Francesca Ingrosso

University of Lorraine, Nancy, Lorraine, France

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Publications (24)61.27 Total impact

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    ABSTRACT: The sensitivity of some infrared bands to the local environment can be exploited to shed light on the structure and the dynamics of biological systems. In particular, the amide I band, which is specifically related to vibrations within the peptide bonds, can give information on the ternary structure of proteins, and can be used as a probe of energy transfer. In this work, we propose a model to quantitatively interpret the frequency shift on the amide I band of a model peptide induced by the formation of hydrogen bonds in the first solvation shell. This method allows us to analyze to what extent the electrostatic interaction, electronic polarization and charge transfer affect the position of the amide I band. The impact of the anharmoniticy of the pontential energy surface on the hydration induced shift is elucidated as well.
    The journal of physical chemistry. B. 09/2014;
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    ABSTRACT: In this work, we present a study of the ability of different semiempirical methods to describe intermolecular interactions in water solution. In particular, we focus on methods based on the Neglect of Diatomic Differential Overlap approximation. Significant improvements of these methods have been reported in the literature in the past years regarding the description of non-covalent interactions. In particular, a broad range of methodologies has been developed to deal with the properties of hydrogen-bonded systems, with varying degrees of success. In contrast, the interactions between water and a molecule containing hydrophobic groups have been little analyzed. Indeed, by considering the potential energy surfaces obtained using different semiempirical Hamiltonians for the intermolecular interactions of model systems, we found that none of the available methods provides an entirely satisfactory description of both hydrophobic and hydrophilic interactions in water. In addition, a vibrational analysis carried out in a model system for these interactions, a methane clathrate cluster, showed that some recent methods cannot be used to carry out studies of vibrational properties. Following a procedure established in our group [M. I. Bernal-Uruchurtu, M. T. C. Martins-Costa, C. Millot, and M. F. Ruiz-López, J. Comput. Chem.21, 572 (2000); W. Harb, M. I. Bernal-Uruchurtu, and M. F. Ruiz-López, Theor. Chem. Acc.112, 204 (2004)], we developed new parameters for the core-core interaction terms based on fitting potential energy curves obtained at the MP2 level for our model system. We investigated the transferability of the new parameters to describe a system, having both hydrophilic and hydrophobic groups, interacting with water. We found that only by introducing two different sets of parameters for hydrophilic and hydrophobic hydrogen atom types we are able to match the features of the ab initio calculated properties. Once this assumption is made, a good agreement with the MP2 reference is achieved. The results reported in this work provide therefore a direction for future developments of semiempirical approaches that are still required to investigate chemical processes in biomolecules and in large disordered systems.
    The Journal of Chemical Physics 07/2014; 141:034106. · 3.12 Impact Factor
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    ABSTRACT: The vibrational relaxation (VR) of the amide I mode of deuterated N -methylacetamide (NMAD) in D2O solution is studied through nonequilibrium simulations using the semiempirical Born-Oppenheimer Molecular Dynamics (SEBOMD) approach to describe the whole solute-solvent system. Relaxation pathways and lifetimes are determined using the Instantaneous Normal Mode (INM) analysis. The relaxation of the amide I mode is characterized by three different time scales, most of the excess energy (80%) being redistributed through intramolecular vibrational energy redistribution (IVR) processes, with a smaller contribution (20%) of intermolecular energy flow into the solvent. The amide II mode is found to contribute modestly (7%) to the relaxation mechanism. The amide I mode and the total vibrational energy decay curves obtained using SEBOMD/INM are in satisfactory agreement with the experimental measurements.
    The journal of physical chemistry. B. 05/2014;
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    ABSTRACT: Electron donor–acceptor (EDA) interactions are widely involved in chemistry and their understanding is essential to design new technological applications in a variety of fields ranging from material sciences and chemical engineering to medicine. In this Letter, we study EDA complexes of carbon dioxide with ketones using several ab initio and density functional theory methods. Energy contributions to the interaction energy have been analyzed in detail using both variational and perturbational treatments. Dispersion energy has been shown to play a key role in explaining the high stability of a non-conventional structure, which can roughly be described by a cooperative EDA interaction.
