Conformational Properties of New Thiosemicarbazone and Thiocarbohydrazone Derivatives and Their Possible Targets

The structure assignment and conformational analysis of thiosemicarbazone KKI15 and thiocarbohydrazone KKI18 were performed through homonuclear and heteronuclear 2D Nuclear Magnetic Resonance (NMR) spectroscopy (2D-COSY, 2D-NOESY, 2D-HSQC, and 2D-HMBC) and quantum mechanics (QM) calculations using Functional Density Theory (DFT). After the structure identification of the compounds, various conformations of the two compounds were calculated using DFT. The two molecules showed the most energy-favorable values when their two double bonds adopted the E configuration. These configurations were compatible with the spatial correlations observed in the 2D-NOESY spectrum. In addition, due to the various isomers that occurred, the energy of the transition states from one isomer to another was calculated. Finally, molecular binding experiments were performed to detect potential targets for KKI15 and KKI18 derived from SwissAdme. In silico molecular binding experiments showed favorable binding energy values for all four enzymes studied. The strongest binding energy was observed in the enzyme butyrylcholinesterase. ADMET calculations using the preADMET and pKCSm software showed that the two molecules appear as possible drug leads.     

Spectroscopic (fluorescence, 1D-ROESY) and theoretical studies of the thiabendazole and β-cyclodextrin inclusion complex

The inclusion complex between the anti-helminthic drug thiabendazole (TBZ) and the β-cyclodextrin (βCD) was characterized in solution using fluorescence and ¹H-Nuclear Magnetic Resonance spectroscopy and studied theoretically by semi empirical PM3 and density functional theory (DFT) quantum mechanical calculations. Thermodynamic stability associated with the formation of the TBZ:βCD inclusion complex in aqueous solution was determined treating the drug’s fluorescence enhancement in the presence of cyclodextrin by a non-linear model, which indicated a moderate host–guest affinity at equilibrium (K 150 ± 31 at 25 °C). Its supramolecular structure in solution was studied through the 1D-ROESY NMR experiment, which produced evidence that the guest molecular encapsulation occurs preferably via the drug’s benzimidazole group. Theoretical study employing molecular optimization with the semi empirical PM3 method provided two energetic-equivalent complex structures that are in accordance with the NMR experimental evidences. Single point energy calculations with DFT at the B3LYP/6-31G (d,p) level suggest the most stable structure of the inclusion complex and further comprehension on the interactions and conformational strains involved in its formation.     

Determination of the Chemical Structure of novel colored 1H-pyrrol-3(2H)-one derivatives formed by Maillard-type reactions

The determination of the chemical structure of a previously unknown Maillard reaction product with an amino acid incorporated in a four-ring structure is reported. The red compounds 1a and 1b , isolated from a thermally treated aqueous solution of furan-2-carbaldehyde and L-alanine, were identified as (S)-4{(E)-1-formyl -2-(2-furyl)ethenyl}-5-(2-furyl)-2-{(E)-(2-furyl)methylidene}-2, 3-dihydro-α-methyl-3-oxo-1H-pyrrole-1-acetic acid and its 2-{(Z)-(2-furyl)methylidene}isomer, respectively, by several 1D- and 2D-NMR techniques, MS, UV, and IR spectroscopy as well as by synthetic experiments. 2D-NOESY and 2D-ROESY experiments performed for conformation analysis indicated the existence of two atropisomers.     

An NMR and DFT investigation on the interconversion of 9-substituented-<Emphasis Type="Italic">N</Emphasis><Superscript><Emphasis Type="Italic">6</Emphasis></Superscript>-hydrazone-8-azaadenine derivatives: proton migration or conformational isomerization?

