Natural Bond Orbital Interpretation Research Articles

The Origin of the Chiral gauche-Conformation Preferences in Chloromethyl Methyl Ether and Analogues Containing S and Se Atoms: A Hybrid-Density Functional Study and Natural Bond Orbital Interpretation

The Origin of the Chiral gauche-Conformation Preferences in Chloromethyl Methyl Ether and Analogues Containing S and Se Atoms: A Hybrid-Density Functional Study and Natural Bond Orbital Interpretation

Computational spectroscopic investigations on structural validation with IR and Raman experimental evidence, projection of ultraviolet-visible excitations, natural bond orbital interpretations, and molecular docking studies under the biological investigation on N-Benzyloxycarbonyl-L-Aspartic acid 1-Benzyl ester

Abstract Experimental Fourier Transform Infra-Red spectrum and Fourier Transform Raman spectrum with Micro Raman spectrum of the N-Benzyloxycarbonyl-L-Aspartic acid 1-Benzyl Ester have been analyzed for molecular structural determination. A hybrid Becke's three-parameter technique with the Lee-Yang-Par (B3LYP) correlation method of Density functional theory (DFT) with 6–311++G(d,p) basic set was used for the investigations on quantum computational spectroscopic calculations. Chemical stabilization energy associated with hyper-conjugative interactions with polarization coefficients and natural Lewis structures were determined by Natural bond orbital analysis. Molecular dynamic simulations with global reactive descriptors were obtained by calculated Frontier molecular orbital energies. The charge density distribution has been visualized by electrostatic potential surfaces. Local reactive behaviors of the chemical compound with the graphical representation of the Fukui functions were obtained. The UltraViolet-Visible light absorptions with different electronic excitations were constructed by the method of Time-dependent DFT. Molecular docking was introduced for N-Benzyloxycarbonyl-L-Aspartic acid 1-Benzyl Ester into different proteins (1ITO, 2ZCO, 1J1J, and COVID-19 proteins).

The Origin of the Chiral gauche-Conformation Preferences in Halomethyl Methyl Ethers. A Hybrid-Density Functional Study and Natural Bond Orbital Interpretation

The effects of the stereoelectronic interaction on the structural and conformational properties of fluoromethyl methyl ether (1) and its analogues containing Cl (2), Br (3), and I (4) atoms were investigated by means of hybrid-density functional based method (B3LYP/Def2-TZVPP) and natural bond orbital (NBO) interpretation. Consistent with the reported experimental data, the chiral gauche conformations of compounds 1–4 are more stable than their corresponding anti conformations. The results showed that the energy barriers of the racemization processes of the chiral gauche-conformations of compounds 1–4 via the plane symmetrical anti conformations are smaller than the plane symmetrical eclipsed transition structures. According to the NBO analysis, the hyperconjugative generalized anomeric effect (HCGAE) increased from compound 1 to compound 4, which explains the increase of the energy discrepancy between their corresponding chiral gauche- and plane symmetrical anti-conformations. In contrast to the trend for the HCGAE, the determined dipole moment discrepancy between the chiral gauche- and plane symmetrical anti-conformations (µanti–µgauche) reduced from compound 1 to compound 4. This fact reveals that there is no correlation between the variations of the conformational preferences in compounds 1–4 and the electrostatic effects associated with the dipole–dipole interactions. There is an excellent agreement between the racemization energy barriers and the proportion between the GAE for compounds 2–4 and compound 1 (i.e., GAEx/GAE1) as well as the difference between the Wiberg Bond Indexes of C1–O2 bonds (Δ[WBIanti-gauche(C1–O2)]). The associations between the HCGAE, pairwise steric exchange energies (PSEE), WBI, dipole moments, orbital integrals, structural parameters, and conformational behaviors of compounds 1–4 have been studied.

