1,721,107 research outputs found
Modelling vibrational relaxation in complex molecular systems
No full textIn this paper we show how it is possible to treat the quantum vibrational relaxation of a chromophore, embedded in a complex atomic-molecular environment, via the explicit solution of the time-dependent Schroedinger equation once using a proper separation between quantum and semiclassical degrees of freedom. The rigorous theoretical framework derived, based on first principles and making use of well defined approximations/assumptions, is utilized to construct a general model for the kinetics of the vibrational relaxation as obtained by the direct evaluation of the density matrix for all the relevant quantum state transitions. Application to (deuterated) N-methylacetamide (the typical benchmark used as a model for the amino acids) shows that the obtained theoretical-computational approach captures the essential features of the experimental process, unveiling the basic relaxation mechanism involving several vibrational state transitions
Statistical Mechanics for Chemical Thermodynamics and Kinetics
No full textThis advanced textbook on theoretical chemistry includes all the fundamental concepts and theoretical approaches to be used when modelling a chemical system (i.e., a molecular system). Starting from the basic principles of quantum mechanics and specifically addressing the concepts and methods to treat quantum-classical systems, the authors derive from first principles the fundamental relations of statistical mechanics and then describe their application to chemical thermodynamics and kinetics. This book provides a rigorous description of the fundamental theoretical principles and derivations addressing sophisticated physical-mathematical issues of special interest in chemistry, thus bridging the gap between basic textbooks and up-to-date specialized publications in both quantum mechanics and statistical mechanics of molecular systems. This is a useful resource for all researchers and/or graduate students interested in the field of theoretical chemistry
Absorption and stationary fluorescent spectra of molecular sensors in solution: A computational study
No full textIn this study we report the application and the extension of a theoretical-computational method for the modelling of absorption and stationary emission (electronic) spectra of flexible and easily polarizable chromophores embedded in complex environments. The method, similar but computationally less expensive than the most popular Quantum Mechanics/Molecular Mechanics (QM/MM) approaches, is based on a combination of Molecular Dynamics simulations, Quantum-Chemical calculations and elementary statistical mechanics. As a test case we have addressed, in the present study, the spectral features of two solvated chromophores, experimentally shown by our group to be very sensitive to the solvent (environment) polarity, formed by a 4-[4-(1-dimethylamino)phenyl]-pyridine moiety linked to an uracil group through an alkyl spacer of different lengths. The method, despite the involved approximations and intrinsic drawbacks, is able of reproducing both the absorption and emission spectra of the above system as well as the sharp dependency of the spectral observables on the environment polarity. In this respect it might represent an efficient tool, alternative to more accurate QM/MM-based approaches, in cases where their application could be made computationally very expensive
Statistical mechanical modeling of chemical reactions in complex systems: The reaction free energy surface
No full textIn this paper, the perturbed matrix method (PMM) is used in combination with basic statistical mechanics, to develop a general theoretical method to model chemical reactions and related molecular processes in complex systems, i.e., liquids, biochemical systems, macromolecules, etc. The main feature of this approach consists of the explicit treatment of the coupling between the reaction center and the fluctuating atomic-molecular environment, providing a rigorous statistical mechanical description of the chemical event. A special attention is dedicated to the approximations and assumptions necessary to use such a theoretical procedure in combination with simulation data
Theoretical-computational modeling of charge transfer and intersystem crossing reactions in complex chemical systems
No full textIn this paper we present a theoretical-computational methodology specifically aimed at describing processes involving internal conversion or intersystem crossing, from atomistic (semiclassical) simulations and, hence, very suitable for treating complex atomic-molecular systems. The core of the presented approach is the evaluation of the diabatic perturbed energy surfaces of a portion of the whole system, treated at the quantum level and therefore preventively selected, in semi-classical interaction with the atomic-molecular environment. Subsequently, the estimation of the coupling between the diabatic surfaces and the inclusion of the obtained observables within a properly designed kinetic model allows the reconstruction of the whole phenomenology directly comparable to the experimental (typically kinetic) data. Application to two systems has demonstrated that the proposed approach can represent a valuable tool, somewhat complementary to other methods based on explicit quantum-dynamical approaches, for the theoretical-computational investigations of large and complex atomic-molecular systems
On the Statistical Regime, Coherence versus Incoherence and Ergodicity of Quantum Vibrational Trajectories in Soft Condensed Molecular Systems
No full textA theoretical-computational procedure, recently proposed for modelling Vibrational Energy Relaxation (VER) processes of a molecule (Quantum Center, QC) embedded in a complex atomic-molecular system, is extended and applied for analyzing in detail the features of the QC density matrix (DM) temporal evolution. The results, obtained using aqueous azide ion as a case study, show the total lack of coherence in the DM, when the system is prepared to be initially in a pure vibrational eigenstate. This finding is fully in line with the statistical interpretation of the process typically adopted also in the experimental studies where the relaxation processes are all described within the typical schemes of chemical kinetics. Consistently, when the initial vibrational state corresponds to an eigenstate mixture, although initially coherent, the DM relaxes to a fully incoherent condition with a mean lifetime related to the one of the diagonal elements relaxation. These specific DM features turn out to be essentially governed by the thermal equilibrium condition of the atomic-molecular classical coordinates which drive the ensemble of the quantum-trajectories toward the observed statistical regime. Finally, from the analysis of a single long timescale quantum vibrational trajectory it also clearly emerges its ergodic behaviour.Vibrational Energy Relaxation (VER) is modelled to provide a rigorous investigation on the accuracy of the statistical regime interpretation of VER kinetics and to characterize the decoherence of quantum vibrational states. Results clearly demonstrate that when considering a typical chromophore in solution (the aqueous azide ion) the thermal equilibrium condition of the atomic-molecular classical coordinates determines the statistical behavior of the quantum-trajectories, with the corresponding density operator (always clearly showing an ergodic behavior) either being incoherent within the whole relaxation process or rapidly loosing its initial coherence. imag
