Francesca Ingrosso

Formation and relaxation of excited states in solution : A new time dependent polarizable continuum model based on time dependent density functional theory

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.

Pathways for H2O bend vibrational relaxation in liquid water.

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 molecules 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.

A time-dependent polarizable continuum model: Theory and application

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.

Ultrafast energy transfer from the intramolecular bending vibration to librations in liquid water

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.

A New Glimpse into the CO2‐Philicity of Carbonyl Compounds

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).

A theoretical investigation of the CO2-philicity of amides and carbamides

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.

Quantum mechanical calculations coupled with a dynamical continuum model for the description of dielectric relaxation; Time dependent Stokes shift of coumarin C153 in polar solvents

Abstract We present here a study of the time dependent Stokes shift, performing quantum-mechanical calculations on coumarin C153 in polar solvents. The electrostatic interaction between the solute and the solvent is treated within the Polarizable Continuum Model, which allows us to use a molecular shaped cavity for the solute. In order to take into account that the sudden change in the solute electronic density after the S0 → S1 excitation can be accompanied by a non instantaneous rearrangement of a component of the solvent polarization, we use a non-equilibrium representation of the solvent response. We have implemented a procedure to calculate the solvation time correlation function (the theoretical counterpart of the Stokes shift), including experimental data of the complex dielectric permittivity \ ge(ω). The results that we have obtained are in good agreement with the experimental measurements. We will report the calculations for water, methanol, acetonitrile and dimethyl sulfoxide as solvents, showing that a correct treatment of dielectric relaxation generally needs a more detailed description of the solvent response than diffusive models.

Importance of Polarization and Charge Transfer Effects to Model the Infrared Spectra of Peptides in Solution.

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.

Vibrational Energy Relaxation of the Amide I Mode of N-Methylacetamide in D2O Studied through Born–Oppenheimer Molecular Dynamics

The vibrational relaxation of the amide I mode of deuterated N-methylacetamide 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%) is redistributed through intramolecular vibrational energy redistribution processes, with a smaller contribution (20%) of intermolecular energy flowing 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 and INM are in satisfactory agreement with the experimental measurements.

Taste for chiral guests: investigating the stereoselective binding of peptides to β-cyclodextrins.

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.