Synthesis,X-ray Molecular Structure,and Semiempirical Calculations of a New Heteroarylpiperazine Derivative

The new piperazine derivative (1) was synthesized by linking a coumarin system to a heteroarylpiperazine via a propyloxy chain. Its molecular structure, as determined by X-ray diffractometry is compared to those computed by three semiempirical methods. PM3 and MNDO give the best accuracy in reproducing the bond distances and angles, respectively. AM1 gives the best agreement with X-ray in reproducing the whole three-dimensional (3D) structure of this molecule. An analysis of these results at the light of other similar previously reported is carried out.     

Synthesis, X-Ray characterization and molecular structure of a novel supramolecular compound of antimony(III); Theoretical investigation on molecular and electronic properties based on the ab initio HF and various DFT methods

A new compound of Sb(III), formulated as (pipzH₂)[Sb₂(pydc)₄].2H₂O (1), was synthesized and characterized by IR, ¹H and ¹³C NMR spectroscopy, elemental analysis and single crystal X-ray diffractometry. The compound (1) is a member of a great family of supramolecular metallic compounds recently derived from a proton transfer ion pair i.e. (pipzH₂)(pydc), where pipz is piperazine and pydcH₂ is pyridine-2,6-dicarboxylic acid. In the title compound with a binuclear structure, Sb(III) atoms are pentacoordinated and the coordination polyhedra show distortion from a regular trigonal bipyramid due to stereochemically active lone pair on metallic centers. The four (pydc)^2? ligands of the formula unit behave differently against metallic centers, i.e. two act as tridentate, and the other two as bidentate ligands. A variety of intermolecular O-H…O, N-H…O and C-H?O hydrogen bonds involving water molecules, cationic and anionic fragments are responsible for the extension of the supramolecular network of the compound. Optimized geometries were calculated for the title compound with the HF, B3LYP, B3PW91, B3P86 and B1LYP methods of theory by using the combination of LanL2DZ basis set with standard basis set 6-31G (d,p). The agreement between the optimized and experimental geometries was in the decreasing order: B3P86, B3PW91, B1LYP, B3LYP and HF. Electronic properties of the title compound were also investigated based on the natural bond orbital (NBO) analysis.     

Experimental and theoretical structural studies on 4-(2-phenylethyl)-5-(2-furyl)-2,4-dihydro-3H-1,2,4-triazole-3-thione

The structural and conformational features of 4-(2-phenylethyl)-5-(2-furyl)-2, 4-dihydro-3H-1,2,4-triazole-3-thione (1a), which can be related to the biological activity, have been investigated by X-ray diffraction and molecular modeling techniques. Ab initio method (RHF/6-31G) and density functional theory (B3LYP/6-31G(D)) have been used to calculate structural parameters, conformations, and relative energy of two tautomeric specious (1a and 1b) of the title compound. The geometry and the conformation of the thione form, 1a, is well reproduced by the DFT (B3LYP/6-31G(D)) method as compared with X-ray structure in which this form is found. The thione form is also predicted to be 14.42 kcal/mol more stable than the thiol form in the gas-phase by the DFT method.     

Synthesis,characterization, spectroscopy,X-ray structure and gaussian hybrid computational investigation of (−)-(S)-1-[2-(benzenesulfonamido)-3-phenylpropanoyl]-4-[(4-methyl)phenyl]thiosemicarbazide

Abstract

The molecule (?)-(S)-1-[2-(benzenesulfonamido)-3-phenylpropanoyl]-4-[(4-methyl)phenyl] thiosemicarbazide was synthesized and its structure analyzed by X-ray diffraction to understand its geometry, and inter/intra-molecular interactions. Theoretical calculations were carried out using DFT and TD-DFT methods with B3LYP/6-31G(d, p) and B3LYP/6-31G?+?(d, p) basis sets. Theoretical bond parameters, harmonic vibration frequencies, and chemical shifts are in good agreement with the experimental results. Electronic properties of the molecule derived from frontier orbitals, molecular electrostatic potential, and theoretical UV-Visible spectrum are validated experimentally.     

