Quantum Theory Of Atoms In Molecules Method Research Articles

A QCT View of the Interplay between Hydrogen Bonds and Aromaticity in Small CHON Derivatives.

The somewhat elusive concept of aromaticity plays an undeniable role in the chemical narrative, often being considered the principal cause of the unusual properties and stability exhibited by certain skeletons. More recently, the concept of aromaticity has also been utilised to explain the modulation of the strength of non-covalent interactions (NCIs), such as hydrogen bonding (HB), paving the way towards the in silico prediction and design of tailor-made interacting systems. In this work, we try to shed light on this area by exploiting real space techniques, such as the Quantum Theory of Atoms in Molecules (QTAIM), the Interacting Quantum Atoms (IQA) approaches along with the electron delocalisation indicators Aromatic Fluctuation (FLU) and Multicenter (MCI) indices. The QTAIM and IQA methods have been proven capable of providing an unbiased and rigorous picture of NCIs in a wide variety of scenarios, whereas the FLU and MCI descriptors have been successfully exploited in the study of diverse aromatic and antiaromatic systems. We used a collection of simple archetypal examples of aromatic, non-aromatic and antiaromatic moieties within organic molecules to examine the changes in delocalisation and aromaticity induced by the Aromaticity and Antiaromaticity Modulated Hydrogen Bonds (AMHB). We observed fundamental differences in the behaviour of systems containing the HB acceptor within and outside the ring, e.g., a destabilisation of the rings in the former as opposed to a stabilisation of the latter upon the formation of the corresponding molecular clusters. The results of this work provide a physically sound basis to rationalise the strengthening and weakening of AMHBs with respect to suitable non-cyclic non-aromatic references. We also found significant differences in the chemical bonding scenarios of aromatic and antiaromatic systems in the formation of AMHB. Altogether, our investigation provide novel, valuable insights about the complex mutual influence between hydrogen bonds and systems.

Structure functionality relationship of flavonoids (myricetin, morin, taxifolin and 3′,4′-dihydroxyflavone). A computational study via the cupric ion probe

The antioxidant and/or prooxidant properties of flavonoids are strongly dependent on their redox metal chelating capacity as well as on the number and positions of hydroxyl groups. In this work the interaction between Cu(II) ion and the set consisting of four flavonoids (myricetin, morin, taxifolin and 3′,4′-dihydroxyflavone) is investigated using density functional theory (DFT) and quantum theory of atoms in molecules (QTAIM). Several potential Cu(II) acceptor sites are considered with respect to the number and positions of hydroxyl (and keto) functional groups within the particular flavonoid moiety. Suitability of the particular Cu(II) acceptor site is discussed from the energetics point of view, i.e. overall stability and interaction energies, electronic transitions are characterized and compared to experimental UV–Vis spectra in DMSO. The nature of the formed Cu-flavonoid chemical bonds is inspected using the bond critical point (BCP) analysis under the formalism of Bader's QTAIM method and the oxidation state of Cu is estimated with respect to the localized d-orbitals and d-populations. An impact of explicit DMSO solvent effects are considered as well.

QCT analysis of molecules containing the first and second period elements based on the PAEM

Quantum chemical topology (QCT) is a branch of theoretical chemistry. We use QCT based on the potential acting on one electron in a molecule (PAEM) to systematically investigate polyatomic molecules containing the first and second period elements. The results and analyses for five series of molecules containing the first and second period elements are presented. The calculated topological characteristics of these molecules, namely, the partitions into atoms, the atomic charges and the absolute value of the PAEM at the bond critical point called Dpb, are compared with those obtained from the quantum theory of atoms in molecules (QTAIM). The values of the PAEMQCT atomic charge are moderate; they are smaller than those obtained from the QTAIM and larger than those obtained from the Hirshfeld method. In PAEMQCT, the Dpb can be utilized to measure the strength of the chemical bond, while in QTAIM method, the electron density at the bcp is related to the bond strength. There is a good linear correlation between the Dpb at the bcp in PAEMQCT and the electron density at the bcp in QTAIM, and their correlation coefficient R is 0.9165.

