G. Vergoten

A new spectroscopic molecular mechanics force field. Parameters for proteins

We present the development of a new spectroscopic molecular mechanics potential for proteins. SPASIBA merges the torsional, van der Waals, electrostatic, and hydrogen bond potentials of AMBER with the Urey–Bradley–Shimanouchi terms for bond lengths and bond angles. To begin, SPASIBA was consistently parametrized to structural, energies, and vibrational frequency data of model compounds representative of the 16 nonaromatic acids: n‐alkanes, alcohols, acids, ethyl methyl sulfide, methyl sulfide in water, ethanethiol, dimethyl disulfide, guanidium ion, propionamide, N‐methylacetamide, N‐methylisobutyramide, and N‐isopropylacetamide. The parameters were then transferred to N‐acetyl‐X methylamides (where X=Gly, L‐Ala, L‐Pro), the L‐Leu, L‐Cys, and L‐Thr amino acids blocked by the carboxylate and ammonium ions, and the right‐handed deca‐alanine and Gly‐L‐Pro‐Gly‐Gly peptides. Results show that SPASIBA reproduces vibrational frequencies (with much higher accuracy than present molecular mechanics potentials), as ...

A vibrational molecular force field of model compounds with biological interest. III: Harmonic dynamics of α : and β-D-galactose in the crystalline state

Abstract The infrared spectra of α- and β- d -galactose were recorded, both in the mid-IR range (4000-500 cm −1 ) and in the far-IR (500-50 cm −1 ). The Raman spectra were also obtained. These spectra constitute the basis of a crystalline-state force field established for these two molecules through a normal coordinate analysis. A modified Urey—Bradley—Shimanouchi force field was combined with an intermolecular potential energy function which includes van der Waals interactions, electrostatic terms and an explicit hydrogen bond function. The force constants were varied, so as to obtain an agreement between the observed vibrational frequencies and the calculated ones of α- d -galactose. The force field obtained was then applied to α- d -galactose O- d 5 and β- d -galactose, in order to test its transferability. The computed potential energy distribution was found to be compatible with previous assignments for d -glucose, particularly for the modes involving C6 and COH groups. For β- d -galactose the same force field was used with changing the force constants due to the C1 and C6 groups.

Champ de forces de symetrie locale de molecules cycliques: III. Interprétation des spectres de vibration du glucose cristallisé sous les deux formes α et β

Abstract This paper reports complete infrared and Raman spectra of crystalline α and β glucose. Some high frequency bands are shown to be characteristic of the anomeric forms but there are significant differences in the low frequency region, despite the fact that the two forms crystallize in the same space group. These spectral data have been interpreted using a normal coordinate treatment of intra and intermolecular vibrations. Firstly, it was necessary to take into account both “tree” and “cycle” redundancies. Concerning the intermolecular vibrations, hydrogen bonds and atom-atom contacts were considered. Assignments of frequencies are given. A relation between the observed differences and the molecular structure modification is established and it is shown that hydrogen bonding is responsible for the differentiation of the α and β glucose low frequency spectra.

Assignment of normal modes for imidazole on the basis of 3-21G and 4-21G Ab Initio Force Fields

Abstract Calculated frequencies and 15 N-shifts for Im normal modes are obtained from normal coordinate analyses carried out using 3–21G and 4–21G ab initio force fields for both theoretical and experimental geometries. They are compared to new experimental data for high resolution FTIR frequencies and 15 N-shifts for Im vapor. Assignments are discussed by considering for each normal mode, potential energy distributions among internal coordinates obtained for both unscaled and scaled frequencies.

Application of three-dimensional molecular hydrophobicity potential to the analysis of spatial organization of membrane domains in proteins. I: Hydrophobic properties of transmembrane segments of Na+, K+-ATPase

A new computer-aided molecular modeling approach based on the concept of three-dimensional (3D) molecular hydrophobicity potential has been developed to calculate the spatial organization of intramembrane domains in proteins. The method has been tested by calculating the arrangement of membrane-spanning segments in the photoreaction center ofRhodopseudomonas viridis and comparing the results obtained with those derived from the X-ray data. We have applied this computational procedure to the analysis of interhelical packing in membrane moiety of Na+, K+-ATPase. The work consists of three parts. In Part I, 3D distributions of electrostatic and molecular hydrophobicity potentials on the surfaces of transmembrane helical peptides were computed and visualized. The hydrophobic and electrostatic properties of helices are discussed from the point of view of their possible arrangement within the protein molecule. Interlocation of helical segments connected with short extramembrane loops found by means of optimization of their hydrophobic/hydrophilic contacts is considered in Part II. The most probable 3D model of packing of helical peptides in the membrane domain of Na+, K+-ATPase is discussed in the final part of the work.

