Showing papers on "Dihedral angle published in 1982"

Molecular-dynamics simulation of a bilayer-membrane

Abstract: We have applied the computer simulation method of molecular dynamics (MD) to a realistic representation of a lipid bilayer, which serves as a model for a biological membrane. The bilayer consists of 2×16 decanoate molecules and is periodic in two dimensions. Interactions include Lennard‐Jones, dihedral, and bond angle potentials while bond lengths are constrained. Head groups are confined near the bilayer surfaces by harmonic forces representing their interaction with the water layer. After equilibration, a simulation extending over 80 ps at 300 K was carried out for a head group surface area of 25 A2. Experimental order parameters are perfectly reproduced. A highly interesting cooperative tilt of the molecules, persisting over several tens of picoseconds, is observed. The molecular plane is strongly correlated with the plane of tilt. The popular kink model for the hydrocarbon chain order and dynamics is not supported. In view of the observed extended spatial correlation, a simulation was also carried out for a bilayer consisting of 2×64 decanoate molecules.

Protein dynamics in solution and in a crystalline environment: a molecular dynamics study.

Abstract: The effect of a solvent and a crystalline environment on the dynamics of proteins is investigated by the method of computer simulation. Three 25-ps molecular dynamics simulations at 300 K of the bovine pancreatic trypsin inhibitor (BPTI), consisting of 454 heavy atoms, are compared: one of BPTI in vacuo, one of BPTI in a box with 2647 spherical nonpolar solvent atoms, and one of BPTI surrounded by fixed crystal image atoms. Both average and time-dependent molecular properties are examined to determine the effect of the environment on the behavior of the protein. The dynamics of BPTI in solution or in the crystal environment are found to be very similar to that found in the vacuum calculation. The primary difference in the average properties is that the equilibrium structure in the presence of solvent or the crystal field is significantly closer to the X-ray structure than is the vacuum result; concomitantly, the more realistic environment leads to a number density closer to experiment. The presence of solvent has a negligible effect on the overall magnitude of the positional or dihedral angle fluctuations in the interior of the protein; however, there are changes in the decay times of the fluctuations of interior atoms. For surface residues, both the magnitude and the time course of the motions are significantly altered by the solvent. There tends to be an increase in the displacements of long side chains and the flexible parts of the main chain that protrude into the solvent. Further, these motions tend to have a more diffusive character with longer relaxation times than in vacuo. The crystal environment has a specific effect on a number of side chains which are held in relatively fixed positions through hydrogen-bond and electric interactions with the neighboring protein atoms. Most of the effects of the solution environment seem to be sufficiently nonspecific that it may be possible to model them by applying a mean field and stochastic dynamic methods.

Bonding in a binuclear metal carbonyl: experimental charge density in Mn2(CO)10

Abstract: X-ray diffraction data (Ag Ka and Mo Net radiation) have been collected at 74 K on dimanganese decacarbonyl Mn2(CO)I 0, and the crystal structure was refined. The atomic positional and thermal parameters were determined from high-angle AgKa data to avoid systematic errors due to bonding effects. The molecular geometry is discussed. The distortions are larger than at room temperature: for example, the torsion angle of the two Mn(CO) 5 fragments is 50.2 °, compared to 47.4 ° at room temperature, and 45 ° for an ideal D4a symmetry. 'X-X' deformation-density maps were computed and averaged over chemically equivalent sites. No significant charge-density accumulation is observed on the Mn-Mn bond. The configuration around the Mn atoms is essentially octahedral, with about 75% of the 3d electrons in the diagonal orbitals (dxy,d~z,dy ~) and the remaining 25% in d: and dx2_/. Atomic charges were determined both by direct integration and by least-squares refinement. Directly integrated charges are very small. Mn seems slightly negative. Both methods of charge integration show a clear difference between axial and equatorial carbonyls, which is confirmed by comparing their electron density with that of free carbon monoxide: the differences are characteristic of a a-bonding n-backbonding mechanism, and are larger for the axial carbonyls than for the equatorial carbonyls. This confirms the stronger bonding of the axial carbonyls, also responsible for the longer C-O bond and the shorter Mn-C bond.

