Solvent effects on the electronic absorption spectrum of camphor using continuum, discrete or explicit approaches

We address the effect of solvation on the lowest electronic excitation energy of camphor. The solvents considered represent a large variation in-solvent polarity. We consider three conceptually different ways of accounting for the solvent using either an implicit, a discrete or an explicit solvation model. The solvatochromic shifts in polar solvents are found to be in good agreement with the experimental data for all three solvent models. However, both the implicit and discrete solvation models are less successful in predicting solvatochromic shifts for solvents of low polarity. The results presented suggest the importance of using explicit solvent molecules in the case of nonpolar solvents. (C) 2009 Elsevier B.V. All rights reserved.

Solvent Effects in Chemical Processes. Water-Assisted Proton Transfer Reaction of Pterin in Aqueous Environment

Pterins are members of a family of heterocyclic compounds present in a wide variety of biological systems and may exist in two forms, corresponding to an acid and a basic tautomer. In this work, the proton transfer reaction between these tautomeric forms was investigated in the gas phase and in aqueous solution. In gas phase, the intramolecular mechanism was carried out for die isolated pterin by quantum mechanical second-order Moller-Plesset Perturbation theory (MP2/aug-cc-pVDZ) calculations and it indicates that the acid form is more stable than the basic form by -1.4 kcal/mol with a barrier of 34.2 kcal/mol with respect to the basic form. In aqueous solution, the role of the water molecules in the proton transfer reaction was analyzed in two separated parts, the direct participation of one water molecule in the reaction path, called water-assisted mechanism, and the complementary participation of the aqueous solvation. The water-assisted mechanism was carried out for one pterin-water cluster by quantum mechanical calculations and it indicates that the acid form is still more stable by -3.3 kcal/mol with a drastic reduction of 70% of the barrier, The bulk solution effect on the intramolecular and water-assisted mechanisms was included by free energy perturbation implemented on Monte Carlo simulations. The bulk water effect is found to be substantial and decisive when the reaction path involves the water-assisted mechanism. In this case, the free energy barrier is only 6.7 kcal/mol and the calculated relative Gibbs free energy for the two tautomers is -11.2 kcal/mol. This value is used to calculate the pK(a) value of 8.2 +/- 0.6 that is in excellent agreement with the experimental result of 7.9.

Solvent assisted decomposition of the tetrahedral intermediate of the transesterification reaction to biodiesel production. A density functional study

B3LYP/6-31 + G(d) calculations were employed to investigate the mechanism of the transesterification reaction between a model monoglyceride and the methoxide and ethoxide anions. The gas-phase results reveal that both reactions have essentially the same activation energy (5.9 kcal mol(-1)) for decomposition of the key tetrahedral intermediate. Solvent effects were included by means of both microsolvation and the polarizable continuum solvation model CPCM. Both solvent approaches reduce the activation energy, however, only the microsolvation model is able to introduce some differentiation between methanol and ethanol, yielding a lower activation energy for decomposition of the tetrahedral intermediate in the reaction with methanol (1.1 kcal mol(-1)) than for the corresponding reaction with ethanol (2.8 kcal mol(-1)), in line with experimental evidences. Analysis of the individual energy components within the CPCM approach reveals that electrostatic interactions are the main contribution to stabilization of the transition state. (C) 2009 Elsevier Ltd. All rights reserved.

Continuum, Discrete, and Explicit Solvation Models for Describing the Low-Lying Absorption Spectrum of the Pterin Acid in Aqueous Environment

The absorption spectrum of the acid form of pterin in water was investigated theoretically. Different procedures using continuum, discrete, and explicit models were used to include the solvation effect on the absorption spectrum, characterized by two bands. The discrete and explicit models used Monte Carlo simulation to generate the liquid structure and time-dependent density functional theory (B3LYP/6-31G+(d)) to obtain the excitation energies. The discrete model failed to give the correct qualitative effect on the second absorption band. The continuum model, in turn, has given a correct qualitative picture and a semiquantitative description. The explicit use of 29 solvent molecules, forming a hydration shell of 6 angstrom, embedded in the electrostatic field of the remaining solvent molecules, gives absorption transitions at 3.67 and 4.59 eV in excellent agreement with the S(0)-S(1) and S(0)-S(2) absorption bands at of 3.66 and 4.59 eV, respectively, that characterize the experimental spectrum of pterin in water environment. (C) 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110: 2371-2377, 2010

Thermodynamic Stabillity of Hydrogen-Bonded Systems in Polar and Nonpolar Environments

