The effect of various partial atomic charges on the bulk and liquid/vacuum interface properties of iodobenzene derivatives at their melting points.

In this work, various atomic charge schemes including natural bond orbital (NBO), electrostatic potential based (CHELPG), and σ-hole model charges were applied in the OPLS-AA force field to investigate their effects on the thermophysical and structural properties of iodobenzene and its derivatives. Molecular dynamics simulations presented in this work show that the studied structural and thermophysical properties are in good agreement with experiments when the CHELPG charge was coupled with the OPLS-AA force field. Also, the arrangement of iodobenzene derivatives in the liquid phase was investigated via combined radial/angular distribution functions (CDFs) analyses and halogen-bonding theory. The most probable orientation of iodobenzene derivatives at the liquid/vacuum interface was assigned by atom density profile and bivariate orientational distribution maps. For all studied iodobenzene derivatives, benzene rings are oriented such that the iodine atoms tend toward the vacuum phase.

A molecular modeling of iodinated organic compounds.

Thermodynamic quantities of some iodinated compounds have been studied by means of ab initio and density functional theory calculations. Since there are some limitations for heavy elements in the fifth row of periodic table such as the iodine atom, a high level of ab initio theory is developed to calculate the energy of iodinated compounds. The standard enthalpies of formation for alkyl iodides and other iodinated organic compounds have been computed and compared with available experimental data. The impact of iodine atoms on the change of enthalpies for deprotonation of iodobenzenes has been studied and a mathematical model is proposed for the effect of iodine on the change of deprotonation. The acidity of diiodophenols as a model for thyroxin hormone has been successfully calculated. The barriers for nucleophilic reactions of substituted methyl iodides are investigated and the energy profiles are characterized by double-well potentials which correspond to pre-reaction and post-reaction complexes, separated by a transition state.

Synthesis, X-ray Structural Characterization, and DFT Calculations of Mononuclear Nickel(II) Complexes Containing Diamine and Methacrylate Ligands.

The mononuclear Ni(II) complexes [Ni(en)2(H2O)2](MAA)2 (1) and [Ni(pn)2(MAA)2] (2), where MAA, en and pn are methacrylate, ethylendiamine and 1,3-propylendiamine, respectively, have been synthesized and characterized by elemental analysis, FT-IR and UV�Vis spectroskopy. Structures of the complexes have been determined by single-crystal X-ray diffraction analyses. In the nickel(II) complexes 1 and 2 nickel(II) ion is six-coordinate and has a distorted octahedral geometry. Ni(II) is bonded to four nitrogen atoms of the two diamines and additionally to two oxygen atoms of aqua ligand in 1, and two oxygen atoms of methacrylate ligands in 2. The theoretical geometries of the studied compounds have been calculated by means of density functional theory (DFT) at the B3LYP/6-311+G(d,p)/LanL2DZ level and considering effective core potential (ECP). The comparison of the results indicates that the employed DFT method yields good agreement with experimental data.

Synthesis, X-ray Structural Characterization, and DFT Calculations of Binuclear Mixed-ligand Copper(II) Complexes Containing Diamine, Acetate and Methacrylate Ligands.

The dinuclear Cu(II) complexes [Cu(en)(MAA)(µ-CH3COO)]2 (1) and [Cu(pn)(MAA)(µ-CH3COO)]2 (2) where MAA, en and pn are methacrylate, ethylendiamine and 1,3-propylendiamine, respectively, have been synthesized and characterized by elemental analysis, FT-IR and UV-Vis spectroscopy. The structures of the complexes have been determined by single-crystal X-ray diffraction analyses. In the dinuclear complexes 1 and 2 the two copper centers are five-coordinated and exhibit distorted square pyramidal geometries. The theoretical geometries of the studied compounds have been calculated by means of density functional theory (DFT) at the B3LYP/6-311+G(d,p)/LanL2DZ level considering effective core potential (ECP).

Electrooxidation of homogentisic acid in aqueous and mixed solvent solutions: experimental and theoretical studies.

Electrochemical behavior of homogentisic acid (HGA) has been studied in both aqueous and mixed solvent solution of water-acetonitrile. Physicochemical parameters of the electrochemical reaction of HGA in these solutions are obtained experimentally by cyclic voltammetry method and are also calculated theoretically using accurate ab initio calculations (G3MP2//B3LYP). Solvation energies are calculated using the available solvation model of CPCM. The pH dependence of the redox activity of HGA in aqueous and the mixture solutions at different temperatures was used for the experimental determination of the standard reduction potential and changes of entropy, enthalpy, and Gibbs free energy for the studied reaction. The experimental standard redox potential of the compound in aqueous solution was obtained to be 0.636 V versus the standard hydrogen electrode. There is a good agreement between the theoretical and experimental values (0.702 and 0.636 V) for the standard electrode potential of HGA. The changes of thermodynamic functions of solvation are also calculated from the differences between the solution-phase experimental values and the gas-phase theoretical values. Finally, using the value of solvation energy of HGA in water and acetonitrile solvents which calculated by the CPCM model of energy, we proposed an equation for calculating the standard redox potential of HGA in mixture solution of water and acetonitrile. A good agreement between the result of electrode potential calculated by the proposed equation and the experimental value confirms the validity of the theoretical models used here and the accuracy of experimental methods.

