Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation

The cooperative folding and unfolding of a beta-hairpin structure are observed in explicit water at native folding conditions through self-guided molecular dynamics simulation. The folded structure agrees excellently with the NMR NOE data. After going through a fully hydrated state, the peptide folds into a beta-hairpin structure in a highly cooperative process. During the folding process it is observed that side chain interaction occurs first, while intrapeptide hydrogen bonds only form at the final stage. On the contrary, the unfolding process starts with the breaking of interstrand hydrogen bonds. Energetic analysis indicates that the driving force of the folding is the intrapeptide interaction, while the solvent interaction opposes the folding.     

Solute-solvent intermolecular vibronic coupling as manifested by the molecular near-field effect in resonance hyper-Raman scattering

Vibronic coupling within the excited electronic manifold of the solute all-trans-β-carotene through the vibrational motions of the solvent cyclohexane is shown to manifest as the "molecular near-field effect," in which the solvent hyper-Raman bands are subject to marked intensity enhancements under the presence of all-trans-β-carotene. The resonance hyper-Raman excitation profiles of the enhanced solvent bands exhibit similar peaks to those of the solute bands in the wavenumber region of 21,700-25,000 cm(-1) (10,850-12,500 cm(-1) in the hyper-Raman exciting wavenumber), where the solute all-trans-β-carotene shows a strong absorption assigned to the 1A(g) → 1B(u) transition. This fact indicates that the solvent hyper-Raman bands gain their intensities through resonances with the electronic states of the solute. The observed excitation profiles are quantitatively analyzed and are successfully accounted for by an extended vibronic theory of resonance hyper-Raman scattering that incorporates the vibronic coupling within the excited electronic manifold of all-trans-β-carotene through the vibrational motions of cyclohexane. It is shown that the major resonance arises from the B-term (vibronic) coupling between the first excited vibrational level (v = 1) of the 1B(u) state and the ground vibrational level (v = 0) of a nearby A(g) state through ungerade vibrational modes of both the solute and the solvent molecules. The inversion symmetry of the solute all-trans-β-carotene is preserved, suggesting the weak perturbative nature of the solute-solvent interaction in the molecular near-field effect. The present study introduces a new concept, "intermolecular vibronic coupling," which may provide an experimentally accessible∕theoretically tractable model for understanding weak solute-solvent interactions in liquid.     

Direct experimental observation of the effect of the base pairing on the oxidation potential of Guanine

The effect of complementary base pairing on the oxidation potential of a guanosine derivative has been determined by cyclic and differential pulse voltammetry in CHCl3. The formation of the Watson-Crick H-bonded complex lowers the oxidation potential of the free molecule by 0.34 V, which compares well with the value obtained by DFT/B3LYP/6-311++g** computations.     

Direct observation of odd-even effect in dilute polymeric solutions: A time-resolved fluorescence anisotropy study

The odd-even effect is demonstrated, for the first time, in dilute polymeric solutions of polyethers, consisting of substituted luminescent quinquephenyl units which are connected by flexible aliphatic chains of 7-12 methylene groups. The effect, which is demonstrated by means of steady state and time resolved fluorescence anisotropy, has been attributed to the different mutual orientation of the luminescent dipoles, in the odd (7, 9, 11) and even (8, 10, 12) polymers. Namely, as the temperature of the solution is lowered the flexible aliphatic chains adopt the nearly all-staggered lowest energy conformation, which results in different mutual orientations of the fluorophores in the two types of polymers.     

Direct observation of protein structural transitions through entire amyloid aggregation processes in water using 2D-IR spectroscopy

