PM3 Level Research Articles

Synthesis, spectroscopic studies, molecular modeling and antimicrobial activity of binuclear Co(II) and Cu(II) complexes of 4,6-diacetylresorcinol

Reactions of 4,6-diacetylresorcinol with different cobalt(II) and copper(II) salts viz., OAc−, Cl−, NO3- and SO42-, yielded a new series of binuclear metal complexes. Reactions of the ligand with these metal ions in the presence of a secondary ligand (L′) [O,O-donor; acetylacetone, N,O-donor; 8-hydroxyquinoline or N,N-donor; 1,10-phenanthroline and N,N,N′,N′-tetramethylethylenediamine] in 1:2:2 (L:M:L′) molar ratio yielded mixed-ligand complexes with different molar ratios. The metal complexes were characterized by elemental and thermal analyses, IR, electronic, ESR and mass spectra as well as conductivity and magnetic susceptibility measurements. The analytical and spectroscopic data suggested that the H2L ligand behaves as a neutral, monobasic or dibasic tetradentate ligand, depending on the type of the anion and secondary ligand used, through the two phenolic and two carbonyl groups. Electronic spectra, magnetic and conductivity measurements showed that all complexes are octahedral with non-electrolytic nature. The profile of ESR spectra of copper(II) complexes suggested the octahedral geometry and the spin Hamiltonian parameters of the complexes were calculated and discussed. Molecular orbital calculations were performed for metal complexes using Hyperchem 7.52 program on the bases of PM3 level and the results correlated with the experimental data. The free ligand and some of its metal complexes showed antimicrobial activity towards some of Gram-positive and Gram-negative bacteria, yeast (Candida albicans) and fungus (Aspergillus fumigatus).

Synthesis and semi-empirical sparkle PM6 study of substituted dithiophosphoric compounds of gadolinium(III)

Seven gadolinium(III) derivatives containing dialkyl and alkylene dithiophosphate chelating ligands [S2P(OR)2]3·2CH3CN (R = Et, n-Pr, n-Bu and Ph) and [S2POR′O]3·2CH3CN (R′ = CH2CMe2CH2, CH2CEt2CH2 and CMe2CMe2) have been synthesized. The metal complexes have been characterized by elemental analyzes, molecular weight determinations, IR, and UV–Visible spectroscopy. Microanalytical data revealed a 1 : 3 metal–ligand ratio in all complexes. Geometries were fully optimized at the semi-empirical sparkle PM6 level of theory using MOPAC2009 and geometrical structures and electronic properties of the complexes have been evaluated. The optimized geometries were confirmed to be minima on the potential energy surfaces through frequency calculations. Absorption spectra of the complexes have been calculated using ORCA2.9 package utilizing the predicted optimized wave functions. Linear and nonlinear static optical susceptibilities for all complexes were calculated at the same level of theory. The polarizability invariants were, in general, well correlated with the molecular volume and the number of carbons within the alkyl moieties. The largest electric properties were exhibited by the phenyl dithiophosphate complex.

Oxidation reactivity of zinc–cysteine clusters in metallothionein

Evaluating the reactivity of the metal-thiolate clusters in metallothionein (MT) is a key step in understanding the biological functions of this protein. The effects of the metal clustering and protein environment on the thiolate reactivity with hydrogen peroxide (H(2)O(2)) were investigated by performing quantum theory calculations with chemical accuracy at two levels of complexity. At the first level, the reactivity with H(2)O(2) of a model system ([(Zn)(3)(MeS)(9)](3-), MeS is methanethiolate) of the β domain cluster of MT was evaluated using density functional theory (DFT) with the mPW1PW91 functional. At the second level of complexity, the protein environment was included in the reactant system and the calculations were performed with the hybrid ONIOM method combining the DFT-mPW1PW91 and the semiempirical PM6 levels of theory. In these conditions, the energy barrier for the oxidation of the most reactive terminal thiolate was 21.5kcalmol(-1). This is 3kcalmol(-1) higher than that calculated for the terminal thiolate in the model system [(Zn)(3)(MeS)(9)](3-) and about 7kcalmol(-1) higher than that obtained for the free thiolate. In spite of this rise of the energy barrier induced by the protein environment, the thiolate oxidation by H(2)O(2) is confirmed as a possible way for metal release from MT. On the other hand, the results suggest that the antioxidant role of MT in the living cell cannot be as important as that of glutathione (which bears a free thiol).

