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1.
The solution structure of coenzyme B12 (5′-deoxyadenosylcobalamin, AdoCbl) and the corresponding cobinamide, AdoCbi+, in which the axial nucleotide has been chemically removed, have been investigated using NMR-restrained molecular dynamics (MD) and simulated annealing (SA) calculations. The nOe cross peaks in the ROESY spectrum of both AdoCbl and AdoCbi+ are consistent with the presence of at least two principal conformations for each compound in solution. In the first, termed the southern conformation, the adenosyl (Ado) ligand is over the C ring of the molecule, the structure observed in the solid state. In the second, the Ado ligand has undergone an anticlockwise rotation and is over C10 in the eastern quadrant of the molecule. A two-state MD/SA simulation was used omitting nOes that arise only from the eastern conformation and that arise only from the southern conformation, respectively. Consensus structures were obtained by averaging the coordinates of 25 annealed structures of the southern and eastern conformations, respectively, of AdoCbl and AdoCbi+, followed by energy minimization. The consensus structure of the southern conformation of AdoCbl agrees well with the solid-state structure and has a very similar corrin fold angle. Several observations show that AdoCbl is considerably more rigid than AdoCbi+, and indeed is one of the most rigid cobalt corrinoids studied by these methods to date: the variability in the conformations of the corrin ring between the family of 25 annealed structure and the consensus structure is much smaller for AdoCbl than for AdoCbi+; during MD simulations, the previously demonstrated flexibility of the corrin ring as gauged by the corrin ruf angle (C5–Co–C15) is preserved for AdoCbi+ but is considerably diminished in AdoCbl because of a decrease in the maximum fold angle and an increase in the minimum fold angle achieved in the latter; the range of values of the Co–C bond length experienced in AdoCbi+ is substantially larger than in AdoCbl; the Ado ligand visits many more orientations relative to the corrin ring in AdoCbi+ than in AdoCbl; the pyrrole rings in AdoCbl undergo smaller deformations than in AdoCbi+; and the “breathing motion” of the corrin ring in which C5, C10 and C15 oscillate from above to below the mean corrin plane is much less pronounced in AdoCbl than in AdoCbi+. This rigidity is attributed to the presence of two bulky ligands in AdoCbl, the Ado ligand in the upper (β) axial position and the 5,6-dimethylbenzimidazole (bzm) ligand in the lower () axial ligand position, in contrast to the other structures which have only one or other of these two bulky ligands. The corrin fold angle in AdoCbl is significantly larger than that in AdoCbi+, a finding that is in agreement with a previous observation that CH3Cbl has a larger fold angle than CH3Cbi+; this implies that base-on corrins are under steric strain.  相似文献   

2.
The reaction of methylzirconocenechloride with 2-bornenyllithium yields (2-bornenyl)methylzirconocene (10a). Carbonylation of 10a takes place exclusively by CO-insertion into the Zr-C(sp2) bond to give Cp2ZrMe(η2-OC-C10H15) (16a). The corresponding hafnium complex 10b reacts analogously to give 16b. Complex 16a was characterized by X-ray diffraction, and found to contain an η2-acyl ligand bonded to zirconium in the thermodynamically favored “O-inside” arrangement with the following bonding parameters: d Zr-C(acyl) = 2.192(7) Å, d Zr-O(acyl) = 2.258(6) Å, d C=O = 1.246(9) Å, angles O(acyl)---Zr---C(acyl) = 32.5(2)°, Zr---C(acyl)---O(acyl) = 76.7(4)°.  相似文献   

3.
A gas electron diffraction study of cyclobutylsilane results in a mixture of equatorial and axial conformers, with the equatorial confomer slightly more stable (Δ G = 0.8 ± 0.4 kJ mol−1). The cyclobutyl ring is distorted with the adjacent bonds longer (C1---C2 = 1.573 (4) Å) than the opposite bonds (C2---C3 = 1.557 (4) Å). The experimental values for the energy difference between the two conformers and for the geometric parameters are reproduced very well by ab initio calculations. The importance of silicon 3d orbitals in the interpretation of ring distortion is ambiguous, but on the basis of the ab initio calculations the participation of silicon 3d functions is negligible.  相似文献   