Amyloid proteins that undergo self-assembly to form insoluble fibrillar aggregates have attracted much attention due to their role in biological and pathological significance in amyloidosis. This study aims to understand the amyloid aggregation dynamics of insulin (INS) in H₂O using two-dimensional infrared (2D-IR) spectroscopy. Conventional IR studies have been performed in D₂O to avoid spectral congestion despite distinct H–D isotope effects. We observed a slowdown of the INS fibrillation process in D₂O compared to that in H₂O. The 2D-IR results reveal that different quaternary structures of INS at the onset of the nucleation phase caused the distinct fibrillation pathways of INS in H₂O and D₂O. A few different biophysical analysis, including solution-phase small-angle X-ray scattering combined with molecular dynamics simulations and other spectroscopic techniques, support our 2D-IR investigation results, providing insight into mechanistic details of distinct structural transition dynamics of INS in water. We found the delayed structural transition in D₂O is due to the kinetic isotope effect at an early stage of fibrillation of INS in D₂O, i.e., enhanced dimer formation of INS in D₂O. Our 2D-IR and biophysical analysis provide insight into mechanistic details of structural transition dynamics of INS in water. This study demonstrates an innovative 2D-IR approach for studying protein dynamics in H₂O, which will open the way for observing protein dynamics under biological conditions without IR spectroscopic interference by water vibrations.

This study aims to understand the structural transition dynamics of INS during amyloid aggregation in H₂O using 2D-IR spectroscopy. The results show that distinct fibrillations in D₂O and H₂O originated from different quaternary structures of INS.     

Direct observation of peptide hydrogel self-assembly

The characterization of self-assembling molecules presents significant experimental challenges, especially when associated with phase separation or precipitation. Transparent window infrared (IR) spectroscopy leverages site-specific probes that absorb in the “transparent window” region of the biomolecular IR spectrum. Carbon–deuterium (C–D) bonds are especially compelling transparent window probes since they are non-perturbative, can be readily introduced site selectively into peptides and proteins, and their stretch frequencies are sensitive to changes in the local molecular environment. Importantly, IR spectroscopy can be applied to a wide range of molecular samples regardless of solubility or physical state, making it an ideal technique for addressing the solubility challenges presented by self-assembling molecules. Here, we present the first continuous observation of transparent window probes following stopped-flow initiation. To demonstrate utility in a self-assembling system, we selected the MAX1 peptide hydrogel, a biocompatible material that has significant promise for use in drug delivery and medical applications. C–D labeled valine was synthetically introduced into five distinct positions of the twenty-residue MAX1 β-hairpin peptide. Consistent with current structural models, steady-state IR absorption frequencies and linewidths of C–D bonds at all labeled positions indicate that these side chains occupy a hydrophobic region of the hydrogel and that the motion of side chains located in the middle of the hairpin is more restricted than those located on the hairpin ends. Following a rapid change in ionic strength to initiate self-assembly, the peptide absorption spectra were monitored as function of time, allowing determination of site-specific time constants. We find that within the experimental resolution, MAX1 self-assembly occurs as a cooperative process. These studies suggest that stopped-flow transparent window FTIR can be extended to other time-resolved applications, such as protein folding and enzyme kinetics.

To facilitate the characterization of phase-transitioning molecules, site-specific non-perturbative infrared probes are leveraged for continuous observation of the self-assembly of fibrils in a peptide hydrogel following stopped-flow initiation.     

Direct observation of a carbene-alcohol ylide

Carboethoxycarbene reacts with methanol-OD to form an ylide. The formation and decay of this ylide was monitored by ultrafast time-resolved IR spectroscopy. The formation and decay of the ylide is linearly dependent on the concentration of methanol-OD in acetonitrile with second-order rate constants of ylide formation (8.4 × 10(9) M(-1) s(-1)) and decay (1.4 × 10(9) M(-1) s(-1)). Similar results were obtained with 1-butanol.     

Direct observation of growth defects in zeolite beta

High-resolution transmission electron microscopy reveals linear, "double pore" defects in the important zeolite beta. Structural interpretation of these defects gives evidence for the mechanism by which the zeolite crystallizes.     

Direct observation of odd-even effect for chiral alkyl alcohols in solution using vibrational circular dichroism spectroscopy

The odd-even effect of chiral alkyl alcohols, (S)-CH(3)CHOHC(n)()H(2)(n)()(+1) (n = 2-8), in solution state has been observed spectroscopically for the first time. The vibrational circular dichroism (VCD) bands at 1148 cm(-)(1) exhibit a clear odd-even effect. The observed VCD bands of (R)-(-)-2-hexanol correspond well to those predicted (population weighted). Density functional theory calculations indicate that the most prevalent conformations in solution are the all-trans forms. The odd-even effect of the VCD bands is ascribed to the alternating terminal methyl motions in the alkyl chains relative to fixed motions near the chiral center in the trans conformations. The conformational sensitivity of VCD for the chiral alcohols in the solution state may be useful for the design of liquid crystals and ligands in the future.     

