1,721,048 research outputs found
Development of fully atomistic approaches to model response properties of complex systems
Full text linkKohn–Sham fragment energy decomposition analysis
Full text linkWe introduce the concept of Kohn-Sham fragment localized molecular orbitals (KS-FLMOs), which are Kohn-Sham molecular orbitals (MOs) localized in specific fragments constituting a generic molecular system. In detail, we minimize the local electronic energies of various fragments, while maximizing the repulsion between them, resulting in the effective localization of the MOs. We use the developed KS-FLMOs to propose a novel energy decomposition analysis, which we name Kohn-Sham fragment energy decomposition analysis, which allows for rationalizing the main non-covalent interactions occurring in interacting systems both in vacuo and in solution, providing physical insights into non-covalent interactions. The method is validated against state-of-the-art energy decomposition analysis techniques and with high-level calculations
Mixed quantum/classical approach to surface-enhanced spectroscopies
Full text linkWe present a novel theoretical approach to calculate the optical response of molecular systems interacting with plasmonic substrates, either metallic or graphene-based
The UV-Visible Absorption Spectra of Coumarin and Nile Red in Aqueous Solution : A Polarizable QM/MM Study
Full text linkWe present a comprehensive computational study of the UV-visible absorption spectra of 7-methoxycoumarin and Nile red in aqueous solution. Our fully atomistic workflow couples classical molecular dynamics (MD) with polarizable QM/MM based on fluctuating charges (QM/FQ) and dipoles (QM/FQF mu). Ensemble-averaged spectra are constructed from the snapshots extracted from the MD, embedding solvent fluctuations and specific solute-solvent interactions in the electronic response of organic dyes. The spectral profiles, obtained at the various levels, reflect the underlying solute-solvent interactions and dynamics, and we rationalize them in terms of hydrogen bonding and frontier molecular orbitals involved in the main electronic transitions. Finally, the simulated spectra and solvatochromic shifts are compared with the available experimental data, showing an overall good agreement and demonstrating the robustness of the computational protocol
Molecular spectroscopy of aqueous solutions: a theoretical perspective
Full text linkComputational spectroscopy is an invaluable tool to both accurately reproduce the spectra of molecular systems and provide a rationalization for the underlying physics. However, the inherent difficulty to accurately model systems in aqueous solutions, owing to water's high polarity and ability to form hydrogen bonds, has severely hampered the development of the field. In this tutorial review we present a technique developed and tested in recent years based on a fully atomistic and polarizable classical modeling of water coupled with a quantum mechanical description of the solute. Thanks to its unparalleled accuracy and versatility, this method can change the perspective of computational and experimental chemists alike
Time-Dependent Multilevel Density Functional Theory
Full text linkWe present a novel three-layer approach based on multilevel density functional theory (MLDFT) and polarizable molecular mechanics to simulate the electronic excitations of chemical systems embedded in an external environment within the time-dependent DFT formalism. In our method, the electronic structure of a target system, the chromophore, is determined in the field of an embedded inactive layer, which is treated as frozen. Long-range interactions are described by employing the polarizable fluctuating charge (FQ) force field. The resulting MLDFT/FQ thus accurately describes both electrostatics (and polarization) and non-electrostatic target-environment interactions. The robustness and reliability of the approach are demonstrated by comparing our results with experimental data reported for various organic molecules in solution
Fully atomistic modeling in computational spectroscopy: tryptophan in aqueous solution as a test case
Full text linkWe present a multiscale computational protocol for the simulation of a wide range of spectroscopic properties─electronic, magnetic, and vibrational─of zwitterionic l-tryptophan in aqueous solution. The approach combines density functional theory (DFT) for the solute with polarizable embedding models (QM/FQ and QM/FQFμ) for the solvent, and incorporates extensive conformational sampling via classical molecular dynamics. The protocol successfully reproduces UV-vis and ECD spectra, including the characteristic S0 → S1 transition and chiroptical features, and captures the negative optical rotation at the sodium D-line with good agreement to experiment. NMR chemical shifts and spin-spin couplings are also computed, and a hybrid QM/FDE/FQFμ scheme is employed to improve the description of solvent-sensitive nuclei. Vibrational spectra (IR, Raman, and ROA) are calculated and analyzed, with all models yielding results consistent with experimental data where available. The comparison between QM/FQ and QM/FQFμ highlights the importance of accurate solvent treatment, especially for chiroptical and magnetic properties
Modeling Raman Spectra in Complex Environments : from Solutions to Surface-Enhanced Raman Scattering
Full text linkThis perspective highlights the essential physicochemical factors required for accurate computational modeling of Raman and Resonance Raman signals in complex environments. It highlights the theoretical challenges for obtaining a balanced quantum mechanical description of the molecular target, integration of target-environment interactions into the Hamiltonian, and explicit treatment of strong interactions such as hydrogen bonding. The dynamical sampling of solute-solvent phase space and the incorporation of plasmonic effects for Surface-Enhanced Raman Scattering (SERS) are also addressed. Through selected applications, we illustrate how these factors influence Raman signals and propose a framework to tackle these challenges effectively, advancing the reliability of theoretical Raman spectroscopy in real-world scenarios
Continuum vs. atomistic approaches to computational spectroscopy of solvated systems
Full text linkMolecular spectral signals can be significantly altered by solvent effects. Among the many theoretical approaches to this problem, continuum and atomistic solvation models have emerged as the most effective for properly describing solvent effects on the spectroscopic signal. In this feature article, we review the continuum and atomistic descriptions as applied to the calculation of molecular spectra, by detailing the similarities and differences between the two approaches from the formal point of view and by analyzing their advantages and disadvantages from the computational point of view. Various spectral signals, of increasing complexity, are considered and illustrative examples, selected to exacerbate the differences between the two approaches, are discussed
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
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