Synthesis, structure and π-delocalization of a phosphaalkenyl based neutral PNP-pincer

Preparation, characterization and structural properties of a novel bis-phosphaalkenyl based PNP-pincer are reported. In this pincer the π-system is delocalized over all three donor sites, which was demonstrated with DFT calculations, UV-Vis measurements and structural findings. As a consequence of this extended delocalization the π-system reveals near coplanarity which is evident from the first crystal structure for an uncomplexed bisphosphaalkenyl PNP-pincer.     

DFT modeling, UV-Vis and IR spectroscopic study of acetylacetone-modified zirconia sol-gel materials

Theoretical and spectroscopic studies of a series of monomeric and dimeric complexes formed through the modification of a zirconium butoxide precursor with acetylacetone and subsequent hydrolysis and/or condensation have been performed by applying DFT/B3LYP/6-31++G(d) and highly accurate RI-ADC(2) methods as well as IR and UV-Vis transmittance and diffuse reflectance spectroscopies. Based on DFT model calculations and simulated and experimental UV-Vis and IR spectra of all the studied structures, the most probable building units of the Zr(IV)-AcAc gel were predicted: the dimeric double hydroxo-bridged complex Zr(2)(AcAc)(2)(OH)(4)(OH)(2br) 9 and the monooxo-bridged complex Zr(2)(AcAc)(2)(OH)(4)O(br)·2H(2)O 12. In both structures, the two AcAc ligands are coordinated to one Zr atom. It was shown that building units 9 and 12 determine the photophysical and vibrational properties of the gel material. The observed UV-Vis and IR spectra of Zr(IV)-AcAc gel were interpreted and a relation between the spectroscopic and structural data was derived. The observed UV-Vis bands at 315 nm and 298/288 nm were assigned to partial ligand-metal transitions and to intra-/inter-AcAc ligand transitions, respectively.     

Quantifying molecular partition into model systems of biomembranes: an emphasis on optical spectroscopic methods

Optical spectroscopies have been intensively used to determine partition coefficients by a plethora of methodologies. The present review is intended to give detailed and useful information for the determination of partition coefficients and addresses several relevant aspects, namely: (i) definition and calculation of the partition coefficient between aqueous and lipidic phases; (ii) partition coefficients vs. "binding" formalisms; (iii) advantages of spectroscopic methodologies over separation techniques; (iv) formalisms for various experimental approaches based on UV-Vis absorption or fluorescence parameters (fluorescence intensity, lifetime, anisotropy and quenching); (v) experimental hints, artifacts and model limitations; and (vi) a brief survey of nonoptical techniques.     

Substitution effect on new Co(II) addition compounds with salicylaldehydes and the nitrogenous bases phen or neoc: Crystal and molecular structures of [Co(5-NO2-salicylaldehyde)2(phen)], [Co(5-CH3-salicylaldehyde)2(neoc)] and [Co(5-Cl-salicylaldehyde)2(neoc)]

The cobalt(II) addition compounds [Co(X-salo)₂(Y)], where X-salo is the anion of substituted salicylaldehydes (X = 3-OCH₃, 5-CH₃, 5-Cl, 5-NO₂ and Y = the neutral 1,10 phenanthroline or neocuproine), were synthesized and characterized by physicochemical and spectral (IR, UV-Vis) data. Theoretical calculations (DFT, ZINDO, TD DFT) with gaussian 03 for the prediction of the electronic spectrum for the compounds, gave good correlation with the experimental one in the solid state and in solution. The cyclic voltammetry study in CH₃CN gave all the expected waves for the redox processes of the metal Co(II) and the ligands phen or neoc and salicylaldehydes. The X-ray diffraction study of three compounds [Co(5-NO₂-salo)₂(phen)], [Co(5-CH₃-salo)₂(neoc)] and [Co(5-Cl-salo)₂(neoc)] verified their analogous proposed octahedral arrangement of the ligands around the cobalt(II) atom.     

