Showing papers on "Dihedral angle published in 1971"

A real-space refinement procedure for proteins

Abstract: This paper describes a procedure which optimizes the fitting of a `model' of a protein to an electron density map. The technique seeks to minimize ∫ (Qo−Qm)2dv where Qo is the observed electron density and Qm is a density associated with a model in terms of which the observed densities are interpreted. Qm consists of a Gaussian density centred on each atomic centre, and a floating background level. Interactions due to overlapping densities of neighbouring atoms are allowed for and the model is normally treated as a flexible chain so that bond lengths are conserved during movement. Alternatively, the atoms may be allowed to move independently. Site occupations and atomic radii are also refinable. The calculation is organized in terms of a `molten zone' of up to ten residues, which moves along the chain one residue at a time, linear or non-linear constraints being applied to preserve chain continuity at each end of the zone. Provision is made for the zone to become active or inactive in predetermined regions of the molecule. A difference map (Qo−Qm) is available at the end of the calculation, as is a molecular listing with revised coordinates and dihedral and inter-bond angles. Inter-bond angles may be treated either as constants or as variables, and if variable may be made elastically stiffer than dihedral angles. The procedure is well suited to maps of 2 to 3 A resolution, but is not limited to this range. It has produced convergent shifts exceeding 1.5 A in a map of 2 A resolution, and, except for shifts exceeding 1 A, convergence is essentially complete in one pass. The procedure has, so far, been applied to four proteins.

Variation of the NH–CαH coupling constant with dihedral angle in the NMR spectra of peptides

Abstract: Proton magnetic resonance data and conformational calculations of a series of model compounds containing a NH-CαH group substituted as in peptides have been used to generate a proton–proton coupling constant–dihedral angle relation for the peptide unit. For those substances used in which the dihedral angle about the N-Cα bond is not fixed, the angle distribution was calculated from conformational theory. Using eight examples in which the number of theoretical assumptions were least, the best values of the coefficients A, B, and C in the expression J(θ) = Acos2θ + B cosθ + Csin2θ were found by a least-squares procedure to be 7.9, −1.55, and 1.35, respectively. This relation gives reasonable values for the dihedral angles ϕ in cyclic oligopeptide structures for which the availability of both NMR data and other structural information allow comparison. When applied to N-acetylamino acid N-methylamides having side chains extending beyond Cβ, however, agreement with the calculated conformational distribution was found for Leu, Met, and Trp, but observed values of J were larger than expected for Val, He, Phe, and Tyr, These disagreements are considered to be the result of interactions not yet taken into account in the usual conformational calculations.

Structures of Norbornane and Norbornadiene as Determined by Gas Electron Diffraction

Abstract: The structures of norbornane and norbornadiene in the gas phase have been investigated by electron diffraction. For the most probable models the rg bond lengths and the bond angles (based on the rα structure) with estimated limits of error are as follows: For norbornadiene: C1–C2=1.5354±0.007 A, C2=C3=1.3432±0.003 A, C1–C7=1.573±0.014 A, ∠C1–C7–C4=94·1±3·0°, and θ (the dihedral angle between the C1–C2–C3–C4 and C4–C5–C6–C1 planes)=115·6±2·2°; For norbornane: C–C(average)=1.5488±0.003 A, C1–C2=1.539±0.012 A, C2–C3=1.557±0.025 A, C1–C7=1.560±0.024 A, ∠C1–C7–C4=93·1±1·7°, and θ=113·1±1·8°. The frame structures of these molecules are similar to each other except for the C2–C3 bond distances. All the C–C–C valence angles are appreciably smaller than the tetrahedral angle (∠C1–C7–C4 in particular). The C1–C7, bridge bonds appear to be longer than the normal C–C single bond. The above structures are compared critically with those reported so far by other investigators. A method for estimation of systematic error...

