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      On the use of the pseudo-diatomic model for experimental evaluation of stabilization energies of weakly bound molecular complexes

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          Stabilization energies of weakly bound molecular complexes, relative to the isolated monomers constituents, have been evaluated experimentally using the pseudo-diatomic (PD) model employing a Lennard-Jones 6-12 potential (LJ), here denominated the PD-LJ model. This method uses spectroscopic data to estimate the potential depth of weakly bound species. In this work we report a systematic comparison between high level ab initio stabilization energy values and the respective experimental data available for a series of binary complexes, aiming to assess the efficaciousness of the PD-LJ model.

          Translated abstract

          Energias de estabilização para complexos moleculares fracamente ligados, relativas aos monomeros isolados, tem sido determinadas experimentalmente através do modelo pseudo-diatômico (PD) o qual faz uso de um potencial do tipo Lennard-Jones 6-12 (LJ), aqui denominado modelo PD-LJ. Este método utiliza dados espectroscópicos para avaliar a profundidade do poço de potencial para sistemas fracamente ligados. Neste trabalho é mostrada uma comparação sistemática entre valores experimentais de energias de estabilização disponíveis na literatura e calculados à nível ab initio para uma série de complexos binários, objetivando avaliar a eficácia do modelo PD-LJ.

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          Most cited references 73

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          Resonating valence bond wave function with molecular orbitals: Application to first-row molecules

          We introduce a method for accurate quantum chemical calculations based on a simple variational wave function, defined by a single geminal that couples all the electrons into singlet pairs, combined with a real space correlation factor. The method uses a constrained variational optimization, based on an expansion of the geminal in terms of molecular orbitals. It is shown that the most relevant non-dynamical correlations are correctly reproduced once an appropriate number \(n\) of molecular orbitals is considered. The value of \(n\) is determined by requiring that, in the atomization limit, the atoms are described by Hartree-Fock Slater determinants with Jastrow correlations. The energetics, as well as other physical and chemical properties, are then given by an efficient variational approach based on standard quantum Monte Carlo techniques. We test this method on a set of homonuclear (Be2, B2, C2, N2, O2, and F2) and heteronuclear (LiF, and CN) dimers for which strong non-dynamical correlations and/or weak van der Waals interactions are present.
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            Puckering Free Energy of Pyranoses: an NMR and Metadynamics--Umbrella Sampling Investigation

            We present the results of a combined metadynamics--umbrella sampling investigation of the puckered conformers of pyranoses described using the gromos 45a4 force field. The free energy landscape of Cremer--Pople puckering coordinates has been calculated for the whole series of alpha and beta aldohexoses, showing that the current force field parameters fail in reproducing proper puckering free energy differences between chair conformers. We suggest a modification to the gromos 45a4 parameter set which improves considerably the agreement of simulation results with theoretical and experimental estimates of puckering free energies. We also report on the experimental measurement of altrose conformers populations by means of NMR spectroscopy, which show good agreement with the predictions of current theoretical models.
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              Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states.

              Molecular dynamics simulation generates large quantities of data that must be interpreted using physically meaningful analysis. A common approach is to describe the system dynamics in terms of transitions between coarse partitions of conformational space. In contrast to previous work that partitions the space according to geometric proximity, the authors examine here clustering based on kinetics, merging configurational microstates together so as to identify long-lived, i.e., dynamically metastable, states. As test systems microsecond molecular dynamics simulations of the polyalanines Ala(8) and Ala(12) are analyzed. Both systems clearly exhibit metastability, with some kinetically distinct metastable states being geometrically very similar. Using the backbone torsion rotamer pattern to define the microstates, a definition is obtained of metastable states whose lifetimes considerably exceed the memory associated with interstate dynamics, thus allowing the kinetics to be described by a Markov model. This model is shown to be valid by comparison of its predictions with the kinetics obtained directly from the molecular dynamics simulations. In contrast, clustering based on the hydrogen-bonding pattern fails to identify long-lived metastable states or a reliable Markov model. Finally, an approach is proposed to generate a hierarchical model of networks, each having a different number of metastable states. The model hierarchy yields a qualitative understanding of the multiple time and length scales in the dynamics of biomolecules.

                Author and article information

                Role: ND
                Journal of the Brazilian Chemical Society
                J. Braz. Chem. Soc.
                Sociedade Brasileira de Química (São Paulo )
                : 8
                : 1
                : 77-82
                [1 ] Universidade Federal de Minas Gerais Brazil
                Product Information: website

                General chemistry

                stabilization energy, weakly bound complexes, ab initio, pseudo-diatomic model


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