New Insights into the Origin of the cis-Configuration Preferences in 1,2-Dihaloethenes: The Importance of the Bonding Orbital Deviations

The origin of the preferences for the cis-configurations in 1,2-difluoroethene (1), 1,2-dichloroethene (2), and 1,2-dibromoethene (3) were explored by means of the G3MP2, LC-ωPBE and CCSD(T) methods with the 6–311+G** basis set on all atoms, and natural bond orbital interpretation. On the basis of the results obtained, the cis-configurations preferences decrease in going from compound 1 to compound 3. Effectively, the deletions of the hyperconjugative interactions from the Fock matrices of the cis- and trans-configurations of compound 1 lead to the increase of the trans-conformation stability (by ~6.11 kcal mol−1) compared with its corresponding cis-conformation. However, the Pauli exchange-type repulsion difference between the cis- and trans-configurations of compound 1 is in favour of the trans-configuration (by ~6.25 kcal mol−1), revealing that the stabilization energies associated with the hyperconjugative interactions do not compensate the destabilizations associated with the exchange component and dipole-dipole interactions. Importantly, the C=C bond paths in the cis-configuration of compound 1 are bent in essentially the same direction (towards the C–F bonds), leading to an increased overlap and a stronger C–C bond, whereas the C–C bond paths in the trans-configuration are bent in opposite directions. Accordingly, the co-operative stabilizations associated with the bending of the C=C bond paths (towards the C–F bonds) and total hyperconjugative generalized anomeric effect overcome the destabilizations associated with the exchange component and dipole–dipole interactions, leading to the preference of the cis-configuration in compound 1. The deletions of all the donor–acceptor electronic interactions from the Fock matrices of the cis- and trans-configurations of compounds 2 and 3 lead to the increase of the trans-conformation stabilities compared with their corresponding cis-conformations, revealing the determining impacts of the hyperconjugative interactions on the configurational preferences in compounds 2 and 3.

Exploring the structural and conformational properties of dioxygen dihalides (halogen = F, Cl, Br)

The structural and conformational properties of dioxygen difluoride (1), dioxygen dichloride (2), and dioxygen dibromide (3) have been investigated by means of the hybrid density functional theory (B3LYP) and the hybrid meta exchange-correlation functional (M06-2X) with the aug-cc-pVQZ, aug-cc-pVTZ, cc-pVTZ, and 6-311++G** basis sets and natural bond orbital interpretation. The results obtained showed that the rotation at the O–O bond by passing from the plane symmetrical trans-(C2h) (or cis-(C2v)) form leads to the O–F bonds breaking. The natural bond order analysis revealed that the O–O bonds in the C2h and C2v forms of compound 1 possess double bond characters and the small bond orders between the oxygen and fluorine atoms results from the strong electron delocalization between the lone pairs of the fluorine atoms (LP4F) and the antibonding orbitals of the adjacent O–O double bond (π*O–O). The lengthening and shortening of the O–F and O–O bonds, respectively, in the trans-(C2h) or cis-(C2v) forms of compound 1 can be interpreted by the decrease of the bonding interactions between the fluorine and oxygen orbitals. The profiles of the orbital amplitudes (or electron densities) of O–O and O–F bonds in the C2h and C2v forms of compound 1 revealed that there are strong electronic repulsions between the πO–O and the lone pairs of oxygen atoms with the lone pairs of fluorine atoms, leading to the dissociation of O–F bonds. It is worth noting that there are strong hyperconjugative interactions between LP2O and the antibonding orbitals of adjacent O–F bonds (σ*O–F) in the skew (C2) form of compound 1, leading to the decrease of the O–O bond length and the increase of the F–O bond length by increasing the πO-O bonding and the σ*O–F antibonding orbital occupations. The increase of the electron delocalization from LP3F to σ*O–O with the decrease of the σ*O–O–σO–O energy gap (results from the increase of the O–O bond length) justifies the similarity between the adiabatic O–O bond dissociation energies in compound 1 and HOOH. The electron delocaizations from LP2O2 to σ*O3–X (X = F (1), Cl (2), Br (3)) decrease drastically from the skew ground state (C2) forms of compound 1 to compound 2 but increase slightly from compound 2 to compound 3, causing the significant increase of the O–O bond length ongoing from compound 1 to compound 2 and the slight decrease from compound 2 to compound 3. Effectively, the conformational properties of compounds 1–3 can be interpreted with the principle of maximum softness.

