Tetramethylammonium Cation: Directionality and Covalency in Its Interactions with Halide Ions

The degree of interpenetration of the van der Waals crusts of two atoms, represented by a penetration index, is defined to better quantify the meaning of the nonbonding contact distances between two atoms, which should allow us to compare different atom pairs on the same footing. The structural trends of the intermolecular contacts between the tetramethylammonium cation (TMA) and halogen atoms are reviewed, and a computational study of model X···TMA ion pairs (X = F, Cl, Br, I, Au) is presented. The results disclose two energy minima, in each of which the anion simultaneously interacts with three hydrogen atoms. The bonding mechanisms in the two cases are discussed based on the results of the tools of the trade that provide a consistent picture in which a distribution of charges significantly varies not only around each different atom but is also strongly dependent on the distance to the central N atom. This behavior, together with some non-negligible covalent character of the interionic interaction, is not predicted from a single-molecular electrostatic potential map of the TMA cation.

Two interaction topologies sustain interactions between the tetramethylammonium cation and halide (or auride) anions. A simple dependence of the interaction energy on the anion’s atomic radius is found, as a result of a refined combination of ionic (major component), covalent, and dispersion forces, in which the interpenetration of the van der Waals crusts of the interacting atoms seems to have a role.

On the importance of π-stacking interactions in the complexes of copper and zinc bearing pyridine-2,6-dicarboxylic acid N-oxide and N-donor auxiliary ligands

Using N- and O-donor ligands in a mixed-ligand system, three new coordination complexes have been X-ray characterized, exhibiting strong π–π stacking interactions.

Experimental and theoretical insights into the formation of weak hydrogen bonds and H⋯H bonding interactions in the solid-state structure of two eucalyptol derivatives

We report the synthesis and X-ray solid-state structure of two eucalyptol derivatives. Both compounds form self-assembled dimers establishing C–H⋯O hydrogen bonds and H⋯H bonding interactions.

Novel 'main-part' isostructuralism in metal complexes with 1-methylimidazole: crystal structures, energy calculations and magnetic properties

Two new transition metal complexes with 1-methylimidazole (1-MeIm) and azide as ligands, namely, [Co(1-MeIm)₄(N₃)₂] (1) and [Ni(1-MeIm)₄(N₃)₂] (2), have been synthesized and characterized by IR, Raman, UV-Vis and XPS spectroscopy. Their crystal structures were solved by single-crystal X-ray diffraction. The supramolecular self-assembly of the two complexes is governed by non-classical C-H⋯N hydrogen bonds and C-H⋯π interactions. Lattice energies and intermolecular interaction energies for various molecular pairs are quantified using the PIXEL method. DFT computational studies to assess the binding energy through modern tools like non-covalent interaction (NCI plots) analysis and reduced density gradient (RDG) analysis have also been carried out. A detailed analysis of geometric descriptors revealed the existence of quasi-isostructural pairs or 'main-part' isostructuralism in a series formed by 1, 2, and a related cadmium complex, being more evident in the 1/2 pair. DFT studies using theoretical models have been used to disclose the relative importance of the H-bond and C-H⋯π noncovalent interactions. Magnetic measurements for compound 1 show weak ferrimagnetic coupling between adjacent M(II) centers, mediated by H-bonding and C-H⋯π non-covalent interactions.

Deciphering the H-Bonding Preference on Nucleoside Molecular Recognition through Model Copper(II) Compounds

