Changes In Torsion Angles Research Articles

The Electronic Spectroscopy of 2,2‘-Binaphthyl in Solution, Cryogenic Matrix and Supersonic Jet

The electronic spectroscopy of 2,2‘-binaphthyl near 330 nm has been investigated by absorption spectroscopy in room-temperature solution and Shpolskii matrix at 4 K and by fluorescence excitation spectroscopy in a supersonic free-jet expansion. In the solution and gas phase, where the molecules are free to form the minimum-energy conformation, the spectra are quite different from those of 1,1‘-binaphthyl and the parent naphthalene. However, when frozen in a matrix, aspects of the electronic spectrum resembled features of the spectra of these molecules. The fluorescence excitation spectrum in the free jet showed several long progressions in the torsional vibration with a characteristic, but anharmonic, frequency of about 30 cm-1. The spectrum was assigned as the 11B ← 11A transition with an origin transition, which, although it could not be observed, was estimated to be at 30 060 ± 30 cm-1. The frequency of 29 members of this progression allowed an accurate torsional potential to be calculated, which was flattened at low energy and approached harmonic at higher energy. The change in equilibrium torsional angle was estimated to be 32° upon electronic excitation, with the excited state being planar (either cis or trans). Several low-frequency vibrations were assigned in the gas phase that probably involve motions of the naphthalene structures as a whole about the central C−C bond. In the matrix, the torsional vibrations were frozen out, which allowed for the observation and tentative assignment of several higher-frequency vibrations resembling those of the bare naphthalene. The origin frequency was measured at 28 460 cm-1. The difference between the gas-phase and solid-phase frequencies was attributed to the constrained structure of the molecule in the matrix.

The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework.

The number of solved structures of macromolecules that have the same fold and thus exhibit some degree of conformational variability is rapidly increasing. It is consequently advantageous to develop a standardized terminology for describing this variability and automated systems for processing protein structures in different conformations. We have developed such a system as a 'front-end' server to our database of macromolecular motions. Our system attempts to describe a protein motion as a rigid-body rotation of a small 'core' relative to a larger one, using a set of hinges. The motion is placed in a standardized coordinate system so that all statistics between any two motions are directly comparable. We find that while this model can accommodate most protein motions, it cannot accommodate all; the degree to which a motion can be accommodated provides an aid in classifying it. Furthermore, we perform an adiabatic mapping (a restrained interpolation) between every two conformations. This gives some indication of the extent of the energetic barriers that need to be surmounted in the motion, and as a by-product results in a 'morph movie'. We make these movies available over the Web to aid in visualization. Many instances of conformational variability occur between proteins with somewhat different sequences. We can accommodate these differences in a rough fashion, generating an 'evolutionary morph'. Users have already submitted hundreds of examples of protein motions to our server, producing a comprehensive set of statistics. So far the statistics show that the median submitted motion has a rotation of approximately 10 degrees and a maximum Calpha displacement of 17 A. Almost all involve at least one large torsion angle change of >140 degrees. The server is accessible at http://bioinfo.mbb.yale. edu/MolMovDB

The introduction of strain and its effects on the structure and stability of T4 lysozyme

In order to try to better understand the role played by strain in the structure and stability of a protein a series of “small-to-large” mutations was made within the core of T4 lysozyme. Three different alanine residues, one involved in backbone contacts, one in side-chain contacts, and the third adjacent to a small cavity, were each replaced with subsets of the larger residues, Val, Leu, Ile, Met, Phe and Trp. As expected, the protein is progressively destabilized as the size of the introduced side-chain becomes larger. There does, however, seem to be a limit to the destabilization, suggesting that a protein of a given size may be capable of maintaining only a certain amount of strain. The changes in stability vary greatly from site to site. Substitution of larger residues for both Ala42 and Ala98 substantially destabilize the protein, even though the primary contacts in one case are predominantly with side-chain atoms and in the other with backbone. The results suggest that it is neither practical nor meaningful to try to separate the effects of introduced strain on side-chains from the effects on the backbone. Substitutions at Ala129 are much less destabilizing than at sites 42 or 98. This is most easily understood in terms of the pre-existing cavity, which provides partial space to accommodate the introduced side-chains. Crystal structures were obtained for a number of the mutants. These show that the changes in structure to accommodate the introduced side-chains usually consist of essentially rigid-body displacements of groups of linked atoms, achieved through relatively small changes in torsion angles. On rare occasions, a side-chain close to the site of substitution may change to a different rotamer. When such rotomer changes occur, they permit the structure to dissipate strain by a response that is plastic rather than elastic. In one case, a surface loop moves 1.2 Å, not in direct response to a mutation, but in an interaction mediated via an intermolecular contact. It illustrates how the structure of a protein can be modified by crystal contacts.

