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

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.

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

Zeitschrift für Physikalische Chemie ◽

10.1515/zpch-2017-1095 ◽

2019 ◽

Vol 233 (3) ◽

pp. 449-469 ◽

Cited By ~ 1

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.

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Stereoelectronic Effects on the Conformational Properties of 1,3-Dioxane, 1,3-Dithiane, and 1,3-Diselenane: An Ab Initio Study and NBO Analysis

Phosphorus Sulfur and Silicon and the Related Elements ◽

10.1080/10426500801963780 ◽

2008 ◽

Vol 183 (10) ◽

pp. 2399-2409

Author(s):

Davood Nori-Shargh ◽

Shamsi Rafatpanah

Keyword(s):

Ab Initio ◽

Nbo Analysis ◽

Ab Initio Study ◽

Stereoelectronic Effects ◽

Conformational Properties

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

Journal of Theoretical and Computational Chemistry ◽

10.1142/s0219633611006797 ◽

2011 ◽

Vol 10 (06) ◽

pp. 803-817 ◽

Cited By ~ 3

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.

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Understanding the isomerization kinetics in the gas phase of a triazole-3-thione derivative: A theoretical approach

Journal of the Serbian Chemical Society ◽

10.2298/jsc181208013k ◽

2019 ◽

Vol 84 (9) ◽

pp. 975-989

Author(s):

Zahra Kazeminejad ◽

Abolfazl Shiroudi ◽

Khalil Pourshamsian ◽

Farhad Hatamjafari ◽

Ahmad Oliaey

Keyword(s):

Lone Pair ◽

Nbo Analysis ◽

State Theory ◽

Ground State Structure ◽

Energy Profiles ◽

Kinetic Rate Constants ◽

Resonance Energies ◽

Stabilization Energies ◽

The Stability ◽

Kinetics Of

The isomerization reactions of the 4-amino-5-methyl-2,4-dihydro- -3H-1,2,4-triazole-3-thione were studied using the B3LYP and M06-2x, as well as the CBS-QB3 theoretical methods. The measured energy profiles were complemented with kinetic rate constants using the transition state theory (TST). Based on the isomers geometries optimized using the CBS-QB3 method, a natural bond orbital (NBO) analysis shows that the stabilization energies of non-bonding lone-pair orbitals [LP(e)S7] to the ?*N2?C3 antibonding orbital increase from isomers 1 to 2. Moreover, the LP(e)S7 ? ?*N2?C3 delocalizations could fairly explain the increase in the occupancies of LP(e)S7 orbitals for isomers 1 and 2 (2 > 1). The studied stabilization energy increases the stability of the ground state structure, and could fairly explain the kinetics of the isomerization reactions 1 and 2 (k2 > k1). NBO results also suggest that the kinetics of these processes are controlled by the LP ??* resonance energies.

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An Ab Initio Study and NBO Analysis of the Stability and Conformational Properties of Hexakis(trimethylelementhyl)benzene (Element = C, Si, Ge, and Sn)

Phosphorus Sulfur and Silicon and the Related Elements ◽

10.1080/10426500600712883 ◽

2006 ◽

Vol 181 (10) ◽

pp. 2419-2434 ◽

Cited By ~ 6

Author(s):

Davood Nori-Shargh ◽

Daryoush Tahmassebi ◽

Mahboobeh Poukalhor ◽

Mostafa Mohammadpour Amini ◽

Saeed Jameh-Bozorghi ◽

...

Keyword(s):

Ab Initio ◽

Nbo Analysis ◽

Ab Initio Study ◽

Conformational Properties ◽

The Stability

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

International Journal of Emerging Research in Management and Technology ◽

10.23956/ijermt.v6i6.292 ◽

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.

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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

Letters in Organic Chemistry ◽

10.2174/1570178615666181022152818 ◽

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.

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