Massimo Ragazzi - Academia.edu (original) (raw)
Papers by Massimo Ragazzi
Journal of Molecular Structure THEOCHEM, 1997
Heparin and other glycosaminoglycans involved in biological processes exist in solution as polyio... more 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 Nand 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. 0 1997 Elsevier Science B.V.
ACS Symposium Series, 1990
Thin Solid Films, 2002
In experiment, Maxwell's displacement current flew through the structure containing a metal e... more In experiment, Maxwell's displacement current flew through the structure containing a metal electrode, an air-gap insulating layer and a Langmuir monolayer situated on the water surface. This contactless arrangement provided a direct insight in the orientational motion of the monolayer constituting molecules. The effect of the surface pressure upon the molecular conformation was monitored by evaluating the vertical component of
International journal of …, 1995
Ab initio computations with different basis sets (up to 6-31 +G**) on methylsulfate and N-methyls... more 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.
Journal Cover
The interaction energy of formyl‐triglycyl amide (FTGA) with water has been analyzed following th... more The interaction energy of formyl‐triglycyl amide (FTGA) with water has been analyzed following the techniques described in the previous papers of this series, where the interaction of water with the naturally occurring amino acids (and some of their zwitter ions) and with the four bases of DNA were examined. FTGA has been chosen in order to obtain a realistic atomic interaction potential of water with the backbone of proteins. Since the peptide linkage (CO–NH) and the terminal formyl group are formed by atoms that are in a different electronic environment than those previously analyzed in this series of papers, new ’’classes’’ of atoms have been added to our pairwise potential library. In the computation of the wavefunction and energy of the FTGA–water complex, we have considered two different conformations of FTGA and a total of 158 positions and orientations of the water molecule. As previously done, the computed SCF–LCAO–MO interaction energies have been fitted with a set of pair potentials of very sim...
The Journal of Chemical Physics, 1979
Macromolecules, 1991
ABSTRACT
Macromolecules, 1984
... Dino R. Ferro* and Massimo Ragazzi Istituto di Chimica della Macromolecole del CNR, Via E. Ba... more ... Dino R. Ferro* and Massimo Ragazzi Istituto di Chimica della Macromolecole del CNR, Via E. Bassini, 15/A, 20133 Milano, Italy. ... bonded to j carbons) and Erxpjkrs = n'k (number of p carbons bonded to k carbons and separated from the observed atom by a j-type a car-bon). ...
Macromolecules, 1992
... Dino R. Ferro,* Stefano V. Meille, and Sergio Brückner §. Istituto di Chimica delle Macro... more ... Dino R. Ferro,* Stefano V. Meille, and Sergio Brückner §. Istituto di Chimica delle Macromolecole del CNR, Via E. Bassini 15, I-20133 Milano, Italy, Dipartimento di Chimica, Politecnico di Milano, Via Mancinelli 7, I-20131 Milano, Italy, and Dipartimento di Scienze e ...
Macromolecular Symposia, 1995
... 89,529-542 (1995) 529 APPLICATIONS OF MOLECULAR MECHANICS TO REFINE AND UNDERSTANDPOLYMERCRYS... more ... 89,529-542 (1995) 529 APPLICATIONS OF MOLECULAR MECHANICS TO REFINE AND UNDERSTANDPOLYMERCRYSTAL STRUCTURES Dino R. Ferro,* Massimo Ragazzi Istituto di Chimica delle Macromolecole del CNR, Via E. Bassini 15, 1-20133 Italy Sergio Briickner ...