Conformational dependence of the vicinal proton coupling constant for the CαCβ bond in peptides

Abstract: We use the nmr data concerning the CαHCβH fragment in eight peptides with rigid side chains to parametrize a Karplus correlation between the vicinal proton Jαβ coupling constant and the dihedral angle θ. When considering molecules containing the fragment CαHαCβHβHβ′, the three-dimensional structure of the model peptides does not need to be known with accurate precision, since each set of Jαβ and Jαβ′ coupling constants is then related to the coefficients of the Karplus equation. A good correlation is observed with the Karplus equation, which is in substantial agreement with the Jαβ coupling constants reported for rigid as well as rotating CαCβ bonds in peptides.

Pitfalls in the use of the torsion angle driving method for the calculation of conformational interconversions

Abstract: Several deficiencies and potential sources of error in the torsion angle driving method, the approach employed most frequently for the simulation of conformational interconversions, have been studied. A general explanation of the observed effects is given in terms of the energy surface and of the effects brought about by “side valleys.” Several examples of molecular mechanics calculations of conformational interconversions, among them the cyclohexane ring inversion, illustrate the problems.

Molecular‐mechanics studies on d(CGCGAATTCGCG)2 and dA12·dT12: An illustration of the coupling between sugar repuckering and DNA twisting

Abstract: Molecular-mechanics calculations have been carried out on the base-paired deoxy dodecanucleoside undecaphosphates d(CGCGAATTCGCG)2 and d(A12)·d(T12). These refinements were carried out using the model-built Arnott B-DNA geometry as initial coordinates (with a helix repaeat of 10.0 residues/turn), as well as helix repeats ranging from 9 to 12 residues/turn. There was some variation in the optimum calculated helix repeat, depending on the dielectric model, the presence or absence of counterions, and the method used for inclusion for nonbonded interactions; the most interesting general result of these calculations was the coupling between furanose sugar puckering and twist. This coupling was observed for all models. With a helix repeat of 9.0 residues/turn, all sugars remain C(2′)endo after refinement; as the helix repear increases to 12.0 residues/turn, the number of sugars repuckering to O(1′)endo and C(3′)endo increases also. With our most rigorous model (i.e., a model with no cutoff distance for nonbonded interactions) and a helix repeat of 10.0 residues/turn, we find a greater tendency for pyrimidine than purine repuckering in d(CGCGAATTCGCG)2, in agreement with the x-ray structural data of Drew et al. [(1981) Proc. Natl. Acad. Sci. USA78, 2179–2185]. We also carried out a number of calculations in which we “forced” one of two deoxy sugars to repucker or one of the C3′-O3′-P-O5′ (ω) torsion angles to change from gauche− to trans using dihedral angle constraints. After the constraints were removed, some of these structures “reverted” to the sugar pucker of the initial structures, while others remained repuckered. In all cases, the energies for repuckered structures after refinement were very similar to energies of the initial structure. Experiments and theory suggest that local conformational fluctuations play an essential role in nmr relaxation of 31P and 13C atoms in double-helical DNA. The results of our previous calculations on hexanucleoside phosphates and the calculations presented there are consistent with an important contribution to nmr relaxation processes of conformational changes in the torsion angle ω′ from gauche− to trans and deoxy sugar repuckering from C(2′)endo to C(3′)endo. Specifically, the calculations presented here indicate a very flexible phosphate backbone in helixes having an intermediate helix repeat of 10 to 11 residues/turn. These helixes may accommodate sugars of variable pucker without significantly disrupting base–base hydrogen-bonding and stacking interactions. All of the variant structures are similar in energy, suggesting that conversion between them can occur on a nanosecond time scale, as observed in nmr relaxation experiments.

