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de la Torre JG, Hernández Cifre JG, Ortega Á, Schmidt RR, Fernandes MX, Pérez Sánchez HE, Pamies R. SIMUFLEX: Algorithms and Tools for Simulation of the Conformation and Dynamics of Flexible Molecules and Nanoparticles in Dilute Solution. J Chem Theory Comput 2009; 5:2606-18. [DOI: 10.1021/ct900269n] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- José García de la Torre
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
| | - José G. Hernández Cifre
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
| | - Álvaro Ortega
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
| | - Ricardo Rodríguez Schmidt
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
| | - Miguel X. Fernandes
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
| | - Horacio E. Pérez Sánchez
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
| | - R. Pamies
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
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García de la Torre J. Dynamic electro-optic properties of macromolecules and nanoparticles in solution: A review of computational and simulation methodologies. Colloids Surf B Biointerfaces 2007; 56:4-15. [PMID: 17125977 DOI: 10.1016/j.colsurfb.2006.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2006] [Revised: 09/14/2006] [Accepted: 10/01/2006] [Indexed: 11/20/2022]
Abstract
This paper reviews some theories, and computational and simulation procedures available for the calculation of the time-course of electro-optic properties of particles in solution. For rigid particles, the time evolution of the properties is directly related to their rotational diffusion; therefore, the computational procedures for the calculation of hydrodynamic properties find a direct application in electro-optics. Several of such computational procedures, based on bead models, are reviewed. For flexible particles, the simultaneous effects the external field and the flexibility can be treated with Brownian dynamics simulation. We illustrate the various procedures, with applications to rigid bent rods and flexible, wormlike or hinged rods, trying to show how the absence or presence of flexibility, and its kind, influences the dynamic electro-optic properties, which are therefore valuable sources of information about the conformation of macromolecules and nanoparticles.
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Affiliation(s)
- J García de la Torre
- Departamento de Quimica Fisica, Facultad de Quimica, Universidad de Murcia, 30071 Murcia, Spain.
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Pérez Sánchez HE, de la Torre JG, Díaz Baños FG. Transient electric birefringence of wormlike macromolecules in electric fields of arbitrary strength: A computer simulation study. J Chem Phys 2005; 122:124902. [PMID: 15836419 DOI: 10.1063/1.1863892] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We have studied the birefringence decay of linear models of macromolecules for two different types of flexibility, the broken-rod chain and the wormlike chain, using a computer simulation of a transient electric birefringence experiment. We have paid particular attention to the influence of the intensity of the orienting field, including two orienting mechanisms, the induced dipole, and the permanent dipole. We have compared wormlike and broken-rod models of the same radius of gyration, finding that they present a different decay curve under the influence of the same intensity of the field. We have seen that these differences are due to the faster relaxation times (smaller in the wormlike chain model) and amplitudes, because, regardless of the type of flexibility, the overall size of a molecule (measured by the radius of gyration) essentially determines the longest relaxation time. We have also analyzed how the relaxation process is affected by the degree of flexibility, the orientation mechanisms, and the intensity of the field. Studying a different aspect, we have paid attention to the deformation of a molecule in a transient electric birefringence experiment as a source of information. In this work we have developed equations to characterize this deformation in terms of one of the components of the gyration tensor, if a dynamic light scattering experiment under the influence of an electric field could be performed. To develop this work we have simulated the Brownian dynamics of the different models, relaxing after the removal of an orienting external electric field of arbitrary strength. A comparison with other methods such a the rigid body treatment or the correlation analysis of Brownian trajectories has also been included. We have seen that differences between the two Brownian dynamics methods are small and that the rigid-body treatment is only an acceptable approximation to obtain the longest relaxation time.
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Affiliation(s)
- H E Pérez Sánchez
- Departamento de Química Física, Universidad de Murcia, 30071 Murcia, Spain
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Pérez Sánchez HE, García de la Torre J, Díaz Baños FG. Influence of Field Strength and Flexibility on the Transient Electric Birefringence of Segmentally Flexible Macromolecules. J Phys Chem B 2002. [DOI: 10.1021/jp014613p] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - F. G. Díaz Baños
- Departamento de Química Física, Universidad de Murcia, 30071 Murcia, Spain
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Carrasco B, Díaz FG, López Martínez MC, García de la Torre J. Birefringence, Deformation, and Scattering of Segmentally Flexible Macromolecules under an External Agent. Steady-State Properties in an Electric Field. J Phys Chem B 1999. [DOI: 10.1021/jp9910385] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- B. Carrasco
- Departamento de Química Física, Universidad de Murcia, 30071 Murcia, Spain
| | - F. G. Díaz
- Departamento de Química Física, Universidad de Murcia, 30071 Murcia, Spain
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