Effect of Conformational Variability on the Drug Resistance of Candida auris ERG11p and FKS1

Candida auris infection has been recognized as an urgent threat to antifungal drug resistance, and the Eagle effect of C. auris FKS1 (1,3-β-d-glucan synthase) wild-type isolates has also been noted. The Eagle effect, namely, where higher concentrations of antifungals reduce fungicidal activity relative to lower concentrations, is a confounding factor of apparent antifungal resistance, but the detailed mechanism remains unclear. Here, we present the conformational variability of mutation sites for ERG11p (lanosterol 14α-demethylase) and FKS1 from deep neural network-based prediction along with the reported X-ray crystallographic and cryo-electron microscopy (cryo-EM) structures of antifungals. The sequence variability maps provide valuable insights into the inconsistent correlation between azole resistance and the mysterious Eagle effect with the dispersion of minimal inhibitory concentration (MIC) for echinocandin resistance. The conformational variability prediction supports the hypothesis that mutations K143R of clade I, VF125AL of clade III, and Y132F of clade IV for C. auris ERG11p make the corresponding site variable and that an increased population of invisible variable conformations potentially contributes to triazole resistance. In contrast, the predicted rigid conformation by the S639F mutation of hot spot region 1 (HS1) for FKS1 suggests that caspofungin (CAS) is involved in an uncompetitive inhibition, and a decreased population of the CAS-bound state of FKS1 with Rho1 leads to drug resistance. The predicted variable HS1 region for FKS1 WT isolates and the rigid one for FKS1 S639F mutants support the in vivo drug response and the in vitro MIC dispersion. A plausible mechanism of the Eagle effect is hereby proposed, namely, that a high concentration of CAS with a high membrane affinity reduces the population of the CAS-bound state of FKS1 with Rho1, as well as accompanying events such as aggregation or association depending on the conformational variability of HS1.

Exceptionally enhanced Raman optical activity (ROA) of amyloid fibrils and their prefibrillar states

Amyloid fibrils form remarkable, multi-layered chiral supramolecular architectures. The proximity of interacting oscillators in the chiral fibril supramolecules is responsible for the unusual sensitivity of vibrational circular dichroism (VCD) for fibril formation. Surprisingly, up to now, such characteristics have not been shown for ROA, although it displays the same vibrational markers of fibrils as VCD, including the amide I band. Here, we report an exceptionally large enhancement of the ROA signal detected for mature amyloid fibrils and their prefibrillar states. Remarkably, the same ROA signal has been obtained for fibrils of homologous lysozymes and the dissimilar protein, insulin, indicating a possible common enhanced ROA spectrum, analogous to that for VCD for all amyloid fibrils investigated to date. The ROA signal is observed at earlier stages of fibril formation than VCD and provides access to a considerably broader range of vibrations. Further studies are necessary to verify the applicability of ROA for the analysis of amyloid fibrils.

Effect of Conformational Variability on Seasonable Thermal Stability and Cell Entry of Omicron Variants

The Omicron BA.1 variant of SARS-CoV-2 preferentially infects through the cathepsin-mediated endocytic pathway, but the mechanism of cell entry has not been solved yet because BA.4/5 is more fusogenic and more efficiently spread in human lung cells than BA.2. It has been unclear why the Omicron spike is inefficiently cleaved in virions compared with Delta, and how the relatively effective reproduction proceeds without the cell entry through plasma membrane fusion. Conformational variability from deep neural network-based prediction correlates well with the thermodynamic stability of variants. The difference of seasonable pandemic variants in summer and those in winter is distinguishable by this conformational stability, and the geographical optimization of variants is also traceable. Further, the predicted conformational variability maps rationalize the less efficient S1/S2 cleavage of Omicron variants and provide a valuable insight into the cell entry through the endocytic pathway. It is concluded that conformational variability prediction is able to complement transformation information on motifs in protein structures for drug discovery.