4.
2-Methyl-2H-cyclopenta[d]pyridazine reacts with trifluoracetic anhydride to give the 5- and 7-trifluoroacetyl products in about a 1:3 ratio. A series of HMO calculations have been made for similar ten π-electron heterocycles in an attempt to predict the positions in the 5-membered rings which would be most reactive to electrophilic substitution. The predictions based on the relative π-electron stabilities of the possible cationic intermediates are in accord with the available experimental data. If the atoms in the 6-ring are numbered 1-6 with the π-excessive heteroatom at the 1-position, then the most reactive site to electrophilic substitution in the 5-ring will be the atom which is linked to either the 1-, 3- or 5-positions. The structures of the major and minor trifluoroacetyl isomers of 2-methyl-2H-cyclopenta[d]pyridazine have been determined by X-ray crystallographic analyses, and the HMO predictions agree with the finding that C(7) is the most reactive position. 2-Methyl-5-trifluoroacetyl-2H-cyclopenta[d]pyridazine crystallizes in the monoclinic space group P21/m, cell constants a = 8·109, b = 6·713, c = 8·768 Å, β = 91·88°, with two molecules per unit cell. All of the atoms have been located and refined by full-matrix least-squares and the final residual is 0·056. The bond lengths appear to be influenced by a contribution of a pyridazinium form to the resonance hybrid. 2-Methyl-5-bromo-7-trifluoroacetyl-2H-cyclopenta[d]pyridazine crystallizes in the orthorhombic space group Pnam, cell constants a = 12·920, b = 12·513, c = 6·752 Å, with four molecules per unit cell. Although the quality of the diffraction data was severely limited by rapid decomposition of the specimen in the X-ray beam, the gross features of the structure were revealed. The residual following isotropic refinement was 0·19.  相似文献   

5.
Bingze Wang    Conghao Deng 《Tetrahedron》1988,44(24):7355-7362
Intramolecular reactions of cyclopropylcarbene in singlet ground state have been studied using HF/3-21G- gradient methods. Relative energies are estimated with 6–31G**. The “super-conjugation” between the cyclopropyl and the p AO at the carbene site stabilizes the carbene and retards its exo-endo isomerization with a barrier of 13.7 kcal/mol. The ring expansion occurs preferably from the exo conformation with a barrier of 12.9 kcal/mol. Two terminals disrotate in different rotation directions before and after the transition state. The ring expansion from the endo conformation is a more energetic pathway. The 1,2 H shift is not competitive to the ring expansion for its much higher barrier.  相似文献   

6.
The crystal structure of N,N′-bis(β-chloroethyl)-glutaramide (NNCEG) has been determined by X-ray diffraction analysis, as part of a research programme on simple model compounds for synthetic polyamides. It crystallizes in the monoclinic system, space group P21 Z = 2, with A = 4·941, B = 28·123, C = 4·835 Å and β = 113°53′. The structure was solved by the heavy atom method and refined to a final R value of 0·079. Each molecule forms hydrogen bonds along two directions (almost the a and the c directions with an angle close to 60°) giving rise to bidimensional layers (parallel to the ac plane with width b/2). A similar system of hydrogen bonds could be postulated for some nylons with odd number of CH2's between amide groups. The molecular conformation different from an all trans conformation is discussed in terms of the barriers to rotation around each bond considered by several authors. The twinning observed in most of the examined crystals is rationalized in terms of simple symmetry operations on molecular conformations of opposite chirality.  相似文献   

7.
An unexpected novel coordination mode of diazoalkanes has been verified via addition of 2-diazopropane to the metal—metal triple bond of bis[dicarbonyl(η5-pentamethylcyclopentadienyl)molybdenum] (MoMo). The dinuclear 1:1 addition product isolated in nearly quantitative yield is structurally characterized by a bent, 4-electron type η12-diazoalkane ligand, with the terminal nitrogen atom symmetrically bridging the metal-metal “single bond” (d(MoMo) 305.0(2) pm; d(Mo---N(1)) 212.0(12) and 212.6(10) pm, respectively) and the second nitrogen atom being bonded to one molybdenum atom only (d(Mo---N(2)) 213.4(13) pm).  相似文献   

