Reactive Molecular Dynamics Simulation of the Structural Damages of the B-DNA Induced by the Oxidation/Nitration of Guanine.

Reactive molecular dynamics simulations (RMD) have been carried out to investigate structural alterations of the dodecamer double-strand B-DNA due to the oxidation/nitration modifications introduced to its guanine bases, including 8-oxoguanine, 8-nitroguanine, and 5-guanidino-4-nitroimidazole, considering two distribution patterns. These modifications may arise in the case of cancer treatment using oxidative/nitrosative reactive nitrogen species as anticancer agents. Results show that these mutations affect structural characteristics of the B-DNA dodecamer in the order 8-nitroguanine > 5-guanidino-4-nitroimidazole ≫ 8-oxoguanine. For instance, the base-pair per turn for these modified B-DNA are changed respectively to 9.79, 10.88 and 10.58 from 10.51 in the native defect-free B-DNA, which is compatible with the experimental value of 10.10. In addition, these mutations allow more water molecules to diffuse into the dodecamer structure and consequently increase the possibility of the penetration of reactive and nonreactive species toward constituting nucleic base-pairs. The largest variation of the B-DNA structure is observed for the mutated B-DNA with 8-nitroguanine modifications applied to its separated CG base-pairs along the dodecamer chain. The structural changes introduced by these nitro-/oxo-modified guanine bases can be considered as a critical step in the damage of the DNA structure and alterations of its function.

Synthesis, characterization, and dye degradation photocatalytic activity of the nano-size copper iron binary oxide.

Magnetic nano-size copper iron binary oxide is synthesized via a sol-gel method using copper and iron nitrates as precursors and citric acid, chicken egg white, and starch as stabilizers followed by annealing at 400 °C and 800 °C in air. The TG-DTG, XRD, FESEM, EDX, VSM, and FT-IR and UV-Vis DRS spectroscopy methods are used for thermal, structural, magnetic, and optoelectronic characterizations. Depending on the stabilizer and annealing temperature, pure CuFe2O4, (CuFe2O4,CuO) or (CuFe2O4,CuO,Fe2O3) phases are formed with nano-size particles of 20-65 nm, having optical band gaps in the range of 2.15-2.60 eV (577-477 nm). Photocatalytic activities of the synthesized nano-size copper iron binary oxide samples are examined for degradation of Nile Blue textile dye displayed first-cycle removal (from water solution) efficiencies of 86.7-93.3%. Considering usage of non-toxic metals and low-cost green stabilizers, good degradation performances, and easy/efficient (magnetic) recyclability, this nano-size catalyst is suggested for further optimization studies for industrial applications.

A molecular dynamics study on magnetic imidazolium-based ionic liquids: the effect of an external magnetic field.

In this paper, we have reported a molecular dynamics (MD) study on the properties of three different magnetic imidazolium-based ionic liquids in the absence and presence of an external magnetic field. In this regard, the volumetric properties such as density and isobaric expansion coefficient, dynamical properties, namely, viscosity, mean square displacement of ions, diffusion coefficients, transport numbers of cations and anions, and electrical conductivity, and structural properties such as radial distribution function (RDF) and spatial distribution function (SDF) of [emim][FeCl4], [bmim][FeCl4] and [hmim][FeCl4] have been studied at different temperatures using molecular dynamics simulations. After studying the different volumetric, structural, and dynamical properties of the above-mentioned magnetic ILs in the absence of a magnetic field, we investigated the effect of an external magnetic field on the structural properties of one of these systems, i.e., [bmim][FeCl4]. In this regard, we established different contributions in the interactions between the external magnetic field and the studied magnetic ionic liquid (MIL). The number density profiles of the studied MIL before and after imposing an external magnetic field of 1.5 T showed a significant variation in the molecular distribution. The results indicated that the external magnetic field reduced the intensity of RDFs due to the reduction in the interactions between different ion sites as a result of changes in their orientations. After applying the external magnetic field, it was observed that due to the oppositely directed forces on the cations and anions, they moved in opposite directions. The snapshots showed that the static motion of the anion was smaller because of its small size. In the presence of an external magnetic field, the ions distributed more homogeneously compared to that observed in the absence of this field. The results of this study can be used in the rational and accurate design of viscomagnetic fluids and reaction systems in the presence and absence of magnetic fields.