The theoretical investigation of solvent effects on the relative stability and 15N NMR shielding of antidepressant heterocyclic drug

The density functional theory (DFT) and Tomasi’s polarized continuum model (PCM) were used for the investigation of solvent polarity and its dielectric constant effects on the relative stability and NMR shielding tensors of antidepressant mirtazapine (MIR). The obtained results indicated that the relative stability in the polar solvents is higher than that in non-polar solvents and the most stable structure was observed in the water at the B3LYP/6-311++G (d,p) level of theory. Also, natural bond orbital (NBO) interpretation demonstrated that by increase of solvent dielectric constant, negative charge on nitrogen atoms of heterocycles and resonance energy for LP(N10) → σ* and π* delocalization of the structure’s azepine ring increase and the highest values of them were observed in water. On the other hand, NMR calculations showed that with an increase in negative charge of nitrogen atoms, isotropic chemical shielding (σiso) around them increase and nitrogen of piperazine ring (N19) has the highest values of negative charge and σiso among nitrogen atoms. NMR calculations also represented that direct solvent effect on nitrogen of pyridine ring (N15) is more than other nitrogens, while its effect on N19 is less than other ones. Based on NMR data and NBO interpretation, it can be deduced that with a decrease in the negative charge on nitrogen atoms, the intramolecular effects on them decrease, while direct solvent effect increases.

Symmetry breaking in the axial symmetrical configurations of enolic propanedial, propanedithial, and propanediselenal: pseudo Jahn–Teller effect versus the resonance-assisted hydrogen bond theory

The origin of the symmetry breaking in the axial symmetrical configurations of enolic propanedial (1), propanedithial (2), and propanediselenal (3) have been investigated by means of time-dependence density functional theory and natural bond orbital interpretations. The results obtained at the quantum chemistry composite (G2MP2, CBS-QB3), ab initio molecular orbital (MP2/6-311++G**), and hybrid density functional theory (B3LYP/6-311++G**) levels of theory showed that the hydrogen-centered synchronous axial symmetrical (C2v) configurations of compounds 1–3 possessing the maximum π-electron delocalization within the M1=C2–C3=C4–M5–H6 keto-enol groups are less stable than their corresponding plane symmetrical (Cs) forms. Importantly, the symmetry breaking in the C2v configurations of the enol forms of compounds 1–3 to their corresponding plane symmetrical Cs configurations is due to the pseudo Jahn–Teller effect (PJTE) by mixing the ground A1 and excited B2 electronic states resulting in a PJT (A1 + B2) ⊗ b2 problem. We may expect that by the decrease of the energy gaps between reference states in the C2v forms that are involved in the PJTE decrease from compound 1 to compound 3, the PJT stabilization energy (PJTSE) may increase but the results obtained showed that the corresponding PJTSEs decrease. This fact can be justified by the increase of the electron delocalizations from the nonbonding orbitals of the C=M moieties to the antibonding orbitals of the H–M bonds, which leads to an increase of the π-electron delocalization within the M1=C2–C3=C4–M5–H6 keto-enol groups. In confrontation between the impacts of the resonance-assisted hydrogen bond and PJTE in the structural and configurational properties of compounds 1–3, PJTE has an overwhelming contribution and causes the symmetry breaking of the C2v configurations to their corresponding Cs forms. The correlations between the structural parameters, synchronicity indices, natural charges, PJTSEs, electron delocalizations, and the hardness of compounds 1–3 have been investigated.

Investigation of solvent effects on the stability and 15N NMR shielding of hallucinogenic harmine using the PCM model and NBO interpretation

Density functional theory (DFT) and Tomasi’s polarized continuum model (PCM) are applied for the investigation of the solvent structure and its dielectric constant effects on the relative stability and nuclear magnetic resonance (NMR) tensors of hallucinogenic harmine. All of the used computational methods indicate that the structural stability in protic polar solvents is higher than that in aprotic polar and nonpolar solvents, and the most stable structure was observed in methanol. Also, the natural bond orbital (NBO) interpretation demonstrates that with an increase in the solvent dielectric constant the resonance energy for LP(N9) → σ* and π* interactions of the strutural pyrrole ring increases while the LP (N9) occupancy decreases, and the highest resonance energy and the lowest occupancy are observed in water and methanol. On the other hand, NMR calculations show that there are the lowest values of Δσdir in water and methanol media for both nitrogen nuclei of the harmine structure.