Direct observation of the transformation of ludwigite to orthopinakiolite

Crystals with the composition Mg_1.5Mn_1.5BO₅ prepared at 1300°C in sealed platinum tubes were studied by high-resolution electron microscopy. The crystals were found to possess the ludwigite structure with very few inherent planar defects. After heating in the electron beam the electron diffraction patterns and electron micrographs showed that the ludwigite structure had rearranged to the orthopinakiolite structure. Two possible mechanisms for such a transformation have been described.     

Intensity enhancement and selective detection of proximate solvent molecules by molecular near-field effect in resonance hyper-Raman scattering

A new molecular phenomenon associated with resonance hyper-Raman (HR) scattering in solution has been discovered. Resonance HR spectra of all-trans-beta-carotene and all-trans-lycopene in various solvents exhibited several extra bands that were not assignable to the solute but were unequivocally assigned to the solvents. Neat solvents did not show detectable HR signals under the same experimental conditions. Similar experiments with all-trans-retinal did not exhibit such enhancement either. All-trans-beta-carotene and all-trans-lycopene have thus been shown to induce enhanced HR scattering of solvent molecules through a novel molecular effect that is not associated with all-trans-retinal. We call this new effect the "molecular near-field effect." In order to explain this newly found effect, an extended vibronic theory of resonance HR scattering is developed where the vibronic interaction including the proximate solvent molecule (intermolecular vibronic coupling) is explicitly introduced in the solute hyperpolarizability tensor. The potential of "molecular near-field HR spectroscopy," which selectively detects molecules existing in the close vicinity of a HR probe in complex chemical or biological systems, is discussed.     

Direct observation for the cyclization of a diarylcarbonyl oxide

Trapping and laser flash spectroscopic experiments showed that the cyclization of diphenylcarbonyl oxide is turned into a very facile process by introducing p-methoxyl substituent, the lifetime of which is as short as 10⁻⁸ s. The trapping with diphenylsulfide and -sulfoxide suggested the intervention of a dioxirane intermediate.     

Charge-transfer-induced twisting of the nitro group

Excited-state relaxation dynamics of 2-amino-7-nitrofluorene (ANF) and 2-dimethylamino-7-nitrofluorene (DMANF) has been investigated in two aprotic solvents, namely acetonitrile and DMSO using femtosecond transient absorption spectroscopic technique. Following photoexcitation to the highly dipolar excited singlet (S1) state, ANF and DMANF undergo mainly two concomitant relaxation processes, namely dipolar solvation and conformational relaxation via twisting of the nitro group to an orthogonal configuration with respect to the aromatic plane. Viscosity dependence of the relaxation dynamics of the S1 states of both ANF and DMANF suggests no involvement of the twisting motion of the amino or dimethylamino group in the charge-transfer process. The twisting of the nitro group is found to be a friction affected diffusive motion, which does not associate with any further charge transfer. The results presented in this paper resolve experimentally the dynamics of the twisting motion of the nitro group for the first time.     

The effect of substituents on the helical twisting power of aldol condensation products of menthone

The helical twisting powers of the E-isomers of aldol condensation products of menthone and aromatic aldehydes are higher than those of the Z-isomers. In order to find out which chiral centre of these menthone derivatives is responsible for the value of the helical twisting in both isomers, the E-isomers of aldol condensation products of 3-methylcyclohexanone and 2-isopropylcyclohexanone were prepared and photoisomerized to form Z-isomers. The physical properties of these species were determined. It was concluded that the strong helical twisting power of the E-isomers of the derivatives of menthone is caused by the chiral carbon atom containing the methyl group in the ring. The relatively low helical twisting power of the Z-isomers and the composition of the E-Z isomers in the photostationary state are determined mainly by the other chiral centre containing the isopropyl group.