Intrinsic Stacking Interactions of Natural and Artificial Nucleobases

2019 ◽  
Author(s):  
Drew P. Harding ◽  
Laura J. Kingsley ◽  
Glen Spraggon ◽  
Steven Wheeler
Keyword(s):  
Gas Phase ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Molecular Descriptors ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Functional Theory ◽  
Binding Partner ◽  
Heavy Atoms ◽  
Wide Range

The intrinsic (gas-phase) stacking energies of natural and artificial nucleobases were explored using density functional theory (DFT) and correlated ab initio methods. Ranking the stacking strength of natural nucleobase dimers revealed a preference in binding partner similar to that seen from experiments, namely G > C > A > T > U. Decomposition of these interaction energies using symmetry-adapted perturbation theory (SAPT) showed that these dispersion dominated interactions are modulated by electrostatics. Artificial nucleobases showed a similar stacking preference for natural nucleobases and were also modulated by electrostatic interactions. A robust predictive multivariate model was developed that quantitively predicts the maximum stacking interaction between natural and a wide range of artificial nucleobases using molecular descriptors based on computed electrostatic potentials (ESPs) and the number of heavy atoms. This model should find utility in designing artificial nucleobase analogs that exhibit stacking interactions comparable to those of natural nucleobases. Further analysis of the descriptors in this model unveil the origin of superior stacking abilities of certain nucleobases, including cytosine and guanine.

Intrinsic Stacking Interactions of Natural and Artificial Nucleobases

2019 ◽  
Author(s):  
Drew P. Harding ◽  
Laura J. Kingsley ◽  
Glen Spraggon ◽  
Steven Wheeler
Keyword(s):  
Gas Phase ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Molecular Descriptors ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Functional Theory ◽  
Binding Partner ◽  
Heavy Atoms ◽  
Wide Range

The intrinsic (gas-phase) stacking energies of natural and artificial nucleobases were explored using density functional theory (DFT) and correlated ab initio methods. Ranking the stacking strength of natural nucleobase dimers revealed a preference in binding partner similar to that seen from experiments, namely G > C > A > T > U. Decomposition of these interaction energies using symmetry-adapted perturbation theory (SAPT) showed that these dispersion dominated interactions are modulated by electrostatics. Artificial nucleobases showed a similar stacking preference for natural nucleobases and were also modulated by electrostatic interactions. A robust predictive multivariate model was developed that quantitively predicts the maximum stacking interaction between natural and a wide range of artificial nucleobases using molecular descriptors based on computed electrostatic potentials (ESPs) and the number of heavy atoms. This model should find utility in designing artificial nucleobase analogs that exhibit stacking interactions comparable to those of natural nucleobases. Further analysis of the descriptors in this model unveil the origin of superior stacking abilities of certain nucleobases, including cytosine and guanine.

Ab Initio Theoretical Studies of Relative Stabilities and IR Spectrum of 5-Methylcytosine Tautomers

2003 ◽  
Vol 2003 (4) ◽  
pp. 195-199 ◽  
Author(s):  
Lida Ghassemzadeh ◽  
Majid Monajjemi ◽  
Karim Zare
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Density Functional ◽  
Relative Energy ◽  
Theoretical Studies ◽  
Functional Theory ◽  
Relative Stabilities ◽  
B3lyp Method ◽  
Wide Range ◽  
Good Agreement

The structure and relative energies of the tautomers of 5-methylcytosine in the gasphase and in different solvents are predicted using MP2 and density functional theory methods. The order of stability for these tautomers is C3>C1>C2>C4>C5>C6 calculated by MP2 and C1>C3>C2>C4>C5>C6 calculated by the B3LYP method. Relative energy calculations are performed in wide range of solvent dielectrics and in all solvents the oxo-amino C1 is predicted as the most stable tautomer. The infrared spectra of two dominant tautomers are calculated in the gas phase using HF and density functional theory. Good agreement between calculated (DFT) and experimental harmonic vibrational frequencies is found.

scholarly journals Unexpected Sandwiched-Layer Structure of the Cocrystal Formed by Hexamethylbenzene with 1,3-Diiodotetrafluorobenzene: A Combined Theoretical and Crystallographic Study