Optical activity of the f–f transitions in trigonal dihedral (D3) lanthanide(III) complexes. I. Theory

Abstract: The theory of natural optical activity in the 4f→4f transitions of trigonal dihedral (D3) lanthanide(III) complexes is developed within the framework of a crystal field model. Within this model, both the chiral and achiral components of the crystal field are represented in terms of multipole‐point charge and multipole‐induced dipole lanthanide–ligand interactions. Electric dipole intensity within the 4f→4f transitions is presumed to arise from interconfigurational mixing between the 4fN, 4fN−1 5d, and 4fN−1 ng configurational states localized on the lanthanide ion, and between the 4fN configurational states of the lanthanide ion and dipolar excitations localized in the ligand environment. Expressions are derived for electronic rotatory strengths, dipole strengths, and dissymmetry factors, and special attention is given to how these quantities are related to the electronic and stereochemical properties of the ligand environment and to the electronic structure of the lanthanide ion. A computational model ba...

Studies of non-crystalline forms of selenium

Abstract: In this work results are presented of various experiments involving the amorphous form of massive selenium, and a structural study performed by X-ray diffraction in the wave vector region 0 A and over a large range of temperature (78 to 683 K). At first, to suppress doubts which subsist in spite of several published reports concerning amorphous material, we examine in detail the dependences of the physical properties and the structural variations on applying a uniaxial compression at 293 K in the metastable form. Comparisons between deformed or non-deformed materials (D a-Se or ND a-Se) are made using measurements of density, longitudinal sound velocity, differential thermal analysis, small angle scattering and careful analysis of the structure factor J(K). The information gained on the structural evolution with temperature is discussed. The variation of Debye temperature, determined from measures of sound velocity between 78 K and 300 K, permits us to calculate the thermal attenuation. In amorphous selenium, the Debye hypotheses are not valid. A temperature variation has no influence on the structure of the amorphous phase. In the viscous phase a slow evolution is observed but only in the liquid phase does a real change of J(K) appear. A disordered chain model is retained to describe the structure of the molecule in amorphous, viscous and liquid selenium. The elementary triangle of the selenium lattice remains constant. The intramolecular deformation is due to a limited variation of the dihedral angle which is random in sign. The limits of variation are reduced weakly by a uniaxial compression and also by an increase of temperature but only for T>Tg; the deformed chains approximate to the hexagonal arrangement. The presence of prolate ellipsoidal voids included between the chains explains the difference in density between the crystallized hexagonal Se and the amorphous material. Finally several simulated models are compared with the experimental J(K) measured at different temperatures. The same uncertainty always remains in the description of the models and the explanation of experiments as a result of the impossibility of separating the two contributive intra and intermolecular disorders.

Raman Spectroscopy of Avidin: Secondary Structure, Disulfide Conformation, and the Environment of Tyrosine?

Abstract: An analysis of the amide I region of Raman spectra indicates that avidin has 10 +/- 5% and 55 +/- 4% of its residues in helical and beta-strand conformations, respectively. Predictions of secondary structure on the basis of the sequence of avidin are consistent with the high percentage of residues in the beta conformation. We observe no differences between the spectra of avidin in solution and in crystals nor is there a significant difference between the secondary structures of avidin and the complex of avidin with biotin. In addition, the ratio of the intensities of the tyrosine doublet at 826 and 855 cm-1 indicates the lone tyrosine side chain of an avidin subunit is in a strong hydrogen bond as a proton acceptor. The Raman data also indicate the single disulfide of an avidin subunit has dihedral angles of 0-50 degrees for each of its two C beta-S bonds and a dihedral angle of 85 +/- 20 degrees for its disulfide bond. We discuss the significance of these results in relation to findings of earlier work on avidin.