The thermodynamic properties of a selected set of benchmark hydrogen-bonded systems (acetic acid dimer and the complexes of acetic acid with acetamide and methanol) was studied with the goal of obtaining detailed information on solvent effects on the hydrogen-bonded interactions using water, chloroform, and n-heptane as representatives for a wide range in the dielectric constant. Solvent effects were investigated using both explicit and implicit solvation models. For the explicit description of the solvent, molecular dynamics and Monte Carlo simulations in the isothermal isobaric (NpT) ensemble combined with the free energy perturbation technique were performed to determine solvation free energies. Within the implicit solvation approach, the polarizable continuum model and the conductor-like screening model were applied. Combination of gas phase results with the results obtained from the different solvation models through an appropriate thermodynamic cycle allows estimation of complexation free energies, enthalpies, and the respective entropic contributions in solution. Owing to the strong solvation effects of water the cyclic acetic acid dimer is not stable in aqueous solution. In less polar solvents the double hydrogen bond structure of the acetic acid dimer remains stable. This finding is in agreement with previous theoretical and experimental results. A similar trend as for the acetic acid dimer is also observed for the acetamide complex. The methanol complex was found to be thermodynamically unstable in gas phase as well as in any of the three solvents. (C) 2010 Wiley Periodicals, Inc. J Comput Chem 31: 2046-2055, 2010

NMR Chemical Shielding and Spin-Spin Coupling Constants of Liquid NH(3): A Systematic Investigation using the Sequential QM/MM Method

The NMR spin coupling parameters, (1)J(N,H) and (2)J(H,H), and the chemical shielding, sigma((15)N), of liquid ammonia are studied from a combined and sequential QM/MM methodology. Monte Carlo simulations are performed to generate statistically uncorrelated configurations that are submitted to density functional theory calculations. Two different Lennard-Jones potentials are used in the liquid simulations. Electronic polarization is included in these two potentials via an iterative procedure with and without geometry relaxation, and the influence on the calculated properties are analyzed. B3LYP/aug-cc-pVTZ-J calculations were used to compute the V(N,H) constants in the interval of -67.8 to -63.9 Hz, depending on the theoretical model used. These can be compared with the experimental results of -61.6 Hz. For the (2)J(H,H) coupling the theoretical results vary between -10.6 to -13.01 Hz. The indirect experimental result derived from partially deuterated liquid is -11.1 Hz. Inclusion of explicit hydrogen bonded molecules gives a small but important contribution. The vapor-to-liquid shifts are also considered. This shift is calculated to be negligible for (1)J(N,H) in agreement with experiment. This is rationalized as a cancellation of the geometry relaxation and pure solvent effects. For the chemical shielding, U(15 N) Calculations at the B3LYP/aug-pcS-3 show that the vapor-to-liquid chemical shift requires the explicit use of solvent molecules. Considering only one ammonia molecule in an electrostatic embedding gives a wrong sign for the chemical shift that is corrected only with the use of explicit additional molecules. The best result calculated for the vapor to liquid chemical shift Delta sigma((15)N) is -25.2 ppm, in good agreement with the experimental value of -22.6 ppm.

Polarization and solvatochromic shift of ortho-betaine in water

Betaine dyes are known to show very large transition energy shifts in different solvents. The ortho-betaine molecule - a simple two-ring prototype of the E-T(30) Reichardt dye - has been investigated theoretically from a combined statistical and quantum mechanics approach. Using sequential Monte Carlo (MC) simulations and MP2/cc-pVDZ calculations the in-water dipole moment of ortho-betaine is obtained as 12.30 +/- 0.05 D. This result shows a considerable increase of 75% compared to the in-vacuum dipole moment. For comparison, the use of a polarizable continuum model using the same MP2/cc-pVDZ leads to an in-water dipole moment of 11.6 D, in good agreement. This large polarization is incorporated in the classical potential for another MC simulation to generate solute-solvent configurations and to obtain the contribution of the polarization effect in the solvatochromic shift. Using statistically uncorrelated configurations and supermolecular INDO/CIS calculations, including the solute and, explicitly, 230 solvent water molecules, the statistically converged calculated shift is obtained here as 6360 cm(-1), in good agreement with the experimental result of 7550 cm(-1). (c) 2007 Elsevier B.V. All rights reserved.