Etude par spectroscopie Raman du chlorhydrate de cocaïne

Raman spectra of cocaine hydrochloride in the polycrystalline state and in saturated aqueous solutions have been recorded at room temperature from 0 to 4000 cm(-1) and at 9 K from 0 to 200 cm(-1) (only for the polycrystalline state). They show that cocaine can be characterized by the following proposed assignments. For the tropane nucleus the frequencies 851 and 786 cm(-1) (piperidine) and 896, 870 cm(-1) (pyrrolidine); these frequencies are assigned to ring carbon stretching vibrations V(C-C) Bands for the ester functional groups can be observed at 1713 cm(-1) (v(CO)) and 1203 cm(-1) (v((C-O-O)). The benzene nucleus is also important in characterization of cocaine hydrochloride because of its bands at 616, 990, 1000, 1026 and 1596 cm(-1). Special reference is made first to the work in the low-frequency range at room temperature and 9 K and secondly to the polarization studies of saturated aqueous solutions in the range 700-1726 cm(-1). The results constitute a pool of analytical characteristics which can be used for toxicological investigations, and also show all the possibilities of Raman spectroscopy in this field.

Molecular modeling of a disialylated monofucosylated biantennary glycan of the N-acetyllactosamine type

The conformations of a disialylated monofucosylated biantennary glycan of theN-acetyllactosamine type were analysed using the Tripos 5.3 force field from the Sybyl software currently used for molecular modelling. The conformation of each glycosidic linkage was calculated when included in oligosaccharide structures of up to 5 units and the influence of the glycosidic environment on the overall structure was measured. The study clearly shows that the conformation of a branched glycan cannot result from the simple addition of the different low energy conformers of each of the glycosidic linkages constituting the glycan structure. The asymmetrical conformation of the two antennae was demonstrated. The lowest energy conformations of the overall glycan structure were built and classified into 5 main models: the Y, T, bird and broken wing conformations already described and a new one called the ‘back folded wing conformation’.

A vibrational molecular force field of model compounds with biological interest. IV. Parameters for the different glycosidic linkages of oligosaccharides

The force field previously obtained for both anomers of glucose has been applied to six disaccharides that are molecules of D‐glucopyranosyl residues. These six disaccharides have different types of glycosidic linkages—that is, α, α trehalose dihydrate (1‐1), sophorose monohydrate (β, 1‐2), laminarabiose (β, 1‐3), maltose monohydrate (α, 1‐4) and cellobiose (β, 1‐4), and gentiobiose (β, 1‐6). From a careful analysis of the infrared and Raman spectra and from harmonic dynamics calculations in the crystalline state, the results show the reliability and the transferability of the set of parameters previously obtained for different carbohydrates. Below 1500 cm−1, observed data and the corresponding calculated frequencies agreed within 5 cm−1 for each of the six disaccharides. The vibrational density of states are well reproduced by these calculations for each molecule, particularly for the fingerprint regions. Moreover, as found by other workers who used sophisticated potential energy functions, no additional terms are needed to express the exoanomeric effect. Specific force constants characteristic of each glycosidic linkage have been derived, particularly for the glycosidic angle bending. More interesting are the values of the internal rotation barriers. It is shown that they are of the same size for both sides of the glycosidic linkage: VC1O1 = VO1Cx′ = 3.29 kcal/mol for an alpha residue and 2.64 kcal/mol for a beta unit (x = 1–6 depends on the position of the glycosidic linkages of the considered disaccharide).

A comparative X-ray diffraction study and ab initio MO calculations on amidocyanopyridinium methylide

Abstract The crystal structure of amidocyanopyridinium methylide, C 8 H 7 N 3 O, has been determined using X-ray diffraction. The compound crystallizes in the monoclinic system, space group P 2 1 / c , with cell dimensions a =4.888 (1) A, b =11.931 (2) A, c =13.406 (2) A, β =105.84° (1) and Z =4. The structure has been refined to a final R =0.040 for 2500 reflections. The ylide carbon–pyridinium nitrogen bond distance is 1.422 (4) A. The refined structure was found to be significantly non-planar. The crystal structure of amidocyanopyridinium methylide is thus the second one, after that of dicyanopyridinium, in which the pyridine ring and the carbanion are almost coplanar. A comparative study using the ab initio procedure shows good agreement with X-ray diffraction data. Indeed, standard deviations between the calculated and the experimental values are 0.017 A and 0.685° for the bond lengths and bond angles, respectively. The energy difference between the calculated and experimental geometries is only 6.902 kcal mol −1 .

The use of the SPASIBA spectroscopic potential for reproducing the structures and vibrational frequencies of a sries of acids: acetic acid, pivalic acid, succinic acid, adipic acid and l-glutamic acid

Abstract Normal coordinate analyses have been performed on acetic, pivalic, succinic and adipic acid dimers (including their deutero analogues) and the l -glutamic acid dimer. It is shown that the calculated potential energy surfaces and harmonic vibrational frequencies are in very good accordance with the experimental results. For all the observed vibrational modes below 1750 cm −1 , the standard deviation between the 381 calculated and observed frequencies is approximately 12 cm −1 . Comparison with previous assignments underlines a quasi-agreement for the four former molecules. In contrast, new assignments are given for some vibrational bands of l -glutamic acid.