Computational study of iron perovskite CH3NH3FeI3 as an alternative to the lead perovskite CH3NH3PbI3 for application in solar cells.

Structural and optical properties of methylammonium iron iodide perovskite CH3NH3FeI3 are studied at DFT-PBE(mBJ)/FP-LAPW + lo level of theory to assess feasibility of the replacement of the toxic lead with the non-toxic iron in the perovskite layer of solar cells. Starting from experimental crystal structure of the Pb perovskite, volume and aspect ratio (c/a) and atomic positions are optimized for the CH3NH3FeI3 structure, and its electronic and optical characteristics are calculated. An index, measuring the raw optical performance of the light harvesting layer of a solar cell is introduced and calculated for the two Fe and Pb perovskites. Comparative values of this index shows that the iron perovskite CH3NH3FeI3 has an acceptable optical performance, ∼61% that of the Pb perovskite CH3NH3PbI3. Analysis of the Brewster angles (θ B) calculated for the TiO2/perovskite and perovskite/spiro interfaces shows that the Fe perovskite solar cell can have better optical harvesting performance by a factor of 1.32, which improves its comparative overall performance up to 80%. As a conclusion, application of iron perovskite CH3NH3FeI3 is promising, especially due to its much lower costs and significantly alleviated environmental hazards of the incorporating solar cells.

Quantum computational study of non-linear optical properties of some phenanthrene derivatives.

Non-linear optical (NLO) behavior of some phenanthrene-based organic molecules is studied using quantum computational MP2 and B3LYP methods with cc-pVDZ basis set. The design of these molecules is based on possible intramolecular charge transfer between electron donor and electron acceptor groups via an aromatic bridge. The -NO2, -CN, -CF3, -C(CF3)C(CF3)2, -SO3H and -C(CN)C(CN)2 acceptors and the -NH2, -N(CH3)2 and pyrrolidinyl donors have been considered. The HOMO and LUMO energies, polarizabilities and first hyperpolarizabilities are calculated for the optimized structures both in the gas phase and in the conductor-like polarizable continuum model (CPCM) of different solvents. Moreover, the energies of the vertical transitions in the UV-Vis range having large oscillator strengths and their corresponding adiabatic transition energies are calculated using TD-DFT-B3LYP/cc-pVDZ method. Also, UV-Vis and infrared spectra are simulated for these designed molecules. Results show that these phenanthrene derivatives have generally very good NLO behavior. Also, NLO properties are enhanced when (-C(CN)C(CN)2 & -NH2) and (-NO2 & pyrrolidinyl) pairs of (acceptor & donor) groups are used. The approach adopted in the present quantum computational study can be used for similar studies for better description and understanding of the NLO responses of the electron donor-bridge-acceptor systems with π-conjugated bridges.

Cyclic Voltammetric Study of 3,5-Diaryl-1-phenyl-2-pyrazolines.

Cyclic voltammetry is used to derive HOMO energies of the 1-phenyl-2-pyrazolines containing electron-donating or electron-withdrawing substituted phenyl rings and or naphthalenyl substitution on the C3- or C5-positions of the heterocyclic ring to investigate the steric and electronic effects of the aryl substitutions and the type of aryl system on their electrochemical behaviors. The optical HOMO-LUMO gaps needed for the calculation of LUMO (excited state) energies of these compounds are obtained from their UV-vis spectra. Results show that the substitution on the C3-aryl ring has significant effect via its π-donor/acceptor ability, compared to the σ-donor/acceptor ability of the C5-aryl ring, on the CV oxidation peak and onset potentials. Comparative analysis showed very good agreement between the experimentally obtained HOMO and (apparent) LUMO energies and the (TD)DFT/6-311++G(d,p) calculated ground and excited states energies. These computational results indicate also that for all chloro- and methoxy-substituted 2-pyrazolines, the HOMO → LUMO is the most intense transition. While the strong acceptor NO2 substitution on all positions of either C3- or C5-aryl rings, except for one compound, increases the intensity of the HOMO → LUMO+1 (LUMO+2) transition significantly, the first (the first two) transition(s) HOMO → LUMO (and HOMO → LUMO+1) has (have) much smaller or negligible intensity (intensities).