Thermodynamic parameters of electrochemical oxidation of L-DOPA: experimental and theoretical studies.

Electrode potential and thermodynamic parameters of the electrochemical reaction of L-DOPA in aqueous solution are obtained experimentally by cyclic voltammetry method and also calculated theoretically using accurate ab initio calculations (G3MP2//B3LYP) along with the available solvation model of CPCM. The pH dependence of the redox activity of L-DOPA in aqueous solution at temperatures in the range of 10-30 °C was used for the experimental determination of the standard reduction potential, changes of entropy, enthalpy, and Gibbs free energy for the studied reaction. The experimental formal redox potential of the two-proton-two-electron reduction process was obtained to be 0.745 V versus standard hydrogen electrode (SHE). The theoretical and experimental values (0.728 and 0.745 V) for the standard electrode potential of L-DOPA are in agreement with each other. The difference between the peak potential of the L-DOPA and the products, which are produced by chemical reactions, has been measured experimentally and also calculated theoretically. There is also an agreement between experimental and theoretical potential difference. Also in this work, the changes of thermodynamic functions of solvation are calculated from the differences between the solution-phase experimental values and the gas-phase theoretical values.

Intermolecular potential energy surface for CS2 dimer.

A new four-dimensional intermolecular potential energy surface for CS(2) dimer is obtained by ab initio calculation of the interaction energies for a range of configurations and center-of-mass separation distances for the first time. The calculations were performed using the supermolecular approach at the Møller-Plesset second-order perturbation (MP2) level of theory with the augmented correlation consistent basis sets (aug-cc-pVxZ, x = D, T) and corrected for the basis-set superposition error using the full counterpoise correction method. A two-point extrapolation method was used to extrapolate the calculated energy points to the complete basis set limit. The effect of using the higher levels of theory, quadratic configuration interaction containing single, double, and perturbative triple excitations QCISD(T) and coupled cluster singles, doubles and perturbative triples excitations CCSD(T), on the shape of potential energy surface was investigated. It is shown that the MP2 level of theory apparently performs extremely poorly for describing the intermolecular potential energy surface, overestimating the total energy by a factor of nearly 1.73 in comparison with the QCISD(T) and CCSD(T) values. The value of isotropic dipole-dipole dispersion coefficient (C(6) ) of CS(2) fluid was obtained from the extrapolated MP2 potential energy surface. The MP2 extrapolated energy points were fitted to well-known analytical potential functions using two different methods to represent the potential energy surface analytically. The most stable configuration of the dimer was determined at R = 6.23 au, α = 90°, ß = 90°, and γ = 90°, with a well depth of 3.980 kcal mol(-1) at the MP2 level of theory. Finally, the calculated second virial coefficients were compared with experimental values to test the quality of the presented potential energy surface.

Benchmark Calculations of Absolute Reduction Potential of Ferricinium/Ferrocene Couple in Nonaqueous Solutions.

High-level ab initio molecular orbital theory is used to obtain benchmark values for the ferricenium/ferrocene (Fc(+)/Fc) couple, the IUPAC recommended reference electrode for nonaqueous solution. The gas-phase ionization energy of ferrocene is calculated using the high-level composite method, G3(MP2)-RAD, and two higher-level variants of this method. These latter methods incorporate corrections for core correlation and, in the case of the highest level considered, use (RO)CCSD(T)/6-311+G(d,p) in place of (RO)CCSD(T)/6-31G(d) as the base level of theory. All methods provide good agreement with one another and the corresponding experimental values. Solvation energies have been calculated using PCM, CPCM, SMD, and COSMO-RS. Using G3(MP2)-RAD-Full-TZ gas-phase energies and COSMO-RS solvation energies, the absolute redox potentials of the Fc(+)/Fc couple have been calculated as 4.988, 4.927, and 5.043 V in acetonitrile, 1,2-dichloroethane, and dimethylsulfoxide solutions, respectively.

Experimental and theoretical studies of redox reactions of o-chloranil in aqueous solution.