Theoretical-computational modelling of the vibrational relaxation of small inorganic species in condensed phase
Full text linkIn this paper we apply a recently developed theoretical-computational procedure for modelling the Vibrational Energy Relaxation (VER) of solvated chromophores represented by small inorganic species. In particular we focus our attention on four different systems, all experimentally well characterized: aqueous cyanide ion and aqueous azide ion, nitrogen dioxide and water both in chloroform. Our method essentially reconstructs the whole vibrational relaxation kinetics (with the chromophore in the ground electronic state) by: (i) determining, through semiclassical Molecular Dynamics (MD) simulation, the electric field (perturbation) produced onto the chromophore by the solvent atom motions; (ii) using the electrostatic perturbation for directly determining the chromophore quantum vibrational dynamics; (iii) calculating the rate constant for the vibrational relaxation as occurring without quantum-classical energy exchange; (iv) introducing the latter effect, a posteriori, hence obtaining the actual relaxation kinetics. Our results, in satisfactory agreement with the available experimental data, show that the VER mechanism is almost entirely determined by the fluctuating perturbation field as produced by the time-dependent motions of the environment atoms (in these cases the solvent) similarly to the well-known effects of the electromagnetic wave causing absorption/emission processes
Revisiting the “Cluster-In-Solvent” Approach for Computational Spectroscopy: The Vibrational Circular Dichroism as a Test Case
Full text linkThe cluster-in-solvent approach, that is, the use of the quantum-mechanical calculation of a spectral observable on a significant number of solute–solvent clusters extracted from semi-classical simulations, is widely used in computational spectroscopy. However, identifying relevant coordinates for cluster selection remains a challenge. We previously developed the Ellipsoid Method for Cluster-in-Solvent (EMCS), an automated strategy for unbiased identification and statistical weighting of clusters. Yet, for larger solutes, EMCS can yield overly large solvent clusters that hinder conformational analysis. Here, we introduce a simple extension of EMCS that reduces cluster size, enabling its application to medium-to-large solutes. The method is validated through the computation of Vibrational Circular Dichroism (VCD) spectra, which are highly sensitive to solute–solvent interactions. Test cases include aqueous L-alanine, aqueous dialanine, and (1S,2S)-trans-1-amino-2-indanol in DMSO. For L-alanine and trans-1-amino-2-indanol, computed spectra closely match experiment, with root-mean-square-deviation (RMSD) values of 10.3 and 8.0, respectively, consistent with previous benchmarks. For aqueous dialanine, the main spectral features were reproduced, though discrepancies in the fine structure remain, likely due to limitations in capturing subtle solvation effects. Overall, the refined EMCS protocol enables efficient and non-arbitrary sampling of solute–solvent clusters, offering a valuable tool for the structural analysis of solvation shells in complex molecular systems
A general theoretical model for electron transfer reactions in complex systems
No full textIn this paper we present a general theoretical-computational model for treating electron transfer reactions in complex atomic-molecular systems. The underlying idea of the approach, based on unbiased first-principles calculations at the atomistic level, utilizes the definition and the construction of the Diabatic Perturbed states of the involved reactive partners (i.e. the quantum centres in our perturbation approach) as provided by the interaction with their environment, including their mutual interaction. In this way we reconstruct the true Adiabatic states of the reactive partners characterizing the electron transfer process as the fluctuation of the electronic density due to the fluctuating perturbation. Results obtained by using a combination of Molecular Dynamics simulation and the Perturbed Matrix Method on a prototypical intramolecular electron transfer (from 2-(9,9'-dimethyl) fluorene to the 2-naphthalene group separated by a steroidal 5-alpha-androstane skeleton) well illustrate the accuracy of the method in reproducing both the thermodynamics and the kinetics of the process
Theoretical–Computational Modeling of CD Spectra of Aqueous Monosaccharides by Means of Molecular Dynamics Simulations and Perturbed Matrix Method
Full text linkThe electronic circular dichroism (ECD) spectra of aqueous d-glucose and d-galactose were modeled using a theoretical–computational approach combining molecular dynamics (MD) simulations and perturbed matrix method (PMM) calculations, hereafter termed MD-PMM. The experimental spectra were reproduced with a satisfactory accuracy, confirming the good performances of MD-PMM in modeling different spectral features in complex atomic–molecular systems, as already reported in previous studies. The underlying strategy of the method was to perform a preliminary long timescale MD simulation of the chromophore followed by the extraction of the relevant conformations through essential dynamics analysis. On this (limited) number of relevant conformations, the ECD spectrum was calculated via the PMM approach. This study showed that MD-PMM was able to reproduce the essential features of the ECD spectrum (i.e., the position, the intensity, and the shape of the bands) of d-glucose and d-galactose while avoiding the rather computationally expensive aspects, which were demonstrated to be important for the final outcome, such as (i) the use of a large number of chromophore conformations; (ii) the inclusion of quantum vibronic coupling; and (iii) the inclusion of explicit solvent molecules interacting with the chromophore atoms within the chromophore itself (e.g., via hydrogen bonds)
- …