The Shape of the Archetypical Oxocarbon Squaric Acid and Its Water Clusters

Herein, a full structural description is presented for the archetypical supramolecular synthone squaric acid (3,4-dihydroxy-3-cyclobutene-1,2-dione), placed in the gas phase by laser ablation and characterized by chirped pulse Fourier transform microwave technique. Free from natural environmental disturbances, two different anti-anti and syn-anti planar forms and the corresponding water clusters have been revealed in a supersonic expansion. The substitution structure of the most stable anti-anti conformer has also been extracted from the analysis of the rotational spectra of the 13 C and 18 O isotopic species in their natural abundance. The interplay between inter- and intramolecular interactions involving hydroxy and carbonyl groups has been analyzed by QTAIM (quantum theory of atoms in molecules) methods for squaric acid and its water clusters to understand their chemical behavior and further rationalize their role in the stabilization of these molecular systems.

How does the total charge and isomerism influence the Ru-NO ammine complexes?

Nitric oxide plays an important role in several physiological processes. This study investigates model ruthenium ammine coordination compounds to control NO bioavailability: cis-[RuCl(NO)(NH3)4]+ (1+), cis-[RuCl(NO)(NH3)4]2+ (12+), cis-[RuCl(NO)(NH3)4]3+ (13+), trans-[RuCl(NO)(NH3)4]+ (2+), trans-[RuCl(NO)(NH3)4]2+ (22+), trans-[RuCl(NO)(NH3)4]3+ (23+), [Ru(NO)(NH3)5]+ (3+), [Ru(NO)(NH3)5]2+ (32+), and [Ru(NO)(NH3)5]3+ (33+). We employed natural population analysis (NPA) atomic charges (qNPA) and the LUMO to identify the main reduction sites in the complexes 1, 2 and 3. For example, in the transformations 12+ → 1+, 22+ → 2+, and 33+ → 32+, the main reduction site was a NO π* orbital, which accounted for the lower electron density of the Ru-NO bond critical point (BCP) in 1+, 2+, and 32+ than 12+, 22+, and 33+, respectively, as shown by the quantum theory of atoms in molecules (QTAIM). The QTAIM method indicated that the electron density was larger in Ru-NO BCP due to the Cl negative cis- and trans-influence in 12+ and 22+, respectively, as compared with the NH3 influence in 33+. Compared to trans-Cl-Ru-NO in 22+, the interacting quantum atoms method demonstrated that cis-Cl-Ru-NO in 12+ displayed (i) a larger repulsive electrostatic energy, which agreed with qNPA, and (ii) a less negative exchange-correlation energy between Ru and the NO nitrogen atom, which agreed with topological analyses performed by the QTAIM method. Thus, the combination of topological and energy decomposition analyses allowed the mechanism behind the Ru-NO bond to be revealed regarding the influence of the total charge and the relative position of the ligands.

Spectral analysis and quantum chemical studies of chair and twist-boat conformers of cycloheximide in gas and solution phases

In this study the conformational behavior of cycloheximide in the gas and solution (CHCl3) phases has theoretically been investigated by spectroscopic and quantum chemical properties using density functional theory (wB97X-D) method with 6–31++G(d,p) basis set, for the first time. The calculated IR results reveal that in the ground state the molecule exits as a mixture of the chair and twist-boat conformers in the gas phase, while the calculated NMR results reveal that it only exits as the chair conformer in the solution phase. In order to obtain the contributions coming from intramolecular interactions to the stability of the conformers in the gas and solution phases, the quantum theory of atoms in molecules (QTAIM), noncovalent interactions (NCI) method, and natural bond orbital analysis (NBO) have been employed. The QTAIM and NCI methods indicated that by intramolecular interactions with bond critical point (BCP) the twist-boat conformer is more stabilized than the chair conformer, while by steric interactions it is more destabilized. Considering that these interactions balance each other, the stabilities of the conformers are understood to be dictated by the van der Waals interactions. The NBO analyses show that the hyperconjugative and steric effects play an important role in the stabilization in the gas and solution phases. Furthermore, to get a better understanding of the chemical behavior of this important antibiotic drug we have evaluated and, commented the global and local reactivity descriptors of the both conformers. Finally, the EPR analysis of γ-irradiated cycloheximide has been done. The comparison of the experimental and calculated data have showed the inducement of a radical structure of (CH2)2ĊCH2 in the molecule. The experimental EPR spectrum has also confirmed that the molecule simultaneously exists in the chair and twist-boat conformers in the solid phase.

