DFT STUDY ON CONFORMATIONAL BEHAVIOR OF HYDROGEN ION ABSTRACTIONS OF CYTOSINE NUCLEOSIDES: AIM AND NBO ANALYSIS

2011 ◽  
Vol 10 (06) ◽  
pp. 803-817 ◽  
Author(s):  
ZAHRA ALIAKBAR TEHRANI ◽  
ALIREZA FATTAHI ◽  
MARJAN JEBELI JAVAN ◽  
MOHAMMAD MAHMOODI HASHEMI
Keyword(s):  
Structural Parameters ◽  
Nbo Analysis ◽  
Basis Sets ◽  
Orbital Method ◽  
Acceptor Interaction ◽  
Hydride Ion ◽  
Stability Order ◽  
The Stability ◽  
Intramolecular Hydrogen ◽  
Hydride Ions

In this paper, we explore theoretically energetic and structural properties of the possible cations formed via hydride ion abstraction at various sites of sugar part of cytosine nucleosides by employing B3LYP exchange-correlation functional with 6-311++G (d,p) orbital basis sets. In general, the hydride ion abstracted sugar cations of cytosine nucleosides have the following stability sequence: caH2′ > caH1′ > caH3′ > caH4′ > caH5′ for cytidine and caH1′ > caH4′ > caH3′ > caH5′ > caH2′ for deoxycytidine. Furthermore, the effect of solvent environment on the stability order of cations integral equation formalism of the polarized model (IEF-PCM) was employed to model aqueous solution. The natural bond orbital method was used for quantitative analysis of the electron delocalization donor–acceptor interaction of various hydride ions abstracted centers of cytosine nucleosides. The role of CH⋯O and HO⋯H intramolecular hydrogen bonds in the stability of cations is investigated based on the results of topological properties of atom in molecule theory. Moreover, variations of significant structural parameters such as puckering amplitudes and phase angles of sugar parts of cytosine nucleosides after cation formation are also found.

A Computational Study of the Conformational Behavior of 2,5-Dimethyl- 1,4-dithiane-2,5-diol and Analogous S and Se: DFT and NBO Study

2020 ◽  
Vol 17 (10) ◽  
pp. 749-759
Author(s):  
Elmira Danaie ◽  
Shiva Masoudi ◽  
Nasrin Masnabadi
Keyword(s):  
Thermodynamic Parameters ◽  
Computational Study ◽  
Structural Parameters ◽  
Nbo Analysis ◽  
Electron Delocalization ◽  
Stereoelectronic Effects ◽  
Conformational Properties ◽  
Molecular Reactivity ◽  
Stabilization Energies ◽  
The Stability

Conformational behaviors of 2,5-dimethyl-1,4-dithiane-2,5-diol (compound 1), 2,5- dimethyl-1,4-dithiane-2,5-dithiol (compound 2) and 2,5-dimethyl-1,4-dithiane-2,5-diselenol (compound 3) were investigated by the B3LYP/6-311+G **, the M06-2X/aug-ccpvdz levels of theory and natural bond orbital NBO analysis. The structures and the structural parameters of the mentioned molecules were optimized by the B3LYP and the M06-2X methods. We assessed the roles and contributions of the effective factors in the conformational properties of the mentioned compounds by means of the B3LYP and M06-2X levels of theory and the NBO interpretations. The stereoelectronic effects of the mentioned molecules were studied using the NBO analysis. The results showed that the stereoelectronic effects were in favor of the (ax,ax) conformers (the most stable conformations), from compound 1 to compound 3; therefore, these effects have impacts on the conformational properties of compounds 1-3, and stabilization energies associated with LP2X→ σ*S1-C2 electron delocalization, where [X= O, S, and Se], for 1-ax, ax conformer has the greatest value between all of the other conformers. Therefore, according to the calculated thermodynamic parameters, the stability of the 1-ax, ax compound was justified by the presence of LP2X→σ*S1-C2 electron delocalization. A molecular orbital explanation was conducted to investigate the correlations between the linear combinations of natural bond orbitals in the HOMOs, LUMOs and the molecular reactivity parameters. There is a direct relationship between the stereoelectronic effects, molecular reactivity and thermodynamic parameters of compounds 1 to 3 as the harder ax, ax conformations with the greater stereoelectronic effects and ΔG(eq-ax) values are more stable than their corresponding eq, eq conformers. Besides frontier molecular orbitals (FMOs), mapped molecular electrostatic potential (MEP) surfaces of conformations of compounds 1 to 3 were investigated.

