Systematic description of molecular deformations with Cremer-Pople puckering and deformation coordinates utilizing analytic derivatives: Applied to cycloheptane, cyclooctane, and cyclo[18]carbon

Potential Energy Surfaces Sampled in Cremer-Pople Coordinates and Represented by Common Force Field Functionals for Small Cyclic Molecules

The complex conformations of the cyclic moieties impact the physical and chemical properties of molecules. In this work, we chose 22 molecules of four-, five-, and six-membered rings and performed a thorough conformational sampling using Cremer-Pople coordinates. With consideration of symmetries, we obtained a total of 1504 conformational structures for four-membered, 5576 for five-membered, and 13509 for six-membered rings. All well-known and many less well-known conformers for each molecule were identified. We represented the potential energy surfaces (PESs) by fitting the data to common analytical force field (FF) functional forms. We found that the general features of PESs can be described by the essential FF functional forms; however, the accuracy of representation can be improved remarkably by including the torsion-bond and torsion-angle coupling terms. The best fit yields R-squared (R²) values close to 1.0 and mean absolute errors in energy less than 0.3 kcal/mol.

Meta-Hybrid Density Functional Theory Prediction of the Reactivity, Stability, and IGM of Azepane, Oxepane, Thiepane, and Halogenated Cycloheptane

The application of plain cycloalkanes and heterocyclic derivatives in the synthesis of valuable natural products and pharmacologically active intermediates has increased tremendously in recent times with much attention being paid to the lower cycloalkane members. The structural and molecular properties of higher seven-membered and nonaromatic heterocyclic derivatives are less known despite their stable nature and vast application; thus, an insight into their structural and electronic properties is still needed. Appropriate quantum chemical calculations utilizing the ab initio (MP2) method, meta-hybrid (M06-2X) functional, and long-range-separated functionals (ωB97XD) have been utilized in this work to investigate the structural reactivity, stability, and behavior of substituents on cycloheptane (CHP) and its derivatives: azepane, oxepane, thiepane, fluorocycloheptane (FCHP), bromocycloheptane (BrCHP), and chlorocycloheptane (ClCHP). Molecular global reactivity descriptors such as Fukui function, frontier molecular orbitals (FMOs), and molecular electrostatic potential were computed and compared with lower members. The results of two population methods CHELPG and Atomic Dipole Corrected Hirshfeld Charges (ADCH) were equally compared to scrutinize the charge distribution in the molecules. The susceptibility of intramolecular interactions between the substituents and cycloalkane ring is revealed by natural bond orbital analysis and intramolecular weak interactions by the independent gradient model (IGM). Other properties such as atomic density of states, intrinsic bond strength index (IBSI), and dipole moments are considered. It is acclaimed that the strain effect is a major determinant effect in the energy balance of cyclic molecules; thus, the ring strain energies and validation of spectroscopic specificities with reference to the X-ray crystallographic data are also considered.

BF3–Catalyzed Diels–Alder Reaction between Butadiene and Methyl Acrylate in Aqueous Solution—An URVA and Local Vibrational Mode Study