The synthetic nucleoside acyclovir is considered an outstanding model of the natural nucleoside guanosine. With the purpose of deepening on the influence and nature of non-covalent interactions regarding molecular recognition patterns, three novel Cu(II) complexes, involving acyclovir (acv) and the ligand receptor N-(2-hydroxyethyl)ethylenediamine (hen), have been synthesized and thoroughly characterized. The three novel compounds introduce none, one or two acyclovir molecules, respectively. Molecular recognition has been evaluated using single crystal X-ray diffraction. Furthermore, theoretical calculations and other physical methods such as thermogravimetric analysis, infrared and UV-Vis spectroscopy, electron paramagnetic resonance and magnetic measurements have been used. Theoretical calculations are in line with experimental results, supporting the relevance of the [metal-N7(acv) + H-bond] molecular recognition pattern. It was also shown that (hen)O-H group is used as preferred H-donor when it is found within the basal coordination plane, since the higher polarity of the terminal (hen)O-H versus the N-H group favours its implication. Otherwise, when (hen)O-H occupies the distal coordination site, (hen)N-H groups can take over.

Role of hydrogen bonds and weak non-covalent interactions in the supramolecular assembly of 9-hydroxyeucaliptol: crystal structure, Hirshfeld surface analysis, and DFT calculations

The compound 1,3,3-trimethyl-2-oxabicyclo[2.2.2]octan-9-ol (9-hydroxyeucaliptol) has been prepared and characterized by single-crystal X-ray diffraction analysis, infrared, Raman, and UV-visible spectroscopies. The molecular geometry of the title compound was also investigated theoretically by density functional theory (DFT) calculations to compare with the experimental data. The substance crystallizes in the trigonal crystal system, space group P3₂ with Z = 9 molecules per unit cell. There are three independent molecules in the crystal asymmetric unit having the same chirality and showing some differences in the orientation of the H-atom of the hydroxyl group. The crystal structure of 9-hydroxyeucaliptol shows that the hydroxyl group presents an anti-conformation with respect to the O-atom of the ether group. The crystal packing of 9-hydroxyeucaliptol is stabilized by intermolecular O-H···O hydrogen bonds involving the hydroxyl groups of different molecules, which play a decisive role in the preferred conformation adopted in solid state. The intermolecular interactions observed in solid state were also studied through the Hirshfeld surface analysis and quantum theory of atoms in molecules (QTAIM) approaches. Energy framework calculations have also been carried out to analyze and visualize the topology of the supramolecular assembly, and the results indicate a significant contribution from electrostatic energy over the dispersion.

X-ray characterization, Hirshfeld surface analysis, DFT calculations, in vitro and in silico lipoxygenase inhibition (LOX) studies of dichlorophenyl substituted 3-hydroxy-chromenones

This work reports the synthesis, X-ray characterization and theoretical study of dichlorophenyl substituted 3-hydroxy-chromenones focusing on the low prevalence of halogen bonds and in vitro and in silico lipoxygenase inhibition (LOX) studies.

A first exploration of isostructurality in transition metal nitroprussides: X-ray analysis, magnetic properties and DFT calculations

Transition metal M(ii) (M = Mn, Fe, Cu, Zn, Cd) nitroprussides with 1-methyl-imidazole were prepared and characterized by spectroscopic techniques, thermal analysis, and powder (Fe complex) and single-crystal XRD.

Interplay of weak noncovalent interactions in alkoxybenzylidene derivatives of benzohydrazide and acetohydrazide: a combined experimental and theoretical investigation and lipoxygenase inhibition (LOX) studies

Three hydrazide-based Schiff bases have been synthesized and characterized by IR, UV-vis and X-ray diffraction methods. A detail analysis of intermolecular interactions has been performed by Hirshfeld surface analysis and DFT calculations.

Crystal engineering with pyrazolyl-thiazole derivatives: structure-directing role of π-stacking and σ-hole interactions

The structure-directing role of a variety of noncovalent interactions in the solid state of pyrazolyl-thiazole derivatives has been analyzed energetically using DFT calculations and by means of Hirshfeld surface analysis.