Conformational in the IR spectra of 1′-hydroxyethyl derivatives of 1,4-benzo-and 5,8-dihydroxy-1,4-naphthoquinones: A DFT study

Detailed conformational analysis of the molecule of ′-hydroxyethyl-1,4-benzoquinone (3) by the B3LYP/cc-pVTZ method revealed predominance of rotamers with the free 1′-OH group in the gas phase. B3LYP/cc-pVTZ calculations with inclusion of solvent (cyclohexane) effect in the framework of the polarizable continuum model predict an increase in the percent-age of such rotamers compared to the corresponding gas-phase values. The results obtained are in qualitative agreement with the experimentally observed pattern of v(OH) bands in the IR spectrum of compound 3 in cyclohexane (hexane) solution. Conformational analysis, including tautomerism and rotamerism, of 2-ethyl-1′,5,8-trihydroxy-1,4-naphthoquinone (2) was performed by the B3LYP method with the 6-31G(d), 6-311G(d), 6-311G(d,p), and cc-pVDZ basis sets. The most abundant tautomeric form of compound 2 is form A in which the substituent bearing 1′-OH group is in the quinonoid nucleus. In the gas phase, the percentage of all rotamers in form A is about 86% (among them, the proportion of rotamers with the free 1′-OH group is more than 60%). The main reason for splitting of the v(OH) bands in the IR spectra of compounds 2 and 3 in solutions in nonpolar solvents is the equilibrium between rotamers with a relatively weak intramolecular hydrogen bond between the 1′-OH group and the carbonyl group and those having no this bond.     

IR and Raman spectra, hydrogen bonds, and conformations of N-(2-hydroxyethyl)-4,6-dimethyl-2-oxo-1,2-dihydropyrimidine (drug Xymedone)

Hydrogen bonds and structure of drug Xymedone in different phase and aggregate states were studied using IR and Raman spectroscopy, IR microscopy, quantum chemical calculations (B3LYP/6-31G*), X-ray powder diffractometry, and DSC and TGA methods. It was found that the synthesized specimen of Xymedone powder is a mixture of two gauche-conformers. First one is bound by intermolecular hydrogen bonds and second one is stabilized by an intramolecular hydrogen bond. Upon the dissolution of Xymedone the conformational equilibrium shifted in favor of conformers of the first or second type depending on the solvent nature.     

Synthesis,characterization, and quantum chemical calculational studies on 3-<Emphasis Type="Italic">p</Emphasis>-methylphenyl-4-amino- 1, 2, 4-triazole-5-thione

The title compound of 3-p-methylphenyl-4-amino-1, 2, 4-triazole-5-thione was synthesized and characterized by elemental analysis, IR, electronic spectra, and X-ray single crystal diffraction. Quantum chemical calculations of the structure, natural bond orbital, and thermodynamic functions of the title compound were performed by using B3LYP/6-311G** and HF-6-311G** methods. Both the methods can well simulate the molecular structure. Vibrational frequencies were predicted, assigned and compared with the experimental values, and B3LYP/6-311G** method is superior to HF/6-311G** method to predict the vibrational frequencies. Electronic absorption spectra calculated by B3LYP/6-311G** method have some red shifts compared with the experimental ones and natural bond orbitals analyses indicate that the two absorption bands are mainly derived from the contribution of n → π^* and π → π^* transitions. On the basis of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations between C ⁰ _p,m , S ⁰ _m , H ⁰ _m , and temperatures.     

Experimental and computational studies on (<Emphasis Type="Italic">Z</Emphasis>)-1-((4-phenylamino)phenylamino)-methylene)naphthalen-2(1<Emphasis Type="Italic">H</Emphasis>)-one

The Schiff base compound (Z)-1-((4-phenylamino)phenylamino)methylene)naphthalen-2(1H)-one has been synthesized and characterized by IR, UV–Vis, and X-ray single-crystal determination. Molecular geometry from X-ray experiment of the title compound in the ground state have been compared using the Hartree–Fock (HF) and density functional method (B3LYP) with 6−31G(d,p) basis set. Calculated results show that density functional theory DFT and HF can well reproduce the structure of the title compound. Using the time-dependent density functional theory (TD-DFT) and Hartree–Fock (TD-HF) methods, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD-DFT method and experimental ones is determined. The energetic behavior of the title compound in solvent media has been examined using B3LYP method with the 6−31G(d,p) basis set by applying the polarizable continuum model (PCM). The total energy of the title compound decreases with increasing polarity of the solvent. In addition, DFT calculations of the title compound, molecular electrostatic potential (MEP), natural bond orbital analysis (NBO), and non-linear optical (NLO) properties were performed at B3LYP/6−31G(d,p) level of theory.     