Conformational Variability Correlation Prediction of Transmissibility and Neutralization Escape Ability for Multiple Mutation SARS-CoV-2 Strains using SSSCPreds

Identifying the fundamental cause of transmissibility of multiple mutation strains and vaccine nullification is difficult in general and is a source of significant concern. The conformational variability of the mutation sites for B.1.617.2 (Δ), B.1.617.1 (κ), B.1.427/429 (ε), P.1 (γ), B.1.351 (β), B.1.1.7 (α), S477N, and the wild-type strain has been assessed using a deep neural-network-based prediction program of conformational flexibility or rigidity in proteins (SSSCPreds). We find that although the conformation of G614 is rigid, which is assigned as a left-handed (LH) α-helix-type one, that of D614 is flexible without the hydrogen bonding latch to T859. The rigidity of glycine, which stabilizes the local conformation more effectively than that of aspartic acid with the latch, thereby contributes to the reduction of S1 shedding, high expression, and increase in infectivity. The finding that the sequence flexibility/rigidity map pattern of B.1.1.7 is similar to that of the wild-type strain but is largely different from those of B.1.351 and P.1 correlates with the minor escape ability of B.1.1.7. The increased rigidity of the amino acid sequence YRYRLFR from the SSSCPreds data of B.1.427/429 near the L452R mutation site contributes to the 2-fold increased B.1.427/B.1.429 viral shedding in vivo and the increase in transmissibility relative to wild-type circulating strains in a similar manner to D614G. The concordance and rigidity ratios of multiple mutation strains such as B.1.617.2 against the wild-type one at the receptor-binding domain (RBD) and receptor-binding motif (RBM) regions provide a good indication of the transmissibility and neutralization escape ability except for binding affinity of mutation sites such as N501Y.

SSSCPreds: Deep Neural Network-Based Software for the Prediction of Conformational Variability and Application to SARS-CoV-2

Amino acid mutations that improve protein stability and rigidity can accompany increases in binding affinity. Therefore, conserved amino acids located on a protein surface may be successfully targeted by antibodies. The quantitative deep mutational scanning approach is an excellent technique to understand viral evolution, and the obtained data can be utilized to develop a vaccine. However, the application of the approach to all of the proteins in general is difficult in terms of cost. To address this need, we report the construction of a deep neural network-based program for sequence-based prediction of supersecondary structure codes (SSSCs), called SSSCPrediction (SSSCPred). Further, to predict conformational flexibility or rigidity in proteins, a comparison program called SSSCPreds that consists of three deep neural network-based prediction systems (SSSCPred, SSSCPred100, and SSSCPred200) has also been developed. Using our algorithms we calculated here shows the degree of flexibility for the receptor-binding motif of SARS-CoV-2 spike protein and the rigidity of the unique motif (SSSC: SSSHSSHHHH) at the S2 subunit and has a value independent of the X-ray and Cryo-EM structures. The fact that the sequence flexibility/rigidity map of SARS-CoV-2 RBD resembles the sequence-to-phenotype maps of ACE2-binding affinity and expression, which were experimentally obtained by deep mutational scanning, suggests that the identical SSSC sequences among the ones predicted by three deep neural network-based systems correlate well with the sequences with both lower ACE2-binding affinity and lower expression. The combined analysis of predicted and observed SSSCs with keyword-tagged datasets would be helpful in understanding the structural correlation to the examined system.

Isolation, Total Synthesis, and Absolute Configuration Determination of Renoprotective Dimeric N-Acetyldopamine-Adenine Hybrids from the Insect Aspongopus chinensis

Aspongdopamines A and B (1 and 2), unusual adducts composed of N-acetyldopamine and adenine were isolated from the insect Aspongopus chinensis. Compounds 1 and 2 are positional isomers both isolated as racemates. Chiral separation assisted by 14-step total synthesis and computation including vibrational circular dichroism calculations allowed us to unambiguously assign the absolute configurations of eight stereoisomers. Renal fibrosis inhibition of the stereoisomers was evaluated in TGF-β1-induced rat kidney epithelial cells.

