Elucidation of Fragmentation Mechanisms of Protonated Peptide Ions and Their Products:  A Case Study on Glycylglycylglycine Using Density Functional Theory and Threshold Collision-Induced Dissociation

2003 ◽  
Vol 125 (30) ◽  
pp. 9229-9236 ◽  
Author(s):  
Houssain El Aribi ◽  
Christopher F. Rodriquez ◽  
David R. P. Almeida ◽  
Yun Ling ◽  
William W.-N. Mak ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Protonated Peptide ◽  
Collision Induced Dissociation ◽  
Peptide Ions ◽  
Functional Theory ◽  
Fragmentation Mechanisms

Understanding collision-induced dissociation of dofetilide: a case study in the application of density functional theory as an aid to mass spectral interpretation

The Analyst ◽  
2013 ◽  
Vol 138 (22) ◽  
pp. 6869 ◽  
Author(s):  
Patricia Wright ◽  
Alexander Alex ◽  
Sophie Harvey ◽  
Teresa Parsons ◽  
Frank Pullen
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Collision Induced Dissociation ◽  
Functional Theory ◽  
Mass Spectral ◽  
Spectral Interpretation

scholarly journals Formation and reactions of the 1, 8-naphthyridine (napy) ligated geminally dimetallated phenyl complexes [(napy)Cu2(Ph)]+, [(napy)Ag2(Ph)]+ and [(napy)CuAg(Ph)]+

2019 ◽  
Vol 25 (1) ◽  
pp. 30-43 ◽  
Author(s):  
Qiuyan Jin ◽  
Jiaye Li ◽  
Alireza Ariafard ◽  
Allan J Canty ◽  
Richard AJ O’Hair
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Ion Trap ◽  
Density Functional Theory Calculations ◽  
Collision Induced Dissociation ◽  
Ion Trap Mass Spectrometry ◽  
Functional Theory ◽  
Organometallic Cations ◽  
Gas Phase Ion

Gas-phase ion trap mass spectrometry experiments and density functional theory calculations have been used to examine the routes to the formation of the 1,8-naphthyridine (napy) ligated geminally dimetallated phenyl complexes [(napy)Cu2(Ph)]+, [(napy)Ag2(Ph)]+ and [(napy)CuAg(Ph)]+ via extrusion of CO2 or SO2 under collision-induced dissociation conditions from their corresponding precursor complexes [(napy)Cu2(O2CPh)]+, [(napy)Ag2(O2CPh)]+, [(napy)CuAg(O2CPh)]+ and [(napy)Cu2(O2SPh)]+, [(napy)Ag2(O2SPh)]+, [(napy)CuAg(O2SPh)]+. Desulfination was found to be more facile than decarboxylation. Density functional theory calculations reveal that extrusion proceeds via two transition states: TS1 enables isomerization of the O, O-bridged benzoate to its O-bound form; TS2 involves extrusion of CO2 or SO2 with the concomitant formation of the organometallic cation and has the highest barrier. Of all the organometallic cations, only [(napy)Cu2(Ph)]+ reacts with water via hydrolysis to give [(napy)Cu2(OH)]+, consistent with density functional theory calculations which show that hydrolysis proceeds via the initial formation of the adduct [(napy)Cu2(Ph)(H2O)]+ which then proceeds via TS3 in which the coordinated H2O is deprotonated by the coordinated phenyl anion to give the product complex [(napy)Cu2(OH)(C6H6)]+, which then loses benzene.

scholarly journals Integrating Density Functional Theory Modeling with Experimental Data to Understand and Predict Sorption Reactions: Exchange of Salicylate for Phosphate on Goethite

Soil Systems ◽  
2020 ◽  
Vol 4 (2) ◽  
pp. 27 ◽  
Author(s):  
James D. Kubicki ◽  
Tsutomu Ohno
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Mineral Water ◽  
Surface Complexes ◽  
Functional Theory ◽  
Complex Models ◽  
Mechanical Approach ◽  
Plant Exudates ◽  
Quantum Mechanical Approach

Density functional theory (DFT) calculations are a quantum mechanical approach that can be used to model chemical reactions on an atomistic scale. DFT provides predictions on structures, thermodynamics, spectroscopic parameters and kinetics that can be compared against experimentally determined data. This paper is a primer on the basics of utilizing DFT for applications in mineral-water interfaces. In our case-study, we use DFT to model the surface complexes of phosphate and salicylate adsorbed onto the (101) and (210) surfaces of α-FeOOH (goethite), as an example of combining DFT and experiment. These three components are important in the phosphorus-organic matter interactions in soils, and by comparing the energies of the two surface complexes, the exchange energy of salicylate for phosphate onto goethite can be estimated. The structures of the surface complexes are predicted and the resulting vibrational frequencies calculated based on these structures are compared to previous observations. Upon verification of reasonable surface complex models, the potential energy of exchanging salicylate for phosphate is calculated and shown to be significantly exothermic. This model result is consistent with observations of plant exudates, such as salicylate freeing adsorbed phosphate in soils under P-limited conditions.

The one-electron self-interaction error in 74 density functional approximations: a case study on hydrogenic mono- and dinuclear systems

2020 ◽  
Vol 22 (28) ◽  
pp. 15805-15830 ◽  
Author(s):  
Dale R. Lonsdale ◽  
Lars Goerigk
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Model Systems ◽  
Electron Model ◽  
Functional Theory ◽  
The One

The one-electron self-interaction error (SIE) is analysed for 74 Density Functional Theory (DFT) approximations in a series of novel one-electron model systems revealing new aspects of the SIE that should be considered in future DFT developments.

The role of exchange–correlation functional on the description of multiferroic properties using density functional theory: the ATiO3 (A = Mn, Fe, Ni) case study

RSC Advances ◽  
2016 ◽  
Vol 6 (103) ◽  
pp. 101216-101225 ◽  
Author(s):  
Renan Augusto Pontes Ribeiro ◽  
Sergio Ricardo de Lazaro ◽  
Carlo Gatti
Keyword(s):  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Multiferroic Properties ◽  
Exchange Correlation

In this study, ab initio density functional theory calculations were performed on ATiO3 (A = Mn, Fe, Ni) materials for multiferroic applications.

scholarly journals Climbing Jacob’s ladder: A density functional theory case study for Ag2ZnSnSe4 and Cu2ZnSnSe4

2020 ◽  
Vol 3 (1) ◽  
pp. 015002
Author(s):  
Daniel Fritsch ◽  
Susan Schorr
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Functional Theory ◽  
Jacob's Ladder

scholarly journals Application of Density Functional Theory in Coordination Chemistry: A Case Study of Group 13 Monohalide as a Ligand

2021 ◽  
Author(s):  
Thayalaraj Christopher Jeyakumar ◽  
Francisxavier Paularokiadoss
Keyword(s):  
Density Functional Theory ◽  
Coordination Chemistry ◽  
Density Functional ◽  
Experimental Studies ◽  
Theoretical Studies ◽  
Dft Methods ◽  
Functional Theory ◽  
Group 13 ◽  
Metal Bonding

The chemistry of Group 13 Monohalide is of great interest due to its isoelectronic relationship with carbon monoxide and dinitrogen. In recent years, theoretical and experimental studies have been evolved on the group-13 atom-based diatomic molecules as a ligand. The synthetic, characterisation and reactivity of various metal complexes have been well discussed in recent reviews. The nature of the metal bonding of these ligands of various types has been explained in addition by the variety of theoretical studies (using DFT methods) such as FMO and EDA. This chapter has a comprehensive experimental and theoretical study of group 13 monohalides as a ligand in coordination chemistry.

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