    Chemical Physics Letters 05/2014; 601:98–102. · 2.15 Impact Factor
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    ABSTRACT: ab initio molecular dynamics simulations of the acetone–CO2 complex (MP2/6-31G(d) level) were performed to investigate the effect of dynamics at finite temperature on the weak electron donor–acceptor intermolecular interactions. In addition, we carried out a study of the free energy of formation of the complex by means of umbrella sampling technique at the MP2 level with a perturbative CCSD(T) correction. The potential of mean force was obtained along a reaction coordinate describing the acetone–CO2 interaction. The results obtained here support some hypothesis that we already explored in past works using static electronic calculations. In particular, when interacting with a molecule having a carbonyl function, carbon dioxide displays both Lewis acid and Lewis base behaviour. This property can be exploited to design molecular systems that are easily solubilised in supercritical CO2.
    Molecular Simulation 01/2014; 40. · 1.06 Impact Factor
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    ABSTRACT: Obtaining compounds of diastereomeric purity is extremely important in the field of biological and pharmaceutical industry, where amino acids and peptides are widely employed. In this work, we theoretically investigate the possibility of chiral separation of peptides by β-cyclodextrins (β-CDs), providing a description of the associated interaction mechanisms by means of Molecular Dynamics (MD) simulations. The formation of host/guest complexes by including a model peptide in the macrocycle cavity is analyzed and discussed. We consider the terminally blocked phenylalanine dipeptide (Ace-Phe-Nme), in the L- and D-configurations, to be involved in the host/guest recognition process. The CD-peptide free energies of binding for the two enantiomers are evaluated through a combined approach that assumes: 1) extracting a set of independent molecular structures from the MD simulation, 2) evaluating the interaction energies for the host/guest complexes by hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) calculations carried out on each structure, for which we also compute 3) the solvation energies through the Poisson-Boltzmann surface area method. We find that chiral discrimination by the CD macrocycle is of the order of 1 kcal/mol, which is comparable to experimental data for similar systems. According to our results, the Ace-(D)Phe-Nme isomer leads to a more stable complex with a β-CD compared to the Ace-(L)Phe-Nme isomer. Nevertheless, we show that the chiral selectivity of β-CDs may strongly depend on the secondary structure of larger peptides. Although the free energy differences are relatively small, the predicted selectivities can be rationalized in terms of host/guest hydrogen bonds and hydration effects. Indeed, the two enantiomers display different interaction modes with the cyclodextrin macrocavity and different mobility within the cavity. This finding suggests a new interpretation for the interactions that play a key role in chiral recognition, which may be exploited to design more efficient and selective chiral separations of peptides.
    The Journal of Physical Chemistry B 01/2013; · 3.61 Impact Factor
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    ABSTRACT: The knowledge of the interactions taking place at a molecular level can help the development of new technological procedures in Chemistry with low environmental impact. In organic, biochemical and pharmaceutical synthesis and in analytical chemistry, important advances in this domain are related to the use of solvents that can be valid alternatives to hazardous organic solvents. In the last decades, a large emphasis has been given to the use of carbon dioxide under supercritical conditions, since the mild temperature and pressure conditions of the fluid can easily be controlled to improve its capacity to solubilize small organic compounds. On the other hand, the solubility of larger molecules and of polar compounds in this medium is generally very low. This has motivated recent theoretical and experimental studies with the purpose of reaching a better understanding of the so-called CO2-philicity of molecules and materials, and very encouraging results have been reported. In this paper, we present an ab initio study of the intermolecular interactions between CO2 and amide and carbamide derivatives, performed on model 1:1 complexes at the MP2/aug-cc-pVTZ//MP2/aug-cc-pVDZ level. Our findings shed some light on the key points to be considered in the design of large CO2-philic molecules, hinting at the use of solubilizer groups in which amide or urea bonds could be involved.