A Vibrational Circular Dichroism Microsampling Accessory: Mapping Enhanced Vibrational Circular Dichroism in Amyloid Fibril Films

We report the first vibrational circular dichroism (VCD) measurement of spatial heterogeneity in a sample using infrared (IR) microsampling. Vibrational circular dichroism spectra are typically measured using a standard IR cell with an IR beam diameter of 10 mm or greater making it impossible to investigate the spatial heterogeneity of a solid film sample. We have constructed a VCD sampling assembly with either 3 mm or 1 mm spatial resolution. An XY-translation stage was used to measure spectra at different spatial locations producing IR and VCD maps of the sample. In addition, a rotating sample stage was employed using a dual photoelastic modulator (PEM) setup to suppress artifacts due to linear birefringence in solid-phase or film samples. Infrared and VCD mapping of an insulin fibril film has been carried out at both 3 and 1 mm spatial resolution, and lysozyme films were mapped at 1 mm resolution. The IR spectra of different spots vary in intensity due primarily to sample thickness. The changes in the VCD intensity across the map largely correlate to corresponding changes in the IR map. Closer inspection of the insulin map revealed changes in the relative intensities of the VCD spectra not present in the parent IR spectra, which indicated differences in the degree of supramolecular chirality of the fibrils in the various spatial regions. For lysozyme films, in addition to different degrees of supramolecular chirality, reversal of the net fibril chirality was observed. The large signal-to-noise ratio observed at 1 mm resolution implies the feasibility of further increasing the spatial resolution by one or two orders of magnitude for protein fibril film samples.

Supramolecular chirality in peptide microcrystals

The vibrational circular dichroism (VCD) spectra of microcrystals of fibril-forming peptides have been measured for the first time. VCD spectra were measured and compared for microcrystals and fibrils formed from the same peptide, human islet amyloid polypeptide (IAPP, amylin). Structural information related to the supramolecular chirality of both the microcrystals and the fibrils, as well as the VCD enhancement mechanisms in fibrils and microcrystals, is obtained from these spectral comparisons. It is concluded that strongly enhanced VCD does not require braiding of two or more filaments that is permitted in fibrils but not microcrystals.

Rapid Filament Supramolecular Chirality Reversal of HET-s (218-289) Prion Fibrils Driven by pH Elevation

Amyloid fibril polymorphism is not well understood despite its potential importance for biological activity and associated toxicity. Controlling the polymorphism of mature fibrils including their morphology and supramolecular chirality by postfibrillation changes in the local environment is the subject of this study. Specifically, the effect of pH on the stability and dynamics of HET-s (218-289) prion fibrils has been determined through the use of vibrational circular dichroism (VCD), deep UV resonance Raman, and fluorescence spectroscopies. It was found that a change in solution pH causes deprotonation of Asp and Glu amino acid residues on the surface of HET-s (218-289) prion fibrils and triggers rapid transformation of one supramolecular chiral polymorph into another. This process involves changes in higher order arrangements like lateral filament and fibril association and their supramolecular chirality, while the fibril cross-β core remains intact. This work suggests a hypothetical mechanism for HET-s (218-289) prion fibril refolding and proposes that the interconversion between fibril polymorphs driven by the solution environment change is a general property of amyloid fibrils.

Is supramolecular filament chirality the underlying cause of major morphology differences in amyloid fibrils?

