Torsional Potential Parameters Research Articles

Extension and validation of the GROMOS 53A6(GLYC) parameter set for glycoproteins.

An extension of the GROMOS 53A6GLYC force field for carbohydrates to encompass glycoprotein linkages is presented. The set includes new atomic charges and incorporates adequate torsional potential parameters for N-, S-, C-, P-, and O-glycosydic linkages, offering compatibility with the GROMOS force field family for proteins. Validation included the description of glycosydic linkage geometries between amino acid and monosaccharide residues, comparison of NMR-derived protein-carbohydrate and carbohydrate-carbohydrate nuclear overhauser effect (NOE) signals for glycoproteins and the effects of glycosylation on protein flexibility and dynamics.

GROMOS 53A6GLYC, an Improved GROMOS Force Field for Hexopyranose-Based Carbohydrates.

An improved parameter set for explicit-solvent simulations of carbohydrates (referred to as GROMOS 53A6GLYC) is presented, allowing proper description of the most stable conformation of all 16 possible aldohexopyranose-based monosaccharides. This set includes refinement of torsional potential parameters associated with the determination of hexopyranose rings conformation by fitting to their corresponding quantum-mechanical profiles. Other parameters, as the rules for third and excluded neighbors, are taken directly from the GROMOS 53A6 force field. Comparisons of the herein presented parameter set to our previous version (GROMOS 45A4), the GLYCAM06 force field, and available NMR data are presented in terms of ring puckering free energies, conformational distribution of the hydroxymethyl group, and glycosidic linkage geometries for 16 selected monosaccharides and eight disaccharides. The proposed parameter modifications have shown a significant improvement for the above-mentioned quantities over the two tested force fields, while retaining full compatibility with the GROMOS 53A6 and 54A7 parameter sets for other classes of biomolecules.

High-resolution synchrotron-based Fourier transform spectroscopy of in the 120–350 cm−1 far-infrared region

The Fourier transform spectrum of the isotopologue of methanol has been recorded in the 120–350 cm−1 far-infrared region at a resolution of 0.00096 cm−1 using synchrotron source radiation at the Canadian Light Source. The study, motivated by astrophysical applications, is aimed at generating a sufficiently accurate set of energy level term values for the ground vibrational state to allow prediction of the centres of the quadrupole hyperfine multiplets for astronomically observable sub-millimetre transitions to within an uncertainty of a few MHz. To expedite transition identification, a new function was added to the Ritz program in which predicted spectral line positions were generated by an adjustable interpolation between the known assignments for the and isotopologues. By displaying the predictions along with the experimental spectrum on the computer monitor and adjusting the predictions to match observed features, rapid assignment of numerous sub-bands was possible. The least squares function of the Ritz program was then used to generate term values for the identified levels. For each torsion-K-rotation substate, the term values were fitted to a Taylor-series expansion in powers of J(J + 1) to determine the substate origin energy and effective B-value. In this first phase of the study we did not attempt a full global fit to the assigned transitions, but instead fitted the sub-band J-independent origins to a restricted Hamiltonian containing the principal torsional and K-dependent terms. These included structural and torsional potential parameters plus quartic distortional and torsion–rotation interaction terms.

Origin of threefold methyl torsional potential in methylindoles

In this article, we present a systematic study on mono-methylindoles to investigate the electronic origin of the threefold symmetric component (V3) of the methyl torsional potential barrier in the ground electronic state (S0). The structures and the torsional potential parameters of these molecules were evaluated from ab initio calculation using Hartree-Fock (HF), second order Mollar Plesset perturbation (MP2) and B3LYP density functional level of theories and Gaussian type basis set 6-31G(d, p). Natural bond orbital (NBO) analysis of these molecules were carried out using B3LYP/6-31G(d, p) level of calculation to understand the formation of the threefold V3 term arising from the changes of various non-covalent interactions during methyl rotation. Our analysis reveals that the contributions from π orbitals play a dominant role in the barrier height determination in this class of molecules. The threefold term in the barrier arises purely from the interactions non-local to the methyl group in case when the methyl group has two single bonds vicinal to it. On the other hand, it is the local interaction that determines the potential energy barrier when the methyl group has one single bond and one double bond vicinal to it. However, in all these cases, the magnitude of the energy barrier depends on the resonance structure formation in the benzene ring frame upon rotation of the methyl group and, therefore, the energetics of the barrier cannot be understood without considering the molecular flexing during methyl rotation.

