scholarly journals Experimental and theoretical investigations of infrared multiple photon dissociation spectra of lysine complexes with Zn2+ and Cd2+

2018 ◽  
Vol 25 (1) ◽  
pp. 97-111 ◽  
Author(s):  
Cameron J Owen ◽  
Georgia C Boles ◽  
Giel Berden ◽  
Jos Oomens ◽  
PB Armentrout
Keyword(s):  
Amino Acid ◽  
Gas Phase ◽  
Single Point ◽  
Basis Sets ◽  
Side Chain ◽  
Amine Group ◽  
Linear Absorption ◽  
Action Spectra ◽  
Phase Structures ◽  
Infrared Multiple Photon Dissociation

The gas-phase structures of zinc and cadmium complexes of lysine (Lys) are investigated via a combination of infrared multiple photon dissociation action spectroscopy and ab initio quantum chemical calculations. In order to unambiguously identify the experimentally observed species, [Zn(Lys−H)]+ and CdCl+(Lys), the action spectra were compared to linear absorption spectra calculated at the B3LYP level of theory, using 6-311+G(d,p) and def2-TVZP basis sets for the zinc and cadmium systems, respectively. Single point energies were also calculated at the B3LYP, B3P86, MP2, and B3LYP-GD3BJ (accounting for empirical dispersion) levels of theory using larger basis sets. Identification of the experimentally formed isomers is possible through good agreement between infrared multiple photon dissociation action spectra and the theoretically predicted spectra. The [Zn(Lys−H)]+ complex adopts a tridentate orientation involving the amino acid backbone amine and deprotonated carboxylic acid groups as well as the side-chain amine group, [Nα,CO−,Nɛ]. The CdCl+(Lys) complex similarly adopts a tridentate chelation involving the amino acid backbone amine and carbonyl groups, as well as the side-chain amine group, [Nα,CO,Nɛ]. In both cases, the identified complexes are the lowest energy gas-phase structures at all levels of theory.

Assessing the impact of anion–π effects on phenylalanine ion structures using IRMPD spectroscopy

2014 ◽  
Vol 16 (44) ◽  
pp. 24223-24234 ◽  
Author(s):  
Michael Burt ◽  
Kathleen Wilson ◽  
Rick Marta ◽  
Moaraj Hasan ◽  
W. Scott Hopkins ◽  
...  
Keyword(s):  
Gas Phase ◽  
Irmpd Spectroscopy ◽  
Phase Structures ◽  
Infrared Multiple Photon Dissociation ◽  
Fluorinated Derivatives ◽  
The Impact

The gas-phase structures of two halide-bound phenylalanine anions (PheX−, X = Cl− or Br−) and five fluorinated derivatives have been identified using infrared multiple photon dissociation (IRMPD) spectroscopy.

scholarly journals Binding motifs of cisplatin interaction with simple biomolecules and aminoacid targets probed by IR ion spectroscopy

2020 ◽  
Vol 92 (1) ◽  
pp. 3-13 ◽  
Author(s):  
Davide Corinti ◽  
Roberto Paciotti ◽  
Nazzareno Re ◽  
Cecilia Coletti ◽  
Barbara Chiavarino ◽  
...  
Keyword(s):  
Biological Activity ◽  
Amino Acid ◽  
Gas Phase ◽  
Quantum Chemical ◽  
Ligand Substitution ◽  
Side Chain ◽  
Binding Motifs ◽  
Distinctive Features ◽  
Ion Spectroscopy ◽  
Vibrational Action

AbstractThe primary intermediates resulting from the interaction of cisplatin, cis-(PtCl2(NH3)2], most widespread antitumor drug, with biomolecular targets are characterized. Electrospray ionization is used to deliver ions formed in solution into the gas phase where they are structurally interrogated by vibrational “action” spectroscopy in conjunction with quantum chemical calculations. The aquation products, cis-[PtX(NH3)2(H2O)]+ (X = Cl, OH), lying along the path responsible for biological activity, are shown to display distinctive features responding to ligation pattern and optimized geometry. The IR spectra of trans-[PtX(NH3)2(H2O)]+ are different, testifying that cis and trans complexes are stable, non interconverting species both in solution and in the gas phase. Ligand substitution by simple nucleophiles (L = pyridine, 4(5)-methylimidazole, thioanisole, trimethylphosphate, acetamide, dimethylacetamide, urea and thiourea) yields cis-[PtCl(NH3)2(L)]+ complexes displaying remarkable regioselectivity whenever L presents multiple candidate platination sites. The incipient formation of cisplatin-derived complexes with the recognized biological amino acid targets L-histidine (His) and L-methionine (Met) has been investigated revealing the primary platination event to be mainly directed at the Nπ atom of the imidazole side chain of His and to the thiomethyl sulfur of Met. The isomer and conformer population of the ensuing cis-[PtCl(NH3)2(Met/His)]+ complexes, sampled in the gas phase, can be ascertained by photofragmentation kinetics on isomer/conformer specific resonances.