Effect of structural defects and chemical functionalisation on the intrinsic mechanical properties of graphene

Due to its unique mechanical properties, graphene can be applied for reinforcement in nanocomposites. We analyse the Young's modulus of graphene at the semi-empirical PM6 level of theory. The internal forces are calculated and the Young's modulus is predicted for a finite graphene sheet when external strain is applied on the system. These results are in a good agreement with theoretical and experimental results from the literature giving values of about 1 TPa for the Young's modulus. Stress-strain curves are computed for elongation up to 20%. In addition, the influence of the presence of a single vacancy, as well as for oxygenation of a vacancy, on the mechanical properties of graphene has been analysed. Our results indicate that when applying the deformation locally onto the system, higher local stress can be induced, as confirmed by Finite Element Analysis. Also, the presence of structural defects in the system will stiffen the system upon low strain, but reduces the elastic limit from more than 20% strain for pristine graphene to less than 10% strain when defects are present.

Hemilabile and luminescent palladium(II) azo-2-phenylindole complexes

The synthesis of three azoderivatives {R1–NN–R2 with R1 = 2-phenylindole and R2 = 4-Me–C6H4– (2a), 4-Cl–C6H4– (2b) or 2-phenylindole (2c)} and the study of their reactivity in front of Pd(II) salts are described. Treatment of 2a or 2b with PdCl2 in a CH2Cl2:CH3OH mixture at 298 K followed by the action of PPh3 produced the cyclopalladated complexes: [Pd(κ2-C,N)Cl(PPh3)] (3a and 3b) with a σ{Pd–C(indole)} bond. For 2c, metallation takes place on the same position but required stronger reaction conditions {Pd(OAc)2 in acetic acid at 398 K}. A comparative study of the spectroscopic and photo-optical properties of ligands 2a–2c and their palladium(II) derivatives (3a–3c) is also reported. Addition of PPh3 to CH2Cl2 solutions of compounds 3a–3c produced the opening of the six-membered metallacycle and the formation of the trans-[Pd(κ1-N)Cl(PPh3)2] derivatives (4a–4c). The crystal structures of 3c·CH2Cl2, 4a, 4b and 4c·3/2CH2Cl2·1/2H2O confirm the mode of binding and the anti-(E) configuration of 2a–2c in the complexes as well as the relative disposition of the remaining ligands bound to the Pd(II) atom. Solution studies reveal that in CDCl3, the Pd–N bond of 4a–4c is hemilabile. Computational studies (at DFT or PM6 level) have also been performed in order to rationalize the high degree of regioselectivity of the cyclopalladation process and the solution behaviour of 4a–4c.

Highly selective and sensitive colourimetric detection of Hg2+ ions by unsymmetrical squaraine dyes

Abstract A novel class of sulphonate group containing unsymmetrical squaraine dyes has been synthesized. These dyes show a selective and sensitive affinity towards Hg2+ in methanol and are practically insensitive to most other environmentally and biologically relevant metal ions. Isothermal titration calorimetric (ITC) studies and High Resolution Mass Spectral (HRMS) analysis indicate a 1:1 binding mode. 1H and 13C NMR of the isolated Dye…Hg2+ adduct showed an unusual addition reaction of Hg2+ along the phenyl-squarate carbon–carbon bond which was also supported by TD-DFT calculations using PM6 level geometries.

