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+.

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 THERMODYNAMIC PROPERTIES OF ORGANIC ACIDS AND SOME THEIR DERIVATIVES

2019 ◽  
Vol 62 (11) ◽  
pp. 38-45
Author(s):  
Vitaly V. Ovchinnikov ◽  
Alexey A. Kulakov ◽  
Irina G. Grigor′eva ◽  
Svetlana A. Maltseva
Keyword(s):  
Experimental Data ◽  
Organic Acids ◽  
Gas Phase ◽  
Thermodynamic Functions ◽  
Bond Energies ◽  
Additional Material ◽  
Electron Pairs ◽  
Valence Electrons ◽  
Heats Of Combustion

The heats of vaporization, combustion, formation, entropy and the heat capacities in different phases of different carbonic acids and their derivatives: acetates, esters with fatty radicals, two-, three- and four-basic acids (52 compounds) were analysed in the framework of one-parametric mathematic equations. The experimental data of all chosen one-, two-, three- and four-basic acids were analyzed. It was determined, that all thermodynamic functions of these types of compounds depend on the number of valence electrons N, from which the sum of lone electron pairs g as represented in the equations Δvap,c,fH° = i ±  f (N-g) and S°(Cp) = i ±  f (N-g) is excluded. The coefficients f in the first equations is in the range of 104-113 kJ mol-1 electron-1, that corresponds to the same values f in the equations, which are mentioned in our earlier papers on the determination of the heats of combustion of organic acids. As concerned of coefficient i in the received equations, necessary to note that situation is not synonymous as with the coefficient f. The magnitudes of this coefficient are different in the equations of vaporization, combustion, formation also as in the equations of entropy and the heat of capacity. On the base of literary experimental data we calculated the 29 new equations, which can be used for the calculation of the same thermodynamic functions for other new organic acids and especially bioorganic substances with the useful properties. Necessary to add, that the received equations can serve as additional material for the calculation of the bond energies of fatty acids and their derivatives in gas phase.

SN2 reactions in the gas phase. Transition states for the reaction: Cl− + RBr = ClR + Br−, where R = CH3, C2H5, and iso-C3H7, from abinitio calculations and comparison with experiment. Solvent effects

1989 ◽  
Vol 67 (8) ◽  
pp. 1262-1267 ◽  
Author(s):  
Kimihiko Hirao ◽  
Paul Kebarle
Keyword(s):  
Experimental Data ◽  
Activation Energy ◽  
Aqueous Solution ◽  
Transition State ◽  
Gas Phase ◽  
Closed Shell ◽  
Basis Set ◽  
Phase Reaction ◽  
Ion Molecule Reactions ◽  
Abinitio Calculations

The geometries and the energies of the reactants, transition state, and products for the gas phase reaction: Cl− + CH3Br = ClCH3 + Br−, were obtained from abinitio calculations using a closed shell SCF method with a MINI basis set developed by Huzinaga etal. The energy changes predicted by the calculations are found in good agreement with the experimental data. The energies and geometries of the reactants and the transition state for the gas phase reactions: Cl− + RBr = ClR + Br−, where R = C2H5 and iso-C3H7, were also obtained. The resulting activation energies follow the same trend as the experimental data: Me < Et < iso-Pr; however, the predicted increase of activation energy is considerably larger. The energies and geometries for the reactants, transition state, and products of the gas phase ion-dihydrate reaction: Cl−(H2O)2 + CH3Br → H2O(ClCH3Br)−H2O → Br−(H2O)2 + CH3Cl were obtained as well. These data provide an interesting comparison with experimental results in aqueous solution. The reaction coordinate of the ion-dihydrate reaction is very much closer to that for aqueous solution than to that for the gas phase. Keywords: nucleophilic substitution reactions, ion–molecule reactions, activation energy.

Density Functional Theory Study of Intermolecular Interaction between RDX and H2O

2013 ◽  
Vol 750-752 ◽  
pp. 1848-1851
Author(s):  
Xiu Lin Zeng ◽  
Xue Hai Ju
Keyword(s):  
Density Functional ◽  
Natural Bond Orbital ◽  
Density Functional Method ◽  
Zero Point ◽  
Functional Method ◽  
Binding Energies ◽  
Basis Set ◽  
Free Energies ◽  
Functional Theory ◽  
Dimerization Process

The density functional method of wB97xD in combination of 6-31+G** basis set was applied to the study of the heterodimers between hexahydro-1,3,5-trinitro-1,3,5-triazine and water. Three stable dimers were located. The binding energies have been corrected for the zero-point vibrational and basis set superposition errors. The largest corrected binding energy is 26.21 kJ/mol. Natural bond orbital analyses and frequency calculations were performed on each optimized structure. The thermodynamic properties of enthalpies, entropies and Gibbs free energies in the dimerization process were presented.

scholarly journals Quantum-Chemical Study on the Relative Stability of Sildenafil Tautomers