The conformations of monensin-A metal complexes in solution determined by NMR spectroscopy

The structures in solution of the Na+, K+ and Rb+ salts of monensin have been determined by the use of NOESY distance restraints and molecular modelling. The structures are similar to those obtained by X-ray diffraction with the exception of a close carboxylate oxygen-to-metal distance and only five observed close metal-to-oxygen ligating interactions. Molecular dynamics involving the derived structure of the sodium salt at increasing relative permittivity sheds light on the mechanism by which monensin binds to and unbinds from sodium ions in the membrane surface. The series of structures as the size of the metal ion increases also shows that the whole monensin molecule adapts to incorporate changes in the ionic radius including changes in torsion angles, changes in heterocyclic ring conformations and changes in the ligation and hydrogen bonding patterns.

A First-Principles Quantum Chemical Analysis of the Factors Controlling Ruffling Deformations of Porphyrins: Insights from the Molecular Structures and Potential Energy Surfaces of Silicon, Phosphorus, Germanium, and Arsenic Porphyrins and of a Peroxidase Compound I Model

Using nonlocal density functional theory calculations, we have examined several factors influencing ruffling deformations of porphyrin and porphyrazine complexes. Because a ruffling distortion is often a direct result of a small macrocycle core size, which, in turn, is brought about by complexation of a central ion with a small ionic radius, this study focuses on the conformations and potential energy surfaces of porphyrin complexes with small central ions (herafter symbolized M) such as SiIV, PV, GeIV, and AsV. The optimized geometries exhibit ruffling torsion angles ranging from 0° for (P)GeIVF2 and (P)SiIV(C⋮CPh)2 to about 55° for [(P)PVF2]+. For relatively substantial ruffling distortions, a good linear correlation has been found between the ruffling torsion angle and the M−N distance for a wide variety of central ions including transition metals, for sterically unhindered porphyrins, and for a database including both experimental and optimized structures. The threshold between ruffling and planar structures is at M−N bond distances of 2.00−2.02 Å for sterically unhindered porphyrins and at 1.85−1.87 Å for porphyrazines. The calculations confirm an experimental observation that electron-withdrawing axial ligands lead to increased ruffling, especially for phosophorous and silicon porphyrins. The ortho hydrogens of axial phenyl ligands and the 2- and 6- hydrogens of axial pyridine ligands can sterically interfere with the porphyrin and contribute to ruffling. In addition to the M−N distance, a number of other geometrical parameters also vary systematically with the ruffling distortion. Thus, the Cα−Cmeso−Cα angle decreases with ruffling and the CβCβ distance and Cα−N−Cα angle increase with ruffling. These structural variations are reflected in a number of ruffling-sensitive vibrational frequencies.. The ruffled D2d geometries of [(P)PVF2]+ and [(P)PVCl2]+ are stabilized by 9.25 and 5.26 kcal/mol, respectively, relative to planar D4h symmetry-constrained optimized geometries. In contrast, the ruffled D2d geometries of [(Pz)PVF2]+ and of all the silicon complexes studied are more stable than the corresponding D4h symmetry-constrained optimized geometries by less than 0.01 kcal/mol. This underscores the extreme softness of ruffling deformations and shows that even fairly large distortions, where the ruffling torsion angle changes by up to 25°, can occur with almost no expenditure of energy. Finally, through a reinvestigation of a recent study of a peroxidase compound I model, we have uncovered a heretofore unsuspected role of Fe(3dxy)-porphyrin(atu) orbital interactions in macrocycle ruffling. Also seen for certain low-spin ferrihemes, this orbital interaction is not important for manganese porphyrins.