A newly synthesized N ⁶ -arylhydrazone-8-azaadenine derivatives (1) showed significant differences in NMR spectra with previously synthesized analogues, specifically, the hydrogens of N^1’H and C^3’H in all the titled compounds showed two groups of signals in their ¹H-NMR spectra. In order to investigate whether the duplication of proton signals were related to a mixture of conformational isomers which rotated around C-N^1’ bond or configurational isomers which resulted from proton migration, variable temperature NMR and 2D-NOESY experiments were carried out in conjunction with density function theory (DFT) calculations at the B3LYP/6-311G (d,p)//B3LYP/6-31G (d,p) level. The results indicated that it was the conformational isomerism rather than hydrogen transfer that induced the reproduction of proton signals, which was attributed to lower barrier energy and larger rate constant of the former process.     

Synthesis,Spectroscopic Characterization,DFT Calculations,and Dynamic Behavior of Mononuclear Macrocyclic Diorganotin(IV) Bis‐Dithiocarbamate Complexes

Nine mononuclear diorganotin(IV) dithiocarbamate complexes 1 – 9 with 19‐, 20‐ and 21‐membered macrocyclic structures were synthesized from dimethyl, di‐n‐butyl, and diphenyltin(IV) dichloride and three bis‐dithiocarbamate ligands derived from secondary bis‐amines having aromatic spacer groups. All compounds were characterized by elemental analysis, mass spectrometry, and spectroscopic methods (IR and ¹H, ¹³C, and ¹¹⁹Sn NMR). Additionally, quantum chemical DFT calculations were performed for the dimethyltin(IV) derivatives in order to model the molecular structures. For one compound series the NMR spectra showed a concentration‐dependent behavior in solution, which was analyzed in detail and permitted to postulate the existence of an equilibrium with the corresponding [2+2] macrocycles.     

Atom accurate structure determination of alprazolam/cyclodextrin inclusion complexes by ROESY and computational approaches

A lot of interest has been seen in computational methods that provide reliable atom accurate structures of different molecular systems. In this article, we describe the complexation of alprazolam (ALP) with three cyclodextrins, i.e., α-, β- and γ-CD. ROESY spectra showed that no complex was formed between ALP and α-CD however, ring A of ALP formed ICs with β- and γ-CD. Therefore, structures of ALP/β-CD and ALP/γ-CD were obtained by a combination of NMR (2D-ROESY) and computational methods by a quantitative ROESY approach. Here we determined the structures of CD ICs by a method recently used in our laboratory and then the structures were obtained independently by DFT (B3LYP functional and def2-TZVP basis set). The structures obtained by both methods were compared with each other. Results demonstrated that our method provides reasonable structures comparable to DFT, and can be used to obtain highly atom accurate structures of CD inclusion complexes. Quantitative ROESY analysis of MM and MD structures consume less time and are cheap as compared to DFT, which is highly CPU demanding and time taking. Negative values of binding energy showed that the process of inclusion was spontaneous and complexes formed were stable. The large negative value of binding energy for ALP/β-CD as compared to ALP/γ-CD showed a higher binding affinity of ALP towards β-CD. FMO studies also revealed the higher HOMO-LOUMO gap for inclusion complexes as compared to pure ALP. Intermolecular H-bonds formed in both the complexes are also one of the forces responsible for inclusion complex formation.     

Valence-band electronic structure of iron phthalocyanine: an experimental and theoretical photoelectron spectroscopy study

