Density Functional Computations on 6-Aminouracil: Effect of Amino Group in the 6th Position on the Watson–Crick Base Pair Uridine–Adenosine

2016 ◽  
Vol 69 (8) ◽  
pp. 881 ◽  
Author(s):  
M. Alcolea Palafox ◽  
V. K. Rastogi
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Water Molecules ◽  
Amino Group ◽  
Infrared And Raman Spectra ◽  
Interaction Energies ◽  
Base Pairs ◽  
Functional Theory ◽  
The Stability ◽  
Density Functional Computations

The predicted infrared and Raman spectra of 6-aminouracil in the solid state by density functional theory methods were analyzed and compared with the experimental spectra. The effect of amino substitution in the sixth position of uridine on the stability of the Watson–Crick (WC) base pairs with deoxyadenosine was evaluated. Different WC pairs of 5-aminouridine, 6-aminouridine, and uridine with deoxyadenosine were simulated, and the counterpoise-corrected interaction energies were determined. 6-Aminouridine produces a stronger WC pair than that involving uridine, and its high dipole moment facilitates interaction with water molecules.

INVESTIGATION OF THE INTERACTION OF HYDROXYL AND HYDROPEROXYL RADICALS WITH ETHENE IN THE PRESENCE OF WATER MOLECULES USING COMPUTATIONAL METHODS

2007 ◽  
Vol 06 (02) ◽  
pp. 377-397
Author(s):  
SEIFOLLAH JALILI ◽  
MINA SOLEIMANI
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Computational Methods ◽  
Density Functional ◽  
Atoms In Molecules ◽  
Water Molecules ◽  
Functional Theory ◽  
Aim Theory ◽  
Thermodynamical Parameters ◽  
The Stability

In this work, the interaction of hydroxyl and hydroperoxyl radicals with ethene in the presence of water molecules and the stability of C 2 H 4 + HO x + ( H 2 O )y; x = 1–2, y = 0–5 clusters were investigated using computational methods. Also, hydrogen bond of these clusters was investigated using Density Functional Theory (DFT) and Atoms in Molecules (AIM) theory. Thermodynamical parameters for the interaction of hydroxyl and hydroperoxyl radicals with ethene in the presence of water molecules were also calculated. We report new results for the interaction of hydroxyl and hydroperoxyl radicals with ethene in the presence of water molecules.

On the Nature of Halide-Water Interactions: Insights from Many-Body Representations and Density Functional Theory

2019 ◽  
Author(s):  
Brandon B. Bizzarro ◽  
Colin K. Egan ◽  
Francesco Paesani
Keyword(s):  
Density Functional Theory ◽  
Charge Transfer ◽  
Molecular Orbital ◽  
Density Functional ◽  
Decomposition Analysis ◽  
Orbital Energy ◽  
Energy Decomposition Analysis ◽  
Interaction Energies ◽  
Many Body ◽  
Functional Theory

<div> <div> <div> <p>Interaction energies of halide-water dimers, X<sup>-</sup>(H<sub>2</sub>O), and trimers, X<sup>-</sup>(H<sub>2</sub>O)<sub>2</sub>, with X = F, Cl, Br, and I, are investigated using various many-body models and exchange-correlation functionals selected across the hierarchy of density functional theory (DFT) approximations. Analysis of the results obtained with the many-body models demonstrates the need to capture important short-range interactions in the regime of large inter-molecular orbital overlap, such as charge transfer and charge penetration. Failure to reproduce these effects can lead to large deviations relative to reference data calculated at the coupled cluster level of theory. Decompositions of interaction energies carried out with the absolutely localized molecular orbital energy decomposition analysis (ALMO-EDA) method demonstrate that permanent and inductive electrostatic energies are accurately reproduced by all classes of XC functionals (from generalized gradient corrected (GGA) to hybrid and range-separated functionals), while significant variance is found for charge transfer energies predicted by different XC functionals. Since GGA and hybrid XC functionals predict the most and least attractive charge transfer energies, respectively, the large variance is likely due to the delocalization error. In this scenario, the hybrid XC functionals are then expected to provide the most accurate charge transfer energies. The sum of Pauli repulsion and dispersion energies are the most varied among the XC functionals, but it is found that a correspondence between the interaction energy and the ALMO EDA total frozen energy may be used to determine accurate estimates for these contributions. </p> </div> </div> </div>

scholarly journals The stability and electronic and photocatalytic properties of the ZnWO4 (010) surface determined from first-principles and thermodynamic calculations

RSC Advances ◽  
2021 ◽  
Vol 11 (38) ◽  
pp. 23477-23490
Author(s):  
Yonggang Wu ◽  
Jihua Zhang ◽  
Bingwei Long ◽  
Hong Zhang
Keyword(s):  
Phase Diagram ◽  
Density Functional Theory ◽  
First Principles ◽  
Density Functional ◽  
Thermodynamic Calculations ◽  
Photocatalytic Properties ◽  
Thermodynamic Approach ◽  
Functional Theory ◽  
Stability Phase Diagram ◽  
The Stability