Structure of a Triple Helical DNA with a Triplex−Duplex Junction

Extended purine sequences on a DNA strand can lead to the formation of triplex DNA in which the third strand runs parallel to the purine strand. Triplex DNA structures have been proposed to play a role in gene expression and recombination and also have potential application as antisense inhibitors of gene expression. Triplex structures have been studied in solution by NMR, but have hitherto resisted attempts at crystallization. Here, we report a novel design of DNA sequences, which allows the first crystallographic study of DNA segment containing triplexes and its junction with a duplex. In the 1.8 A resolution structure, the sugar-phosphate backbone of the third strand is parallel to the purine-rich strand. The bases of the third strand associate with the Watson and Crick duplex via Hoogsteen-type interactions, resulting in three consecutive C(+).GC, BU.ABU (BU = 5-bromouracil), and C(+).GC triplets. The overall conformation of the DNA triplex has some similarity to the B-form, but is distinct from both A- and B-forms. There are large changes in the phosphate backbone torsion angles (particularly gamma) of the purine strand, probably due to the electrostatic interactions between the phosphate groups and the protonated cytosine. These changes narrow the minor groove width of the purine-Hoogsteen strands and may represent sequence-specific structural variations of the DNA triplex.

Conformational assignment of the N-terminal residues of the small domain (Ala 12–Val 49) of pig cytosolic aspartate aminotransferase using the acap computer program

Conformational changes of the aspartate aminotransferase N-terminal small domain residues Ala12–Val49 that occur upon substrate binding were evaluated using Amino Acid Conformation Assignment of Proteins ( acap) computer program (Version 1.07). In the segment considered, four residues (Val15, Asp27, Gly36 and Gly38) underwent backbone torsional angle changes of such magnitude that led to different conformers, while the other residues underwent change in backbone torsional angles without change in their conformational assignment. The residues that changed conformational assignment migrated to adjacent conformational centers of the Ramachandran map. In addition to confirming the importance of three residues for enzyme's function (Ala12, Gly36, Gly38), the conformational analysis revealed an additional potentially significant residue (Asp27). These findings are consistent with X-ray studies and literature values for aspartate aminotransferase (AspAT), showing that the acap program can be successfully used in determinig conformational assignment of amino acid residues within proteins. The approach can be used to predict amino acid residue function in cases where it would be difficult to infer such information from the X-ray studies.

Stable formation of a pyrimidine-rich loop hairpin in a cruciform promoter

We have determined the solution structure of a TCC-loop hairpin in the cruciform promoter for the bacteriophage N4 virion RNA polymerase (N4 vRNAP). This hairpin and its complementary GGA-loop hairpin are extruded at physiological superhelical density and are required for vRNAP recognition. Contrary to its complementary GGA-loop, the three pyrimidines in the TCC-loop are all unpaired. However, with the help of two juxtaposed stem Watson-Crick G·C base-pairs, each nucleotide in the loop employs a special method to stabilize the hairpin structure. The resulting structures display extensive loop base-stacking rearrangement yet minor backbone distortion, which is largely accomplished through some loop ζ and α torsional angle changes. Consistent with the structural studies, UV melting of the GAAGCTCCGCTTC hairpin revealed a higher melting temperature (66 °C) than that of the GAACGTCCCGTTC hairpin (58 °C) with reversed stem G·C base-pairs, indicating significant contribution from the extra three loop-stem H-bonds. Thermodynamic parameters ΔG°25 of the GAAGCTCCGCTTC hairpin and its complementary GAAGCGGAGCTTC hairpin are −4.1 and −4.3 kcal/mol respectively, indicating approximately equal contribution of each hairpin to the cruciform formation of the N4 virion RNA polymerase promoter. No significant loop dynamics in the microsecond to millisecond NMR time-scale was observed, and the abundant well-defined exchangeable and non-exchangeable proton NOEs allowed us to efficiently determine a well-converged family for the final structures of the TCC-loop hairpin.