The unique enhanced sensitivity of vibrational circular dichroism (VCD) to the formation and development of amyloid fibrils in solution is extended to four additional fibril-forming proteins or peptides where it is shown that the sign of the fibril VCD pattern correlates with the sense of supramolecular filament chirality and, without exception, to the dominant fibril morphology as observed in AFM or SEM images. Previously for insulin, it has been demonstrated that the sign of the VCD band pattern from filament chirality can be controlled by adjusting the pH of the incubating solution, above pH 2 for “normal” left-hand-helical filaments and below pH 2 for “reversed” right-hand-helical filaments. From AFM or SEM images, left-helical filaments form multifilament braids of left-twisted fibrils while the right-helical filaments form parallel filament rows of fibrils with a flat tape-like morphology, the two major classes of fibril morphology that from deep UV resonance Raman scattering exhibit the same cross-β-core secondary structure. Here we investigate whether fibril supramolecular chirality is the underlying cause of the major morphology differences in all amyloid fibrils by showing that the morphology (twisted versus flat) of fibrils of lysozyme, apo-α-lactalbumin, HET-s (218–289) prion, and a short polypeptide fragment of transthyretin, TTR (105–115), directly correlates to their supramolecular chirality as revealed by VCD. The result is strong evidence that the chiral supramolecular organization of filaments is the principal underlying cause of the morphological heterogeneity of amyloid fibrils. Because fibril morphology is linked to cell toxicity, the chirality of amyloid aggregates should be explored in the widely used in vitro models of amyloid-associated diseases.

The transition from the native to the acid-state characterized by multi-spectroscopy approach: study for the holo-form of bovine α-lactalbumin

The transition of the holo-form of bovine α-lactalbumin from the native (N) to the pH-generated acidic-state (A-state) was analyzed by probing its tertiary and secondary structure using a concerted spectroscopic approach combining near- and far-UV circular dichroism (CD), electrospray ionization ion mobility mass spectrometry (ESI-IM-MS), vibrational circular dichroism (VCD), and Fourier transform infrared spectroscopy (FTIR) in the attenuated total reflection (ATR) and transmission (TR) modes. The spectroscopic results, which relied on the interaction of an electromagnetic field with different molecular targets, confirmed the decay of extensive rigid side-chain packing interactions during the pH-induced N→A-state transition and revealed the targets' dependence on secondary structural changes. Independent analyses of the spectral changes using two methods of multivariate analysis, such as principal component analysis and two-dimensional correlation spectroscopy, revealed small but significant differences in the secondary structure as a result of the all-or-none transition. The cooperativity of the transition was quantitatively described using values corresponding to the mid-point (tm) and width of the transition (Δtm). The averages of the two parameters, calculated using the data collected by the different probes, were equal to 3.5±0.2 and 0.6±0.1(SE), respectively. The variable two-state nature of the cooperative N→A-state transition confirmed that the protonation of the side chain carboxyl groups on the Asp and Glu residues and that the release of a Ca(2+) ion induced structural changes on both the secondary and tertiary levels. The changes have been confirmed by results obtained from the concerted spectroscopic approach.

Data mining of supersecondary structure homology between light chains of immunogloblins and MHC molecules: absence of the common conformational fragment in the human IgM rheumatoid factor

It is shown that fuzzy search and data mining techniques of supersecondary structure homology for subunits of proteins using conformational code patterns of α-helix-type (3β5α4β) and β-sheet-type (6α4β4β) fragments can be used to extract correlations between fragments of MHC class I molecules and the light chain of immunoglobulins. The new method of conformational pattern analysis with fuzzy search of structural code homology reflects well the shape of main chain rather than secondary structure in comparison with the DSSP method. Further, the data mining technique using the combination of h- and s-fragment patterns can quantify the supersecondary structure homology between any subunits of proteins with different amino acid sequences. Characteristic fragment patterns (string "shhshss"), which were sandwiched between two identical amino acid sequences His and Pro, were found in light chains of various types of immunogloblins, α-chain and β-2 microglobulin of MHC class I and α-chain and β-chain of MHC class II, but not in heavy chains of Fab immunoglobulin fragments and T cell receptors (TCR). Leukocyte immunoglobulin-like receptors (LILR) are related by the conformational fragment (string "shhshss") to β-2 microglobulins as a type of pair forms (string "sohsss"). Further, human IgM rheumatoid factor, one of the immunogloblins, did not strongly exhibit the conformational fragment pattern. Nonclassic MHC class I molecules CD1D, MIC-A, and MIC-B, which have functions to activate NKT, NK, and T cells, did not also clearly show the patterns. These code-driven mining techniques can be utilized as a metadata-generating tool for systems biology to elucidate the biological function of such conformational fragments of MHC I and II molecules, which come in contact with various signal ligands on the surface of T cells and natural killer cells.

