Graph theory-based reaction pathway searches and DFT calculations for the mechanism studies of free radical-initiated peptide sequencing mass spectrometry (FRIPS MS): a model gas-phase reaction of GGR tri-peptide

2020 ◽  
Vol 22 (9) ◽  
pp. 5057-5069 ◽  
Author(s):  
Jae-ung Lee ◽  
Yeonjoon Kim ◽  
Woo Youn Kim ◽  
Han Bin Oh
Keyword(s):  
Graph Theory ◽  
Dft Calculations ◽  
Gas Phase ◽  
Density Functional ◽  
Reaction Pathway ◽  
Peptide Sequencing ◽  
Phase Reaction ◽  
Functional Theory ◽  
Fragmentation Mechanisms ◽  
Gas Phase Fragmentation

A new approach for elucidating gas-phase fragmentation mechanisms is proposed: graph theory-based reaction pathway searches (ACE-Reaction program) and density functional theory (DFT) calculations.

EXPRESS: Hydration and Ion-Pair Formation of NaNO3(aq): A Vibrational Spectroscopic and Density Functional Theory Study

2021 ◽  
pp. 000370282098686
Author(s):  
Wolfram Rudolph ◽  
Dieter Fischer ◽  
Gert Irmer
Keyword(s):  
Dft Calculations ◽  
Gas Phase ◽  
Heavy Water ◽  
Density Functional ◽  
Plane Deformation ◽  
Deformation Mode ◽  
Solute Concentration ◽  
Small Contribution ◽  
Functional Theory ◽  
Raman Analysis

Qualitative and quantitative Raman and infrared (IR) measurements on NaNO3 solutions have been carried out over a wide concentration range (5.56 · 10-6 – 7.946 mol/L) in water and heavy water. The Raman spectra were measured from 4000 cm-1 to low wavenumbers at 45 cm-1. Band fit analysis on the profile of the 1047 cm-1 – band, ν1(a1') NO3- measured at high resolution at 0.85 cm-1 produced a small contribution at 1027 cm-1 of the isotopomer N16O218O-(aq). The effect of solute concentration on the Raman and IR bands has been systematically recorded. Extrapolation of the experimental data resulted in values for all the nitrate-bands of the “free” i.e. fully hydrated NO3-(aq). However, even in dilute solutions the vibrational symmetry of the hydrated NO3-(aq) is broken and the antisymmetric N-O stretch, which is degenerate for the isolated anion, is split by 56 cm-1. At concentrations > 2.5 mol/L direct contact between Na+ and NO3- was observed and accompanied by large band parameter changes. DFT calculations on NO3-(H2O)n (n=1-3) led to optimized geometries and vibrational frequencies which reproduced the measured ones within an accuracy of 1%. A hydrated gas phase species Na+(H2O)10NO3- was optimized resulting in the geometry and symmetry of the nitrate which is bound in an antisymmetric bidentate fashion with the nitrate possessing C1. The ν1 Na+-(OH2) breathing mode in aqueous solution appears at 189 cm-1 whereas in heavy water ν1 Na+-(OD2) is shifted to 175.6 cm-1 due to the isotope effect. DFT calculations on hydrated Na+(OH2)n gas phase clusters provided realistic Na+-hydrate structures with n = 4 and 5 which resembled the measured frequency of ν1 Na+-OH2 mode quite well. Quantitative Raman analysis employing the symmetric stretching band, ν1(a1') NO3-, has been carried out down to concentrations as low as 5.56 · 10-6 mol/L. The in-plane deformation mode ν4(e') in the Raman scattering at higher concentrations has been used as an indicator band for detecting directly coordinated NO3-.

Gas-phase COS activation by U+: Reaction mechanisms and bonding analysis

2017 ◽  
Vol 16 (02) ◽  
pp. 1750010
Author(s):  
Lidan Zhang ◽  
Jiguang Du ◽  
Gang Jiang
Keyword(s):  
Gas Phase ◽  
Reaction Mechanisms ◽  
Density Functional ◽  
Main Product ◽  
Natural Bond Orbital ◽  
Experimental Result ◽  
Phase Reaction ◽  
Functional Theory ◽  
Energy Profiles ◽  
Bonding Properties

Density functional theory (DFT) calculations were used to investigate the gas phase reaction of U[Formula: see text] with COS to produce US[Formula: see text]CO and UO[Formula: see text]CS. It is shown that the two reactions are exothermic and the formation of UO[Formula: see text]CS has the lower energy barrier which agrees with the experimental result that UO[Formula: see text] is the main product. The reaction mechanisms and the potential energy profiles (CPEPs) considering different spin states were presented in detail. Diverse analyses including atoms in molecules, natural bond orbital were used to study the bonding properties of all the involved species.

