scholarly journals Thermochemistry of Guanine Tautomers Re-Examined by Means of High-Level CCSD(T) Composite Ab Initio Methods

2019 ◽  
Vol 72 (8) ◽  
pp. 607 ◽  
Author(s):  
Amir Karton
Keyword(s):  
Ab Initio ◽  
Gas Phase ◽  
Basis Set ◽  
Energy Window ◽  
Small Energy ◽  
Composite Methods ◽  
Wide Range ◽  
Complete Basis Set ◽  
Enol Tautomer ◽  
High Level

We obtained accurate gas-phase tautomerization energies for a set of 14 guanine tautomers by means of high-level thermochemical procedures approximating the CCSD(T) energy at the complete basis set (CBS) limit. For the five low-lying tautomers, we use the computationally demanding W1-F12 composite method for obtaining the tautomerization energies. The relative W1-F12 tautomerization enthalpies at 298K are: 0.00 (1), 2.37 (2), 2.63 (3), 4.03 (3′), and 14.31 (4) kJmol−1. Thus, as many as four tautomers are found within a small energy window of less than 1.0kcalmol−1 (1kcalmol−1=4.184kJmol−1). We use these highly accurate W1-F12 tautomerization energies to evaluate the performance of a wide range of lower-level composite ab initio procedures. The Gn composite procedures (G4, G4(MP2), G4(MP2)-6X, G3, G3B3, G3(MP2), and G3(MP2)B3) predict that the enol tautomer (3) is more stable than the keto tautomer (2) by amounts ranging from 0.36 (G4) to 1.28 (G3(MP2)) kJmol−1. We also find that an approximated CCSD(T)/CBS energy calculated as HF/jul-cc-pV{D,T}Z+CCSD/jul-cc-pVTZ+(T)/jul-cc-pVDZ results in a root-mean-square deviation (RMSD) of merely 0.11kJmol−1 relative to the W1-F12 reference values. We use this approximated CCSD(T)/CBS method to obtain the tautomerization energies of 14 guanine tautomers. The relative tautomerization enthalpies at 298K are: 0.00 (1), 2.20 (2), 2.51 (3), 4.06 (3′), 14.30 (4), 25.65 (5), 43.78 (4′), 53.50 (6′), 61.58 (6), 77.37 (7), 82.52 (8′), 86.02 (9), 100.70 (10), and 121.01 (8) kJmol−1. Using these tautomerization enthalpies, we evaluate the performance of standard and composite methods for the entire set of 14 guanine tautomers. The best-performing procedures emerge as (RMSDs are given in parentheses): G4(MP2)-6X (0.51), CCSD(T)+ΔMP2/CBS (0.52), and G4(MP2) (0.64kJmol−1). The worst performers are CCSD(T)/AVDZ (1.05), CBS-QB3 (1.24), and CBS-APNO (1.38kJmol−1).

scholarly journals Density Functional Theory and Complete Basis Set Ab Initio Computational Study of Five-, Six-, Seven- and Eight-hydrogen Coordinated Carbon Cations

1999 ◽  
Vol 23 (8) ◽  
pp. 502-503
Author(s):  
Branko S. Jursic
Keyword(s):  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Computational Study ◽  
Basis Set ◽  
Functional Theory ◽  
Complete Basis ◽  
Complete Basis Set ◽  
High Level

High level ab initio and density functional theory studies are performed on highly protonated methane species.