Homoselenocysteine — An oxygen or selenium acid in the gas phase?

2010 ◽  
Vol 88 (8) ◽  
pp. 744-753 ◽  
Author(s):  
Marcela Hurtado ◽  
Otilia Mó ◽  
Manuel Yáñez
Keyword(s):  
Gas Phase ◽  
Global Minimum ◽  
Group Structure ◽  
Hydroxyl Group ◽  
Amino Group ◽  
Deprotonated Form ◽  
Protonated Amino Group ◽  
Stability Order ◽  
The Stability ◽  
Intramolecular Hydrogen

The potential energy surface of l-homoselenocysteine (HSEC) has been explored through the use of B3LYP/6-311+G(d,p) calculations. In this survey, seventy-seven different conformers have been located. These local minima can be classified in four groups, A–D. Structures A, B, and D are stabilized by intramolecular hydrogen bonds (IMHBs) with the amino group acting as the hydrogen bond (HB) donor and the carbonyl group (structures A and D) or the hydroxyl group (structure B) as HB acceptors. The structures in set C present an IMHB with the amino group acting as the HB acceptor and the hydroxyl group as the HB donor. The stability order decreases in the following order: A > B > C > D. From their relative stabilities it can be concluded that only three of these conformers, namely A1, A4, and A5, would exist in the gas phase at room temperature. The most stable deprotonated form corresponds to a Se-deprotated species stabilized by a strong IMHB between the hydroxyl group and the Se atom. However, a direct deprotonation of the most stable neutrals lead to O-deprotonated species, which eventually isomerize to yield the global minimum. Hence, we can conclude that, quite unexpectedly, HSEC behaves as a Se acid in the gas phase, its intrinsic acidity being 1374 kJ mol–1 at the B3LYP/6-311++G(3df,2p) level of theory. The most stable protonated forms are systematically the N-protonated ones, the global minimum being a structure stabilized through an IMHB involving the protonated amino group as the HB donor and the SeH group as the HB acceptor. The calculated gas-phase proton affinity (PA) at the B3LYP/6-311++G(3df,2p) level of theory is 930 kJ mol–1.

scholarly journals Coordination Behavior of Ni2+, Cu2+, and Zn2+ in Tetrahedral 1-Methylimidazole Complexes: A DFT/CSD Study

2018 ◽  
Vol 2018 ◽  
pp. 1-8 ◽  
Author(s):  
Samuel Tetteh
Keyword(s):  
Density Functional ◽  
Population Analysis ◽  
Substantial Reduction ◽  
Nbo Analysis ◽  
Basis Sets ◽  
Dft Methods ◽  
Functional Theory ◽  
Formal Charge ◽  
Coordination Behavior ◽  
The Stability

The interaction between nickel (Ni2+), copper (Cu2+), and zinc (Zn2+) ions and 1-methylimidazole has been studied by exploring the geometries of eleven crystal structures in the Cambridge Structural Database (CSD). The coordination behavior of the respective ions was further investigated by means of density functional theory (DFT) methods. The gas-phase complexes were fully optimized using B3LYP/GENECP functionals with 6-31G∗ and LANL2DZ basis sets. The Ni2+ and Cu2+ complexes show distorted tetrahedral geometries around the central ions, with Zn2+ being a perfect tetrahedron. Natural bond orbital (NBO) analysis and natural population analysis (NPA) show substantial reduction in the formal charge on the respective ions. The interaction between metal d-orbitals (donor) and ligand orbitals (acceptor) was also explored using second-order perturbation of the Fock matrix. These interactions followed the order Ni2+ > Cu2+ > Zn2+ with Zn2+ having the least interaction with the ligand orbitals. Examination of the frontier orbitals shows the stability of the complexes in the order Ni2+ > Cu2+ < Zn2+ which is consistent with the Irving–Williams series.

