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The synthesis of four novel amide compounds (R1C(O)NHR2) is reported, which contain both bulky (R1=phenyl and adamantyl) and hydrophilic (R2=hydroxyl, methoxyl) groups. The incorporation of such substituents provides compounds with unique properties that combine steric hindrance and hydrophilicity. The synthesized amides were fully characterized by 1H and 13C nuclear magnetic resonance (NMR) and analysed using infrared (IR) and Raman spectroscopy to investigate their vibrational properties in the solid phase, specifically focusing on the amide‐type normal modes of vibrations. Furthermore, the crystal structures of three derivatives were determined by single‐crystal X‐ray diffraction, which provided insights into their molecular arrangements. The occurrence of N−H⋅⋅⋅O=C hydrogen bonding intermolecular interaction is clearly observed and characterized by Hirschfeld surface analysis. Topology analysis using the Quantum Theory of Atom in Molecules and Crystals (QTAIM−C) were employed to investigate the electronic properties of the isolated amide molecules and to analyse the intermolecular interactions within the crystalline structure. The periodic calculations for the crystal revealed a higher electronic density in the C−N bond, indicating an increased covalent character in this bond compared with the C=O bond. This observation indicates the presence of resonance‐assisted hydrogen bonds within the amide core, leading to π electronic delocalization. [ABSTRACT FROM AUTHOR]

Two eucalyptol derivatives, namely 1,3,3-trimethyl-2-oxabicycle[2.2.2]oct-5-yl acetate (4) and 1,3,3-trimethyl-2-oxabicycle[2.2.2]oct-5,8-yl acetate (6) have been synthesized and characterized. Their crystal structures have been solved by single-crystal X-ray diffraction methods indicating that the molecular conformation of both compounds is stabilized by intramolecular C–H⋯O bonds between the H-atoms of the methyl group from the eucalyptol moiety and the O-atom of the acetoxy group. In addition, we have performed a detailed investigation of the intermolecular interactions that stabilize the crystal packing of both structures by using Hirshfeld surface analysis and their associated two-dimensional fingerprint plots. The analysis reveals that the solid-state structure of compounds 4 and 6 is mainly stabilized by C–H⋯O hydrogen bonds and H⋯H bonding interactions. These interactions have also been described and studied energetically using DFT calculations. The nature and strength of these intermolecular contacts have been rationalized by using several computational tools including molecular electrostatic potential (MEP) surfaces, natural bond orbital analysis (NBO), Bader's theory of atoms in molecules (QTAIM) and non-covalent interaction plot (NCI plot) index methods. Furthermore, the intermolecular contacts observed in the crystal lattice of both compounds were experimentally studied through vibrational (IR and Raman) and 1H and 13C NMR spectra. The computational molecular docking analysis of the compounds has been carried out against five potential leishmanial drug targets and the main protease of SARS-CoV-2. [ABSTRACT FROM AUTHOR]

Synthetic novgorodovaite analog Ca2( C2O4) Cl4·2H4O is identical to its natural counterpart. It crystallizes in the monoclinic I2/m space group with a = 6.9352(3), b = 7.3800(4), c = 7.4426(3) Å, β = 94.303(4)°, V = 379.85(3) Å3 and Z = 2. The heptahydrate analog, Ca2( C2O4)Cl4·7H4O, crystallizes as triclinic twins in the P1 space group with a = 7.3928(8), b = 8.9925(4), c = 10.484(2) Å, α = 84.070(7), β = 70.95(1), γ = 88.545(7)°, V = 655.3(1) Å3 and Z = 2. The crystal packing of both calcium oxalate-chloride double salts favors the directional bonding of oxalate, C2O4 2-, ligands to calcium ions as do other related calcium oxalate minerals. The π-bonding between C and O atoms of the C2O4 2- oxalate group leaves sp2-hydridised orbitals of the oxygen atoms available for bonding to Ca. Thus, the Ca-O bonds in both calcium oxalate-chloride double salts are directed so as to lie in the plane of the oxalate group. This behavior is reinforced by the short O...O distances between the oxygens attached to a given carbon atom, which favors them bonding to a shared Ca atom in bidentate fashion. Strong bonding in the plane of the oxalate anion and wide spacing perpendicular to that plane due to repulsion between oxalate π-electron clouds gives rise to a polymerized structural units which are common to both hydrates, explaining the nearly equal cell constants ~7.4 Å which are defined by the periodicity of Ca-oxalate chains in the framework (monoclinic b ≈ triclinic a). When compared with novgorodovaite, the higher water content of Ca2( C2O4) Cl4·7H4O leads to some major differences in their structures and ensuing physical properties. While novgorodovaite has a three-dimensional framework structure, in the higher hydrate, the highly polar water molecules displace chloride ions from the calcium coordination sphere and surround them through OwH···Cl hydrogen bonds. As a result, polymerization in Ca2( C2O4)Cl4·7H4O solid is limited to the formation of two-dimensional Ca2( C2O4)(H4O)5 slabs parallel to (001), inter-layered with hydrated chloride anions. This layered structure accounts for (001) being both a perfect cleavage and a twin interface plane. The infrared and Raman spectra of both salts are also briefly discussed. [ABSTRACT FROM AUTHOR]