    Theoretical Chemistry Accounts 01/2013; 132. · 2.14 Impact Factor
  • Francesca Ingrosso, Branka Maria Ladanyi
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    ABSTRACT: The density dependence of the local structure and of collective dynamics of a polar fluid fluoroform along an isotherm at a temperature of 1.03 T(c), in the near-critical (NC) region, were studied by classical molecular dynamics (MD) simulations. In the case of local structure we focus on local density inhomogeneities and on orientational pair correlations that are relevant to dielectric properties and light scattering intensities. Our results show that the density dependence of the frequency shifts of fluoroform ν(2) and ν(3) modes correlates well with that of intermolecular dipole-dipole interactions. Our study of collective dynamics deals with dipole and polarizability anisotropy relaxation, experimentally-accessible through far-infrared absorption, depolarized light scattering and optical Kerr effect. Our MD simulations were performed using an all-atom nonpolarizable potential model of fluoroform. Contributions of induced dipoles to dielectric properties were included using first order perturbation theory and this approach was also used to include interaction-induced contributions to polarizability anisotropy relaxation. For interactions involving induced dipoles we calculated and compared the results of a distributed polarizability model to a model with a single polarizable site located at the center-of-mass. Using a projection scheme that allows us to identify the contributions from different relaxation mechanisms, we found that dipole relaxation is dominated by collective reorientation, while in the case of polarizability anisotropy, relaxation processes related to translational dynamics make a major contribution over most of the fluid density range. The dielectric properties of fluoroform in the NC region were calculated and compared to the corresponding measurements. We found the dielectric constant and the far-infrared absorption spectrum to be in good agreement with experiments.
    The Journal of Physical Chemistry B 12/2012; · 3.61 Impact Factor
  • Muhannad Altarsha, Francesca Ingrosso, Manuel F Ruiz-Lopez
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    ABSTRACT: We report a theoretical study on non-conventional structures of 1:1 complexes between carbon dioxide and carbonyl compounds. These structures have never been reported before but are relevant for understanding the solubility of carbonyl compounds in supercritical CO(2) . The work is based on the results of ab initio calculations at the MP2 and CCSD(T) levels using aug-cc-pVDZ and aug-cc-pVTZ basis sets. Investigated systems include aldehydes, ketones and esters, together with some fluorinated derivatives. The results are interpreted in terms of natural bond orbital analyses. Harmonic vibrational frequency calculations have also been done in order to compare them with available experimental data. We show for the first time that complexes where CO(2) behaves globally as a Lewis base are stable in the case of ketones and esters, but not in the case of aldehydes, and their stability is similar to that of traditional complexes in which CO(2) behaves as a Lewis acid. This finding considerably modifies the concept of CO(2) -philicity and may have important ramifications in the development of green reactions in supercritical CO(2) .
    ChemPhysChem 07/2012; 13(14):3397-403. · 3.35 Impact Factor
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    ABSTRACT: Structural properties of peracetylated β-cyclodextrin in supercritical carbon dioxide were investigated by means of molecular dynamics simulations. The study indicated a strong reduction of the cavity accessibility to guest molecules, compared to native β-cyclodextrin in water. Indeed, the cavity is self-closed during the largest part of the simulation, which agrees well with suggestions made on the basis on high-pressure NMR experiments. Self-closure happens because one glucose unit undergoes a main conformational change (from chair to skew) that brings one of the acetyl groups in the wide rim of the cyclodextrin to the cavity interior. This arrangement turns out to be quite favorable, persisting for several nanoseconds. In addition to the wide rim self-closure, a narrow rim self-closure may also occur, though it is less likely and exhibits short duration (<1 ns). Therefore, the number of solvent molecules reaching the cavity interior is much smaller than that found in the case of native β-cyclodextrin in water after correction to account for different molar densities. These findings support the weak tendency of the macromolecule to form host-guest complexes in this nonconventional medium, as reported by some experiments. Finally, Lewis acid/base interactions between the acetyl carbonyl groups and the solvent CO(2) molecules were analyzed through ab initio calculations that revealed the existence of a quite favorable four-member ring structure not yet reported. The ensemble of these results can contribute to establish general thermodynamic principles controlling the formation of inclusion complexes in supercritical CO(2), where the hydrophilicity/hydrophobicity balance is not applicable.
