Metallofullerenes as Robust Single-Atom Catalysts for Adsorption and Dissociation of Hydrogen Molecules: A Density Functional Study.

Hydrogen is currently considered as the best alternative for traditional fuels due to its sustainable and ecofriendly nature. Additionally, hydrogen dissociation is a critical step in almost all hydrogenation reactions, which is crucial in industrial chemical production. A cost-effective and efficient catalyst with favorable activity for this step is highly desirable. Herein, transition-metal-doped fullerene (TM@C60) complexes are designed and investigated as single-atom catalysts for the hydrogen splitting process. Interaction energy analysis (Eint) is also carried out to demonstrate the stability of designed TM@C60 metallofullerenes, which reveals that all the designed complexes have higher thermodynamic stability. Furthermore, among all the studied metallofullerenes, the best catalytic efficiency for hydrogen dissociation is seen for the Sc@C60 catalyst Ea = 0.13 eV followed by the V@C60 catalyst Ea = 0.19 eV. The hydrogen activation and dissociation processes over TM@C60 metallofullerenes is further elaborated by analyzing charge transfer via the natural bond orbital and electron density difference analyses. Additionally, quantum theory of atoms in molecule analysis is carried out to investigate the nature of interatomic interactions between hydrogen molecules and TMs@C60 metallofullerenes. Overall, results of the current study declare that the Sc@C60 catalyst can act as a low cost, highly efficient, and noble metal-free single-atom catalyst to efficiently catalyze hydrogen dissociation reaction.

Chiral Recognition of Amino Acids Using CC2 Porous Organic Cages.

Enantiomers have the same physical properties but different chemical properties due to the difference in the orientation of groups in space and thus Chiral discrimination is quite necessary, as an enantiomer of drug can have lethal effects. In this study, we used the CC2 cage for chiral discrimination of amino acids using density functional theory. The results indicated the physisorption of amino acids in the central cavity of the cage. Among the four selected amino acids, proline showed maximum interactions with the cage and maximum chiral discrimination energy is also observed in the case of proline that is 2.78 kcal/mol. Quantum theory of atoms in molecules and noncovalent interaction index analyses showed that the S enantiomer in each case has maximum interactions. The charge transfer between the analyte and surface is further studied through natural bond orbital analysis. It showed sensitivity of cage for both enantiomers, but a more pronounced effect is seen for S enantiomers. In frontier molecular orbital analysis, the least EH-L gap is observed in the case of R proline with a maximum charge transfer of -0.24 e-. Electron density difference analysis is carried out to analyze the pattern of the charge distribution. The partial density of state analysis is computed to understand the contribution of each enantiomer in overall density of the complexes. Our results show that S-CC2 porous organic cages have a good ability to differentiate between two enantiomers. S-CC2 porous organic cages efficiently differentiated the S enantiomer from the R enantiomers of selected amino acids.

Determination of the Absolute Configuration of Ballonigrin Lactone A Using Density Functional Theory Calculations.

We report the determination of the absolute configuration of a diterpenoid, namely, ballonigrin lactone A (BLA), by comparison of the computed optical rotations, [α]D, of its two diastereomers using density functional theory (DFT) calculations to the experimental [α]D value of +22.4. One of the diastereomers having configurations 4S, 5R, 6S, 10S, 15S was named "α-BLA," and the other one with configuration 4S, 5R, 6S, 10S, 15R was called "ß-BLA". Six conformers for each diastereomer (α-BLA and ß-BLA) of BLA were identified through their conformational analysis. [α]D values of these six conformations for each diastereomer were calculated using DFT at the mPW1PW91/6-311G(d,p)/SMDChloroform level of theory, leading to the conformationally averaged [α]D values of -96.8 for α-BLA and +65.1 for ß-BLA. Thus, it was found that the experimental [α]D value of +22.4 was of 4S, 5R, 6S, 10S, 15R, i.e., ß-BLA. Experimental and computed nuclear magnetic resonance (NMR) data were also compared, and this comparison was in accordance with the conclusion drawn from the comparison of [α]D values. Finally, the results were augmented with the calculation of the DP4 analysis, and the probability obtained also endorsed our earlier calculations.

Mini review: Instrumentation for vibrational circular dichroism spectroscopy, still a role for dispersive instruments.

Vibrational circular dichroism (VCD) has become a standard method for determination of absolute stereochemistry, particularly now that reliable commercial instrumentation has become available. These instruments use a now well-documented Fourier transform infrared-based approach to measure VCD that has virtually displaced initial dispersive infrared-based designs. Nonetheless, many papers have appeared reporting dispersive VCD data, especially for biopolymers. Instrumentation designed with these original methods, particularly after more recent updates optimizing performance in selected spectral regions, has been shown still to have advantages for specific applications. This article presents a mini-review of dispersive VCD instrument designs and includes sample spectra obtained for various biopolymer (particularly peptide) samples. Complementary reviews of Fourier transform-VCD designs are broadly available.

Spiral superstructures of amyloid-like fibrils of polyglutamic acid: an infrared absorption and vibrational circular dichroism study.