Electron-diffraction study of the molecular structure of dimethyldisulphide, (CH3)2S2

Abstract: The molecular structure of (CH3)2S2 has been studied by gas-phase electron diffraction. The results confirm a published microwave study, but are superior in precision. The orientation of the methyl groups was refined and it is established that the C—H bonds are staggered (or nearly so) with respect to the S—S bond. The principal parameters are C—H = 1.090±0.007 A, S—C = 1.806±0.002 A, S—S = 2.022±0.003 A, ∠SSC = 104.1±0.3°; the dihedral angle of the CSSC skeleton is 83.9±0.9°. The S—S length is significantly shorter than found in H2S2. The work differs from a standard structure analysis in that two sets of data were used, based on different treatments of the background. Slight differences in some of the less well determined parameters were observed.

Couplings into Methylene Groups: a New Nuclear Magnetic Resonance Approach to Stereochemistry

Abstract: A method of assigning dihedral angles to hydrogens adjacent to a methylene function by using computer analyzed n.m.r. coupling constants in a modified Karplus equation is presented. The "Dihedral Angle Estimation by the Ratio Method" (DAERM) is based on the assumption that, although the magnitudes of the Karplus constants, k1 and k2, vary, the ratio of k1 to k2 is a constant. Dihedral angles computed in this way seem not to be influenced by the effects of ring strain and substituent electronegativity. The conformational preferences of several four- to six-membered ring Systems, some containing oxygen and sulfur atoms, have been investigated by this method. Molecular features such as ring puckering and flattening are indicated by DAERM as are some subtle electrostatic influences.

Structure and Rotational Isomerism of Ethylenediamine as Studied by Gas Electron Diffraction

Abstract: The structure and the rotational isomerism of ethylenediamine have been investigated by means of gas electron diffraction. Evidence has been given for the presence of one conformer (gauche) in the vapor phase (at 50–120°C); the N–C–C–N dihedral angle measured from the cis position is 64·0±4°, and the fraction of any other isomer, if present, is estimated to be less than 5%. A theoretical prediction based on the SCF-CNDO/2 method has essentially accounted for this finding. The rg distances and the angles based on the ra structure determined by a least-squares analysis on molecular intensities, with estimated limits of error, are as follows: C–C=1.545±0.008 A, C–N=1.469±0.004 A, ∠C–C–N=110.2±0.7°, C–H=1.109±0.01 A, ∠C–C–H=111·9±5°, and ∠H–C–H=112·7±8°.

The Crystal and Molecular Structure of 2,5-Distyrylpyrazine

Abstract: 2,5-Distyrylpyrazine(C20H16N2), which has photo-polymerizability in the crystalline state, crystallizes in the orthorhombic system with cell dimensions of a=20.638, b=9.599, and c=7.655 A, including four molecules in the unit cell. The space group is Pbca. The structure has been determined by the direct method and refined by the block-diagonal-matrix least-squares method using three-dimensional data. The molecules is not planar; the average plane of the pyrazine ring makes a dihedral angle of 12.09° with that of the benzene ring. The molecules are spaced by the c-translation forming an almost parallel plane-to-plane stack. In this stack, the ethylenic double bonds approach each other at the shortest intermolecular distances of 3.939 A, since the long axis of the molecule makes an angle of about 30° with the c-axis. Therefore, the polymerization may occur between these double bonds to form a cyclobutane ring.

Consistent force field calculations on 2,5‐diketopiperazine and its 3.6‐dimethyl derivatives

Abstract: The minimum energy conformations are calculated for 2, 5-diketopiperazine (DKP) and its 3,6-dimethyl derivatives (DL-DMDKP and LL-DMDKP), using a consistent force field approach developed previously. The energy function parameters that were not required in earlier calculations on alkanes, amides, mid lactams are fitted to spectral and conformational data on the diketopiperazines. Vibrational assignments are suggested for DKP. Conformational energies are also determined over a range of selected values for ring dihedral angles, and the shape of the potential energy functions is examined over deviations from planarity. DKP and LL-DMDKP are found to have non-planar minimum energy conformations, separated from planar by less than a kcal/mole. DL-DMKP exhibits a nearly flat trough about the planar conformation. Calculations of minimum energies with one dihedral angle coordinate constrainted show a coupling between bond angles and dihedral angles in agreement with recent suggestions of Benedetti.

Nuclear magnetic resonance studies of lysine-vasopressin: structural constraints.