Electronic and steric effect manifestations in the structure of 9-Azidoacridine

The crystal structure of 9-azidoacridine (9AA) was determined by X-ray structure analysis (the compound crystallizes in the rhombic system). The crystallographically independent fragment of the structure of 9AA was found to contain two molecules. Both molecules were nonplanar, and the azido group was displaced out of the acridine nucleus plane by 34.6° (molecule A) and 28.6° (molecule B). The barriers to azido group rotations about the C-N bond were calculated by the semiempirical PM3 and nonempirical DFT B3LYP quantum-chemical methods. According to the B3LYP/6-31G^* calculations, the structures with the azido group situated in the acridine nucleus plane and perpendicularly to this plane are 0.21 and 1.66 kcal/mol, respectively, higher in energy than the completely optimized structure, in which the dihedral angle between the azido group and acridine nucleus planes is 32°. The PM3 method overestimates the steric strain energy of 9AA and underestimates the energy of azido group conjugation with the acridine nucleus compared with B3LYP calculations.     

A new rosane-type diterpenoid from Stachys parviflora and its density functional theory studies

A new rosane-type diterpenoid (1) has been isolated from the chloroform fraction of Stachys parviflora. Structure of 1 was proposed based on 1D and 2D NMR techniques including correlation spectroscopy, heteronuclear multiple quantum coherence, heteronuclear multiple bond correlation and nuclear Overhauser effect spectroscopy. A theoretical model for the electronic and spectroscopic properties of compound 1 is also developed. The geometries and electronic properties were modelled at B3LYP/6-31G^* and the theoretical scaled spectroscopic data correlate nicely with the experimental data.     

Thermodynamic stability of 2,4,6-tris(nitromethyl)-1,3,5-triazine: an experimental and theoretical study

The molecular geometries and electronic structures of 2,4,6-tris(nitromethyl)-1,3,5-triazine isomers were investigated by the density functional method DFT/B3LYP/6-311++G** to elucidate the structural factors responsible for the stability of these systems. It was shown that a characteristic feature of the nitromethyl tautomer (1) of 2,4,6-tris (nitromethyl)-1,3,5-triazine consists in nonvalence interactions between an oxygen atom of nitro group and a carbon atom of triazine ring, which are probably due to Coulomb attraction between them. The tautomer with the 2,4,6-tris (nitromethylene)-hexahyrdo-1,3,5-triazine structure (2) is stabilized trough direct polar conjugation between the amino and nitro groups at the double bond. Structural strain of the molecule with the 2,4,6-tris(aci-nitromethyl)-1,3,5-triazine structure (3) is the reason for its thermodynamic instability. X-ray data indicate that the compound under study exists in the triazine tautomeric form 1 and the distances between oxygen atoms of nitro group and carbon atom of the triazine ring are shortened. NMR data suggest the existence of triazine in the nitromethyl form 1 in acetonitrile and acetone and a tautomeric equilibrium between the nitromethyl and nitromethylene forms in a more polar solvent (DMSO). The results obtained suggest a Coulomb-type stabilization of the 2,4,6-tris(nitromethyl)-1,3,5-triazine molecule in the gas phase, in the crystal, and in nonpolar solvents.     

Hybrid-DFT Study and NBO Analysis of the Stereoelectronic Interaction Effects (Associated with the Anomeric Effects) on the Conformational Properties of 2,3,5,6-Tetrahalo-1,4-dioxanes and Their Analogs Containing S and Se Atoms

NBO analysis and hybrid density functional theory–based method (B3LYP/6-311+G**) was used to study the anomeric effects (AE), dipole–dipole interactions, and steric repulsion effects on the conformational properties of 2,3,5,6-tetrahalo-1,4-dioxane [halo = F (1), Cl (2), Br (3)], 2,3,5,6-tetrahalo-1,4-dithiane [halo = F (4), Cl (5), Br (6)], and 2,3,5,6-etrahalo-1,4-diselenane [halo = F (7), Cl (8), Br (9)]. B3LYP/6-311+G** results revealed a strong axial preference in compounds 1–3. Gibbs free energy difference (G _eq–G _ax) values (e.g., ΔG _eq-ax) between the axial and equatorial conformations of compound 1 to compound 3 are 8.19, 3.86, and 3.13 kcal mol^?1, respectively, as calculated by the B3LYP/6-311+G** level of theory. On the other hand, the NBO analysis of donor–acceptor (bond–antibond) interactions revealed that the AE for compounds 1–3 are ?12.26, ?16.46, and ?18.11 kcal mol^?1, respectively. Contrary to the increase of the AE values from compound 1 to compound 3, the increase of the steric repulsions (e.g., 1,3-syn-axial repulsions) could fairly explain the decrease of the axial conformation stability in compounds 1–3 compared to their equatorial conformations. Further, the correlations between the AE, structural parameters, and conformational behavior of compounds 4–9 have been investigated.     