Electron spin fluctuation in intense laser fields.

The effects of the orientation, wavelength and carrier-envelope phase of laser pulses on the spin fluctuation in HeH2+ and LiH3+ molecular ions in their bound electronic states, during their interactions with linearly polarized intense laser pulses, were investigated by solving numerically the time-dependent Dirac equation with the Foldy-Wouthuysen transformation. The results of this study showed that an increase in the wavelength of the laser pulse at a fixed intensity reduces the lifetime of the coherent spin states and increases the sensitivity of the spin vector to the applied laser field in both HeH2+ and LiH3+ species. This sensitivity also depends on the carrier-envelope phase of the laser pulse due to the asymmetry of these systems. Furthermore, the influence of spin-orbit coupling on the dynamics of the spin in the interaction of the highly charged atomic species, N6+, with ultra-intense laser pulses was investigated by considering different initial orbitals and spin polarizations. The results show that significantly different spin-forces are induced when an interaction starts with two parallel and perpendicular polarized spin states with respect to the direction of the laser pulse propagation. Furthermore, spin-orbit coupling affects the quantization of the spin space and results in asymmetric spin fluctuation depending on the initial spin polarization state and the electron orbital momentum, which is induced by the electric field of the laser pulse.

Molecular dynamics simulations of electric field induced water flow inside a carbon nanotorus: a molecular cyclotron.

A nano-flow is induced by applying gigahertz rotating electric fields (EFs) of different strengths and frequencies on a carbon nanotorus filled with water molecules, using molecular dynamics simulations. This nano-flow, which may also be regarded as a molecular cyclotron motion, needs a rising time to establish and to follow the rotating EF depending on the applied EF strength and frequency. For establishment of a steady cyclotron motion in the carbon nanotorus, EFs of higher strengths and lower frequencies are required. Furthermore, the response of the orientations of the water molecules to the direction of the rotating EF is faster than that of their positions. In this study, it is also shown that the free motion of the nanotorus carbon atoms speeds up establishment of cyclotron motion.

Spin dynamics in HeH2+ molecular ion in intense laser fields.

A theoretical study is carried out on the effect of non-dipole interactions on the electron spin dynamics in the asymmetric diatomic HeH2+ in its first excited state in intense linearly polarized laser fields. The Foldy-Wouthuysen transformation is used to solve the Dirac equation numerically without BOA. Effects of the phase of the laser pulse and alignment of the molecule on the relativistic characteristics, such as the pure spin and the pure spin-orbit current densities, spin-orbit force and spin torque, are investigated. The results of this study demonstrate that population oscillates between the two spin states during the course of interaction and its configuration depends on the molecular axis orientation and initial phase of the laser pulse. Also, a small polarization takes place in the spin states, even in the absence of the spin-orbit coupling. Furthermore, spin and spin-orbit current densities are phase-dependent and affected differently by the phase of the laser pulse.

Elucidation of Molecular Mechanisms Behind the Self-Assembly Behavior of Chitosan Amphiphilic Derivatives Through Experiment and Molecular Modeling.

