Preparation,crystal structure and characterization of 2,4,6-trinitro-3,5-dimethylbenzoic acid monohydrate

In the present work, we synthesized 2,4,6-trinitro-3,5-dimethylbenzoic acid (TNDMBA). Single crystal of TNDMBA·H₂O was cultured from aqueous solution using a slow evaporation method at 30°C. The crystal structure was determined by X-ray single-crystal diffraction analysis. The crystal belongs to the monoclinic system with space group P2(1)/c having unit cell parameters of a = 17.24(3) Å, b = 6.032(1) Å, and c = 16.359(4) Å. There are two kinds of intermolecular H-bond interactions between H₂O and TNDMBA, which is different from typical carboxylic acids that form H-bond dimers across crystallographic centers of inversion. The title compound was characterized by FT-IR, DSC, and TG-DTG technologies, and calculated by using density functional theory (DFT) method. The calculated results show that the structural parameters from the theory are close to those of the crystal structure from the experiments. The compound is composed of three nitro groups and one carboxyl group, and it can be used as a potential energetic combustion catalyst in industry.     

Influences of the molecule–electrode interface structure on the conducting characteristics of the gold-4,4 bipyridine-gold molecular junction

Two popular models of the gold-4,4 bipyridine (44BPD)-gold molecular junction, i.e., the direct contact of the 44BPD molecule with the Au(1 1 1) surface and the intermediary contact through one extra gold atom on each side, were studied using density functional theory calculations under periodic boundary conditions. The relative position of the Fermi level is changed by the extra gold atom from well below the LUMO (lowest unoccupied molecular orbital) of the 44BPD molecule in the direct contact model to within the energy range of the LUMO in the intermediary contact model, indicating that the local structure of the contact can significantly affect the conducting characteristics of the junction. The dependence of the molecule–electrode interaction on the interface structure was also investigated in details.     

A theoretical study of the structure and vibrations of 2,4,6-trinitrotolune

Theoretical calculations of the structure, internal rotations and vibrations of 2,4,6-trinitrotolune, TNT, in the gas phase were performed at the B3LYP/6-31G* and B3LYP/6-311+G** levels of theory. Two genuine energy minimum structures were found. In both structures the 4-nitro group is planar to the phenyl ring, while the 2,6-nitro groups are slightly out of plane with the phenyl ring due to steric interaction with the methyl group. The two structures are related by internal rotations of the methyl and 2, or 6-nitro group. The lowest energy route for interconversion between them is a concerted motion of the methyl group and 2 or 6 nitro group in a ‘cog wheel’ type of mechanism. The geometry of the low energy structure A is closest to that observed in the crystal structures of TNT, where all three nitro groups are out of plane with the phenyl ring. FTIR and Raman spectra of solid TNT and ¹³C, ¹⁵N enriched TNT are presented and assigned with the help of the B3LYP/6-311+G** calculations on A. The lower level B3LYP/6-31G* calculation fails to predict the correct vibrational coupling between the nitro and phenyl groups. The B3LYP/6-311+G** calculation gives a good prediction of the nitro vibrations and the isotopic shifts observed for TNT isotopomers.     

First-principles study of crystalline mono-amino-2,4,6-trinitrobenzene, 1,3-diamino-2,4,6-trinitrobenzene, and 1,3,5-triamino-2,4,6-trinitrobenzene

The electronic structure and thermodynamic properties of crystalline mono-amino-2,4,6-trinitrobenzene (MATB), 1,3-diamino-2,4,6-trinitrobenzene (DATB), and 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) have been comparatively studied using density functional theory in the local density approximation. An analysis of electronic structure shows that the CNO₂ bonds in the three solids are easier to be broken in the thermal decomposition than the CNH₂ bonds. The calculated thermodynamic properties show that the order of their thermodynamic stability is TATB > DATB > MATB and their decomposition reactions are favorable under high temperature. Finally, an attempt is made to correlate the impact sensitivity of the three solids with their band gap. The result shows that there is the relationship between the band gap and impact sensitivity.     