Normal and reversed supramolecular chirality of insulin fibrils probed by vibrational circular dichroism at the protofilament level of fibril structure

Fibrils are β-sheet-rich aggregates that are generally composed of several protofibrils and may adopt variable morphologies, such as twisted ribbons or flat-like sheets. This polymorphism is observed for many different amyloid associated proteins and polypeptides. In a previous study we proposed the existence of another level of amyloid polymorphism, namely, that associated with fibril supramolecular chirality. Two chiral polymorphs of insulin, which can be controllably grown by means of small pH variations, exhibit opposite signs of vibrational circular dichroism (VCD) spectra. Herein, using atomic force microscopy (AFM) and scanning electron microscopy (SEM), we demonstrate that indeed VCD supramolecular chirality is correlated not only by the apparent fibril handedness but also by the sense of supramolecular chirality from a deeper level of chiral organization at the protofilament level of fibril structure. Our microscopic examination indicates that normal VCD fibrils have a left-handed twist, whereas reversed VCD fibrils are flat-like aggregates with no obvious helical twist as imaged by atomic force microscopy or scanning electron microscopy. A scheme is proposed consistent with observed data that features a dynamic equilibrium controlled by pH at the protofilament level between left- and right-twist fibril structures with distinctly different aggregation pathways for left- and right-twisted protofilaments.

VCD to determine absolute configuration of natural product molecules: secolignans from Peperomia blanda

The absolute configuration and solution-state conformers of three peperomin-type secolignans isolated from Peperomia blanda (Piperaceae) are unambiguously determined by using vibrational circular dichroism (VCD) spectroscopy associated with density functional theory (DFT) calculations. Advantages of VCD over the electronic form of CD for the analysis of diastereomers are also discussed. This work extends our growing knowledge about secondary metabolites within the Piperaceae family species while providing a definitive and straightforward method to assess the absolute stereochemistry of secolignans.

Spontaneous inter-conversion of insulin fibril chirality

Amyloid fibrils are associated with many neurodegenerative diseases and are considered to be the energetically most favorable form of proteins. Here we report that a small pH change initiates spontaneous transformation of insulin fibrils from one polymorph to another. As a result, fibril supramolecular chirality overturns both accompanying morphological and structural changes.

Experimental and theoretical polarized Raman linear difference spectroscopy of small molecules with a new alignment method using stretched polyethylene film

This paper reports the development of the new technique of Raman linear difference (RLD) spectroscopy and its application to small molecules: anthracene and nucleotides adenosine-5'-monophosphate, thymidine-5'-monophosphate, guanosine-5'-monophosphate, and cytidine-5'-monophosphate. In this work we also present a new alignment method for Raman spectroscopy where stretched polyethylene films are used as the matrix. Raman spectra using light polarized along the orientation direction and perpendicular to it are reported. The polyethylene (PE) film spectra are consistent with powder samples and films deposited on quartz. RLD spectra determined from the difference of the parallel and perpendicular polarized light Raman spectra are also reported. The equations describing RLD are derived, and RLD spectra of anthracene and thymidine are calculated from these equations using Density Functional Theory and assuming perfect orientation of the samples. Because of the wealth of spectroscopic information in the vibrational spectra of biomolecules together with our ability to calculate spectra as a function of orientation, we conclude that RLD has the potential to provide structural information for biological samples that currently cannot be extracted from any other method.

