scholarly journals Decarboxylation versus Acetonitrile Loss in Silver Acetate and Silver Propiolate Complexes, [RCO2Ag2(CH3CN)n]+ (where R = CH3 and CH3C≡C; n = 1 and 2)

2015 ◽  
Vol 68 (9) ◽  
pp. 1385 ◽  
Author(s):  
Jiawei Li ◽  
George N. Khairallah ◽  
Richard A. J. O'Hair
Keyword(s):  
Dft Calculations ◽  
Gas Phase ◽  
Density Functional ◽  
Ion Trap ◽  
Fragmentation Pathway ◽  
Binding Energies ◽  
Silver Acetate ◽  
Bond Forming ◽  
Fragmentation Reactions ◽  
A Minor

Gas-phase experiments using collision-induced dissociation in an ion trap mass spectrometer have been used in combination with density functional theory (DFT) calculations (at the B3LYP/SDD6–31+G(d) level of theory) to examine the competition between decarboxylation and loss of a coordinated acetonitrile in the unimolecular fragmentation reactions of the silver acetate and silver propiolate complexes, [RCO2Ag2(CH3CN)n]+ (where R = CH3 and CH3C≡C; n = 1 and 2), introduced into the gas-phase via electrospray ionisation. When R = CH3, loss of acetonitrile is the sole reaction channel observed for both complexes (n = 1 and 2), consistent with DFT calculations, which highlight that the barriers for decarboxylation 2.18 eV (n = 2) and 1.96 eV (n = 1) are greater than the binding energies of the coordinated acetonitriles (1.60 eV for n = 2; 1.64 eV for n = 1). In contrast, when R = CH3C≡C, decarboxylation is the main fragmentation pathway observed for both complexes (n = 1 and 2), with loss of acetonitrile only being a minor product channel. This is consistent with DFT calculations, which reveal that the barriers for decarboxylation are 1.17 eV (n = 2) and 1.16 eV (n = 1), which are both below the binding energies of the coordinated acetonitriles (1.55 eV for n = 2; 1.56 eV for n = 1). The barrier for decarboxylation of [CH3C≡CCO2Ag2]+ is 1.22 eV, which is less than the 2.06 eV reported for decarboxylation of [CH3CO2Ag2]+ (Al Sharif et al. Organometallics, 2013, 32, 5416). The observed ease of decarboxylation of silver propiolate complexes in the gas-phase is consistent with the recently reported use of silver salts in metal catalysed decarboxylative C–C and C–X bond forming reactions of propiolic acids.

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.

Conformational polymorphism in a Schiff-base macrocyclic organic ligand: an experimental and theoretical study

2010 ◽  
Vol 66 (5) ◽  
pp. 527-543 ◽  
Author(s):  
Leonardo Lo Presti ◽  
Raffaella Soave ◽  
Mariangela Longhi ◽  
Emanuele Ortoleva
Keyword(s):  
Schiff Base ◽  
Solid State ◽  
Dft Calculations ◽  
Gas Phase ◽  
Phase Ii ◽  
Density Functional ◽  
Organic Ligand ◽  
Stable Phase ◽  
Stable Form ◽  
Molecular Conformations