PURPOSE: Chitosan-based polymeric micelles (CBPMs) are considered as promising carriers for delivery of anticancer drugs, imaging agents and genes. To optimize the physicochemical, pharmaceutical and biological properties of CBPMs, the molecular mechanisms behind the self-assembly behavior of chitosan (CHI) amphiphilic derivatives are elucidated. METHODS: This study has two stages. In the experimental stage, dexamethasone (DEX) as a hydrophobic group is grafted to CHI in three degrees of substitution in order to obtain CHI derivatives with different degrees of hydrophobicity. These new CHI amphiphilic derivatives (CHI_DEXs) form micelles in water where their critical aggregation concentration (CAC), size and zeta potential are measured. Through comparing the results of these measurements, the change of self-assembly behavior of CHI_DEXs in response to increasing their hydrophobicity is evaluated. Correlating this evaluation with the results of the 13 MD simulations conducted on CHI_DEXs in atomistic molecular dynamics (MD) simulation stage, reveals the molecular mechanisms behind the self-assembly behavior of CHI_DEXs. RESULTS: Our evaluation of the experimental results reveals that increasing hydrophobicity of a CHI amphiphilic derivative would not necessarily cause it to form micelles with lower CAC value, smaller size and lower zeta potential. The MD simulations reveal that there exists a balance between intra- and inter-chain interactions which is responsible for the self-assembly behavior of CHI amphiphilic derivatives. CONCLUSION: An increase in DS of the hydrophobic group triggers a cascade of molecular events that shifts the balance between intra- and inter-chain interactions leading to changes in the CAC, size and zeta potential of the CBPMs.

Theoretical studies on the deacylation step of acylated Candida Antarctica lipase B: structural and reaction pathway analysis.

The deacylation step of acylated Candida Antarctica lipase B, which was acylated with methylcaprylate (MEC) and acetylcholine (ACh), has been studied by using density functional theory method. Free energies of the entire reaction were calculated for enzyme deacylation by water and hydrogen peroxide that represented hydrolysis and perhydrolysis reactions, respectively. The calculations displayed that a stepwise mechanism there was with the enzyme-product complex being a deep minimum on the free energy surfaces of both of two reactions. The tetrahedral intermediate formation was the rate-determining step of all reactions, which needed 8.1 to 10.5kcalmol(-1) for activation in different reactions. In the second stage of the reaction, fewer free energy barriers, between 4.7 and 5.9kcalmol(-1), were identified to enable the proton transfer from His224 to Ser105 and the breakdown of the tetrahedral intermediate. These calculated activation free energies approved theoretical possibility of both of two reactions for two substrates. Finally, an applied tool examined the interactions role in the stability and energy levels of different chemical species.

Reaction mechanism and free energy profile for acylation of Candida Antarctica lipase B with methylcaprylate and acetylcholine: density functional theory calculations.

Candida Antarctica lipase B (CALB), a specific enzyme to catalyze the hydrolysis of esters, can be a good candidate for acetylcholine (ACh) hydrolysis instead of acetylcholinesterase. The catalytic mechanism of the CALB acylation, as the first stage in the hydrolysis reaction, with ACh and methylcaprylate (MEC) has been examined by using density functional theory technique. The significant emphasis of this article is on the free energy barriers for the acylation step of hydrolysis reactions. Computed free energy barriers of the first step are 9.2 and 15.9 kcal mol(-1), but for the second step are 7.9 and 11.6 kcal mol(-1) for MEC and ACh respectively. Activation free energies are in the comparable and acceptable range and imply both of two reactions are theoretically possible. The stability role of the adjacent amino acids was examined by using two applied tools. It is exposed that the oxyanion hole residues decrease energy barriers by stabilizing the transition state structures.

Metastable excited states of OBr2- and OCl2- dianions.

Electronic stabilities, structures, properties, and spectroscopic constants of the halogen oxide dianions OBr2- and OCl2- and their singly charged anions which are of astrophysical and laboratory interests have been studied. The X2Σ states of OBr2- and OCl2- are metastable with PECs having smooth wells with minima located at R=1.859 Å and 1.776 Å, and Coulomb barriers of 40402.54987 cm(-1) and 43746.63462 cm(-1) heights located at RRCB=2.100 Å and 1.922 Å, respectively, both without any vibrational states. While, the B2Σ state of OBr2- and the A2Σ state of OCl2- are metastable with PECs having wells deep enough to suite several bound states, with minima located at Re=1.773 Å and 1.6430 Å, and Coulomb barriers of 191437.45813 cm(-1) and 180550.70294 cm(-1) heights located at RRCB=2.658 Å and 2.4480 Å, with De=1.26470 eV and 1.60837 eV, respectively. The OBr- and OCl- singly charged anions are stable in their ground states. Based on the calculated Frank-Condon factors, it is concluded that metastable excited state OBr2- and OCl2- dianions and ground state OBr- and OCl- singly charged anions can be formed via electron capture processes.

