The application of BTEM to UV-vis and UV-vis CD spectroscopies: the reaction of Rh4(CO)12 with chiral and achiral ligands

Two different organometallic ligand substitution reactions were investigated: (1) an achiral reactive system consisting of Rh₄(CO)₁₂ + PPh₃  Rh₄(CO)₁₁PPh₃ + CO in n-hexane under argon; and (2) a chiral reactive system consisting of Rh₄(CO)₁₂ + (S)-BINAP  Rh₄(CO)₁₀BINAP + 2CO in cyclohexane under argon. These two reactions were run at ultra high dilution. In both multi-component reactive systems the concentrations of all the solutes were less than 40 ppm and many solute concentrations were just 1–10 ppm. In situ spectroscopic measurements were carried out using UV–vis (Ultraviolet–visible) spectroscopy and UV–vis CD spectroscopy on the reactive organometallic systems (1) and (2), respectively. The BTEM algorithm was applied to these spectroscopic data sets. The reconstructed UV–vis pure component spectra of Rh₄(CO)₁₂, Rh₄(CO)₁₁PPh₃ and Rh₄(CO)₁₀BINAP as well as the reconstructed UV–vis CD pure component spectra of Rh₄(CO)₁₀BINAP were successfully obtained from BTEM analyses. All these reconstructed pure component spectra are in good agreement with the experimental reference spectra. The concentration profiles of the present species were obtained by performing a least square fit with mass balance constraints for the reactions (1) and (2). The present results indicate that UV–vis and UV–vis-CD spectroscopies can be successfully combined with an appropriate chemometric technique in order to monitor reactive organometallic systems having UV and Vis chromophores.     

Synthesis, characterization and some properties of novel bis(pentafluorophenyl)methoxyl substituted metal free and metallophthalocyanines

The preparation of some new tetrakis[bis(pentafluorophenyl)methoxyl] substituted metal free and metallophthalocyanine (MPcs) complexes were achieved by the tetramerization of 4-[bis(pentafluorophenyl)methoxy]phthalonitrile with Li metal in pentan-1-ol or metal [Co(II) or Zn(II)] acetates in DMAE, respectively. The structures of the target compounds were confirmed by elemental analysis, IR, UV–vis, ¹H NMR, ¹⁹F NMR and mass spectroscopic methods. MPcs are soluble only in strong and medium polar solvents while the metal free one is soluble in weakly, medium and strong polar solvents. The temperature and frequency dependence of the electrical conductivities were studied on spin coated films of the compounds using dc and impedance spectroscopy techniques in the frequency range from 40 to 10⁵ Hz and within the temperature range from 290 to 440 K. The temperature dependence of the exponent s and conductivity, σ_ac, were completely in agreement with the prediction of the hopping model. The redox properties of the complexes were determined by cyclic voltammetry. The nature of the redox processes was also confirmed using spectroelectrochemical measurements.     

Development of a conformational search strategy for flexible ligands: A study of the potent μ-selective opioid analgesic fentanyl

Summary An extensive conformational search of the potent opioid analgesic, fentanyl, was performed using the semiempirical quantum mechanical method AM1 and the CHARMm potential energy function. A combination of two procedures was used to search the conformational space for fentanyl, which included nested dihedral scans, geometry optimization and molecular dynamics simulation at different temperatures. In addition, the effect of a continuum solvent environment was taken into account by use of appropriate values for the dielectric constant in the CHARMm computations.The results of the conformational search allowed the determination of the probable conformation of fentanyl in polar and nonpolar solvents and of three candidate conformers for its bioactive form.     

Study of Imidazolium Ionic Liquids:Temperature-dependent Fluorescence and Molecular Dynamics Simulation

The steady-state fluorescence spectra and molecular dynamics simulations were explored to investigate the temperature dependent organization in some imidazolium ionic liquids:1-butyl-3-methylimidazolium hexafluo-rophosphate([bmim][PF6]),1-ethyl-3-methylimidazolium ethylsulfate([emim][EtSO4]) and 1-butyl-3-methylimida-zolium tetrafluoroborate([bmim][BF4]).The pure room temperature ionic liquids(ILs) exhibit a large red shift at more than an excitation wavelength of around 340 nm,which demonstrates the hetero...     

Comprehensive ab initio calculation and simulation on the low-lying electronic states of TlX (X = F, Cl, Br, I, and At)

The low-lying electronic states of TlX (X=F, Cl, Br, I, and At) are investigated using the configuration interaction based complete active space third-order perturbation theory [CASPT3(CI)] with spin-orbit coupling accounted for. The potential energy curves and the corresponding spectroscopic constants are reported. The results are grossly in good agreement with the available experimental data. The absorption spectra are simulated as well to reassign the experimental bands. The present results are also useful for guiding future experimental measurements.     

