Halogen Bonding Organocatalysis Enhanced through Intramolecular Hydrogen Bonds

Recent results indicate a halogen bond donor is strengthened through direct interaction with a hydrogen bond to the electron-rich belt of the halogen. Here, this Hydrogen Bond enhanced Halogen Bond...

Crystal structure, Hirshfeld surface analysis, and DFT studies of N-(2-chlorophenylcarbamothioyl)cyclohexanecarboxamide

N-(2-Chlorophenylcarbamothioyl)cyclohexanecarboxamide was characterized by a single crystal X-ray diffraction study. Crystal data for this compound, C14H17ClN2OS; Monoclinic, space group P21/n with Z = 4, a = 5.2385(10) Å, b = 17.902(4) Å, c = 15.021(3) Å, β = 90.86(3)°, V = 1408.5(5) Å3, T = 153(2) K, μ(MoKα) = 0.413 mm-1, Dcalc = 1.400 g/cm3, 9840 reflections measured (7.082° ≤ 2Θ ≤ 50.378°), 2519 unique (Rint = 0.0406, Rsigma = 0.0335) which were used in all calculations. The final R1 was 0.0397 (I > 2σ(I)) and wR2 was 0.0887 (all data). The puckering parameters (q2 = 0.019(3) Å, q3 = 0.578(3) Å, θ = 1.0(3)° and φ = 51(8)°) of the title compound show that the cyclohexane ring adopts a chair conformation. The molecular conformation of the title compound is stabilized by intramolecular hydrogen bonds (N2-H2⋅⋅⋅Cl1, N2-H2⋅⋅⋅O1, and C2-H2A⋅⋅⋅S1) and intermolecular hydrogen bonds (N1-H1⋅⋅⋅S1i and C9-HA⋅⋅⋅S1ii: 2-x, 2-y, 1-z). The intramolecular hydrogen bonds (N2-H2⋅⋅⋅O1 and C2-H2A⋅⋅⋅S1) are also form two pseudo-six-membered rings. Density functional theory optimized structure in the gaseous phase at B3LYP/6-311G(d,p) level of theory has been compared with the experimentally defined molecular structure. The molecular orbitals HOMO and LUMO with the energy gap for the title compound are calculated and the estimated energy gap (ΔE) between the HOMO and LUMO energies levels of the title compound is 3.5399 eV, which implies that the title molecule is very reactive. The Hirshfeld surface analysis reveals that the most important contributions to crystal packing are from H···H (49.0%), H···C/C···H (12.5%), H···Cl/Cl···H (10.9%), and H···S/S···H (10.0%) interactions. The energy-framework calculations are used to analyze and visualize the three-dimensional topology of the crystal packing. The intermolecular energy analysis confirmed a significant contribution of dispersion to the stabilization of molecular packings in the title compound.

A novel сalcium trifluoroacetate structure

Objectives. The study was devoted to considering the features of the synthesis and crystal structure of calcium trifluoroacetate Ca2(CF3COO)4·8CF3COOH and investigating the products of its thermal behavior.Methods. The compositions of the proposed structural form were characterized by various physicochemical methods (X-ray diffraction, IR spectroscopy), and the products of thermal decomposition were determined under dynamic vacuum conditions.Results. The reaction between calcium carbonate and 99% trifluoroacetic acid yielded a new structural type of calcium trifluoroacetate Ca2(CF3COO)4·8CF3COOH (I) in the form of colorless prismatic crystals unstable air. X-ray diffraction results confirmed the composition I: space group P21, with unit cell parameters: a = 10.0193(5) Å, b = 15.2612(7) Å, c = 16.3342(8) Å, β = 106.106(2)°, V = 2399.6(2) Å3, Z = 2. The structure is molecular, constructed from Ca2(CF3COO)4·8CF3COOH dimers. The end molecules of the trifluoroacetic acid were involved in the formation of intramolecular hydrogen bonds with oxygen atoms of the bidentate bridging anions CF3COO−. There were strongly pronouncedsymmetric and asymmetric absorption bands of COO and CF3-groups in the IR spectrum of the resulting compound in the range of 1200–1800 cm−1. The definite peak of the oscillation of the OH-group at 3683 cm−1 corresponds to the trifluoroacetic acid molecules present in the structure. The broadpeak of the valence oscillations in the range of 3300–3500 cm−1 is caused by the presence of intramolecular hydrogen bonds. Decomposition began at 250°C and 10−2 mm Hg with calcium fluoride CaF2 as the final decomposition product.Conclusions. We obtained a previously undescribed calcium–trifluoroacetic acid complex whose composition can be represented by Ca2(CF3COO)4·8CF3COOH. The crystal island structure is a dimeric molecule where the calcium atoms are bound into dimers by four trifluoroacetate groups. The complex was deposited in the Cambridge Structural Data Bank with a deposit number CCDC 2081186. Although the compound has a molecular structure, thermal decomposition leads to the formation of calcium fluoride characterized by a small particle size, which may further determine its applications.

Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces

Our long-term investigations have been devoted the characterization of intramolecular hydrogen bonds in cyclic compounds. Our previous work covers naphthazarin, the parent compound of two systems discussed in the current work: 2,3-dimethylnaphthazarin (1) and 2,3-dimethoxy-6-methylnaphthazarin (2). Intramolecular hydrogen bonds and substituent effects in these compounds were analyzed on the basis of Density Functional Theory (DFT), Møller–Plesset second-order perturbation theory (MP2), Coupled Clusters with Singles and Doubles (CCSD) and Car-Parrinello Molecular Dynamics (CPMD). The simulations were carried out in the gas and crystalline phases. The nuclear quantum effects were incorporated a posteriori using the snapshots taken from ab initio trajectories. Further, they were used to solve a vibrational Schrödinger equation. The proton reaction path was studied using B3LYP, ωB97XD and PBE functionals with a 6-311++G(2d,2p) basis set. Two energy minima (deep and shallow) were found, indicating that the proton transfer phenomena could occur in the electronic ground state. Next, the electronic structure and topology were examined in the molecular and proton transferred (PT) forms. The Atoms In Molecules (AIM) theory was employed for this purpose. It was found that the hydrogen bond is stronger in the proton transferred (PT) forms. In order to estimate the dimers’ stabilization and forces responsible for it, the Symmetry-Adapted Perturbation Theory (SAPT) was applied. The energy decomposition revealed that dispersion is the primary factor stabilizing the dimeric forms and crystal structure of both compounds. The CPMD results showed that the proton transfer phenomena occurred in both studied compounds, as well as in both phases. In the case of compound 2, the proton transfer events are more frequent in the solid state, indicating an influence of the environmental effects on the bridged proton dynamics. Finally, the vibrational signatures were computed for both compounds using the CPMD trajectories. The Fourier transformation of the autocorrelation function of atomic velocity was applied to obtain the power spectra. The IR spectra show very broad absorption regions between 700 cm−1–1700 cm−1 and 2300 cm−1–3400 cm−1 in the gas phase and 600 cm−1–1800 cm−1 and 2200 cm−1–3400 cm−1 in the solid state for compound 1. The absorption regions for compound 2 were found as follows: 700 cm−1–1700 cm−1 and 2300 cm−1–3300 cm−1 for the gas phase and one broad absorption region in the solid state between 700 cm−1 and 3100 cm−1. The obtained spectroscopic features confirmed a strong mobility of the bridged protons. The inclusion of nuclear quantum effects showed a stronger delocalization of the bridged protons.

Perturbating Intramolecular Hydrogen Bonds through Substituent Effects or Non-Covalent Interactions

An analysis of the effects induced by F, Cl, and Br-substituents at the α-position of both, the hydroxyl or the amino group for a series of amino-alcohols, HOCH2(CH2)nCH2NH2 (n = 0–5) on the strength and characteristics of their OH···N or NH···O intramolecular hydrogen bonds (IMHBs) was carried out through the use of high-level G4 ab initio calculations. For the parent unsubstituted amino-alcohols, it is found that the strength of the OH···N IMHB goes through a maximum for n = 2, as revealed by the use of appropriate isodesmic reactions, natural bond orbital (NBO) analysis and atoms in molecules (AIM), and non-covalent interaction (NCI) procedures. The corresponding infrared (IR) spectra also reflect the same trends. When the α-position to the hydroxyl group is substituted by halogen atoms, the OH···N IMHB significantly reinforces following the trend H < F < Cl < Br. Conversely, when the substitution takes place at the α-position with respect to the amino group, the result is a weakening of the OH···N IMHB. A totally different scenario is found when the amino-alcohols HOCH2(CH2)nCH2NH2 (n = 0–3) interact with BeF2. Although the presence of the beryllium derivative dramatically increases the strength of the IMHBs, the possibility for the beryllium atom to interact simultaneously with the O and the N atoms of the amino-alcohol leads to the global minimum of the potential energy surface, with the result that the IMHBs are replaced by two beryllium bonds.