Ab initio determination of optical rotatory dispersion in the conformationally flexible molecule (R)-epichlorohydrin

Ab initio optical rotation data from linear-response coupled-cluster and density-functional methods are compared to both gas-phase and liquid-phase polarimetry data for the small, conformationally flexible molecule epichlorohydrin. Three energy minima exist along the C-C-C-Cl dihedral angle, each with strong, antagonistic specific rotations ranging from ca. -450 to +500 deg/[dm (g/mL)] at 355 nm. Density-functional theory (specifically the B3LYP functional) consistently overestimates the optical rotations of each conformer relative to coupled-cluster theory (in agreement with our earlier observations for conformationally rigid species), and we attribute this to density-functional theory's underestimation of the lowest-lying excitation energies of epichlorohydrin. Length- and velocity-gauge formulations of the coupled-cluster response function lead to slightly different specific rotations (ca. 7% at short wavelengths). We have determined well-converged Gibbs free energy differences among the conformers using complete-basis-set extrapolations of coupled-cluster energies including triple excitations to obtain Boltzmann-averaged specific rotations for comparison to the gas-phase results. The length-gauge coupled-cluster data agree remarkably well with experiment, with the velocity-gauge coupled-cluster and density-functional data bracketing the experimental results from below and above, respectively. Liquid-phase conformer populations reported earlier by Polavarapu and co-workers from combined infrared absorption and theoretical analyses differ markedly from the gas-phase populations, particularly for polar solvents. Nevertheless, Boltzmann-averaged specific rotations from both coupled-cluster and density-functional calculations agree well with the corresponding experimental intrinsic rotations, although the theoretical specific rotations for the individual conformers do not take solvent effects into account. PCM-based estimates of conformer populations lead to poor agreement with experiment.     

Optical rotatory dispersion of 2,3-hexadiene and 2,3-pentadiene

The specific rotation of (P)-2,3-hexadiene (1) was measured as a function of wavelength for the gas phase, the neat liquid, and solutions. There was a surprisingly large difference between the gas phase and condensed phase values. The specific rotation was calculated using B3LYP and CCSD, and the difference in energy between the three low energy conformers was estimated at the G3 level. The Boltzmann-averaged CCSD-calculated rotations using the gauge independent velocity gauge representation, as well as the B3LYP values, are in agreement with the gas-phase experimental values. In order to avoid possible problems associated with the conformers of 1, 2,3-pentadiene (2) also was examined. Here again, there was a large difference between the gas-phase and condensed-phase specific rotations, with the CCSD velocity gauge (and B3LYP) results being close to the gas-phase experimental values. The possibility that 2,3-pentadiene could be distorted on going from the gas to liquid phase, thereby accounting for the effect of phase on the specific rotation, was examined via a Monte Carlo statistical mechanics simulation. No effect on the geometry was found. Specific rotations of 1 found in solutions were similar to those for the liquid phase, indicating that the phase difference was not due to association.     

Compactization of rigid-chain amphiphilic macromolecules with local helical structure

Conformational characteristics of amphiphilic macromolecules with secondary local helical structuring are studied by the method of molecular dynamics for different properties of a helix (bending angles between neighboring vectors of the bond and internal rotation angle) and different rigidities of its fixation. Extended helices with high distances between helical turns and dense helices in which neighboring turns directly adjoin each other are studied. As the quality of a solvent deteriorates, extended helices experience a well-pronounced coil-globule transition, whose amplitude increases with an increase in chain rigidity, while the dimensions of dense helices gradually change. In a poor solvent, extended helices formed “collagen-like” structures, flexible chains of dense helices produce hairpin structures, and rigid macromolecules of dense helices form rodlike globules with an almost ideal local helical order. Independently of helix parameters, a deterioration in solvent quality leads to stabilization of the local secondary structure.     

