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Papers by Adrián Kalstein

Theoretical Chemistry Accounts, 2011

Intramolecular vibrational dynamics of polyatomic molecules in solution can be addressed through ... more Intramolecular vibrational dynamics of polyatomic molecules in solution can be addressed through normal mode analysis based on either equilibrium normal modes (ENMs) or instantaneous normal modes (INMs). While the former offers a straightforward way of examining experimental spectra, the latter provides a decoupled shorttime description of the vibrational motions of the molecule. In order to reconcile both representations, a realistic assignment of the INMs in terms of the ENMs is needed. In this paper, we describe a novel method to assign the INMs using the ENMs as templates, which provides a unique relationship between the two sets of normal modes. The method is based specifically on the use of the so-called Min-Cost or Min-Sum algorithm, duly adapted to our problem, to maximize the overlaps between the two sets of modes. The identification of the INMs as the system evolves with time then allows us to quantify the vibrational energy stored in each INM and so monitor the flows of intramolecular vibrational energy within the solute molecule. We also discuss the degree of mixing of the INMs and characterize the way they change with time by means of the corresponding autocorrelation functions. The usefulness of the method is illustrated by carrying out equilibrium molecular dynamics (MD) simulations of the deuterated N-methylacetamide (NMAD) molecule in D 2 O solution.

The Journal of Physical Chemistry A, 2010

Nonequilibrium molecular dynamics (MD) simulations and instantaneous normal mode (INMs) analyses ... more Nonequilibrium molecular dynamics (MD) simulations and instantaneous normal mode (INMs) analyses are used to study the vibrational relaxation of the C-H stretching modes (ν(s)(CH₃)) of deuterated N-methylacetamide (NMAD) in aqueous (D2O) solution. The INMs are identified unequivocally in terms of the equilibrium normal modes (ENMs), or groups of them, using a restricted version of the recently proposed Min-Cost assignment method. After excitation of the parent ν(s)(CH₃) modes with one vibrational quantum, the vibrational energy is shown to dissipate through both intramolecular vibrational redistribution (IVR) and intermolecular vibrational energy transfer (VET). The decay of the vibrational energy of the ν(s)(CH₃) modes is well fitted to a triple exponential function, with each characterizing a well-defined stage of the entire relaxation process. The first, and major, relaxation stage corresponds to a coherent ultrashort (τ(rel) = 0.07 ps) energy transfer from the parent ν(s)(CH₃) modes to the methyl bending modes δ(CH₃), so that the initially excited state rapidly evolves into a mixed stretch-bend state. In the second stage, characterized by a time of 0.92 ps, the vibrational energy flows through IVR to a number of mid-range-energy vibrations of the solute. In the third stage, the vibrational energy accumulated in the excited modes dissipates into the bath through an indirect VET process mediated by lower-energy modes, on a time scale of 10.6 ps. All the specific relaxation channels participating in the whole relaxation process are properly identified. The results from the simulations are finally compared with the recent experimental measurements of the ν(s)(CH₃) vibrational energy relaxation in NMAD/D₂O(l) reported by Dlott et al. (J. Phys. Chem. A 2009, 113, 75.) using ultrafast infrared-Raman spectroscopy.

The Journal of Chemical Physics, 2010

A nonequilibrium molecular dynamics (MD) study of the vibrational relaxation of the amide I mode ... more A nonequilibrium molecular dynamics (MD) study of the vibrational relaxation of the amide I mode of deuterated N-methylacetamide (NMAD) in aqueous (D(2)O) solution is carried out using instantaneous normal modes (INMs). The identification of the INMs as they evolve over time, which is necessary to analyze the energy fluxes, is made by using a novel algorithm which allows us to assign unequivocally each INM to an individual equilibrium normal mode (ENM) or to a group of ENMs during the MD simulations. The time evolution of the energy stored in each INM is monitored and the occurrence of resonances during the relaxation process is then investigated. The decay of the amide I mode, initially excited with one vibrational quantum, is confirmed to fit well to a biexponential function, implying that the relaxation process involves at least two mechanisms with different rate constants. By freezing the internal motions of the solvent, it is shown that the intermolecular vibration-vibration channel to the bending modes of the solvent is closed. The INM analysis reveals then the existence of a major and faster decay channel, which corresponds to an intramolecular vibrational redistribution process and a minor, and slower, decay channel which involves the participation of the librational motions of the solvent. The faster relaxation pathway can be rationalized in turn using a sequential kinetic mechanism of the type P-->M+L-->L, where P (parent) is the initially excited amide I mode, and M (medium) and L (low) are specific midrange and lower-frequency NMAD vibrational modes, respectively.