The ab initio study and NBO interpretation of solvent effects on the structural stability and the chemical reactivity of penicillin-V conformations

Quantum mechanics (QM) methods were used to examine the electronic structure and the relative stability of penicillin-V (PV) conformations in the gas phase and the different solvent media. The effects of solvent dielectric constant and the computational methods were analyzed on the conformational stability of β-lactam-thiazolidine bicyclic system, its geometry and its reactivity. Our findings indicated that in the PV, the axial form of thiazolidine ring is more stable than equatorial form one in all of the tested media. This is in agreement with the NMR studies performed on PV that indicate the axial conformation is the dominant form in solid state. Furthermore, the atomic charges computations and natural bond orbital Interpretation (NBO) represented that by increasing the solvent dielectric constant, the charge values on the C5 and C7 atoms of the β-lactam ring decrease, while HOMO–LUMO gap and occupancy values of the contained bonds in β-lactam ring of the interested structures increase. Hence, the β-lactam ring possesses the lowest reactivity against nucleophilic attacks and the highest stability in presence of implicit waters. However, it can be concluded that the structural stability of penicillin-V conformations is controlled by solvent’s polarity and its dielectric constant, the electrophilic nature of β-lactam ring and HOMO–LUMO gap.

Hybrid-DFT Study and NBO Interpretation of the Configurational Behavior of 2-Halotetrahydrothiopyran S-Oxides

Natural bond orbital (NBO) interpretation and hybrid density functional theory (hybrid-DFT: B3LYP/Def2-TZVPP)-based methods were used to investigate the impacts of the generalized anomeric effects (GAE), electrostatic, and steric interactions on the conformational properties of cis and trans isomers of 2-fluoro-, 2-chloro-, and 2-bromotetrahydrothiopyran S-oxide (1–3). The results obtained showed that the trans-axial configurations are the most stable forms of compounds 1–3. Based on the results obtained, the instability of the second lowest energy-minimum (cis-equatorial configuration, with axial S˭O and equatorial C‒X bonds, X = halogen atoms) increases from compound 1 to compound 3. This trend is also observed for the third lowest energy-minimum (i.e., the trans-equatorial configuration). Contrary to the trend observed for the cis- and trans-equatorial forms, the instability of the cis-axial form compared to the trans-axial form, increases from 1 to 2 but decreases slightly from 2 to 3. The correlations between the GAE, bond orders, steric effects, ΔG, Δμ, structural parameters, and conformational and configurational behaviors of compounds 1–3 have been investigated. Supplemental materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfur, and Silicon and the Related Elements to view the free supplemental file.

Complete basis set, hybrid-DFT study and NBO interpretation of conformational analysis of 2-methoxytetrahydropyran and its thiopyran and selenopyran analogues in relation to the anomeric effect

2-Methoxytetrahydropyran (1), -thiopyran (2) and -selenopyran (3) have been chosen as model compounds to investigate the origin of the anomeric effect (AE). The impacts of the hyperconjugation, electrostatic and steric interactions on the conformational preferences of compounds 1–3 have been analysed by means of complete basis set-4, hybrid-density functional theory (B3LYP/6-311+G**) based methods and natural bond orbital (NBO) interpretation. Both levels of theory showed that the axial conformations of compounds 1–3 are more stable than their equatorial conformations. The Gibbs free energy difference (G eq–G ax) values (i.e. ΔG eq–ax) between the axial and equatorial conformations increase from compound 1 to compound 2 but decrease from compound 2 to compound 3. Based on the NBO results obtained, the AE associated with the electron delocalisation [i.e. Σ(endo-AEeq + exo-AEeq) − Σ(endo-AEax + exo-AEax)] increase slightly from compound 1 to compound 2 but decrease from compound 2 to compound 3. Similar trend is also observed for the differences between the calculated total steric exchange energy values [i.e. Δ(TSEE)eq–ax]. On the other hand, the calculated differences between the dipole moment values of the axial and equatorial conformations [i.e. Δ(μeq–μax)] decrease from compound 1 to compound 3. These findings led to the proposal that the AE associated with the electron delocalisation (the hyperconjugation effect) is more significant for the explanation of the conformational preferences of compounds 1–3 than the electrostatic model. The correlations between the AE associated with the electron delocalisation, bond orders, TSEE, ΔG eq–ax, dipole–dipole interactions, structural parameters and conformational behaviours of compounds 1–3 have been investigated.