Infrared Multiple Photon Dissociation Action Spectroscopy of Protonated Unsymmetrical Dimethylhydrazine and Proton-bound Dimers of Hydrazine and Unsymmetrical Dimethylhydrazine

2021 ◽  
Author(s):  
Christopher P. McNary ◽  
Maria Demireva ◽  
Jonathan Martens ◽  
Giel Berden ◽  
Jos Oomens ◽  
...  
Keyword(s):  
Gas Phase ◽  
Action Spectroscopy ◽  
Phase Structures ◽  
Unsymmetrical Dimethylhydrazine ◽  
Infrared Multiple Photon Dissociation

The gas-phase structures of protonated unsymmetrical 1,1-dimethylhydrazine (UDMH) and the proton-bound dimers of UDMH and hydrazine are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy utilizing light generated by...

Competition between salt bridge and non-zwitterionic structures in deprotonated amino acid dimers

2018 ◽  
Vol 20 (23) ◽  
pp. 15641-15652 ◽  
Author(s):  
Sven Heiles ◽  
Giel Berden ◽  
Jos Oomens ◽  
Evan R. Williams
Keyword(s):  
Amino Acid ◽  
Functional Groups ◽  
Salt Bridge ◽  
Side Chain ◽  
Infrared Multiple Photon Dissociation ◽  
Bridge Structures

The effect of side chain functional groups on salt bridge structures in deprotonated amino acid homodimers is investigated using both infrared multiple photon dissociation spectroscopy between 650 and 1850 cm−1 and theory.

Serine O-sulfation probed by IRMPD spectroscopy

2015 ◽  
Vol 17 (39) ◽  
pp. 25891-25904 ◽  
Author(s):  
Roberto Paciotti ◽  
Cecilia Coletti ◽  
Nazzareno Re ◽  
Debora Scuderi ◽  
Barbara Chiavarino ◽  
...  
Keyword(s):  
Gas Phase ◽  
Irmpd Spectroscopy ◽  
Phase Structures ◽  
Infrared Multiple Photon Dissociation

The gas phase structures of (de)protonatedO-sulfoserine ions have been revealed by infrared multiple photon dissociation (IRMPD) spectroscopy and computations.

scholarly journals Side-chain effects on the structures of protonated amino acid dimers: A gas-phase infrared spectroscopy study

2018 ◽  
Vol 429 ◽  
pp. 115-120 ◽  
Author(s):  
Jongcheol Seo ◽  
Waldemar Hoffmann ◽  
Sebastian Malerz ◽  
Stephan Warnke ◽  
Michael T. Bowers ◽  
...  
Keyword(s):  
Infrared Spectroscopy ◽  
Amino Acid ◽  
Gas Phase ◽  
Side Chain ◽  
Spectroscopy Study ◽  
Protonated Amino Acid

Polypeptides Folding: Rules for the Calculation of the Backbone Dihedral Angles φ starting from the Amino Acid Sequence

2020 ◽  
Author(s):  
Michele Larocca
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Theoretical Approach ◽  
Polypeptide Chain ◽  
Hydrophobic Effect ◽  
Side Chain ◽  
Dihedral Angles ◽  
Mechanical Forces ◽  
Specific Chemical

<p>Protein folding is strictly related to the determination of the backbone dihedral angles and depends on the information contained in the amino acid sequence as well as on the hydrophobic effect. To date, the type of information embedded in the amino acid sequence has not yet been revealed. The present study deals with these problematics and aims to furnish a possible explanation of the information contained in the amino acid sequence, showing and reporting rules to calculate the backbone dihedral angles φ. The study is based on the development of mechanical forces once specific chemical interactions are established among the side chain of the residues in a polypeptide chain. It aims to furnish a theoretical approach to predict backbone dihedral angles which, in the future, may be applied to computational developments focused on the prediction of polypeptide structures.</p>

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