1,721,071 research outputs found
Implementation and validation of DFT-D for molecular vibrations and dynamics: The benzene dimer as a case study
No full textSemi-empirical correction to density functional theory for dispersion (DFT-D) has been implemented for energies, analytical gradients, and Hessians in order to explore potential energy surfaces by means of a complete set of first-principle methods. The impact of nonbonding interactions on structures, binding energies and zero-point energy contributions as well as on ab initio molecular dynamics trajectories have been investigated for the well known case of benzene dimer. While the static results are in remarkable agreement with the most sophisticated post-Hartree-Fock approaches, the low cost of DFT-D allows to unravel dynamical aspects too, which are mandatory for situations ruled by weak interactions
Non-periodic boundary conditions for ab initio molecular dynamics in condensed phase using localized basis functions
No full textComputation of protein pK's values by an integrated density functional theory/polarizable contimuum model approach
No full textThis paper describes the extension of our computational strategy for pK predictions of small molecules to large solutes. The basic computational tool results from the coupling of quantum mechanical methods rooted in the density functional theory with the most recent version of the Polarizable Continuum Model. However, a third level is introduced, which includes solute regions far from the reactive center, which are described at a simplified level. This partition, together with the recent implementation of fast cavity generation, powerful iterative solvers, and fast multipole technology, allows us to tackle solutes of the dimension of a small protein. The problems and perspectives of this methodology are analyzed with special reference to the behavior of different Polarizable Continuum Model versions on the challenging playground represented by the pK's of the different histidine residues occurring in the human prion protein
Accurate density functional calculations of near-edge X-ray and optical absorption spectra of liquid water using nonperiodic boundary conditions: The role of self-interaction and long-range effects
No full textMicrosolvation of the Zn(II) ion in aqueous solution: A hybrid QM/MM MD approach using non-periodic boundary conditions
No full textQuantum mechanical computations and spectroscopy: From small rigid molecules in the gas phase to large flexible molecules in solution
No full textInterpretation of structural properties and dynamic behavior of molecules in solution is of fundamental importance to understand their stability, chemical reactivity, and catalytic action. While information can be gained, in principle, by a variety of spectroscopic techniques, the interpretation of the rich indirect information that can be inferred from the analysis of experimental spectra is seldom straightforward because of the subtle interplay of several different effects, whose specific role is not easy to separate and evaluate. In such a complex scenario, theoretical studies can be very helpful at two different levels: (i) supporting and complementing experimental results to determine the structure of the target molecule starting from its spectral properties; (ii) dissecting and evaluating the role of different effects in determining the observed, spectroscopic properties. This is the reason why computational spectroscopy is rapidly evolving from a highly specialized research field into a versatile and widespread tool for the assignment of experimental spectra and their interpretation in terms of chemical physical effects. In such a situation, it becomes important that both computationally and experimentally oriented chemists are aware that new methodological advances and integrated computational strategies are available, providing reliable estimates of fundamental spectral parameters not only for relatively small molecules in the gas phase but also for large and flexible molecules in condensed phases.In this Account, we review the most significant methodological contributions from our research group in this field, and by exploiting some recent results of their application to the computation of IR, UV-vis, NMR, and EPR spectral parameters, we discuss the microscopic mechanisms underlying solvent and vibrational effects on the spectral parameters.After reporting some recent achievements for the study of excited states by first principle quantum mechanical approaches, we focus on the treatment of environmental effects by means of mixed discrete-continuum solvent models and on effective methods for computing vibronic contributions to the spectra. We then discuss some new developments, mainly based on time-dependent approaches, allowing us to go beyond the determination of spectroscopic parameters toward the simulation of line widths and shapes.Although further developments are surely needed to improve the accuracy and effectiveness of several items in the proposed approach, we try to show that the first important steps toward a direct. comparison between the results obtained in vitro and those obtained in silico have been made, making easier fruitful crossovers among experiments, computations and theoretical models, which would be decisive for a deeper understanding of the spectral behavior associated with complex systems and processes
Theoretical study of the electronic structure and absorption spectra of molecular liquids
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