Raise the anchor! Synthesis, X-ray and NMR characterization of 1,3,5-triazinanes with an axial tert-butyl group

N-t-Bu-N',N''-Disulfonamide-1,3,5-triazinanes were synthesized and characterized by X-ray single crystal structure analysis. In the course of the X-ray structure elucidation, the first solid experimental evidence of the axial position of the tert-butyl group in unconstrained hexahydro-1,3,5-triazacyclohexanes was obtained. Dynamic low-temperature NMR analysis allowed to fully investigate a rare case of crystallization-driven unanchoring of the tert-butyl group in the chair conformation of saturated six-membered cycles. DFT calculations show that the use of explicit solvent molecules is necessary to explain the equatorial position of the t-Bu group in solution. Otherwise, the axial conformer is the thermodynamically stable isomer.

Intermolecular interactions in antipyrine-like derivatives 2-halo-N-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)benzamides: X-ray structure, Hirshfeld surface analysis and DFT calculations

Based on experimental and computational data, a complex network of intermolecular interactions has been rationalized for antipyrine compounds.

Recurrent π–π stacking motifs in three new 4,5-dihydropyrazolyl–thiazole–coumarin hybrids: X-ray characterization, Hirshfeld surface analysis and DFT calculations

Two different π–π stacking modes are described, studied and characterized in the crystal structures of 4,5-dihydropyrazolyl–thiazole–coumarin hybrids, including a partial aliphatic ring.

Synthesis, X-ray characterization and theoretical study of 3a,6:7,9a-diepoxybenzo[de]isoquinoline derivatives: on the importance of F⋯O interactions

This manuscript reports the synthesis, X-ray characterization and theoretical study of 3a,6:7,9a-diepoxybenzo[de]isoquinoline derivatives focusing on the importance of F···O interactions.

Synthesis, Structure, and Biological Assays of Novel Trifluoromethyldiazepine–Metal Complexes

A new series of CuII, NiII, CoII, and MnIII complexes have been synthesised from the (6Z)-6-(7-trifluoromethyl-1,2,3,4-tetrahydro-5H-1,4-diazepin-5-ylidene)cyclohexa-2,4-dien-1-one (HDZP) ligand. These complexes were characterised by elemental, spectroscopic (IR and UV-vis), and thermal analysis. The crystal structure of Cu-DZP was solved by X-ray diffraction methods. The complex crystallises in the monoclinic P21/c space group, with two molecules per unit cell. The crystal lattice is stabilised by different intra and intermolecular interactions. Hirshfeld surface analysis was employed to obtain additional information about interactions that are responsible for the crystal packing. Quantitative examination of the fingerprint plots indicated the dominant contribution of H⋯H and H⋯X (X=O, F) interactions in the crystal packing. In addition, C–H⋯chelate ring (CR) and C–H⋯π interactions are described in detail and evaluated using DFT calculations. The antibacterial properties and the mechanism of inhibition of the main bacterial resistant mechanism, the biofilm, of the metal complexes and free ligand were investigated. [Mn(DZP)3]·2H2O was the most active complex against the Pseudomonas aeruginosa biofilm formation with an inhibition of 40%. However, none of the complexes inhibit more than 25% of the Gram negative bacteria microbial development. The most meaningful result was the bactericidal effect of [Co(DZP)2(H2O)2]·2H2O against the Gram positive bacteria, Staphylococcus aureus, which inhibits the bacterial development and significantly reduces the biofilm formation at low concentration.

Enol-imino-Keto-enamine Tautomerism in a Diazepine Derivative: How Decisive Are the Intermolecular Interactions in the Equilibrium?

The strange tautomeric equilibrium behavior exhibited by a new o-hydroxyphenyl diazepine derivative when the compound is analyzed both in solution and solid state opens the structural study of the enol-imino-keto-enamine forms and the influence of the intermolecular interactions in their equilibrium. The expected enol-imino form, in which the enol is part of a phenyl system and a strong O-H···N intramolecular hydrogen bond is established, results the most stable tautomer in gas phase (theoretical calculations) and was detected by NMR spectroscopy when the compound was dissolved in aprotic solvents. Nevertheless, the keto-enamine form ,in which the keto group integrates a cyclohexadienone moiety and the aromaticity of the phenol is lost, was the only tautomer in the crystal lattice according to single-crystal X-ray diffraction, vibrational spectroscopy, and diffuse reflectance results. The last form was also found as the main tautomer in UV-vis and NMR spectroscopy when a protic solvent was employed.

