Increasing Normal Modes Analysis Accuracy:  The SPASIBA Spectroscopic Force Field Introduced into the CHARMM Program

Abstract

In the present work, the SPASIBA spectroscopic force field has been introduced into the CHARMM program. The SPASIBA force field combines the van der Waals and electrostatic interactions as originally found into CHARMM with Urey-Bradley-Shimanouchi terms for bond stretching, valence angle bending, torsional and improper torsional internal coordinates. SPASIBA has a vibrational spectroscopic origin, and it has largely proven its efficiency in reproducing experimental data such as vibrational wavenumbers, dipole moments, rotational barriers, conformational energy differences, and moments of inertia. The SPASIBA parameters have been included into CHARMM by way of a particular library which directly activates calculations of the specific energetic terms.

The SPASIBA Force Field for Chondroitin Sulfate: Vibrational Analysis of d-Glucuronic and N-acetyl-d-Galactosamine 4-Sulfate Sodium Salts

“…Torsional potentials related to ring bonds and exocylic hydroxyl groups were deduced from spectroscopic data on crystal forms of monosaccharides and extended to a variety of glycosidic linkages appearing in disaccharides. 14,15 Examination of the low-frequency region (76-300 cm -1 ) reveals a good agreement with the DFT predictions, in particular, for the monosaccharide ring normal modes involving CT-CT, CT-O5, and exocyclic hydroxyl group torsional librations and ring deformations.…”

“…The SPASIBA force field is a spectroscopic molecular-mechanics-derived empirical potential function first devoted to proteins 13 and extended to a large variety of chemical groups such as alkanes, alkenes, amino acids, ethers, esters, thiols, alcohols, saccharides, and phospholipids. [14][15][16][17][18][19][20] Not only does this force field appear to be an adequate tool for molecular mechanics studies of monosaccharides, but it has also been extended to force constant determination related to various glycosidic linkages along the etablishment of Ramachandran's φ, ψ maps. 14,15 The SPASIBA force field has been developed in our group for many years.…”

“…[14][15][16][17][18][19][20] Not only does this force field appear to be an adequate tool for molecular mechanics studies of monosaccharides, but it has also been extended to force constant determination related to various glycosidic linkages along the etablishment of Ramachandran's φ, ψ maps. 14,15 The SPASIBA force field has been developed in our group for many years. It is able to reproduce at the same time structures energies and vibrational spectra with a much higher precision on the latter than commonly available force fields.…”

“…This is the main reason it has recently been introduced into the CHARMM package. 15 Therefore, the SPASIBA force field is a molecular force field which can be used with high confidence, particularly in molecular dynamics simulations where it has to be reliable over the whole potential energy surface rather than in the vicinity of the minima, since the parameters deduced from spectra reflect the curvature of the potential surface. The philosophy of SPASIBA and all the procedures for parameter determination have been given in detail in a series of papers corresponding to thermally excited modes (see refs 13-15 and references therein).…”

Structural differences between the putative carbohydrate-recognition domains of human IL-1 alpha, IL-1 beta and IL-1 receptor antagonist obtained by in silico modeling

“…tripos.com]. The Tripos force field was mainly used except for the internal rotation and electrostatic terms for carbohydrates specific parameters as previously determined [23]. In particular, partial atomic charges were calculated using quantum chemical methods based on the Density Functional Theory (B3LYP hybrid functional and 6-31G* basis set).…”