Chiral action at a distance: remote substituent effects on the optical activity of calyculins A and B

[structure--see text] Calyculins A and B differ only by the (E)- vs (Z)-configuration at C(2). Yet, they show a large difference in optical rotations. We demonstrate a new strategy that provides a physical analysis of this long-range chiro-optical effect by Boltzmann-averaged atomic contribution mapping. The polarizability characteristics of the CN substituent rather than the perturbation of the stereogenic centers or the introduction of asymmetry into the polyene chain give rise to the remarkable difference in rotation angles.     

Chiral induction in quinoline-derived oligoamide foldamers: assignment of helical handedness and role of steric effects

Chiral groups attached to the end of quinoline-derived oligoamide foldamers give rise to chiral helical induction in solution. Using various chiral groups, diastereomeric excesses ranging from 9% to 83% could be measured by NMR and circular dichroism. Despite these relatively weak values and the fact that diastereomeric helices coexist and interconvert in solution, the right-handed or left-handed helical sense favored by the terminal chiral group could be determined unambiguously using X-ray crystallography. Assignment of chiral induction was performed in an original way using the strong tendency of racemates to cocrystallize, and taking advantage of slow helix inversion rates, which allowed one to establish that the stereomers observed in the crystals do correspond to the major stereomers in solution. The sense of chiral helical induction was rationalized on the basis of sterics. Upon assigning an Rs or Ss chirality to the stereogenic center using a nomenclature where the four substituents are ranked according to decreasing sizes, it is observed that Rs chirality always favors left-handed helicity and Ss chirality favors right-handed helicity (P). X-ray structures shed some light on the role of sterics in the mechanism of chiral induction. The preferred conformation at the stereocenter is apparently one where the bulkiest group should preferentially point away from the helix, the second largest group should be aligned with the helix backbone, and the smallest should point to the helix.     

Foldamer dynamics expressed via Markov state models. II. State space decomposition

The structural landscape of poly-phenylacetylene (pPA), otherwise known as m-phenylene ethynylene oligomers, has been shown to consist of a very diverse set of conformations, including helices, turns, and knots. Defining a state space decomposition to classify these conformations into easily identifiable states is an important step in understanding the dynamics in relation to Markov state models. We define the state decomposition of pPA oligomers in terms of the sequence of discretized dihedral angles between adjacent phenyl rings along the oligomer backbone. Furthermore, we derive in mathematical detail an approach to further reduce the number of states by grouping symmetrically equivalent states into a single parent state. A more challenging problem requires a formal definition for knotted states in the structural landscape. Assuming that the oligomer chain can only cross the ideal helix path once, we propose a technique to define a knotted state derived from a helical state determined by the position along the helical nucleus where the chain crosses the ideal helix path. Several examples of helical states and knotted states from the pPA 12-mer illustrate the principles outlined in this article.     

Optical activity induced by helical arrangements of tryptamine and 4-chlorobenzoic acid in their cocrystal

Optical rotatory powers of chiral cocrystals formed from the achiral molecules tryptamine and 4-chlorobenzoic acid were determined by the HAUP (high accuracy universal polarimeter) method. These cocrystals belonged to space group P2(1)2(1)2(1), and their absolute configuration was confirmed by the Flack parameter. In the M-crystal, 2-fold helical arrangements are formed in a counterclockwise direction between the two components through the quaternary ammonium salt bridge, hydrogen bond, and the aromatic pi-piinteraction along the c axis, while clockwise helices alone exist in the P-crystal. Large rotatory powers rho(3)(M) = -355 and rho(3)(P) = +352 deg mm(-)(1) were obtained along the c axis in the M- and P-crystal, respectively, at 632.8 nm and 303 K. The magnitude was 10 to 100 times larger than those for ordinary organic crystals. Further, it was confirmed that the negative sign was induced by the counterclockwise helical structures and the positive sign by the clockwise helices. In contrast, the rotations along the a and b axis which are in perpendicular directions to the screw axis were rho(1)(M) = +138, rho(1)(P) = -140 deg mm(-)(1), and rho(2)(M) = -56, rho(2)(P) = +58 deg mm(-)(1), much smaller than rho(3)(M) and rho(3)(P) . The results revealed that the helically arranged aromatic pi electrons as well as the helical ionic and hydrogen bond networks in the crystal contributed to the enhancement of the magnitude of these rotations.     