Diethylaminophenyl-based Schiff base Cu(ii) and V(iv) complexes: experimental and theoretical studies and cytotoxicity assays

A combined experimental and theoretical study and cytotoxicity assays of diethylaminophenyl-based Schiff base Cu(ii) and VO(iv) complexes are reported. The Cu(ii) complex shows interesting chelate ring⋯π interactions in the crystal structure.

New coordination polymers based on 2-methylimidazole and transition metal nitroprusside containing building blocks: synthesis, structure and magnetic properties

In this study, we report the synthesis, structural and magnetic properties of coordination polymers based on transition metal nitroprussides and 2-methylimidazole as ligands.

Exploring weak intermolecular interactions in thiocyanate-bonded Zn(ii) and Cd(ii) complexes with methylimidazole: crystal structures, Hirshfeld surface analysis and luminescence properties

We report the synthesis, spectroscopy and X-ray crystal structures of four Cd(ii) and Zn(ii) coordination compounds with imidazole derivatives and thiocyanate as co-ligands.

A detailed exploration of intermolecular interactions in 4-(4-dimethylaminobenzylideneamino)-N-(5-methyl-3-isoxazolyl)benzenesulfonamide and related Schiff bases: Crystal structure, spectral studies, DFT methods, Pixel energies and Hirshfeld surface analysis

The Schiff base of the title has been synthesized and its crystal structure determined by single-crystal X-ray diffraction. The compound was characterized by IR, Raman, ¹H NMR, ¹³C NMR and electronic absorption spectra. DFT calculations provide the quantum chemical basis for the observed molecular conformation. A study of intermolecular interactions of the title compound is compared with seven other closely related structures and reveals that molecules in most of the compounds are linked by a cooperative effect of strong and weak hydrogen bonds, CH^…π, and π^…π stacking interactions, and also lp^…π contacts. Lattice energy calculations indicate that the dispersion component is the major contribution, with the coulombic term playing a significant role in the total energy. Interaction energies for molecular pairs involving NH···N bonds indicate a dominant contribution to packing stabilization coming from coulomb component. Hirshfeld surfaces and 2D-fingerprint plots allowed us to visualize different intermolecular contacts and its relative contributions to total surface in each compound. The analysis of electrostatic potential (ESP) maps correlates well with the computed energies providing evidences on the dominant electrostatic nature of NH···N and NH···O interactions.

Structure and bonding of 2,2,2-trichloroethylacetate: An experimental gas phase and computational study

The structural and conformational properties of 2,2,2-trichloroethylacetate, H3CCO2CH2CCl3, have been determined in the gas phase using gas electron diffraction (GED). The experimental measurements were complemented by MP2 and DFT quantum-chemical calculations. Two conformers separated by a shallow rotational barrier have been identified, one of C 1 (syn-gauche) and the other of C s symmetry (syn-anti). All calculations indicate that syn-gauche is preferred in terms of enthalpy, whereas syn-anti seems to be slightly more stable regarding Gibbs free energy. In the gas-phase structure determination, dynamic models based on different potential energy surface scans were used. The one from dispersion-corrected density functional theory, predicting a preference of syn-gauche by 1.7kJmol−1, was found to describe the experimental data best. One- and two-conformer models had to be rejected due to correlations and unrealistically large amplitudes. Experimentally determined structural parameters are in good agreement with both, quantum-chemical calculations as well as GED data for related compounds. Interacting quantum atoms (IQA) analyses revealed that interplay between the carbonyl group and the hydrogen as well as chlorine atoms of the trichloroethyl group accounts for most of the stabilisation of the C 1 conformer. With intramolecular symmetry-adapted perturbation theory (I-SAPT) analyses it was possible to further elucidate the nature of dominant interactions in the two conformers. Herein, preference of syn-gauche can for the most part be attributed to electrostatic and to some extent to induction and dispersion interplays. In contrast this conformer is severely destabilised through steric repulsion. These results were supported by NBO analyses.