The crystal structure of sodium and magnesiumtris(oxalato)chromato(III) nona hydrate, NaMg[Cr(C2O4)3]·9H2O, has been determined by X-ray diffraction methods. It crystallizes in the trigonalP3c1 space group with (in the hexagonal setting)a = b = 16.9635(4),c = 12.5247(3) Å, andZ = 6 molecules per unit cell. The Cr(III) and sodium ions are in octahedral environments coordinated to three oxalate molecules and arranged in a honeycomb-like layered structure perpendicular to the crystalc-axis. There are three different octahedral [Mg(H2O)6]2+hydrated ions that fill the honeycomb holes giving rise to electrically neutral Na[Mg(H2O)6][Cr(oxalato)3] crystal slabs. Neighboring slabs are bridged by the remaining three water molecules through H-bonds and therefore the whole crystal can be more properly described as Na[Mg(H2O)6][Cr(oxalato)3]·3H2O. Also, the structure of isomorphous NaMg[Al(C2O4)3]·9H2O compound has been re-examined and compared with the chromium(III) complex. Infrared and Raman spectra of both complexes were also recorded and briefly discussed. [ABSTRACT FROM PUBLISHER]

The molecular structure of two mixed and closely related conformers of the title compound, C13H16O2, found in the solid with unequal occupancies has been determined by X-ray diffraction methods. The substance crystallizes in the monoclinic Pca21 space group with a =17.279(2), b =5.1716(7), c =12.549(2)Å, and Z = 4 molecules per unit cell. The structure was solved from 1314 reflections with I >2σ(I) and refined to an agreement R1-factor of 0.049. The minor conformer (34.7%) is nearly mirror-related to and extensively overlapped with the major one. The skeleton of the 4-hydroxyacetophenone molecular fragment and the prenyl group,—(CH2)—(CH) = C(CH3)2, pendant arm attached to it are both planar and perpendicular to each other. A strong intermolecular O—H···O bond links neighboring molecules in the lattice to produce a polymeric structure. The conformational structures of the compound in the gas phase have been calculated by the DFT method and the geometrical results have been compared with the X-ray data. These data allow a complete assignment of vibration modes in the solid state FTIR and Raman spectra. The calculated 1H and 13C chemicals shifts are in good agreement with the corresponding experimental NMR spectra of the compound in solution. [Copyright &y& Elsevier]

In this study 2-(2′-furyl)-4,5-1H-dihydroimidazole (1) was prepared and then characterized by infrared, Raman, and multidimensional nuclear magnetic resonance (NMR) spectroscopies. The crystal and molecular structures of 1 were determined by X-ray diffraction methods. The density functional theory (DFT) and second-order Møller–Plesset theory (MP2) with Pople's basis set show that there are two conformers for the title molecule that have been theoretically determined in the gas phase, and that only one of them, conformer I, is present in the solid phase. NMR spectra observed for 1 were successfully compared with the calculated chemical shifts at the B3LYP/6-311++G** level theorized for this conformer. The harmonic vibrational frequencies for the optimized geometry of the latter conformer were calculated at the B3LYP/6-311++G** level in the approximation of the isolated molecule. For a complete assignment of the IR and Raman spectra in the solid phase of 1, DFT calculations were combined with Pulaýs scaled quantum mechanics force field (SQMFF) methodology to fit the theoretical frequency values to the experimental ones. Copyright © 2009 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

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Abstract: Structural and conformational properties of 1H-Isoindole-1,3(2H)-dione, 2-[(methoxycarbonyl)thio] (S-phthalimido O-methyl thiocarbonate) are analyzed using a combined approach including X-ray diffraction, vibrational spectra and theoretical calculation methods. The vibrational properties have been studied by infrared and Raman spectroscopies along with quantum chemical calculations (B3LYP and B3PW91 functional in connection with the 6-311++G** and aug-cc-pVDZ basis sets). The crystal structure was determined by X-ray diffraction methods. The substance crystallizes in the monoclinic P21/c space group with a =6.795(1), b =5.109(1), c =30.011(3)Å, β =90.310(3)° and Z =4 molecules per unit cell. The conformation adopted by the Nh name="sbnd" />Cs syn (Cbond in synperiplanar orientation with respect to the Nbond). The experimental molecular structure is well reproduced by the MP2/aug-cc-pVDZ method. [Copyright &y& Elsevier]