A Systematic DFT Study of Two Elementary Steps Involving Hydrogen Peroxide and the Hydroxyl Radical in the Fenton Reaction

2018 ◽  
Author(s):  
Danilo Carmona ◽  
David Contreras ◽  
Oscar A. Douglas-Gallardo ◽  
Stefan Vogt-Geisse ◽  
Pablo Jaque ◽  
...  
Keyword(s):  
Hydrogen Peroxide ◽  
Hydroxyl Radical ◽  
Ab Initio ◽  
Fenton Reaction ◽  
Basis Set ◽  
Basis Sets ◽  
Dft Methods ◽  
Elementary Steps ◽  
Oxygen Oxygen ◽  
Complete Basis Set

The Fenton reaction plays a central role in many chemical and biological processes and has various applications as e.g. water remediation. The reaction consists of the iron-catalyzed homolytic cleavage of the oxygen-oxygen bond in the hydrogen peroxide molecule and the reduction of the hydroxyl radical. Here, we study these two elementary steps with high-level ab-initio calculations at the complete basis set limit and address the performance of different DFT methods following a specific classification based on the Jacob´s ladder in combination with various Pople's basis sets. Ab-initio calculations at the complete basis set limit are in agreement to experimental reference data and identified a significant contribution of the electron correlation energy to the bond dissociation energy (BDE) of the oxygen-oxygen bond in hydrogen peroxide and the electron affinity (EA) of the hydroxyl radical. The studied DFT methods were able to reproduce the ab-initio reference values, although no functional was particularly better for both reactions. The inclusion of HF exchange in the DFT functionals lead in most cases to larger deviations, which might be related to the poor description of the two reactions by the HF method. Considering the computational cost, DFT methods provide better BDE and EA values than HF and post--HF methods with an almost MP2 or CCSD level of accuracy. However, no systematic general prediction of the error based on the employed functional could be established and no systematic improvement with increasing the size in the Pople's basis set was found, although for BDE values certain systematic basis set dependence was observed. Moreover, the quality of the hydrogen peroxide, hydroxyl radical and hydroxyl anion structures obtained from these functionals was compared to experimental reference data. In general, bond lengths were well reproduced and the error in the angles were between one and two degrees with some systematic trend with the basis sets. From our results we conclude that DFT methods present a computationally less expensive alternative to describe the two elementary steps of the Fenton reaction. However, choice of approximated functionals and basis sets must be carefully done and the provided benchmark allows a systematic validation of the electronic structure method to be employed

scholarly journals Non-Covalent Interactions Involving Alkaline-Earth Atoms and Lewis Bases B: An ab Initio Investigation of Beryllium and Magnesium Bonds, B···MR2 (M = Be or Mg, and R = H, F or CH3)

Inorganics ◽  
2019 ◽  
Vol 7 (3) ◽  
pp. 35 ◽  
Author(s):  
Ibon Alkorta ◽  
Anthony Legon
Keyword(s):  
Ab Initio ◽  
Lewis Acids ◽  
Alkaline Earth ◽  
Basis Set ◽  
Covalent Bonds ◽  
Lewis Bases ◽  
Complete Basis Set ◽  
Definition Of ◽  
The Individual ◽  
Equilibrium Dissociation

Geometries, equilibrium dissociation energies (De), intermolecular stretching, and quadratic force constants (kσ) determined by ab initio calculations conducted at the CCSD(T)/aug-cc-pVTZ level of theory, with De obtained by using the complete basis set (CBS) extrapolation [CCSD(T)/CBS energy], are presented for the B···BeR2 and B···MgR2 complexes, where B is one of the following Lewis bases: CO, H2S, PH3, HCN, H2O or NH3, and R is H, F or CH3. The BeR2 and MgR2 precursor molecules were shown to be linear and non-dipolar. The non-covalent intermolecular bond in the B···BeR2 complexes is shown to result from the interaction of the electrophilic band around the Be atom of BeR2 (as indicated by the molecular electrostatic potential surface) with non-bonding electron pairs of the base, B, and may be described as a beryllium bond by analogy with complexes such as B···CO2, which contain a tetrel bond. The conclusions for the B···MgR2 series are similar and a magnesium bond can be correspondingly invoked. The geometries established for B···BeR2 and B···MgR2 can be rationalized by a simple rule previously enunciated for tetrel-bonded complexes of the type B···CO2. It is also shown that the dissociation energy, De, is directly proportional to the force constant, kσ, in each B···MR2 series, but with a constant of proportionality different from that established for many hydrogen-bonded B···HX complexes and halogen-bonded B···XY complexes. The values of the electrophilicity, EA, determined from the De for B···BeR2 complexes for the individual Lewis acids, A, reveal the order A = BeF2 > BeH2 > Be(CH3)2—a result that is consistent with the −I and +I effects of F and CH3 relative to H. The conclusions for the MgR2 series are similar but, for a given R, they have smaller electrophilicities than those of the BeR2 series. A definition of alkaline-earth non-covalent bonds is presented.

