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

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.

Distinct conformational properties determined by implicit and explicit representation of protein-solvent interactions. An analytical and computer simulation study

In the protein folding problem, solvent-mediated forces are commonly represented by intra-chain pairwise contact energy. Although this approximation has proven to be useful in several circumstances, it is limited in some other aspects of the problem. Here we show that it is possible to achieve two models to represent the chain-solvent system. one of them with implicit and other with explicit solvent, such that both reproduce the same thermodynamic results. Firstly, lattice models treated by analytical methods, were used to show that the implicit and explicitly representation of solvent effects can be energetically equivalent only if local solvent properties are time and spatially invariant. Following, applying the same reasoning Used for the lattice models, two inter-consistent Monte Carlo off-lattice models for implicit and explicit solvent are constructed, being that now in the latter the solvent properties are allowed to fluctuate. Then, it is shown that the chain configurational evolution as well as the globule equilibrium conformation are significantly distinct for implicit and explicit solvent systems. Actually, strongly contrasting with the implicit solvent version, the explicit solvent model predicts: (i) a malleable globule, in agreement with the estimated large protein-volume fluctuations; (ii) thermal conformational stability, resembling the conformational hear resistance of globular proteins, in which radii of gyration are practically insensitive to thermal effects over a relatively wide range of temperatures; and (iii) smaller radii of gyration at higher temperatures, indicating that the chain conformational entropy in the unfolded state is significantly smaller than that estimated from random coil configurations. Finally, we comment on the meaning of these results with respect to the understanding of the folding process. (C) 2009 Elsevier B.V. All rights reserved.

First study on the thermo-solvatochromism in aqueous 1-(1-butyl)-3-methylimidazolium tetrafluoroborate: A comparison between the solvation by an ionic liquid and by aqueous alcohols

The thermo-solvatochrornic behaviors of 2,6-diphenyl-4-(2,4,6-triphenylpyridinium-1-yl) phenolate, RB; 2,6-dichloro-4-(2,4,6-triphenyloyridinium-1-yl) phenolate, WB; 2,6-dibromo-4-[(E)-2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePMBr(2); 2,6-dibromo-4-[(E)-2-(1-n-octylpyridinium-4-yl)ethenyl] phenolate, OcPMBr(2), have been investigated in binary mixtures of the ionic liquid, IL, 1-(1-butyl)-3-methylimidazolium tetrafluorborate, [BuMeIm][BF(4)], and water (W), in the temperature range from 10 to 60 degrees C. Plots of the empirical solvent polarities, ET (probe) in kcal mol(-1), versus the mole fraction of water in the binary mixture, chi(w) showed nonlinear, i.e., nonideal behavior. Solvation by these IL-W mixtures shows the following similarities to that by aqueous aliphatic alcohols: The same solvation model can be conveniently employed to treat the data obtained; it is based on the presence in the system-bulk medium and probe solvation shell of IL, W, and the ""complex"" solvent 1:1 IL-W. The origin of the nonideal solvation behavior appears to be the same, preferential solvation of the probe, in particular by the complex solvent. The strength of association of the IL-W complex, and the polarity of the IL are situated between the corresponding values of aqueous methanol and aqueous ethanol. Temperature increase causes a gradual desolvation of all probes employed. A difference between solvation by IL-W and aqueous alcohols is that probe-solvent hydrophobic interactions appear to play a minor role in case of the former mixture, probably because solvation is dominated by hydrogen-bonding and Coulombic interactions between the ions of the IL and the zwitterionic probes.

Thermo-solvatochromism in binary mixtures of water and ionic liquids: on the relative importance of solvophobic interactions

