The Experts below are selected from a list of 57 Experts worldwide ranked by ideXlab platform

Andrea C. Vaiana - One of the best experts on this subject based on the ideXlab platform.

  • Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue?
    Journal of chemical theory and computation, 2007
    Co-Authors: Pascal Auffinger, Thomas E. Cheatham, Andrea C. Vaiana
    Abstract:

    Realistic all-atom simulation of biological systems requires accurate modeling of both the biomolecules and their ionic environment. Recently, ion nucleation phenomena leading to the rapid growth of KCl or NaCl clusters in the vicinity of biomolecular systems have been reported. To better understand this phenomenon, molecular dynamics simulations of KCl aqueous solutions at three (1.0, 0.25, and 0.10 M) concentrations were performed. Two popular water models (TIP3P and SPC/E) and two Lennard-Jones Parameter sets (AMBER and Dang) were combined to produce a total of 80 ns of molecular dynamics trajectories. Results suggest that the use of the Dang cation Lennard-Jones Parameters instead of those adopted by the AMBER force-field produces a more accurate description of the ionic solution. In the later case, formation of salt aggregates is probably indicative of an artifact resulting from misbalanced force-field Parameters. Because similar results were obtained with two different water Parameter sets, the simu...

  • Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue?
    Journal of Chemical Theory and Computation, 2007
    Co-Authors: Pascal Auffinger, Thomas E. Cheatham Iii, Andrea C. Vaiana
    Abstract:

    Realistic all-atom simulation of biological systems requires accurate modeling of both the biomolecules and their ionic environment. Recently, ion nucleation phenomena leading to the rapid growth of KCl or NaCl clusters in the vicinity of biomolecular systems have been reported. To better understand this phenomenon, molecular dynamics simulations of KCl aqueous solutions at three (1.0, 0.25, and 0.10 M) concentrations were performed. Two popular water models (TIP3P and SPC/E) and two Lennard-Jones Parameter sets (AMBER and Dang) were combined to produce a total of 80 ns of molecular dynamics trajectories. Results suggest that the use of the Dang cation Lennard-Jones Parameters instead of those adopted by the AMBER force-field produces a more accurate description of the ionic solution. In the later case, formation of salt aggregates is probably indicative of an artifact resulting from misbalanced force-field Parameters. Because similar results were obtained with two different water Parameter sets, the simulations exclude a water model dependency in the formation of anomalous ionic clusters. Overall, the results strongly suggest that for accurate modeling of ions in biomolecular systems, great care should be taken in choosing balanced ionic Parameters even when using the most popular force-fields. These results invite a reexamination of older data obtained using available force-fields and a thorough check of the quality of current Parameters sets by performing simulations at finite (>0.25 M) instead of minimal salt conditions.

Angel Mulero - One of the best experts on this subject based on the ideXlab platform.

  • Prediction of the enthalpy of vapourisation for anhydrides, formates, acetates, propionates, butyrates, esters, and ethers
    Physics and Chemistry of Liquids, 2008
    Co-Authors: I. Cachadiña, Angel Mulero, M.i. Parra
    Abstract:

    Four analytical correlations based on the use of the corresponding states principle were used to calculate the enthalpy of vapourisation of fluids. Three of these correlations require as inputs the critical temperature and the acentric factor. The fourth requires a molecular Lennard–Jones Parameter and the acentric factor. Results for 184 polar and non-polar fluids grouped into 9 families are compared with the values accepted by the Design Institute for Physical Property (DIPPR) project. Recommendations are given for the use of each model and for the choice of the adequate model for each family of fluids.

  • Vaporization Enthalpy: Corresponding-States Correlations Versus DIPPR Database
    Journal of Physical and Chemical Reference Data, 2007
    Co-Authors: I. Cachadiña, Angel Mulero
    Abstract:

    Data for the vaporization enthalpy accepted in the Design Institute for Physical Property Data® (DIPPR®) database are compared with those given by general correlations based on the corresponding-states method. In particular, four analytical predictive correlations were used. Three of them require as input the critical temperature and the acentric factor. The fourth requires a molecular Lennard-Jones Parameter and the acentric factor. Results obtained for 1576 fluids indicate that the recommended model for an overall use, in order to reproduce the DIPPR data, is the one proposed by Sivaraman et al. [Ind. Eng. Chem. Fundam. 23, 97 (1984)].