New Journal of Chemistry, 2010
A series of oligomers constituting alternating thiophene and fluorenone residues, designed to eva... more A series of oligomers constituting alternating thiophene and fluorenone residues, designed to evaluate the effect upon both electronic properties and packing of the moiety sequence in the light of donor-acceptor concept, were synthesised and studied by cyclic voltammetry, optical spectroscopy, and XRD investigations into crystals, films, and powders. Moreover, ab initio calculations, based on Density Functional Theory, were carried out on selected molecules. A clear indication of close-packing induction by fluorenone in the oligomers, together with the factors determining the electrical and optical properties, are derived and presented. In the light of the performance of selected compounds in prototypes of p-type FET devices and bulk heterojunction solar cells, some general indications of chemical structure requirements for applications such as photovoltaic cells are described.
Tetrahedron, 1988
The conformation of the hexahydrocannabinol derivative (-I-(6~,9R.10aR)-6.6,9-trimethy1-6e.7,8.9.... more The conformation of the hexahydrocannabinol derivative (-I-(6~,9R.10aR)-6.6,9-trimethy1-6e.7,8.9.10,10a-harahydro-6H-dib~so[~,~]pyran (HHC) has been determined by land 2-D NOR experiments. the latter obtained with a pulse sequence which strongly reduces the contribution of the main diagonal. lJCH and 3J H have been measured in heteronuclear J-resolved 2-D spectra obtain s both with the gated decoupling technique, and with "spinflip" of directly attached protons ("semiselective" 2-D J-spectroscopy). Gn the baais of the NGR effects, it can be concluded that the conformation of the pyran ring is essentially half-chair. This result is consistent with the 3JaI s measured between the geminal methyl carbons at C-6 and H-6a; at leaat one of the two couplings appears to be sensibly lowered b thenearby oxygen. Tbe J 5'
Macromolecules, 1986
... Dino R. Ferro* and Massimo Ragazzi Istituto di Chimica della Macromolecole del CNR, Via E. Ba... more ... Dino R. Ferro* and Massimo Ragazzi Istituto di Chimica della Macromolecole del CNR, Via E. Bassini, 15/A, 20133 Milano, Italy. ... bonded to j carbons) and Erxpjkrs = n'k (number of p carbons bonded to k carbons and separated from the observed atom by a j-type a car-bon). ...
Macromolecular Theory and Simulations, 2001
Journal of the American Chemical Society, 1986
... Mono-and Oligosaccharides: NMR and Force-Field Studies Din0 R. Ferro,*+ August0 Provasoli,+ M... more ... Mono-and Oligosaccharides: NMR and Force-Field Studies Din0 R. Ferro,*+ August0 Provasoli,+ Massimo Ragami,+ Giangiacomo Torri,* Benito Casu,* Giuseppe Gatti,f Jean-Claude Jacquinet,l Pierre Sinay,l Maurice Petitou," and Jean Choay" ...
Carbohydrate Research, 1992
Carbohydrate Research, 1990
The 1H-n.m.r. 3J values for the L-iduronic acid (IdoA) residues for solutions in D2O of natural a... more 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.
Carbohydrate Research, 1995
The conformation of models of the epoxy-derivative of the glycosaminoglycan heparin has been stud... more The conformation of models of the epoxy-derivative of the glycosaminoglycan heparin has been studied by molecular mechanics calculations using a MM2-like force field extended with parameters for the oxirane ring. Two dimers, two trimers and several higher homologs modeling heparin epoxide were investigated, assuming the preferred 5H0 ring form of 2,3-anhydro-alpha-L-guluronic acid residue. Two-dimensional (phi; psi) maps of dimers showed the location of the energetically preferred conformers. Starting from the most stable dimer conformers, structures of trimers and other oligomers were derived and optimized, with an exhaustive search of the preferred sidechain conformers. The effect of solvation on conformation was analyzed using a continuum model of solvent. The present calculations indicate a significant flexibility of the heparin epoxide chain.
Carbohydrate Research, 1991
Search by Subject Search using Medical Subject Headings (< b> MeSH</b>), a controlled... more Search by Subject Search using Medical Subject Headings (< b> MeSH</b>), a controlled vocabulary for indexing life sciences content.< br/> Note that some records do not have MeSH. These include Patents and the latest PubMed and PubMed Central records.