The thermo-solvatochromism of 2,6-dibromo-4-[(E)-2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePMBr(2), has been studied in mixtures of water, W, with ionic liquids, ILs, in the temperature range of 10 to 60 degrees C, where feasible. The objectives of the study were to test the applicability of a recently introduced solvation model, and to assess the relative importance of solute-solvent solvophobic interactions. The ILs were 1-allyl-3-alkylimidazolium chlorides, where the alkyl groups are methyl, 1-butyl, and 1-hexyl, respectively. The equilibrium constants for the interaction of W and the ILs were calculated from density data; they were found to be linearly dependent on N(C), the number of carbon atoms of the alkyl group; van't Hoff equation (log K versus 1/T) applied satisfactorily. Plots of the empirical solvent polarities, E(T) (MePMBr(2)) in kcal mol(-1), versus the mole fraction of water in the binary mixture, chi(w), showed non-linear, i.e., non-ideal behavior. The dependence of E(T) (MePMBr(2)) on chi(w), has been conveniently quantified in terms of solvation by W, IL, and the ""complex"" solvent IL-W. The non-ideal behavior is due to preferential solvation by the IL and, more efficiently, by IL-W. The deviation from linearity increases as a function of increasing N(C) of the IL, and is stronger than that observed for solvation of MePMBr(2) by aqueous 1-propanol, a solvent whose lipophilicity is 12.8 to 52.1 times larger than those of the ILs investigated. The dependence on N(C) is attributed to solute-solvent solvophobic interactions, whose relative contribution to solvation are presumably greater than that in mixtures of water and 1-propanol.

Thermo-solvatochromism of merocyanine polarity probes - What are the consequences of increasing probe lipophilicity through annelation?

The question raised in the title has been answered by comparing the solvatochromism of two series of polarity probes, the lipophilicities of which were increased either by increasing the length of an alkyl group (R) attached to a fixed pyridine-based structure or through annelation (i.e., by fusing benzene rings onto a central pyridine-based structure). The following novel solvatochromic probes were synthesized: 2,6-dibromo-4-[(E)-2-(1-methylquinolinium-4-yl)ethenyl]-phenolate (MeQMBr(2)) and 2,6-dibromo-4-[(E)-2-(1-methyl-acridinium-4- yl) ethenyl)]phenolate (MeAMBr(2) The solvatochromic behavior of these probes, along with that of 2,6dibromo-4-[(E)-2-(1-methylpyridinium-4-yl)ethenyl]phenol-ate(MePMBr(2)) was analyzed in terms of increasing probe lipophilicity, through annelation. Values of the empirical solvent polarity scale [E(T)(MePMBr(2))] in kcalmol(-1) correlated linearly with ET(30), the corresponding values for the extensively employed probe 2,6-diphenyl-4-(2,4,6-triphenylpyridinium-1-yl)phenolate (RB). On the other hand, the nonlinear correlations of ET(MeQMBr(2)) or ET(MeAMBr(2)) with E(T)(30) are described by second-order polynomials. Possible reasons for this behavior include: i) self-aggregation of the probe, ii) photoinduced cis/trans isomerization of the dye, and iii) probe structure- and solvent-dependent contributions of the quinonoid and zwitterionic limiting formulas to the ground and excited states of the probe. We show that mechanisms (i) and (ii) are not operative under the experimental conditions employed; experimental evidence (NMR) and theoretical calculations are presented to support the conjecture that the length of the central ethenylic bond in the dye increases in the order MeAMBr(2) > MeQMBr(2) > MePMBr(2), That is, the contribution of the zwitterionic limiting formula predominates for the latter probe, as is also the case for RB, this being the reason for the observed linear correlation between the ET(MePMBr2) and the ET(30) scales. The effect of increasing probe lipophilicity on solvatochromic behavior therefore depends on the strategy employed. Increasing the length of R affects solvatochromism much less than annelation, because the former structural change hardly perturbs the energy of the intramolecular charge-transfer transition responsible for solvatochromism. The thermo-solvatochromic behavior (effect of temperature on solvatochromism) of the three probes was studied in mixtures of water with propanol and/or with DMSO. The solvation model used explicitly considers the presence of three ""species"" in the system: bulk solution and probe solvation shell [namely, water (W), organic solvent (Solv)], and solvent-water hydrogen-bonded aggregate (Solv-W). For aqueous propanol, the probe is efficiently solvated by Solv-W; the strong interaction of DMSO with W drastically decreases the efficiency of Solv-W in solvating the probe, relative to its precursor solvents. Temperature increases resulted in desolvation of the probes, due to the concomitant reduction in the structured characters of the components of the binary mixtures.