4,6-二甲氧基-2-[甲氧脲基硫代脲基]嘧啶的合成、晶体结构和理论计算

利用2-氨基-4,6-二甲氧基嘧啶在干燥条件下与硫氰酸钾、氯甲酸甲酯在乙酸乙酯溶液中反应制得4-(4,6-二甲氧基嘧啶-2-基)-3-硫代脲酸甲酯, 在二甲基甲酰胺溶液中培养出单晶, 通过X射线单晶结构分析法测定分子结构和晶体结构, 晶体属单斜晶系, 空间群为C2/m, 晶胞参数为: a＝1.6672(3) nm, b＝0.66383(12) nm, c＝1.1617(2) nm, β＝109.275(2)°, V＝1.2136(4) nm³, D_c＝1.490 g/cm³, μ＝0.281 mm^－1, F(000)＝568, Z＝4, R₁＝0.0341, wR₂＝0.1042. 运用Gaussian 03程序, 在6-311G的基组水平上, 用HF, MP2以及B3LYP三种计算方法对标题化合物进行了几何全优化, 并对其成键情况及自然键轨道(NBO)进行了分析.     

Structural and electronic properties of a Benzoin monomer

In the present work, we report structural and electronic properties of a benzoin monomer named as 2-oxo-1,2-diphenylethyl-2-bromopropanoate (C₁₇H₁₄BrO₃). The previously synthesized compound is characterized by single crystal X-ray diffraction. The optimized molecular geometry (bond lengths, and bond angles), HOMO-LUMO analysis and molecular electrostatic potential (MEP) are calculated by density functional theory (DFT) and Hartree-Fock (HF) methods with 6-311G(d) basis set in the neutral ground state and using DFT methods for singly oxidized doublet, singly reduced doublet, and neutral triplet state for the benzoin compound. The X-ray structure determination of the compound is compatible with the geometric parameters calculated at B3LYP/6-311G(d). In the triplet state the HOMO-LUMO energy gap of 2.39?eV which indicates semi-conductor property is recommended for the photovoltaic devices.     

An Ab Initio Study and NBO Analysis of the Stability and Conformational Properties of Hexakis(trimethylelementhyl)benzene (Element = C,Si, Ge,and Sn)

Ab initio molecular orbital and density functional theory were used to investigate energetic and structural properties of the various conformations of hexa-tertbutylbenzene (1), hexakis(trimethylsilyl)benzene (2), hexakis (trimethylgermyl)benzene (3), and hexakis(trimethylstannyl)benzene (4). HF/3-21G//HF/3-21G and B3LYP/3-21G//HF/3-21G results revealed that the Twist-Boat (TB) conformer of compound 1 is more stable than the 1-Chair (C), 1-Boat (B), and 1-Planar (P) conformers. B3LYP/3-21G//HF/3-21G results show that the 1- TB conformer is more stable than 1- C, 1- B, and 1- P conformers of about 1.13, 4.34, and 99.94 kcal mol^?1 , respectively. Contrary to the stability order of compound 1 conformers, the C conformer of compounds 2–4 is more stable than TB, B, and P conformations, as calculated by B3LYP/3-21G//HF/3-21G and HF/3-21G//HF/3-21G levels of theory. The energy gap between the C and P conformers in compounds 1–4 is decreased in the following order: ΔE(4: C, P) < ΔE (3: C, P) < ΔE(2: C, P) < ΔE (1: C, P). This fact can be explained in terms of the increase of C _aromatic -M (M═C, Si, Ge, and Sn) bond lengths and the decrease of steric (van der Waals) repulsions in the previously discussed compounds. For compounds 1–3, the calculations were also performed at the B3LYP/ 6-31G*//HF/3-21G level of theory. However, the comparison showed that the results at B3LYP/3-21G//HF/3-21G methods correlated well with those obtained at the B3LYP/6-31G*// HF/6-31G method. Further, NBO analysis revealed that in compounds 1–4, the resonance energy associated with the σ_M-C1 to σ*_C2-C3 delocalization is 5.20, 9.68, 11.15, and 12.27 kcal mol^?1, respectively. These resonance energy values could explain the easiness of the ring flipping processes of C, B, and TB conformers of compounds 4 to 1. Also, the NBO results showed that by an increase of the σ_M-C1 → σ *_C2-C3 resonance energies in compounds 1–4, the σ_M-C1 bonding orbital occupancies decrease. This fact could fairly explain the increase of the C_aryl-M bond length from compound 1 to 4. The NBO results are also in good agreement with the calculated energy barriers for the ring flipping of the chair conformations in compounds 1–4, as calculated by B3LYP and HF methods.     

