Cooperative Hydrogen-Bonding in Adenine−Thymine and Guanine−Cytosine Base Pairs. Density Functional Theory and Møller−Plesset Molecular Orbital Study

2003 ◽  
Vol 107 (33) ◽  
pp. 6441-6443 ◽  
Author(s):  
Amparo Asensio ◽  
Nadya Kobko ◽  
J. J. Dannenberg
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bonding ◽  
Molecular Orbital ◽  
Density Functional ◽  
Base Pairs ◽  
Functional Theory ◽  
Molecular Orbital Study ◽  
Moller Plesset ◽  
Cooperative Hydrogen Bonding ◽  
Adenine Thymine

Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment

2001 ◽  
Vol 114 (12) ◽  
pp. 5149-5155 ◽  
Author(s):  
Marcus Elstner ◽  
Pavel Hobza ◽  
Thomas Frauenheim ◽  
Sándor Suhai ◽  
Efthimios Kaxiras
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bonding ◽  
Nucleic Acid ◽  
Density Functional ◽  
Stacking Interactions ◽  
Acid Base ◽  
Base Pairs ◽  
Functional Theory ◽  
Nucleic Acid Base

CONFORMATIONAL PROPERTIES AND INTRAMOLECULAR HYDROGEN BONDING OF 3-AMINO-PROPENESELENAL: AN AB INITIO AND DENSITY FUNCTIONAL THEORY STUDIES

2013 ◽  
Vol 12 (04) ◽  
pp. 1350025 ◽  
Author(s):  
HEIDAR RAISSI ◽  
FARZANEH FARZAD ◽  
SHAHIRA ESLAMDOOST ◽  
FARIBA MOLLANIA
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bonding ◽  
Molecular Orbital ◽  
Continuum Model ◽  
Density Functional ◽  
Intramolecular Hydrogen Bonding ◽  
Stationary Points ◽  
Functional Theory ◽  
Polarized Continuum Model ◽  
Intramolecular Hydrogen

In the present work a conformational analysis of 3-amino-propeneselenal (APS) was performed using several computational methods, including DFT (B3LYP), MP2 and G2MP2. Harmonic vibrational frequencies were estimated at the same levels to confirm the nature of the stationary points found and also to account for the zero point vibrational energy (ZPVE) correction. Two intramolecular hydrogen bonds (HBs) established between the polar groups were identified by the structural geometric parameters. The excited-state properties of intramolecular hydrogen bonding in hydrogen bonded systems have been investigated theoretically using the time dependent density functional theory (TDDFT) method. The influence of the solvent on the stability order of conformers and the strength of intramolecular hydrogen bonding was considered using the polarized continuum model (PCM), the self-consistent isodensity polarized continuum model (SCI-PCM) and the integral equation formalism-polarizable continuum model (IEF-PCM) methods. The "atoms in molecules" theory of Bader was used to analyze critical points and to study the nature of HB in these systems. Natural bond orbital (NBO) analysis was also performed for better understanding the nature of intramolecular interactions. The calculated the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies show that charge transfer occur within the molecule. Further verification of the obtained transition state structures were implemented via intrinsic reaction coordinate (IRC) analysis. Calculations of the 1 H NMR chemical shift at GIAO/B3LYP/6–311++G** level of theory are also presented.

scholarly journals Computational Evaluation of Intermolecular Interaction in Poly(Styrene-Maleic Acid)-Water Complexes Using Density Functional Theory

2021 ◽  
Vol 21 (6) ◽  
pp. 1537
Author(s):  
Daru Seto Bagus Anugrah ◽  
Laura Virdy Darmalim ◽  
Permono Adi Putro ◽  
Liana Dewi Nuratikah ◽  
Nurwarrohman Andre Sasongko ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Molecular Orbital ◽  
Maleic Acid ◽  
Density Functional ◽  
Basis Set ◽  
Water Molecules ◽  
Functional Theory ◽  
High Hydrogen