Abstract: The 220-MHz proton NMR spectra of lysine-vasopressin and some related compounds are examined in deuterated dimethyl sulfoxide to obtain structural information that must be satisfied by any proposed conformation of the molecule. This structural information is in the form of dihedral angles (for rotation about the NH-CαH bonds) from coupling constants, possible hydrogen bonding of the CONH2 and backbone amide groups from the temperature-dependence of the chemical shift, and aromatic ring-aromatic ring interaction from the effect of the magnetically anisotropic groups on the chemical shift.

Structures of Bicyclo[2.2.2]octene and Bicyclo[2.2.2]octadiene as Studied by Gas Electron Diffraction

Abstract: Bicyclo[2.2.2]oct-2-ene and bicyclo[2.2.2]octa-2,5-diene have been investigated by gas electron diffraction. They are found to have C2v symmetry in respect of the thermal-average nuclear positions. The structural parameters with estimated limits of error (the γg bond lengths and the angles difined in the γα structure) determined by a leastsquares analysis on the molecular intensities are as follows for octene and octadiene, respectively: C(sp3)–C(sp3) (weighted average of the C1–C7, and C7–C8 bonds)=1.549±0.008 and 1.553±0.017 A, C(sp2)–C(sp3)=1.509±0.015 and 1.521±0.008 A, C(sp2)–C(sp2)=1.341±0.008 and 1.339±0.005 A, C(sp3)–H (average)=1.112±0.008 and 1.105±0.012 A, ∠C–C=C=114.2±0.6° and 113.5±0.5°, The dihedral angle θ between the C1–C2–C3 C4 and C1–C6–C5–C4 planes=121.2±2.1° and 123.4±2.2°, ∠C=C–H=122.4±6.0° and 125.5±4.0°, ∠H–C–H=109.2±4.0° and 111.3±7.0°. A conformational analysis based on an empirical prescription of strain energies, similar to that of Jacob et al., and a molecular-orbital analysis ...

Approximate Treatment of the Conformational Characteristics of a Cyclic Nonapeptide, Cyclolinopeptide A

Abstract: Possible conformations for a cyclic nonapeptide that are consistent with conformation-dependent information obtained from an NMR investigation of the peptide in solution are presented. These several conformations are deduced from the myriad of possible conformations by eliminating from consideration all cyclic species having one or more residues in a conformation that does not correspond to the vicinal coupling constants observed by NMR between the amide and α-protons. A Karplus-like relation connecting the dihedral angle [unk]′ and the vicinal coupling JNα between N—H and Cα—Hα is used to test this correspondence. A further reduction in the number of cyclic conformations under consideration is made possible by rejecting the conformations that have a high intramolecular conformational energy. The intramolecular conformational energy of the cyclic nonapeptide is estimated by summing the independent residue energies. These have been calculated by others with approximate potential functions to account for the intrinsic torsional potentials and the nonbonded steric (6-12 potential) and electrostatic (monopole-monopole) interactions solely dependent upon one or both of the residue rotations, [unk] and Ψ, about the N—Cα and Cα—C bonds, respectively.

Conformational energy map of a dipeptide unit in relation to infrared and nuclear magnetic resonance data.

Abstract: The variation of energy of the conformation of a dipeptide unit with the dihedral angles \phi and \psi is a fundamental aspect, which is of great importance to the study of protein structure. Good reviews are available dealing with the energy changes associated with the variation of different parameters such as bond lengths, bond angles, dihedral angles etc. Also recently, attempts have been made to obtain satifactory expression for hydrogen bond energy as a function of the parameters relating to it . Although various results of interest in relation to the conformation of polypeptides and proteins have been worked out from such theory, the theoretical results have not been dirertly tested in many cases in relation to available data from physicochemical studies on a dipeptide unit, or fragments of simple compounds which sufficiently approximate to it. The purpose of this prelimiiiary note is to point out the possibility of making such tests and to indicate some results which show reasonable agreement with data obtained from infrared arid NMR studies.