Toxic Interaction between Dibutyl Phthalate and Human Serum Albumin: Spectroscopic and Molecular Modeling Investigations

Because of the widely usage of Dibutyl phthalate (DBP), its residue exist extensively in the environment and can enter human body, being potential harmful. Human serum albumin (HSA) is a major transporter for endogenous and exogenous compounds in vivo. The aim of this study was to examine the interaction of HSA with DBP through spectroscopic and molecular modeling methods. The experiments revealed that DBP binds to site I (subdomain IIA) of HSA mainly through hydrophobic interactions, illustrated by the calculated ΔH and ΔS. Furthermore, molecular docking was applied to define the specific binding sites, the results of which show that DBP mainly interacts with the positively charged amino acid residues LEU 219, PHE 223, LEU 234, LEU 238, ALA 258, LEU 260, and ILE 290 predominately through hydrophobic interactions, in accordance with the conclusion of thermodynamic analysis. The binding of DBP can cause conformational and some microenvironmental changes of HSA, revealed by UV‐vis absorption, synchronous fluorescence, and circular dichroism results. The accurate and full basic data in the work is beneficial to clarifying the binding mechanism of DBP with HSA in vivo and understanding its effect on protein function during the blood transportation process.     

Synchronous fluorescence and UV-vis spectrometric study of the competitive interaction of chlorpromazine hydrochloride and Neutral Red with DNA using chemometrics approaches

In this study, we have shown with the use of UV–vis spectrophotometry and the constant wavelength synchronous fluorescence spectroscopy (CW-SFS) techniques that the pharmaceutical drug, chlorpromazine hydrochloride (CPZ), intercalates into the deoxyribonucleic acid (DNA) double helix by partial exchange with the Neutral Red (NR) molecular probe.

We have also demonstrated that with the use of three-way data plots, it is clear that it is important to have well-defined methodology for the selection of the important CW-SFS method parameter, Δλ. Ad hoc selection of this parameter, or even that based on experience, can readily lead to serious errors, which subsequently can be transferred to the interpretation of results. The said three-way plots provide a straightforward diagrammatic method, which improves the selection process of a satisfactory value for Δλ.

Finally, we used PARAFAC modeling to resolve the complex three-way CW-SFS data, which provided simultaneously the concentration information for the three reaction components, NR, CPZ and NR-DNA, for the system at equilibrium. This PARAFAC analysis indicated that the intercalation of the CPZ molecule into the DNA proceeds by exchanging with the NR probe, and can be attributed to two parallel reactions.     

Some polyhydroxy azo–azomethine derivatives of salicylaldehyde: Synthesis, characterization, spectroscopic, molecular structure and antimicrobial activity studies

Some new substituted polyhydroxy azo–azomethine compounds were prepared by reaction of tris(hydroxymethyl)aminomethane with (E)-2-hydroxy-5-(phenyldiazenyl) benzaldehyde and its substituted derivatives. The structures of azo and azo–azomethine compounds were determined by IR, UV–vis, ¹H NMR and ¹³C NMR spectroscopic techniques, and/or X-ray diffraction studies. According to IR spectra, all azo–azomethine compounds adopt keto form in solid state. UV–vis analysis has shown the presence of keto–enol tautomerism in solution for all azo–azomethine compounds, except that for nitro substituted derivative, enol form is dominantly favored in solution. At the same time, above mentioned derivative compounds were studied in vitro for their antimicrobial properties. Among the phenylazosalicylaldehyde series compound tested, 4-phenylazosalicylaldehyde, 4-(3-chlorophenylazo)salicylaldehyde, 4-(2-chlorophenylazo)salicylaldehyde, 4-(4-fluorophenylazo)salicylaldehyde, 4-(3-chlorophenylazo)salicylaldehyde and 4-(4-ethylphenylazo)salicylaldehyde showed a weak antimicrobial activity only against gram positive bacteria. On the contrary, phenylazosalicylaldehyde series compounds were reacted tris(hydroxmethyl)aminomethane, that exhibited a strong antimicrobial activity against gram positive bacteria, yeast and mould. Moreover, while the 2-{[1,3-dihydroxy-2-(hydroxymethyl)propan-2-ylimino]methyl}phenol did not show an inhibition on tested microorganism, the addition of phenyldiazine groups to 2-{[1,3-dihydroxy-2-(hydroxymethyl)propan-2-ylimino]methyl}phenol resulted in a strong increases in antimicrobial activity.     

Considerations on the recognition of the D1 receptor by agonists

Summary A model of the mechanism for recognition of the D1 receptor has been developed. Conformational analysis for 10 agonists from diverse chemical families was carried out as a first step toward the characterization of the bioactive form. First, maximum structural overlap of the features common to all ligands allowed a simple identification of the candidate bioactive form for each ligand. At a second level of characterization, steric and electronic properties were computed for all accessible structures to analyze those properties that may modulate receptor recognition.     

