Competing intramolecular NHOC hydrogen bonds and extended intermolecular network in 1-(4-chlorobenzoyl)-3-(2-methyl-4-oxopentan-2-yl) thiourea analyzed by experimental and theoretical methods

Non-Covalent Interactions in Molecular Systems: Thermodynamic Evaluation of the Hydrogen-Bond Strength in Amino-Ethers and Amino-Alcohols

The intramolecular hydrogen bond (intra-HB) is one of the best-known examples of non-covalent interactions in molecules. Among the different types of intramolecular hydrogen bonding, the NH⋅⋅⋅O hydrogen bond in amino-alcohols and amino-ethers is one of the weakest. In contrast to the strong OH⋅⋅⋅N intramolecular hydrogen bond, the strength of the NH⋅⋅⋅O bond can hardly be measured with conventional spectroscopic methods, even for simple amino-alcohols, since the band belonging to the NH⋅⋅⋅O conformer merges with the free OH band. In this work, we developed a combination of G4 calculations, and a method based on experimental vaporization enthalpies to determine the NH⋅⋅⋅O hydrogen bonding strength. The archetypal compounds for this study are 2-amino-1-ethanol and 3-amino-1-propanol as well as their respective methoxy analogs. Based on these molecules, different series were studied to investigate various factors influencing NH⋅⋅⋅O intra-HB strength. In the first series, the influence of alkylation near the hydroxy or methoxy group and the amino group in sterically hindered aminoalcohols was examined. In the second series, the influence of alkylation of the amino-group was investigated. In the third series, the effect of extending the alkyl chain between functional groups was studied.

A Dual Approach on Experimental, Theoretical Insight of Structural Elucidation, Hirshfeld Surface Analysis, Optical and Electrochemical Properties of Acyl Thiourea-Ethynyl Hybrid Derivatives

Hybrid moieties of ethynylated-thiourea, Th1 and Th2 have been synthesised via the addition reaction between ethynyl derivatives and 4-tert-butylbenzoyl isothiocyanate in acetone, and were characterised by selected spectroscopic methods (i.e., ¹H and ¹³C NMR, UV-visible, FT-IR) and elemental analysis. Thermogravimetric analysis indicated that Th1 and Th2 were relatively stable up to ca. 210 °C. Single-crystal X-ray diffraction was used to identify the crystal structure of Th2 in which the centre of 1-acyl thiourea moiety (-C(O)NHC(S)NH) exhibits S conformation. The Hirshfeld surface analysis has allowed visualizing the crystal packing, which is characterised by the prolonged intermolecular N-H⋯O = C and N-H⋯S = C hydrogen-bonding interactions within Th2 molecule. Electrochemical data of both compounds correspondingly exhibit irreversible redox potential processes. Besides, frontier molecular orbitals and Natural Bond Orbital population analysis were computed at the B3LYP/6-31G (d, p) level of approximation, suggesting strong delocalization of the electronic density through a conjugated π-system involving the ethynyl-phenyl and thiourea groups.

GRAPHICAL ABSTRACT

Figure of molecular structure for acyl thiourea-ethynyl derivative. Two derivatives of acyl thiourea-ethynyl were synthesised and characterised by selected spectroscopic methods such as 1H and 13C NMR, UV-visible, FT-IR, elemental, thermal, electrochemical, X-ray diffraction, and density functional theory (DFT) calculation for molecular orbitals and natural bond orbital population analysis.

Probing the Effect of Halogen Substituents (Br, Cl, and F) on the Non-covalent Interactions in 1-(Adamantan-1-yl)-3-arylthiourea Derivatives: A Theoretical Study

The effect of halogen substituents (X = Br, Cl, and F) on the crystal packing and intra- and intermolecular interactions in four adamantane-thiourea hybrid derivatives is investigated using different theoretical tools. The bromo and chloro derivatives exhibit 3D isostructurality as evident from lattice parameters, molecular conformation, and crystal packing. The density functional theory study suggests that the molecular conformation of the parent (unsubstituted) and fluoro derivatives exhibits a stable low energy anti-syn conformation. In contrast, bromo and chloro derivatives adopt stable and relatively high energy minima on their potential energy surfaces. Hirshfeld surface analysis reveals the effect of halogen substituents on the intermolecular contacts. The halogen atoms mainly reduce the contribution of H···H contacts toward crystal packing. PIXEL energy analysis indicates the strong dimer formed by N-H···S hydrogen bonds in all four structures. It also revealed that a vast number of H···H contacts observed in different dimers of these structures either presented along with other conventional interactions or solely stabilize the dimeric topology. The topological parameters for intermolecular interactions in these structures suggest an intermediate bonding character between shared and closed-shell interactions for N-H···S hydrogen bonds in the parent and chloro derivatives. In contrast, the N-H···S hydrogen bond in other structures is of a closed-shell interaction. Among four derivatives, the fluoro derivative is weakly packed in the solid state based on the PIXEL method's lattice energy calculation.