Quantifying molecular partition into model systems of biomembranes: an emphasis on optical spectroscopic methods

Optical spectroscopies have been intensively used to determine partition coefficients by a plethora of methodologies. The present review is intended to give detailed and useful information for the determination of partition coefficients and addresses several relevant aspects, namely: (i) definition and calculation of the partition coefficient between aqueous and lipidic phases; (ii) partition coefficients vs. “binding” formalisms; (iii) advantages of spectroscopic methodologies over separation techniques; (iv) formalisms for various experimental approaches based on UV-Vis absorption or fluorescence parameters (fluorescence intensity, lifetime, anisotropy and quenching); (v) experimental hints, artifacts and model limitations; and (vi) a brief survey of nonoptical techniques.     

Electrochemical and spectroelectrochemical studies of complexes of 1,10-phenanthroline-5,6-dione

Electrochemical and spectroelectrochemical (UV-Vis, IR, EPR) of pd (pd = 1,10-phenanthroline-5,6-dione), Pt(N,N′-pd)Cl2, Pd(N,N′-pd)Cl₂, [Ru(bpy)₂(N,N′-pd)]Cl₂ (bpy = 2,2′-bipyridine) and Pt(O,O′-pd)(PPh₃)₂, where N,N′ and O,O′ refers to coordination of pd to the metal centre via N and O atoms, respectively, reveals that the electron transfer processes between +0.5 and −1.25 V all occur at the pd ligand in agreement with DFT calculations. The two CO groups carry a significant amount of the negative charge in mono-reduced pd¹⁻. The mode of coordination of pd has a greater influence on its redox chemistry than the metal centre or the ancillary ligands.     

Enhancement of the chiroptical response of α-amino acids via N-substitution for molecular structure determination using vibrational circular dichroism

The chiroptical response in the form of vibrational circular dichroism (VCD) in the midinfrared region is found to be enhanced when a hydrogen of amino group of l -tryptophan is substituted with acetyl, acryloyl, or maleyl group. The order of preference for VCD enhancement is found to be acryloyl > acetyl > maleyl group. The resulting experimental VCD spectra are also found to be satisfactorily reproduced by the quantum mechanical (QM) predicted spectra. The QM predicted spectra were simulated using the conformer populations, (a) predicted by Gibbs energies and (b) optimized to maximize the similarity between experimental and predicted VCD spectra. It is found that the conformer populations predicted by Gibbs energies do not yield the maximum possible similarity between experimental and the QM predicted spectra. This work identifies the N-substitution of α-amino acids and determining the conformer populations that best reproduce the experimental spectra as two new approaches for molecular structure determination.     

Effects of surfactant, salt and solvent on the structure and activity of adenosine deaminase: molecular dynamic and spectrophotometric studies

Effects of sodium dodecyl sulfate, dodecyltrimethylammonium bromide, sodium chloride, sodium sulfate, methanol and ethanol, on the structure and activity of adenosine deaminase (ADA) were investigated by UV-Vis, circular dichroism spectrophotometry and molecular dynamics (MDs) studies. Relative activity, experimental and computational helix content, total accessible surface area (ASA) and exposed charged surface area (ECSA) were obtained. The relative activity of ADA in the absence and the presence of denaturants were compared with structural results. It was shown that an increase in the surface area and a decrease in the amount of helicity are associated with a decrease in the activity of ADA.     

Identification of intermediate and product from methemoglobin-catalyzed oxidation of <Emphasis Type="Italic">o</Emphasis>-phenylenediamine in two-phase aqueous—organic system

Methemoglobin (metHb) was used as a mimetic enzyme for peroxidase to catalyze the oxidation reaction of o-phenylenediamine (OPDA) with H2O2 functioning as an oxidant. A reaction intermediate was obtained in two-phase aqueous-organic system and an absorption peak at 710 nm was confirmed to be that of the intermediate in relation to OPDA. The isolated product and intermediate were characterized by UV-Vis and IR spectrophotometry and HPLC-tandem mass spectrometry. The results showed that the product is 2,3-diaminophenazine, the molecular mass of the intermediate is 212 daltons, and a conceivable structure of the intermediate is suggested. Combining the catalyzed reaction mechanism of peroxidase and our experimental results, a conceivable oxidation reaction mechanism of OPDA and H2O2 using metHb as catalyst is proposed.     