2021 ◽  
Author(s):  
Wojciech Piotr Oziminski ◽  
Igor Wiśniewski
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Water Solution ◽  
Quantum Chemical Study ◽  
Basis Set ◽  
Steric Interaction ◽  
Free Energies ◽  
Dft Methods ◽  
Enol Tautomer ◽  
Tautomeric Mixture

Abstract The tautomeric equilibrium of Sildenafil molecule was theoretically studied using B3LYP and M06-2X Density Functional Theory (DFT) methods in connection with aug-cc-pVDZ correlation consistent basis set. Calculations were performed for gas phase and water solution conditions modelled by Polarizable Continuum Model (PCM). Three tautomeric forms are possible. Two keto forms: A – where the tautomeric proton in more distant from carbonyl group, B – where it is closer, and one enol form denoted C. Both DFT methods qualitatively give similar tautomer stability order: B>A>C. The B tautomer is dominant in gas phase and water environment, whereas the C tautomer is too high in energy to be present in the tautomeric mixture. Regarding the A tautomer, it is not present in the gas phase but is present in small amounts in water solution. According to B3LYP/ aug-cc-pVDZ the relative Gibbs free energies for A and C relative to B, are 10.05 kcal/mol and 11.91 kcal/mol for gas phase and 5.49 kcal/mol and 12.49 kcal/mol for water solution. According to M06-2X/aug-cc-pVDZ the relative Gibbs free energies for A and C are 9.12 kcal/mol and 10.60 kcal/mol for gas phase and 4.27 kcal/mol and 10.23 kcal/mol for water solution. Therefore, for in vivo conditions we expect that the B tautomer is dominant and there may exist small amounts of the A tautomer. The C enol tautomer is not present at all. This picture is very different from the parent tautomeric system: 4-hydroxypyrimidine/4-pyrimidinone where the C enol tautomer is less stable than keto B only by about 1 kcal/mol in the gas phase and the A keto tautomer is the least stable and not present in the tautomeric mixture. In order to understand these differences we performed additional calculations for series of parent molecules starting from 4-hydroxypyrimidine/4-pyrimidinone, going through two in-between model molecules and ending at Sildenafil molecule. We found that the most important reasons of C form destabilization are: dearomatization of the 6-membered ring caused by the fusion with pyrazole ring, lack of strong intramolecular hydrogen bond in C form of Sildenafill and presence of destabilizing steric interaction of oxygen and nitrogen atoms of two 6-memberd rings in this tautomer.

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.

scholarly journals Computer Simulation of Small Magnetic Clusters of 3d-Transition Metals of the Iron Subgroup Using the Hybrid Density Functional Method

2020 ◽  
pp. 21-26
Author(s):  
S.A. Beznosyuk ◽  
A.G. Blyum ◽  
M.S. Zhukovsky ◽  
T.M. Zhukovsky ◽  
А.S. Masalimov
Keyword(s):  
Experimental Data ◽  
Density Functional ◽  
Density Functional Method ◽  
Calculated Data ◽  
Functional Method ◽  
Binding Energies ◽  
Basis Set ◽  
Magnetic Clusters ◽  
Spin Multiplicity ◽  
Hybrid Density Functional

This paper presents the results of s study focused on the stability of small 3d-transition-metal magnetic clusters (metals of an iron subgroup) in spin-polarized states using the hybrid density functional method. Computer modeling and full variational optimization of geometric structures of clusters were performed for various values of the spin multiplicity of electronic states. The binding energies, the bond lengths, and the frequencies of atomic zero-point vibrations in small clusters with a nuclearity of n = 2, 3, 4, 5, 6 were calculated depending on the metal (Fe, Co, Ni) and spin multiplicity M in the zero-charge state. The calculations were carried out using the hybrid density functional B3LYP method in the def2-TZVP basis set of the ORCA package algorithms. A comparison of the calculated results with the available experimental data is presented. It is shown that the calculated data obtained by the hybrid density functional method are in satisfactory agreement with the experimental data for “naked” clusters in inert media both for the spin multiplicity of the ground state and for the energy of atomic shock dissociation of clusters in inert gas flows.