    The Journal of Physical Chemistry B 03/2012; 116(13):3982-90. · 3.61 Impact Factor
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    ABSTRACT: We present a study of the infrared spectrum of N-methyl acetamide (NMA) performed by using molecular dynamics (MD) with a quantum electronic Hamiltonian. A recently developed method, based on the Born–Oppenheimer approximation and on a semiempirical level of quantum chemistry (SEBOMD), is employed. We focus on the solvent effect on the infrared spectrum of the solute, on its geometry, and on its electrostatic properties. We thus run simulations of NMA in the gas phase and in water (64 solvent molecules with periodic boundary conditions), taking into account its two different conformers—cis and trans. The use of a semiempirical electronic Hamiltonian allows us to explore much larger time scales compared to density functional theory based MD for systems of similar size. NMA represents a simple model system for peptide bonds: those infrared bands that are more significant as a signature of the peptide bond (amide I, II, and III and the N–H stretch) are identified, and the solvent shift is evaluated and compared to experiments. We find a satisfying agreement between our model and experimental measurements, not only for the solvent shift but also for the structural and electrostatic properties of the solute. On the other hand, when a molecular mechanics, nonpolarizable force field is used to run MD, very little or nil solvent effect is observed. By analyzing our results, we propose an explanation of this discrepancy by stressing the importance of mutual polarization and charge transfer in an accurate modeling of the solute–solvent interactions.
    Journal of Chemical Theory and Computation. 04/2011; 7(6).
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    ABSTRACT: The mechanism of the H2O bend vibrational relaxation in liquid water has been examined via classical MD simulations and an analysis of work and power contributions. The relaxation is found to be dominated by energy flow to the hindered rotation of the bend excited water molecule. This energy transfer, representing approximately 2/3 of the transferred energy, is due to a 2:1 Fermi resonance for the centrifugal coupling between the water bend and rotation. The remaining energy flow (approximately 1/3) from the excited water bend is dominated by transfer to the excited water molecule's first four water neighbors, i.e., the first hydration shell, and is itself dominated by energy flow to the two water molecules hydrogen (H)-bonded to the hydrogens of the central H2O. The energy flow from the produced rotationally excited central molecule is less local in character, with approximately half of its rotational kinetic energy being transferred to water molecules outside of the first hydration shell, whereas the remaining half is preferentially transferred to the two first hydration shell water molecules donating H-bonds to the central water oxygen. The overall energy flow is well described by an approximate kinetic scheme.
    The Journal of Physical Chemistry A 09/2009; 113(31):8949-62. · 2.77 Impact Factor
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    ABSTRACT: A theoretical study of the water bend-to-libration energy transfer in liquid H(2)O has been performed by means of nonequilibrium classical molecular dynamics computer simulations. Attention has been focused on the time scale and mechanism of the decay of the fundamental H(2)O bend vibration and the related issue of the decay of water librational (hindered rotational) excitations, including the important role of that for the excited molecule itself. The time scales found are 270 fs for the decay of the average energy of an H(2)O molecule excited to the nu = 1 state of the bending oscillator and less than 100 fs for excess rotational (librational) kinetic energy, both consistent with recent ultrafast infrared experimental results. The energy flow to the excited molecule rotation and through the first several solvent shells around the excited water molecule is discussed in some detail.