Polymorphism in the highly flexible organic Schiff-base macrocycle ligand 3,6,9,17,20,23-hexa-azapentacyclo(23.3.1.111,15.02,6.016,20)triaconta-1(29),9,11,13,15(30),23,25,27-octaene (DIEN, C24H30N6) has been studied by single-crystal X-ray diffraction and both solid-state and gas-phase density functional theory (DFT) calculations. In the literature, only solvated structures of the title compound are known. Two new polymorphs and a new solvated form of DIEN, all obtained from the same solvent with different crystallization conditions, are presented for the first time. They all have P\bar 1 symmetry, with the macrocycle positioned on inversion centres. The two unsolvated polymorphic forms differ in the number of molecules in the asymmetric unit Z′, density and cohesive energy. Theoretical results confirm that the most stable form is (II°), with Z′ = 1.5. Two distinct molecular conformations have been found, named `endo' or `exo' according to the orientation of the imine N atoms, which can be directed towards the interior or the exterior of the macrocycle. The endo arrangement is ubiquitous in the solid state and is shared by two independent molecules which constitute an invariant supramolecular synthon in all the known crystal forms of DIEN. It is also the most stable arrangement in the gas phase. The exo form, on the other hand, appears only in phase (II°), which contains both the conformers. Similarities and differences among the occurring packing motifs, as well as solvent effects, are discussed with the aid of Hirshfeld surface fingerprint plots and correlated to the results of the energy analysis. A possible interconversion path in the gas phase between the endo and the exo conformers has been found by DFT calculations; it consists of a two-step mechanism with activation energies of the order of 30–40 kJ mol−1. These findings have been related to the empirical evidence that the most stable phase (II°) is also the last appearing one, in accordance with Ostwald's rule.

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.

Charge transfer complexes between 2-, 3- and 4-aminopyridines and some π-acceptors in the gas phase and in chloroform: DFT calculations

2016 ◽  
Vol 15 (04) ◽  
pp. 1650029 ◽  
Author(s):  
Nuha Ahmed Wazzan
Keyword(s):  
Charge Transfer ◽  
Dft Calculations ◽  
Gas Phase ◽  
Density Functional ◽  
Molecular Structures ◽  
Basis Set ◽  
Charge Transfer Complexes ◽  
Good Correspondence ◽  
Electronic Distribution ◽  
Picryl Chloride

This work reports density functional theory (DFT) calculations on the molecular structures, electronic distribution, and UV-Vis and IR spectroscopy analysis of charge transfer complexes between aminopyridines (APYs), namely 2-APY, 3-APY and 4-APY, as electron-donors and some [Formula: see text]-electron-acceptors, namely chloranil (CHL), tetracyanoethylene (TCNE) and picryl chloride (PC), formed in the gas phase at the B3LYP/6-31[Formula: see text]G(d,p) method/basis set, and in chloroform at the same method/basis set using PCM as solvation model. Good correspondence was generally obtained between the calculated parameters and the experimental ones.

Fragmentation Reactions of All 64 Deprotonated Trinucleotide and 16 Mixed Base Tetranucleotide Anions via Tandem Mass Spectrometry in an Ion Trap.

2000 ◽  
Vol 53 (4) ◽  
pp. 307 ◽  
Author(s):  
Ana K. Vrkic ◽  
Richard A. J. O'Hair ◽  
Simon Foote
Keyword(s):  
Mass Spectrometry ◽  
Proton Transfer ◽  
Ion Trap ◽  
Fragmentation Pathway ◽  
Intramolecular Proton Transfer ◽  
Base Loss ◽  
Phosphodiester Bond ◽  
Neutral Base ◽  
Fragmentation Reactions ◽  
Direct Dissociation

The gas-phase fragmentation reactions of the [M–H]– ions derived from all 64 trinucleotides and 16 isomeric tetranucleotides each containing adenine, thymine, guanine and cytosine were examined using multistage mass spectrometry (MS/MS and MS3) collision-induced dissociation in an ion trap mass spectrometer. The initial fragmentation pathway involved neutral base loss predominantly from the 5´ terminus, along with minor 3´ and internal base loss in the order A > T > G > C to form [M–H–BH]– ‘non-sequence’ ions. The resultant [M–H–BH]– ions often fragment via intramolecular proton transfer with concomitant cleavage of the 3´ C–O phosphodiester bond to yield an ion–molecule complex, which undergoes either direct dissociation or proton transfer to yield the w-type or (a–B)-type ‘sequence’ ions respectively.