Conformational consequences of intramolecular hydrogen bonding by OH to the directional lone-pair of sulfur in derivatives of methyl phenyl sulfide, diphenyl sulfide, and diphenyl disulfide

Abstract: Complete spectral parameters for the 1H nmr spectra of 2-hydroxyphenyl methyl sulfide, 2, 2-hydroxyphenyl phenyl sulfide, 3, bis(2-hydroxy-3-tert-butyl-5-methylphenyl) sulfide, 4, and bis(2-hydroxyphenyl) disulfide, 5, are reported for CCl4 solutions at 305 K. For 2 the parameters are consistent only with a conformation in which the C—S—C plane is roughly perpendicular to the aromatic plane. The conformational determinant is the hydrogen bond which forces the mainly 3p orbital on sulfur into the benzene plane. In 3 a similar arrangement is found about the sulfur atom, with the phenyl group lying in the C—S—C plane and therefore perpendicular to the hydroxyphenyl plane (skew conformation). In 4 two hydrogen bonds exist, yielding a gable (twist) conformation. Compound 5 exists in the axial conformation with probable C2 symmetry, the CSSC dihedral angle and the CCSS torsion angles all being near 90°. For none of the compounds is there any evidence for interactions.

Atomic models of amorphous selenium

Abstract: A critical review of the literature has been carried out on the structure of amorphous selenium. Two molecular models were then constructed to follow the conclusions derived from the survey and to also fit newly obtained radial distribution functions for bulk quenched amorphous selenium. These computer models followed four criteria: (1) the molecules were disordered chains; (2) the chains were packed to maximize Van der Waals attractions; (3) the close-packing was achieved by letting the magnitude of the dihedral angle vary slightly and by letting the phase of the dihedral angle vary randomly; (4) closed rings were assumed to be few in number and thus negligible in fitting the RDF. It was found that the percentage of cis and trans configurations in the molecules could vary widely and still be consistent with both the radial distribution function and with physical criteria. Thus the cis/trans ratio, or the phase of the dihedral angle, is not unique for amorphous selenium. The structure of a-Se may be described as consisting of coiled disordered chains which are packed in such a way as to minimize the Van der Waals bond lengths in a minimum cluster which has a radius of 11 A.

Optical activity of the f–f transitions in trigonal dihedral (D3) lanthanide(III) complexes. II. Calculations

Abstract: Calculations of dipole strengths, rotatory strengths, and dissymmetry factors associated with the 4f↔4f transitions of trigonal dihedral (D 3) lanthanide(III) complexes are reported. These calculations, based on a theoretical model described in the previous paper [J. Chem. Phys. 76, 1595 (1982)], represent the first attempt to quantitatively account for the chiroptical properties of lanthanide systems. As model systems, tris‐terdentate chelate structures formed by oxydiacetate (ODA2−) ligands and the trivalent lanthanide ions Pr3+, Eu3+, Tb3+, and Ho3+ are considered. Calculations are reported for both isotropic and oriented samples of the Ln(ODA)3 3− systems. Parameters varied in the computational model include ligand geometry, ligand charges and polarizabilities, and lanthanide crystal field coefficients. The results of the calculations are applied to the interpretation of lanthanide CD/absorption and CPL/emission spectra. Special emphasis is given to the r e l a t i v e chiroptical strengths predicted for term‐to‐term transitions and to the ligand structure parameters having the greatest influence on the chiroptical properties. The calculated results demonstrate that the theoretical model correctly accounts for most of the qualitative aspects of lanthanideoptical activity as observed by experiment. In a few cases, the calculations also achieve quantitative or semiquantitative agreement with experimental observation. However, the model as applied in this study is not sufficiently refined to permit reliable calculations of lanthanide chiroptical spectra at the level of crystal field component resolution.

Beiträge zur Chemie des Phosphors, 116 Kernresonanzspektren und Kristallstruktur von Tri-tert-butylcyclotriphosphan / Contributions to the Chemistry of Phosphorus, 116 NMR Spectra and Crystal Structure of Tri-tert-butylcyclotriphosphane