The electronic structure of iron phthalocyanine (FePc) in the valence region was examined within a joint theoretical-experimental collaboration. Particular emphasis was placed on the determination of the energy position of the Fe 3d levels in proximity of the highest occupied molecular orbital (HOMO). Photoelectron spectroscopy (PES) measurements were performed on FePc in gas phase at several photon energies in the interval between 21 and 150 eV. Significant variations of the relative intensities were observed, indicating a different elemental and atomic orbital composition of the highest lying spectral features. The electronic structure of a single FePc molecule was first computed by quantum chemical calculations by means of density functional theory (DFT). The hybrid Becke 3-parameter, Lee, Yang and Parr (B3LYP) functional and the semilocal 1996 functional of Perdew, Burke and Ernzerhof (PBE) of the generalized gradient approximation (GGA-)type, exchange-correlation functionals were used. The DFT/B3LYP calculations find that the HOMO is a doubly occupied π-type orbital formed by the carbon 2p electrons, and the HOMO-1 is a mixing of carbon 2p and iron 3d electrons. In contrast, the DFT/PBE calculations find an iron 3d contribution in the HOMO. The experimental photoelectron spectra of the valence band taken at different energies were simulated by means of the Gelius model, taking into account the atomic subshell photoionization cross sections. Moreover, calculations of the electronic structure of FePc using the GGA+U method were performed, where the strong correlations of the Fe 3d electronic states were incorporated through the Hubbard model. Through a comparison with our quantum chemical calculations we find that the best agreement with the experimental results is obtained for a U(eff) value of 5 eV.     

Cyclometalated iridium(III) complex of 6‐hydroxydipyrido[3,2‐a:2′,3′‐c]phenazine: synthesis,and acid–base and avid DNA binding properties

A new cyclometalated Ir(III) complex [Ir(ppy)₂(hdppz)]PF₆ (Hppy = 2‐phenylpyridine and hdppz = 6‐hydroxydipyrido[3,2‐a:2′,3′‐c]phenazine) was synthesized and characterized. The pH effects on the UV–vis absorption spectra were studied and ground‐state acid ionization constant pK_a values of the complex were derived. The calf thymus DNA (ct‐DNA) binding properties of the complex were investigated with UV‐vis absorption spectrophotometric titrations, DNA competitive binding with ethidium bromide, DNA melting experiments, viscosity measurements and density functional theory (DFT) calculations. The complex was demonstrated to act as a ct‐DNA intercalator with a large DNA binding constant value of (6.06 ± 0.32) × 10⁶ M ⁻¹ in 50 mM NaCl. The avid DNA binding affinity observed was rationalized by the DFT calculations. Copyright © 2011 John Wiley & Sons, Ltd.     

Theoretical and Experimental Studies on the Metal Complex of Diethylenetriamino-trioxo-molybdenum(Ⅵ)[MoO3(NH2C2H4NHC2H4NH2)]

For diethylenetriamino-trioxo-molybdenum(VI), density functional theory (DFT) method calculations of the structure, atomic charge distributions, electronic spectra, natural po- pulation analyses and thermodynamic properties at different temperatures have been performed by B3LYP method using LANL2DZ, CEP-121G and CEP-31G basis sets, respectively. The calculated results show that B3LYP/LANL2DZ method can best reproduce the molecular structure. The atomic charge distribution analyses indicate that during forming the complex, the ligand of diethyl- enetriamine donates negative charges to MoO3 and these charges are accepted by molybdenum(VI) atom as well as three oxygen atoms. The electronic spectra calculations indicate that B3LYP/ LANL2DZ results are nearest to experimental data among the three methods and electronic tran- sitions are mainly derived from the contribution of bands π→π*. The calculation of the second order optical nonlinearity was carried out, and the molecular hyperpolarizability was 0.7881*10-30 esu.     

Theoretical and Experimental Studies on the Metal Complex of Diethylenetriamino-trioxo-molybdenum(VI) [MoO_3(NH_2C_2H_4NHC_2H_4NH_2)]

1 INTRODUCTION Molybdenum is a biologically important trace ele- ment that occurs in the redox-active sites of moly- bdoenzymes involving in nitrogen, sulfur or carbon metabolism. The structural chemistry of molybde- num complexes has aroused considerable interest in view of its higher oxidation states to form a number of compounds containing MoO groups, and informa- tion on these is very useful in understanding the behavior of MO groups generally[1~3]. Molybdenum oxide-based solids hav…     

Synthesis,crystal feature and spectral characterization of paeonol derived Schiff base ligands and their Cu(II) complexes with antimicrobial activity