  • Evaluation of correlations for prediction of the normal boiling enthalpy
    Fluid Phase Equilibria, 2006
    Co-Authors: I. Cachadiña, Angel Mulero
    Abstract:

    Abstract Ten analytical models were used to calculate the enthalpy of vaporization of fluids at the boiling temperature. The correlations considered were six specific expressions valid only at that temperature, and four general correlations valid for any temperature. Most of these models require as inputs the critical properties and the acentric factor, but one of the specific models requires only the molecular weight (and, obviously, the boiling temperature). One of the models is a correlation requiring a molecular Lennard–Jones Parameter and the acentric factor as inputs. Results for 290 fluids are compared with the values given by the DIPPR project.

  • Boiling enthalpy from correlations Results for 83 families of fluids
    Thermochimica Acta, 2006
    Co-Authors: Angel Mulero, I. Cachadiña
    Abstract:

    Ten analytical models were used to calculate the enthalpy of vaporization of fluids at the boiling temperature. The correlations considered were six specific expressions valid only at that temperature, and four general correlations valid for any temperature. Most of these models require as inputs the critical properties and the acentric factor, but one of the specific models requires only the molecular weight (and, obviously, the boiling temperature). One of the models is a correlation requiring a molecular Lennard-Jones Parameter and the acentric factor as inputs. Results for 1591 polar and non-polar fluids, grouped into 83 families, are compared with the values given by the DIPPR project.

Pascal Auffinger - One of the best experts on this subject based on the ideXlab platform.

  • Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue?
    Journal of chemical theory and computation, 2007
    Co-Authors: Pascal Auffinger, Thomas E. Cheatham, Andrea C. Vaiana
    Abstract:

    Realistic all-atom simulation of biological systems requires accurate modeling of both the biomolecules and their ionic environment. Recently, ion nucleation phenomena leading to the rapid growth of KCl or NaCl clusters in the vicinity of biomolecular systems have been reported. To better understand this phenomenon, molecular dynamics simulations of KCl aqueous solutions at three (1.0, 0.25, and 0.10 M) concentrations were performed. Two popular water models (TIP3P and SPC/E) and two Lennard-Jones Parameter sets (AMBER and Dang) were combined to produce a total of 80 ns of molecular dynamics trajectories. Results suggest that the use of the Dang cation Lennard-Jones Parameters instead of those adopted by the AMBER force-field produces a more accurate description of the ionic solution. In the later case, formation of salt aggregates is probably indicative of an artifact resulting from misbalanced force-field Parameters. Because similar results were obtained with two different water Parameter sets, the simu...

  • Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue?
    Journal of Chemical Theory and Computation, 2007
    Co-Authors: Pascal Auffinger, Thomas E. Cheatham Iii, Andrea C. Vaiana
    Abstract:

    Realistic all-atom simulation of biological systems requires accurate modeling of both the biomolecules and their ionic environment. Recently, ion nucleation phenomena leading to the rapid growth of KCl or NaCl clusters in the vicinity of biomolecular systems have been reported. To better understand this phenomenon, molecular dynamics simulations of KCl aqueous solutions at three (1.0, 0.25, and 0.10 M) concentrations were performed. Two popular water models (TIP3P and SPC/E) and two Lennard-Jones Parameter sets (AMBER and Dang) were combined to produce a total of 80 ns of molecular dynamics trajectories. Results suggest that the use of the Dang cation Lennard-Jones Parameters instead of those adopted by the AMBER force-field produces a more accurate description of the ionic solution. In the later case, formation of salt aggregates is probably indicative of an artifact resulting from misbalanced force-field Parameters. Because similar results were obtained with two different water Parameter sets, the simulations exclude a water model dependency in the formation of anomalous ionic clusters. Overall, the results strongly suggest that for accurate modeling of ions in biomolecular systems, great care should be taken in choosing balanced ionic Parameters even when using the most popular force-fields. These results invite a reexamination of older data obtained using available force-fields and a thorough check of the quality of current Parameters sets by performing simulations at finite (>0.25 M) instead of minimal salt conditions.