Amyloid fibrils, which are often associated with certain degenerative disorders, reveal a number of intriguing spectral properties. However, the relationship between the structure of fibrils and their optical traits remains poorly understood. Poly(L-glutamic) acid is a model polypeptide shown recently to form amyloid-like fibrils with an atypical infrared amide I' band at 1595 cm(-1), which has been attributed to the presence of bifurcated hydrogen bonds coupling C═O and N-D groups of the main chains to glutamate side chains. Here we show that this unusual amide I' band is observed only for fibrils grown from pure enantiomers of the polypeptide, whereas fibrils precipitating from equimolar mixtures of poly(L-glutamic) and poly(D-glutamic) acids have amide I' bands at 1684 and 1612 cm(-1), which are indicative of a typical intermolecular antiparallel ß-sheet. Pure enantiomers of polyglutamic acid form spirally twisted superstructures whose handedness is correlated to the amino acid chirality, while fibrils prepared from the racemate do not form scanning electron microscopy (SEM)-detectable mesoscopically ordered structures. Vibrational circular dichroism (VCD) spectra of ß-aggregates prepared from mixtures of all L- or D-polyglutamic acid in varying ratios indicate that the enhancement of VCD intensity correlates with the presence of the twisted superstructures. Our results demonstrate that both IR absorption and enhanced VCD are sensitive to subtle packing defects taking place within the compact structure of amyloid fibrils.

Experimental and theoretical spectroscopic study of 3(10)-helical peptides using isotopic labeling to evaluate vibrational coupling.

Coupling between the amide linkages in a peptide or protein is the key physical property that gives vibrational spectra and circular dichroism sensitivity to secondary structures. By use of (13)C isotopic labeling on individual and pairs of amide C═O groups, the amide I band for selected residues was effectively isolated in designed hexa- and octapeptides having dominant 3(10)-helical conformations. The resultant frequency and intensity responses were measured with IR absorption, vibrational circular dichroism (VCD), and Raman spectroscopies and simulated with density functional theory (DFT) based computations. Band fitting the spectral components and correlating the results to the computed coupling between selected labeled positions were used to determine coupling constant signs and to estimate their magnitudes for specific sequences. The observed frequency and intensity patterns, and their variation between IR and VCD with label position in the sequence, follow the theoretical predictions to a large degree, but are complicated by end effects that alter the local force field (FF) for some residues in these short peptides. These FF variations were overestimated in the theoretical models which may be evidence of structural variations not included in the model. By analyzing the simulations with different coupling models, the coupling constants were determined to lie in a range (positive) +3-5 cm(-1) for sequential residues (i,i+1) and with (negative) -3 cm(-1) as an upper bound for alternate ones (i,i+2). The sequential amide coupling for 3(10)-helices is weaker than for α-helices but has the same sign and is larger than and oppositely signed as compared to 3(1)-, or poly-(Pro)(n) type-II, helices.

Inter-residue coupling and equilibrium unfolding of PPII helical peptides. Vibrational spectra enhanced with (13)C isotopic labeling.

Unordered proteins, unfolded peptides, and several "random coil" models have been shown to have local conformations similar to that of polyproline II (PPII). Inter-residue coupling of selected residues in a series of related peptides having predominantly PPII conformations were measured using IR, VCD, and Raman spectra of selected variants that were doubly C(1)-labeled with (13)C on the amide C═O. The characteristics of the (13)C═O component of the IR, VCD, and Raman amide I' bands and their sensitivity to the local structure of the peptide are compared to predictions based on DFT level calculations for related structures and used to estimate coupling interactions between pairs of C═O groups along the backbone of this helical structure. In the PPII case, the coupling is relatively weak, due to the extended structure, yet by combining IR, Raman, and VCD observations with results of DFT level model calculations, we have determined bounds for experimental interaction constants for this structure. Correlation of properties for PPII structures with those of "random coils" can be done by comparing Pro(n) and Pro-rich sequences with Lys-rich sequences. The experimental band shifts and implied couplings reflect the computed results in both cases. Thermal unfolding of these peptides appears to be multistate, with monotonic spectral changes but little evidence of a cooperative (sigmoidal) transition. For the Lys-rich series, a transition from PPII to α-helix structure was induced by TFE addition, and the spectra were fit to an equilibrium model. These spectral changes show a large variation in (13)C═O coupling that occurs with a local conformational change from PPII- to α-helical, which is both well-fit by our theoretical results and offers a new site-specific method of assigning local PPII/disordered vs α-helical (or other) structure.

Comparison of vibrational circular dichroism instruments: development of a new dispersive VCD.

A dispersive vibrational circular dichroism (VCD) instrument has been designed and optimized for the measurement of mid-infrared (MIR) bands such as the amide I and amide II vibrational modes of peptides and proteins. The major design considerations were to construct a compact VCD instrument for biological molecules, to increase signal-to-noise (S/N) ratio, to simultaneously collect and digitize the sample transmission and polarization modulation signals, and to digitally ratio them to yield a VCD spectrum. These were realized by assembling new components using design factors adapted from previous VCD instruments. A collection of spectra for peptides and proteins having different dominant secondary structures (alpha-helix, beta-sheet, and random coil) measured for identical samples under the same conditions showed that the new instrument had substantially improved S/N as compared with our previous dispersive VCD instrument. These instruments both provide protein VCD for the amide I that are comparable to or somewhat better than those measurable with commercial Fourier transform (FT) VCD instruments if just the amide I band in the spectra is obtained at modest resolution (8 cm(-1)) with the same total data collection time on each type of instrument.