Abstract: Structural and conformational properties of the molecule bis[isopropoxy(thiocarbonyl)]sulfide, [(CH3)2CHOC(S)]2S, have been studied by vibrational spectroscopy (IR and Raman) and quantum chemical calculations (HF and B3LYP with 6-31+G∗ basis sets). The crystal and molecular structure of the title compound was determined by X-ray diffraction methods. It crystallizes in the monoclinic C2/c space group with a =8.4007(4), b =13.5936(5), c =10.3648(5)Å, β =106.024(4)° and Z =4 molecules per unit cell. The molecules are sited on a crystallographic twofold axis passing through the sulphide atom and arranged in layers perpendicular to the b-axis. The solid state IR and Raman spectra of the compound give no sign of any other rotamer. [Copyright &y& Elsevier]

Abstract: Pure O-methyl N-methoxycarbonyl thiocarbamate CH3OC(S)N(H)C(O)OCH3 (I) and O-ethyl N-methoxycarbonyl thiocarbamate, CH3CH2OC(S)N(H)C(O)OCH3 (II), are quantitatively prepared by the addition reaction between the CH3OC(O)NCS and the corresponding alcohols. The compounds are characterized by multinuclear (1H and 13C) and bi-dimensional (13C HSQC) NMR, GC–MS and FTIR spectroscopy techniques. Structural and conformational properties are analyzed using a combined approach involving crystallographic data, vibration spectra and theoretical calculations. The low-temperature (150K) crystal structure of II was determined by X-ray diffraction methods. The substance crystallizes in the monoclinic space group P21/n with a =4.088(1)Å, b =22.346(1)Å, c =8.284(1)Å, β =100.687(3)° and Z =4 molecules per unit cell. The conformation adopted by the thiocarbamate group –OC(S)N(H)– is syn (Cbond in synperiplanar orientation with respect to the N–H single bond), while the methoxycarbonyl Cbond is in antiperiplanar orientation with respect to the N–H bond. The non-H atoms in II are essentially coplanar and the molecules are arranged in the crystal lattice as centro-symmetric dimeric units held by N−H···Sn bonds [d(N···S)=3.387(1)Å, ∠(N−H···S)=166.4(2)°]. Furthermore, the effect of the π electronic resonance in the structural and vibrational properties is also discussed. [Copyright &y& Elsevier]

Abstract: The molecular structure of the title complex, [Cu(C6H14N4O2)2(H2O)]CO3 ·H2O, was determined by single crystal X-ray diffractometry. It crystallizes in the monoclinic space group P21, with Z =2. The Cu(II) ion is in a square pyramidal environment, trans coordinated at the basis by two argininate groups acting as bidentate ligands through their amino nitrogen and carboxylate oxygen atoms. The coordination around copper is completed by a water molecule at the pyramid apex. The infrared, Raman and electronic spectra are briefly discussed on the basis of the structural peculiarities of the complex. [Copyright &y& Elsevier]

A new perfluoromethylated vinylogous amide, (Z)‐4,4,4‐trifluoro‐1‐(2‐hydroxyphenyl)‐3‐(2‐methoxyethylamino)‐2‐buten‐1‐one, is chosen as an example to investigate the bonding interactions in solid state. The Z, s‐cis form is the dominant conformation in both solution and solid state. Intramolecular hydrogen bonding determines this conformational preference in a nonpolar solvent (NMR spectra). Carbonyl and phenol groups are sensitive to the intra‐ and intermolecular contacts (vibrational spectra). The supramolecular assembly (X‐ray diffraction) is governed by NH⋯O and OH⋯O strong intermolecular hydrogen bonds giving rise to center‐symmetric R22(16) and R22(12) graph‐set motifs. The π‐stacking, F⋯H and F⋯F interactions are also discussed (Hirshfeld analysis). [ABSTRACT FROM AUTHOR]

The crystal structure of Ba(NH4)[Co(CN)6]·4H2O complex was determined by X-ray diffraction methods. It crystallizes in the hexagonal P63/m space group with a = b =7.6882(2)Å, c =14.4764(4)Å, and Z =2 molecules per unit cell. The structure was solved from 475 reflections with I >2σ(I) and refined to an agreement R1-factor of 0.0214. The cobaltocyanide anion has an octahedral shape with its Co(III) ion sited at a crystallographic special position of point symmetry (S 6) [d(Co-C)=1.886(3)Å and d(C–N)=1.143(4)Å]. The barium ion is in a 9-fold environment at a crystal special position (C 3 h ), coordinated to cyanide N-atoms of neighboring complexes [d(Ba–N)=2.862(3)Å] and to one type of water molecule laying onto an m mirror plane [d(Ba–Ow)=2.924(4)Å]. The ammonium ion and the other type of water molecule share four symmetry-related C 3 lattice sites with equal occupancy. Under the P63 subspace group these four sites split into two independent pairs of C 3 sites, one occupied by two symmetry-related ammonium ions, the other by two (disordered) water molecules. The complex was characterized by UV–Vis, IR and Raman spectroscopy and the thermal decomposition was studied to investigate the formation of BaCoO3− δ . This compound, in its hexagonal form, could be synthesized at temperatures as low as 675°C. At 750°C a new orthorhombic poly-type is obtained in a mixture with the hexagonal form which is associated with the appearance of oxygen vacancies. These temperatures of synthesis and reaction times are lower than those reported by ceramic and sol–gel synthesis. These soft treatments gave rise to homogeneous particles of small grain size. [ABSTRACT FROM AUTHOR]