Development of a model for the rational design of molecular imprinted polymer: Computational approach for combined molecular dynamics/quantum mechanics calculations

A new rational approach for the preparation of molecularly imprinted polymer (MIP) based on the combination of molecular dynamics (MD) simulations and quantum mechanics (QM) calculations is described in this work. Before performing molecular modeling, a virtual library of functional monomers was created containing forty frequently used monomers. The MD simulations were first conducted to screen the top three monomers from virtual library in each porogen-acetonitrile, chloroform and carbon tetrachloride. QM simulations were then performed with an aim to select the optimum monomer and progen solvent in which the QM simulations were carried out; the monomers giving the highest binding energies were chosen as the candidate to prepare MIP in its corresponding solvent. The acetochlor, a widely used herbicide, was chosen as the target analyte. According to the theoretical calculation results, the MIP with acetochlor as template was prepared by emulsion polymerization method using N,N-methylene bisacrylamide (MBAAM) as functional monomer and divinylbenzene (DVB) as cross-linker in chloroform. The synthesized MIP was then tested by equilibrium-adsorption method, and the MIP demonstrated high removal efficiency to the acetochlor. Mulliken charge distribution and ¹H NMR spectroscopy of the synthesized MIP provided insight on the nature of recognition during the imprinting process probing the governing interactions for selective binding site formation at a molecular level. We think the computer simulation method first proposed in this paper is a novel and reliable method for the design and synthesis of MIP.     

Method for evaluation of density functional integrals in molecular calculations

Numerical methods for computing variationally optimized molecular orbitals within the Hartree–Fock approximation are augmented to include correlation functionals of the density in the energy and the numerical methods for carrying this out are described. The approach is applied explicitly to the Colle–Salvetti correlation energy functional. It is found that the gradient terms in the Colle–Salvetti functional present numerical problems associated with the low-density behavior, but also that they make a relatively small contribution to the correlation energy. In the three cases considered, HF, H₂O and N₂, it is found that the Colle–Salvetti correction considerably underestimates the correlation energies obtained in coupled-cluster theory.     

Paramagnetic NMR shift,spectroscopic and molecular modeling studies of lanthanide(III)-morin complexes

Studies on nine-coordinate lanthanide complexes of morin are described. The complexes were characterized by elemental analysis, molar conductance, UV–Vis spectra, IR spectra, thermal analysis and NMR spectra. Molecular modeling studies were also carried out. The complexes are non-electrolytes in DMSO. TGA showed anhydrous nature of the complexes. The electronic spectra of the complexes were recorded in methanol. ¹H NMR spectra of lanthanum, praseodymium, neodymium, samarium and dysprosium complexes have been studied in DMSO-d₆. The complexes do not dissociate in DMSO and retain their coordination. ¹H NMR spectra of paramagnetic and diamagnetic complexes exhibit downfield as well as upfield shifts of morin resonances that shows change in geometry during coordination.     

Relativistic perturbation theory of molecular structure

Summary The recently developed relativistic double perturbation theory is extended to handle relativistic changes of molecular structure more easily. This is achieved by simple coordinate scalings. Accurate higher order mixed perturbation energies for H ₂ ⁺ are calculated. The relativistic changes of bond energy,DE, of bond length,R _e , and especially of force constant,k, and of anharmonicity,a, are large, up to 100%·(Z/c)². The dominant contributions tok anda are due to the indirect change of the nonrelativistick anda connected with the relativistic change of bond length. Accordingly the relativistic changes obey Badger's and Gordy's rules (–RDEk).Dedicated to Prof. Klaus Ruedenberg in appreciation of his fundamental contributions to both formal theory and physical explanations in quantum chemistry     

Electronic and geometrical structures of cyclopropanes, part 51. fluorocyclopropanes. linear correlation of orbital energies with C–C bond lengths. further improvement of the two-orbitals model

The electronic and geometrical structures of fluorocyclopropanes (1–12) have been analysed using DFT B3LYP calculations. A linear relationship, Δɛ_ω=−0.172 Δr−0.171 (n=12, R=0.931), between Δɛ_ω (in eV), the difference of the energies of the Walsh orbitals ω_S and ω_A, and Δr (in pm), the difference of vicinal and distal C–C bond lengths, is established. Correcting the orbital splitting by the basic value at Δr=0.00 pm, an even better linear correlation Δɛ_ω ^eff=0.0720 Δr (n=12, R=0.984) is obtained. The results confirm the general applicability of the two-orbitals model for the relationship between geometrical and electronic structures for substituted cyclopropanes. ¹For Part 4 see Ref. [17].     