Spectroscopic and theoretical studies of some N,N-diethyl-2-[(4 `-substituted)phenylsulfonyl]acetamides

The analysis of the IR carbonyl band of the N,N-diethyl-2-[(4`-substituted)phenylsulfonyl]acetamides Et(2)NC(O)CH(2)S(O)(2)-C(6)H(4)-Y (Y = OMe 1, Me 2,1-13, Cl 4, Br 5, NO(2) 6) supported by B3LYP/6-31G(d,p) calculations for 3, indicated the existence of three pairs (anti and syn) of cis (c) and gauche (g(1) and g(2)) conformers in the gas phase, being the gauche conformers significantly more stable than the cis ones. The anti geometry is more stable than the syn one, for each pair of cis and gauche conformers. The summing up of the orbital (NBO analysis) and electrostatic interactions justifies quite well the populations and the v(CO) frequencies of the anti and syn pairs of c, g(1) and g(2) conformers. The IR higher carbonyl frequency component whose population is ca. 10%, in CCl(4), may be ascribed to the least stable and most polar cis conformer pair (in the gas phase) and the lower frequency component whose population is ca. 90%, to the summing up of the populations of the two most stable and least polar gauche conformer pairs (g(1) and g(2)) (in the gas phase). The reversal of the cis(c)/gauche (g(1) + g(2)) population ratio observed in chloroform ca. 60% (cis)/40% (gauche) and the occurrence of the most polar cis(c) conformer only, in acetonitrile, strongly suggests the coalescence of the two gauche components in a unique carbonyl band in solution. A further support to this rationalization is given by the single point PCM solvation model performed by HF/6-31G(d,p) method, which showed a progressive increase of the c/(g(1) + g(2)) ratio going from gas to CCl(4), to CHCl(3) and to CH(3)CN. X-ray single crystal analysis of 4 indicates that this compound assumes, in the solid state, the syn-clinal (gauche) conformation with respect to the [O=C-CH(2)-S] moiety, and the most stable anti geometry relative to the [C(O)N(CH(2)CH(3))(2)] fragment. In order to obtain larger energy gain from the crystal packing the molecules of 4 are linked in centrosymmetric dimers through two C-H center dot center dot center dot O interactions (C-H([O-Ph])center dot center dot center dot O([SO2])) forming a step ladder. (C) 2011 Elsevier B.V. All rights reserved.

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.

Reaction-diffusion stochastic lattice model for a predator-prey system

We have the purpose of analyzing the effect of explicit diffusion processes in a predator-prey stochastic lattice model. More precisely we wish to investigate the possible effects due to diffusion upon the thresholds of coexistence of species, i. e., the possible changes in the transition between the active state and the absorbing state devoid of predators. To accomplish this task we have performed time dependent simulations and dynamic mean-field approximations. Our results indicate that the diffusive process can enhance the species coexistence.

Liquid polymorphism, order-disorder transitions and anomalous behavior: A Monte Carlo study of the Bell-Lavis model for water

The Bell-Lavis model for liquid water is investigated through numerical simulations. The lattice-gas model on a triangular lattice presents orientational states and is known to present a highly bonded low density phase and a loosely bonded high density phase. We show that the model liquid-liquid transition is continuous, in contradiction with mean-field results on the Husimi cactus and from the cluster variational method. We define an order parameter which allows interpretation of the transition as an order-disorder transition of the bond network. Our results indicate that the order-disorder transition is in the Ising universality class. Previous proposal of an Ehrenfest second order transition is discarded. A detailed investigation of anomalous properties has also been undertaken. The line of density maxima in the HDL phase is stabilized by fluctuations, absent in the mean-field solution. (C) 2009 American Institute of Physics. [doi:10.1063/1.3253297]

Understanding solvation

The effects of solvents on different chemical phenomena, including reactivity, spectroscopic data, and swelling of biopolymers can be rationalized by use of solvatochromic probes, substances whose UV-vis spectra, absorption, or emission are sensitive to the properties of the medium. Thermo-solvatochromism refers to the effect of temperature on solvatochromism. The study of both phenomena sheds light on the relative importance of the factors that contribute to solvation, namely, properties of the probe, those of the solvent (acidity, basicity, dipolarity/polarizability, and lipophilicity), and the temperature. Solvation in binary solvent mixtures is complex because of ""preferential solvation"" of the probe by some component of the mixture. A recently introduced solvent exchange model is based on the presence in the binary solvent mixture of the organic component (molecular solvent or ionic liquid), S, water, W, and a 1:1 hydrogen-bonded species (S-W). Solvation by the latter is more efficient than by its precursor solvents, due to probe-solvent hydrogen-bonding and hydrophobic interactions; dimethyl sulfoxide (DMSO)-W is an exception. Solvatochromic data are employed in order to explain apparently disconnected phenomena, namely, medium effect on the pH-independent hydrolysis of esters, (1)H NMR data of water-ionic liquid (IL) mixtures, and the swelling of cellulose.