Gas-phase structure of 2,2,2-trichloroethyl chloroformate studied by electron diffraction and quantum-chemical calculations

The molecular structure and conformational properties of 2,2,2-trichloroethyl chloroformate, ClC(O)OCH2CCl3 were determined experimentally using gas-phase electron diffraction (GED) and theoretically based on quantum-chemical calculations at the MP2 and DFT levels of theory. Further experimental measurements such as UV-visible, IR and Raman spectroscopy were complemented with the corresponding theoretical studies. All experimental results and calculations confirm the presence of two conformers namely anti-gauche (C1 symmetry) and anti-anti (Cs symmetry). The conformational preference was rationalised by NBO and AIM analyses. Molecular properties such as ionisation potential, electronegativity, chemical potential, chemical hardness and softness were deduced from HOMO-LUMO analyses. The TD-DFT approach was applied to assign the electronic transitions observed in the UV-visible spectrum. A detailed interpretation of the infrared and Raman spectra of the title compound are reported. Using calculated frequencies as a guide, IR and Raman spectra also provide evidence for the presence of both C1 and Cs conformers.

Quantum chemical studies on molecular structure, spectroscopic (IR, Raman, UV-Vis), NBO and HOMO-LUMO analysis of 1-benzyl-3-(2-furoyl) thiourea

Vibrational and electronic spectra for 1-benzyl-3-(2-furoyl) thiourea were calculated by using density functional method (B3LYP) with different basis sets. The complete assignment of all vibrational modes was performed on basis of the calculated frequencies and comparing with the reported IR and Raman spectra for that thiourea derivative. UV-visible absorption spectra of the compound dissolved in methanol were recorded and analyzed using time dependent density functional theory (TD-DFT). The calculated values for the geometrical parameters of the title compound are consistent with the ones reported from XRD studies. The stability of the molecule, related to hyper-conjugative interactions, and electron delocalization were evaluated using natural bond orbital (NBO) analysis. Intra-molecular interactions were studied by AIM approach. The HOMO and LUMO analysis are used to determine the charge transfer within the molecule. Molecular electrostatic potential map was performed by the DFT method.

Vibrational studies (FTIR and Raman), conformational analysis, NBO, HOMO-LUMO and reactivity descriptors of S-methyl thiobutanoate, CH3CH2CH2C(O)SCH3

In the present article, the molecular structure of S-methyl thiobutanoate, CH3CH2CH2C(O)SCH3 was determined by ab initio (MP2) and DFT calculations using different basis sets. The infrared and Raman spectra for the liquid phase were also recorded and the bands observed were assigned to the vibrational normal modes. The experimental and calculations confirm the presence of two most stable conformers, one with pseudo anti-syn conformation and another with gauche-syn conformation. The study was completed using natural bond orbital (NBO) and AIM analysis. The molecular properties like dipole moment, molecular electrostatic potential surface (MEP) and HOMO-LUMO molecular orbitals were calculated to get a better insight of the properties of the title molecule. Global and local reactivity descriptors were computed in order to predict reactivity and reactive sites on the molecule for nucleophilic, electrophilic and radical attacks.