DNA stretching and compression: large-scale simulations of double helical structures

Computer-simulated elongation and compression of A- and B-DNA structures beyond the range of thermal fluctuations provide new insights into high energy “activated” forms of DNA implicated in biochemical processes, such as recombination and transcription. All-atom potential energy studies of regular poly(dG)·poly(dC) and poly(dA)·poly(dT) double helices, stretched from compressed states of 2.0 Å per base-pair step to highly extended forms of 7.0 Å per residue, uncover four different hyperfamilies of right-handed structures that differ in mutual base-pair orientation and sugar-phosphate backbone conformation. The optimized structures embrace all currently known right-handed forms of double-helical DNA identified in single crystals as well as non-canonical forms, such as the original “Watson-Crick” duplex with trans conformations about the P—O5′ and C5′—C4′ backbone bonds. The lowest energy minima correspond to canonical A and B-form duplexes.The calculations further reveal a number of unusual helical conformations that are energetically disfavored under equilibrium conditions but become favored when DNA is highly stretched or compressed. The variation of potential energy versus stretching provides a detailed picture of dramatic conformational changes that accompany the transitions between various families of double-helical forms. In particular, the interchanges between extended canonical and non-canonical states are reminiscent of the cooperative transitions identified by direct stretching experiments. The large-scale, concerted changes in base-pair inclination, brought about by changes in backbone and glycosyl torsion angles, could easily give rise to the observed sharp increase in force required to stretch single DNA molecules more than 1.6–1.65 times their canonical extension.Our extended duplexes also help to tie together a number of previously known structural features of the RecA-DNA complex and offer a self-consistent stereochemical model for the single-stranded/duplex DNA recognition brought in register by recombination proteins. The compression of model duplexes, by contrast, yields non-canonical structures resembling the deformed steps in crystal complexes of DNA with the TATA-box binding protein (TBP). The crystalline TBP-bound DNA steps follow the calculated compression-elongation pattern of an unusual “vertical” duplex with base planes highly inclined with respect to the helical axis, exposed into the minor groove, and accordingly accessible for recognition.Significantly, the double helix can be stretched by a factor of two and compressed roughly in half before its computed internal energy rises sharply. The energy profiles show that DNA extension-compression is related not only to the variation of base-pair Rise but also to concerted changes of Twist, Roll, and Slide. We suggest that the high energy “activated” forms calculated here are critical for DNA processing, e.g. nucleo-protein recognition, DNA/RNA synthesis, and strand exchange.

Ab Initio Studies of Disilazanes: Structures and Vibrational Properties of Hexachloro-, Hexamethyl-, and Tetrachlorodisilazane

The structures of hexachlorodisilazane, NH(SiCl3)2, and hexamethyldisilazane, NH(SiMe3)2, have been calculated at HF/6-31G* and MP2/6-31G* levels. Both contain planar HNSi2 skeletons and show the expected staggering of the substituents as seen along the Si‚‚‚Si direction, as previously found in the electron diffraction structure of the hexamethyl compound. Unlike the latter, however, the ab initio structures both belong to the C2 point group. Force fields for these two molecules and for tetrachlorodisilazane, NH(SiHCl 2)2, were calculated at the HF level and scaled to produce vibration frequencies for comparison with previously obtained spectra. For NH(SiCl3)2, all but five of the fundamentals are satisfactorily assigned. Seven scale factors could be refined, other factors being transferred from model compounds. For the hexamethyl compound, the interpretation was less detailed. In all three molecules the out-of-plane NH bending motion is found to be associated with fundamentals around or below 400 cm -1 , far lower than previous assignments. The force constant for this motion is greatly reduced as chlorine substituents are replaced by methyl groups, which shows the sensitivity of the stability of the planar system to the inductive effect of substituents. For tetrachlorodisilazane, NH(SiHCl2)2, earlier spectra were reanalyzed and evidence was found for the presence of two conformers, as suggested by previous ab initio investigations. The vibrational properties of the SiH bonds were explored by extending the ab initio calculations to a series of nonequilibrium structures, with the object of mapping variations in the SiH bond with change in torsional angle. This bond is strongest in the skeletal plane and weakest at right angles to the latter, which is in accordance with an n(N)-U*(Si-H) orbital interaction. However the orientation of the other silyl group also influences SiH bond strength. Long-range interactions are found between the stretching motions of both SiH and SiCl bonds. The former appear to arise from dipole-dipole interactions between the SiH bonds, but the source of the latter remains obscure. The form of the observed OSiH spectrum suggests that signal averaging conceals the splittings expected from both interactions and bond strength variation. Electrical properties of the SiH and SiCl bonds are examined.