A combined computational and experimental study of the [Co(bpy)3](2+/3+) complexes as one-electron outer-sphere redox couples in dye-sensitized solar cell electrolyte media.

A combined experimental and computational investigation conducted to understand the nature of the interactions between cobalt II/III redox mediators ([Co(bpy)3](2+/3+)) and their impact on the performance of the corresponding dye-sensitized solar cells (DSCs) is reported. The fully optimized equilibrium structures of cobalt(II/III)-tris-bipyridine complexes in the gas phase and acetonitrile solvent are obtained by the density functional B3LYP method using LanL2DZ and 6-31G(d,p) basis sets. The harmonic vibrational frequencies, infrared intensities and Raman scattering activities of the complexes are also calculated. The scaled computational vibrational wavenumbers show very good agreement with the experimental values. Calculations of the electronic properties of the complexes are also performed at the TD-B3LYP/6-31G(p,d)[LanL2DZ] level of theory. Detailed interpretations of the infrared and Raman spectra of the complexes in different phases are reported. Detailed atomic orbital coefficients of the frontier molecular orbitals and their major contributions to electronic excitations of the complexes are also reported. These results are in good agreement with the experimental electrochemical values. Marcus diagram is derived for the electron transfer reaction Co(II) + D35(+)→ Co(III) + D35 using the Co-N bond length as a reaction coordinate.

Characterization of gold-thiol-8-hydroxyquinoline self-assembled monolayers for selective recognition of aluminum ion using voltammetry and electrochemical impedance spectroscopy.

Gold electrode surface is modified via covalent attachment of a synthesized thiol functionalized with 8-hydroxyquinoline, p-((8-hydroxyquinoline)azo) benzenethiol (SHQ), for the first time. The behavior of the nanostructured electrode surface (Au-SHQ) is characterized by electrochemical techniques including cyclic and differential pulse voltammetry (CV and DPV), and electrochemical impedance spectroscopy (EIS). The modified surface is stable in a wide range of potentials and pHs. A surface pKa of 6.0±0.1 is obtained for Au-SHQ electrode using surface acid/base titration curves constructed by CV and EIS measurements as a function of pH. These results helped to determine the charge state of the surface as a function of pH. The gold modified electrode surface showed good affinity for sensing the Al(III) ion at pH 5.5. The sensing process is based on (i) accumulation and complex formation between Al(III) from the solution phase and 8HQ function on the Au electrode surface (recognition step) and (ii) monitoring the impedance of the Au-SHQ-Al(III) complex against redox reaction rate of parabenzoquinone (PBQ) (signal transduction step). The PBQ is found to be a more suitable probe for this purpose, after testing several others. Thus, the sensor was tested for quantitative determination of Al(III) from the solution phase. At the optimized conditions, a linear response, from 1.0×10(-11) to 1.2×10(-5) M Al(III) in semi-logarithmic scale, with a detection limit of 8.32×10(-12) M and mean relative standard deviation of 3.2% for n=3 at 1.0×10(-7) M Al(III) is obtained. Possible interferences from coexisting cations and anions are also studied. The results show that many ions do not interfere significantly with the sensor response for Al(III). Validity of the method and applicability of the sensor are successfully tested by determination of Al(III) in human blood serum samples.

Ground and excited states of the diatomic dianion Cl2(2-).

The QCISD(T)/aug-cc-pVQZ and CIS/aug-cc-pVQZ calculations have been carried out to obtain potential energy curves (PECs) of the Cl2(2-) diatomic dianion in order to address possibility of its formation in the merged beam fragmentation of Cl2(-) questioned based on the observation of the Cl(-)+Cl+e(-) channel. Results show that two of the excited states, namely A(1)Σg and a(3)Σg are metastable with PECs having wells deep enough to suite several bound states, with minima located at Re=2.8280 Å and Re=2.5972 Å, and Coulomb barriers of 1648.288 and 1403.835 cm(-1) heights located at 4.0320 and 3.6130 Å, respectively. Transition probabilities and tunneling predissociation lifetimes corresponding to these metastable states are also calculated and analyzed. Ground state X(1)Σg and excited states B(1)Σu, C(1)Πg and D(1)Πu calculated for this dianion are all repulsive. Calculated Franck-Condon factors suggest that Cl2(2-) can be produced in its excited states via an electron impact process initiating from the ground states of Cl2 and Cl2(-) .

