On the stabilization of the carbonate dianion by sulfur dioxide

2010 ◽  
Vol 88 (11) ◽  
pp. 1125-1135 ◽  
Author(s):  
Friedrich Grein ◽  
Justin K. Chan ◽  
Idlir Liko
Keyword(s):  
Sulfur Dioxide ◽  
Oxygen Atom ◽  
Gas Phase ◽  
Single Point ◽  
Basis Set ◽  
Water Molecules ◽  
Electron Detachment ◽  
Optimized Geometries

The stabilization in the gas phase of the carbonate dianion [Formula: see text] by SO2 molecules is being investigated. The geometries of various isomers of [Formula: see text] (SO2)n and [Formula: see text] (SO2)n, for n = 1–4, have been optimized by the B3PW91/6−311+G(3df) method. Single-point CCSD and CCSD(T) energies at the DFT-optimized geometries were obtained for n = 1–3, using the 6−311+G(d) basis set. For n = 1 and 2, the monoanionic clusters are adiabatically more stable than the dianionic ones. However, starting at n = 3, they become less stable. The CCSD adiabatic electron detachment energy of the dianionic cluster switches from −0.39 eV for n = 2 to +0.20 eV for n = 3. The vertical electron detachment energy turns positive at n = 2, with a CCSD value of 1.35 eV. Several of the less stable dianionic, and most of the monoionic clusters, are characterized by the transfer of an oxygen atom from CO3 to SO2, forming [Formula: see text] or [Formula: see text] units, owing to [Formula: see text] + CO2 being more stable than [Formula: see text] + SO2. For the stabilization of the sulfate dianion by stepwise hydration, studied both experimentally and theoretically by other groups, a minimum of three water molecules was required.

scholarly journals Molecular Mechanisms of Succinimide Formation from Aspartic Acid Residues Catalyzed by Two Water Molecules in the Aqueous Phase

2021 ◽  
Vol 22 (2) ◽  
pp. 509
Author(s):  
Tomoki Nakayoshi ◽  
Koichi Kato ◽  
Shuichi Fukuyoshi ◽  
Ohgi Takahashi ◽  
Eiji Kurimoto ◽  
...  
Keyword(s):  
Gas Phase ◽  
Aspartic Acid ◽  
Aqueous Phase ◽  
Molecular Mechanisms ◽  
Model Compound ◽  
Reaction Pathway ◽  
Single Point ◽  
Water Molecules ◽  
Age Related ◽  
Optimized Geometries

Aspartic acid (Asp) residues are prone to nonenzymatic isomerization via a succinimide (Suc) intermediate. The formation of isomerized Asp residues is considered to be associated with various age-related diseases, such as cataracts and Alzheimer’s disease. In the present paper, we describe the reaction pathway of Suc residue formation from Asp residues catalyzed by two water molecules using the B3LYP/6-31+G(d,p) level of theory. Single-point energies were calculated using the MP2/6-311+G(d,p) level of theory. For these calculations, we used a model compound in which an Asp residue was capped with acetyl and methylamino groups on the N- and C-termini, respectively. In the aqueous phase, Suc residue formation from an Asp residue was roughly divided into three steps, namely, iminolization, cyclization, and dehydration, with the activation energy estimated to be 109 kJ mol−1. Some optimized geometries and reaction modes in the aqueous phase were observed that differed from those in the gas phase.

Structures, binding energies, and thermodynamic functions of NH4+, NH3•+, and their H2O complexes

1993 ◽  
Vol 71 (9) ◽  
pp. 1368-1377 ◽  
Author(s):  
David A. Armstrong ◽  
Arvi Rauk ◽  
Dake Yu
Keyword(s):  
Experimental Data ◽  
Gas Phase ◽  
Thermodynamic Functions ◽  
Hydration Shell ◽  
Binding Energies ◽  
Basis Set ◽  
Free Energies ◽  
Hydrated Complexes ◽  
Optimized Geometries ◽  
First Hydration Shell