Configurations and conformations of glycosyl sulfoxides

2010 ◽  
Vol 88 (11) ◽  
pp. 1154-1174 ◽  
Author(s):  
Hong Liang ◽  
Micheline MacKay ◽  
T. Bruce Grindley ◽  
Katherine N. Robertson ◽  
T. Stanley Cameron
Keyword(s):  
Solid State ◽  
Dft Calculations ◽  
Gas Phase ◽  
Density Functional ◽  
Lone Pair ◽  
Azido Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Comparison Of The Results ◽  
P Type

X-ray crystallographic studies of two axial glycosyl sulfoxides having RS configurations (derivatives of phenyl 2-azido-2-deoxy-1-thio-α-d-galactopyranoside S-oxide) show that they adopt anti conformations in the solid state, in contrast to previous observations and assumptions. Density functional theory (DFT) calculations at the B3lYP6–311G+(d,p)/6–31G(d) level confirm that anti conformations of both phenyl and methyl RS glycosyl sulfoxides of 2-azido-2-deoxy-α-d-pyranosides are more stable than exo-anomeric conformations in the gas phase. 1D NOE measurements indicate that the more polar exo-anomeric conformers are only populated to a slight extent in solution. The anti conformations are distorted so that the glycosyl substituents are closer to being eclipsed with H1. This distortion allows S n → σ* overlap if the sulfur lone pair is a p-type lone pair. Evidence for this overlap comes from short C1–S bond distances, as short as the comparable bond distances in the X-ray crystal structure and in the results from DFT calculations for the SS glycoside, which does adopt the expected exo-anomeric conformation, both in the solid state and in solution, and has normal n → σ* overlap. For 2-deoxy derivatives not bearing a 2-azido group, gas-phase DFT calculations at the same level indicate that the anti- and exo-anomeric conformers have comparable stabilities. Comparison of the results of the two series shows that electronegative substituents in equatorial orientations at C2 destabilize conformations with parallel S–O arrangements, the conformation favored by having an endocyclic C–O dipole antiparallel to the S–O dipole, by about 2.5 kcal mol–1 (1 cal = 4.184 J). An equatorial glycosyl sulfoxide, (SS) phenyl 3,4,6-tri-O-acetyl-2-deoxy-2-phthalimido-1-thio-β-d-glucopyranoside S-oxide, also adopts an anti conformation in the solid state as shown by X-ray diffraction. It also adopts this conformation in solution, in contrast to studies of other equatorial glycosyl sulfoxides.

scholarly journals Copper mediated decyano decarboxylative coupling of cyanoacetate ligands: Pesci versus Lewis acid mechanism

2015 ◽  
Vol 44 (19) ◽  
pp. 9230-9240 ◽  
Author(s):  
Jiawei Li ◽  
George N. Khairallah ◽  
Vincent Steinmetz ◽  
Philippe Maitre ◽  
Richard A. J. O'Hair
Keyword(s):  
Mass Spectrometry ◽  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Ion Trap ◽  
Functional Theory ◽  
Decomposition Reactions ◽  
Decarboxylative Coupling ◽  
Gas Phase Ion ◽  
Sequential Decomposition

A combination of gas-phase ion trap multistage mass spectrometry (MSn) experiments and density functional theory (DFT) calculations have been used to examine the mechanisms of the sequential decomposition reactions of copper cyanoacetate anions, [(NCCH2CO2)2Cu]−.

Is acyl migration to the aglycon avoidable in 2-acyl assisted glycosylation reactions?

2004 ◽  
Vol 82 (7) ◽  
pp. 1157-1171 ◽  
Author(s):  
Attila Bérces ◽  
Dennis M Whitfield ◽  
Tomoo Nukada ◽  
Iwona do Santos Z. ◽  
Agnes Obuchowska ◽  
...  
Keyword(s):  
Proton Transfer ◽  
Dft Calculations ◽  
Density Functional ◽  
Acyl Migration ◽  
Carbonyl Oxygen ◽  
Acyl Transfer ◽  
Protecting Group ◽  
Neighboring Group ◽  
Bond Forming ◽  
Anomeric Carbon