Robust model predictive controller with output feedback and target tracking

A model predictive controller (MPC) is proposed, which is robustly stable for some classes of model uncertainty and to unknown disturbances. It is considered as the case of open-loop stable systems, where only the inputs and controlled outputs are measured. It is assumed that the controller will work in a scenario where target tracking is also required. Here, it is extended to the nominal infinite horizon MPC with output feedback. The method considers an extended cost function that can be made globally convergent for any finite input horizon considered for the uncertain system. The method is based on the explicit inclusion of cost contracting constraints in the control problem. The controller considers the output feedback case through a non-minimal state-space model that is built using past output measurements and past input increments. The application of the robust output feedback MPC is illustrated through the simulation of a low-order multivariable system.

Loss of Ergodicity in the Transition from Annealed to Quenched Disorder in a Finite Kinetic Ising Model

We consider a kinetic Ising model which represents a generic agent-based model for various types of socio-economic systems. We study the case of a finite (and not necessarily large) number of agents N as well as the asymptotic case when the number of agents tends to infinity. The main ingredient are individual decision thresholds which are either fixed over time (corresponding to quenched disorder in the Ising model, leading to nonlinear deterministic dynamics which are generically non-ergodic) or which may change randomly over time (corresponding to annealed disorder, leading to ergodic dynamics). We address the question how increasing the strength of annealed disorder relative to quenched disorder drives the system from non-ergodic behavior to ergodicity. Mathematically rigorous analysis provides an explicit and detailed picture for arbitrary realizations of the quenched initial thresholds, revealing an intriguing ""jumpy"" transition from non-ergodicity with many absorbing sets to ergodicity. For large N we find a critical strength of annealed randomness, above which the system becomes asymptotically ergodic. Our theoretical results suggests how to drive a system from an undesired socio-economic equilibrium (e. g. high level of corruption) to a desirable one (low level of corruption).

The complementary exponential geometric distribution: Model, properties, and a comparison with its counterpart

In this paper, we proposed a new two-parameter lifetime distribution with increasing failure rate, the complementary exponential geometric distribution, which is complementary to the exponential geometric model proposed by Adamidis and Loukas (1998). The new distribution arises on a latent complementary risks scenario, in which the lifetime associated with a particular risk is not observable; rather, we observe only the maximum lifetime value among all risks. The properties of the proposed distribution are discussed, including a formal proof of its probability density function and explicit algebraic formulas for its reliability and failure rate functions, moments, including the mean and variance, variation coefficient, and modal value. The parameter estimation is based on the usual maximum likelihood approach. We report the results of a misspecification simulation study performed in order to assess the extent of misspecification errors when testing the exponential geometric distribution against our complementary one in the presence of different sample size and censoring percentage. The methodology is illustrated on four real datasets; we also make a comparison between both modeling approaches. (C) 2011 Elsevier B.V. All rights reserved.

Numerical Solution of the Upper-Convected Maxwell Model for Three-Dimensional Free Surface Flows

This work presents a finite difference technique for simulating three-dimensional free surface flows governed by the Upper-Convected Maxwell (UCM) constitutive equation. A Marker-and-Cell approach is employed to represent the fluid free surface and formulations for calculating the non-Newtonian stress tensor on solid boundaries are developed. The complete free surface stress conditions are employed. The momentum equation is solved by an implicit technique while the UCM constitutive equation is integrated by the explicit Euler method. The resulting equations are solved by the finite difference method on a 3D-staggered grid. By using an exact solution for fully developed flow inside a pipe, validation and convergence results are provided. Numerical results include the simulation of the transient extrudate swell and the comparison between jet buckling of UCM and Newtonian fluids.