Chirality and diastereoselection of Δ/Λ-configured tetrahedral zinc complexes through enantiopure Schiff base complexes: combined vibrational circular dichroism, density functional theory, 1H NMR, and X-ray structural studies

The metal-centered Δ/Λ-chirality of four-coordinated, nonplanar Zn(A(^)B)(2) complexes is correlated to the chirality of the bidentate enantiopure (R)-A(^)B or (S)-A(^)B Schiff base building blocks [A(^)B = (R)- or (S)-N-(1-(4-X-phenyl)ethyl)salicylaldiminato-κ(2)N,O with X = OCH(3), Cl, Br]. In the solid-state the (R) ligand chirality induces a Λ-M configuration and the (S) ligand chirality quantitatively gives the Δ-M configuration upon crystallization as deduced from X-ray single crystal studies. The diastereoselections of the pseudotetrahedral zinc-Schiff base complexes in CDCl(3) solution were investigated by (1)H NMR and by vibrational circular dichroism (VCD) spectroscopy. The appearance of two signals for the Schiff-base -CH═N- imine proton in (1)H NMR indicates an equilibrium of both Δ- and Λ-diastereomers with a diastereomeric ratio of roughly 20:80% for all three ligands. VCD proved to be very sensitive to the metal-centered Δ/Λ-chirality because of a characteristic band representing coupled vibrations of the two ligand's C═N stretch modes. The absolute configuration was assigned on the basis of agreement in sign with theoretical VCD spectra from Density Functional Theory calculations.

Determination of absolute configuration of chiral molecules using vibrational optical activity: a review

Determination of the absolute handedness, known as absolute configuration (AC), of chiral molecules is an important step in any field related to chirality, especially in the pharmaceutical industry. Vibrational optical activity (VOA) has become a powerful tool for the determination of the AC of chiral molecules in the solution state after nearly forty years of evolution. VOA offers a novel alternative, or supplement, to X-ray crystallography, permitting AC determinations on neat liquid, oil, and solution samples without the need to grow single crystals of the pure chiral sample molecules as required for X-ray analysis. By comparing the sign and intensity of the measured VOA spectrum with the corresponding ab initio density functional theory (DFT) calculated VOA spectrum of a chosen configuration, one can unambiguously assign the AC of a chiral molecule. Comparing measured VOA spectra with calculated VOA spectra of all the conformers can also provide solution-state conformational populations. VOA consists of infrared vibrational circular dichroism (VCD) and vibrational Raman optical activity (ROA). Currently, VCD is used routinely by researchers in a variety of backgrounds, including molecular chirality, asymmetric synthesis, chiral catalysis, drug screening, pharmacology, and natural products. Although the application of ROA in AC determination lags behind that of VCD, with the recent implementation of ROA subroutines in commercial quantum chemistry software, ROA will in the future complement VCD for AC determination. In this review, the basic principles of the application of VCD to the determination of absolute configuration in chiral molecules are described. The steps required for VCD spectral measurement and calculation are outlined, followed by brief descriptions of recently published papers reporting the determination of AC in small organic, pharmaceutical, and natural product molecules.

Absolute configuration and selective trypanocidal activity of gaudichaudianic acid enantiomers

Gaudichaudianic acid, a prenylated chromene isolated from Piper gaudichaudianum, has been described as a potent trypanocidal compound against the Y-strain of Trypanosoma cruzi. We herein describe its isolation as a racemic mixture followed by enantiomeric resolution using chiral HPLC and determination of the absolute configuration of the enantiomers as (+)-S and (-)-R by means of a combination of electronic and vibrational circular dichroism using density functional theory calculations. Investigation of the EtOAc extract of the roots, stems, and leaves from both adult specimens and seedlings of P. gaudichaudianum revealed that gaudichaudianic acid is biosynthesized as a racemic mixture from the seedling stage onward. Moreover, gaudichaudianic acid was found exclusively in the roots of seedlings, while it is present in all organs of the adult plant. Trypanocidal assays indicated that the (+)-enantiomer was more active than its antipode. Interestingly, mixtures of enantiomers showed a synergistic effect, with the racemic mixture being the most active.