Domain motions in actin

Previous crystallographic investigations have shown that actin can undergo large conformational changes, even when complexed to the same actin binding protein. We have conducted a formal analysis of domain motions in actin, using the four available crystal structures, to classify the mechanism as either hinge or shear and to quantify the magnitude of these changes. We demonstrate that actin consists of two rigid cores, a semi-rigid domain and three conformationally variable extended loops. Confirming predictions about the nature of the domain rotation in actin based on its structural similarity to hexokinase, we show, using an algorithm previously used only to identify protein hinges, that residues at the interface between the two rigid cores undergo a shear between alternative conformations of actin. Rotations of less than 7° in the torsion angles of five residues in the polypeptides that connect the rigid cores enable one actin conformation to be transformed into another. Because these torsion angle changes are small, the interface between the domains is maintained. In addition, we show that actin secondary structure elements, including those outside the rigid cores, are conformationally invariant among the four crystal structures, even when actin is complexed to different actin binding proteins. Finally, we demonstrate that the current F-actin models are inconsistent with the principles of actin conformational change identified here.

Conformational flexibility of di- and tetrahydropyrimidine rings in nucleic acid bases. An ab initio [formula omitted] study

Using ab initio HF 6–31 G∗∗ method of calculation it is shown that dihydropyrimidinone and tetrahydropyrimidin-2,4-dione rings in the uracil, thymine, cytosine, isocytosine and guanine molecules are not conformationally rigid. A change in the relevant torsion angles of ± 20° causes an energy increase of about 1.5 kcal/mol. The main reason for conformational flexibility is the non-aromatic and anti-aromatic character of the cyclic π-systems in these molecules. A decrease in the exocyclic double bond polarity and the presence of electron-donating substituents increase the non-rigidity of the pyrimidine rings.

Structural basis of DNA recognition and mechanism of quadruplex formation by the beta subunit of the Oxytricha telomere binding protein.

Interactions of the beta subunit of the Oxytricha nova telomere binding protein with the telomeric DNA sequences, d(T4G4)2 and dT6(T4G4)2, have been investigated in vitro using Raman and fluorescence spectroscopies. Raman difference spectra show that the beta subunit binds to both d(T4G4)2 and dT6(T4G4)2 but promotes the formation of a parallel-stranded quadruplex only in dT6(T4G4)2, thus demonstrating the importance of the telomeric 5' tail for in vitro recognition and guanine quadruplex formation. While d(T4G4)2 is not a suitable substrate for quadruplex promotion by the beta subunit, the Raman spectra reveal other structural rearrangements of this DNA strand upon beta subunit binding, including changes in guanine glycosyl torsion angles from syn to anti and disruption of carbonyl hydrogen-bonding interactions. The conformation of d(T4G4)2 in the beta:d(T4G4)2 complex is suggested as a plausible intermediate along the pathway to formation of the parallel-stranded guanine quadruplex. Fluorescence band shifts indicate that at least one of the two tryptophans of the beta subunit is shielded from solvent as a consequence of DNA binding in both the beta:dT6(T4G4)2 and beta:d(T4G4)2 complexes. However, the Raman spectra of these complexes suggest no significant changes in the beta subunit secondary structure attendant with DNA binding. A model for beta subunit binding by Oxytricha telomeric DNA sequences and a mechanism for quadruplex formation are proposed. A key feature of this model is the use of a telomeric hairpin secondary structure as the recognition motif.