Four novel Schiff bases PNL-4OMe, PNL-4Br, PNL-4F, PNL-3,4-F₂, and their copper(II) complex with [M(L)₂(H₂O)₂] arrangement was synthesized using Paeonol and various aromatic substituted amines. Characterization has been done through FT-IR, ESI Mass, TG-DTA, DFT, magnetic measurements, elemental analysis, and Thermogravimetric analysis. Paeonol derived new bond formation in Schiff bases and changes in frequencies during complexation have been confirmed through FT-IR spectra. All complexes are thermally stable, paramagnetic, and have non-electrolytic behavior. The antimicrobial activity was also tested against Gram-positive bacteria; S. aureus, B. subtilis, and Gram-negative bacteria; E. coli, P. aeruginosa. Single-crystal X-ray data provide evidence that PNL-3,4-F₂ is recrystallizing in a triclinic system with P-1(2) space group and confirms the intramolecular H-bonding and short Vander Waal type interactions. Non-covalent interactions and π … π stacking surface interactions in PNL-3,4-F₂ were studied with Hirshfeld analysis. H-atoms have the highest interactions with other atoms of neighbouring molecules compared to all other atoms. DFT calculations were performed on the electronic structure of ligand PNL-3,4-F₂ and its copper(II) complex and discussed.     

Geometrical and electronic structure of small copper nanoclusters: XANES and DFT analysis

The geometrical and electronic structure of small copper nanoclusters was studied by density functional theory (DFT) and analysis of X-ray absorption spectra. It was shown that the icosahedral geometry of small copper nanoclusters of 13 atoms was energetically more stable than cuboctahedral geometry. The binding energies in these structures were compared; the theoretical XANES spectra were compared with experiment. The paper gives the results of ab initio calculations of the electronic structure of copper clusters differing in size.     

Ab initio/DFT electronic structure calculations, spectroscopic studies and normal coordinate analysis of 2-chloro-5-bromopyridine

FT-IR (4000-400 cm(-1)) and FT-Raman (3500-50 cm(-1)) spectral measurements of solid sample of 2-chloro-5-bromopyridine have been done. Ab initio and DFT calculations have been performed giving energies, optimized structures, harmonic vibrational frequencies, depolarization ratios, IR intensities, Raman activities and atomic displacements. Furthermore, force field calculations have been performed by normal coordinate analysis. A complete assignment of the observed spectra, based on spectral correlations, electronic structure calculations and normal coordinate analysis, has been proposed. The results of the calculations have been used to simulate IR and Raman spectra for the molecule that showed good agreement with the observed spectra. The SQM method, which implies multiple scaling of the DFT force fields, has been shown superior to the uniform scaling approach. The energy and oscillator strength calculated by Time-dependent DFT results are in good agreement with the experimental results.     

Geometries and stabilities of Ag n v (v?=?±1, 0; n?=?21–29) clusters

We performed a systematical study on the lowest-energy structures of the medium-sized silver clusters Ag _n (n?=?21?C29) by using a genetic algorithm coupled with a tight-binding method, and the DFT calculations with Perdew?CWang generalized-gradient approximation. The corresponding cluster ions were also searched based on the neutral cluster structures. It is found that the Ag_21?C23 prefer icosahedron or double-icosahedron as core structures. Ag _n (n?=?24?C27) favor a bulk-like fcc stacking motif. Ag₂₈ and Ag₂₉ tend to high symmetrical structures. The relative stabilities, the ionization potentials and electronic affinities of silver clusters analyzed in the paper are consistent with the experimental data. It is interesting to find that the experimental spectra fit reasonable well the optical absorption spectra obtained with the structures calculated by us.     