Improved calculations of compactness and a reevaluation of continuous compact units

A new method for calculating compactness (Z) that uses look-up table-based algorithms for area and volume computations is introduced. These algorithms can be used in any iterative area orvolume calculation, are more than 1000 times faster than the originalalgorithms, and have equal or better precision. With the faster algorithms it is now possible to calculate the compactness of all continuous units in a protein, and to precisely locate the optimal compact units without the screening functions and limited resolution used previously. These methods have been incorporated into a fully automatic domain finding algorithm, and this method has been applied to the 21 proteins originally analyzed as well as 12 additional proteins. This method is robust, and yields similar units even when applied to coordinates of protein crystals grown under different experimental conditions. © 1993 Wiley-Liss, Inc.     

Insights into electronic and structural properties of novel Pd(II) salen-type complexes

Novel palladium(II) complexes with salen-type ligands based on 3-methylsalicyladehyde and a set of aliphatic diamines (C1 to C4) have been synthesised and characterized by spectroscopic techniques (UV-Vis and FTIR), Density Functional Theory (DFT) calculations and single-crystal X-ray diffraction for C1 and C4. X-ray diffraction analysis of these complexes was focused on coordination sphere and supramolecular arrangements. In the two compounds, the molecules form dimers, being the most relevant intermolecular interactions the hydrogen bonds of the type C-H?O, C-H?π and π?π stacking interactions between the six-membered metallocycles.Electronic spectra of all Pd(II) complexes are dominated by charge transfer and intraligand bands at λ < 400 nm. DFT calculations showed that the HOMO is ligand-dominated, with the metal contribution being ∼18% for all complexes. This suggests that the structural/electronic differences between the ligands do not influence significantly the participation of metal orbitals in HOMO. All the complexes exhibit dipole moments with the same direction, from the aldehyde moiety towards the imine bridge with C2 and C3 showing quite similar values, μ_C2 = 5.49 and μ_C3 = 5.54 D, whereas complexes C1 and C4 show slightly higher values: μ_C1 = 5.79 and μ_C4 = 6.17 D. The magnitude of bond lengths and angles predicted by DFT calculations are comparable to those determined by X-ray crystallography.The experimental vibrational frequencies of the Pd(II) complexes were correlated with the values estimated by DFT calculations. The good agreement between the experimental and theoretical vibrational data allowed the assignment of relevant IR bands to molecular vibration modes.     

Synthesis, characterization, crystal structures and DNA binding studies of nickel(II) hydrazone complexes

A series of octahedral and square-planar Ni(II) complexes have been synthesized from two different types of hydrazone ligands. The isolated complexes have been characterized by means of analytical and spectroscopic techniques. The structures of two of the complexes have been determined by single crystal X-ray diffraction study. The binding modes of the complexes with DNA and their ability to bind DNA have been investigated by UV-Vis absorption titration, ethidium bromide fluorescence displacement experiments, and viscometry measurements and cyclic voltammetry studies. The experimental results show that the mode of binding of the complexes to DNA is combination of different mode of interaction.     