I. Cachadiña - One of the best experts on this subject based on the ideXlab platform.

  • Prediction of the enthalpy of vapourisation for anhydrides, formates, acetates, propionates, butyrates, esters, and ethers
    Physics and Chemistry of Liquids, 2008
    Co-Authors: I. Cachadiña, Angel Mulero, M.i. Parra
    Abstract:

    Four analytical correlations based on the use of the corresponding states principle were used to calculate the enthalpy of vapourisation of fluids. Three of these correlations require as inputs the critical temperature and the acentric factor. The fourth requires a molecular Lennard–Jones Parameter and the acentric factor. Results for 184 polar and non-polar fluids grouped into 9 families are compared with the values accepted by the Design Institute for Physical Property (DIPPR) project. Recommendations are given for the use of each model and for the choice of the adequate model for each family of fluids.

  • Vaporization Enthalpy: Corresponding-States Correlations Versus DIPPR Database
    Journal of Physical and Chemical Reference Data, 2007
    Co-Authors: I. Cachadiña, Angel Mulero
    Abstract:

    Data for the vaporization enthalpy accepted in the Design Institute for Physical Property Data® (DIPPR®) database are compared with those given by general correlations based on the corresponding-states method. In particular, four analytical predictive correlations were used. Three of them require as input the critical temperature and the acentric factor. The fourth requires a molecular Lennard-Jones Parameter and the acentric factor. Results obtained for 1576 fluids indicate that the recommended model for an overall use, in order to reproduce the DIPPR data, is the one proposed by Sivaraman et al. [Ind. Eng. Chem. Fundam. 23, 97 (1984)].

  • Evaluation of correlations for prediction of the normal boiling enthalpy
    Fluid Phase Equilibria, 2006
    Co-Authors: I. Cachadiña, Angel Mulero
    Abstract:

    Abstract Ten analytical models were used to calculate the enthalpy of vaporization of fluids at the boiling temperature. The correlations considered were six specific expressions valid only at that temperature, and four general correlations valid for any temperature. Most of these models require as inputs the critical properties and the acentric factor, but one of the specific models requires only the molecular weight (and, obviously, the boiling temperature). One of the models is a correlation requiring a molecular Lennard–Jones Parameter and the acentric factor as inputs. Results for 290 fluids are compared with the values given by the DIPPR project.

  • Boiling enthalpy from correlations Results for 83 families of fluids
    Thermochimica Acta, 2006
    Co-Authors: Angel Mulero, I. Cachadiña
    Abstract:

    Ten analytical models were used to calculate the enthalpy of vaporization of fluids at the boiling temperature. The correlations considered were six specific expressions valid only at that temperature, and four general correlations valid for any temperature. Most of these models require as inputs the critical properties and the acentric factor, but one of the specific models requires only the molecular weight (and, obviously, the boiling temperature). One of the models is a correlation requiring a molecular Lennard-Jones Parameter and the acentric factor as inputs. Results for 1591 polar and non-polar fluids, grouped into 83 families, are compared with the values given by the DIPPR project.

Karim Mazeau - One of the best experts on this subject based on the ideXlab platform.

  • Atomic partial charges and one Lennard-Jones Parameter crucial to model cellulose allomorphs
    Cellulose, 2014
    Co-Authors: Pan Chen, Yoshiharu Nishiyama, Karim Mazeau
    Abstract:

    The influence of the non-bonded Parameters, i.e., Lennard-Jones and the partial atomic charges, on the predicted unit cell dimensions of different allomorphs of cellulose were studied in the framework of the GROMOS force field. Systematic variation of partial atomic charges revealed the particular importance of charge distribution at the proximity of glycosidic linkage to the monoclinic angles. Furthermore, the unit cell Parameters were better predicted when the repulsive term of the united atom CH1 (carbon atoms bearing one hydrogen) was optimized. The a -axis of cellulose I_β was over estimated by more than 7 and 8.3 % in GROMOS-53A6 and GROMOS-56A_carbo respectively, but gave prediction within 0.2 % from experimental value, i.e. within experimental accuracy, when the CH1 repulsion term was optimized and CHARMM charge set was imported. At the same time, the average deviation from experimental values of the lattice Parameters of four allomorphs was improved from 2.36 to 1.18 % for GROMOS-53a6 and from 2.53 to 1.75 % for GROMOS-56A_carbo.