Synthesis, DFT calculations of structure, vibrational and thermal decomposition studies of the metal complex Pb[Mn(C3H2O4)2(H2O)2]

The metallo-organic complex Pb[Mn(C3H2O4)2(H2O)2] was synthesized and characterized by IR and Raman spectroscopy and powder X-ray diffraction methods. The cell parameters for the complex were determined from powder X-ray diffraction using the autoindexing program TREOR, and refined by the Le Bail method with the Fullprof program. A hexagonal unit cell was determined with a=b=13.8366(7)Å, c=9.1454(1)Å, γ=120°. The DFT calculated geometry of the complex anion [Mn(C3H2O4)2(H2O)2](2-) is very close to the experimental data reported for similar systems. The IR and Raman spectra and the thermal analysis of the complex indicate that only one type of water molecules is present in the structure. The thermal decomposition of Pb[Mn(C3H2O4)2(H2O)2] at 700 °C in air produces PbO and Pb2MnO4 as final products. The crystal structure of the mixed oxide is very similar to that reported for Pb3O4.

Ab-initio and DFT calculations on molecular structure, NBO, HOMO-LUMO study and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde

The experimental and theoretical study on the molecular structure and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde (DMABA) is presented. The IR and Raman spectra were recorded in solid state. Optimized geometry, vibrational frequencies and various thermodynamic parameters of the title compound were calculated using DFT methods and are in agreement with the experimental values. A detailed interpretation of the IR and Raman spectra of the title compound were reported. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using NBO analysis and AIM approach. The HOMO and LUMO analysis were used to determine the charge transfer within the molecule and some molecular properties such as ionization potential, electron affinity, electronegativity, chemical potential, hardness, softness and global electrophilicity index. The TD-DFT approach was applied to assign the electronic transitions observed in the UV-visible spectrum measured experimentally. Molecular electrostatic potential map was performed by the DFT method. According to DSC measurements, the substance presents a melting point of 72.34°C and decomposes at temperatures higher than 193°C.

Structural, vibrational and electronic characterization of 1-benzyl-3-furoyl-1-phenylthiourea: an experimental and theoretical study

The compound 1-benzyl-3-furoyl-1-phenylthiourea was synthesized and characterized through IR and Raman spectroscopy and its molecular structure was determined.

Synthesis, crystal structure, conformational and vibrational properties of 6-acetyl-2,2-dimethyl-chromane

The 6-acetyl-2,2-dimethyl-chromane compound was synthesized and characterized by IR, Raman, UV-Visible and (1)H NMR spectroscopies. Its solid state structure was determined by X-ray diffraction methods. The substance crystallizes in the triclinic P-1 space group with a=5.9622(5) Å, b=10.342(1) Å, c=10.464(1) Å, α=63.81(1)°, β=81.923(9)°, γ=82.645(9)°, and Z=2 molecules per unit cell. Due to extended π-bonding delocalization a substantial skeletal fragment of the molecule is planar. The vibrational modes were calculated at B3LYP/6-31G(d,p) level and all of them assigned in the IR and Raman spectra. The DFT calculated (1)H NMR spectrum (chemical shifts) were in good agreement with the experimental data. The electronic (UV-Visible) spectrum was calculated using TD-DFT method in gas phase and it was correlated with the experimental data. The assignment and analysis of the frontier HOMO and LUMO orbitals indicate that the absorption bands are mainly originated from π→π(*) transitions. According to DSC measurements the substance presents a melting point of 93°C and decomposes at temperatures higher than 196°C.

DFT calculations of structure and vibrational properties of 2,2,2-trichloroethylacetate, CH(3)CO(2)CH(2)CCl(3)

The molecular structure and conformational properties of 2,2,2-trichloroethylacetate, CH(3)CO(2)CH(2)CCl(3), were determined by ab initio (MP2) and DFT quantum chemical calculations at different levels of theory. The theoretical study was complemented with experimental measurements such as IR and Raman spectroscopy. The experimental and calculations confirm the presence of two conformers, one with anti, gauche conformation (C1 symmetry) and another with anti, anti form (Cs symmetry). The conformational preference was studied using the total energy scheme, NBO and AIM analysis. The infrared spectra of CH(3)CO(2)CH(2)CCl(3) are reported in the liquid and solid phases and the Raman spectrum in liquid phase. Using calculated frequencies as a guide, evidence for both C1 and Cs conformers is obtained in the IR and Raman spectra.