Supramolecular architecture in 1:1 cocrystal of N-carbamothioylacetamide and N,N'-thiocarbonyldiacetamide from the attempted synthesis of 1,3-diacetyl-2-thioxoimidazolidine-4,5-dione (a thioparabanic acid derivative)

An attempt to synthesize thioparabanic acid as precursor to other fused heterocyclic compounds, by a microwave assisted multistep one-pot reaction yielded a co-crystal of N-carbamothioylacetamide (NCTA) and N,N'-thiocarbonyldiacetamide (NNTCA) which is being reported in this paper. The structure of N-carbamothioylacetamide and N,N'-thiocarbonyldiacetamide from the attempted synthesis of 1,3-diacetyl-2-thioxoimidazolidine-4,5-dione, C₅H₈N₂O₂S.C₃H₆N₂OS, has triclinic (P-1) symmetry. It is of interest with respect to biological application. The structure displays inter- and intra-molecular hydrogen bonding through -C=O···H interactions. Similarly, -C=S···H hydrogen bonding interactions are present, providing additional intermolecular stability to the co-crystal. For application as a potential drug candidate, a density functional theory (DFT) simulation of the antioxidant activities of the co-crystal and its individual components (NCTA and NNTCA) has been performed. The computed redox potentials indicate that the study compounds show comparable antioxidant activities with ascorbic acid (AA) for a one electron transfer process. Meanwhile, for a two-electron process, AA showed significant antioxidant advantage over the titled compound.

Synthesis, characterization, antimicrobial and cytotoxic activity of novel half-sandwich Ru(II) arene complexes with benzoylthiourea derivatives

Three new ruthenium(II)-arene complexes, [Ru(η⁶-p-cymene)(L¹)Cl₂] (C1) where L¹ is N-((4 methoxyphenyl)carbamothioyl)benzamide; [Ru(η⁶-p-cymene)(L²)Cl₂] (C2) where L² is 4-(3-benzoylthioureido)benzoic acid and [Ru(η⁶-p-cymene)(L³)Cl₂] (C3) where L³ is methyl 4-(3- benzoylthioureido)benzoate have been synthetized, characterized and evaluated for their antimicrobial and anticancer activity. Characterization was performed using ¹H and ¹³C NMR, IR spectroscopy, mass spectrometry, electrical conductivity measurements and X-Ray diffraction analysis. X-Ray diffraction analysis of C1 showed typical expected "piano-stool" geometry with ruthenium coordinated to ligand via nitrogen and sulfur atoms of benzoylthiourea derivatives. Interesting, in herein described complex, upon coordination the four-membered ring was formed, instead of six-membered chelate common for this type of ligands. Cytotoxic activity was determined in human cervix adenocarcinoma (HeLa) cell line and IC₅₀ values ranged from 29.68 to 52.36 μM and the complexes were more active than related ligands (except in case of C2 where it is found that IC₅₀ value is close to IC₅₀ value of related ligand). Complex [Ru(η⁶-p-cymene)(L¹)Cl₂] (C1) expressed the highest cytotoxic activity with IC₅₀ value of 29.7 μM. Complexes and ligands were tested against nine Gram-positive and Gram-negative bacteria and one yeast- Candida albicans. Clinical Candida spp. strains from microbiological laboratories were included in testing processes as well. Minimum inhibitory concentrations values ranged from 62.5 μg/ml for complexes against Candida albicans to over 1000 μg/ml for several bacterial species.

Crystal structure of bis(2-((allylcarbamothioyl)imino)-4-methylthiazol-3-ido-κ2 N,S)palladium(II), C16H20N6PdS4

C16H20N6PdS4, monoclinic, C2/c (no. 15), a = 13.2801(8) Å, b = 18.5771(8) Å, c = 10.2577(5) Å, β = 121.906(2)°, V = 2148.29(19) Å3, Z = 4, R gt(F) = 0.0300, WR ref(F 2) = 0.0721, T = 293 K.