8.
Solid state 13C NMR experiments on poly(p-biphenylene terephthalate) with long n-dodecyl side chains have been carried out over a wide range of temperatures, in order to elucidate conformational and dynamical behavior of the polyester in the crystalline state and thermotropic liquid crystalline state. From these experimental results, it is found that at temperatures from room temperature to 80 °C the n-alkyl side chains take both of the immobile and the mobile regions, and at temperatures above 120 °C take only the mobile region. In the immobile region the n-alkyl side chains are in the all-trans zigzag conformation and in the mobile state are undergoing fast exchange between the trans and gauche conformations. On the other hand, the terephthalate moiety of the main chain undergoes rotational motion after the melt of n-alkyl side chains as the temperature is increased.  相似文献   

9.
Using ab initio gradient calculations at the Hartree—Fock level, the structures of formylphosphine and acetyldimethylphosphine were determined as a function of the torsional angle around the central PCAC bond. Split valence-shell basis sets, augmented by a set of polarization d-functions on the phosphorus atom, were used.

For both molecules, the existence of a single total-energy minimum corresponding to the amide-type conformation (C1 symmetry) was demonstrated. Full optimization of all the geometrical parameters was made at the stable conformation and at the transition states for internal rotation of the acyl group. The rotation barriers in the acylphosphines are considerably lower than in the analogous amides. In contrast to the latter, the steric factors in acylphosphines are relatively more important in their effect on the potential-curve shape as compared with electronic factors. Although the calculated geometric parameters of the acylphosphines are indicative of a certain contribution of p — π conjugation in the stable conformation, the magnitude of the effect is quite small. In all the computed acetyldimethylphosphine conformations, the PCAc bond length is greater than that of PCMe. A similar regularity was earlier noted in analysis of experimental data on carbon—halogen bond lengths.  相似文献   


10.
The crystal and molecular structures of 2′-amino-6′-dibutylamino-3′-methylspiro[isobenzofuran-1(3H), 9′[9H]xanthen]-3-one (1), 2′-amino-6′-(N-cyclohexyl-N-methylamino)-3′-methylspiro[isobenzofuran-1(3H), 9′[9H]xanthen]-3-one (2) and 2′-(2-chlorophenyl)amino-6′-dibutylaminospiro[isobenzofuran-1(3H), 9′[9H]xanthen-3-one (3) have been determined by single-crystal X-ray diffraction analysis. Atom-atom non-bonded potential energy and semiempirical quantum chemical calculations have been performed. The xanthene rings of 1 to 3 are slightly bent and the phthalide rings are planar. The phthalide ring moieties are almost perpendicular (88.9(1)–93.5(5)°) to the xanthene rings. The bond lengths C(6)---O(2) are apparently extended from the normal C(sp3---O (lactone) length. The temperature factors for one butyl group C(32)---C(35)) of 1 increase gradually toward the terminal carbon. The temperature factors for C(30)---C(33) of 2 indicate large vibrations and these are reflected in short bond lengths. Two butyl groups of 3 are disordered and these C---C bond lengths are short and long alternately. Atomic net charges around spirocarbon C(6) and toward N(1) to C(6) indicate the weak alternative system in the colorless form. As the xanthene ring has a planar geometry, the π electron density migration will easily occur from the auxochromes attached to the phthalide ring to the xanthene ring.  相似文献   