Structural and spectroscopic studies of peptoid oligomers with alpha-chiral aliphatic side chains

Substantial progress has been made in the synthesis and characterization of various oligomeric molecules capable of autonomous folding to well-defined, repetitive secondary structures. It is now possible to investigate sequence-structure relationships and the driving forces for folding in these systems. Here, we present detailed analysis by X-ray crystallography, NMR, and circular dichroism (CD) of the helical structures formed by N-substituted glycine (or "peptoid") oligomers with alpha-chiral, aliphatic side chains. The X-ray crystal structure of a N-(1-cyclohexylethyl)glycine pentamer, the first reported for any peptoid, shows a helix with cis-amide bonds, approximately 3 residues per turn, and a pitch of approximately 6.7 A. The backbone dihedral angles of this pentamer are similar to those of a polyproline type I peptide helix, in agreement with prior modeling predictions. This crystal structure likely represents the major solution conformers, since the CD spectra of analogous peptoid hexamers, dodecamers, and pentadecamers, composed entirely of either (S)-N-(1-cyclohexylethyl)glycine or (S)-N-(sec-butyl)glycine monomers, also have features similar to those of the polyproline type I helix. Furthermore, this crystal structure is similar to a solution NMR structure previously described for a peptoid pentamer comprised of chiral, aromatic side chains, which suggests that peptoids containing either aromatic or aliphatic alpha-chiral side chains adopt fundamentally similar helical structures in solution, despite distinct CD spectra. The elucidation of detailed structural information for peptoid helices with alpha-chiral aliphatic side chains will facilitate the mimicry of biomolecules, such as transmembrane protein domains, in a distinctly stable form.     

Synthesis of Conjugated Optically Active Polymetallocenes

The development of methodology for synthesizing new materials in which metal atoms are linked by hydrocarbons whose electronic conjugation is unbroken is described. The fundamental idea is to twist the hydrocarbons into helices. By attaching bulky groups to their precursors, the helices can be made to twist mainly in one direction. The molecules synthesized are helicenes capped by five-membered rings to which metals are attached. If the size of the helix is chosen appropriately, a polymeric structure forms in which hydrocarbon rings and metal atoms alternate. An oligomer with Structure 22 is the first such material prepared. It and related structures might be precursors of molecular solenoids, examples of which are not yet known.     

Helix formation in alpha,gamma- and beta,gamma-hybrid peptides: theoretical insights into mimicry of alpha- and beta-peptides

Alpha,gamma- and beta,gamma-hybrid peptides, which are composed of two different homologous amino acid constituents in alternate order, are suggested as novel classes of peptide foldamers. On the basis of a systematic conformational search employing the methods of ab initio MO theory, the possibilities for the formation of periodic secondary structures in these systems are described. The conformational analysis provides a great number of helix conformers widely differing in energy, which can be arranged into three groups: (i) helices with all hydrogen bonds formed in forward direction along the sequence, (ii) helices with all hydrogen bonds in backward direction, and (iii) helices with alternate hydrogen-bond directions (mixed or beta-helices). Most stable are representatives of beta-helices, but their stability decreases considerably in more polar environments in comparison to helix conformers from the other two classes. There is a great similarity between the overall topology of the most stable hybrid peptide helices and typical helices of peptides which are exclusively composed of a single type of homologous amino acids. Thus, the helices of the beta,gamma-hybrid peptides mimic perfectly those of the native alpha-peptides as, for instance, the well-known alpha-helix, whereas the most stable helix conformers of alpha,gamma-hybrid peptides correspond well to the overall structure of beta-peptide helices. The two suggested novel hybrid peptide classes expand considerably the pool of peptide foldamers and may be promising tools in peptide design and in material sciences.     