Comment on "Structural and vibrational studies on 1-(5-Methyl- [1,3,4] thiadiazol-2-yl)-pyrolidin-2-ol" [Spectrochimica Acta Part A, 152 (2016) 252-261]. The importance of intramolecular OH⋯N hydrogen bonding in the conformational properties of thiadiazol-pyrrolidin-2-ol bearing species

The title paper [1] reports a study on the spectroscopic and physicochemical properties of 1-(5-methyl- [1,3,4]thiadiazol-2-yl)-pyrrolidin-2-ol (MTPN) based on experimental and theoretical data. The latter ones are based on the computed molecular structure for a rather unusual conformer. Here, after a careful analysis of the conformational space of MTPN, the most stable conformation was determined for the molecule isolated in a vacuum, which results to be 21.9kJ/mol more stable than the conformer reported previously. Our study also includes the closely related species 1-(5-trifluoromethyl- [1,3,4]thiadiazol-2-yl)-pyrrolidin-2-ol (FMTPN). An intramolecular OH⋯N hydrogen bond determines the conformational behavior of the [1,3,4]thiadiazol-2-yl)-pyrrolidin-2-ol group as demonstrated by Natural Bond Orbital population analysis.

On the roles of close shell interactions in the structure of acyl-substituted hydrazones: An experimental and theoretical approach

The 2-(phenyl-hydrazono)-succinic acid dimethyl ester compound was synthesized by reacting phenylhydrazine with dimethylacetylene dicarboxylate at room temperature and characterized by elemental analysis, infrared, Raman, (1)H and (13)C NMR spectroscopies and mass spectrometry. Its solid state structure was determined by X-ray diffraction methods. The X-ray structure determination corroborates that the molecule is present in the crystal as the hydrazone tautomer, probably favored by a strong intramolecular N-H···O=C hydrogen bond occurring between the carbonyl (-C=O) and the hydrazone -C=N-NH- groups. A substantial fragment of the molecular skeleton is planar due to an extended π-bonding delocalization. The topological analysis of the electron densities (Atom in Molecule, AIM) allows characterization of intramolecular N-H···O interaction, that can be classified as a resonant assisted hydrogen bond (RAHB). Moreover, the Natural Bond Orbital population analysis confirms that a strong hyperconjugative lpO1→σ*(N2-H) remote interaction between the C2=O1 and N2-H groups takes place. Periodic system electron density and topological analysis have been applied to characterize the intermolecular interactions in the crystal. Weak intermolecular interactions determine the crystal packing, and the prevalence of non-directional dispersive contributions are inferred on topological grounds. The IR spectrum of the crystalline compound was investigated by means of density functional theory calculations carried out with periodic boundary conditions on the crystal, showing excellent agreement between theory and the experiments. The vibrational assignment is complemented with the analysis of the Raman spectrum.

Synthesis, X-ray crystal structure, thermal behavior and spectroscopic analysis of 1-(1-naphthoyl)-3-(halo-phenyl)-thioureas complemented with quantum chemical calculations

Two novel 1-(1-naphthoyl)-3-(halo-phenyl) substituted thioureas, namely 1-(1-naphthoyl)-3-(2,4-di-fluoro-phenyl)-thiourea (1) and 1-(1-naphthoyl)-3-(3-chloro-4-fluoro-phenyl)-thiourea (2), were synthesized and fully characterized. The X-ray crystal and molecular structures have been determined resulting in a planar acylthiourea group, with the C=O and C=S adopting a pseudo-antiperiplanar conformation. An intramolecular N-H⋯O=C hydrogen bond occurs between the thioamide and carbonyl groups. The crystal packing of both compounds is characterized by extended intermolecular N-H⋯S=C and N-H⋯O=C hydrogen-bonding interactions involving the acylthiourea moiety. Compound 2 is further stabilized by π-stacking between adjacent naphthalene and phenyl rings. The thermal behavior, as well as the vibrational properties, studied by infrared and Raman spectroscopy data complemented by quantum chemical calculations at the B3PW91/6-311++G(d,p) support the formation of these intra- and intermolecular hydrogen bonds. Furthermore, the UV-Vis spectrum is interpreted in terms of TD-DFT quantum chemical calculations with the shapes of the simulated absorption spectra in good accordance with the experimental data.

Synthesis, X-ray, NMR, FT-IR, UV/vis, DFT and TD-DFT studies of N-(4-chlorobutanoyl)-N'-(2-, 3- and 4-methylphenyl)thiourea derivatives

A new isomers of thiourea derivatives, namely N-(4-chlorobutanoyl)-N'-(2-methylphenyl)-thiourea (1a), N-(4-chlorobutanoyl)-N'-(3-methylphenyl)thiourea (1b) and N-(4-chlorobutanoyl)-N'-(4-methylphenyl)thiourea (1c) have been synthesized by refluxing mixture of equimolar amounts of 4-chlorobutanoylisothiocyanate with 2, 3 or 4-toluidine, respectively. The three isomers were characterized by spectroscopic (UV/vis, FT-IR and NMR) and X-ray crystallography techniques. To investigate the isomerization effect on spectroscopic data, DFT and TD-DFT calculations have been carried out using five hybrid functionals (B3LYP, B3P86, CAM-B3LYP, M06-2X and PBE0) to predict UV/vis absorption bands (n→π∗ and π→π∗), (1)H and (13)C NMR chemical shifts, FT-IR vibration modes and X-ray parameters (bonds, bond angles and torsion angles) for 1a, 1b and 1c isomers. The results showed that the isomerization effect is significant on λ(MAX) absorption bands, while for IR and NMR the effect is negligible. In accordance with previous studies, B3LYP, B3P86 and PBE0 gave the most reliable to predict the excitation energies of thiourea derivatives.