Internal rotation potential functions of the acryloyl chloride molecule in the ground (S 0) and excited (S 1) electronic states

The internal rotation potential function of the acryloyl chloride molecule in the S 0 and S 1 electronic states was reproduced using systems of torsional vibration levels obtained for its trans and cis isomers by analyzing the vibrational structure of the UV spectrum of the molecule. The kinematic factor F in the S 0 ground state was calculated including geometric parameter relaxation as a function of internal rotation angle. The torsional potential parameters in the S 0 state obtained in this work were substantially different from those determined from the infrared Fourier-transform spectrum ignoring the resonance perturbation of the level with v = 3. The form of the internal rotation potential function and the higher stability of the trans isomer (the main isomer) were substantiated by high-level quantum-mechanical calculations.

Electronic spectra of molecules with two C3 v internal rotors: Torsional analysis of the [formula omitted] LIF spectrum of biacetyl

The laser-induced fluorescence excitation spectrum of the biacetyl A 1 A u ( S 1)– X 1 A g ( S 0) transition in the region from 22 182 to 22 800 cm −1 shows a complicated absorption line spectrum, which is believed to arise from a long progression in the torsional vibrations of the two equivalent methyl tops in this molecule. In this paper, we discuss three topics: (i) a numerical calculation of these energy levels using a kinetic and potential energy formalism and constants from the literature [M.L. Senent, D.C. Moule, Y.G. Smeyers, A. Toro-Labbé, F.J. Peqalver, J. Mol. Spectrosc. 164 (1994) 66], (ii) a qualitative description of the calculated energy level pattern using local-mode ideas applied to the two equivalent methyl rotors together with G 36 permutation-inversion group symmetry species, and (iii) a least-squares refinement of the torsional potential parameters based on results of some of our high-resolution rotational analyses, followed by a comparison of energy levels calculated from the refined parameters with a low-resolution spectrum taken in the region from 0 to 500 cm −1 above the A– X band origin. Concerning (ii), we find that the two vibrational levels with one quantum of torsional excitation are best described by a normal mode formulation, but that many levels with more than one quantum of torsional excitation are better described by a local-mode formulation. Concerning (iii), we obtain low-order molecular constants quite similar to those reported by Senent et al., but higher-order constants which are quite different. Our calculated spectrum agrees well with the low-resolution spectrum, but full confirmation of the present interpretation for levels with three or more quanta of torsion excited will require high-resolution studies of additional bands.

A new GROMOS force field for hexopyranose‐based carbohydrates

A new parameter set (referred to as 45A4) is developed for the explicit-solvent simulation of hexopyranose-based carbohydrates. This set is compatible with the most recent version of the GROMOS force field for proteins, nucleic acids, and lipids, and the SPC water model. The parametrization procedure relies on: (1) reassigning the atomic partial charges based on a fit to the quantum-mechanical electrostatic potential around a trisaccharide; (2) refining the torsional potential parameters associated with the rotations of the hydroxymethyl, hydroxyl, and anomeric alkoxy groups by fitting to corresponding quantum-mechanical profiles for hexopyranosides; (3) adapting the torsional potential parameters determining the ring conformation so as to stabilize the (experimentally predominant) (4)C(1) chair conformation. The other (van der Waals and nontorsional covalent) parameters and the rules for third and excluded neighbors are taken directly from the most recent version of the GROMOS force field (except for one additional exclusion). The new set is general enough to define parameters for any (unbranched) hexopyranose-based mono-, di-, oligo- or polysaccharide. In the present article, this force field is validated for a limited set of monosaccharides (alpha- and beta-D-glucose, alpha- and beta-D-galactose) and disaccharides (trehalose, maltose, and cellobiose) in solution, by comparing the results of simulations to available experimental data. More extensive validation will be the scope of a forthcoming article. (c) 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1400-1412, 2005.

Barriers to Methyl Torsion in 2-Fluoro-6-chlorotoluene: Additivity of ortho-Substituent Effects in S0, S1, and D0