Quantum chemical investigation on the structural and electronic properties of α-, β-, and γ-cyclodextrin complexes: DFT and QTAIM analysis

To characterize the structural, thermochemical and electronic aspects in complexes of leucine, vanillin and mechlorethamine with α-, β-, and γ-cyclodextrins (CDs), a density functional theory (DFT) study has been conducted in combination with quantum theory of atoms in molecules (QTAIM) analysis. The QTAIM method has been utilized to explore the nature of various possible interactions between leucine, vanillin and mechlorethamine with CDs in terms of bond critical points (BCPs). HOMO and LUMO and atomic charges studies show charge transfer occurs between drugs and cyclodextrins. This behavior has been also investigated via QTAIM charge analysis. On the other hand, based on QTAIM electronic energy indicators we have discussed electrostatic character of interactions between vanillin, leucine and mechlorethamine with inner surface CDs in the coordination sphere.

Electronic properties of the AsCO, AsSiO and AsGeO radicals: Linear or cyclic?

Quantum chemical analysis was performed on the AsCO, AsSiO, and AsGeO isomers with the objective of describing several electronic properties of these radicals: (i) the nature of their global minimum in the ground state; (ii) analysis of the bond nature using the natural bond orbital and Quantum Theory of Atoms in Molecules (QTAIM) methodologies; (iii) their atomic charge distributions; (iv) the energy gaps among the species and their isomerization pathways; and (v) their heats of formation at 0K and 298K. The main question emphasized in this study is whether the global minimum of the AsCO, AsSiO, and AsGeO radicals in their ground state corresponds to a linear or cyclic geometry. An inspection of the energy profiles shows that for the AsCO radical, the global minimum in the ground state is a linear isomer. In contrast, the AsSiO and AsGeO isomers exhibit a cyclic arrangement at the global minimum. Moreover, we additionally investigated whether the cyclic species have a cyclic or T-shaped structure. This was answered through an analysis using the QTAIM and natural bond orbital methods, which confirmed their cyclic nature. The QTAIM analysis predicted a ring critical point in the cyclic structures, which is characteristic of a cyclic geometry rather than a T-shaped one.

The Complexation of the Anticancer Drug ThioTEPA with Methylated DNA Base Guanine: Combined Ab Initio and QTAIM Investigation.

Non-covalent complexes of methylated nitrogenous DNA base guanine (m(9) Gua) with 1 to 6 molecules of anticancer drug ThioTEPA (1,1',1''-phosphorothioyltriaziridine) have been investigated by molecular modeling techniques (molecular docking and DFT geometry optimization), ab initio wavefunction calculations and the quantum theory of atoms in molecules (QTAIM). The accuracy of complex structures predicted by standard molecular docking techniques have been assessed by comparing them with ab initio calculations, and the most important differences have been discussed. Obtained stabilization enthalpies (kcal/mol) for the m(9) Gua⋅⋅⋅(ThioTEPA)n complexes with n=1…6 have been found to be -15.6, -26.5, -38.4, -49.6, -60.5 and -69.3 respectively. The non-covalent interactions revealed by the QTAIM method have been shown to be a dominating factor responsible for the complex stability, with hydrogen bonds of NH⋅⋅⋅N type being the most important interactions in small (n=1 to 4) and CH⋅⋅⋅N bonds - in large (n=5, 6) complexes. The obtained results may help to understand ThioTEPA-DNA interactions and clarify the mechanism of the drug action.