STUDY OF INTRAMOLECULAR HYDROGEN BONDING IN ORTHO-SUBSTITUTED ACETANILIDE COMPOUNDS USING COMPUTATIONAL METHODS

2004 ◽  
Vol 03 (04) ◽  
pp. 527-542 ◽  
Author(s):  
SEIFOLLAH JALILI ◽  
MOJDEH AKHAVAN
Keyword(s):  
Hydrogen Bonding ◽  
Density Functional ◽  
Structural Parameters ◽  
Intramolecular Hydrogen Bonding ◽  
Basis Sets ◽  
Structural Factors ◽  
Functional Theory ◽  
Aim Theory ◽  
Moller Plesset ◽  
Intramolecular Hydrogen

The intramolecular hydrogen bonding formation in ortho-substituted compounds of Acetanilide, ortho-hydroxy Acetanilide and ortho-nitro Acetanilide, was investigated using Density Functional Theory (DFT), Møller-Plesset second-order (MP2) method and "Atoms in Molecules (AIM)" theory. It was found that in each case, the cis isomer is more stable than the trans isomer and ortho-nitro Acetanilide forms a stronger hydrogen bond than ortho-hydroxy Acetanilide. The effects of hydrogen bonding on structural parameters of the considered systems were studied using Becke's functional (B3LYP) and at the ab initio MP2 level in conjunction with different basis sets and suitable structural factors. The results are in agreement with the results of AIM theory.

HUMO-LUMO Studies on Methyl Orange Doped ZTS Crystals for Laser Applications

2018 ◽  
Vol 6 (6) ◽  
pp. 362
Author(s):  
G. Suresh ◽  
K. Sambath Kumar ◽  
P. Ambalavanan ◽  
P. Kumaresan
Keyword(s):  
Molecular Electrostatic Potential ◽  
Nbo Analysis ◽  
Inorganic Materials ◽  
Thermo Gravimetric ◽  
Laser Applications ◽  
Charge Delocalization ◽  
Device Applications ◽  
Warming Rate ◽  
The Stability ◽  
Homo Lumo

Zinc Thiourea Sulphate (ZTS), crystal is a magnificent metal natural compound, which consolidates the upsides of both natural and inorganic materials when contrasted and other customary non-linear optical materials and in this way can be utilized as a part of a more extensive scope of uses. Late endeavors at delivering new recurrence transformation materials have concentrated essentially on expanding the extent of the NLO properties that can recurrence twofold low pinnacle control sources, for example, diode lasers.  The thermo gravimetric examination (TGA) and differential warm investigation (DTA) were completed utilizing Seiko warm analyzer at warming rate 20°C/min in air to decide the warm dependability of the compound. ZTS crystals were developed by moderate cooling procedure. This empowers the development of mass gems along all the three bearings at an ideal pH. FTIR examines demonstrate that in the spectra of ZTS there is a move in the recurrence band in the low-recurrence district which uncovers that thiourea shapes sulfur-to-zinc securities in the ZTS crystals. The stability and charge delocalization of the molecule were also studied by natural bond orbital (NBO) analysis. The HOMO-LUMO energies describe the charge transfer takes place within the molecule. Molecular electrostatic potential has been analyzed.  The developments try in extensive scale with this enhanced pH qualities is required to yield mass crystal appropriate for laser combination tests and SHG device applications.

Molecular Investigations of the Newly Synthesized Azomethines as Antioxidants: Theoretical and Experimental Studies

2019 ◽  
Vol 19 (6) ◽  
pp. 419-433 ◽  
Author(s):  
Siyamak Shahab ◽  
Masoome Sheikhi ◽  
Liudmila Filippovich ◽  
Evgenij Dikusar ◽  
Anhelina Pazniak ◽  
...  
Keyword(s):  
Density Functional ◽  
Energy Gap ◽  
Experimental Studies ◽  
Antioxidant Property ◽  
Nbo Analysis ◽  
Antioxidant Potential ◽  
Functional Theory ◽  
Homo And Lumo ◽  
Intramolecular Hydrogen ◽  
Activity Mechanism