Ab initio calculations are performed for [Formula: see text] and [Formula: see text] complexes for n = 0–5. For n = 0 and 1, the geometries of the complexes are optimized at the HF/6-31 + G* and MP2/6-31 + G* levels, and the energies are evaluated at the G2 level. For n = 2–5, the geometry optimizations and frequency calculations are carried out at the HF/6-31 + G* level, and the MP2/6-31 + G* energies are calculated at the HF optimized geometries. Basis set superposition errors are corrected by the Boys–Bernardi scheme at the HF/6-31 + G* level. The gas phase thermodynamic properties [Formula: see text] are evaluated as functions of temperature using standard statistical methods. Based on the calculated binding energies and the thermodynamic functions, the incremental changes in enthalpies and free energies, ΔHn and ΔGn, for the gas phase equilibria (H2O)n−1 M+ + H2O → (H2O)nM+ for M+ = NH4+ and NH3•+, are evaluated in comparison with the experimental data for [Formula: see text] the present results suggest conformations for the hydrated complexes observed in the experiments. The total free energy change for filling the first hydration shell is significantly more negative for NH3•+ than for NH4+.

scholarly journals Computational Study of the Dissociation Reactions of Secondary Ozonide

Atmosphere ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 100 ◽  
Author(s):  
Mansour H. Almatarneh ◽  
Shefa’ F. Alrebei ◽  
Mohammednoor Altarawneh ◽  
Yuming Zhao ◽  
Abd Al-Aziz Abu-Saleh
Keyword(s):  
Barrier Height ◽  
Computational Study ◽  
Reaction Pathway ◽  
Single Point ◽  
Water Dimer ◽  
Basis Set ◽  
Basis Sets ◽  
Water Molecules ◽  
Point Energy ◽  
Secondary Ozonide

This contribution presents a comprehensive computational study on the reactions of secondary ozonide (SOZ) with ammonia and water molecules. The mechanisms were studied in both a vacuum and the aqueous medium. All the molecular geometries were optimized using the B3LYP functional in conjunction with several basis sets. M06-2X, APFD, and ωB97XD functionals with the full basis set were also used. In addition, single-point energy calculations were performed with the G4MP2 and G3MP2 methods. Five different mechanistic pathways were studied for the reaction of SOZ with ammonia and water molecules. The most plausible mechanism for the reaction of SOZ with ammonia yields HC(O)OH, NH3, and HCHO as products, with ammonia herein acting as a mediator. This pathway is exothermic and exergonic, with an overall barrier height of only 157 kJ mol−1 using the G3MP2 method. All the reaction pathways between SOZ and water molecules are endothermic and endergonic reactions. The most likely reaction pathway for the reaction of SOZ with water involves a water dimer, in which the second water molecule acts as a mediator, with an overall barrier height of only 135 kJ mol−1 using the G3MP2 method. Solvent effects were found to incur a significant reduction in activation energies. When the second H2O molecule acts as a mediator in the reaction of SOZ with water, the barrier height of the rate-determining step state decreases significantly.

scholarly journals A computational study of cysteine and glutathione binding to Au8 cluster

10.29007/8c3l ◽  
2020 ◽  
Author(s):  
Thanh Si Nguyen ◽  
Vu Nhat Pham
Keyword(s):  
Gas Phase ◽  
Potential Energy Surfaces ◽  
Density Functional ◽  
Computational Study ◽  
Gold Cluster ◽  
Basis Set ◽  
Functional Theory ◽  
Metal Atoms ◽  
Energy Surfaces ◽  
Optimized Geometries

The interaction between the Au8 cluster with cysteine (Cys) and glutathione (GSH) is investigated by means of density functional theory (DFT) using the PBE functional in conjunction with the cc-pVTZ basis set for non-metal atoms and the cc-pVTZ-PP basis set for gold. Harmonic vibrational frequencies are also calculated to confirm optimized geometries as local minima or transition states on the potential energy surfaces. The computed results show that these molecules prefer to anchor on the gold cluster via the sulfur atom with the adsorption energies of 20.3 and 30.8 kcal/mol for CYS and GSH, respectively, in the gas phase. In water, such values are considerably reduced, namely 19.0 kcal/mol for CYS and 26.4 kcal/mol for GSH. If a visible light with a frequency of v = 6x1014 Hz (500 nm) is applied, the time for the recovery of CYS and GSH from the most stable complexes will be about 1.24 and 6.03x107 seconds at 298 K in the gas phase. Such values significantly reduce to 0.14 and 4.08x104 in water. Thus, the Au8 cluster could be a promising material for designing tiny sensors in CYS and GSH selective detection.

