1,720,984 research outputs found
Modeling light-matter interaction in complex embedded systems
No full textSystems in the condensed phase are characterized by a high degree of complexity due to their large size and variety of intermolecular interactions at the microscopic level. Computational spectroscopy is a valuable tool for the investigation of complex systems, but it requires ad hoc modeling able to reduce the computational cost to simulate effectively realistic scenarios. To this end, I have developed a set of computational tools for the calculation of spectroscopic properties of chemical systems embedded in the external environment (solvents or nanostructured plasmonic materials). The first part of the thesis focuses on solvated systems. Starting from the classical, atomistic, and fully polarizable model based on the Fluctuating Charges (Fluctuating Dipoles) force field, I propose two complementary multiscale approaches for the simulation of spectroscopic properties: the first is based on a hybrid quantum-classical description of the environment for the first-principles description of short-range non-electrostatic interactions between solute and solvent. The second aims at cost-effective simulations of absorption spectra of large embedded substrates through the coupling of a polarizable embedding with the Time-Dependent Density Functional Tight-Binding approach. In the second part of the thesis, I focus on the description of surface-enhanced spectroscopies, in which the environment consists of plasmonic nanostructured materials that may impressively amplify the electromagnetic field experienced by the adsorbed target thanks to the surface plasmon resonance phenomenon. In this framework, I extend the classical, atomistic frequency-dependent Fluctuating Charges model to the simulation of the optical properties of noble metal nanoparticles and graphene-based materials composed of millions of atoms. The agreement with ab initio and experimental data is remarkable, also in the case of non-homogeneous plasmonic silver-gold alloyed nanoparticles. The model is then coupled to a DFT Hamiltonian for the simulation of Surface-Enhanced Raman Scattering spectra
Atomistic QM/Classical Modeling of Surface-Enhanced Infrared Absorption
Full text linkWe present a multiscale quantum mechanics/classical (QM/MM) approach for modeling surface-enhanced infrared absorption (SEIRA) spectra of molecules adsorbed on plasmonic nanostructures. The molecular subsystem is described at the density functional theory (DFT) level, while the plasmonic material is represented using fully atomistic, frequency-dependent Fluctuating Charges (omega FQ) and Fluctuating Charges and Dipoles (omega FQF mu) models. These schemes enable an accurate and computationally efficient description of the plasmonic response of both graphene-based materials and noble metal nanostructures, achieving accuracy comparable to that of ab initio methods. The proposed methodology is applied to the calculation of SEIRA spectra of adenine adsorbed on gold nanoparticles and graphene sheets. The quality and robustness of the approach are assessed through comparison with surface-enhanced Raman scattering (SERS) spectra and available experimental data. The results demonstrate that the proposed framework provides a reliable route to simulate vibrational responses of plasmon-molecule hybrid systems
PROCEDIMENTO IN-SILICO DI IDENTIFICAZIONE DEL DESIGN DI UN SENSORE PLASMONICO NANOSTRUTTURATO
No full textEffective yet Reliable Computation of EPR Spectra in Solution by a QM/MM Approach: Interplay between Electrostatics and Non-electrostatic Effects
Full text linkIn this paper, we have extended to the calculation of hyperfine coupling constants, the model recently proposed by some of the present authors
[Giovannini et al., J. Chem. Theory Comput. 13, 4854–4870 (2017)] to include Pauli repulsion and dispersion effects in Quantum Mechanical/
Molecular Mechanics (QM/MM) approaches. The peculiarity of the proposed approach stands in the fact that repulsion/dispersion
contributions are explicitly introduced in the QM Hamiltonian. Therefore, such terms not only enter the evaluation of energetic properties
but also propagate to molecular properties and spectra. A novel parametrization of the electrostatic fluctuating charge force field has
been developed, thus allowing a quantitative reproduction of reference QM interaction energies. Such a parametrization has been then tested
against the prediction of EPR parameters of prototypical nitroxide radicals in aqueous solutions
Quantum dynamics of dissipative polarizable media
No full textClassical polarizable approaches have become the gold standard for simulating complex systems and processes in the condensed phase. These methods describe intrinsically dissipative polarizable media, requiring a formal definition within the framework of open quantum systems. We present a Hamiltonian formulation for the quantum dynamics of polarizable sources based on a generalized theory of the damped harmonic oscillator, using pseudoboson theory to characterize their coherent state dynamics. We then apply our theory to the study of the
optical response of two plasmonic systems. Furthermore, by exploiting the phase-space formulation of quantum