Synthesis, characterization, DFT studies and DNA binding of mixed platinum (II) complexes containing quinoxaline and 1,2-dithiolate ligands

The complexes Pt(pq)Cl2(1) and Pt(pq)(bdt) (2) (where pq = 2-(2'pyridyl)quinoxaline and bdt=benzene-1,2-dithiolate) have been synthesized and fully characterized by UV-visible (UV-Vis), Fourier Transformer Infrared Spectra (FTIR), 1 and 2D NMR and cyclic voltammetry (CV). Interactions of the tested systems (the aforementioned complexes 1 and 2) and the free ligands pq and bdt with double stranded calf thymus DNA (CT-DNA) were studied by UV-spectrophotometric (melting curves) and circular dichroism (CD) measurements. The results suggest that both complexes 1 and 2, are able to form adducts with DNA and to distort the double helix by changing the base stacking. Complex 2 forms stronger adducts to CT-DNA than complex 1 and this is probably due to the substitution of the chlorine atoms of 1 by the 1,2-dithiolate ligand (bdt) in 2. The latter induces an extensive distortion in the planarity of 2 as density functional theory (DFT) calculations reveal. Besides, the light absorbing complex 2 possess intense mixed metal ligand to ligand charge transfer (MM'LLCT) transition in the visible region of the spectrum and could act as photoluminescent metal-based probe for the study of DNA binding. Thus, the photocleavage of DNA by 2 has been studied by UV-Vis and CD spectra and monitored by agarose gel electrophoresis. Under our experimental conditions, it is unclear that complex 2 can photocleave DNA. Furthermore, the ability of 2 to inhibit proliferation of human tumor cell lines was tested and the results indicate some cytoxytic effect on the SF-286 cells.     

Computational molecular characterization of the flavonoid Morin and its Pt(II), Pd(II) and Zn(II) complexes

In this work, we make use of a model chemistry within density functional theory (DFT) recently presented, which is called M05-2X, to calculate the molecular structure of the flavonoid Morin and its Pt(II), Pd(II) and Zn(II) complexes, as well to predict their IR and UV-Vis spectra, the dipole moment and polarizability, the free energy of solvation in different solvents as an indication of solubility, the HOMO and LUMO orbitals, and the chemical reactivity parameters that arise from Conceptual DFT. The calculated values are compared with the available experimental data for these molecules.     

Ternary uranyl hydroxo acetate complexes: A computational study of structure, energetics, and stability constants

We studied computationally uranyl monohydroxo monoacetate complexes in aqueous solution using a scalar relativistic all-electron density functional method. Such ternary uranyl complexes may serve as models of ternary uranyl humate complexes which are important for the speciation of uranyl in the environment. As for simple uranyl monocarboxylate complexes, we calculated bidentate coordination to be slightly preferred due to entropy and solvation effects. Compared to uranyl acetate, uranyl hydroxo acetate exhibits an elongated uranyl bond and a short U-OH bond of ∼214 pm. The latter may provide a signature for direct identification of such ternary complexes by EXAFS. As expected from the lower charge of uranyl monohydroxide, complexation by acetate is less exoenergetic than acetate complexation of uranyl. In contrast, experimental complexation constants of uranyl humate and uranyl hydroxo humate are quite similar. Thus, one may question the interpretation of experimental results that assign simple ternary complexes as result of uranyl humate complexation at neutral pH.     

A Comparative Semiempirical, Ab initio and DFT Study of Decarbonylation of Cyclic Ketones Part 1: Thermal Fragmentation of Cyclopropanone

Calculations using different quantum mechanical methods including semiempirical (MNDO,AM1 and PM3), ab initio (RHF and MP2 calculations using the 6-311G and 6-311++G^** basis sets), and density functional theory (LSDA, BP, MIXBP and B3LYP, i.e., B3LYP/6-311+G**//B3LYP/6-31G*) have been performed on the thermal fragmentation of cyclopropanone to ethylene and carbon monoxide. All RHF calculations predict a concerted single step mechanism for this conversion. The estimated activation energies vary from 34.4 to 54.6 kcal·mol^-1, mainly localized around 37±2 kcal·mol^-1, depending on the method. Whereas the calculated RHF reaction energies also varied from 14.5 to -33.3 kcal·mol^-1, the B3LYP/6-311+G**//B3LYP/6-31G* method predicts the experimental value (-17.7 kcal·mol^-1) within experimental uncertainties. Remarkably, semiempirical AM1 and PM3 methods and simple DFT calculations, LSDA, predict comparable results to the more advanced methods. UHF ab initio calculations predict the same single step mechanism, whereas a multistep biradical mechanism with an unrealistically low activation energy is favored by the semiempirical methods. Structures of the activated complex of the single step mechanism, estimated by different methods, are very similar and consistent with a nonlinear cheletropic [_2s + _2a] reaction, as predicted by the orbital symmetry rules and earlier EHT calculations.Electronic Supplementary Material available.     