Journal of Molecular Structure THEOCHEM, 1997
Heparin and other glycosaminoglycans involved in biological processes exist in solution as polyio... more 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 Nand 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. 0 1997 Elsevier Science B.V.
ACS Symposium Series, 1990
Thin Solid Films, 2002
In experiment, Maxwell's displacement current flew through the structure containing a metal e... more In experiment, Maxwell's displacement current flew through the structure containing a metal electrode, an air-gap insulating layer and a Langmuir monolayer situated on the water surface. This contactless arrangement provided a direct insight in the orientational motion of the monolayer constituting molecules. The effect of the surface pressure upon the molecular conformation was monitored by evaluating the vertical component of
International journal of …, 1995
Ab initio computations with different basis sets (up to 6-31 +G**) on methylsulfate and N-methyls... more 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.
Journal Cover
The interaction energy of formyl‐triglycyl amide (FTGA) with water has been analyzed following th... more The interaction energy of formyl‐triglycyl amide (FTGA) with water has been analyzed following the techniques described in the previous papers of this series, where the interaction of water with the naturally occurring amino acids (and some of their zwitter ions) and with the four bases of DNA were examined. FTGA has been chosen in order to obtain a realistic atomic interaction potential of water with the backbone of proteins. Since the peptide linkage (CO–NH) and the terminal formyl group are formed by atoms that are in a different electronic environment than those previously analyzed in this series of papers, new ’’classes’’ of atoms have been added to our pairwise potential library. In the computation of the wavefunction and energy of the FTGA–water complex, we have considered two different conformations of FTGA and a total of 158 positions and orientations of the water molecule. As previously done, the computed SCF–LCAO–MO interaction energies have been fitted with a set of pair potentials of very sim...
The Journal of Chemical Physics, 1979
Macromolecules, 1991
ABSTRACT
Macromolecules, 1984
... Dino R. Ferro* and Massimo Ragazzi Istituto di Chimica della Macromolecole del CNR, Via E. Ba... more ... Dino R. Ferro* and Massimo Ragazzi Istituto di Chimica della Macromolecole del CNR, Via E. Bassini, 15/A, 20133 Milano, Italy. ... bonded to j carbons) and Erxpjkrs = n'k (number of p carbons bonded to k carbons and separated from the observed atom by a j-type a car-bon). ...
Macromolecules, 1992
... Dino R. Ferro,* Stefano V. Meille, and Sergio Brückner §. Istituto di Chimica delle Macro... more ... Dino R. Ferro,* Stefano V. Meille, and Sergio Brückner §. Istituto di Chimica delle Macromolecole del CNR, Via E. Bassini 15, I-20133 Milano, Italy, Dipartimento di Chimica, Politecnico di Milano, Via Mancinelli 7, I-20131 Milano, Italy, and Dipartimento di Scienze e ...
Macromolecular Symposia, 1995
... 89,529-542 (1995) 529 APPLICATIONS OF MOLECULAR MECHANICS TO REFINE AND UNDERSTANDPOLYMERCRYS... more ... 89,529-542 (1995) 529 APPLICATIONS OF MOLECULAR MECHANICS TO REFINE AND UNDERSTANDPOLYMERCRYSTAL STRUCTURES Dino R. Ferro,* Massimo Ragazzi Istituto di Chimica delle Macromolecole del CNR, Via E. Bassini 15, 1-20133 Italy Sergio Briickner ...
New Journal of Chemistry, 2010
A series of oligomers constituting alternating thiophene and fluorenone residues, designed to eva... more A series of oligomers constituting alternating thiophene and fluorenone residues, designed to evaluate the effect upon both electronic properties and packing of the moiety sequence in the light of donor-acceptor concept, were synthesised and studied by cyclic voltammetry, optical spectroscopy, and XRD investigations into crystals, films, and powders. Moreover, ab initio calculations, based on Density Functional Theory, were carried out on selected molecules. A clear indication of close-packing induction by fluorenone in the oligomers, together with the factors determining the electrical and optical properties, are derived and presented. In the light of the performance of selected compounds in prototypes of p-type FET devices and bulk heterojunction solar cells, some general indications of chemical structure requirements for applications such as photovoltaic cells are described.