mechanics and the integrability of quadratic Hamiltonians, we derive a self-consistent relation for the emitted
electric field of the polarizable medium under the semiclassical approximation, based on exact formulas for
medium polarization. Finally, we derive the master equation describing the open dynamics of a quantum system
interacting with the quantum polarizable medium, along with analytical expressions for correlation functions
calculated over arbitrary Gaussian states
Correction to “Going Beyond the Limits of Classical Atomistic Modeling of Plasmonic Nanostructures”
Full text linkThis corrects the article DOI: 10.1021/acs.jpcc.1c04716.In the original paper, the Fermi energy values εF are incorrect. This affects the data in Figure 5 and the discussion of numerical results. As reported in ref 29, the Fermi energy can be computed from n2D, i.e., graphene 2D electron density (see eq 8 in the original paper) by exploiting the following equation: (Formula and Table Presented)
Fully Atomistic Modeling of Realistic Plasmonic Materials: Assessing the Performance of Iterative Solvers
Full text linkThe fully atomistic modeling of real-size plasmonic nanostructures is
computationally demanding, therefore most calculations are limited to
small-to-medium sized systems. However, plasmonic properties strongly depend on
the actual shape and size of the samples. In this paper we substantially extend
the applicability of classical, fully atomistic approaches by exploiting
state-of-the-art numerical iterative Krylov-based techniques. In particular, we
focus on the recently developed FQ model, when specified to carbon
nanotubes, graphene-based nanostructures and metal nanoparticles. The
performance of Generalized Minimal Residual (GMRES) and Quasi-Minimum Residual
(QMR) algorithms is studied, with special emphasis on the dependence of the
convergence rate on the dimension of the structures (up to 1 million atoms) and
the physical parameters entering the definition of the atomistic approach.Comment: 15 pages, 15 figure
Modeling Infrared and Vibrational Circular Dichroism Spectra of Complex Systems: the DFTB/Fluctuating Charges Route
No full textSimulating vibrational spectra of large biomolecular systems in aqueous environments remains a challenge in computational chemistry due to the complex interactions between solutes and solvents. In this study, we employ the density functional tight-binding (DFTB) method, coupled with the fluctuating charges (FQ) force field, to simulate infrared (IR) and vibrational circular dichroism (VCD) spectra of solvated large biomolecules. We focus on three representative systems: the doxorubicin/DNA intercalation complex, ubiquitin, and hen egg white lysozyme. By using molecular dynamics (MD) trajectories to sample the conformational space, we compute spectra for multiple snapshots, employing different DFTB Hamiltonians, including SCC-DFTB, DFTB3, and GFN1-xTB. Our results demonstrate the accuracy and computational efficiency of the DFTB/FQ method in reproducing experimental spectral features, particularly for large, solvated systems which cannot be afforded by other ab initio methodologies. The results of this work highlight the potential of DFTB/FQ as a scalable method for simulating vibrational properties in complex molecular systems
Multiscale frozen density embedding/molecular mechanics approach for simulating magnetic response properties of solvated systems
Full text link: We present a three-layer hybrid quantum mechanical/quantum embedding/molecular mechanics approach for calculating nuclear magnetic resonance (NMR) shieldings and J-couplings of molecular systems in solution. The model is based on the frozen density embedding (FDE) and polarizable fluctuating charges (FQ) and fluctuating dipoles (FQFμ) force fields and permits the accurate ab initio description of short-range nonelectrostatic interactions by means of the FDE shell and cost-effective treatment of long-range electrostatic interactions through the polarizable force field FQ(Fμ). Our approach's accuracy and potential are demonstrated by studying NMR spectra of Brooker's merocyanine in aqueous and nonaqueous solutions
Modeling UV/Vis Absorption Spectra of Food Colorants in Solution: Anthocyanins and Curcumin as Case Studies
Full text linkWe present a comprehensive computational study of UV/Vis absorption spectra of significant food colorants, specifically anthocyanins and curcumin tautomers, dissolved in polar protic solvents, namely water and ethanol. The absorption spectra are simulated using two fully polarizable quantum mechanical (QM)/molecular mechanics (MM) models based on the fluctuating charge (FQ) and fluctuating charge and dipoles (FQF mu) force fields. To accurately capture the dynamical aspects of the solvation phenomenon, atomistic approaches are combined with configurational sampling obtained through classical molecular dynamics (MD) simulations. The calculated QM/FQ and QM/FQF mu spectra are then compared with experiments. Our findings demonstrate that a precise reproduction of the UV/Vis spectra of the studied pigments can be achieved by adequately accounting for configurational sampling, polarization effects, and hydrogen bonding interactions
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