Crystal and molecular structure of bis-(2,2-bipyridylamine)copper(II) perchlorate

Abstract: The crystal structure of bis-(2,2′-bipyridylamine)copper(II) perchlorate, [Cu(C10H9N3)2](ClO4)2, was determined from single crystal X-ray diffraction data which was measured on a diffractometer. The crystals are monoclinic, space group C2/c, with a= 9·35, b= 12·88, c= 19·69 A, β= 102·8°, and Z= 4. The structure was solved by conventional Patterson and Fourier methods. The two-fold axis of the space group is utilized by the complex with the pyridine nitrogen atoms co-ordinating to the copper in a pseudotetrahedral arrangement. The dihedral angle between the N–Cu–N planes of the two ligands is 55·6°. This geometry seems to result from steric interaction between the ligands.

Electronic Structure of Lone Pairs. II. Disulfides and Acyl Thiol

Abstract: The electronic structure and the electronic transition of three cyclic disulfides, (CH2)3S2, (CH2)4S2, and (CH3)2S2, are calculated by the semi-empirical ASMO SCF method in order to study the interaction of the neighbouring lone pairs of the S–S bond in connection with the ability of reductive scission. It is concluded that the absorption at 2500–3000 A is the transition of n–σ* and that the variation in the maximum for the various cyclic disulfides and the chain disulfide are induced by the change in the dihedral angle that a molecule can take. The electronic structure and the reactivity of (CH3)2S2, CH3SSH, and CH3SCOCH3 are then discussed on the basis of an extended Huckel calculation. It is suggested that there is the possibility of an interaction between two molecules, R2S2, through the S–S bond of each molecule, in the HO of one molecule and in the LV of another.

The n.m.r. spectra and conformations of cyclic compounds part V. Mechanism of CH·CH coupling in heterocyclic compounds

Abstract: The 1H spectra of some five-membered heterocyclic olefins and related compounds are reported and analysed. The observation of some weak, hitherto ignored transitions in the AA′BB′ spectrum of the CH2·CH2 groups removes the deceptive simplicity of the spectrum and gives well determined and non-equal values of Jcis and Jtrans.The mechanisms contributing to the CH·CH couplings in these systems are considered in detail. It is concluded that (a) ring buckle and the known dihedral angle dependence satisfactorily accounts for the values in carbocyclic rings; (b) these contributions plus angle deformations and the orientation of the electronegative substituents account for the values in saturated five-membered heterocyclics. (c) No reasonable combination of these mechanisms provides a quantitative explanation of the large couplings observed in the five-membered heterocyclic olefins investigated.Possible reasons for this are given.

Crystal and molecular structure of a root inhibitor fromEucalyptus grandis, 4-ethyl-1-hydroxy-4,8,8,10,10-pentamethyl-7,9-dioxo-2,3-dioxabicyclo [4.4.0]decene-5

Abstract: The crystal structure of C15H22O5, a root inhibitor isolated from adult leaves ofEucalyptus grandis, has been determined by direct methods with Cukα diffractometer data and refined by full-matrix least-squares calculations toR = 0·046 for 1829 statistically significant reflexions. The compound, a racemate, crystallizes in the monoclinic space groupP21/c, with unit cell dimensionsa = 11·767,b = 12·063,c = 10·906 A, β = 103·2° andZ = 4. The molecular skeleton consists of a 2,3-dioxabicyclo[4.4.0]decene system with one hydroxyl, two carbonyl, one ethyl and five methyl side groups. The dihedral angle at the peroxide bond is 76·8° and the O-O bond distance is 1·480 A. The molecules are linked in the c direction by hydrogen bonds between the hydroxyl group and one of the carbonyl oxygen atoms.

Crystal structure of (Me3Sn)2N2C

Abstract: The crystal structure of (Me3Sn)2N2C has been determined by single-crystal X-ray diffraction, and the absolute configuration established for the particular crystal employed. The crystals are hexagonal, space group P6422, a= 8·74(1), c= 14·28(2)A, Z= 3. The structure consists of an infinite helical network of planar trimethyltin groups linked by linear NCN units. The nitrogen atoms complete a trigonal-bipyramidal arrangement about tin, with Sn–N 2·47(1) and Sn–C (mean) 2·14(2)A. The Sn2NCNSn2 moieties have exact D2(222) symmetry with a dihedral angle of 68° between the two Sn2NC planes; C–N 1·24(2)A and angle SnNC 117·6(4)°. The structure can be considered to be intermediate between carbodi-imide, cyanamide, and ionic extremes.