Abstract: A complete analysis of the ³¹P, ¹³C and ¹H NMR spectra of tri-tert-butyl-cyclotriphosphane (1) was carried out and the resulting NMR parameters were correlated with the X-ray data of the molecule. It was found, that increasing P-P-C-bond angles correspond to a downfield shift and an increase of the absolute values of the negative ¹J(PP) and ¹J(PC) coupling constants. Generally, the chemical shifts of cyclotriphosphanes as well as of larger cyclic phosphanes depend on the endo- and exocyclic bond angles, the dihedral angle between the electron lone pairs of adjacent P-atoms, and the β-effect. On the basis of the X-ray and chemical shift data of 1, the bond angles of other cyclotriphosphanes can be deduced from their δ(³¹P) values. 1 crystallizes triclinically in the space group P1 with Z = 4 formula units. The X-ray analysis confirms the NMR-spectroscopically determined three-membered ring structure with the tert-butyl substituents on either side of the ring plane. Due to steric hindrance between the two tert-butyl groups in cis position, the corresponding P-P-C-bond angles show the largest values so far observed for organylcyclophosphanes.

The influence of symmetry on the conformational dependences of scalar and vectorial properties for double‐rotor molecules

Abstract: We show how specific parameters of double‐rotor molecules can be characterized by up to six symmetry indices depending on whether the molecule is linear, bent planar, or gauche and whether the parameter is scalar or vectorial, aggregate, mononuclear, or binuclear. These symmetry indices can be used to select the distinct, nonzero, harmonic coefficients in the limited Fourier‐series expansions of the parameters as functions of the dihedral angles. Illustrative applications are given to the numerical calculations of the torsional potentials for the isomers of xylene and of the hyperfine couplings for the protons in propyl.

A theoretical investigation of the sulfur—selenium bond

Abstract: A theoretical ab initio study of HSH, HSeH, HOOH, HOSH, HSSH, HSSeH, HSeSeH, HSSSH, HSeSSH, HSSeSH, HSeSeSH, HSeSSeH and HSeSeSeH has been performed using minimal Gaussian basis sets. Full geometry optimization has been carried out for HSH and HSeH. For the four-atom molecules only the chalcogen —chalcogen bond length and the dihedral angle have been optimized while other bond parameters are held fixed at experimental values. The geometries of the five-atom molecules have not been optimized. The calculated bond parameters of HSH and HSeH are in good agreement with the experimental values. The optimum XY (X, Y  S, Se) bond lengths are somewhat larger than the values estimated from IR and microwave data. The electronic structures of the molecules indicate that the SS, SeS and SeSe bonds are very similar. The total energy change calculated for the interconversion reaction between these bonds is small, as indicated by experimental studies. This may well explain why the rearrangement reactions between various Se n S 8— n molecules are possible both in solution and in the molten state. A possible mechanism for the rearrangement is discussed.

Electronic Absorption Spectra and Geometry of Molecular Ions Generated from Stilbene and Related Compounds. II. Radical Ions of (E)-Stilbene and Related Compounds

Abstract: The electronic absorption spectra of radical ions produced by γ-ray irradiation of (E)-stilbene and related compounds in frozen matrices were measured. On illumination and on controlled warming, the spectra of the radical ions of sterically uncrowded stilbenes and diphenylacetylene remained almost unchanged, while those of the radical ions of sterically crowded stilbenes changed noticeably. Examination of the spectra and of their changes led to the following conclusions: (a) The relaxed geometry of the radical ions of sterically uncrowded stilbenes is planar or nearly planar; (b) in the unrelaxed geometries of the radical ions of (E)-α,β-dialkylstilbenes the torsion angles of the Ph–C bonds are nearly as large as in the parent molecules, and on relaxation these angles become smaller and the torsion angle of the central ethylenic bond deviates from 0° to a considerable extent; (c) for the radical ions of ortho-substituted (E)-stilbenes the geometrical change on relaxation is comparatively small.