Intra- and intermolecular hydrogen bonding and conformation in 1-acyl thioureas: an experimental and theoretical approach on 1-(2-chlorobenzoyl)thiourea

The vibrational analysis (FT-IR and FT-Raman) for the new 1-(2-chlorobenzoyl)thiourea species suggests that strong intramolecular interactions affect the conformational properties. The X-ray structure determination corroborates that an intramolecular N-H⋯OC hydrogen bond occurs between the carbonyl (-CO) and thioamide (-NH2) groups. Moreover, periodic system electron density and topological analysis have been applied to characterize the intermolecular interactions in the crystal. Extended N-H⋯SC hydrogen-bonding networks between both the thioamide (N-H) and carbamide (NH2) groups and the thiocarbonyl bond (CS) determine the crystal packing. The Natural Bond Orbital (NBO) population analysis demonstrates that strong hyperconjugative remote interactions are responsible for both, intra and intermolecular interactions. The Atom in Molecule (AIM) results also show that the N-H⋯Cl intramolecular hydrogen bond between the 2-Cl-phenyl ring and the amide group characterized in the free molecule changes to an N⋯Cl interaction as a consequence of crystal packing.

Intermolecular interactions in crystalline 1-(adamantane-1-carbonyl)-3-substituted thioureas with Hirshfeld surface analysis

The 1-acyl thiourea synthon is characterized through a complete Hirshfeld surface analysis for a series of six closely related 1-(adamantane-1-carbonyl) thioureas.

Hydrogen-bonded complexes between dimethyl sulfoxide and monoprotic acids: molecular properties and IR spectroscopy

MP2/6-31++G(d,p) and DFT B3LYP/6-31++G(d,p) calculations were performed of the structure, binding energies, and vibrational modes of complexes between dimethyl sulfoxide (DMSO) as a proton acceptor and monoprotic linear acids HX (X = F, Cl, CN) as well as monoprotic carboxylic acids HOOCR (R = -H, -CH3, -C6H5) in 1:1 and 1:2 stoichiometric ratios. The results show that two different structures are possible in the 1:2 ratio: in the first, the DMSO molecule interacts with both acid molecules (leading to a "Y" structure); in the second, the DMSO interacts with only one monoprotic acid. The second structure shows a lower stability per hydrogen bond. The spontaneities of the reactions to form the 1:1 and 1:2 complexes are greatly influenced by the X group of the linear acid. With the exception of HCN, all the reactions are spontaneous. In the 1:2 complexes with Y structure, we observed that the hydrogen atoms of the linear acid are coupled in symmetric and asymmetric modes, while this type of coupling is absent from the other 1:2 complexes.

Intramolecular hydrogen bond in biologically active o-carbonyl hydroquinones

Intramolecular hydrogen bonds (IHBs) play a central role in the molecular structure, chemical reactivity and interactions of biologically active molecules. Here, we study the IHBs of seven related o-carbonyl hydroquinones and one structurally-related aromatic lactone, some of which have shown anticancer and antioxidant activity. Experimental NMR data were correlated with theoretical calculations at the DFT and ab initio levels. Natural bond orbital (NBO) and molecular electrostatic potential (MEP) calculations were used to study the electronic characteristics of these IHB. As expected, our results show that NBO calculations are better than MEP to describe the strength of the IHBs. NBO energies (∆Eij(2)) show that the main contributions to energy stabilization correspond to LP-->σ* interactions for IHBs, O1…O2-H2 and the delocalization LP-->π* for O2-C2=Cα(β). For the O1…O2-H2 interaction, the values of ∆Eij(2) can be attributed to the difference in the overlap ability between orbitals i and j (Fij), instead of the energy difference between them. The large energy for the LP O2-->π* C2=Cα(β) interaction in the compounds 9-Hydroxy-5-oxo-4,8, 8-trimethyl-l,9(8H)-anthracenecarbolactone (VIII) and 9,10-dihydroxy-4,4-dimethylanthracen-1(4H)-one (VII) (55.49 and 60.70 kcal/mol, respectively) when compared with the remaining molecules (all less than 50 kcal/mol), suggests that the IHBs in VIII and VII are strongly resonance assisted.