This report unequivocally separates orthoester formation from acyl transfer for the first time and indicates possible routes to eliminate 2-O-acyl transfer during glycosylation reactions. Experimental evidence is shown that acyl transfer from 2-O-acyl-3,4,6-tri-O-benzyl-D-galactopyranose-derived glycosyl donors decreases in the order formyl > acetyl > pivaloyl. The 2-O-benzoyl derivatives are more variable, in some cases transferring easily, and in others not at all. Density functional theory (DFT) calculations of the structure and energetics of dioxolenium ion and related intermediates suggest that a proton transfer pathway from the nucleophile to O-2 provides an explanation for the observed trends. These DFT calculations of the proton transfer pathway support a mechanism in which a relay molecule is involved. Further DFT calculations used a constraint based on linear combinations of six bond lengths to establish the sequence of bond breaking and bond forming. The calculated anomeric carbon to former carbonyl oxygen bond that breaks during acyl transfer is the longest in the formyl case and shortest in those that exhibit little or no acyl transfer. Rotation about the aromatic to carbonyl Ph—C(=O) bond is different from the alkyl series. Analysis of this proposed TS led to the postulate that 2,6-substitution may hinder rotation even more. Thus, the 2,6-dimethylbenzoyl analogue was synthesized and it does not transfer directly or by rearrangement of its readily formed orthoester. DFT calculations suggested that 2,6-dimethoxybenzoyl should also not transfer easily. Experimentally, this proved to be the case and this new 2-O-acyl protecting group cleaves at 50 °C with a 1 mol/L solution of LiOH in methanol. Thus, a calculated transition state has led to a prototype of a protecting group that solves a major problem in oligosaccharide synthesis.Key words: glycosylation, carbohydrates, quantum chemistry, reaction mechanism, neighboring-group effects.

scholarly journals Calculation of Phase Diagrams and First-Principles Study of Germanium Impacts on Phosphorus Distribution in Czochralski Silicon

2021 ◽  
Author(s):  
Hongqun Dong ◽  
Xiaoma Tao ◽  
Mervi Paulasto-Kröckel
Keyword(s):  
Dft Calculations ◽  
Phase Diagrams ◽  
Density Functional ◽  
Binary Systems ◽  
Nearest Neighbors ◽  
Binding Energies ◽  
P System ◽  
Low Resistivity ◽  
Co Doping ◽  
Equilibrium Segregation

AbstractPhosphorus (P) is one of the most widely used donor dopants for fabricating a low-resistivity silicon (Si) substrate. However, its volatile nature and the relatively small equilibrium segregation coefficient in Si at the melting temperature of Si impede the efficient and effective growth of low-resistivity Czochralski (CZ) Si single crystal. The primary objective of this work is to theoretically perceive the influence of germanium co-doping on the heavily P-doped Si crystal by means of CALculation of PHase Diagrams (CALPHAD) approaches and density functional theory (DFT) calculations. Phase equilibria at the Si-rich corner of the Si-Ge-P system has been thermodynamically extrapolated based on robust thermodynamic descriptions of involved binary systems, where Si-P and Ge-P have been re-assessed in this work. Phase diagram calculation results indicate that at a given P concentration (e.g. 0.33 at.% P) Ge co-doping lowers the solidification temperature of the Si(Ge, P) alloys, as well as the relevant equilibrium segregation coefficients of P in the doped Si. DFT calculations simulated the formation of (i) monovacancy in Si as well as (ii) solutions of Si(P) and Si(Ge) with one dopant substitutionally inserted in 64- and 216-atom Si cubic supercells. Binding energies were calculated and compared for Ge-Ge, Ge-P and P-P bonds positioning at the first nearest-neighbors (1NN) to the third nearest-neighbors (3NN). P-P bonds have the largest bonding energy from 1NN to 3NN configurations. The climbing image nudged elastic band method (CL-NEB) was utilized to calculate the energy barriers of P 1NN jump in the 64-atom Si cubic supercell with/without a neighboring Ge atom. With Ge present, a higher energy barrier for P 1NN jump was obtained than that without involving Ge. This indicates that Ge can impede the P diffusion in Si matrix.

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