The phenomenon of conglomerate crystallization of organic compounds. Part 4. The structures of 2,2?-biphenyldisulfide (I) and 2,2?-biphenyldisulfide monoxide (II)

A racemic solution of 2,2′-biphenyldisulfide (I), C12H8S2, produces conglomerate crystals of (I) belonging in space group P3221 (no. 154) with lattice constants: a = 7.38 (3) A, b = 7.38 (3), c = 16.20 (2) A; V = 766.6 A3 and d(calc; M.W. = 216.32, z = 3) = 1.406 g-cm−3, d(meas) = 1.47 g-cm−3. A total of 1150 data were collected over the range of 4° ≤ 2θ ≤ 60° using film data (Weissenberg); of these, 448 [independent and with I ≥ 3σ(I)] were used in the structural analysis. Refinement converged to final residuals of 0.080 and 0.082 for R(F) and RW(F), respectively. The molecule is located at the twofold axis of the space group. A solution of 2,2′-biphenyldisulfide mono-oxide (II), C12H8S2O, produces centrosymmetric crystals of II belonging in space group P21/c with lattice constants: a = 9.947 (1) A, b = 7.162 (2), c = 15.420 (3) A, and β = 107.56 (1)°; V = 107.56 (1) A3 and d(calc; M.W. = 232.31, Z = 4) = 1.473 g-cm−3. A total of 2114 data were collected over the range of 4° ≤ 2θ ≤ 50°; of these, 1089 [independent and with I ≥ 2.5σ(I)] were used in the structural analysis. Data were corrected for absorption (μ = 4.539 cm−1), and the relative transmission coefficients ranged from 0.9198 to 0.9998. Refinement converged to final residuals of 0.0313 and 0.0300 for R(F) and Rw(F), respectively. For I, the central six-membered ring C4S2 contains a helical C2S2 fragment whose conformational chirality is defined by a torsional angle of 59.98°. The benzene rings are the expected, planar hexagons characteristic of aryl rings. By comparison with I, the torsional angle of the C2S2 fragment of the mono-oxide is diminished (52.9°) by the introduction of the S=O fragment. We believe alteration of molecules (such as functionalization) causing large changes in torsional angles of helical fragments of molecules may play a role in the selection of their crystallization mode; however, it is not the only factor dictating that choice, which is also affected by steric hindrance to the formation of short intermolecular contacts leading, in the solid state, to the formation of homochiral, infinite helical strings, as we shall demonstrate in the text. This study clearly shows the influence of those contacts on the formation of the strings. © 1998 John Wiley & Sons, Inc. Heteroatom Chem 9:65–74, 1998

Internal reorganization energy in return electron transfer within geminate radical ion pairs

The internal reorganization energies λ v for return electron transfer (ET) reactions within geminate radical ion pairs were studied using the extended Nelsen method. In the ET systems studied, the common acceptor was 9,10-dicyanoanthracene (DCA). The donors were methyl-substituted compounds of benzene, biphenyl, naphthalene and phenanthrene. The calculated results indicated that the λ v values were associated mainly with the carbon atoms of the aromatic rings and the atoms linked directly to the aromatic rings. Systems with similar substituted conditions are expected to have similar internal reorganization energies. For systems in which the two aromatic rings of the donor can rotate relative to each other, the calculated λ v values include a contribution from the change in torsional angle in the ET process. Compared with the system in which the donor is a fluorene molecule, the contributions of the torsional angles (low-frequency vibration) to λ v were estimated.

Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches.

A statistical analysis of known structures is made for an assessment of the utility of short-range energy considerations. For each type of amino acid, the potentials governing (1) the torsions and bond angle changes of virtual C alpha-C alpha bonds and (2) the coupling between torsion and bond angle changes are derived. These contribute approximately -2 RT per residue to the stability of native proteins, approximately half of which is due to coupling effects. The torsional potentials for the alpha-helical states of different residues are verified to be strongly correlated with the free-energy change measurements made upon single-site mutations at solvent-exposed regions. Likewise, a satisfactory correlation is shown between the beta-sheet potentials of different amino acids and the scales from free-energy measurements, despite the role of tertiary context in stabilizing beta-sheets. Furthermore, there is excellent agreement between our residue-specific potentials for alpha-helical state and other thermodynamic based scales. Threading experiments performed by using an inverse folding protocol show that 50 of 62 test structures correctly recognize their native sequence on the basis of short-range potentials. The performance is improved to 55, upon simultaneous consideration of short-range potentials and the nonbonded interaction potentials between sequentially distant residues. Interactions between near residues along the primary structure, i.e., the local or short-range interactions, are known to be insufficient, alone, for understanding the tertiary structural preferences of proteins alone. Yet, knowledge of short-range conformational potentials permits rationalizing the secondary structure propensities and aids in the discrimination between correct and incorrect tertiary folds.