Synthesis and characterization of silver nanoparticle/kaolinite composites

Ag nanoparticles were synthetized in the interlamellar space of a layered kaolinite clay mineral. Disaggregation of the lamellae of non-swelling kaolinite was achieved by intercalation of dimethyl sulfoxide. The kaolinite was suspended in aqueous AgNO₃ solution and, after adsorption of Ag⁺, the ions were reduced with NaBH₄. The interlamellar space limits particle growth (d_ave=3.8–4.2 nm); however, larger silver particles may be formed on the exterior surface of kaolinite with d_ave=5.6–10.5 nm diameter. The diameter of the particles prepared in this way is depending on the initial AgNO₃ concentration. The silver nanoparticles prepared were characterized by UV–vis spectroscopy, X-ray diffraction (XRD), Small angle X-ray scattering (SAXS), X-ray photoelectron spectroscopy (XPS) and Transmission electron microscopy (TEM).     

苝二酸酐与嘧啶衍生物的氢键组装

Semi-empirical AM1 method was used to study 1:1 and 1:2 hydrogen bond complexes formed with perylene dianhydride and pyridine derivatives. The weak interaction energy become bigger as the number of hydrogen bonds increases. The donor groups on the host and electron-withdrawing groups on the guest molecules favor hydrogen bonding interactions, and the formation of hydrogen bonding leads to electron density flow from the host to the guest molecules. Electronic spectra of these complexes were computed using INDO/SCI method. Blue-shift of the electronic absorption spectra for the complexes, comparing that of the host,takes place, and the first peaks for different complexes changed slightly. These are in agreement with the experimental results. The cause of blue-shift was discussed, and the electronic transitions were assigned based on theoretical calculations. The potential curve of double proton transfer in the complex was calculated, and the transition state and activated energy relative to the N-H bond were obtained.     

An experimental and theoretical study of the electronic spectra of tetraethylammonium [bis(1,3-dithiole-2-thione-4,5-dithiolato)M(III)] and tetraethylammonium [bis(1,3-dithiole-2-one-4,5-dithiolato)M(III)] (M = Sb or Bi)

Metal complexes of dmit and related ligands, such as dmio, have been studied extensively over the last few decades: [dmit](2-) = bis(1,3-dithiole-2-thione-4,5-dithiolato); [dmio](2-) = bis(1,3-dithiole-2-one-4,5-dithiolato). While much effort has been placed on determining structural properties, very few vigorous spectroscopic studies of these metal complexes have been undertaken. The spectroscopic features of the infrared, Raman and UV-vis spectra, previously reported, have largely been used to characterize compounds. In particular, many details of the electronic structure are still to be revealed. We now report a detailed analysis of the UV-vis spectra of the [M(dmit)](-1) and [M(dmio)](-1) anions, where M = Sb(III) or Bi(III). Experimental spectra were deconvoluted and analysed by several theoretical methodologies, including ab initio CI, TD and CISD calculations. The results led to the assignments of several MLCT/LMCT bands, occurring between 390 and 300 nm, and the confirmation of metal orbital contributions to the HOMO-LUMO boundary.     

Rotational isomerism of vinyl ethers of azines based on the data of IR spectroscopy and quantum-chemical AM1 calculations

The IR spectra of vinyl ethers of azines have two C=C stretching vibration bands of the vinyl group at 1620 and 1640 cm⁻¹, which correspond to thes-cis and nonplanars-trans conformers, respectively. According to the results of AM1 calculations, the hetaryl fragment and the vinyl group in thes-trans conformers of all the ethers under study are twisted out of the C−O−C plane by ∼30°. In thes-cis conformation, the angle of rotation of the heterocycle with respect to the vinyloxy group varies from 45 to 90°. The character of the change in the intensity of the v(C=C) absorption bands of the doublet under changes of the temperature indicates that thes-trans conformer is energetically favorable. The exception is 5-vinyloxyacridine for which thes-cis conformation is more favorable. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2439–2442, December, 1998.     

Separation of variables and search algorithm for internal rotation coordinates and kinematic coefficients in the theory of nuclear motions in polyatomic molecules

The construction algorithm is proposed for the internal rotation coordinates in polyatomic molecules. It is based on the properties of the matrix of kinematic coefficients when an excessive system of natural coordinates is introduced. The approximations providing the separation of variables are considered. The exact form of the kinetic energy operator is given.     

A computer assisted procedure of assignments of vibration–rotation bands of asymmetric and symmetric top molecules

An advanced graphically oriented interactive program package for assignments of complex (perturbed) vibration–rotation spectra of asymmetric and symmetric top molecules has been developed. In addition to the well known Loomis–Wood algorithm, the new procedure takes advantage of a precise knowledge of the lower (e.g. ground) vibrational state energies, works with a realistic approximation of effective Hamiltonians for lower as well as upper vibrational states, and allows an instant combination difference inspection of spectral lines by the graphical representation of the appropriate parts of the analyzed experimental spectrum. Being constrained to the combination difference checking, the new algorithm can directly assign the correct rotational quantum numbers as well as ‘quality weights’ estimating relative accuracies of the identified lines.     