Metal Oxide Nanoparticles: Size-Dependence of Quantum-Mechanical Properties

Most of physicochemical properties of nanoparticles alter with their varying size. Therefore, understanding the size-property relationships is essential to design nanoparticles characterized by desired features. We have studied those relationships based on a series of 6 representative metal oxides molecular clusters with diameters ranging from 5 Å to 50 Å. We investigated effects of the variation in the clusters size on values of the selected molecular (quantum-mechanical) parameters, that could be consider as potential nanodescriptors for QSAR/QSPR studies. We noticed that the studied parameters change according to two main schemes: (i) increase/decrease non-linearly till it reaches a given value (saturation point) and (ii) increase/decrease linearly with size of a nanoparticle. Our results show that the saturation effect for some molecular properties of nanometer-sized metal oxides can be reached even in clusters containing dozens of atoms. Calculations based on small clusters representing smaller fragments of a nanoparticle at semiempirical PM6 level of the quantum-mechanical theory can be efficiently used for investigation and prediction of the properties of nanometer-scale metal oxides; they are not computationally demanding. We believe that the molecular properties calculated this way would be utilized in future as structural descriptors for quantitative modeling of the relationships between structure and activity of nanomaterials (Nano-QSAR). Keywords: Band gap, nanoparticle, metal oxide, descriptors, size, Nano-QSAR, macro-quantum, nanoparticles, electrophilicity, ZnO nanoparticles, Density Functional Theory, non-linear properties, titanium, parameterization

Metal Oxide Nanoparticles: Size-Dependence of Quantum-Mechanical Properties

Most of physicochemical properties of nanoparticles alter with their varying size. Therefore, understanding the size-property relationships is essential to design nanoparticles characterized by desired features. We have studied those relationships based on a series of 6 representative metal oxides molecular clusters with diameters ranging from 5 Å to 50 Å. We investigated effects of the variation in the clusters size on values of the selected molecular (quantum-mechanical) parameters, that could be consider as potential nanodescriptors for QSAR/QSPR studies. We noticed that the studied parameters change according to two main schemes: (i) increase/decrease non-linearly till it reaches a given value (saturation point) and (ii) increase/decrease linearly with size of a nanoparticle. Our results show that the saturation effect for some molecular properties of nanometer-sized metal oxides can be reached even in clusters containing dozens of atoms. Calculations based on small clusters representing smaller fragments of a nanoparticle at semiempirical PM6 level of the quantum-mechanical theory can be efficiently used for investigation and prediction of the properties of nanometer-scale metal oxides; they are not computationally demanding. We believe that the molecular properties calculated this way would be utilized in future as structural descriptors for quantitative modeling of the relationships between structure and activity of nanomaterials (Nano-QSAR).

X-ray structure and computational study for N-acryloyl-l-valine, a versatile monomer for preparing smart drug delivery carriers

The title compound (NAV) has been synthesized by the acylation reaction of l-valine with acryloyl chloride, in alkaline solution. The X-ray crystal and molecular structure was solved and refined in the P212121 space group and was characterized by an almost coplanar H2CCHC(O)N(H)C system, CCCN, CCCO and (C)CC(O)N(H)C torsion angles being +anti periplanar (+ap) (trans, +172(1)°), −syn periplanar (−sp, cys) (−8(1)°), and (−ap, trans) (−175(1)°). The carboxylic group plane is almost perpendicular to the amide plane (dihedral angle: 83(1)°) and the OCC(H)N(H) torsion angle is−sp, cys (−28(1)°). The CO bond distance at amide is 1.240(3)Å, whereas the CO bond distances at carboxylic group are 1.200(3) and 1.303(3)Å, respectively allowing an easy assignment of protonation site.The molecule has been theoretically analyzed via the methods of density functional theory DFT and semi-empirical quantum mechanics at PM3 level (SEQMPM3) in order to examine the conformational surface at the gas phase and in the presence of solvent molecules. The DFT computations at B3LYP/6-311++G** are the most reliable ones among those performed in this work (SEQMPM3, and B3LYP/6-31G**) as the agreement between computed and XRD bond parameters is excellent. Even the conformations are very reliable and the effect of the solvent was evaluated in a box of water molecules (at SEQMPM3) and through the PCM method at DFT for water, methanol, chloroform and other solvents.

Structural diversity in binuclear complexes of alkaline earth metal ions with 4,6-diacetylresorcinol