scholarly journals Global accurate diabatic potential surfaces for the reaction H + Li2

RSC Advances ◽  
2020 ◽  
Vol 10 (64) ◽  
pp. 39226-39240
Author(s):  
Ruilin Yin ◽  
Nan Gao ◽  
Jing Cao ◽  
Yanchun Li ◽  
Dequan Wang ◽  
...  
Keyword(s):  
Ab Initio ◽  
Adiabatic Potential ◽  
Basis Set ◽  
Potential Surfaces ◽  
High Level

The adiabatic potential energies for the lowest three states of a Li2H system are calculated with a high level ab initio method (MCSCF/MRCI) with a large basis set.

The cubyl cation rearrangements

2016 ◽  
Vol 52 (16) ◽  
pp. 3403-3405 ◽  
Author(s):  
Said Jalife ◽  
Sukanta Mondal ◽  
Jose Luis Cabellos ◽  
Gerardo Martinez-Guajardo ◽  
Maria A. Fernandez-Herrera ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Gas Phase ◽  
Dynamics Simulations ◽  
High Level

Born–Oppenheimer molecular dynamics simulations and high-level ab initio computations predict that the cage-opening rearrangement of the cubyl cation to the 7H+-pentalenyl cation is feasible in the gas phase.

Rearrangement of the Fulminate Anion (CNO-) to the Cyanate Anion (OCN-). Possible Intermediacy of the Oxazirinyl Anion

1986 ◽  
Vol 39 (6) ◽  
pp. 913 ◽  
Author(s):  
WK Li ◽  
J Baker ◽  
L Radom
Keyword(s):  
Gas Phase ◽  
Electron Correlation ◽  
Basis Set ◽  
Intramolecular Rearrangement ◽  
Molecular Orbital Calculations ◽  
Potential Well ◽  
Electron Loss ◽  
Diffuse Function ◽  
Moller Plesset ◽  
High Level

The rearrangement of the fulminate anion (CNO-) to the cyanate anion (OCN-) has been examined by using high-level ab initio molecular orbital calculations which include a diffuse-function-augmented polarization basis set and electron correlation incorporated at the full fourth-order Moller-Plesset level (MP4). The reaction is predicted to be exothermic by 275 kJ mol-1. Our best calculations indicate theinvolvement of a metastable cyclic oxazirinyl anion intermediate. However, this lies in an extremely shallow potential well and, in contrast to the predictions of semiempirical calculations, is unlikely to have more than a fleeting existence. The fulminate and cyanate anions are calculated to be stable with respect to electron loss and stable with respect to intramolecular rearrangement; accordingly, both should be observable gas-phase species.

scholarly journals How accurate are approximate quantum chemical methods at modelling solute–solvent interactions in solvated clusters?

2020 ◽  
Vol 22 (7) ◽  
pp. 3855-3866 ◽  
Author(s):  
Junbo Chen ◽  
Bun Chan ◽  
Yihan Shao ◽  
Junming Ho
Keyword(s):  
Ab Initio ◽  
Quantum Chemical ◽  
Interaction Energies ◽  
Chemical Methods ◽  
Dft Methods ◽  
Solvent Interactions ◽  
Quantum Chemical Methods ◽  
Composite Methods ◽  
Wide Range

In this paper, the performance of ab initio composite methods, and a wide range of DFT methods is assessed for the calculation of interaction energies of thermal clusters of a solute in water.

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