Precise description of single and double ionization of hydrogen molecule in intense laser pulses.

A new simulation box setup is introduced for the precise description of the wavepacket evolution of two electronic systems in intense laser pulses. In this box, the regions of the hydrogen molecule H(2), and singly and doubly ionized species, H(2) (+) and H(2) (+2), are well discernible and their time-dependent populations are calculated at different laser field intensities. In addition, some new regions are introduced and characterized as quasi-double ionization and their time-dependencies on the laser field intensity are calculated and analyzed. The adopted simulation box setup is special in that it assures proper evaluation of the second ionization. In this study, the dynamics of the electrons and nuclei of the hydrogen molecule are separated based on the adiabatic approximation. The time-dependent Schrödinger and Newton equations are solved simultaneously for the electrons and the nuclei, respectively. Laser pulses of 390 nm wavelength at four different intensities (i.e., 1 × 10(14), 5 × 10(14), 1 × 10(15), and 5 × 10(15) W cm(-2)) are used in these simulations. Details of the central H(2) region are also presented and discussed. This region is divided into four sub-regions related to the ionic state H(+)H(-) and covalent (natural) state HH. The effect of the motion of nuclei on the enhanced ionization is discussed. Finally, some different time-dependent properties are calculated, their dependencies on the intensity of the laser pulse are studied, and their correlations with the populations of different regions are analyzed.

Voltammetric oxidation of 2-oxo-1,2,3,4-tetrahydropyrimidin-5-carboxamides: substituent effects.

Electrochemical oxidation of a series of 20 substituted 2-oxo-1,2,3,4-tetrahydropyrimidin-5-carboxamides (THPMs) in acetonitrile has been studied using voltammetric methods at a glassy carbon electrode to investigate the influence of the substituents on the 4- and 5-positions of the heterocyclic ring. Analysis of the results shows that the electronic nature and steric hindrance of the substituents, especially their orientations toward the heterocyclic ring, determine their effects on the oxidation potential. Analysis of the computational results obtained at the DFT-B3LYP/6-31++G** level of theory suggests a mechanism in which the first electron removal occurs from either the N(1) of the heterocyclic ring or N(17) of the amide substitution. This process is followed by a fast proton removal resulting in the formation of stable allylic and/or benzylic radicals which then undergo further oxidation to the 2-oxo-1,2-dihydropyrimidin-5-carboxamides (DHPMs).

Ultrasound-assisted dehydrogenation of 5-acetyl-3,4-dihydropyrimidin-2(1H)-ones.

In this study, various 5-acetyl-3,4-dihydropyrimidin-2(1H)-ones were synthesized and the dehydrogenation of these compounds by potassium peroxydisulfate in aqueous acetonitrile under thermal and sono-thermal conditions were investigated. Whereas the effect of the nature of 4-substituent influences the rate of reaction, the application of sonic waves decreases drastically the time of thermal reaction.

Characterization of a candidate multi-pole molecular switch using computational techniques.

An organic molecule, designed in this study, is proposed as a candidate molecular switch and characterized using the B3LYP/6-31G* computational method. Structural and electronic properties of this molecular switch (M) and its singly charged (M+ and M-) species in their lowest and the first higher spin states are calculated and analyzed. Molecular volume and electronic spatial extent (ESE) of this nanoswitch undergo negligibly small changes (<2%) upon charging. Furthermore, the small difference between the calculated dipole moments of the M+ and M- species shows that switching between negative and positive poles does not significantly affect the charge transfer performance of this molecular switch. Natural bond orbital (NBO) and spin density distributions are also calculated and analyzed. A preliminary study on the response of the proposed molecular switch to the external electric field approves its function as a multi-pole nanoswitch controlled by a bias voltage.