A new approach to helical primary structures of four-membered rings: (P)- and (M)-tetraspiro[3.0.0.0.3.2.2.2]hexadecane

A new approach to helical primary structures of four-membered rings uses a cycloaddition of a trimethylenketeniminium salt to suitable tailored methylenecyclobutanes to assemble the desired carbon framework. The results are short and effective syntheses of (M)-trispiro[3.0.0.3.2.2]tridecane [(M)-5], and (P)- and (M)-tetraspiro[3.0.0.0.3.2.2.2]hexadecane [(P)- and (M)-24]. Unlike helices of three-membered rings, the specific rotation decreases, as the length of the helix increases.     

Elongation and contraction of molecular springs. Synthesis, structures, and properties of bridged [7]thiaheterohelicenes

A series of bridged [7]thiaheterohelicenes 3a-c and 4 with a variety of helical pitches have been prepared from racemic and optical pure 2,13-bis(hydroxymethyl)dithieno[3,2-e:3',2'-e']benzo[1,2-b:4,3-b']bis[1]benzothiophene (1) in order to investigate the helical structures in solution. Recrystallizations of (PM)-3a, (PM)-3b, (PM)-3c, and (P)-4 from hexane-dichloromethane gave crystals suitable for X-ray crystallography, while recrystallization of (PM)-4 with benzene gave an inclusion complex with a stoichiometry of (PM-4)(4).(C(6)H(6)). X-ray analyses of (PM)-3a-c, (PM-4)(4).(C(6)H(6)), and (P)-4 indicate that the dihedral angles between terminal thiophene rings of the helical framework significantly vary from 22 degrees for 4 to 59 degrees for 3c. This represents as increase of 37 degrees or 168%. Although the (13)C NMR and UV absorption spectra of bridged helicenes 3a-c and unbridged helicene 5 are essentially the same, the molar rotation of 5 is very large compared with those of 3a-c and 4. A red shift (15 nm) in the circular dichroism (CD) spectrum is observed for 4, suggesting that this compound is more planar than 3a-c in solution. In the series of [7]thiaheterohelicenes studied, the minimum helical pitch is 2.70 A for 4.     

Assessing the mechanical properties of a molecular spring

We report on the dramatic effect of increasing helix diameter on the hybridization of oligopyridine-dicarboxamide strands into double helices. Upon replacing a single pyridine by a 1,8-diazaanthracene unit within an oligomeric strand, a 4.7 A enlargement of the helix diameter occurs parallel to the long anthracene axis. This structure change results in a spectacular stabilization of the double helical hybrids derived from these strands (factors of over 10(7)). Detailed investigations of the hybridization process using X-ray crystallography, NMR, fluorescence measurements and molecular mechanics calculations allowed us to assign the duplex stabilization to two enthalpic effects. First, the increase in diameter results in an augmented surface, involved in intermolecular pi-pi stacking. Second, the enlarged diameter leads to a lower tilt angle of the helical strand, with respect to the helix axis, which in turn results in smaller dihedral angles at the aryl-amide linkages and thus a considerably lowered enthalpic cost of the spring-like extension of the strands during the hybridization process. These results provide novel insights into how subtle tuning of molecular components may result in considerable and rationalizable changes in double helical supramolecular architectures.     

Helical foldamer-catalyzed enantioselective 1,4-addition reaction of dialkyl malonates to cyclic enones

The introduction of a five-membered ring α,α-disubstituted α-amino acid into l-Leu-based heptapeptides preferentially induced right-handed (P) helical structures. Using 5 ～ 20 mol% of a single helical foldamers-catalyst, enantioselective 1,4-addition reactions of dialkyl malonates to cycloalk-2-enones (5 ～ 7 rings) proceeded to give chiral 3-substituted cycloalkanones with 94 ～ 99% ee in moderate chemical yields, regardless of the ring size of substrates.     