11.
The crystal and molecular structures of 2′-amino-6′-dibutylamino-3′-methylspiro[isobenzofuran-1(3H), 9′[9H]xanthen]-3-one (1), 2′-amino-6′-(N-cyclohexyl-N-methylamino)-3′-methylspiro[isobenzofuran-1(3H), 9′[9H]xanthen]-3-one (2) and 2′-(2-chlorophenyl)amino-6′-dibutylaminospiro[isobenzofuran-1(3H), 9′[9H]xanthen-3-one (3) have been determined by single-crystal X-ray diffraction analysis. Atom-atom non-bonded potential energy and semiempirical quantum chemical calculations have been performed. The xanthene rings of 1 to 3 are slightly bent and the phthalide rings are planar. The phthalide ring moieties are almost perpendicular (88.9(1)−93.5(5)°) to the xanthene rings. The bond lengths C(6)---O(2) are apparently extended from the normal C(sp3)---O (lactone) length. The temperature factors for one butyl group C(32)---C(35)) of 1 increase gradually toward the terminal carbon. The temperature factors for C(30)---C(33) of 2 indicate large vibrations and these are reflected in short bond lengths. Two butyl groups of 3 are disordered and these C---C bond lengths are short and long alternately. Atomic net charges around spirocarbon C(6) and toward N(1) to C(6) indicate the weak alternative system in the colorless form. As the xanthene ring has a planar geometry, the π electron density migration will easily occur from the auxochromes attached to the phthalide ring to the xanthene ring.  相似文献   

12.
Microwave spectra of allylsilane and its 13C and deuterium substituted species have been measured and assigned for the skew isomer. The rs structure was determined with the aid of several assumptions. Some of the parameters determined are; r(C=C) = 1.328 ± 0.007 Å, r(C---C) = 1.492 ± 0.008 Å, (CCC) = 126.7 ± 0.8°, (CCSi) = 111.6 ± 0.5° and τ(CCCSi) = 106.8 ± 1.1°. Dipole moments and their components were also determined for the CH2 = CHCH2SiH3 and CH2=CHCH2SiD3 species. Hyperconjugation between the C=C π bond and the C---Si σ bond is discussed.  相似文献   

13.
The 1H, 2H and 13C NMR spectra of phenyl acetate, phenyl acetate-[13CO] and phenyl acetate-[C2H3] dissolved in a nematic liquid crystalline solvent have been analysed to yield dipolar coupling, Dij. These have been interpreted using the additive potential model to provide information on the molecular conformation, resulting in three possible shapes for V(φ), the potential energy for rotation about the ring-oxygen bond. A comparison with the results of molecular orbital calculations leads to the conclusion that a potential with a minimum at 54.4° ± 0.1° is the most probable.  相似文献   

14.
The complex Fe(η6-C5H5CMe3)2 crystallizes in the centrosymmetric triclinic space group P (Ci1; No. 2) with unit cell dimensions of a 8.770(1) Å, b 8.878(1) Å, c 11.991(1) Å, 107.56(1)°, β 90.85(1)°, γ 90.13(1)°, V 890.0(2) Å3 and Z = 2. A full sphere of data was collected on a four-circle diffractometer. The structure was solved and refined to R 7.93% for all 3155 independent reflections and R 4.98% for those 2002 data with | F0 | > 6σ. | F0 |. The molecules lie on crystallographic inversion centers at 0, 0, 0 and 1/2, 0, 1/2; the crystallographic asymmetric unit therefore consists of two independent half molecules. The molecule centered at 0, 0, 0 (molecule “A”) is ordered and well-defined; that centered on 1/2, 0, 1/2 (molecule “B”)is probably disordered, as indicated by larger “thermal parameters” and a greater range of apparent interatomic distances. Discussion em phasizes the geometry of molecule A, which has precise Ci symmetry with Fe(1A)-B(1A) 2.297(4) Å and Fe(1A)-C(ring) distances ranging from 2.057(6) Å to 2.138(4) Å.  相似文献   