Adsorption Behavior of 5-Fluorouracil on Au(111): An In Situ STM Study

The biological effects of chemical substitution of DNA bases triggered several investigations of their physicochemical properties This paper studies the adsorption behavior of a halogenated uracil, 5-fluorouracil (5FU). at the electrochemical interface of Au(111) and sulfuric acid solution. Upon modulation of the electric field across the interface, four distinct phases could be inferred by means of cyclic voltammetry (CV) At negative potentials relative to the SCE electrode, limited by the threshold of hydrogen evolution, no molecular species could be detected by scanning tunneling microscopy (STM) at the reconstructed Au(111)-(23 x root 3) surface, indicating that any physisorbed molecules are randomly distributed Incursion into more positive potentials increases the surface population but doer not form any two-dimensional (2D) physisorbed ordered structure Instead, we observed metastable structures that are only detectable. on surfaces with high defect density At sufficiently high positive potentials. limited by gold oxidation, the molecules are chemisorbed in a (3 x 2 root 3) ordered structure. with the aromatic ring perpendicular to the surface We report the densest chemisorbed monolayer for pyrimidine-derivative molecules (area per molecule 0 14 +/- 0 04 nm(2)). A comparison of the adsorption behavior of uracil derivatives has been made based on recent results of chemical substitution and solvent effects. We propose that pi-stacking is enhanced when halogens are incorporated in the uracil structure, in a similar fashion to what is observed in then crystal structure

Aromatic nitro substitution reaction between 4-nitro-N-n-butyl-1,8-naphthalimide and n-heptanethiol in water-methanol binary mixtures

The second-order rate constants of thiolysis by n-heptanethiol on 4-nitro-N-n-butyl-1,8-naphthalimide (4NBN) are strongly affected by the water-methanol binary mixture composition reaching its maximum at around 50% mole fraction. In parallel solvent effects on 4NBN absorption molar extinction coefficient also shows a maximum at this composition region. From the spectroscopic study of reactant and product and the known H-bond capacity of the mixture a rationalization that involves specific solvent H-donor interaction with the nitro group is proposed to explain the kinetic data. Present findings also show a convenient methodology to obtain strongly fluorescent imides, valuable for peptide and analogs labeling as well as for thio-naphthalimide derivatives preparations. Copyright (C) 2008 John Wiley & Sons, Ltd.

Conformational behavior of different possible ways of oligoglycine formation in a solvent-free environment

The possible ways for glycine oligopeptide formation in gas phase, both in the extended P-strand like conformation and folded 2(7)-ribbon like conformations are analyzed using quantum chemical calculations. We focus on the sequential formation of peptide bond through upgradation of the immediate lower order molecule and observe the consequences in other related processes like oligoglycine formation through simultaneous peptide linkage of n glycine monomers and interchange of molecular conformation through peptide linkage. A comparison is made between the structures and binding energies obtained for both conformers. All binding energies are increased by the zero-point energy contribution. The role of electron correlation effects is briefly analyzed. The folded 2(7)-ribbon-like conformations in vacuo are found to be more stable in comparison to the extended structure. (c) 2007 Elsevier B.V. All rights reserved.

Analysis of Agonist and Antagonist Effects on Thyroid Hormone Receptor Conformation by Hydrogen/Deuterium Exchange

Thyroid hormone receptors (TRs) are ligand-gated transcription factors with critical roles in development and metabolism. Although x-ray structures of TR ligand-binding domains (LBDs) with agonists are available, comparable structures without ligand (apo-TR) or with antagonists are not. It remains important to understand apo-LBD conformation and the way that it rearranges with ligands to develop better TR pharmaceuticals. In this study, we conducted hydrogen/deuterium exchange on TR LBDs with or without agonist (T(3)) or antagonist (NH(3)). Both ligands reduce deuterium incorporation into LBD amide hydrogens, implying tighter overall folding of the domain. As predicted, mass spectroscopic analysis of individual proteolytic peptides after hydrogen/deuterium exchange reveals that ligand increases the degree of solvent protection of regions close to the buried ligand-binding pocket. However, there is also extensive ligand protection of other regions, including the dimer surface at H10-H11, providing evidence for allosteric communication between the ligand-binding pocket and distant interaction surfaces. Surprisingly, C-terminal activation helix H12, which is known to alter position with ligand, remains relatively protected from solvent in all conditions suggesting that it is packed against the LBD irrespective of the presence or type of ligand. T(3), but not NH(3), increases accessibility of the upper part of H3-H5 to solvent, and we propose that TR H12 interacts with this region in apo-TR and that this interaction is blocked by T(3) but not NH(3.) We present data from site-directed mutagenesis experiments and molecular dynamics simulations that lend support to this structural model of apo-TR and its ligand-dependent conformational changes. (Molecular Endocrinology 25: 15-31, 2011)