THEORETICAL STUDY OF MECHANISM FOR THE ATMOSPHERIC REACTION CF3CHFO2 + NO

2013 ◽  
Vol 12 (01) ◽  
pp. 1250101 ◽  
Author(s):  
YA-NA WENG ◽  
XIAO-JUAN YAN ◽  
SHU-JIN LI
Keyword(s):  
Density Functional ◽  
Energy Surface ◽  
Single Point ◽  
Basis Set ◽  
Stationary Points ◽  
Cluster Method ◽  
Radical Pairs ◽  
Functional Theory ◽  
Point Energy ◽  
Optimized Geometries

The mechanism of the reaction CF3CHFO2 + NO was investigated using ab initio and density functional theory (DFT). The optimized geometries for all stationary points on the reaction energy surface were calculated using MP2 and B3LYP methods with the aug-cc-pVDZ basis set. Single-point energy calculations were performed using the coupled cluster method with single, double and perturbative triple configurations, CCSD(T). The most important energy minima on the potential energy surface (PES) were found corresponding to two conformers of the peroxynitrite association adducts, cis- CF3CHFOONO and trans- CF3CHFOONO , and the nitrate, CF3CHFONO2 . The radical pairs ( CF3CHFO + NO2 ) and the nitrate are formed through the breaking of the peroxy bond of trans- CF3CHFOONO and the rearrangement of cis- CF3CHFOONO , respectively. The nitrate can be decomposed to carbonylated species ( CF3CHO or CF3CFO ), nitryl fluoride (NO2F), nitrous acid (HONO), and radical pairs ( CF3CHFO + NO2 ), which are of potential atmospheric importance.

Theoretical studies of sulfite – sulfur dioxide clusters, SO32−(SO2)n: structure and stability of SnO2n+1 anions, n = 1–5

2013 ◽  
Vol 91 (10) ◽  
pp. 1018-1031 ◽  
Author(s):  
Justin K. Chan ◽  
Sonya Burrill ◽  
Friedrich Grein
Keyword(s):  
Sulfur Dioxide ◽  
Density Functional Calculations ◽  
Density Functional ◽  
Basis Set ◽  
Theoretical Studies ◽  
Electron Detachment ◽  
Structure And Stability

Density functional calculations using the B3PW91 functional with the 6-311+G(3df) basis set were performed on the addition of n = 1–4 SO2 molecules to SO3− and SO32−. Geometry optimizations were performed for a large number of possible structures. At n = 4, the dianionic cluster becomes adiabatically more stable than the monoanionic one, with an adiabatic electron detachment energy of 0.30 eV. Monoanionic clusters are characterized by the O–S–O–SO3 moiety having long O–S bonds to SO2 molecules. Dianionic clusters, however, prefer S–S bonding of O3S–O–S(O) with SO2.

Konkurrierende Liganden: Theophyllin als nicht- und stark koordinierender Ligand in Quecksilber(II)-Komplexen / Competing Ligands: Theophylline as Non- and Strongly Coordinating Ligand in Mercury(II) Complexes

2006 ◽  
Vol 61 (6) ◽  
pp. 758-765 ◽  
Author(s):  
Matthias Nolte ◽  
Ingo Pantenburg ◽  
Gerd Meyer
Keyword(s):  
Oxygen Atom ◽  
Water Molecule ◽  
Aqueous Solutions ◽  
Single Crystal ◽  
Coordination Polymers ◽  
Water Molecules ◽  
Slow Evaporation ◽  
Monoclinic Symmetry ◽  
X Ray ◽  
Chloride Ligand

[{Hg(CF3)2}(ThpH)(H2O)](H2O) (1), [{Hg4(Thp)4}(ClO4)4(H2O)8](H2O)4 (2), [{Hg(ThpH)2} (NO3)](NO3) (3) and {Hg(Thp)Cl}(H2O) (4) (ThpH = theophylline, C7H8N4O2) have been synthesized by slow evaporation of aqueous solutions of the mercuric salts Hg(CF3)2, Hg(ClO4)2, Hg(NO3)2, or HgCl2 and theophylline. Their crystal structures were determined on the basis of single crystal X-ray data. The coordination polymers 1 and 2 crystallize with triclinic symmetry, P1̅ (no. 2), with a = 468.8(2), b = 1256.4(5), c = 1445.5(6) pm, α = 67.15(3), β = 89.21(3), γ = 89.40(3)° and a = 833.6(1), b = 1862.7(2), c = 2182.9(2) pm, α = 111.61(1), β = 90.98(1), γ = 95.51(1)°, respectively. 3 and 4 crystallize with monoclinic symmetry, Pc (no. 7), a =1194.1(1), b=1258.8(2), c=735.5(2) pm, β =96.96(2)° and P21/n (no. 14), a=1069.0(2), b =911.6(1), c=1089.9(2) pm and β = 96.87(2)°. In 1 the theophylline molecules are non-coordinating to mercury and leave the Hg(CF3)2 molecule unchanged. Only weak electrostatic attractions to one keto-oxygen atom of theophylline and one water molecule hold this co-crystallisate together. In 2, the theophyllinate anion, Thp−, strongly coordinates with both N(7) and N(9) to HgII forming a large ring with eight Hg atoms that incorporates the water molecules. One sort of nitrate ions in 3 is weakly attached to HgII with the theophylline molecules still bound strongly through N(9). The chloride ligand and the theophyllinate ion seem to have the same strengths as ligands in 4 as they are both attached to HgII with the shortest distances possible