A new series of binuclear and mixed-ligand complexes with the general formula: [M2(HnL)mLx′(H2O)yClz]; where M=Mg(II), Ca(II), Sr(II) and Ba(II); H2L=4,6-diacetylresorcinol, the secondary ligand L′=acetylacetone (acac), 8-hydroxyquinoline (8-HQ) or 2,2′-bipyridyl (Bipy), n=0–2, m=1,2, x=0,1,2,4, y=0,2,4,5 and z=0–2; have been synthesized. They have been characterized by the analytical and spectral methods (IR, 1H NMR and mass) as well as TGA and molar conductivity measurements. The spectroscopic and conductance data suggested that the H2L ligand behaves as a neutral, monobasic or dibasic tetradentate ligand, depending on the basicity of the secondary ligand, through the two phenolic and two carbonyl groups. Binuclear octahedral geometry has been assigned to all of the prepared complexes in various molar ratios 2:2; 2:2:2; 1:2:1 and 1:2:4 (L:M:L′). Molecular orbital calculations were performed for the ligands and their complexes using Hyperchem 7.52 program on the bases of PM3 level and the results were correlated with the experimental data. The ligand and some of its alkaline metal(II) complexes showed antibacterial activity towards some of Gram-positive and Gram-negative bacteria, yeast (Candida albicans) and fungus (Aspergillus fumigatus).

Density functional study of copper‐exchanged zeolites and related microporous materials: Adsorption of nitrosyls

AbstractDFT periodic, ONIOM, and cluster studies with all‐electron basis sets are applied to Cu(I) exchanged zeolites and silicoalumino‐phosphate analogs with faujasite and chabazite topology. The reactivity of the cations at different cation positions is probed by NO adsorption. In the ONIOM approach, the cation center and the nearest framework environment are described by DFT, whereas a larger part of the structure is modeled at the semiempirical PM6 level. The importance of including all electrons explicitly in the periodic model computations is outlined by comparison of the results with those from ONIOM and previous plane‐wave studies. The Cu(I) cations reside at distinct extraframework cation sites in the vicinity of the double six‐membered rings (D6R) and upon adsorption they experience a displacement from their previous position. A full optimization with all‐electron basis set is a prerequisite for proper elucidation of the coordination of the transition metal cations by the framework oxygen atoms. © 2012 Wiley Periodicals, Inc.

MACRONONE, A NOVEL DIEPOXYLIGNAN FROM BARK OF <i>MAHKOTA DEWA</i> (<i>Phaleria macrocarpa</i> (<i>Scheff.</i>) Boerl.) AND ITS ANTIOXIDANT ACTIVITY

Mahkota dewa (Phaleria macrocarpa (Scheff.) Boerl.) which is belong to family of Thymelaeaceae is one of Indonesian traditional medicines. Chemical constituent has been isolated from bark of mahkota dewa. Sample was extracted with methanol. Concentrated methanol extract was extracted by n-hexane, chloroform and ethyl acetate. A Compound that separated and purified by column chromatography from ethyl acetate extract is a red spherical crystal (m.p. 94-95 °C). Its spot gave yellow fluorescence at TLC plate (UV366) and has optical rotation of -9.3°(c. 2 mg/mL, methanol). Structure elucidation by UV, IR, 1H-NMR, 13C-NMR and NMR 2 dimension (HMQC, COSY, HMBC and DEPT-135) spectroscopy show that the compound gives a name macronone. Computational chemistry calculation using Hyperchem on the level of semiempirical method PM3 was confirmed the conformation of macronone. DPPH method shows that macronone has lower antioxidant activity compare to the ethyl acetate extract.

Novel isoxazole polycyclic aromatic hydrocarbons as DNA-intercalating agents

The third generation of isoxazole polycyclic aromatic hydrocarbons, acting as DNA-intercalator agents and possessing the binding constants in the range 104–105 M−1, in order to easily diffuse targeting remotely implanted tumors, has been synthesized in good yields according to the 1,3-dipolar cycloaddition methodology. The structure of the obtained cycloadducts has been determined by NOE experiments and supported by computational studies at PM3 level. All the obtained compounds have been tested for their in vitro cytotoxic activity and the most potent of them, (3RS,5SR)-2-benzyl-N,N-dimethyl-3-(pyren-1-yl)isoxazolidine-5-carboxamide (7d), showed an IC50 of 4 μM upon the human lung cancer (A-549) cells. Moreover, compound 7d showed binding constant for the intercalation with calf thymus DNA, poly-d(AT)2 and poly-d(GC)2 of 1.7 × 105 M−1, 1.6 × 105 M−1 and 0.3 × 105 M−1, respectively. Biological and docking studies showed that, in vitro, these compounds complex by intercalation between base pairs, approaching the DNA from its minor groove with a preference for the AT nucleobases pairs.