: In this study, the antioxidant property of new synthesized azomethins has been investigated as theoretical and experimental. Methods and Results: Density functional theory (DFT) was employed to investigate the Bond Dissociation Enthalpy (BDE), Mulliken Charges, NBO analysis, Ionization Potential (IP), Electron Affinities (EA), HOMO and LUMO energies, Hardness (η), Softness (S), Electronegativity (µ), Electrophilic Index (ω), Electron Donating Power (ω-), Electron Accepting Power (ω+) and Energy Gap (Eg) in order to deduce scavenging action of the two new synthesized azomethines (FD-1 and FD-2). Spin density calculations and NBO analysis were also carried out to understand the antioxidant activity mechanism. Comparison of BDE of FD-1 and FD-2 indicate the weal antioxidant potential of these structures. Conclusion: FD-1 and FD-2 have very high antioxidant potential due to the planarity and formation of intramolecular hydrogen bonds.

Quantum Mechanical Investigation of Geometrical Structure and Dynamic Behavior of h-BNNT (9,9-5) and h-AlNNT (9,9-5)Single-Walled Nanotubes: NBO Analysis

2019 ◽  
Vol 16 (9) ◽  
pp. 705-717
Author(s):  
Mehrnoosh Khaleghian ◽  
Fatemeh Azarakhshi
Keyword(s):  
Carbon Nanotubes ◽  
Density Functional ◽  
Structural Parameters ◽  
Energy Levels ◽  
Nbo Analysis ◽  
Electronic Energy ◽  
Boron Nitride Nanotubes ◽  
Basis Set ◽  
B3lyp Method ◽  
Mechanical Investigation

In the present research, B45H36N45 Born Nitride (9,9) nanotube (BNNT) and Al45H36N45 Aluminum nitride (9,9) nanotube (AlNNT) have been studied, both having the same length of 5 angstroms. The main reason for choosing boron nitride nanotubes is their interesting properties compared with carbon nanotubes. For example, resistance to oxidation at high temperatures, chemical and thermal stability higher rather than carbon nanotubes and conductivity in these nanotubes, unlike carbon nanotubes, does not depend on the type of nanotube chirality. The method used in this study is the density functional theory (DFT) at Becke3, Lee-Yang-Parr (B3LYP) method and 6-31G* basis set for all the calculations. At first, the samples were simulated and then the optimized structure was obtained using Gaussian 09 software. The structural parameters of each nanotube were determined in 5 layers. Frequency calculations in order to extract the thermodynamic parameters and natural bond orbital (NBO) calculations have been performed to evaluate the electron density and electrostatic environment of different layers, energy levels and related parameters, such as ionization energy and electronic energy, bond gap energy and the share of hybrid orbitals of different layers.

Numerical and Experimental Approaches to Investigate the Stability of a Motorcycle Vehicle

2006 ◽  
Author(s):  
Federico Cheli ◽  
Marco Bocciolone ◽  
Marco Pezzola ◽  
Elisabetta Leo
Keyword(s):  
Degrees Of Freedom ◽  
Structural Parameters ◽  
Experimental Tests ◽  
Roll Angle ◽  
Longitudinal Motion ◽  
Reference Trajectory ◽  
Steering Angle ◽  
Steady State Condition ◽  
The Stability ◽  
Linearized Model

The study of motorcycle’s stability is an important task for the passenger’s safety. The range of frequencies involved for the handling stability is lower than 10 Hz. A numerical model was developed to access the stability of a motorcycle vehicle in this frequency range. The stability is analysed using a linearized model around the straight steady state condition. In this condition, the vehicle’s vertical and longitudinal motion are decoupled, hence the model has only four degrees of freedom (steering angle, yaw angle, roll angle and lateral translation), while longitudinal motion is imposed. The stability was studied increasing the longitudinal speed. The input of the model can be either a driver input manoeuvre (roll angle) or a transversal component of road input able to excite the vibration modes. The driver is introduced in the model as a steering torque that allows the vehicle to follow a reference trajectory. To validate the model, experimental tests were done. To excite the vehicle modes, the driver input was not taken into account considering both the danger for the driver and the repeatability of the manoeuvre. Two different vehicle configurations were tested: vehicle 1 is a motorcycle [7] and vehicle 2 is a scooter. Through the use of the validated model, a sensitivity analysis was done changing structural (for example normal trail, steering angle, mass) and non structural parameters (for example longitudinal speed).

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