Density-functional tight-binding for phosphine-stabilized nanoscale gold clusters

We report a parameterization of the second-order density-functional tight-binding (DFTB2) method for the quantum chemical simulation of phosphine-ligated nanoscale gold clusters, metalloids, and gold surfaces. Our parameterization extends the previously released DFTB2 “auorg” parameter set by connecting it to the electronic parameter of phosphorus in the “mio” parameter set. Although this connection could technically simply be accomplished by creating only the required additional Au–P repulsive potential, we found that the Au 6p and P 3d virtual atomic orbital energy levels exert a strong influence on the overall performance of the combined parameter set. Our optimized parameters are validated against density functional theory (DFT) geometries, ligand binding and cluster isomerization energies, ligand dissociation potential energy curves, and molecular orbital energies for relevant phosphine-ligated Au_n clusters (n = 2–70), as well as selected experimental X-ray structures from the Cambridge Structural Database. In addition, we validate DFTB simulated far-IR spectra for several phosphine- and thiolate-ligated gold clusters against experimental and DFT spectra. The transferability of the parameter set is evaluated using DFT and DFTB potential energy surfaces resulting from the chemisorption of a PH₃ molecule on the gold (111) surface. To demonstrate the potential of the DFTB method for quantum chemical simulations of metalloid gold clusters that are challenging for traditional DFT calculations, we report the predicted molecular geometry, electronic structure, ligand binding energy, and IR spectrum of Au₁₀₈S₂₄(PPh₃)₁₆.

We report a parameterization of the density-functional tight-binding (DFTB) method for the accurate prediction of molecular, electronic and vibrational structure of phosphine-ligated nanoscale gold clusters, metalloids, and gold surfaces.     

Molecular docking studies and structural&electronic analysis of gefarnate

This study focused on the structural/electronic features of an anti-ulcer agent, gefarnate. The molecular geometry of the compound was calculated using Gaussian 09 W software and the structure was optimized using the DFT/B3LYP method with the 6–31++G(d,p) basis set ground state. Also, in silico studies like molecular docking studies and ADME/T estimation were carried out using web-based tools and software. The protein used in these calculations is the crystal structure of the 3U6J, VEGFR2 kinase domain in complex with a pyrazolone inhibitor. The binding energy for the gefarnate molecule-VEGFR2 kinase complex has been computed as −8.6 kcal/mol. The compound showed no toxicity properties including cytotoxic, mutagenic, carcinogenic, or immunogenic.     

Infrared and electronic spectra of copper (II) complex of maleonitriledithiolate and 4,4'-dimethyl-2, 2'-bipyridine and their theoretical studies

The molecular structure and binding, as well as infrared and electronic spectroscopic properties for the title complex Cu(mnt)(dmbpy)(mnt(2-)=maleonitriledithiolate, dmbpy=4,4'-dimethyl-2,2'-bipyridine) were studied in this paper. With semi-empirical PM3 and non-empirical DFT (B3LYP/6-311G*) methods, the molecular geometry of the complex was optimized and corresponding vibrational spectra in the gaseous state were obtained. The calculated results derived from DFT were more reasonable than those from PM3. The point group of Cu(mnt)(dmbpy) in isolated gaseous state was C(2), in which Cu(II) adopted a distorted tetrahedral geometry and the dihedral angle between the N(2)Cu and S(2)Cu planes was about 29.814 degrees. And a complete assignment to the IR spectra of such a complicated molecule was exhibited. With ZINDO/S method an electronic spectrum was calculated. The results showed that the calculated values generally agreed with the observed ones. And a detailed explain was made on its electronic spectra.     

Structure and vibrational spectra of copper(II) 2-pyridylmethanolate tetrahydrate

In the memory of Prof. Ing. Ladislav Valko, DrSc. (1930–2013) A room-temperature synthesis of copper(II) 2-pyridylmethanolate tetrahydrate, [CuL₂] · 4H₂O, with nearly quantitative yields with its structure redetermined at 213 K is presented. In agreement with the X-ray structure data, the DFT quantum-chemical calculations confirmed the planar structure of CuL₂ (C _2h symmetry). The measured IR and Raman spectra were interpreted using the DFT calculations and some erroneous assignments in the previous studies have been corrected.