Synthesis,Crystal Structure,Quantum Chemical Analysis,Electrochemical Behavior,and Antibacterial and Photocatalytic Activity of Co Complex with Pyridoxal-(S-Methyl)-isothiosemicarbazone Ligand

New complex Co(III) with ligand Pyridoxal-S-methyl-isothiosemicarbazone, (PLITSC) was synthesized. X-ray analysis showed the bis-ligand octahedral structure of the cobalt complex [Co(PLITSC-H)₂]BrNO₃·CH₃OH (compound 1). The intermolecular interactions governing the crystal structure were described by the Hirsfeld surface analysis. The structure of compound 1 and the corresponding Zn complex (([Zn(PLTSC)(H₂O)₂]SO₄·H₂O)) were optimized at the B3LYP/6–31 + G (d,p)/LanL2DZ level of theory, and the applicability was assessed by comparison with the crystallographic structure. The natural bond orbital analysis was used for the discussion on the stability of formed compounds. The antibacterial activity of obtained complexes towards S. aureus and E. coli was determined, along with the effect of compound 1 on the formation of free radical species. Activity of compound 1 towards the removal of methylene blue was also investigated. The voltammograms of these compounds showed the reduction of metal ions, as well as the catalyzed reduction of CO₂ in acidic media.     

Insight into the C-F bond mechanism of molecular analogs for antibacterial drug design

The activities of biological molecules usually rely on both of intra-molecular and intermolecular interactions between their function groups. These interactions include interonic attraction theory, Van der Waal’s forces and the function of geometry on the individual molecules, whether they are naturally or synthetic. The purpose of this study was to evaluate the antibacterial activity of C-F bond compound using combination of experiments verification and theoretical calculation. We target on the insect natural products from the maggots of Chrysomyis megacephala Fabricius. Based on density functional theory(DFT) and B3LYP method, a theoretical study of the C-F bond on fluoride was designed to explore compounds 2 and 4 antibacterial structure–activity relationship. With the progress in DFT, first-principle calculation based on DFT has gradually become a routine method for drug design, quantum chemistry and other science fields.     

Ab Initio Study of Ring Flipping of the Overcrowded Peri-Substituted Naphthalenes

Ab inintio molecular orbital and density functional theory method were used to investigate the structural and dynamic behavior of 1,8-di-tert-butyl naphthalene (1), 1,8-bis(trimethylsilyl)naphthalene (2), 1,8-bis(trimethylgermyl)naphthalene (3), and 1,8-bis(trimethylstannyl)naphthalene (4). HF/3-21G//HF/3-21G results revealed that the ring flipping barrier height of compound 1–4 is 92.59, 32.13, 26.76, and 15.46 kJ mol^?1 respectively. The obtained results show that the transition state structure for ring flipping of the bulky-groups is in a planar form with naphthalene ring. Contrary to compound 1, the ring flipping of compounds 2–4 occurred easily at room temperature. Also, MP2/3-21G//HF/3-21G energy calculation, show that the enantiomerization energy of compounds 1–4 are 97.99, 33.24, 26.80, and 15.38 kJ·mol^?1 respectively. The required energy for ring inversion of compounds 1–4 are 85.09, 27.26, 21.54, and 10.21 kJ mol^?1 respectively, as calculated by B3LYP/3-21G//HF/3-21G method. It can be concluded that the lower energy barrier of the ring flipping of compounds 2–4 is related to the increasing of the bond lengths of Si—C, Ge—C, and Sn—C, in contrast to C—C bond.     

A mixed experimental and theoretical study on chelidamate copper(II) complex with 4-methylpyrimidine

A new chelidamate complex, [Cu(chel)(H₂O)₂(mpd)] (chel = chelidamate; mpd = 4-methylpyrimidine), has been synthesized and characterized through a combination of single crystal X-ray analysis, electron paramagnetic resonance (EPR), ultraviolet-visible (UV-vis), and fourier transform infrared spectroscopy (FT-IR). The complex has six-coordinate distorted octahedral geometry around Cu(II). The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and angles) have been calculated using Density Functional Theory (DFT)/B3LYP and Hartree Fock quantum chemical methods with 6-31G(d, p) basis set by Gaussian 09W software. The EPR spectrum of the compound showed that the paramagnetic center has rhombic symmetry. The EPR studies were carried out using the following unrestricted hybrid density functionals: B3LYP, CAM-B3LYP, HSEH1PBE, WB97XD, MPW1PW91, and BPV86. The UV–vis absorption spectra have been examined in different media and compared with the calculated one using TD-DFT method by applying the polarizable continuum model. Natural bond orbital property of complex has been performed by DFT/B3LYP with 6-31G (d, p) basis set.