Synthesis, spectroscopic studies and nonlinear optical behavior of N,N′-bis(2-hydroxy-1-naphthylmethylidene)-1-methyl-1,2-diaminoethane-N,N′,O,O′-nickel(II)

A Schiff base complex N,N′-bis(2-hydroxy-1-naphthylmethylidene)-1-methyl-1,2- diaminoethane-N,N′,O,O′-nickel(II) has been synthesized. The title compound has been characterized by FT-IR and UV–vis spectroscopies. The UV–vis experiments indicate that the compound has solvatochromism in the UV region, implying non-zero molecular first hyperpolarizability. To investigate microscopic second-order nonlinear optical (NLO) behavior of the examined complex, the electric dipole moments (μ) and the first static hyperpolarizabilities (β) were computed using Finite Field second-order Møller Plesset (FF MP2) perturbation procedure. According to ab initio quantum mechanical calculations, the title complex exhibits non-zero β values, revealing microscopic second-order NLO behavior.     

Six-dimensional tunneling dynamics of internal rotation in hydrogen peroxide molecule and its isotopomers

The six-dimensional torsion-vibration Hamiltonian of the H₂O₂ molecule and its H/D- and ¹⁸O/¹⁶O-isotopomers is derived. The Hamiltonian includes the kinetic energy operator, which depends on the tunneling coordinate, and the potential energy surface represented as a quartic polynomial with respect to the small-amplitude transverse coordinates. Parameters of the Hamiltonian were obtained from DFT calculations of the equilibrium geometries, eigenvectors, and eigenfrequencies of normal vibrations at the stationary points corresponding to the ground state and both the cis- and trans-transition states, carried out with the B3LYP density functional and 6-311+G(2d,p) basis set. The quantum dynamics problem is solved using the perturbative instanton approach generalized for the excited states situated above the barrier top. Vibration-tunneling spectra are calculated for the ground state and low-lying excited states with energies below 2000 cm^–1. Strong kinematic and squeezed potential couplings between the large-amplitude torsional motion and bending modes are shown to be responsible for the vibration-assisted tunneling and for the dependence of tunneling splittings on the quantum numbers of small-amplitude transverse vibrations. Mode-specific isotope effects are predicted.     

Synthesis and DFT study of the spectral behavior of new 4‐hydroxycoumarins

4‐Hydroxycoumarins are compounds with a lot of applications as drugs and herbicides. They have very interesting spectral and chemical properties, which are investigated theoretically and experimentally. Some new 4‐hydroxycoumarins with arylydene‐β‐ketoester or arylydene‐2,4‐pentanedione side chain were synthesized by two step synthetic scheme. Their structure was characterized by UV–vis, IR, and ¹H NMR methods. The spectral behavior of the optimized structures of these compounds was reproduced by the hybrid DFT methods B3LYP and B3P86 with 6‐31G** and aug‐cc‐pVDZ basis sets. Electronic excited states and vibrational frequencies were calculated. HF method was also used for comparison, because of the lack of electronic correlation. The theoretical spectra were compared with the experimental ones. A lot of compounds show good agreement between experimental and some of the theoretical data, especially obtained by aug‐cc‐pVDZ basis set. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Enumeration of internal rotation reactions and their reaction graphs

Threefold and twofold internal rotation reactions and their reaction graphs are enumerated using the generalized wreath product method developed by the author in an earlier paper. The correspondence between reaction directed graphs (digraphs) and finite topologies on isomers is established. It is shown that the reaction digraphs can be represented by Borel fields. Atropisomerism in polyphenyl compounds is discussed. Applications to spontaneous generation of optical activity and NMR spectroscopy are considered. Borel fields are enumerated by bumping squares of the upper rows of Young diagrams starting from the Young diagram containing just one row.     

ESI MS, spectroscopic and PM5 semiempirical studies of Colchicine complexes with lithium, sodium and potassium salts

The colchicine complexes with Li⁺, Na⁺ and K⁺ cations have been synthesized and studied by ESI MS, ¹H and ¹³C NMR, FT-IR and PM5 semiempirical methods. It has been shown that colchicine forms stable complexes of 1:1 stoichiometry with monovalent metal cations. For Li⁺ cations also formation of the 2:1 stoichiometry complexes has been detected. The most stable structures of the complexes are those in which the acetamide groups are involved in the coordination process. The structures of the colchicine complexes with Li⁺, Na⁺ and K⁺ cations are visualized and discussed in details.