The high application of Poly(styrene-maleic acid) (PSMA) in an aqueous environment, such as biomedical purposes, makes the interaction between PSMA and water molecules interesting to be investigated. This study evaluated the conformation, the hydrogen bond network, and the stabilities of all the possible intermolecular interactions between PSMA with water (PSMA−(H2O)n, n = 1–5). All calculations were executed using the density functional theory (DFT) method at B3LYP functional and the 6–311G** basis set. The energy interaction of PSMA–(H2O)5 complex was –56.66 kcal/mol, which is classified as high hydrogen bond interaction. The Highest Occupied Molecular Orbital (HOMO) – Lowest Unoccupied Molecular Orbital (LUMO) energy gap decreased with the rise in the number of H2O molecules, representing a more reactive complex. The strongest hydrogen bonding in PSMA–(H2O)5 wasformed through the interaction on O72···O17–H49 with stabilizing energy of 50.32 kcal/mol, that analyzed by natural bond orbital (NBO) theory. The quantum theory atoms in molecules (QTAIM) analysis showed that the hydrogen bonding (EHB) value on O72···O17–H49 was –14.95 kcal/mol. All computational data revealed that PSMA had moderate to high interaction with water molecules that indicated the water molecules were easily transported and kept in the PSMA matrix.

Possible use of BN-modified fullerene as a nano-biosensor to detect adenine–thymine Watson–Crick base pair in mutagenic tautomeric form: Theoretical approach

2015 ◽  
Vol 14 (01) ◽  
pp. 1550003 ◽  
Author(s):  
Shamoon Ahmad Siddiqui ◽  
Tabish Rasheed ◽  
Nadir Bouarissa ◽  
A. Al-Hajry
Keyword(s):  
Density Functional Theory ◽  
Electronic Structure ◽  
Theoretical Approach ◽  
Electronic Structures ◽  
Density Functional ◽  
Tautomeric Form ◽  
Theoretical Calculations ◽  
Base Pairs ◽  
Functional Theory ◽  
Adenine Thymine

The present work deals with the theoretical investigation of electronic structure features and stability of adenine–thymine (AT) and rare tautomer of adenine–thymine (rAT) base pairs along with their complexes with Cu 2+ cation and their interactions with BN doped fullerene ( C 58 BN ). All the calculations have been performed with density functional theory using B3LYP functional. Electronic structures of the two base pairs are almost identical. Hence, it is rather difficult to distinguish between the two base pairs on the basis of their electronic properties. As per our theoretical calculations, we have observed that, BN modified fullerene could act as a nano-biosensor for detection of mispairing between these two complementary bases as well as their Cu 2+ complexes.

MOLECULAR STRUCTURE, VIBRATIONAL ASSIGNMENTS, CONFORMATIONAL STABILITY, GROUND AND EXCITED STATE HYDROGEN-BONDING ANALYSIS OF 2-NITROSO VINYL AMINE

2013 ◽  
Vol 12 (07) ◽  
pp. 1350072 ◽  
Author(s):  
FARIBA MOLLANIA ◽  
HEIDAR RAISSI
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bonding ◽  
Excited State ◽  
Molecular Orbital ◽  
Density Functional ◽  
Dominant Factor ◽  
Potential Energy Distribution ◽  
Functional Theory ◽  
Stability Order ◽  
The Stability

In the present work, a detailed conformational study is performed using several computational methods, including density functional theory (DFT) (B3LYP), MP2 and G2MP2 on 2-Nitroso vinyl amine (NVA) in order to determine the stability order of conformers and the various possibilities of intramolecular hydrogen bonding (HB) formation. Four conformers exhibit HB . This feature, although not being the dominant factor in energetic terms, appears to be of foremost importance to define the geometry of the molecule. According to our theoretical results, oximimine conformers are more stable than the corresponding nitrosoamine and nitrosoimine analogues. Theoretical calculations show the following order for intramolecular HB strength in the conformers of title compound: [Formula: see text] The nature of intramolecular HB has been investigated by means of the Bader theory of atoms in molecules (AIM) and natural bond orbital (NBO) analysis. Also, Harmonic Oscillator Model of Aromaticity (HOMA) index as a geometrical indicator of a local aromaticity are investigated. The influence of the solvent on the stability order of conformers and the strength of intramolecular HB is considered using the Onsager reaction field model. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies confirm that charge transfer occur within the molecule. Further verification of the obtained transition state structures were implemented via intrinsic reaction coordinate (IRC) analysis. Calculations of the 1 H NMR chemical shift at GIAO/B3LYP/6–311++G** levels of theory are also presented. The excited-state properties of intramolecular HB in H -bonded systems have been investigated theoretically using the time-dependent density functional theory (TD-DFT) method. The complete vibrational assignment for three H -bonded conformers has been made on the basis of the calculated potential energy distribution (PED).

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>

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