Local and nonlocal density functional calculations of the molecular structure of isomeric thiadiazoles

The chemistry of thiadiazoles and their derivatives is of considerable interest in chemistry owing to their pharmacological and potential industrial applications. In this context, a detailed study of isomeric thiadiazole molecules has been done using local (SVWN; Slater, and Vosko, Wilk and Nusair) and nonlocal (BLYP; Becke, and Lee, Yang and Parr) density functionals and optimizing the molecular geometries by means of the gradient technique. A charge sensitivity analysis of the studied molecule has been performed by resorting to density functional theory, obtaining several sensitivity coefficients such as the molecular energy, net atomic charges, global and local hardness, global and local softness and Fukui functions. With these results and the analysis of the dipole moments, the molecular electrostatic potentials and the total electron density maps, several conclusions have been inferred about the preferred sites of chemical reaction of the studied compounds. The condensed Fukui functions are shown to be one of the best criteria for predicting chemical reactivity.     

Vibrational energies,bonding nature,electronic properties,spectroscopic investigations and analysis of 3-bromo-4-Chlorobenzophenone

In this present study, we investigated pharmaceutically active of 3-Bromo-4-chlorobenzophenone. Structural, electronic properties (HOMO-LUMO, MEP) are investigated using DFT tool. Vibrational spectral analysis for FT-IR and FT-Raman are made of headline molecule. Electronic transition properties are discussed with the help of UV–Vis spectral analysis. Biologically active sites are found from MEP analysis. Electron delocalization properties are studied explored from HOMO-LUMO band gap energy. Moreover, intra molecular interactions are explained from NBO method. Molecular docking studies are performed to find the interactions various pathologies. The topological properties of the electron density have been analyzed.     

Investigation on the isoform selectivity of novel kinesin-like protein 1 (KIF11) inhibitor using chemical feature based pharmacophore,molecular docking,and quantum mechanical studies

Kinesin-like protein (KIF11) is a molecular motor protein that is essential in mitosis. Removal of KIF11 prevents centrosome migration and causes cell arrest in mitosis. KIF11 defects are linked to the disease of microcephaly, lymph edema or mental retardation. The human KIF11 protein has been actively studied for its role in mitosis and its potential as a therapeutic target for cancer treatment. Pharmacophore modeling, molecular docking and density functional theory approaches was employed to reveal the structural, chemical and electronic features essential for the development of small molecule inhibitor for KIF11. Hence we have developed chemical feature based pharmacophore models using Discovery Studio v 2.5 (DS). The best hypothesis (Hypo1) consisting of four chemical features (two hydrogen bond acceptor, one hydrophobic and one ring aromatic) has exhibited high correlation co-efficient of 0.9521, cost difference of 70.63 and low RMS value of 0.9475. This Hypo1 is cross validated by Cat Scramble method; test set and decoy set to prove its robustness, statistical significance and predictability respectively. The well validated Hypo1 was used as 3Dquery to perform virtual screening. The hits obtained from the virtual screening were subjected to various scrupulous drug-like filters such as Lipinski’s rule of five and ADMET properties. Finally, six hit compounds were identified based on the molecular interaction and its electronic properties. Our final lead compound could serve as a powerful tool for the discovery of potent inhibitor as KIF11 agonists.     

Solvatochromism, hyperpolarizability, molecular and crystal structure of betaine dye 4-(2,4,6-triphenylpyridinium-1-yl)-phenolate

Solvatochromic effect of 4-(2,4,6-triphenylpyridinium-1-yl)-phenolate hydrate, 1, was determined. CT absorption band, which gave the shift from 23,880 (in water solution) to 14,440 cm⁻¹ (in anisole solution) allowed the molecular second order polarizability β_CT to be estimated as 59.5×10⁻³⁰ cm⁵ esu⁻¹. The crystal structure of 1 was determined: C₂₉H₂₁NO·5.78H₂O; orthorhombic, C222₁, a=15.005(9), b=24.356(4), c=7.5097(9) Å; V=2744.5(17) Å³, Z=4, D_X=1.224 g cm⁻¹; λ=0.71073 Å (Mo Kα); μ=0.087 mm⁻¹; final R₁=0.0551 for 2882 reflections [I>2σ(I)]. The molecules of 1, in an anti-parallel arrangement, form columns along the c-axis through stacking between the pyridinium ring and a phenyl ring in para position of the neighbouring molecule. Water molecules filling channels between the columns are disordered. Two of water molecules are connected by hydrogen bonds with negatively charged oxygen atom of 1. Powdered samples of 1 revealed only weak SHG response as measured using HRS method in relation to urea standard.     