Quantum chemical investigation on the structural and electronic properties of zinc–salphen complex: DFT and QTAIM analysis

To characterize the structural, thermochemical and electronic aspects in complexation of zinc cation with N, N′-bissalicylidene phenylenediimine dianion (salphen) Schiff base ligand, a Density Functional Theory (DFT) study has been conducted in combination with Quantum Theory of Atoms in Molecules (QTAIM) analysis. Comparison of our calculated structural parameters of Zn–salphen complex with the available X-ray crystallographical data reveals that both functionals (B3LYP and M06) can well reproduce X-ray structure of the complex with a near accuracy. Then, we have examined the effect of three solvents, benzene, DMF and methanol, on thermochemistry of complexation by calculating the enthalpy and Gibbs free energy changes. In the next step, QTAIM method has been utilized to explore the nature of various possible interactions in Zn–salphen complex in terms of Bond Critical Points (BCPs). Topological study of electron density and its Laplacian clearly predicted that the bond strength of imine (CN) and phenoxide (CPhO) moieties in salphen ligand decreases through the complexation. This behavior has been also investigated via QTAIM charge analysis. Moreover, it has been demonstrated that there are two HH bond interactions with the stabilizing effect on the complexation process. On the other hand, based on QTAIM electronic energy indicators we have discussed the electrostatic character of interactions between zinc cation with N and O atoms of salphen in the coordination sphere.

Electron-topological, energetic and π-electron delocalization analysis of ketoenamine-enolimine tautomeric equilibrium.

The ketoenamine-enolimine tautometic equilibrium has been studied by the analysis of aromaticity and electron-topological parameters. The influence of substituents on the energy of the transition state and of the tautomeric forms has been investigated for different positions of chelate chain. The quantum theory of atoms in molecules method (QTAIM) has been applied to study changes in the electron-topological parameters of the molecule with respect to the tautomeric equilibrium in intramolecular hydrogen bond. Dependencies of the HOMA aromaticity index and electron density at the critical points defining aromaticity and electronic state of the chelate chain on the transition state (TS), OH and HN tautomeric forms have been obtained.

Bonding Properties Related with Chiral Discrimination in Dinuclear Metal Complexes of Group 10

AbstractA series of neutral dinuclear homo‐ and heterochiral complexes formed by hydrazine (a molecule with axial chirality), a metal atom of group 10 (Ni, Pd, Pt), and halogen atoms (F, Cl, Br, I) was studied by computational methods including density functional theory. In the optimized structures the heterochiral complexes were always found to be energetically favored. The chiral discrimination depends on the contributions coming from the metal atoms and the halogen anions attached to them. Moreover, the relative energies of the optimized complexes are correlated with the electronegativity of the metals and the halogens as well as with the relative distances of the bond critical points in the metal–nitrogen bonds. Also the smaller deviation of the ligand–metal–ligand angles from the ideal value of 90° corresponds to the heterochiral complexes. An analysis of the bonding properties reveals a complex mechanism for the behavior of the electron lone pairs of the nitrogen and halogen atoms. The electronic properties of the optimized complexes were studied by NBO (Natural Bond Orbital) and QTAIM (Quantum Theory of Atoms in Molecules) methods. An NBO analysis of the energy differences between the stabilizing energies related to the interactions between an electron lone pair of the coordinated nitrogen atom and the opposite M–X antibonding orbital explain the differences of the total energies between the diastereomeric heterochiral and homochiral complexes. The stabilizing energies have systematically more negative values in the heterochiral complexes; this can be interpreteted as a measure of the trans influence. Small energy values related to the cis influence were found mainly in the nickel complexes. The M–N bonds in the heterochiral complexes are more polar with a higher bond order than that in the homochiral ones, as shown by QTAIM methods. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)