Solvatochromic shifts vs nanosolvation patterns: Uracil in water as a test case

Zazza, Costantino; Olsen, Jógvan Magnus Haugaard; Kongsted, Jacob

doi:10.1016/j.comptc.2011.07.020

Cited by 6 publications

(11 citation statements)

References 56 publications

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“…However, CIS showed the bright transition for uracil is from S 0 to S 1 , whereas this result is inconsistent with most other (gas phase) computations that determine the bright transition to be S 0 → S 2 . 36,37,39,43,44 The solvent effects on uracil and its excited-state properties have been studied using implicit models [22][23][24]26 and explicit solvent treatments via uracil−water complexes, 26,27,30,45,46 QM/ MM, 25 the effective fragment potential water model, 29 and also the fragment molecular orbital method. 28 However, the effect of solvent on the resonance Raman spectrum of uracil has not yet been investigated.…”

Section: Introductionmentioning

confidence: 99%

“…We focus on uracil in part due to the challenges associated with the computational determination of the states involved in its UV–vis absorption, for example, reordering of the π → π* and n → π*excited states due to solvation. ,,− TD-DFT is used to simulate the resonance Raman spectrum of uracil and to assist in the interpretation of its experimental spectrum . The chemical structure and the atomic indices of uracil are shown in Figure .…”

Section: Introductionmentioning

confidence: 99%

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Simulation of the Resonance Raman Spectrum for Uracil

Sun

Brown

2014

J. Phys. Chem. A

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The resonance Raman spectrum of uracil is simulated using the Herzberg-Teller short-time dynamics formalism. The ground-state geometry is optimized at the levels of PBE0/aug-cc-pVTZ and B3LYP/aug-cc-pVTZ, respectively. The gradient of the bright excited state is computed using time-dependent density functional theory and spin-flip time-dependent density functional theory. The excited-state calculations are carried out in both the gas phase and implicit water using the conductor-like polarizable continuum model. The ground-state equilibrium structure is found to impact the resulting resonance Raman spectrum significantly. The simulated resonance Raman spectrum using the long-range corrected functionals, that is, CAMB3LYP and LC-BLYP, and based on the PBE0/aug-cc-pVTZ optimized ground-state structure shows better agreement with the experimental spectrum than using standard hybrid functionals, that is, PBE0 and B3LYP. The solvation effect leads to a change in the energetic order of the n → π* and π → π* excited states, and it improves the agreement with the experimental spectrum, especially with regard to the relative intensities of the peaks with frequencies greater than 1600 cm(-1).

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Simulation of the Resonance Raman Spectrum for Uracil

Sun

Brown

2014

J. Phys. Chem. A

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“…(16) (17) In these equations, ρ(ν) is the probability density of the vertical transition frequency, ν ref , n(ν ref ), and |μ 0,i | ν ref 2 are the frequency at the center of each bin, the corresponding number of MD frames, and mean transition dipole square norm within the bin, respectively. Moreover, ℏ = h/(2π) with h being the Planck constant, ϵ 0 is the vacuum dielectric constant, c is the light speed, and σ 2 is the variance produced by the semiclassical vibrations due to other semi-classical internal coordinates neglected in eqs 14 and 15 (σ = 0.0011 a.u.…”

Section: Methodsmentioning

confidence: 99%

“…The Perturbed Matrix Method (PMM) − is used to study the quantum mechanical behavior of localized phenomena in a complex system. − At variance with gas phase, events occurring in condensed phases involve contributions characterized by strongly different energy and time regimes, tuned, in general, by a huge number of degrees of freedom. In such cases, a brute force first-principle strategy in which the forces of the whole system are computed on the fly is hardly feasible unless oversimplified quantum mechanical models are employed. − Whenever one is interested in local phenomena tuned by the environment, hybrid Quantum-Mechanics–Molecular-Mechanics (QM/MM) approaches are the methods of choice for reliable yet feasible simulations.…”

Section: Introductionmentioning

confidence: 99%

Flexible and Comprehensive Implementation of MD-PMM Approach in a General and Robust Code

Carrillo

Galdo

Aschi

et al. 2017

J. Chem. Theory Comput.

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The Perturbed Matrix Method (PMM) approach to be used in combination with Molecular Dynamics (MD) trajectories (MD-PMM) has been recoded from scratch, improved in several aspects, and implemented in the Gaussian suite of programs for allowing a user-friendly and yet flexible tool to estimate quantum chemistry observables in complex systems in condensed phases. Particular attention has been devoted to a description of rigid and flexible quantum centers together with powerful essential dynamics and clustering approaches. The default implementation is fully black-box and does not require any external action concerning both MD and PMM sections. At the same time, fine-tuning of different parameters and use of external data are allowed in all the steps of the procedure. Two specific systems (Tyrosine and Uridine) have been reinvestigated with the new version of the code in order to validate the implementation, check the performances, and illustrate some new features.

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“…54,56,65,66 One important aspect is that for these two excitations two quite different shifts are obtained upon solvation: The n → π * transition, the lowest excitation in vacuum, experiences a strong blue shift of about +0.5 eV while a clear red shift of about −0.2 eV is found for the π → π * transition, the second-lowest excitation, eventually leading to an inverted order for the two connected excited states due to the fact that they are only separated by about 0.4 eV in vacuum. For uracil it is thus in particular necessary to obtain also the correct order of these two states, which can be used to assess the accuracy of a method.…”

Section: B Uracil In Watermentioning

confidence: 99%

Solvatochromic shifts from coupled-cluster theory embedded in density functional theory

Höfener¹,

Gomes

Visscher³

2013

The Journal of Chemical Physics

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Building on the framework recently reported for determining general response properties for frozen-density embedding [S. Höfener, A. S. P. Gomes, and L. Visscher, J. Chem. Phys. 136, 044104 (2012)], in this work we report a first implementation of an embedded coupled-cluster in density-functional theory (CC-in-DFT) scheme for electronic excitations, where only the response of the active subsystem is taken into account. The formalism is applied to the calculation of coupled-cluster excitation energies of water and uracil in aqueous solution. We find that the CC-in-DFT results are in good agreement with reference calculations and experimental results. The accuracy of calculations is mainly sensitive to factors influencing the correlation treatment (basis set quality, truncation of the cluster operator) and to the embedding treatment of the ground-state (choice of density functionals). This allows for efficient approximations at the excited state calculation step without compromising the accuracy. This approximate scheme makes it possible to use a first principles approach to investigate environment effects with specific interactions at coupled-cluster level of theory at a cost comparable to that of calculations of the individual subsystems in vacuum.

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Solvatochromic shifts vs nanosolvation patterns: Uracil in water as a test case

Cited by 6 publications

References 56 publications

Simulation of the Resonance Raman Spectrum for Uracil

Simulation of the Resonance Raman Spectrum for Uracil

Flexible and Comprehensive Implementation of MD-PMM Approach in a General and Robust Code

Solvatochromic shifts from coupled-cluster theory embedded in density functional theory

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