Crystals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 379 ◽  
Author(s):  
Yu Zhang ◽  
Jian-Ge Wang ◽  
Weizhou Wang
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Layer Structure ◽  
Noncovalent Interactions ◽  
Density Functional Theory Calculations ◽  
Stacking Interactions ◽  
Halogen Bonds ◽  
Functional Theory ◽  
Π Stacking ◽  
Cocrystal Structure

The cocrystal formed by hexamethylbenzene (HMB) with 1,3-diiodotetrafluorobenzene (1,3-DITFB) was first synthesized and found to have an unexpected sandwiched-layer structure with alternating HMB layers and 1,3-DITFB layers. To better understand the formation of this special structure, all the noncovalent interactions between these molecules in the gas phase and the cocrystal structure have been investigated in detail by using the dispersion-corrected density functional theory calculations. In the cocrystal structure, the theoretically predicted π···π stacking interactions between HMB and the 1,3-DITFB molecules in the gas phase can be clearly seen, whereas there are no π···π stacking interactions between HMB molecules or between 1,3-DITFB molecules. The attractive interactions between HMB molecules in the corrugated HMB layers originate mainly in the dispersion forces. The 1,3-DITFB molecules form a 2D sheet structure via relatively weak C–I···F halogen bonds. The theoretically predicted much stronger C–I···π halogen bonds between HMB and 1,3-DITFB molecules in the gas phase are not found in the cocrystal structure. We concluded that it is the special geometry of 1,3-DITFB that leads to the formation of the sandwiched-layer structure of the cocrystal.

scholarly journals Computational Studies on the Molecule 1-(2-Hydroxyethyl)-5-Fluorouracil in Gas Phase and Aqueous Solution and Prediction of Its Confinement inside Capped Nanotubes

2019 ◽  
Vol 2019 ◽  
pp. 1-14
Author(s):  
Y. Tadjouteu Assatse ◽  
G. W. Ejuh ◽  
F. Tchoffo ◽  
J. M. B. Ndjaka
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Molecular Descriptors ◽  
Structural Parameters ◽  
Computational Studies ◽  
Functional Theory ◽  
Quantum Molecular Descriptors ◽  
Nlo Properties ◽  
Oniom Method ◽  
Good Agreement

Density functional theory (DFT) calculations were performed on a fluorouracil derivative at the B3LYP/6−31+G(d) level. Furthermore, the ONIOM method was performed to investigate the possibility of its confinement inside capped nanotubes. The results found of the structural parameters of the optimized molecule are in good agreement with experimental data. The analysis of thermodynamic properties leads us to predict that the confinement of the studied molecule inside capped nanotubes SWCNT(12,0), SWCNT(14,0), and SWCNT(16,0) is possible. The large Eg values found suggest a good stability for the studied molecule. The predicted nonlinear optical (NLO) properties of the studied molecule are much greater than those of urea. Thereby, it is a good candidate as second-order NLO material. The calculated ∆Gsol values suggest that the studied molecule is more soluble than the 5-FU molecule. The results of quantum molecular descriptors show that the studied molecule is hard electrophile and strongly reactive.

Solvent effects on nonlinear optical response of certain tetrammineruthenium(II) complexes of modified 1,10-phenanthrolines

2013 ◽  
Vol 91 (12) ◽  
pp. 1303-1309 ◽  
Author(s):  
Muhammad Ramzan Saeed Ashraf Janjua ◽  
Asif Mahmood ◽  
Farooq Ahmad
Keyword(s):  
Optical Properties ◽  
Gas Phase ◽  
Solvent Effects ◽  
Density Functional ◽  
Nonlinear Optical ◽  
Structural Modification ◽  
Solvent Polarity ◽  
Nonlinear Optical Properties ◽  
Functional Theory ◽  
Wide Range