Theoretical Chemistry Accounts, 2011

Intramolecular vibrational dynamics of polyatomic molecules in solution can be addressed through ... more Intramolecular vibrational dynamics of polyatomic molecules in solution can be addressed through normal mode analysis based on either equilibrium normal modes (ENMs) or instantaneous normal modes (INMs). While the former offers a straightforward way of examining experimental spectra, the latter provides a decoupled shorttime description of the vibrational motions of the molecule. In order to reconcile both representations, a realistic assignment of the INMs in terms of the ENMs is needed. In this paper, we describe a novel method to assign the INMs using the ENMs as templates, which provides a unique relationship between the two sets of normal modes. The method is based specifically on the use of the so-called Min-Cost or Min-Sum algorithm, duly adapted to our problem, to maximize the overlaps between the two sets of modes. The identification of the INMs as the system evolves with time then allows us to quantify the vibrational energy stored in each INM and so monitor the flows of intramolecular vibrational energy within the solute molecule. We also discuss the degree of mixing of the INMs and characterize the way they change with time by means of the corresponding autocorrelation functions. The usefulness of the method is illustrated by carrying out equilibrium molecular dynamics (MD) simulations of the deuterated N-methylacetamide (NMAD) molecule in D 2 O solution.

The Journal of Physical Chemistry A, 2010

Nonequilibrium molecular dynamics (MD) simulations and instantaneous normal mode (INMs) analyses ... more Nonequilibrium molecular dynamics (MD) simulations and instantaneous normal mode (INMs) analyses are used to study the vibrational relaxation of the C-H stretching modes (ν(s)(CH₃)) of deuterated N-methylacetamide (NMAD) in aqueous (D2O) solution. The INMs are identified unequivocally in terms of the equilibrium normal modes (ENMs), or groups of them, using a restricted version of the recently proposed Min-Cost assignment method. After excitation of the parent ν(s)(CH₃) modes with one vibrational quantum, the vibrational energy is shown to dissipate through both intramolecular vibrational redistribution (IVR) and intermolecular vibrational energy transfer (VET). The decay of the vibrational energy of the ν(s)(CH₃) modes is well fitted to a triple exponential function, with each characterizing a well-defined stage of the entire relaxation process. The first, and major, relaxation stage corresponds to a coherent ultrashort (τ(rel) = 0.07 ps) energy transfer from the parent ν(s)(CH₃) modes to the methyl bending modes δ(CH₃), so that the initially excited state rapidly evolves into a mixed stretch-bend state. In the second stage, characterized by a time of 0.92 ps, the vibrational energy flows through IVR to a number of mid-range-energy vibrations of the solute. In the third stage, the vibrational energy accumulated in the excited modes dissipates into the bath through an indirect VET process mediated by lower-energy modes, on a time scale of 10.6 ps. All the specific relaxation channels participating in the whole relaxation process are properly identified. The results from the simulations are finally compared with the recent experimental measurements of the ν(s)(CH₃) vibrational energy relaxation in NMAD/D₂O(l) reported by Dlott et al. (J. Phys. Chem. A 2009, 113, 75.) using ultrafast infrared-Raman spectroscopy.

The Journal of Chemical Physics, 2010

A nonequilibrium molecular dynamics (MD) study of the vibrational relaxation of the amide I mode ... more A nonequilibrium molecular dynamics (MD) study of the vibrational relaxation of the amide I mode of deuterated N-methylacetamide (NMAD) in aqueous (D(2)O) solution is carried out using instantaneous normal modes (INMs). The identification of the INMs as they evolve over time, which is necessary to analyze the energy fluxes, is made by using a novel algorithm which allows us to assign unequivocally each INM to an individual equilibrium normal mode (ENM) or to a group of ENMs during the MD simulations. The time evolution of the energy stored in each INM is monitored and the occurrence of resonances during the relaxation process is then investigated. The decay of the amide I mode, initially excited with one vibrational quantum, is confirmed to fit well to a biexponential function, implying that the relaxation process involves at least two mechanisms with different rate constants. By freezing the internal motions of the solvent, it is shown that the intermolecular vibration-vibration channel to the bending modes of the solvent is closed. The INM analysis reveals then the existence of a major and faster decay channel, which corresponds to an intramolecular vibrational redistribution process and a minor, and slower, decay channel which involves the participation of the librational motions of the solvent. The faster relaxation pathway can be rationalized in turn using a sequential kinetic mechanism of the type P-->M+L-->L, where P (parent) is the initially excited amide I mode, and M (medium) and L (low) are specific midrange and lower-frequency NMAD vibrational modes, respectively.