In this study we investigate the Diels–Alder reaction between methyl acrylate and butadiene, which is catalyzed by BF3 Lewis acid in explicit water solution, using URVA and Local Mode Analysis as major tools complemented with NBO, electron density and ring puckering analyses. We considered four different starting orientations of methyl acrylate and butadiene, which led to 16 DA reactions in total. In order to isolate the catalytic effects of the BF3 catalyst and those of the water environment and exploring how these effects are synchronized, we systematically compared the non-catalyzed reaction in gas phase and aqueous solution with the catalyzed reaction in gas phase and aqueous solution. Gas phase studies were performed at the B3LYP/6-311+G(2d,p) level of theory and studies in aqueous solution were performed utilizing a QM/MM approach at the B3LYP/6-311+G(2d,p)/AMBER level of theory. The URVA results revealed reaction path curvature profiles with an overall similar pattern for all 16 reactions showing the same sequence of CC single bond formation for all of them. In contrast to the parent DA reaction with symmetric substrates causing a synchronous bond formation process, here, first the new CC single bond on the CH2 side of methyl acrylate is formed followed by the CC bond at the ester side. As for the parent DA reaction, both bond formation events occur after the TS, i.e., they do not contribute to the energy barrier. What determines the barrier is the preparation process for CC bond formation, including the approach diene and dienophile, CC bond length changes and, in particular, rehybridization of the carbon atoms involved in the formation of the cyclohexene ring. This process is modified by both the BF3 catalyst and the water environment, where both work in a hand-in-hand fashion leading to the lowest energy barrier of 9.06 kcal/mol found for the catalyzed reaction R1 in aqueous solution compared to the highest energy barrier of 20.68 kcal/mol found for the non-catalyzed reaction R1 in the gas phase. The major effect of the BF3 catalyst is the increased mutual polarization and the increased charge transfer between methyl acrylate and butadiene, facilitating the approach of diene and dienophile and the pyramidalization of the CC atoms involved in the ring formation, which leads to a lowering of the activation energy. The catalytic effect of water solution is threefold. The polar environment leads also to increased polarization and charge transfer between the reacting species, similar as in the case of the BF3 catalyst, although to a smaller extend. More important is the formation of hydrogen bonds with the reaction complex, which are stronger for the TS than for the reactant, thus stabilizing the TS which leads to a further reduction of the activation energy. As shown by the ring puckering analysis, the third effect of water is space confinement of the reacting partners, conserving the boat form of the six-member ring from the entrance to the exit reaction channel. In summary, URVA combined with LMA has led to a clearer picture on how both BF3 catalyst and aqueous environment in a synchronized effort lower the reaction barrier. These new insights will serve to further fine-tune the DA reaction of methyl acrylate and butadiene and DA reactions in general.

Bonding Character, Electron Delocalization, and Aromaticity of Cyclo[18]Carbon (C18 ) Precursors, C18 -(CO)n (n=6, 4, and 2): Focusing on the Effect of Carbonyl (-CO) Groups

The bonding character, electron delocalization, and aromaticity of the cyclo[18]carbon (C₁₈ ) precursors, C₁₈ -(CO)_n (n=6, 4, and 2), have been studied by combining quantum chemical calculations and various electronic wavefunction analyses with different physical bases. It was found that C₁₈ -(CO)_n (n=6, 4, and 2) molecules exhibit alternating long and short C-C bonds, and have out-of-plane and in-plane dual π systems (π^out and πⁱⁿ ) perpendicular to each other, which are consistent with the relevant characteristics of C₁₈ . However, the presence of carbonyl (-CO) groups significantly reduced the global electron conjugation of C₁₈ -(CO)_n (n=6, 4, and 2) compared to C₁₈ . Specifically, the -CO group largely breaks the extensive delocalization of πⁱⁿ system, and the π^out system is also affected by it but to a much lesser extent; as a consequence, C₁₈ -(CO)_n (n=6, 4, and 2) with larger n shows weaker overall aromaticity. Mostly because of the decreased but still apparent π^out electron delocalization in the C₁₈ -(CO)_n (n=6, 4, and 2), a notable diatropic induced ring current under the action of external magnetic field is observed, demonstrating the clear aromatic characteristic in the molecules. The correlation between C₁₈ -(CO)_n (n=6, 4, and 2) and C₁₈ in terms of the gradual elimination of -CO from the precursors showed that the direct elimination of two CO molecules in C₁₈ -(CO)_n (n=6, 4, and 2) has a synergistic mechanism, but it is kinetically infeasible under normal conditions due to the high energy barrier.