Adsorption Forms of Water Molecules on Gas-Phase Platinum Clusters Pt3+ Studied by Vibrational Photodissociation Spectroscopy

2019 ◽  
Vol 233 (6) ◽  
pp. 881-894 ◽  
Author(s):  
Fumitaka Mafuné ◽  
Manami Abe ◽  
Satoshi Kudoh
Keyword(s):  
Density Functional Theory ◽  
Dft Calculations ◽  
Gas Phase ◽  
Vibrational Spectra ◽  
Density Functional ◽  
Molecular Form ◽  
Vibrational Excitation ◽  
Water Molecules ◽  
Functional Theory ◽  
Platinum Clusters

Abstract The vibrational spectra of Pt3(H2O)m+ (m = 1–4) cluster were measured in the 3000–3800 cm−1 range via infrared photodissociation (IRPD) spectroscopy. The IRPD spectra were recorded through the photodissociation of Pt3(H2O)m+-Ar (m = 1–3) complexes and Pt3(H2O)4+ cations upon vibrational excitation. The spectra were compared to the vibrational spectra of several stable isomers obtained by density functional theory (DFT) calculations and the adsorption forms of the water molecules were subsequently discussed. The IRPD spectra of all the studied Pt3(H2O)m+ cations exhibited intense peaks at ∼3600 and 3700 cm−1. This suggested that the water molecules mainly adsorb onto the Pt clusters in molecular form and that each molecule binds directly to a Pt atom via its O atom side. For the water-rich Pt3(H2O)4+ cations, all four water molecules were directly bound to the Pt atoms; however, according to the DFT calculations, the fourth H2O molecule could bind to a first-layer water molecule through hydrogen bonding.

A theoretical study of the nitration of eugenol with the nitronium ion

2011 ◽  
Vol 76 (12) ◽  
pp. 1529-1548
Author(s):  
Ricardo Ugarte ◽  
Guillermo Salgado ◽  
Luis Basáez
Keyword(s):  
Carbon Atom ◽  
Gas Phase ◽  
Density Functional ◽  
Molecular Electrostatic Potential ◽  
Reaction Pathway ◽  
Minimum Energy ◽  
Stationary Points ◽  
Functional Theory ◽  
Π Complex ◽  
Ring Carbon Atom

The nitration of eugenol was investigated by using density functional theory (DFT) calculations. Potential energy surface and molecular electrostatic potential of eugenol was constructed in order to find, respectively, the minimum energy conformers and the possible sites for electrophilic attack. Stationary points were located and characterized at the B3LYP/6-311++G(2d,2p) level of theory. A strongly bound π-complex was found, in which the distance between the nitrogen atom of the NO2 moiety and the C1 carbon atom of the aromatic ring is 2.15 Å in the gas phase and 2.06 Å in dichloromethane. The most favorable σ-complex or Wheland intermediate is the result from the interaction between the nitrogen and the C6 ring carbon atom. The transition state that connects both complexes is more resembling the σ-complex. The nitronium ion exothermically reacts with eugenol to give the π-complex without an energy barrier. The next stage of the reaction pathway, π-complex → σ-complex, is endothermic and involves a Gibbs energy of activation of 7.9–8.0 kcal mol–1 (gas phase) and 8.3–8.9 kcal mol–1 (CH2Cl2).

Intrinsic Stacking Interactions of Natural and Artificial Nucleobases

2019 ◽  
Author(s):  
Drew P. Harding ◽  
Laura J. Kingsley ◽  
Glen Spraggon ◽  
Steven Wheeler
Keyword(s):  
Gas Phase ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Molecular Descriptors ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Functional Theory ◽  
Binding Partner ◽  
Heavy Atoms ◽  
Wide Range

The intrinsic (gas-phase) stacking energies of natural and artificial nucleobases were explored using density functional theory (DFT) and correlated ab initio methods. Ranking the stacking strength of natural nucleobase dimers revealed a preference in binding partner similar to that seen from experiments, namely G > C > A > T > U. Decomposition of these interaction energies using symmetry-adapted perturbation theory (SAPT) showed that these dispersion dominated interactions are modulated by electrostatics. Artificial nucleobases showed a similar stacking preference for natural nucleobases and were also modulated by electrostatic interactions. A robust predictive multivariate model was developed that quantitively predicts the maximum stacking interaction between natural and a wide range of artificial nucleobases using molecular descriptors based on computed electrostatic potentials (ESPs) and the number of heavy atoms. This model should find utility in designing artificial nucleobase analogs that exhibit stacking interactions comparable to those of natural nucleobases. Further analysis of the descriptors in this model unveil the origin of superior stacking abilities of certain nucleobases, including cytosine and guanine.

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