The structures and vibrational frequencies of a series of aliphatic alcohols as obtained using the spectroscopic potential SPASIBA

Tristram, Frankie; Durier, V.; Vergoten, Gérard

doi:10.1016/0022-2860(95)09183-1

Cited by 7 publications

(8 citation statements)

References 18 publications

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“…The rms for wavenumbers are quite comparable and in agreement with the value obtained by Tristram et al In the present work, the nonbonded parameters and atomic charges were taken from the CHARMM22 library. The dipole moment and optimized geometries obtained from SPASIBA/CHARMM are in quite good accordance with the experimental data, but the torsional barrier for the Me−C bond is, however, calculated with a lower value (0.85 kcal mol -1 ) than for the experimental one (1.07 kcal mol -1 ).…”

Section: Resultssupporting

confidence: 91%

“… a ν, stretching; νs and νa, symmetric and antisymmetric stretchings; τ, torsion; Δν, mean deviation; δ and ρ, in-plane bending and rocking deformations; δs and δa, symmetric and antisymmetric deformations. b Calcd; see ref . …”

Section: Resultsmentioning

confidence: 99%

“…The SPASIBA molecular mechanics force field is a spectroscopic molecular force field that treats bonds and bond angles by Urey−Bradley−Shimanouchi terms. , These terms have been previously combined with the torsional, van der Waals, and electrostatic terms of protein force fields, such as the AMBER or the CHARMM force fields, to provide a means to investigate the relationship between molecular spectra of proteins and their conformational properties. Previous studies have demonstrated that root-mean-square deviations between the observed and calculated vibrational frequencies for a large variety of chemical groups are in the 10−15 wavenumber range. − This level of agreement originates from the fact that the SPASIBA spectroscopic force field takes into account particular terms that have not been treated by other molecular mechanics force fields. These terms are directly related to the gem and/or tetrahedral redundancies.…”

Section: Introductionmentioning

confidence: 97%

See 2 more Smart Citations

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

et al. 2004

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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.

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Section: Resultssupporting

confidence: 91%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

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

et al. 2004

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“…Empirical Force Field. The SPASIBA force field is a spectroscopic molecular-mechanics-derived empirical potential function first devoted to proteins and extended to a large variety of chemical groups such as alkanes, alkenes, amino acids, ethers, esters, thiols, alcohols, saccharides, and phospholipids. − 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. , …”

Section: Methodsmentioning

confidence: 99%

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

et al. 2006

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Normal-mode analyses were carried out on the two components of the chondroitin 4-sulfate linear glycosaminoglycan, a copolymer implying alternate D-glucuronate beta-(1-->3) and N-acetyl-D-galactosamine 4-sulfate beta-(1-->4) (hereafter named D-galactosamine 4-sulfate) residues. Scaled quantum mechanical calculations (SQM) using the density functional theory approach at different levels of theory (B3LYP/6-31G** and B3LYP/6-31++G**) were performed to obtain correct vibrational assignments. The SPASIBA empirical force field parameters were then obtained from both theoretical predictions and observed IR and Raman data. It is shown that calculations including diffuse functions at the B3LP/6-31++G** level and the introduction of the Na+ counterion are necessary to give correct assignments of the CO2- symmetric (nu(s)) and antisymmetric (nu(a)) stretching modes for the glucuronic carboxylate residue.

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“… − tested and enhanced several force fields in order to obtain the vibrational frequencies of a series of alkanes. Similar approaches have been applied to alcohols . Buck et al .…”

Section: Introductionmentioning

confidence: 99%

OH-Stretching Red Shifts in Bulky Hydrogen-Bonded Alcohols: Jet Spectroscopy and Modeling

2006

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The available database for OH-stretching bands of jet-cooled aliphatic alcohol dimers is extended to systems including 1-adamantanol and 2-adamantanol, using a heated pulsed nozzle coupled to an FTIR spectrometer. This database is used to simplify and parametrize the standard Wang et al. AMBER/parm99.dat force field for the prediction of hydrogen-bond-induced red shifts, as it avoids complications due to mode coupling and cooperativity. Apart from subtle chiral recognition effects, the performance of the simple model in describing steric, electronic, and conformational influences on the red shifts is remarkable, as exemplified by predictions for mixed-alcohol dimers. The resulting semiempirical approach can complement quantum chemical calculations, in particular for larger systems, although the good performance is rather specific to red shift predictions.

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The structures and vibrational frequencies of a series of aliphatic alcohols as obtained using the spectroscopic potential SPASIBA

Cited by 7 publications

References 18 publications

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

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

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

OH-Stretching Red Shifts in Bulky Hydrogen-Bonded Alcohols: Jet Spectroscopy and Modeling

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