The techniques of resonant two-photon ionization (R2PI) and pulsed-field ionization (PFI) were used to measure the absorption spectra of 2-fluoro-6-chlorotoluene (S1) and of 2-fluoro-6-chlorotoluene+ (D0, the cation ground state) for internally cold molecules in a pulsed nozzle expansion. The adiabatic ionization potential is 72 943 ± 5 cm-1 = 9.0438 ± 0.0006 eV. We assign much of the low-frequency torsional and vibrational structure in both S1 and D0. Analysis yields the one-dimensional model torsional potential parameters V3‘ = 139.4 ± 2.0 cm-1 and V6‘ = −7 ± 5 cm-1 in S1 and V3+ = 192.7 ± 2.0 cm-1 and V6+ = 20 ± 5 cm-1 in D0. In earlier work, ab initio calculations at the HF/6-31G* level found V3‘‘ = 230 cm-1 in S0. An interlocking combination of experimental band intensities and ab initio calculations shows that, in all three electronic states, the minimum energy conformation places one methyl CH bond in the plane of the ring pseudo-trans to the chlorine substituent, i.e., on the same side of the ring as the fluorine substituent. The 3-fold barrier heights exhibit a kind of additivity of ortho-substituent effects. That is, in S0, S1, and D0 the torsional potential of 2-fluoro-6-chlorotoluene is approximately equal to the algebraic sum of the potential for o-fluorotoluene plus the potential for o-chlorotoluene shifted in phase by 180°. This is true to high accuracy in S0 and S1; it is qualitatively true in D0 as well. We argue that the dominant contribution to the barrier in all three states is steric repulsion between the methyl group and a lone pair on each halogen, with the weaker methyl−fluorine interaction partially canceling the stronger methyl−chlorine interaction. The approximate invariance of the torsional potential upon π excitation to S1 and upon π ionization to D0 is unusual among 3-fold symmetric molecules. We attribute this to alignment of the π molecular orbitals (essentially Hückel orbitals) so as to have approximate C2v symmetry about the methyl rotor axis. In effect, fluorine and chlorine act as equivalent, weak π donors. Thus, 2-fluoro-6-chlorotoluene has a substantial 3-fold barrier due to net steric repulsion, but behaves much like a 6-fold molecule with respect to effects of π excitation or ionization.

Analysis of the torsional Raman spectrum of a pyramidal molecule, dimethylamine

Overtone Raman spectra of dimethylamine (DMA) are analyzed yielding accurate torsional potential parameters. Neglecting the inversion motion of the amino-hydrogen in DMA the group G 18 is the proper molecular symmetry group to analyze the measured torsional Raman spectrum. The character table of G 18 for this basically pyramidal molecule has been derived and is reported here explicitly. The torsional potential parameters are fitted with the introduction of additional terms in the Hamiltonian odd in α i , α i being the torsional angle of top i. The mutual top-top interaction terms yield a significant distortion of the torsional potential surface.

Gas- and liquid-phase NMR studies of conformational exchange in N,N-diisopropylacetamide

The gas-phase free activation energy, Δ G ≠, for internal rotation about the carbon—nitrogen bond in N,N-diisopropylacetamide is 14.3 (0.1) kcal mol −1. For neat N,N-diisopropylacetamide, and solutions in CCl 4, CDCl 3, dimethylsulphoxide (DMSO) and D 2O, Δ G ≠ values are 16.1 (0.1), 15.6 (0.01), 16.4 (0.1), 16.4 (0.1) and 17.8 (0.1) kcal mol −1, respectively. Phase effects on the kinetic parameters for this amide are similar to those found for amides studied previously; this is compatible with solvent internal pressure effects and consistent with a process that proceeds via a transition state that has greater steric requirements than the ground-state configurations. We also demonstrate that gas-phase dynamic NMR can provide valuable data for evaluating the accuracy of molecular mechanics and semiempirical molecular orbital calculations, as well as for generating torsional potential parameters useful for their parameterization. These calculations have extreme importance in the future development of the ability to model the structural and dynamic characteristics of proteins and other biologically important molecules.

The torsional Raman spectra of partially deuterated ethane molecules. I. One conformer derivatives: CH3CD3, CH3CH2D, CH3CHD2, CH2DCD3, and CHD2CD3

The torsional Raman spectra of one-conformer partially deuterated derivatives of ethane, CH3CD3, CH3CH2D, CH3CHD2, CH2DCD3, and CHD2CD3 have been experimentally investigated with an improved conventional Raman spectrometer. The recorded spectra have been interpreted with a rotational–torsional effective Hamiltonian and a simple model for the torsional dependence of the molecular polarizability. The effective threefold torsional potential parameters for CH3CD3 (V3=997.72 cm−1, V6=8.45 cm−1 ) have been taken from the recent literature, whilst the following parameters were obtained for the other derivatives: CH3CH2D, V3=1007 cm−1, V6=7.3 cm−1; CH3CHD2, V3=1003 cm−1, V6=8.5 cm−1; CH2DCD3, V3=993 cm−1, V6=8.2 cm−1; CHD2CD3, V3=995 cm−1, V6=6.7 cm−1. The estimated accuracy of these parameters is of the order of ±2 cm−1.

Conformational disorder in conjugated polymers

Conformational disorder plays an important role in determining the electronic properties of conjugated polymers. To obtain a better theoretical description of the role and extent of conformational disorder, we derive the π electron correlation length and the bond correlation length in terms of the effective torsional potential and geometry of the conjugated polymer chains. These quantites are related to the conjugation lengths and persistence lengths of the chain, which are computed for polyacetylene, polydiacetylene, polythiophene, and polypyrrole. In spite of uncertainties in the torsional potential parameters for these materials, good qualitative agreement is found between experiment and theory.