Alkynide and acetonitrile activation by strained AlPC(2) heterocycles

Bicyclic compounds with annulated four- (AlPC(2)) and five-membered (P(2)C(3)) rings activate and capture Al-alkynides and acetonitrile at room temperature to afford bicyclic compounds with unique six-membered Al(2)PC(3) and AlNPC(3) heterocycles.     

alpha and piDL helical states of alternating poly(gamma-benzyl D-L-glutamate) in solution.

As in solid state, strictly alternating poly(gamma-benzyl D-L-glutamate) in solution can adopt two different helical conformations. Besides the alpha helix, a second helical conformation is found at higher temperatures in dioxane and chloroform, the properties of which correspond to that of the piDL4 helix. As the molecules have a finite length a screw sense is favored for both helical forms thus giving rise to optical activity allowing the study of the transconformation by optical rotatory dispersion and circular dichroism besides infrared and dielectric measurements. Thus, as the temperature is raised the equilibria right-left handed alpha helices and alpha-piDL helical forms can be followed. The favored screw senses are determined by the number of interacting side chains for the alpha helix and by the number of hydrogen bonds which are formed in the piDL helical conformation. The side chain-side chain interactions in the alpha helix are experimentally shown to be attractive.     

Matrix isolation and low temperature solid state FTIR spectroscopic study of alpha-furil

Alpha-furil [C(4)H(3)O-C(=O)-C(=O)-C(4)H(3)O] has been isolated in argon and xenon matrices and studied by FTIR spectroscopy, supported by DFT(B3LYP)/6-311++G(d,p) calculations. The obtained spectra were fully assigned and revealed the presence in the matrices of three different conformers, all of them exhibiting skewed conformations around the intercarbonyl bond with the two C(4)H(3)O-C(=O) fragments nearly planar. The three conformers differ in the orientation of the furan rings relative to the carbonyl groups: the most stable conformer, I (C(2) symmetry; O=C-C=O intercarbonyl dihedral equal to 153.1 degrees), has both furan rings orientated in such a way that one of their beta-hydrogen atoms approaches the oxygen atom of the most distant carbonyl group, forming two H-C=C-C-C=O six-membered rings; the second most stable conformer, II (C(1) symmetry; O=C-C=O intercarbonyl dihedral equal to 126.9 degrees ), has one furan ring orientated as in I, while the second furan group is rotated by ca. 180 degrees (resulting in an energetically less favourable H-C=C-C=O five-membered ring); in the third conformer, III (C(2) symmetry; O=C-C=O dihedral equal to 106.2 degrees ), both furan rings assume the latter orientation relative to the dicarbonyl group. The theoretical calculations predicted the two higher energy forms being 5.85 and 6.22 kJ mol(-1) higher in energy than the most stable form, respectively, and energy barriers for conformational interconversion higher than 40 kJ mol(-1). These barriers are high enough to prevent observation of conformational isomerization for the matrix isolated compound. The three possible conformers of alpha-furil were also found to be present in CCl(4) solution, as well as in a low temperature neat amorphous phase of the compound prepared from fast condensation of its vapour onto a suitable 10 K cooled substrate. On the other hand, in agreement with the available X-ray data [S. C. Biswas, S. Ray and A. Podder, Chem. Phys. Lett., 1987, 134, 541], the IR spectra obtained for the neat low temperature crystalline state reveals that, in this phase, alpha-furil exists uniquely in its most stable conformational state, I.     

ORD and CD studies of poly[(S)(−)-N-α-methylbenzylethylenimine]

The advantages of chiral N-substituted polyethylenimines for the chiroptical study of macromolecular conformations in solution have been considered. Poly[(S)(?)-N-α-methylbenzylethylenimine] (poly-3) and five model compounds have been obtained and their chiroptical properties studied. The cyclic dimer and tetramer of imine 3 are suitable models for the chiroptical study of configurational and conformational behaviour of randomly coiled and helical poly-3 in solution. Unlike the disordered poly-3 in acidified solvents and the configurational models in various solvents, helical poly-3 in hydrocarbon solvents has positive optical rotation and positive CD-band of the tertiary amine chromophore at 223 nm. The appearance of this inherently chiral chromophore of the helix explains the observed changes of the sign and values of the optical rotation of poly-3 in various solvents which are mainly caused by conformational transformations of the main chain. The presence of helical conformations of poly-3 in solution are also confirmed by optical rotation data of stereocopolymers and the concentration dependence data of ORD curves of poly-3. This conclusion agrees with NMR and i.r.-data.     