Ab initio and density functional theory calculations of molecular structure and vibrational spectrum of ethyl azidoacetate

Here we report ab initio and density functional results for molecular properties of ethyl azidoacetate (N₃CH₂COOC₂H₅) and for the corresponding singly ionized structure (N₃CH₂COOC₂H₅⁺). Ab initio ionization energies based on Koopmans’ theorem are in excellent agreement with the experimental data from ultraviolet photoelectron spectroscopy. DFT adiabatic energy differences between neutral and ionized structures are very sensitive to electronic correlation effects and are not in very good agreement with experiment. The results for the structure and vibrational frequencies are compared with the experimental data of related molecular structures.     

Preparation, crystal structure and thermal decomposition study of some trimethylsilyl esters of dicarbamic acids

Some new trimethylsilylated dicarbamic acid esters 1–9 and 10 were prepared. Their thermal decomposition was studied in n-alkanes as media. The reactions were monitored by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS), respectively. Some N-silylated cyclic ureas 11–15 were also prepared from the corresponding esters 2–6 by thermolysis. The crystal structures of 2, 5 and 8 are also discussed. The crystal and molecular structures of 2 and 5 have very similar characteristics. Both molecules are sited via their molecular centre of symmetry on crystallographic inversion centres. The Carbamate groups are planar in all three cases as expected. An analysis of the data showed that the force due to Si---O conjugation which constrains the Si atom into the plane of the carbamate group is comparable to the crystal packing forces with a small out-of-plane movement being not unfavourable.     

Molecular structure and conformational stability of allylisocyanate—post-Hartree–Fock and density functional theory studies

The molecular structure and conformational stability of allylisocyanate (CH₂CHCH₂NCO) molecule was studied using the ab initio and DFT methods. The geometries of possible conformers, C-gauche (δ=120°, θ=0°) (δ=C=C–C–N and θ=C–C–N=C) and C-cis N-trans (δ=0° and θ=180°) were optimized employing HF/6-31G^*, MP2/6-31G^* levels of theory of ab initio and BLYP, B3LYP, BPW91 and B3PW91 methods of DFT implementing the atomic basis set 6-311+G(d,p). The structural and physical parameters of the above conformers were discussed with the experimental and theoretical values of the related molecules, methylisocyanate and 3-fluoropropene. It has been found that the N=C=O bond angle is not linear as the experimental result for both the conformers and the theoretical bond angle is 173°. The rotational potential energy surfaces have been performed at the HF/6-31G^*, and MP2/6-31G^* levels of theory. The Fourier decomposition potentials were analysed at the HF/6-31G^*, and MP2/6-31G^* levels of theory. The HF/6-31G^* level of theory predicted that the C-gauche conformer is more stable than the C-cis N-trans conformer by 0.41 kJ/mol, but the MP2 and DFT methods predicted the C-cis N-trans conformer is found to be more stable than the C-gauche conformer. The calculated chemical hardness value at the HF/6-31G^* level of theory predicted the C-cis N-trans form is more stable than C-gauche form, whereas the chemical hardness value at the MP2/6-31G^* level of theory favours the slight preference towards the C-gauge conformer.     

Synthesis, crystal structure and density functional theoretical studies on phenyl-thiocarbamic acid-O-pyridin-4-ylmethyl ester

The title compound of phenyl-thiocarbamic acid-O-pyridin-4-ylmethyl ester has been synthesized and characterized by elemental analysis, IR, electronic spectroscopy and X-ray single crystal diffraction. Density functional theory (DFT) method calculations of the structure, atomic charge distributions and the thermodynamic properties at different temperatures have been performed. Calculated results show that DFT method at B3LYP/6-311G^** level can well reproduce the structure of the title compound. The predicted vibrational frequencies are compared with the experimental ones and they support each other on the whole. The atoms of sulfur, oxygen and the atom of nitrogen from pyridine ring all have bigger negative charges, which make the title compound become a multidentate organic ligand. The correlation equations of the thermodynamic properties of and with temperature are also obtained.     

表观价态异常分子EuS2和Eu2S的泛函理论研究

用密度泛函理论方法研究了EUS2和Eu2S的分子结构、电子结构和成健情况．结果表明EuS2有弯曲构型和直线构型，而Eu2S只有弯曲构型．在S－S和Eu－Eu之间存在化学使．在这两个分子中，Eu和S的价届满足8电子规律，保持其正常价态．第一电离势和原子化能的计算值与实验结果符合较好．相对论效应对分子几何构型和振动基频影响较小，对分子轨道能级顺序和键能有较显著的影响，但旋轨偶合起的作用不大