Near-infrared and mid-infrared Fourier transform vibrational circular dichroism of proteins in aqueous solution

Vibrational circular dichroism (VCD) of a series of proteins in H(2)O solution with differing secondary structure are reported for the first time in the near-infrared (NIR) region as well as the NH-stretching region. The Fourier transform (FT) near-infrared (NIR) measurements were carried out between 6000 to 4000 cm(-1). FT-VCD measurements were simultaneously carried out for the mid-infrared (mid-IR) region from 2000 to 800 cm(-1) for direct comparison to VCD in the NIR region. The NIR VCD spectra of proteins show distinct spectral features for different protein structural motifs, indicating a valuable new method to study protein conformations. The principal VCD transitions in the NIR region are two combination bands, the amide A-II and B-II bands, of the amide A and B fundamentals with the amide II fundamental, and the second overtone of the amide II, referred to as the amide 3 x II band. VCD in the amide A and B band region consisting primarily of NH stretching motions were successfully obtained in H(2)O for the first time for an insulin fibril sample. Similar to the enhanced VCD signal observed in amide I and II regions, the amide A and B VCD of insulin fibril shows strong intensity enhancements, providing an additional valuable probe of protein fibril growth and development in solution. The relative sensitivities of the mid-IR, N-H stretching, and NIR regions are discussed.

A revised conformational code for the exhaustive analysis of conformers with one-to-one correspondence between conformation and code: application to the VCD analysis of (S)-ibuprofen

A revised conformational code for the exhaustive analysis of conformers of all classes of molecules is proposed and applied to the vibrational circular dichroism (VCD) analysis of (S)-ibuprofen. The revised code can strictly define the conformation of compounds with relatively high-symmetry substituents and is especially useful for visualizing conformational changes in ligands and proteins. The conformational analysis of (S)-ibuprofen using the code in the solution state reveals that the four energetically preferred conformations, ibut-3alpha2alpha sigma(phpa-3alpha sigma2alpha), ibut-3alpha2alpha tau(phpa-3alpha tau2alpha), ibut-2beta3beta tau(phpa-3alpha tau2alpha), and ibut-2beta3beta sigma(phpa-3alpha sigma2alpha), exist in the monomer and dimer forms. In CDCl(3) solution, the dimer form is stabilized as the "U"-shape, and the ease of crystallization is largely ascribed to the conformation of phpa-3alpha2alpha for (S)-ibuprofen. The new version of the conformational code has the possibility to be used as a tool for the exhaustive analysis of conformers of all kinds of chemical compounds, conformome analysis, and in the future for metabolome, proteome, and genome analyses.

Structure and absolute configuration of ginkgolide B characterized by IR- and VCD spectroscopy

Experimental and calculated (B3LYP/6-31G(d)) vibrational circular dichroism (VCD) and IR spectra are compared, illustrating that the structure and absolute configuration of ginkgolide B (GB) may be characterized directly in solution. A conformational search for GB using MacroModel and subsequent DFT optimizations (B3LYP/6-31G(d)) provides a structure for the lowest energy conformer which agrees well with the structure determined by X-ray diffraction. In addition, a conformer at an energy of 7 kJ mol(-1) (B3LYP/6-311+G(2d,2p)) with respect to the lowest energy conformer is predicted, displaying different intramolecular hydrogen bonding. Differences between measured and calculated IR and VCD spectra for GB at certain wavenumbers are rationalized in terms of interactions with solvent, intermolecular GB-GB interactions, and the potential presence of more than one conformer. This is the first detailed investigation of the spectroscopic fingerprint region (850-1300 cm(-1)) of the natural product GB employing infrared absorption and VCD spectroscopy.

Vibrational Circular Dichroism: A New Tool for the Solution-State Determination of the Structure and Absolute Configuration of Chiral Natural Product Molecules

Vibrational circular dichroism (VCD) has been used in recent years to determine the absolute configuration of a number of natural product chiral molecules. In this brief review, these applications will be described and the methodology of VCD determination of absolute configuration (AC) will be explained. The principal advantages of VCD versus X-ray crystallography for absolute configuration determination are: 1) only solution-state samples are needed and therefore single crystals are not required, 2) high enantiomeric sample purity is not required, 3) high chemical purity is not required as long as impurities are not chiral and 4) solution-state conformations are obtained as an extra feature of the AC determination.