The electrochemical reduction of o-chloranil (OCA) in aqueous solution has been studied experimentally and theoretically. The effects of temperature and pH on various thermodynamic parameters were studied by means of cyclic voltammetry. The pH dependence of the redox activity of OCA in aqueous solution at temperatures in the range 25-40 degrees C was used for the experimental determination of the standard reduction potentials of both the one-proton-two-electron (0.67 V) and two-proton-two-electron (0.79 V) reduction processes. The temperature dependency of the equilibrium constants of studied reactions has been used in order to determine enthalpy, entropy, and Gibbs energy changes of the reactions. It is found that the two studied redox reactions of OCA are strongly affected by solvation effects and controlled by entropy contributions to the Gibbs free energies. High-level ab initio calculations (G3 and CBS-QB3 using the CPCM solvation model) have been employed to calculate the reduction potentials of OCA in aqueous solution for the one-proton-two-electron (0.65 and 0.69 V at the respective levels of theory) and two-proton-two-electron (0.81 and 0.83 V) reactions, which are in excellent agreement with the corresponding experimental values. The acidic strength of the reduced form of OCA in aqueous solution, pK(a), has been also calculated (5.2) and is also in excellent agreement with the experimental value (5.0). The agreement mutually verifies the accuracy of experimental method and the validity of the mathematical model.

Comparison of G3 and G4 theories for radical addition and abstraction reactions.

A test set of 21 radical addition and 28 hydrogen abstraction reactions has been studied at the W1, G4, G3X, G3X(MP2), and G3X(MP2)-RAD levels of theory with a view to establishing whether the recently introduced G4 theory offers improved performance over the G3 methods. All methods tested approximated the benchmark W1 values to within a mean absolute deviation (MAD) of 4 kJ mol(-1) or less, although maximum absolute deviations for problematic reactions (such as radical addition to thiocarbonyl compounds) can be as much as 10 kJ mol(-1) for the G3 methods. The new noncanceling higher-level correction (HLC) term in G4 was found to be capable of mitigating these errors in radical addition, but it introduced a systematic error to the reaction energies of the abstraction reactions, and its format may therefore require re-examination. G3 methods were shown to offer "chemical accuracy" even for these problematic cases, provided they were corrected to the W1 level of theory via an ONIOM-based approach.

Determination of the absolute redox potential of Rutin: experimental and theoretical studies.

The conditional formal potential, E degrees', of Rutin has been studied by cyclic voltammetry using a Rutin film deposited at the multi-wall carbon nanotubes modified glassy carbon electrode (GCE) as the working electrode in different pH phosphate buffered solutions. The experimental standard redox potential, E degrees, of Rutin is obtained to be 0.88 V versus SHE (Standard Hydrogen Electrode). High-level ab initio calculations have been also performed on a chemical model of Rutin and the absolute reduction potential has been calculated. The theoretical standard reduction potential relative to SHE (0.83 V) is in relatively good agreement with experiment.

One-electron oxidation and reduction potentials of nitroxide antioxidants: a theoretical study.

High-level ab initio calculations have been used to determine the oxidation and reduction potentials of a large number of nitroxides including derivatives of piperidine, pyrrolidine, isoindoline, and azaphenalene, substituted with COOH, NH2, NH3+, OCH3, OH, and NO2 groups, with a view to (a) identifying a low-cost theoretical procedures for the determination of electrode potentials of nitroxides and (b) studying the effect of substituents on these systems. Accurate oxidation and reduction potentials to within 40 mV (3.9 kJ mol(-1)) of experimental values were found using G3(MP2)-RAD//B3-LYP/6-31G(d) gas-phase energies and PCM solvation calculations at the B3-LYP/6-31G(d) level. For larger systems, an ONIOM method in which G3(MP2)-RAD calculations for the core are combined with lower-cost RMP2/6-311+G(3df,2p) calculations for the full system, was able to approximate G3(MP2)-RAD values (to within 1.6 kJ mol(-1)) at a fraction of the computational cost. The overall ring structure has more effect on the electrode potentials than the inclusion of substituents. Azaphenalene derivatives display the lowest oxidation potentials and least negative reduction potentials and are thus the most promising target to function as antioxidants in biological systems. Piperidine and pyrrolidine derivatives have intermediate oxidation potentials but on average pyrrolidine derivatives display more negative reduction potentials. Isoindoline derivatives show higher oxidation potentials and more negative reduction potentials. Within a ring, the substituents have a relatively small effect with electron donating groups such as amino and hydroxy groups stabilizing the oxidized species and electron withdrawing groups such as carboxy groups stabilizing the reduced species, as expected.

Should contemporary density functional theory methods be used to study the thermodynamics of radical reactions?