PSEUDOPOTENTIAL STUDIES ON THE ELECTRONIC STRUCTURE OF LANTHANUM MONOHALIDES LaF, LaCl, LaBr, AND LaI

2005 ◽  
Vol 04 (spec01) ◽  
pp. 583-592 ◽  
Author(s):  
XIAOYAN CAO ◽  
MICHAEL DOLG
Keyword(s):  
Experimental Data ◽  
Binding Energies ◽  
Basis Set ◽  
Basis Sets ◽  
Relativistic Energy ◽  
Molecular Constants ◽  
Orbit Splitting ◽  
Calculated Binding Energy ◽  
Atomic Spin ◽  
Spin Orbit Splitting

Relativistic energy-consistent small-core lanthanide pseudopotentials of the Stuttgart–Köln variety and corresponding valence basis sets have been used for the investigation of the ground state (1Σ+) lanthanum monohalides LaF , LaCl , LaBr , and LaI . The molecular constants were derived from coupled-cluster calculations, taking into account corrections for atomic spin-orbit splitting as well as basis set superposition errors. With the exception of the binding energies for LaI the theoretical values for LaF (Re = 2.034 Å, De = 6.73 eV , ωe = 574 cm -1), LaCl (Re = 2.517 Å, De = 5.11 eV , ωe = 339 cm -1), LaBr (Re = 2.664 Å, De = 4.47 eV , ωe = 236 cm -1), and LaI (Re = 2.891 Å, De = 3.65 eV , ωe = 186 cm -1) show good agreement with the experimental data. The calculated binding energy (3.65 eV) for LaI is in-between the two conflicting estimated experimental data (2.97 eV, 4.29 eV).

scholarly journals Quantum-chemical study on the relative stability of sildenafil tautomers

2021 ◽  
Author(s):  
Wojciech Piotr Oziminski ◽  
Igor Wiśniewski
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Water Solution ◽  
Quantum Chemical Study ◽  
Basis Set ◽  
Steric Interaction ◽  
Free Energies ◽  
Dft Methods ◽  
Enol Tautomer ◽  
Tautomeric Mixture

AbstractThe tautomeric equilibrium of sildenafil molecule was theoretically studied using B3LYP and M06-2X density functional theory (DFT) methods in connection with aug-cc-pVDZ correlation consistent basis set. Calculations were performed for gas phase and water solution conditions modelled by polarizable continuum model (PCM). Three tautomeric forms are possible. Two keto forms: A — where the tautomeric proton in more distant from carbonyl group and B — where it is closer, and one enol form denoted, C. Both DFT methods qualitatively give similar tautomer stability order: B > A > C. The B tautomer is dominant in gas phase and water environment, whereas the C tautomer is too high in energy to be present in the tautomeric mixture. Regarding the A tautomer, it is not present in the gas phase but is present in small amounts in water solution. According to B3LYP/aug-cc-pVDZ, the relative Gibbs-free energies for A and C relative to B are 10.05 kcal/mol and 11.91 kcal/mol for gas phase and 5.49 kcal/mol and 12.49 kcal/mol for water solution. According to M06-2X/aug-cc-pVDZ, the relative Gibbs-free energies for A and C are 9.12 kcal/mol and 10.60 kcal/mol for gas phase and 4.27 kcal/mol and 10.23 kcal/mol for water solution. Therefore, for in vivo conditions, we expect that the B tautomer is dominant, and there may exist small amounts of the A tautomer. The C enol tautomer is not present at all. This picture is very different from the parent tautomeric system: 4-hydroxypyrimidine/4-pyrimidinone where the C enol tautomer is less stable than keto B only by about 1 kcal/mol in the gas phase and the A keto tautomer is the least stable and not present in the tautomeric mixture. In order to understand these differences, we performed additional calculations for a series of parent molecules starting from 4-hydroxypyrimidine/4-pyrimidinone, going through two in-between model molecules and ending at Sildenafil molecule. We found that the most important reasons of C form destabilization are dearomatization of the 6-membered ring caused by the fusion with pyrazole ring, lack of strong intramolecular hydrogen bond in C form of sildenafil and presence of destabilizing steric interaction of oxygen and nitrogen atoms of two 6-memberd rings in this tautomer.

Theoretical binding affinities and spectra of complexes formed by a cyclic β-peptoid with amino acids

2010 ◽  
Vol 64 (4) ◽  
Author(s):  
Yu Sun ◽  
Jinpei Du ◽  
Ying Wang ◽  
Shi Wu
Keyword(s):  
Amino Acids ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Binding Energies ◽  
Basis Set ◽  
Binding Affinities ◽  
Functional Theory ◽  
Guest Molecules ◽  
The Density Functional Theory ◽  
Optimized Geometries

AbstractBinding affinities of a cyclic β-peptoid to amino acids were studied using the density functional theory (DFT) at the B3LYP/6-311G(d,p) level after the basis set superior error (BSSE). The host molecule possesses binding ability to amino acids since the binding energies of the complexes formed are negative. The complexes were stabilized via hydrogen bonds between the host and the guest molecules. Based on the B3LYP/6-31G(d) optimized geometries, electronic spectra of the complexes were calculated using the INDO/CIS method. 13C NMR spectra and nucleus-independent chemical shift (NICS) values of the complexes were computed at the B3LYP/6-31G(d) level. Carbon atoms in the carboxyl groups of the complexes are shifted downfield relative to those of the host. Some complexes exhibit aromaticity although the host shows anti-aromaticity. Formation of hydrogen bonds leads to cyclic current formation in these complexes.

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