Dino R. Ferro

Conformer populations of L-iduronic acid residues in glycosaminoglycan sequences

The 1H-n.m.r. 3J values for the L-iduronic acid (IdoA) residues for solutions in D2O of natural and synthetic oligosaccharides that represent the biologically important sequences of dermatan sulfate, heparan sulfate, and heparin have been rationalized by force-field calculations. The relative proportions of the low-energy conformers 1C4, 2S0, and 4C1 vary widely as a function of sequence and of pattern of sulfation. When IdoA or IdoA-2-sulfate units are present inside saccharide sequences, only 1C4 and 2S0 conformations contribute significantly to the equilibrium. This equilibrium is displaced towards the 2S0 form when IdoA-2-sulfate is preceded by a 3-O-sulfated amino sugar residue, and towards the 1C4 form when it is a non-reducing terminal. For terminal non-sulfated IdoA, the 4C1 form also contributes to the equilibrium. N.O.e. data confirm these conclusions. Possible biological implications of the conformational flexibility and the counter-ion induced changes in conformer populations are discussed.

A force-field study of the conformational characteristics of the iduronate ring

Methods of molecular mechanics were applied to investigate the conformation of the (methyl 2‐O‐sulfate‐4‐methyl‐α‐L‐idopyranose) uronic acid (DMIS), in order to correlate the peculiar vicinal proton coupling constants observed in polysaccharides containing the iduronate ring to the conformational characteristics of this sugar ring. We found three conformers with comparable energies, namely the two chair forms 1C4 and 4C1 and the skew‐boat form 2S0(L); the latter is separated from each chair form by a barrier of about 9 kcal/mol. Along the pseudorotational path three additional minima (3S1, 1S3, and 1S5) were found, yet at least 4 kcal/mol higher than 2S0. The results obtained for the relative energies of the three conformers and the conformation of the side groups were affected by the inclusion of the electrostatic term and, in particular, by the charge assigned to the ionic groups of DMIS. However, the conformational properties of the idopyranosidic ring in DMIS (and in related compounds) should still be interpreted in terms of equilibrium among these three conformers only.

Conformation of the pentasaccharide corresponding to the binding site of heparin for antithrombin III.

The conformation in solution of the pentasaccharide methyl glycoside (As-G-A*-Is-AM; 1), which represents the binding site of heparin for Antithrombin III, has been investigated using molecular mechanics and 1H-n.m.r. spectroscopy. The pentasaccharide has a rather rigid (As-G-A*) and a more flexible (Is-AM) region. A simplified model of 1, comprising two conformations, corresponding to the 1C4 and the 2S0 forms of the iduronate residue, and modified at the G-A* glycosidic linkage with respect to the energy minimum, reproduces most of the observed 3J values and n.O.e. enhancements. The possible role in the binding to Antithrombin III of a low-energy conformer, not observed in solution, is discussed.

Bridging the gap – structure determination of the red polymorph of tetrahexylsexithiophene by Monte Carlo simulated annealing, first-principles DFT calculations and Rietveld refinement

The crystal structure of the red polymorph of tetrahexylsexithiophene (THST) is solved from X-ray powder diffraction data by a direct-space Monte Carlo simulated-annealing approach. First-principles density functional theory (DFT) calculations are used to distinguish between three nearly identical solutions in the space groups C2/m, C2 and P\bar{1} and to improve the overall accuracy of the crystal structure. The correct space group is found to be C2/m. In all space groups, the thiophene backbone is planar and the hexyl side chains assume an all-trans conformation except for two terminal methyl residues, which adopt a gauche orientation. The ability of first-principles DFT calculations to provide atomic coordinates of single-crystal quality is demonstrated by lattice-energy minimization of the known crystal structure of the yellow polymorph of THST. The combination of Monte Carlo simulated annealing, first-principles DFT calculations and Rietveld refinement presented in this paper is generally applicable. It provides a powerful alternative to standard approaches in cases where the information content of the powder diffraction pattern alone is insufficient to distinguish between different structure solutions. DFT calculations can also provide invaluable guidance in Rietveld refinement.