Complete basis set, hybrid-density functional theory study, and natural bond orbital interpretations of the conformational behavior of halocarbonyl, thiocarbonyl, and selenocarbonyl isocyanates

Complete basis set CBS-QB3, hybrid-density functional theory (B3LYP/Def2-TZVPP) based methods and NBO interpretation were used to investigate the impacts of the stereoelectronic effects and electrostatic and steric interactions on the conformational properties of halocarbonyl isocyanates (halo = F (1), Cl (2), and Br (3)), halothiocarbonyl isocyanates (halo = F (4), Cl (5), and Br (6)), and haloselenocarbonyl isocyanates(halo = F (7), Cl (8), and Br (9)). Both methods showed that the Z-conformations of compounds 1, 4, and 7 are more stable than their corresponding E conformations, but the stability of the E conformations, when compared with the corresponding Z conformations, increases from compound 1 to compound 3, compound 4 to compound 6, and also from compound 7 to compound 9. The NBO analysis showed that the generalized anomeric effect (GAE) is in favor of the Z conformations of compounds 1, 4, and 7. The GAE values calculated (i.e., GAEE–GAEZ) increase from compound 1 to compound 3, compound 4 to compound 6, and also from compound 7 to compound 9. On the other hand, there are none of the same trends between the calculated total dipole moment and the Gibbs free energy difference values between the E and Z conformations (i.e., ΔμE–Z and ΔGE–Z) of compounds 1–3, 4–6, and 7–9. Accordingly, the GAE succeeds in accounting for the increase of the E conformation stability from compound 1 to compound 3, compound 4 to compound 6, and also from compound 7 to compound 9. Therefore, the GAE associated with the electron delocalization, not the total dipole moment changes (i.e., ΔμE–Z), is a reasonable indicator of the total energy difference in compounds 1–3, 4–6, and 7–9. There is a direct correlation between the calculated GAE and Δ[r2–6(E) – r2–6(Z)] parameters. Importantly, there are interesting through-space electron delocalizations (LP2X6→π*C4–O5) that justify the increase of the E conformation stability from compound 1 to compound 3, compound 4 to compound 6, and also from compound 7 to compound 9, when compared with their corresponding Z conformations. The correlations between the GAE, bond orders, total steric exchange energies (TSEE), ΔGZ–E, ΔμE–Z, structural parameters, and conformational behaviors of compounds 1–9 were investigated.

Complete basis set, hybrid-DFT study, and NBO interpretations of the conformational behavior of 1,2-dihaloethanes

The conformational behavior of 1,2-difluoroethane (1), 1,2-dichloroethane (2), 1,2-dibromoethane (3), and 1,2-diiodoethane (4) have been analyzed by means of complete basis set CBS-QB3, hybrid-density functional theory (B3LYP/Def2-TZVPP) based methods and natural bond orbital (NBO) interpretation. Both methods showed the expected greater stability of the gauche conformation of compound 1 compared to its anti conformation. Contrary to compound 1, the anti conformations of compounds 2–4 are more stable than their gauche conformation. The stability of the anti conformation compared to the gauche conformation increases from compound 1 to compound 4. The NBO analysis of donor–acceptor (σ → σ*) interactions showed that the generalized anomeric effect (GAE) is in favor of the gauche conformation of compound 1. Contrary to compound 1, GAE is in favor of the anti conformations of compounds 2–4. The GAE values calculated (i.e., GAEanti − GAEgauche) increase from compound 1 to compound 4. On the other hand, the calculated dipole moment values for the gauche conformations decrease from compound 1 to compound 4. In the conflict between the GAE and dipole moments, the former succeeded in accounting for the increase of the anti conformation stability from compound 1 to compound 4. There is a direct correlation between the calculated GAE, ∆[r c–c(G) − r c–c(A)] and ∆[r c–x(A) − r c–x(G)] parameters. The correlations between the GAE, bond orders, total steric exchange energies (TSEEs), ΔG Anti–Gauche, ΔG ‡(Gauche → Gauche′, C 2v), ΔG ‡(Anti → Gauche, C 2), dipole–dipole interactions, structural parameters, and conformational behaviors of compounds 1–4 have been investigated.