Interplay of Rotational and Pseudorotational Motions in Flexible Cyclic Molecules

Solutions to the time-independent nuclear Schrödinger equation associated with the pseudorotational motion of three flexible cyclic molecules are presented and discussed. Structural relaxations related to the pseudorotational motion are described as functions of a pseudorotation angle ϕ which is formulated according to the definition of ring-puckering coordinates originally proposed by Cremer and Pople ( J. Am. Chem. Soc. 1975, 97 (6), 1354-1358). In order to take into account the interplay between pseudorotational and rotational motions, the rovibrational Hamiltonian matrices are formulated for the rotational quantum numbers J = 0 and J = 1. The rovibrational Hamiltonian matrices are constructed and diagonalized using a Python program developed by the authors. Suitable algorithms for (i) the construction of one-dimensional cuts of potential energy surfaces along the pseudorotation angle ϕ and (ii) the assignment of the vibrorotational wave functions (which are needed for the automatic calculation of rotational transition energies J = 0 → J = 1) are described and discussed.

DFT computational study towards investigating psychotropic drugs, promazine and trifluoperazine adsorption on graphene, fullerene and carbon cyclic ring nanoclusters

Detection and qualification process related to impurities assume importance in pharmacological drug development programmes and the present article gives the structural and spectral characterisation of phenothiazine derivatives, promazine (PME) and trifluoperazine (TPE) and their self-assembly with graphene/fullerene/carbon ring (CG/CF/CR) systems theoretically. The investigation of adsorption behaviour of these compounds can provide valuable information about its reactivity, electronic and structural properties. Three-dimensional electrostatic potential diagrams were mapped. The frontier orbital energies and energy band gaps of the molecules were computed. Delocalization of charge density between the bonding or lone pair and antibonding orbitals is calculated by NBO analysis. Docking was executed to investigate binding areas of chemical compounds. Bioactivity scores show that the pharmacokinetic and pharmacological properties of the ligands are appropriate leading to be considered potential drug agents. The obtained theoretical wavenumber results of the present study were fully compatible with the experimental results.

Aromaticity of Even-Number Cyclo[n]carbons (n = 6-100)

The recently synthesized cyclo[18]carbon molecule has been characterized in a number of studies by calculating electronic, spectroscopic, and mechanical properties. However, cyclo[18]carbon is only one member of the class of cyclo[n]carbons—standalone carbon allotrope representatives. Many of the larger members of this class of molecules have not been thoroughly investigated. In this work, we calculate the magnetically induced current density of cyclo[n]carbons in order to elucidate how electron delocalization and aromatic properties change with the size of the molecular ring (n), where n is an even number between 6 and 100. We find that the Hückel rules for aromaticity (4k + 2) and antiaromaticity (4k) become degenerate for large C_n rings (n > 50), which can be understood as a transition from a delocalized electronic structure to a nonaromatic structure with localized current density fluxes in the triple bonds. Actually, the calculations suggest that cyclo[n]carbons with n > 50 are nonaromatic cyclic polyalkynes. The influence of the amount of nonlocal exchange and the asymptotic behavior of the exchange–correlation potential of the employed density functionals on the strength of the magnetically induced ring current and the aromatic character of the large cyclo[n]carbons is also discussed.

TAO-DFT investigation of electronic properties of linear and cyclic carbon chains

It has been challenging to adequately investigate the properties of nanosystems with radical nature using conventional electronic structure methods. We address this challenge by calculating the electronic properties of linear carbon chains (l-CC[n]) and cyclic carbon chains (c-CC[n]) with n = 10-100 carbon atoms, using thermally-assisted-occupation density functional theory (TAO-DFT). For all the cases investigated, l-CC[n]/c-CC[n] are ground-state singlets, and c-CC[n] are energetically more stable than l-CC[n]. The electronic properties of l-CC[n]/c-CC[n] reveal certain oscillation patterns for smaller n, followed by monotonic changes for larger n. For the smaller carbon chains, odd-numbered l-CC[n] are more stable than the adjacent even-numbered ones; c-CC[[Formula: see text]]/c-CC[4m] are more/less stable than the adjacent odd-numbered ones, where m are positive integers. As n increases, l-CC[n]/c-CC[n] possess increasing polyradical nature in their ground states, where the active orbitals are delocalized over the entire length of l-CC[n] or the whole circumference of c-CC[n].