Tetrahedron, 1988
The conformation of the hexahydrocannabinol derivative (-I-(6~,9R.10aR)-6.6,9-trimethy1-6e.7,8.9.... more The conformation of the hexahydrocannabinol derivative (-I-(6~,9R.10aR)-6.6,9-trimethy1-6e.7,8.9.10,10a-harahydro-6H-dib~so[~,~]pyran (HHC) has been determined by land 2-D NOR experiments. the latter obtained with a pulse sequence which strongly reduces the contribution of the main diagonal. lJCH and 3J H have been measured in heteronuclear J-resolved 2-D spectra obtain s both with the gated decoupling technique, and with "spinflip" of directly attached protons ("semiselective" 2-D J-spectroscopy). Gn the baais of the NGR effects, it can be concluded that the conformation of the pyran ring is essentially half-chair. This result is consistent with the 3JaI s measured between the geminal methyl carbons at C-6 and H-6a; at leaat one of the two couplings appears to be sensibly lowered b thenearby oxygen. Tbe J 5'
Macromolecules, 1986
... Dino R. Ferro* and Massimo Ragazzi Istituto di Chimica della Macromolecole del CNR, Via E. Ba... more ... Dino R. Ferro* and Massimo Ragazzi Istituto di Chimica della Macromolecole del CNR, Via E. Bassini, 15/A, 20133 Milano, Italy. ... bonded to j carbons) and Erxpjkrs = n'k (number of p carbons bonded to k carbons and separated from the observed atom by a j-type a car-bon). ...
Macromolecular Theory and Simulations, 2001
Journal of the American Chemical Society, 1986
... Mono-and Oligosaccharides: NMR and Force-Field Studies Din0 R. Ferro,*+ August0 Provasoli,+ M... more ... Mono-and Oligosaccharides: NMR and Force-Field Studies Din0 R. Ferro,*+ August0 Provasoli,+ Massimo Ragami,+ Giangiacomo Torri,* Benito Casu,* Giuseppe Gatti,f Jean-Claude Jacquinet,l Pierre Sinay,l Maurice Petitou,&amp;amp;quot; and Jean Choay&amp;amp;quot; ...
Carbohydrate Research, 1992
Carbohydrate Research, 1990
The 1H-n.m.r. 3J values for the L-iduronic acid (IdoA) residues for solutions in D2O of natural a... more 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.
Carbohydrate Research, 1995
The conformation of models of the epoxy-derivative of the glycosaminoglycan heparin has been stud... more The conformation of models of the epoxy-derivative of the glycosaminoglycan heparin has been studied by molecular mechanics calculations using a MM2-like force field extended with parameters for the oxirane ring. Two dimers, two trimers and several higher homologs modeling heparin epoxide were investigated, assuming the preferred 5H0 ring form of 2,3-anhydro-alpha-L-guluronic acid residue. Two-dimensional (phi; psi) maps of dimers showed the location of the energetically preferred conformers. Starting from the most stable dimer conformers, structures of trimers and other oligomers were derived and optimized, with an exhaustive search of the preferred sidechain conformers. The effect of solvation on conformation was analyzed using a continuum model of solvent. The present calculations indicate a significant flexibility of the heparin epoxide chain.
Carbohydrate Research, 1991
Search by Subject Search using Medical Subject Headings (< b> MeSH</b>), a controlled... more Search by Subject Search using Medical Subject Headings (< b> MeSH</b>), a controlled vocabulary for indexing life sciences content.< br/> Note that some records do not have MeSH. These include Patents and the latest PubMed and PubMed Central records.