    The Journal of Physical Chemistry A 07/2009; 113(24):6657-65. · 2.77 Impact Factor
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    ABSTRACT: The spectroscopic behavior of 6-propionyl-2-(N,N-dimethyl)aminonaphthalene (PRODAN) is investigated in different environments, ranging from homogeneous solutions of different polarities to diffuse interfaces mimicking membranes. The variety of experimental data as well as computational results present in the literature still do not clarify the nature of the emission process; in particular, it is not well-established whether fluorescence in such a molecule occurs from a planar or from a twisted intramolecular charge transfer state. The first part of the work is thus devoted to better understand how the electronic transition processes occur in homogeneous solvents. The effect of the medium polarity as well as the hydrogen bond formation are studied. In the second part of the paper, a first attempt to interpret the experimental results of PRODAN in unilamellar vesicles is carried out. The complexity of the still-open questions about the photophysics of PRODAN has prompted us to base the study on quantum-mechanical calculations performed at various levels of theory, namely, DFT, TDDFT, CIS, and SAC-CI, and to include the effects of the environment in a self-consistent way. This is achieved by using the integral equation formalism version of the polarizable continuum model (IEFPCM). IEFPCM is a quite versatile approach, being able to treat equilibrium and nonequilibrium solvation in both homogeneous and heterogeneous media.
    The Journal of Physical Chemistry B 02/2008; 112(2):414-23. · 3.61 Impact Factor
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    ABSTRACT: Results are presented for an investigation of intermolecular electron transfer (ET) in solution by means of quantum calculations. The two molecules that are involved in the ET reaction form a solvent-separated radical ion pair. The solvent plays an important role in the ET between the two molecules. In particular, it can give rise to specific solute-solvent interactions with the solutes. An example of specific interactions is the formation of a hydrogen bond between a protic solvent and one of the molecules involved in the ET. We address the study of this system by means of quantum calculations on the solutes immersed in a continuum solvent. However, when the solvent can give rise to hydrogen bond formation with the negatively charged ion after ET, we explicitly consider solvent molecules in the solute cavity, determining the hydrogen bond energetic contribution to the overall interaction energy. Solute-solvent pair distribution functions, showing the different arrangement of solvent molecules before and after ET in the first solvation shell, are reported. We provide results of the solvent reorganization energy from quantum calculations for both the two isolated fragments and the ion pair in solution. Results are in agreement with available experimental data.
    The Journal of Physical Chemistry B 01/2007; 110(49):25115-21. · 3.61 Impact Factor
  • Giorgio Cinacchi, Francesca Ingrosso, Alessandro Tani
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    ABSTRACT: Computer simulation results are presented for an atomistic pair potential model of 1,4-dioxane which takes into account molecular flexibility. The model has been conceived to be applied to the study of solvatochromism and solvation dynamics in the presence of the polar probe coumarin C153. Computer simulations on the pure liquid have produced thermodynamical, structural, and dynamical data in good agreement with available experimental measures. This constitutes a valuable test of the 1,4-dioxane all-atom model employed. The study of solute-solvent interactions for C153 in 1,4-dioxane has been motivated by the aim of casting light, through simulations, on the interesting experimental findings according to which such a solvent behaves as a "polar" solvent with respect to dynamic solvation properties. Molecular dynamics is particularly suitable to model the process and provides an interpretation of the so-called "dioxane anomaly". An investigation of the structure of the solvation shell and of the dynamics of solvation is presented and discussed. In particular, the satisfactory accordance between simulated and experimental solvation response implies that the simulations give a reliable description of both solute and solvent at a molecular level and reinforces the idea that the explicit inclusion of discrete solvent molecules is needed for a realistic treatment of solvation phenomena in which the local structure of the liquid plays a key role.
    The Journal of Physical Chemistry B 08/2006; 110(27):13633-41. · 3.61 Impact Factor
  • Francesca Ingrosso, Branka M Ladanyi
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    ABSTRACT: Molecular dynamics (MD) simulations of a probe solute (coumarin C153) in supercritical fluoroform are used to study time-dependent solute-solvent interactions. We study the dynamics of solvent reorganization in response to electronic excitation of C153 at a temperature of 1.03 T(c) (the critical temperature) and a series of densities above and below the critical density. Simulations of a two-site and five-site models of fluoroform are presented and compared. The time-dependent solvation response after solute electronic excitation is studied in the two cases, and the five-site results present an earlier onset of exponential decay that is closer to what is expected to be the experimental response. This is confirmed by comparison to experiment. In addition to obtaining the solvation response from nonequilibrium MD trajectories, approximate solvation responses were obtained from equilibrium time correlations of the fluctuations in the solvation energy change in the presence of ground- and excited-state solutes. For the five-site model, the equilibrium excited-state response shows stronger density dependence than the ground-state one. The nonequilibrium response appears to have an intermediate decay rate between the two equilibrium functions. The solute-partial-charge-solvent-induced-dipole interaction was also taken into account by means of a perturbative approach, which improved the agreement with experimental measurements available at densities corresponding to 1.4-1.6 rho(c) (where rho(c) the critical density). From the comparison between the two models, it is possible to conclude that an atomistic description is necessary for correctly representing the portion of solvation dynamics that is related to reorientation. This consideration is supported by providing results for orientational time correlation functions and by comparing the correlation times with the experimental ones.