Coordinating properties of alkylated 6-aminopurines. electrostatic potential distributions for 3-methyladenine and 9-methyladenine and preparation and structure of cis-diamminebis(3-methyladenine)platinum(ii) nitrate trihydrate

Abstract: Electrostatic potential maps have been computed for 3-methyladenine and 9-methyladenine under the INDO molecular orbital approximation. These maps clearly indicate a shift in the attractive electrophilic site from N ( 1) of the six-membered pyrimidine ring to N(7) of the five-membered imidazole ring and a marked increase in molecular dipole moment on going from the 9-substituted to the 3-substituted purine. These features help to rationalize the increased ligating power of 3-alkylated 6-aminopurines over 9-alkylated 6-aminopurines. The synthesis, solution ‘H NMR spectrum, and solid-state molecular and crystal structure of cis-diamminebis(3-methyladenine)platinum(II) nitrate trihydrate, ~ is [ (NH~)~Pt(3-MeA) ,1(N03)2.3H20, are also reported. The compound crystallizes in the triclinic system, space group P1, with a = 10.877 (4) A, b = 15.395 (5) A, c = 7.604 (2) A, CY = 103.33 ( 2 ) O , p = 102.90 (2)O, y = 99.94 (2)O, V = 1173.6 A3, Z = 2 (based on a molecular weight of 705.52 for [Pt(NH3)2(C,N,H,)2](N03)2.3H20), Dmcasd = 1.99 (1) g ~ m ~ , and Dmld = 1.99 g ~ m ~ . The crystal structure was solved by conventional Patterson and Fourier methods and refined by full-matrix least-squares techniques to an R value of 0.044. The C ~ S [ ( N H , ) ~ R ( ~ M ~ A ) ~ ] ~ + cation is essentially square planar with the two independent 3-MeA ligands showing N(7)-Pt bonding and is arranged in a head-to-tail fashion such that the complex cation possesses approximate C2 molecular symmetry. Principal geometrical parameters are as follows: Pt-N(ammine) = 2.039 (6) A, 2.031 (6) A; Pt-N(7)(3-MeA) = 2.010 (4) A, 2.004 (4) A; N(ammine)-Pt-N(ammine) = 90.6 (2)O; N(7)-Pt-N(7) = 89.5 (2)’; interbase dihedral angle = 90.6O; base/PtN, coordination plane dihedral angle = 98.9, 11 1.8’. The extended crystal structure exhibits two different types of base-stacking interactions and two different kinds of base pairing through hydrogen bonds. There is also an extensive network of hydrogen bonds. Further stabilization is afforded by base/nitrate anion stacking. The IH N M R spectrum of the platinated 3-MeA ligand is compared to that of the free base and to the spectra of several Co(III)-3-alkylated 6-aminopurine complexes. The present complex affords a model for an N(7)J,.AMP-Pt-N(7)Y-AMP type cross-linking mode that is perhaps applicable to the binding of Pt(I1) antitumor drugs to DNA. It is suggested that such a cross-link would demand about the same degree of local denaturation of a polynucleotide as one of the type N(7),,.GMp-Pt-N(7),t.GMP.

Dipole moments, spectroscopy, and ground and excited state conformations of cycloalkane-1,2-diones

Abstract: The dipole moments of a series of α,α,ω,ω-tetramethylcycloalkane-1,2-diones with a ring size varying between 4 and 8 carbon atoms, and of di-t-butylglyoxal, camphorquinone, and homoadamantane-4,5-dione have been measured. The (time-averaged) dihedral angle Φ between the carbonyl groups of these compounds has been calculated from the dipole moments. The HeI photoelectron spectra showed that the ionization potentials of the two different non-bonding MOs (N+ and N–) hardly vary with the ring size and thus with Φ. The u.v. absorption spectra exhibit two bands; the long wavelength band shifts from ca. 330 nm for a substrate with perpendicular diketo-geometry to ca. 450 or 500 nm for a planar transoid and planar cisoid diketo-conformation, respectively. The second absorption band is found for all compounds at ca. 285 nm. The fluorescence and phosphorescence bands shift in a regular way relative to the long wavelength absorption band, viz. the shift is maximal for Φ 90° and minimal for Φ 0 or 180°. The data show in a quantitative way that 1,2-diketones emit from excited states with coplanar diketo-geometry.

A 13C cross polarization–magic angle spinning (CP-MAS) n.m.r. study of crystalline cyclohexa-amylose inclusion complexes. Conformation-dependent 13C chemical shifts are related to the dihedral angles of glycosidic linkages

Abstract: 13 C Chemical shifts of the C-1 and C-4 atoms of crystalline cyclohexa-amylose enclosing a variety of guest molecules are significantly displaced as a result of host–guest interaction and are related to the dihedral angles (ϕ and ψ) at the linkages.