Structural and spectroscopic properties of N,N-diethyl- (I) and N-tert-butyl-N′-methoxycarbonylsulfenyl urea (II) are analyzed using a combined approach with data obtained from X-ray diffraction, vibrational spectra and quantum chemical calculations. The molecular structures of CH3OC(O)SN(H)C(O)N(CH2CH3)2 (I) and CH3OC(O)SN(H)C(O)N(H)C(CH3)3 (II), the later co-crystallized with ethyl acetate (II 1/2EtOAc), were determined by X-ray diffraction methods. Compound I crystallizes in the triclinic space group P-1 and II·0.5EtOAc in the orthorhombic space group Pnma. In I, there are two independent but closely related molecules in the asymmetric unit whose conformations differ only in the orientation of the terminal N(CH2CH3)2 groups. Neighboring molecules in I exhibit N-H⋯O interaction giving rise to a polymeric chains. The conformation of the O-C=O-S-N-C=O-N skeleton of II is almost identical to the corresponding one of both molecules of I. Neighboring molecules in II are linked through bifurcated N-H⋯O⋯H-N interactions giving rise to a polymeric chain. The vibrational properties have been studied by FTIR and FT-Raman spectroscopy along with quantum chemical calculations at the B3LYP/6-311+G* level. [Copyright &y& Elsevier]

Abstract: The formation and characterisation of a polymeric copper complex produced by chemical reaction between copper (II) ions and 3-mercapto-1-propanesulphonate sodium salt (MPSA) were studied. The formation of this complex, followed by sequential UV–visible spectroscopic measurements, involves the reduction of Cu(II) ions to Cu(I) by MPSA, the latter being oxidised to bis-(3-sulphopropyl)-disulphide (SPS), a dimer of MPSA. In the presence of oxygen, the re-oxidation of Cu(I) to Cu(II) results in the formation of polymeric complex species consisting of [Cu(SO3(CH2)3S–S(CH2)3SO3)(H2O)4] units. Single crystal X-ray diffraction shows that this polymeric copper complex crystallizes in the monoclinic C2/c space group. The Cu(II) ion in the complex structure lies on an inversion centre in an elongated octahedral environment, equatorially coordinated to four water molecules and axially to two MPSA ligands through one of their sulphonic oxygen atoms. The complex units are arranged in the lattice as polymeric [Cu(SPS)(H2O)4] n molecules extending along the crystal [101] direction. The IR and Raman spectra as well as TGA and DTA data are reported. The stepwise thermal decomposition from room temperature up to 1000°C begins with the loss of water molecules and ends with the formation of copper sulphide species. [Copyright &y& Elsevier]

• Seven haloalkyl chromones (-CF2H, -CCl2H, -CF2CF3) linked to bromine and bromomethyl substituents were characterized and studied. • The crystal structure of 3-dibromomethyl-2-difluoromethyl chromone was determined by X-ray diffraction methods. • The Hirshfeld Surface Analysis showed non-covalent interactions O⋯Br, π⋯π and F⋯H hydrogen bonds. • AIM and NCI analysis of weak interactions were perform in compound 5. A set of seven new chromones with 2-haloalkyl (-CF 2 H, -CCl 2 H, -CF 2 CF 3) and 3-bromo and bromomethyl substituents were synthesized. The novel compounds were studied by DFT calculations and characterized by vibrational spectroscopy (IR and Raman) in solid state, and NMR (1H, 13C and 19F) and UV–vis spectroscopy in solution. The crystal structure of 3-dibromomethyl-2-difluoromethyl chromone was determined by X-ray diffraction. Due to extended π-bond delocalization, the organic framework is planar and lies on a crystallographic m-mirror plane. The intermolecular non-covalent interactions of 3-dibromomethyl-2-difluoromethyl chromone, as π⋯π stacking arrangements, F⋯H hydrogen bonds and O⋯Br contacts were evaluated by Hirshfeld surfaces analysis. These intermolecular contacts, which affect the absorption bands location of the involved groups, were also detected in the vibrational spectra. [ABSTRACT FROM AUTHOR]