Solvatochromic and lonochromic Effects of Iron(II)bis-(1,10-phenanthroline)dicyano: a Theoretical Study

Solvatochromic and ionochromic effects of the iron(II)bis(1,10-phenanthroline)dicyano (Fe(phen)(2)(CN)(2)) complex were investigated by means of combined DFT/TDDFT calculations using the PBE and B3LYP functionals. Extended solvation models of Fe(phen)(2)(CN)(2) in acetonitrile and aqueous solution, as well as including interaction with Mg(2+), were constructed. The calculated vertical excitation energies reproduce well the observed solvatochromism in acetonitrile and aqueous solutions, the ionochromism in acetonitrile in the presence of Mg(2+), and the absence of ionochromic effect in aqueous solution. The vertical excitation energies and the nature of the transitions were reliably predicted after inclusion of geometry relaxation upon aqueous micro- and global solvation and solvent polarization effect in the TDDFT calculations. The two intense UV-vis absorption bands occurring for all systems studied are interpreted as transitions from a hybrid Fe(II)(d)/cyano N(p) orbital to a phenanthroline pi* orbital rather than a pure metal-to-ligand-charge transfer (MLCT). The solvatochromic and ionochromic blue band shifts of Fe(phen)(2)(CN)(2) were explained with preferential stabilization of the highest occupied Fe(II)(d)/cyano N(p) orbitals as a result of specific interactions with water solvent molecules or Mg(2+) ions in solution. Such interactions occur through the CN(-) groups in the complex, and they have a decisive role for the observed blue shifts of UV-vis absorption bands.

Tailored Media for Homogeneous Cellulose Chemistry: Ionic Liquid/Co-Solvent Mixtures

Co-solvents can minimize two of the major problems associated with the use of ionic liquids (ILs) as solvents for homogeneous derivatization of cellulose: high viscosity and limited miscibility with non-polar reagents or reaction products. Thus, the effects of 18 solvents and 3 binary solvent mixtures on cellulose solutions in three ILs were systematically studied with respect to the solution phase behavior. The applicable limits of these mixtures were evaluated and general guidelines for the use of co-solvents in cellulose chemistry could be advanced: Appropriate co-solvents should have EN T values (normalized empirical polarity) > 0.3, very low ``acidity`` (alpha < 0.5), and relatively high ""basicity`` (beta >= 0.4). Moreover, novel promising co-solvents and binary co-solvent mixtures were identified.

A physical organic chemistry approach to dissolution of cellulose: effects of cellulose mercerization on its properties and on the kinetics of its decrystallization

The effects of alkali treatment on the structural characteristics of cotton linters and sisal cellulose samples have been studied. Mercerization results in a decrease in the indices of crystallinity and the degrees of polymerization, and an increase in the alpha-cellulose contents of the samples. The relevance of the structural properties of cellulose to its dissolution is probed by studying the kinetics of cellulose decrystallization, prior to its solubilization in LiCl/N,N-dimethylacetamide (DMAc). Our data show that the decrystallization rate constants and activation parameters are only slightly dependent on the physico-chemical properties of the starting celluloses. This multi-step reaction is accompanied by a small enthalpy and large, negative, entropy of activation. These results are analyzed in terms of the interactions within the biopolymer chains during decrystallization, as well as those between the two ions of the electrolyte and both DMAc and cellulose.

Matrix effects observed during pesticides residue analysis in fruits by GC

The influence of the sample matrix in the CC-electron-capture detection analysis of the pesticides dimethoate, diazinon, chlorothalonil.. parathion methyl and fenitrothion in fruits samples has been studied. Experiments have been carried out where the pesticide responses in standard solutions prepared in selected solvent were compared with their response when present in apple, mango, papaya, banana, pineapple and melon extracts. The presence of matrix effects (MEs) and their extent were shown to be simultaneously influenced by several factors (matrix concentration, matrix type, pesticide concentration, analytical range). Pronounced MEs were observed particularly for dimethoate and diazinon in all matrices tested; in lower concentrations, all pesticides presented significant ME. The other pesticides presented variable ME. Higher ME enhancement was detected at lower pesticide concentration levels of and/or at higher matrix concentration solutions. The ME detected for fenitrothion, in the analytical range evaluated, were dependent on matrix type. For each pesticide, solvent and matrix-matched calibrations were compared for all fruit samples, and it could be concluded that quantitation based on standard solutions prepared in blank matrix extract (matrix-matched calibration) should be used to compensate the MEs and to obtain more accurate results for the pesticides studied.