Polarization Force Fields for Peptides Implemented in ECEPP2 and MM2

Torrens, Francisco

doi:10.1080/08927020008022384

Cited by 18 publications

(8 citation statements)

References 42 publications

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“…In previous papers, both noninteracting induced dipole (NID) and interacting induced dipole (ID) polarization models were implemented in the program molecular mechanics (MM2) 41. The polarizing force field (MMID2) was described elsewhere 42–44. In this work, MMID2 has been improved to include terms specific for five‐ and six‐coordination.…”

Section: Introductionmentioning

confidence: 99%

Nature of O₂, CO, and CN binding to hemoprotein models

Torrens

2004

Int J of Quantum Chemistry

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Parametrization of a molecular-mechanics program to include terms specific for five-and six-coordinate transition metal complexes results in computersimulated structures of hemo complexes. The principal new feature peculiar to five-and six-coordination is a term that measures the effect of electron-pair repulsion modified by the ligand electronegativity and takes into account the different structural possibilities. The work consists in the modification of program molecular mechanics for penta and hexacoordination. The model system takes into account the structural differences of the fixing center in the hemoglobin subunits. The customary proximal histidine is added. The macrocycle hemo IX is wholly considered in our model. The calculations show clearly that certain conformations are much more favorable that others for fixing O 2 . From the O 2 binding in hemoglobin and myoglobin and in simple Fe porphyrin models, it is concluded that the bent O 2 ligand is best viewed as bound superoxide, O 2 Ϫ .

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Section: Introductionmentioning

confidence: 99%

Nature of O₂, CO, and CN binding to hemoprotein models

Torrens

2004

Int J of Quantum Chemistry

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“…An optimized version of our program POLAR, including the whole interacting induced‐dipole polarization model, has been implemented in the program molecular mechanics (MM2), its extension to transition metals (MMX) and empirical conformational energy program for peptides (ECEPP2). The new versions are called MMID2 37, MMXID 38, and ECEPPID2 39.…”

Section: Methodsmentioning

confidence: 99%

Net charge and polarizability of zeolitic Brønsted acidic sites

Torrens¹,

Castellano²

2007

Int J of Quantum Chemistry

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ABSTRACT:The interacting induced-dipoles polarization model, implemented in our program POLAR, is used for the calculation of the effective polarizability of the zeolitic bridged OH group, which results much higher than that of the free silanol group. A high polarizability is also calculated for the bridged OH group with a Si 4ϩ , in the absence of Lewis-acid promotion of silanol by Al 3ϩ . The crystal polarizability is estimated from the Clausius-Mossotti relationship. Siliceous zeolites are lowpermittivity isolators. The interaction of a weak base with the zeolitic OH can be considered as a local bond. Only when cations are located in the zeolite micropore, next to tetrahedra that contain trivalent cations, are large electrostatic fields generated. They are short ranged, and the positive cation charges are compensated.

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“…The calculation of molecular polarizabilities has been carried out by the interacting induced dipoles polarization model [ 35 , 36 , 37 ] that calculates tensor effective anisotropic point polarizabilities by the method of Applequist et al . [ 38 , 39 , 40 ].…”

Section: Interacting Induced Dipoles Polarization Model For Molecularmentioning

confidence: 99%

“…The new versions are called MMID [ 35 , 36 ] and ECEPPID [ 37 ]. In both programs, the polarization energy can be now calculated by three options: (1) no polarization, (2) non-interacting induced dipoles polarization model and (3) interacting induced dipoles polarization model.…”

Section: Interacting Induced Dipoles Polarization Model For Molecularmentioning

confidence: 99%

Molecular Polarizability of Sc and C (Fullerene and Graphite) Clusters

Torrens

2001

Molecules

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A method (POLAR) for the calculation of the molecular polarizability <α> is presented. It uses the interacting induced dipoles polarization model. As an example, the method is applied to Scn and Cn (fullerene and one-shell graphite) model clusters. On varying the number of atoms, the clusters show numbers indicative of particularly polarizable structures. The <α> are compared with reference calculations (PAPID). In general, the Scn calculated (POLAR) and Cn computed (POLAR and PAPID) are less polarizable than what is inferred from the bulk. However, the Scn calculated (PAPID) are more polarizable than what is inferred. Moreover, previous theoretical work yielded the same trend for Sin, Gen and GanAsm small clusters. The high polarizability of the Scn clusters (PAPID) is attributed to arise from dangling bonds at the surface of the cluster.

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Polarization Force Fields for Peptides Implemented in ECEPP2 and MM2

Cited by 18 publications

References 42 publications

Nature of O₂, CO, and CN binding to hemoprotein models

Nature of O₂, CO, and CN binding to hemoprotein models

Net charge and polarizability of zeolitic Brønsted acidic sites

Molecular Polarizability of Sc and C (Fullerene and Graphite) Clusters

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Polarization Force Fields for Peptides Implemented in ECEPP2 and MM2

Cited by 18 publications

References 42 publications

Nature of O2, CO, and CN binding to hemoprotein models

Nature of O2, CO, and CN binding to hemoprotein models

Net charge and polarizability of zeolitic Brønsted acidic sites

Molecular Polarizability of Sc and C (Fullerene and Graphite) Clusters

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Product

Resources

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Nature of O₂, CO, and CN binding to hemoprotein models

Nature of O₂, CO, and CN binding to hemoprotein models