15.
The solution structure of Cobeta-5'-deoxyadenosylimidazolylcobamide, Ado(Im)Cbl, the coenzyme B(12) analogue in which the axial 5,6-dimethylbenzimidazole (Bzm) ligand is replaced by imidazole, has been determined by NMR-restrained molecular modeling. A two-state model, in which a conformation with the adenosyl moiety over the southern quadrant of the corrin and a conformation with the adenosyl ligand over the eastern quadrant of the corrin are both populated at room temperature, was required by the nOe data. A rotation profile and molecular dynamics simulations suggest that the eastern conformation is the more stable, in contrast to AdoCbl itself in which the southern conformation is preferred. Consensus structures of the two conformers show that the axial Co-N bond is slightly shorter and the corrin ring is less folded in Ado(Im)Cbl than in AdoCbl. A study of the thermolysis of Ado(Im)Cbl in aqueous solution (50-125 degrees C) revealed competing homolytic and heterolytic pathways as for AdoCbl but with heterolysis being 9-fold faster and homolysis being 3-fold slower at 100 degrees C than for AdoCbl. Determination of the pK(a)'s for the Ado(Im)Cbl base-on/base-off reaction and for the detached imidazole ribonucleoside as a function of temperature permitted correction of the homolysis and heterolysis rate constants for the temperature-dependent presence of the base-off species of Ado(Im)Cbl. Activation analysis of the resulting rate constants for the base-on species show that the entropy of activation for Ado(Im)Cbl homolysis (13.7 +/- 0.9 cal mol(-1) K(-1)) is identical with that of AdoCbl (13.5 +/- 0.7 cal mol(-1) K(-1)) but that the enthalpy of activation (34.8 kcal mol(-1)) is 1.0 +/- 0.4 kcal mol(-1) larger. The opposite effect is seen for heterolysis, where the enthalpies of activation are identical but the entropy of activation is 5 +/- 1 cal mol(-1) K(-1) less negative for Ado(Im)Cbl. Extrapolation to 37 degrees C provides a rate constant for Ado(Im)Cbl homolysis of 2.1 x 10(-9) s(-1), 4.3-fold smaller than for AdoCbl. Combined with earlier results for the enzyme-induced homolysis of Ado(Im)Cbl by the ribonucleoside triphosphate reductase from Lactobacillus leichmannii, the catalytic efficiency of the enzyme for homolysis of Ado(Im)Cbl at 37 degrees C can be calculated to be 4.0 x 10(8), 3.8-fold, or 0.8 kcal mol(-1), smaller than for AdoCbl. Thus, the bulky Bzm ligand makes at best a <1 kcal mol(-1) contribution to the enzymatic activation of coenzyme B(12).  相似文献   

16.
The overall conformational order of the alkyl tail of the lyotropic lamellar phase of the dimethyldodecyl amineoxide, (CH3)2ON+(CH2)11CH3 (DDAO)---H2O system (75.7 wt.%) has been studied by using Fourier transform infrared spectroscopy. The spectral region 1000–1400 cm−1, covering the CH2 wagging modes and the methyl umbrella modes of DDAO, has been recorded in the temperature interval 3–60°C and at different mole fractions of gramicidin-D with respect to DDAO (Xg = 0.03, 0.05 and 0.1) for both DDAO-H2O and DDAO-D2O systems. It has been shown that the DDAO amphiphile molecules of the lamellar phase reorganise in a phase-like transition near 25–30°C. The DDAO-water system does not show any significant bands corresponding to a double gauche conformation at 1355 cm−1 nor to a gauche-transgauche (kinked) conformation at 1367 cm−1. These bands are probably present but hidden in the broad low-frequency side of the CH3 umbrella band at 1377 cm−1. Upon incorporation of gramicidin into the lamellar phase both head group and acyl chain spectra of the lipid change in such a way as to indicate a decreased “ordering” of the molecules, as judged by comparison with spectra of the same molecule in a micellar environment, and with increased fluidity of the acyl chains.  相似文献   

