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Derivation of class II force fields: V. Quantum force field for amides, peptides, and related compounds

โœ Scribed by Maple, J. R.; Hwang, M.-J.; Jalkanen, K. J.; Stockfisch, T. P.; Hagler, A. T.


Publisher
John Wiley and Sons
Year
1998
Tongue
English
Weight
403 KB
Volume
19
Category
Article
ISSN
0192-8651

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โœฆ Synopsis


V these coupling and anharmonic contributions. Both force field representations are assessed in terms of their ability to fit the observables. They have also been tested by calculating the properties of 11 stationary states of these amide molecules. Optimized structures, vibrational frequencies, and conformational energies obtained from the quantum calculations and from both the QMFF and the HDFF are compared. Several strained and derivatized compounds including urea, formylformamide, and butyrolactam are included in these tests to assess ลฝ . the range of applicability transferability of the force fields. It was found that the class II coupled anharmonic force field reproduced the structures, energies, and vibrational frequencies significantly more faithfully than the class I harmonic diagonal force field. An important measure, rms energy deviation, was found to be 1.06 kcalrmol with the class II force field, and 2.30 kcalrmol with the harmonic diagonal force field. These deviations represent the error in relative configurational energy differences for strained and distorted structures calculated with the force fields compared with quantum mechanics. This provides a measure of the accuracy that might be expected in applications where strain may be important such as calculating the energy of a system as it ลฝ . approaches a rotational barrier, in ligand binding to a protein, or effects of introducing substituents into a molecule that may induce strain. Similar results were found for structural properties. Protein dynamics is becoming of everincreasing interest, and, to simulate dynamic properties accurately, the dynamic behavior of model compounds needs to be well accounted for. To this end, the ability of the class I and class II force fields to reproduce the vibrational frequencies obtained from the quantum energy surface was assessed. An rms deviation of 43 cm y1 was achieved with the coupled anharmonic force field, as compared to 105 cm y1 with the harmonic diagonal force field. Thus, the analysis presented here of the class II force field for the amide functional group demonstrates that the incorporation of anharmonicity and coupling terms in the force field significantly improves the accuracy and transferability with regard to the simulation of structural, energetic, and dynamic properties of amides.


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Derivation of class II force fields. VI.
โœ M.-J. Hwang; X. Ni; M. Waldman; C. S. Ewig; A. T. Hagler ๐Ÿ“‚ Article ๐Ÿ“… 1998 ๐Ÿ› Wiley (John Wiley & Sons) ๐ŸŒ English โš– 399 KB ๐Ÿ‘ 2 views

The methodology for deriving class II force fields has been applied to acetal, hemiacetal, and carbohydrate compounds. A set of eighteen model compounds containing one or more anomeric centers was selected for generating the quantum mechanical energy surface, from which the force field was derived a