Characterization and DNA interaction of the Pt(II)(pq)(bdt) complex: A theoretical and experimental research

A mononuclear complex Pt(pq)(bdt) (1) (where pq = 2-(2′pyridyl)quinoxaline and bdt = benzene-1,2-dithiolate) has been prepared and characterized by NMR spectroscopy, ES mass spectroscopy and elemental analysis. Furthermore, its molecular and electronic structure has been fully elucidated by means of the density functional theory (DFT) and time-dependent density functional theory (TDDFT). The former reveals an extensive distortion of the planarity of complex 1, while the latter an intense mixed metal ligand to ligand charge transfer (MM′LLCT) transition in the visible region of the spectrum. Interactions of complex 1, the free ligands pq and bdt with double stranded calf thymus DNA before and after illumination were studied by UV-spectrophotometric (melting curves) and circular dichroism (CD) measurements, indicating that complex 1 is able to form adducts with DNA and to distort the double helix by changing the base stacking. Under our experimental conditions, it is unclear that complex 1 can photocleave DNA. Viscosity changes of calf thymus DNA (CT-DNA) in the presence of an incremental amount of complex 1 demonstrate that in very low ratios, [1]/[DNA]  0.02, this complex binds intercalatively to the DNA, while in higher ratios a partial or a non-classical interacalation should occur due to the tetrahedral distortion of the molecule and the existence of the dithiolato-ligand.     

Spectroscopic,electrochemical, docking and molecular dynamics studies on the interaction of three oxovanadium (IV) Schiff base complexes with bovine serum albumin and their cytotoxicity against cancer

This study was designed to investigate the interaction of three oxovanadium (IV) Schiff base complexes with bovine serum albumin (BSA) by means of various spectroscopic and electrochemical methods along with molecular docking study and molecular dynamics simulations. Binding constants were estimated by fluorescence and UV-Vis spectroscopy. The results indicated a good affinity of the complexes for BSA in which furyl derivative had more activity. Molecular docking study showed that these complexes have the similar binding modes and located within subdomain IB in site III of BSA. The supporting of molecular docking and molecular dynamics results by experimental data, confirms the validity of the interactions data obtained by these methods. Biological activity against cancer cell showed that furyl derivative has higher activity than other complexes. Pharmaceutical analysis also showed that, these complexes potentially can be used as anticancer agents.     

QM/MM investigation of structure and spectroscopic properties of a vanadium-containing peroxidase

We present a comprehensive analysis of the most likely ground state configuration of the resting state of vanadium dependent chloroperoxidase (VCPO) based on quantum mechanics/molecular mechanics (QM/MM) evaluations of ground state properties, UV-vis spectra and NMR chemical shifts. Within the QM/MM framework, density functional theory (DFT) calculations are used to characterize the resting state of VCPO via time-dependent density functional theory (TD-DFT) calculations of electronic excitation energies and NMR chemical shifts. Comparison with available experimental data allows us to determine the most likely protonation state of VCPO, a state which results in a doubly protonated axial oxygen, a site largely stabilized by hydrogen bonds. We found that the bulk of the protein that is beyond the immediate layer surrounding the cofactor, has an important electrostatic effect on the absorption maximum. Through examination of frontier orbitals, we analyze the nature of two bound water molecules and the extent to which relevant residues in the active site influence the spectroscopy calculations.