17.
The molecular structures of n-hexane were determined by RHF/4-21G ab initio geometry optimization at 30° grid points in its three-dimensional τ1(C11–C8–C5–C1), τ2(C14–C11–C8–C5), τ3(C17–C14–C11–C8) conformational space. Of the resulting 12×12×12=1728 grid structures, 468 are symmetrically non-equivalent and were optimized constraining the torsions τ1, τ2, and τ3 to the respective grid points, while all other structural parameters were relaxed without any constraints. From the results, complete parameter surfaces were constructed using natural cubic spline functions, which make it possible to calculate parameter gradients, |P|=[(∂P/∂τi)2+(∂P/∂τj)2]1/2, where P is a C–C bond length or C–C–C angle. The parameter gradients provide an effective measure of the torsional sensitivity of the system and indicate that dynamic activities in one part of the molecule can significantly affect the density of states, and thus the contributions to vibrational entropy, in another part. This opens the possibility of dynamic entropic conformational steering in complex molecules; i.e. the generation of free energy contributions from dynamic effects of one part of a molecule on another. When the conformational trends in the calculated C–C bond lengths and C–C–C angles are compared with average parameters taken from some 900 crystallographic structures containing n-hexyl fragments or longer C–C bond sequences, some correlation between calculated and experimental trends in angles is found, in contrast to the bond lengths for which the two sets of data are in complete disagreement. The results confirm experiences often made in crystallography. That is, effects of temperature, crystal structure and packing, and molecular volume effects are manifested more clearly in bond lengths than bond angles which depend mainly on intramolecular properties. Frequency analyses of the τ1, τ2 and τ3 torsional angles in the crystal structures show conformational steering in the sense that, if τ1 is trans peri-planar (170°≤τ1≤180°; −180°≤τ1≤−170°), the values of τ2 and τ3 are clustered closely around the ideal gauche (±60°) and trans (±180°) positions. In contrast, when τ1 is in the region (50°≤τ1≤70°), there is a definite increase in the populations of τ2 and τ3 at −90 and −150°.  相似文献   

18.
19.
The kinetics of the thermal Co-C bond homolysis of the complexes of a vitamin B(12) binding protein (haptocorrin) with a series of analogs of neopentylcobalamin modified in side chain structure have been studied. The analogs include the C13 epimer in which the e propionamide side chain adopts an "upwardly" axial conformation and a series of c side chain-modified analogs, including the c-monocarboxylate, the c-N-methylamide, the c-N,N-dimethylamide, and the c-N-isopropylamide. Activation parameters for the thermal homolysis of these complexes show that the previously observed stabilization of alkylcobalamins by haptocorrin is due to both enthalpic and entropic factors. With the exception of that for the analog having the bulkiest c side chain substituent, neopentylcobalamin-c-N-isopropylamide, the enthalpies of activation are independent of analog structure, but the entropies of activation increase with the steric bulk of the c side chain and with the number of "upwardly" projecting side chains, as previously observed for protein-free neopentylcobalamin and its analogs. The results are discussed in terms of the solvent cage effect on Co-C bond homolysis and the importance of corrin ring side chain thermal motions to the entropy of activation for this reaction.  相似文献   

20.
We present the results of Q.N.S. studies for two members of the homologous series of alkoxyazoxybenzenes, CnH2n+1O-ϕ-N2O-ϕ-OCnH2n+1; PAP (n = 2) and POAB (n = 3). The Q.N.S. measurements were performed on the non-deuteriated (d0-PAP and d0-POAB) and the chain deuteriated samples, d10-PAP and d14-POAB. Three models were fitted to the experimental data: (1) uniaxial rotational diffusion of the molecule around the axis with the smallest moment of inertia, (2) uniaxial rotational diffusion of the two moieties of the molecule around the N-ϕ bonds, (3) 180° instantaneous jumps of the two moieties of the molecule around N-ϕ bonds. We have assumed the molecule to exist in the trans conformation. The translational diffusion of the molecules and the methyl groups' reorientation were neglected. It turned out that model (3) does not describe the experimental data well. Models (1) and (2) describe the experimental data equally well, giving no preference for the axis of rotation. However, comparison of our results with those obtained from dielectric relaxation suggests the choice of model (2) as responsible for the Q.N.S. data. The correlation times determined by fitting to both rotational diffusion models are of the order of several picoseconds. However, the correlation times determined for d10-PAP and d14-POAB are two or three times longer than for d0-PAP and d0-POAB, respectively, which indicates the existence of additional motion of the end chains.  相似文献   

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