Structural and Optical Isomers of Nonamethoxy Cyclotriveratrylene: Separation and Physical Characterization

The paper concerns the structural and optical isomers of nonamethoxy-tribenzocyclononene (compound 1). In the first part of the paper it is shown that 1 exists in two structural isomers: a rigid crown (c-1) with C3 symmetry and a flexible saddle (s-1) with C1 symmetry. The latter, not previously known, can be prepared from the as-synthesized c-1 by quenching a hot solution (or the melt) followed by HPLC separation. The crown/saddle equilibrium, isomerization kinetics, and associated thermodynamic parameters in various organic solvents are reported. Carbon-13 MAS NMR, X-ray diffraction, and differential scanning calorimetry (DSC) of polycrystalline c-1 and s-1 racemates are also reported. The different melting points of the isomers and their rapid isomerization in the melt result in unconventional DSC thermograms involving multiple endothermic and exothermic transitions. The second part of the paper concerns the chiral properties of 1. Both the saddle and crown isomers are structurally chiral, but due to the fast pseudorotation of s-1 in solution, it cannot be separated into its enantiomers. Those of c-1 were separated by HPLC using a chiral column. Their X-ray structure and melting points differ considerably from those of the racemate. This and their fast racemization in the melt lead to complex DSC thermograms with multiple transitions. Solutions of the neat enantiomers exhibit a relatively small specific optical rotation. In the UV they show circular dichroism for the B1u and B2u transitions, with the latter exhibiting a clear couplet structure. Infrared and vibrational circular dichroism spectra of the enantiomers in solution are reported. Comparison of these spectra with quantum mechanical simulations provides unambiguous identification of the enantiomers.

Near-infrared excited Raman optical activity

Measurements of near-infrared scattered circular polarization Raman optical activity (SCP-ROA) are presented using laser excitation at 780 nm for samples of S-(-)-alpha-pinene and L-alanyl-L-alanine. These are the first measurements of ROA outside the blue-to-green visible region between 488 and 532 nm. Comparison of Raman and ROA intensities measured with excitation at 532 and 780 nm demonstrate that the expected frequency to the fourth-power dependence for Raman scattering and the corresponding fifth-power dependence for ROA are observed. It can be concluded that, to within this frequency dependence, the same level of efficiency of Raman and ROA measurements using commercial instrumentation with 532 nm excitation is maintained with the change to near-infrared excitation at 780 nm.

Synthesis and vibrational circular dichroism of enantiopure chiral oxorhenium(V) complexes containing the hydrotris(1-pyrazolyl)borate ligand

The infrared and vibrational circular dichroism (VCD) spectra of six chiral oxorhenium(V) complexes, bearing a hydrotris(1-pyrazolyl)borate (Tp) ligand, have been investigated. These complexes are promising candidates for observation of parity violation (symmetry breaking due to the weak nuclear force). New chiral oxorhenium complexes have been synthesized, namely, [TpReO(eta2-O(CH3)CH2CH2O-O,O)] (4a and 4b) diastereomers and [TpReO(eta2-N(CH3)CH2CH2O-N,O)] (5) and [TpReO(eta2-N(tBu)CH2CH2O-N,O)] (6) enantiomers. All compounds could be obtained in enantiomerically pure form by using either column chromatography or HPLC over chiral columns. VCD spectroscopy of these compounds and of [TpReO(eta2-N(CH3)CH(CH3)CH(Ph)O-N,O)] (2) and [TpReO(eta2-N(CH2)3CHCO2-N,O)] (3) (with chiral bidentate ligands derived, respectively, from ephedrine and proline) were studied. This allowed the absolute configuration determination of all compounds together with their conformational analysis, by comparing calculated and experimental spectra. This is the first VCD study of rhenium complexes which further demonstrates the applicability of VCD spectroscopy in determining the chirality of inorganic complexes.