The ZnWO4 (010) surface termination stability is studied using a density functional theory-based thermodynamic approach. The stability phase diagram shows that O-Zn, DL-W, and DL-Zn terminations of ZnWO4 (010) can be stabilized.

scholarly journals Hydration Dependent Band Gap Tunability of Self-Assembled Phenylalanine-Tryptophan Nanotubes

2020 ◽  
Author(s):  
Hugo Souza ◽  
Antonio Chaves Neto ◽  
Francisco Sousa ◽  
Rodrigo Amorim ◽  
Alexandre Reily Rocha ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Band Gap ◽  
Electronic Properties ◽  
Building Block ◽  
Density Functional ◽  
Tight Binding ◽  
Water Molecules ◽  
Confined Water ◽  
Functional Theory ◽  
Tight Binding Method

In this work, we investigate the effects of building block separation of Phenylalanine-Tryptophan nanotube induced by the confined water molecules on the electronic properties using density-functional theory based tight-binding method. <div><br></div>

scholarly journals Supramolecular Complexes of Cucurbiturils with Second Group Metal Salts and Hydrates and Histamine

INEOS OPEN ◽  
2021 ◽  
Vol 4 ◽  
Author(s):  
Yu. A. Borisov ◽  
◽  
S. S. Kiselev ◽  
Keyword(s):  
Aqueous Solution ◽  
Density Functional Theory ◽  
Density Functional ◽  
Metal Salts ◽  
Supramolecular Complexes ◽  
Water Molecules ◽  
Functional Theory ◽  
Guest Molecules ◽  
First Time ◽  
Formation Energies

The interaction of cucurbiturils (Q6, Q7, and Q8) with Ca and Ba chlorides and iodides are studied for the first time by density functional theory. The thermodynamic parameters for the formation of host–guest complexes are calculated. The structures of complexes of Q6 and Q7 with one and two guest molecules are established. The energy parameters for the transfer of Be2+ and Ba2+ cations from an aqueous solution into the cavity of Q7 containing n water molecules are defined. The dependences of the formation energies for complexes Q7WnBe2+ and Q7WnBa2+ on the number of water molecules are shown to be parabolic, with the energy minima at n = 5 and n = 6, respectively. It is found that Q7 can form in an aqueous solution supramolecular complexes with protonated histamine (HA) and neutral histamine in the presence of Ca2+ ions.

Predicting the stability of ternary intermetallics with density functional theory and machine learning

2018 ◽  
Vol 148 (24) ◽  
pp. 241728 ◽  
Author(s):  
Jonathan Schmidt ◽  
Liming Chen ◽  
Silvana Botti ◽  
Miguel A. L. Marques
Keyword(s):  
Machine Learning ◽  
Density Functional Theory ◽  
Density Functional ◽  
Functional Theory ◽  
The Stability

Impact of N-(2-aminoethyl) Glycine Unit on Watson-Crick Base Pairs

2019 ◽  
Vol 233 (3) ◽  
pp. 449-469 ◽  
Author(s):  
Indumathi Karunakaran ◽  
Abiram Angamuthu ◽  
Praveena Gopalan
Keyword(s):  
Density Functional ◽  
Structural Parameters ◽  
Base Pairs ◽  
Functional Theory ◽  
Amide Bonds ◽  
Highest Occupied Molecular Orbital ◽  
Minimal Distortion ◽  
Stabilization Energies ◽  
The Stability ◽  
Lowest Unoccupied Molecular Orbitals

Abstract We aim to understand the structure and stability of the backbone tailored Watson-Crick base pairs, Guanine-Cytosine (GC), Adenine-Thymine (AT) and Adenine-Uracil (AU) by incorporating N-(2-aminoethyl) glycine units (linked by amide bonds) at the purine and pyrimidine sites of the nucleobases. Density functional theory (DFT) is employed in which B3LYP/6-311++G∗∗ level of theory has been used to optimize all the structures. The peptide attached base pairs are compared with the natural deoxyribose nucleic acid (DNA)/ribonucleic acid (RNA) base pairs and the calculations are carried out in both the gas and solution phases. The structural propensities of the optimized base pairs are analyzed using base pair geometries, hydrogen bond distances and stabilization energies and, compared with the standard reference data. The structural parameters were found to correlate well with the available data. The addition of peptide chain at the back bone of the DNA/RNA base pairs results only with a minimal distortion and hence does not alter the structural configuration of the base pairs. Also enhanced stability of the base pairs is spotted while adding peptidic chain at the purine site rather than the pyrimidine site of the nucleobases. The stability of the complexes is further interpreted by considering the hydrogen bonded N–H stretching frequencies of the respective base pairs. The discrimination in the interaction energies observed in both gas and solution phases are resulted due to the existence of distinct lowest unoccupied molecular orbitals (LUMO) in the solution phase. The reactivity of the base pairs is also analyzed through the in-depth examinations on the highest occupied molecular orbital (HOMO)-LUMO orbitals.

Sign in / Sign up

Export Citation Format

Share Document