Comparative Study of Vibrational Spectra of Two Bioactive Natural Products Lupeol and Lupenone Using MM/QM Method

This work deals with the theoretical study on the molecular structure and vibrational spectra of two well-known natural products: lupeol and lupenone. The spectra were interpreted with the aid of normal mode analysis following full-structure optimization carried out with the hybrid two-level ONIOM (B3LYP/6-31G: PM3) method. A detailed interpretation of the infrared spectra of Lupeol and Lupenone is also reported in the present work. The similarities and differences between the vibrational spectra of the two molecules studied have been highlighted. The scaled theoretical wave numbers are in perfect agreement with the experimental values. The thermodynamic calculations related to the title compounds were also performed at B3LYP/6-31G: PM3 level of theory. Quantum chemical calculations have been carried out to understand the dynamical behavior of the bioactive molecules Lupeol and Lupenone.

Quantum tautomerization in porphycene and its isotopomers: Path-integral molecular dynamics simulations

Path-integral molecular dynamics simulations have been performed for porphycene and its isotopic variants in order to understand the effect of isotopic substitution of inner protons on the double proton transfer mechanism. We have used an on-the-fly direct dynamics technique at the semiempirical PM6 level combined with specific reaction parameterization. Our quantum simulations show that double proton transfer of the unsubstituted porphycene at T=300K mainly occurs via a so-called concerted mechanism through the D2h second-order saddle point. In addition, we found that both isotopic substitution and temperature significantly affect the double proton transfer mechanism. For example, the contribution of the stepwise mechanism increases with a temperature increase. We have also carried out hypothetical simulations with the porphycene configurations being completely planar. It has been found that out-of-plane vibrational motions significantly decrease the contribution of the concerted proton transfer mechanism.

Redistribution of carbonyl stretch mode energy in isolated and solvated N-methylacetamide: Kinetic energy spectral density analyses

The vibrational energy transfer from the excited carbonyl stretch mode in N-deuterated N-methylacetamide (NMA-d), both in isolation and in a heavy water cluster, is studied with nonequilibrium molecular dynamics (NEMD) simulations, employing a quantum mechanical/molecular mechanical (QM∕MM) force field at the semiempirical PM3 level. The nonequilibrium ensemble of vibrationally excited NMA-d is prepared by perturbing the positions and velocities of the carbonyl C and O atoms and its NEMD trajectories are obtained with a leap-frog algorithm properly modified for the initial perturbation. In addition to the time-domain analysis of the kinetic and potential energies, a novel method for the spectral analysis of the atomic kinetic energies is developed, in terms of the spectral density of kinetic energy, which provides the time-dependent changes of the frequency-resolved kinetic energies without the complications of normal mode analysis at every MD time step. Due to the QM description of the solute electronic structure, the couplings among the normal modes are captured more realistically than with classical force fields. The energy transfer in the isolated NMA-d is found to proceed first from the carbonyl bond to other modes with time scales of 3 ps or less, and then among the other modes over 3-21 ps. In the solvated NMA-d, most of the excess energy is first transferred to other intramolecular modes within 5 ps, which is subsequently dissipated to solvent with 7-19 ps time scales. The contribution of the direct energy transfer from the carbonyl bond to solvent was only 5% with ~7 ps time scale. Solvent reorganization that leads to destabilization of the electrostatic interactions is found to be crucial in the long time relaxation of the excess energy, while the water intramolecular modes do not contribute significantly. Detailed mode-specific energy transfer pathways are deduced for the isolated and solvated NMA-d and they show that the energy transfer in NMA-d is a highly cooperative process among the intramolecular modes and there is no single dominant pathway with more than 30% of transient contribution.

Amylose–Vanillin Complexation Assessed by a Joint Experimental and Theoretical Analysis

A joint experimental and theoretical study has been carried out on the amylose–vanillin complex, demonstrating its formation by X-ray diffraction as well as UV/visible and circular dichroism spectroscopic techniques. Theoretical simulations substantiate these experimental data and the variations of properties upon complexation by evidencing the stability of the inclusion of vanillin in the helical cavity as well as by explaining the related changes of the linear (chiro-)optical properties. In particular, the circular dichroism (CD) signature of the vanillin inclusion complex results from a geometrical distortion induced by the complexation with the surrounding amylose helix. The use of the ONIOM technique mixing B3LYP and PM6 levels of approximation to include the interactions between different layers (together with the IEFPCM model to describe the solvent) appears to be a satisfactory methodology to simulate both the UV and CD spectra for these compounds.