    The Journal of Physical Chemistry B 06/2006; 110(20):10120-9. · 3.61 Impact Factor
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    ABSTRACT: In this paper a novel approach to study the formation and relaxation of excited states in solution is presented within the integral equation formalism version of the polarizable continuum model. Such an approach uses the excited state relaxed density matrix to correct the time dependent density functional theory excitation energies and it introduces a state-specific solvent response, which can be further generalized within a time dependent formalism. This generalization is based on the use of a complex dielectric permittivity as a function of the frequency, epsilonomega. The approach is here presented in its theoretical formulation and applied to the various steps involved in the formation and relaxation of electronic excited states in solvated molecules. In particular, vertical excitations (and emissions), as well as time dependent Stokes shift and complete relaxation from vertical excited states back to ground state, can be obtained as different applications of the same theory. Numerical results on two molecular systems are reported to better illustrate the features of the model.
    The Journal of Chemical Physics 04/2006; 124(12):124520. · 3.12 Impact Factor
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    ABSTRACT: We present a study of local density augmentation around an attractive solute (i.e., giving rise to more attractive interaction with the solvent than solvent-solvent interactions) in supercritical fluoroform. This work is based on molecular dynamics simulations of coumarin 153 in supercritical fluoroform at densities both above and below the critical density, ranging from dilute gas-like to liquid-like, at a reduced temperature (T/T(c)) of 1.03. We focused on studying the structure of the solvation shell and the variation of the solute electronic absorption and emission shifts with density. Quantum calculations at the density functional theory (DFT) level were run on the solute in the ground state, and time-dependent DFT calculations were performed in the solute excited state in order to determine the solute-solvent potential parameters. The results obtained for the Stokes shift are in agreement with the experimental measurements. To evaluate local density augmentation from simulations, we used two different definitions, one based on the solvation number and the other derived from solvatochromic shifts. In the former case, the agreement with experimental results is good, while, in the latter case, better agreement is achieved by perturbatively including the induced-dipole contribution to the solvation energy.
    The Journal of Physical Chemistry B 04/2006; 110(10):4953-62. · 3.61 Impact Factor
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    ABSTRACT: This work presents an extention of the polarizable continuum model to explicitly describe the time-dependent response of the solvent to a change in the solute charge distribution. Starting from an initial situation in which solute and solvent are in equilibrium, we are interested in modeling the time-dependent evolution of the solvent response, and consequently of the solute-solvent interaction, after a perturbation in this equilibrium situation has been switched on. The model introduces an explicit time-dependent treatment of the polarization by means of the linear-response theory. Two strategies are tested to account for this time dependence: the first one employs the Debye model for the dielectric relaxation, which assumes an exponential decay of the solvent polarization; the second one is based on a fitting of the experimental data of the solvent complex dielectric permittivity. The first approach is simpler and possibly less accurate but allows one to write an analytic expression of the equations. By contrast, the second approach is closer to the experimental evidence but it is limited to the availability of experimental data. The model is applied to the ionization process of N,N-dimethyl-aniline in both acetonitrile and water. The nonequilibrium free-energy profile is studied both as a function of the solvent relaxation coordinate and as a function of time. The solvent reorganization energy is evaluated as well.
    The Journal of Chemical Physics 05/2005; 122(15):154501. · 3.12 Impact Factor