In this research paper, we have reported solvent effects on nonlinear optical properties of tetrammineruthenium(II) complexes of modified 1,10-phenanthrolines. Polarizability and hyperpolarizability were calculated in the gas phase, benzene (ε = 2.3), THF (ε = 7.52), dichloromethane (ε = 8.93), acetone (ε = 21.01), methanol (ε = 33.00), acetonitrile (ε = 36.64), and water (ε = 80.10) using density functional theory. These solvents cover a wide range of polarities. The results of theoretical investigation have shown that nonlinear optical properties significantly increased with the increase of solvent polarity. Solvent strongly affected hyperpolarizability as compared with polarizability. Nonlinear optical properties were also changed by the change of functional. Hyperpolarizability significantly changed with the change of functional as compared with polarizability. The results of this study indicate that like structural modification, polarity of the medium can significantly change the nonlinear optical properties.

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 Solution-Processed OLEDs Based on Thermally Activated Delayed Fluorescence Copper(I) Complexes with Intraligand Charge-Transfer Excited State

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 1125
Author(s):  
Teng Teng ◽  
Jinfan Xiong ◽  
Gang Cheng ◽  
Changjiang Zhou ◽  
Xialei Lv ◽  
...  
Keyword(s):  
Charge Transfer ◽  
Density Functional ◽  
Delayed Fluorescence ◽  
Quantum Yields ◽  
Functional Theory ◽  
Solution Processed ◽  
Thermally Activated Delayed Fluorescence ◽  
Light Emitting ◽  
Thermally Activated ◽  
Wide Range

A new series of tetrahedral heteroleptic copper(I) complexes exhibiting efficient thermally-activated delayed fluorescence (TADF) in green to orange electromagnetic spectral regions has been developed by using D-A type N^N ligand and P^P ligands. Their structures, electrochemical, photophysical, and electroluminescence properties have been characterized. The complexes exhibit high photoluminescence quantum yields (PLQYs) of up to 0.71 at room temperature in doped film and the lifetimes are in a wide range of 4.3–24.1 μs. Density functional theory (DFT) calculations on the complexes reveal the lowest-lying intraligand charge-transfer excited states that are localized on the N^N ligands. Solution-processed organic light emitting diodes (OLEDs) based on one of the new emitters show a maximum external quantum efficiency (EQE) of 7.96%.

scholarly journals A machine learning platform for the discovery of materials

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Carl E. Belle ◽  
Vural Aksakalli ◽  
Salvy P. Russo
Keyword(s):  
Machine Learning ◽  
Density Functional ◽  
Gw Approximation ◽  
Dft Methods ◽  
Functional Theory ◽  
Unit Cell Size ◽  
Learning Platform ◽  
Photovoltaic Materials ◽  
Wide Range ◽  
Quantum Espresso

AbstractFor photovoltaic materials, properties such as band gap $$E_{g}$$ E g are critical indicators of the material’s suitability to perform a desired function. Calculating $$E_{g}$$ E g is often performed using Density Functional Theory (DFT) methods, although more accurate calculation are performed using methods such as the GW approximation. DFT software often used to compute electronic properties includes applications such as VASP, CRYSTAL, CASTEP or Quantum Espresso. Depending on the unit cell size and symmetry of the material, these calculations can be computationally expensive. In this study, we present a new machine learning platform for the accurate prediction of properties such as $$E_{g}$$ E g of a wide range of materials.

Graph theory-based reaction pathway searches and DFT calculations for the mechanism studies of free radical-initiated peptide sequencing mass spectrometry (FRIPS MS): a model gas-phase reaction of GGR tri-peptide

2020 ◽  
Vol 22 (9) ◽  
pp. 5057-5069 ◽  
Author(s):  
Jae-ung Lee ◽  
Yeonjoon Kim ◽  
Woo Youn Kim ◽  
Han Bin Oh
Keyword(s):  
Graph Theory ◽  
Dft Calculations ◽  
Gas Phase ◽  
Density Functional ◽  
Reaction Pathway ◽  
Peptide Sequencing ◽  
Phase Reaction ◽  
Functional Theory ◽  
Fragmentation Mechanisms ◽  
Gas Phase Fragmentation

A new approach for elucidating gas-phase fragmentation mechanisms is proposed: graph theory-based reaction pathway searches (ACE-Reaction program) and density functional theory (DFT) calculations.

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