perform H-atom abstraction.

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