The Consistent Force Field: Development of Potential Energy Functions for Conformational Analysis

Rasmussen, Kjeld; Engelsen, Søren B.; Fabricius, Jesper; Rasmussen, Birgit

doi:10.1007/978-94-011-1974-0_22

Cited by 18 publications

(29 citation statements)

References 6 publications

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“…Molecular mechanics calculations were performed with the Consistent Force Field (CFF) program for conformational analysis, − which was further modified to cope with the electrostatic models. Crystal simulations were carried out by using the Williams variant of the Ewald lattice summation method , with a spherical and abrupt cutoff limit of 14 Å and convergence constants of 0.2 Å -1 , 0.2 Å -1 , and 0.0 for Coulomb, dispersion, and repulsion lattice summation terms.…”

Section: Methods and Calculationsmentioning

confidence: 99%

“…Crystal simulations were carried out by using the Williams variant of the Ewald lattice summation method , with a spherical and abrupt cutoff limit of 14 Å and convergence constants of 0.2 Å -1 , 0.2 Å -1 , and 0.0 for Coulomb, dispersion, and repulsion lattice summation terms. The parameters for the set of potential energy functions were determined by combining trial and error guesses with the optimization algorithm which is a variant of the general least-squares method (the Levenberg−Marquardt algorithm). , …”

Section: Methods and Calculationsmentioning

confidence: 99%

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Why Are Copper(II) Amino Acid Complexes Not Planar in Their Crystal Structures? An ab Initio and Molecular Mechanics Study

Sabolović

Liedl

1999

Inorg. Chem.

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This paper presents geometries of copper(II) chelates with l-alanine, l-leucine, and l-N,N-dimethylvaline optimized by the hybrid density functional method B3LYP. According to the molecular quantum mechanics results, a square-planar copper(II) coordination geometry is electronically favored in vacuo. Deviations from the planar configuration observed in the crystal state should be attributed to sterical intramolecular and/or intermolecular effects. This paper proposes a new molecular mechanics model for tetracoordinated copper(II) amino acidates to investigate these effects in detail. The empirical parameter set for the selected potential energy functions was optimized both with respect to the X-ray crystal structures (internal coordinates and unit cell constants) and with respect to the quantum mechanically derived valence angles around copper. To test this newly developed force field (FF), the equilibrium geometries of 10 molecules are predicted in vacuo and in approximate crystalline surrounding. The results were compared with their ab initio and experimental crystal structures, respectively. The unit cell volumes were reproduced in a range from −7.0% to 2.1%. The total root-mean-square deviations between the experimental and FF in crystal internal coordinates were 0.017 Å in the bond lengths, 2.2° in the valence angles, and 3.6° in the torsion angles. The force field is capable of reproducing the changes in the chelate rings' torsion angles caused by the crystal packing forces and successfully explains the nonplanarity of Cu(II) amino acid complexes in their crystal structures.

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Section: Methods and Calculationsmentioning

confidence: 99%

Section: Methods and Calculationsmentioning

confidence: 99%

Why Are Copper(II) Amino Acid Complexes Not Planar in Their Crystal Structures? An ab Initio and Molecular Mechanics Study

Sabolović

Liedl

1999

Inorg. Chem.

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“…Computer modeling of biomolecular systems and large organic molecules is currently dominated by molecular mechanics calculations due to the advantage in speed. Several high quality force fields, such as AMBER,20, 21 CFF,22, 23 CHARMM,24, 25 COMPASS,26 GROMOS,27 SPASIBA,28 MM3,29 MM4,30 OPLS–AA,31 and MMFF9432, 33 have been developed and are commonly used for elucidating structures and properties of molecules in gas, liquid, and crystal phases. Currently, each force field has significant strength in the area where it was specifically parameterized, that is, MMFF94 performs well for predicting the structures and relative conformational energies of a wide range of organic molecules while the OPLS–AA potential is well suited for describing intermolecular interactions 32, 34.…”

Section: Introductionmentioning

confidence: 99%

Parameterization of OPLS–AA force field for the conformational analysis of macrocyclic polyketides

2002

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The parameters for the OPLS-AA potential energy function have been extended to include some functional groups that are present in macrocyclic polyketides. Existing OPLS-AA torsional parameters for alkanes, alcohols, ethers, hemiacetals, esters, and ketoamides were improved based on MP2/aug-cc-pVTZ and MP2/aug-cc-pVDZ calculations. Nonbonded parameters for the sp(3) carbon and oxygen atoms were refined using Monte Carlo simulations of bulk liquids. The resulting force field predicts conformer energies and torsional barriers of alkanes, alcohols, ethers, and hemiacetals with an overall RMS deviation of 0.40 kcal/mol as compared to reference data. Densities of 19 bulk liquids are predicted with an average error of 1.1%, and heats of vaporization are reproduced within 2.4% of experimental values. The force field was used to perform conformational analysis of smaller analogs of the macrocyclic polyketide drug FK506. Structures that adopted low-energy conformations similar to that of bound FK506 were identified. The results show that a linker of four ketide units constitutes the shortest effector domain that allows binding of the ketide drugs to FKBP proteins. It is proposed that the exact chemical makeup of the effector domain has little influence on the conformational preference of tetraketides.

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“…While model 7 keeps the values of the partial charges equal to the charge parameters, model 8 allows the partial charge assignment and neutralization to be done by a special charge redistribution algorithms that is part of the CFF program. 22 In this algorithm the X is treated as a highly electronegative halogen, in accordance with the assumption that the "dummy" atoms represent the electron pair. The partial charge assignments inside the nine molecules due to the charge parameters given in Table 2 are found in Table 3.…”

Section: Resultsmentioning

confidence: 99%

In Vacuo and In Crystal Molecular-Mechanical Modeling of Copper(II) Complexes with Amino Acids

Sabolović¹,

Rasmussen²

1995

Inorg. Chem.

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The Consistent Force Field: Development of Potential Energy Functions for Conformational Analysis

Cited by 18 publications

References 6 publications

Why Are Copper(II) Amino Acid Complexes Not Planar in Their Crystal Structures? An ab Initio and Molecular Mechanics Study

Why Are Copper(II) Amino Acid Complexes Not Planar in Their Crystal Structures? An ab Initio and Molecular Mechanics Study

Parameterization of OPLS–AA force field for the conformational analysis of macrocyclic polyketides

In Vacuo and In Crystal Molecular-Mechanical Modeling of Copper(II) Complexes with Amino Acids

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