The performance of a variety of DFT functionals (BLYP, PBE, B3LYP, B3P86, KMLYP, B1B95, MPWPW91, MPW1B95, BB1K, MPW1K, MPWB1K, and BMK), together with the ab initio methods RHF, RMP2, and G3(MP2)-RAD, and with ONIOM methods based on combinations of these procedures, is examined for calculating the enthalpies of a range of radical reactions. The systems studied include the bond dissociation energies (BDEs) of R-X (R = CH3, CH2F, CH2OH, CH2CN, CH2Ph, CH(CH3)Ph, C(CH3)2Ph; X = H, CH3, OCH3, OH, F), RCH(Ph)-X (R = CH3, CH3CH2, CH(CH3)2, C(CH3)3, CH2F, CH2OH, CH2CN; X = H, F), R-TEMPO (R = CH3, CH2CH3, CH(CH3)2, C(CH3)3, CH2CH2CH3, CH2F, CH2OH, CH2CN, CH(CN)CH3, CH(Cl)CH3; TEMPO = 2,2,6,6,-tetramethylpiperidin-1-yloxyl) and HM1M2-X (M1, M2 = CH2CH(CH3), CH2CH(COOCH3), CH2C(CH3)(COOCH3); X = Cl, Br), the beta-scission energies of RXCH2* and RCH2CHPh* (R = CH3, CH2CH3, CH(CH3)2, C(CH3)3; X = O, S, CH2), and the enthalpies of several radical addition, ring-opening, and hydrogen- and chlorine-transfer reactions. All of the DFT methods examined failed to provide an accurate description of the energetics of the radical reactions when compared with benchmark G3(MP2)-RAD values, with all methods tested showing unpredictable deviations of up to 40 kJ mol-1 or more in some cases. RMP2 also shows large deviations from G3(MP2)-RAD in the absolute values of the enthalpies of some types of reaction and, although it fares somewhat better than the DFT methods in modeling the relative values, it fails for substituents capable of strongly interacting with the unpaired electron. However, it is possible to obtain cost-effective accurate calculations for radical reactions using ONIOM-based procedures in which a high-level method, such as G3(MP2)-RAD, is only used to model the core reaction (which should contain all substituents alpha to the reaction center), and the full system is modeled using a lower-cost procedure such as RMP2.

Accurate calculation of absolute one-electron redox potentials of some para-quinone derivatives in acetonitrile.

Standard ab initio molecular orbital theory and density functional theory calculations have been used to calculate absolute one-electron reduction potentials of several para-quinones in acetonitrile. The high-level composite method of G3(MP2)-RAD is used for the gas-phase calculations and a continuum model of solvation, CPCM, has been employed to calculate solvation energies. To compare the theoretical reduction potentials with experiment, the reduction potentials relative to a standard calomel electrode (SCE) have also been calculated and compared to experimental values. The average error of the calculated reduction potentials using the proposed method is 0.07 V without any additional approximation. An ONIOM method in which the core is studied at G3(MP2)-RAD and the substituent effect of the rest of the molecule is studied at R(O)MP2/6-311+G(3df,2p) provides an accurate low-cost alternative to G3(MP2)-RAD for larger molecules.

Computational electrode potential of a coumestan derivative: theoretical and experimental studies.

Electrode potential of a coumestan derivative, an important biological molecule, in aqueous solution is computed theoretically using Self-Consistent Field (SCF) theory at the level of Hartree--Fock and employing 6-31G(d) basis set and also obtained experimentally by employing electrochemical technique of cyclic voltammetry (CV). Frequency calculations have been carried out and thermal corrections and entropies have been taken into account. Polarizable continuum model is used to describe the solvent. The theoretical and experimental values for the standard electrode potential of the studied coumestan are in excellent agreement with each other and there is only 0.001 V discrepancy between experiment and theory. The agreement mutually verifies the accuracy of experimental method and the validity of mathematical model.

Selective and non-selective determination of heavy metal ions in flowing solutions by fast stripping cyclic voltammetry.

A simple and fast stripping voltammetric detection method has been designed for selective and non-selective measurements of heavy metal ions in a flow-injection system. A special computer numerical method is introduced for calculating the analyte signal and noise reduction, where the signal is calculated based on the partial and total charge exchange at electrode surface. For a selective determination, the currents are integrated in the range of the oxidation and reduction of the analyte. For non-selective measurements, the integration range is set for the whole potential scan range (including oxidation and reduction of the Au surface). The time for stripping has been shown to be less than 300 ms. The main advantages of the detection method are as follows: first, removal of oxygen from the measured solution is not required; second, it is sufficiently fast for the determination of heavy metal ions in various chromatographic analysis methods. The limit of detection for tested ions was between 3 x 10(-9) and 6 x 10(-10) M, and the relative standard deviation at 50 ppb Pb2+ was 4.7% for 10 runs.