Tetrahexylsexithiophene: crystal structure and molecular mechanics calculations

SUMMARY: The synthesis, crystal structure and detailed molecular mechanics calculations, including crystal packing interactions, of tetrahexylsubstituted sexithienylene are presented. Unexpectedly the molecule, which arranges in the P-1 space group, displays no herringbone arrangement, thienylenic rings are far from coplanarity and the alkylic side chains present different conformations. Molecular mechanics fully accounts for these findings. From crystal packing computations it is derived that different arrangements are unable to lower the packing energy, due to the closeness of two alkyl chains on the same side of the thienylenic backbone, which prevents interspersion of non-parallel molecules.

An improved force field for conformational analysis of sulfated polysaccharides

A force field to be used in molecular mechanics studies of sulfated polysaccharides with explicit account of water and counterion interactions was derived from the analysis of six crystal structures of sulfated monosaccharide salts. The force field is based on Allingers MM2, and was developed starting from the parameters used in previous studies of heparin and related oligosaccharides. While the novel parameters have been derived empirically, use of the atomic charge distribution obtained from ab initio quantum‐mechanical computations, at the 6–31 + G** level, improves the quality of structural fitting significantly. The overall discrepancy between the positions of the nonhydrogen atoms determined by X‐ray diffractometry and those corresponding to the minimum‐energy structure is 0.21 Å. While most geometrical features of both carbohydrate and sulfate moieties are reproduced satisfactorily, in some cases (particularly in the case of the Na+ salt of α‐methyl‐4‐O‐sulfogalactopyranoside) the hydrogen bond pattern is altered by energy minimization, probably due to errors in the balance of the strong electrostatic forces.

Treatment of ionic species in force-field calculations: Sulfate and carboxylate groups in carbohydrates

Ab initio computations with different basis sets (up to 6-31 + G* *) on methylsulfate and N-methylsulfate anions and on the ionic and neutral forms of acetic acid are presented. The atomic charges for the O-sulfo group, computed using the Merz-Kollman method at the highest level of theory, were inserted in a MM2-derived force-field; its current parametrization affords a 0.22 A root-mean-square deviation with respect to five crystal structures of sulfated monosaccharides.

Copolymer Microstructures of Ethylene Norbornene Copolymers Prepared with Homogeneous Metallocene Based Catalysts

Series of ethylene-norbornene copolymers were synthesized in the presence of zirconocenes with different symmetries and ligand patterns and at different norbornene/ethylene ratios. Copolymers were characterized by 13C NMR spectroscopy; Inadequate NMR sequences were used also. The comparison of 13C NMR spectra of copolymers prepared with different norbornene content and the correlation between 13C NMR chemical shifts and conformational structures of the chain on the basis of molecular mechanics calculations were performed. Preliminary assignments were revised and new comonomer sequences such as ENNE which contain meso and racemo NN dyads were assigned.

Toward a realistic force field for the treatment of ionic sugars

Heparin and other glycosaminoglycans involved in biological processes exist in solution as polyions: their specific activities are likely to depend on the geometrical arrangement of the charged (sulfate, carboxylate, amino) groups. Force-field methods, widely used in investigating molecular interactions, rely on proper interatomic potentials. However, in the case of these groups, little work has been done previously. Here we present a new parameter subset (to supplement an MM2-based force field) for N-and O-sulfate groups in sugars. Ab initio computations (RHF and MP2/6-31+ G∗∗) on model compounds, in particular Mesulfate and N-Me-sulfate, yielded a set of atomic charges and the value of the energy barrier to bond rotations. Experimental crystal structures of ionic monosaccharides (five O-sulfated and one N-sulfated) were taken as standard for fitting a number of parameters and as starting points for energy minimizations in which counterions and water molecules were also considered within the crystallographic environment. Models computed using the current parameter set fit the six experimental structures with an overall root-mean-square deviation of 0.21 A with respect to the heavy-atom positions.