Peptide models. XIV. Ab initio study on the role of side-chain backbone interaction stabilizing the building unit of right- and left-handed helices in peptides and proteins

Previous ab initio computations revealed that the conformational building unit of the right-handed helix (ϕ ≈ −54°, ψ ≈ −45°) is not an energy minimum on two-dimensional-type Ramachandran potential energy surfaces (E = E{ϕ, ψ}). Theoretical investigations were performed on several single-amino-acid diamides such as For-Gly-NH₂, For-L-Ala-NH₂, Ac-L-Ala-NHMe, and For-L-Val-NH₂ containing amino acid residues (e.g., Ala) which can often be found in helices as shown by X-ray data analysis of globular proteins. The current ab initio [self-consistent field (SCF)] results (based on four different basis sets [3-21G, 4-21G, 4-21G^*, and 6-31G^*]) presented point toward an intrinsic (i.e., non-environmental-assisted) stability of the right-handed helical subconformation of a simple amino acid diamide if the residue contains a polar side chain. Such is the case for a serine derivative when its (SINGLE BOND)CH₂OH side chain is favorably oriented. For the For-L-Ser-NH₂ model compound two slightly different right-handed helical backbone conformations were determined. Depending on the relative orientation of the side chain, the conformational monomer of the 3₁₀ helix (a sharper helical structure with an [i, i + 3]-type H-bond network) as well as the building block of the “standard” α-helix (the regular helical structure with an [i, i + 4]-type H-bond network) were determined computationally by geometry optimization. © 1997 John Wiley & Sons, Inc.     

Stereoelectronic and steric effects in the collagen triple helix: toward a code for strand association

Collagen is the most abundant protein in animals. The protein consists of a helix of three strands, each with sequence X-Y-Gly. Natural collagen is most stable when X is (2S)-proline (Pro) and Y is (2S,4R)-4-hydroxyproline (4R-Hyp). We had shown previously that triple helices in which X is (2S,4S)-4-fluoroproline (4S-Flp) or Y is (2S,4R)-4-fluoroproline (4R-Flp) display hyperstability. This hyperstability arises from stereoelectronic effects that preorganize the main-chain dihedral angles in the conformation found in the triple helix. Here, we report the synthesis of strands containing both 4S-Flp in the X-position and 4R-Flp in the Y-position. We find that these strands do not form a stable triple helix, presumably because of an unfavorable steric interaction between fluoro groups on adjacent strands. Density functional theory calculations indicate that (2S,3S)-3-fluoroproline (3S-Flp), like 4S-Flp, should preorganize the main chain properly for triple-helix formation but without a steric conflict. Synthetic strands containing 3S-Flp in the X-position and 4R-Flp in the Y-position do form a triple helix. This helix is, however, less stable than one with Pro in the X-position, presumably because of an unfavorable inductive effect that diminishes the strength of the interstrand 3S-FlpC=O...H-NGly hydrogen bond. Thus, other forces can counter the benefits derived from the proper preorganization. Although (Pro-Pro-Gly)7 and (4S-Flp-4R-Flp-Gly)7 do not form stable homotrimeric helices, mixtures of these two peptides form stable heterotrimeric helices containing one (Pro-Pro-Gly)7 strand and two (4S-Flp-4R-Flp-Gly)7 strands. This stoichiometry can be understood by considering the cross sections of the two possible heterotrimeric helices. This unexpected finding portends the development of a "code" for the self-assembly of determinate triple helices from two or three strands.