1,721,060 research outputs found
Non covalent interactions in RNA and DNA base pairs: a quantum-mechanical study of the coupling between solvent and electronic density
No full textIt is well-known that a solvent can modify the relative importance of the different constituents (electrostatic and dispersion) of non-covalent interactions, but much less is known about how these solvent-induced modifications specifically couple with the polarization of the electronic
density and electronic correlation. Here we present a quantum mechanical analysis of the effects of the solvent on the non covalent interactions (both stacking and hydrogen bonding) in base pairs using a hierarchy of combinations between a MP2 correlated description for the
base pairs and the polarizable continuum model (PCM) for the solvent. A comparison of the results obtained in these different combinations of increasing accuracy allows us to better analyze the important role played by the coupling between correlated electronic densities and solvent polarization in determining the relative importance of stacking and hydrogen bonding effects
Energies, structures and electronic properties of molecules in solution with the C-PCM solvation model
No full textFinite elements molecular surfaces in continuum solvent models for large chemical systems
No full textSolvation of Coumarin 153 in Supercritical Fluoroform
No full textWe present a study of local density augmentation around an attractive solute (i.e., giving rise to more attractive interaction with the solvent than solvent-solvent interactions) in supercritical fluoroform. This work is based on molecular dynamics simulations of coumarin 153 in supercritical fluoroform at densities both above and below the critical density, ranging from dilute gaslike to liquidlike, at a reduced temperature (T/Tc) of 1.03. We focused on studying the structure of the solvation shell and the variation of the solute electronic absorption and emission shifts with density. Quantum calculations at the density functional theory (DFT) level were run on the solute in the ground state, and time-dependent DFT calculations were performed in the solute excited state in order to determine the solute-solvent potential parameters. The results obtained for the Stokes shift are in agreement with the experimental measurements. To evaluate local density augmentation from simulations, we used two different definitions, one based on the solvation number and the other derived from solvatochromic shifts. In the former case, the agreement with experimental results is good, while, in the latter case, better agreement is achieved by perturbatively including the induced-dipole contribution to the solvation energy
On the Calculation of Vibrational Frequencies for Molecules in Solution Beyond the Harmonic Approximation
No full textWe report some results on the calculation of vibrational spectra of molecules in condensed phase with accounting simultaneously for anharmonicity and solute-solvent
interactions, the latter being described by means of the polarizable continuum model (PCM).
Density functional theory force fields are employed as well as a new implementation of the
PCM cavity and its derivatives. The results obtained for formaldehyde and simple peptide
prototypes show that our approach is able to yield a quantitative agreement with experiments
for vacuo-to-solvent harmonic and anharmonic frequency shifts
How the environment controls absorption and fluorescence spectra of PRODAN: a quantum-mechanical study in homogeneous and heterogeneous media
No full textThe spectroscopic behavior of 6-propionyl-2-(N,N-dimethyl)aminonaphthalene (PRODAN) is investigated in different environments, ranging from homogeneous solutions of different polarities to diffuse interfaces mimicking membranes. The variety of experimental data as well as computational results present in the literature still do not clarify the nature of the emission process; in particular, it is not well-established whether fluorescence in such a molecule occurs from a planar or from a twisted intramolecular charge transfer state. The first part of the work is thus devoted to better understand how the electronic transition processes occur in homogeneous solvents. The effect of the medium polarity as well as the hydrogen bond formation are studied. In the second part of the paper, a first attempt to interpret the experimental results of PRODAN in unilamellar vesicles is carried out. The complexity of the still-open questions about the photophysics of PRODAN has prompted us to base the study on quantum-mechanical calculations performed at various levels of theory, namely, DFT, TDDFT, CIS, and SAC-CI, and to include the effects of the environment in a self-consistent way. This is achieved by using the integral equation formalism version of the polarizable continuum model (IEFPCM). IEFPCM is a quite versatile approach, being able to treat equilibrium and nonequilibrium solvation in both homogeneous and heterogeneous media
Self Consistent Field and Polarizable Continuum Model: a new strategy of solution for the coupled equations
No full textWe present a new strategy for the solution of the self-consistent field (SCF) equations when solvent effects are included by means of the polarizable continuum model (PCM). By exploiting the recently introduced variational formalism of the PCM (VPCM), we are able to recast the self-consistent reaction field problem as an energy functional of both electronic and polarization degrees of freedom. The variational minimization of such a functional leads to the free energy of the solvated molecule at a given geometry. In this contribution we describe an effective procedure and its implementation to achieve the solution of such a variational problem. Moreover, we present numerical evidence that the new approach is superior to the traditional one in terms of performance, especially when a relatively inexpensive semiempirical method is used to describe medium- and large-size solutes
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
A state-specific polarizable continuum model time dependent density functional theory method for excited state calculations in solution
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