Spectroscopic, Morphological, and Mechanistic Investigation of the Solvent‐Promoted Aggregation of Porphyrins Modified in meso‐Positions by Glucosylated Steroids

Solvent-driven aggregation of a series of porphyrin derivatives was studied by UV/Vis and circular dichroism spectroscopy. The porphyrins are characterised by the presence in the meso positions of steroidal moieties further conjugated with glucosyl groups. The presence of these groups makes the investigated macrocycles amphiphilic and soluble in aqueous solvent, namely, dimethyl acetamide/water. Aggregation of the macrocycles is triggered by a change in bulk solvent composition leading to formation of large architectures that express supramolecular chirality, steered by the presence of the stereogenic centres on the periphery of the macrocycles. The aggregation behaviour and chiroptical features of the aggregates are strongly dependent on the number of moieties decorating the periphery of the porphyrin framework. In particular, experimental evidence indicates that the structure of the steroid linker dictates the overall chirality of the supramolecular architectures. Moreover, the porphyrin concentration strongly affects the aggregation mechanism and the CD intensities of the spectra. Notably, AFM investigations reveal strong differences in aggregate morphology that are dependent on the nature of the appended functional groups, and closely in line with the changes in aggregation mechanism. The suprastructures formed at lower concentration show a network of long fibrous structures spanning over tens of micrometres, whereas the aggregates formed at higher concentration have smaller rod-shaped structures that can be recognised as the result of coalescence of smaller globular structures. The fully steroid substituted derivative forms globular structures over the whole concentration range explored. Finally, a rationale for the aggregation phenomena was given by semiempirical calculations at the PM6 level.

Sulfonamide as an Activating Group for the Synthesis of Poly(aryl ether sulfonamide)s by Nucleophilic Aromatic Substitution

Poly(aryl ether sulfonamide)s were produced utilizing the sulfonamide moiety as a new activating group for nucleophlic aromatic substitution polymerization. The activated monomer, 2,4-difluoro-N,N-dimethylbenzenesulfonamide, was synthesized in high yields through a simple substitution reaction between 2,4-difluorobenzenesulfonyl chloride and dimethyl amine. The reactivity of this monomer in a nucleophilic aromatic substitution mechanism was estimated using semiempirical calculations at the PM3 level, as well as by 1H, 13C and 19F NMR spectroscopy. The data support the sulfonamide as sufficiently electron-withdrawing to activate aryl fluorides for substitution by phenoxide nucleophiles. Model reactions with tert-butylphenol confirm that the aryl fluorides of 2,4-difluoro-N,N-dimethylbenzenesulfonamide can be displaced in quantitative yields and suggest the process is suitable for forming polymers. A variety of novel polymers were produced employing bisphenol A, 4,4′-biphenol, bisphenol AF and hydroquinone as comonomers. The polymers were characterized by gel permeation chromatography, solution viscometry, NMR spectroscopy, thermogravimetric analysis, and differential scanning calorimetry. The high molecular weight poly(aryl ether sulfonamide)s exhibit moderate to high glass transition temperatures ranging from 163 to 199 °C. The polymers were shown to be thermally stable with 5% weight loss occurring from 398 to 442 °C in a nitrogen atmosphere.

Structural and quantum chemical analysis on 4,4′-di(2-hydroxybenzylamino)diphenylmethane

The title compound is analyzed by X-ray diffraction. ONIOM(B3LYP/6-31G(d,p):PM3) is used to investigate the optimized calculation and the frequency analysis of the molecule, in which the PM3 method was used for carbon and hydrogen atoms of the benzene ring and the B3LYP/6-31G(d,p) method was used for the other parts. Energy changes in the molecule are numerically investigated by the flexible scan at PM3 level. The nature of intramolecular interactions that stabilize the structure in vacuo and solid is studied. The results reveal that the molecule is flexible and molecular conformations can easily be mutually transformed through very small potential barriers.