Local Dynamics of Poly(ethylene oxide) in Solution. 1. Localization of Chain Motion

Fully atomistic molecular dynamics simulations have been performed on a solution consisting of a poly(ethylene oxide) (PEO) chain of 54 repeat units and 207 toluene molecules at 338 K and 1 bar. The local dynamics of the PEO chain have been examined. Equilibration in a given torsional potential well occurs in about 1.5 ps. Average conformational transition times are 7.4 and 9.0 ps for CO and CC torsions, respectively. Changes in atomic positions or torsional angles accompanying conformational transitions are localized within 8−10 atoms along the polymer chain, in good agreement with simulations of hydrocarbon polymers. About 15% of transitions are correlated with a second transition at the next-neighbor position. In addition to trans-centered cooperative transition pairs that have previously been observed in polyethylene simulations, a variety of types of gauche-centered pairs occur quite frequently.

3-Halocyclohexanones. Torsion angle changes after cation-carbonyl complexation dictate the facial selectivity in reactions with nucleophiles: An ab initio investigation

The geometrical changes that take place after complexation of the carbonyl oxygen of 3-halocyclohexanones with prototypical cations such as H + and Li + were calculated using ab initio MO methods at 6-31G level. The torsion angle changes interpret rationally the experimentally known axial preference of the 3-eq-derivatives and the axial preference (predicted from transition state calculations) of the 3-ax-species. Stereoelectronic effects in 3-ax-halocyclohexanones and 1,3-dipolar interactions in 3-eq-halocyclohexanones after complexation of the carbonyl oxygen with cations such as H + and Li + account for the experimentally observed and the predicted diastereoselectivities, respectively, of these molecules. The complexation induces pyramidalization of the carbonyl carbon and controls the p orbial to adopt an energetically favorable orientation (ax or eq) for capture by a nucleophile.

The directional changes in torsion angles alone after complexation of the carbonyl oxygen with a prototypical cation such as H + predict the facial selectivity of substituted cyclohexanones. An ab initio investigation

H + was taken as a prototypical cation for complexation with the carbonyl oxygen of 3-oxa-, 3,5-dioxa-, and 3-thiacyclohexanones. The geometries of the complexes were fully optimized using ab initio MO calculations with 6-31G basis set. The complexation desymmetrizes the molecular geometry further to an extent that the torsion angle changes on the axial face can be rationally used for the prediction of the facial selectivity in reactions with nucleophiles. The torsion angle changes are sensitive to the nature, position, and orientation of the substitutents. Based on the theory of stereoelectronic control and corroborated by ab initio MO calculations, a simple approach to the prediction of facial control in reactions of selected substituted cyclohexanones with nucleophiles is described. Some evidence is also presented against the known transition state models.

Conformations and Relative Stabilities of the Cis and Trans Isomers in a Series of Isolated N-Phenylamides

The gas-phase conformations of a series of isolated N-phenylamides have been determined from vibrationally resolved electronic spectra obtained by resonant two-photon ionization in a supersonic jet expansion. Both the cis and trans isomers of formanilide were identified, with the cis isomer in 6.5% abundance. The spectral features displayed by this isomer are consistent with a nonplanar geometry which undergoes a large change in the phenyl torsional angle following electronic excitation. The more abundant trans isomer of formanilide adopts a planar structure and is stabilized by 2.5 kcal/mol with respect to the cis isomer. In the excited electronic state the relative stabilities of the two isomers are reversed. Acetanilide, in contrast, is found exclusively as the trans isomer, also having a planar structure. N-Methyl substitution causes a reversal of the relative isomer stabilities found in formanilide and leads to an isomer distribution consisting of approximately 90% E and 10% Z in N-methylformanilide....