scholarly journals Absorption mechanism, structural and electronic properties of MC19 (M = B and Si) fullerenes with 1-acetylpiperazine

2017 ◽  
Vol 36 (1-2) ◽  
pp. 797-804
Author(s):  
Özgür Alver ◽  
Cemal Parlak ◽  
Mohamed I Elzagheid ◽  
Ponnadurai Ramasami
Keyword(s):  
Electronic Properties ◽  
Gas Phase ◽  
Basis Set ◽  
Stable Complex ◽  
Absorption Mechanism ◽  
Boron Doped ◽  
Structural And Electronic Properties ◽  
Influence Of Water ◽  
Vibrational Bands ◽  
Silicon Doped

The interaction mechanisms of undoped, silicon- and boron-doped C20 fullerenes and 1-acetylpiperazine (1-ap) were investigated. Stability, electronic properties, influence of water on the solubility and stability, molecular parameters, descriptive vibrational bands and nuclear magnetic resonance shielding values are reported. The quantum mechanical calculations were carried out using the M06-2X functional and the 6-31G(d) basis set. It is observed that all the complexes are more stabilized in water compared to the gas phase. The most stable complex was found as silicon-doped fullerene interacting with the carbonyl edge of 1-ap releasing energy of 64.13 kcal/mol in water.

Theoretical study on NO3-initiated oxidation of acenaphthene in the atmosphere

2008 ◽  
Vol 86 (2) ◽  
pp. 129-137 ◽  
Author(s):  
Xiaohui Qu ◽  
Qingzhu Zhang ◽  
Wenxing Wang
Keyword(s):  
Product Information ◽  
Environmental Concern ◽  
Single Point ◽  
Basis Set ◽  
Orbital Theory ◽  
Night Time ◽  
Point Energy ◽  
Secondary Reactions ◽  
Favorable Reaction ◽  
High Level

Acenaphthene is widespread and toxic, and thus of substantial environmental concern. The reaction with NO3 radicals is an important atmospheric loss process of acenaphthene at night time. In this work, the mechanism for the NO3-initiated atmospheric oxidation reaction of acenaphthene has been studied using high level molecular orbital theory. Geometries of all the related species have been optimized at the MPWB1K level with the 6–31G(d,p) basis set. The single-point energy calculations have been carried out at the MPWB1K/6–311+G(3df,2p) level. The possible secondary reactions were also studied. Several energetically favorable reaction pathways were revealed for the first time.Key words: acenaphthene, NO3 radicals, reaction mechanism, product information, oxidation degradation.

scholarly journals Unknown Knowns: Case Studies in Uncertainties in the Computation of Thermochemical Parameters

2020 ◽  
Author(s):  
John Simmie
Keyword(s):  
Heat Capacity ◽  
Gas Phase ◽  
Basis Set ◽  
Statistical Thermodynamic ◽  
Vibrational Modes ◽  
Heavy Atoms ◽  
New Methods ◽  
Formation Enthalpies ◽  
Thermochemical Parameters

<div>Both the computation of, and the uncertainties associated, with gas-phase molar formation enthalpies are now quite well established for systems comprised of tens of ‘heavy’ atoms chosen from the commonest elements. The same cannot be said for derived thermochemical quantities such as entropy, heat capacity and an enthalpy function. Whilst the application of well known statistical thermodynamic relations is mostly understood, the determination of the uncertainty with which such values can be obtained has been little studied — apart, that is, for a general protocol devised by Goldsmith et al. [J. Phys. Chem. A, 2012, 116, 9033–9057]. Specific examples from that work are explored here and it is shown that their estimates are overly pessimistic. It is also evident that for some species the calculated thermochemical parameters show very little variation with either the level of theory, or basis set, or treatment of vibrational modes — this renders the inclusion of such species in databases designed to validate new methods of limited value.<br></div>

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