The Strain Energy, Geometrical Structure, and Spin–Spin Coupling Constants of Cyclic Hydrocarbons

Abstract: The thermochemical data and spin–spin coupling constants (SSCC) are compared with the geometrical parameters of molecules investigated in the gas phase by electron diffraction and microwave spectroscopy. Cycloalkanes CnH2n, cycloalkenes CnH2n–2, cyclo-1,3-dienes, bicyclo[n.1.0]alkanes, and bicyclo[n.m.1]alkanes have been chosen as objects of investigation. Using the method of least squares, 13 empirical equations, relating the strain energy and the SSCC, on the one hand, to the internuclear distances and the valence and dihedral angles, on the other, have been fitted. The equations can be used to estimate the characteristics of compounds which have not been investigated. The bibliography includes 170 references.

On the fluctuation-dissipation theorem for interacting brownian particles

Abstract: The correct form of the fluctuation-dissipation theorem for interacting brownian particles contains a term due to the interparticle force, which has usually been ignored in brownian dynamics (BD) simulations. In order to estimate its size, a BD simulation of n-butane has been performed. The term appears to be virtually zero. Besides, the process of energy transfer through the molecule has been studied. It displays two time scales. Energy relaxation involving the bond length and bond angle degrees of freedom takes less than 1 ps, whereas the energy is only completely redistributed after about 100 ps, which is due to the weak coupling of the atoms through the dihedral degree of freedom.

Conformation‐dependent Raman bands of phospholipid surfaces. 3—head group Ortho‐phosphate stretching vibrations

Abstract: Vibrational frequencies of diethyl phosphate were calculated for rotamers for which the dihedral angle about the PO and CO bonds varied. The frequencies predicted for the symmetric and antisymmetric OPO stretches, the symmetric and antisymmetric ionic PO2− stretches, and the CC stretches are found to be sensitive to the PO and CO dihedral angles. The results of Raman temperature and solvent studies of diethyl phosphate are reported and are found to be in good agreement with the conclusions obtained from the normal coordinate analyses. Frequencies of diethyl phosphate rotamers having the geometries of crystalline glycerophosphorylcholine (GPC), crystalline GPC CdCCl2, and amorphous GPC CdCl2 were calculated and compared to the Raman spectra of these phospholipid head group models. The normal coordinate analyses are in good agreement with Raman spectra. These results indicate that the observed frequencies of phosphate group vibrations may be compared to the normal coordinate analyses of diethyl phosphate rotamers to monitor conformation in phospholipid head groups (and other organic ortho -phosphates). The Raman symmetric OPO stretch bandwidth may be used to monitor rotational freedom or broadening due to the distribution of differing conformations.

Comprehensive conformational analysis of (Gly‐Pro‐Pro)n and (Gly‐Pro‐Hyp)n related to collagen

Abstract: A complete analysis of all possible conformations with correct hydrogen bonds of the collagen II type was performed on the basis of developed simultaneous equations. Using a unimodal search (by varying Ψ3), the energetically favorable structure was obtained. No other energetically satisfactory structural solutions are possible. The next aim was to obtain a precise model of the molecule. The program used includes a subroutine for continual deformation of the pyrrolidine rings. The set of parameters determining the structure consists of 14 independent variables (8 dihedral and 6 bond angles). As starting points for the energy optimization, conformations produced by scanning and some structures from previous work were used. The final structures (practically the same for both polymers) have helix parameters h = 0.285 nm and t = 52°, which are in excellent agreement with the 7/2 symmetry of diffraction data. The conformations of the pyrrolidine rings are of the B type, i.e., C2-Cβ-exo-Cγ-endo. For both polypeptides, the conformations of imino acids in position 3 of the triplet are the same; in position 2, however, they are slightly different. The difference in diffraction patterns for the 7/2 and 10/3 helices is discussed.