Directional hydrogen bonding in the MM3 force field. I

1994 ◽  
Vol 7 (11) ◽  
pp. 591-609 ◽  
Author(s):  
Jenn-Huel Lii ◽  
Norman L. Allinger
Keyword(s):  
Hydrogen Bonding ◽  
Force Field ◽  
Mm3 Force Field

Ring inversion pathways of exo- and endo-calix[4]arenes studied by means of the MM3 force field

1995 ◽  
Vol 36 (37) ◽  
pp. 6665-6668 ◽  
Author(s):  
Iris Thondorf ◽  
Jorg Brenn ◽  
Wolfgang Brandta ◽  
Volker Bohmerb
Keyword(s):  
Force Field ◽  
Ring Inversion ◽  
Mm3 Force Field

scholarly journals Simulating Absorption Spectra of Flavonoids in Aqueous Solution: A Polarizable QM/MM Study

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5853
Author(s):  
Sulejman Skoko ◽  
Matteo Ambrosetti ◽  
Tommaso Giovannini ◽  
Chiara Cappelli
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Hydrogen Bonding ◽  
Force Field ◽  
Absorption Spectra ◽  
Computational Study ◽  
Md Simulations ◽  
Quantum Mechanical ◽  
Hydrogen Bonding Interactions

We present a detailed computational study of the UV/Vis spectra of four relevant flavonoids in aqueous solution, namely luteolin, kaempferol, quercetin, and myricetin. The absorption spectra are simulated by exploiting a fully polarizable quantum mechanical (QM)/molecular mechanics (MM) model, based on the fluctuating charge (FQ) force field. Such a model is coupled with configurational sampling obtained by performing classical molecular dynamics (MD) simulations. The calculated QM/FQ spectra are compared with the experiments. We show that an accurate reproduction of the UV/Vis spectra of the selected flavonoids can be obtained by appropriately taking into account the role of configurational sampling, polarization, and hydrogen bonding interactions.

MMPEP: Development and evaluation of peptide parameters for Allinger's MMP2(85) programme, including calculations on crambin and insulin

1988 ◽  
Vol 66 (11) ◽  
pp. 2687-2702 ◽  
Author(s):  
Saul Wolfe ◽  
Donald Fredric Weaver ◽  
Kiyull Yang
Keyword(s):  
Hydrogen Bonding ◽  
Force Field ◽  
Van Der Waals ◽  
Heavy Atom ◽  
Van Der Waals Interactions ◽  
Heavy Atoms ◽  
Minimization Procedure ◽  
Natural Result ◽  
Experimental Crystal ◽  
Initial Starting

Allinger's MMP2(85) program has been converted to an IBM environment, and the dimensions expanded to a current maximum of 999 atoms. Substantial additional expansion will be possible. An all-atom set of parameters, which permit Allinger's comprehensive force field to be applied to the molecular mechanics treatment of peptides, has been determined. These parameters, termed MMPEP, contain 21 atom types: 5 for carbon, 6 for hydrogen, 5 for nitrogen, 4 for oxygen, and 1 for sulfur, and are based on crystallographic heavy atom bond lengths and bond angles, vibrational and microwave spectra, and ab initio calculations. To minimize the conformational energy of a peptide from an initial starting geometry, all internally stored parameters are released, and replaced by PEPCON, a 360-line external file containing the MMPEP parameters.The ability of the MMPEP parameterization of MM85 to reproduce experimental crystal structures has been tested on several peptides and polypeptides, and the use of a dielectric constant ε = 78.5 D leads to the following results: Ala-Ala-Gly (rms = 0.261); Gly-Gly-Val (rms = 0.349); glutathione (rms = 0.417); crambin (327 heavy atoms; rms = 0.310 for all heavy atoms); insulin (389 heavy atoms; rms = 0.646 for all heavy atoms); the origins of deviations can be interpreted. No problems have been encountered in the application of the Newton–Raphson minimization procedure to such large molecules as crambin and insulin, even though all possible nonbonded interactions have been retained. On the IBM 3081 computer, real time minimization of trip)eptides requires 1–2 min, crambin requires 250 min, and insulin 200 min. Since hydrogen bonding in Allinger's force field is a natural result of electrostatic and van der Waals interactions, in MMPEP hydrogen bonding is taken into account through the large number of hydrogen atom types and their different bond moments and van der Waals radii.

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