Minor Conformer Research Articles

NMR studies of DNA support the role of pre-existing minor groove variations in nucleosome indirect readout.

We investigated how the intrinsic sequence-dependent properties probed via the phosphate linkages (BI ↔ BII equilibrium) influence the preferred shape of free DNA, and how this affects the nucleosome formation. First, this exploits NMR solution studies of four B-DNA dodecamers that together cover 39 base pairs of the 5' half of the sequence 601, of special interest for nucleosome formation. The results validate our previous prediction of a systematic, general sequence effect on the intrinsic backbone BII propensities. NMR provides new evidence that the backbone behavior is intimately coupled to the minor groove width. Second, application of the backbone behavior predictions to the full sequence 601 and other relevant sequences demonstrates that alternation of intrinsic low and high BII propensities, coupled to intrinsic narrow and wide minor grooves, largely coincides with the sinusoidal variations of the DNA minor groove width observed in crystallographic structures of the nucleosome. This correspondence is much poorer with low affinity sequences. Overall, the results indicate that nucleosome formation involves an indirect readout process implicating pre-existing DNA minor groove conformations. It also illustrates how the prediction of the intrinsic structural DNA behavior offers a powerful framework to gain explanatory insight on how proteins read DNA.

Theoretical study of the structural stability of molecular chain sheet models of cellulose crystal allomorphs.

The structural stabilities of the molecular chain sheets constituting the crystal structures of the cellulose allomorphs Iα, Iβ, II, and IIII were investigated by density functional theory (DFT) optimization of the isolated chain sheet models with finite dimensions. The DFT-optimized chain sheet models of the two native cellulose crystals developed a right-handed twist with a similar amount of twisting. The DFT-optimized cellulose II (010) and (020) models twisted in opposite directions with right- and left-handed chirality, respectively. The cellulose IIII (1-10) model retained the initial flat structure after the DFT-optimization. The structural features of the DFT-optimized chain sheet models were reflected in the structures of the parent crystal models observed in solvated molecular dynamics (MD) simulations. The minor conformations of the hydroxymethyl groups proposed in the real crystal structures were detected in the MD crystal models and the DFT-optimized (010) model of cellulose II. The crystal chain packing and crystal conversions are interpreted in terms of principal chain sheet stacking.

Conformational analysis of an anti-androgenic, (E,E)-8-hydroxygermacrene B, using NOESY and dynamic NMR spectroscopy

(E,E)-8-Hydroxygermacrene B was prepared by ketone reduction of germacrone, a naturally occurring compound from Curcuma aeruginosa Roxb. with NaBH4 at low temperature (4°C). This compound showed remarkable in vitro anti-androgenic activity (IC50 0.15±0.022mM) applicable to male baldness treatments. NMR analysis at −50°C indicated that there were four conformational isomers of (E,E)-8-hydroxygermacrene B in a ratio of 48:40:8:4. The major conformers were assigned by 1H NMR and 2D-NOESY NMR spectroscopy as having methyl groups at C-10 and C-4 in up–down (UD) orientations (48% predominance) and UU (40%). 1H NMR spectra implied another two minor conformers with these methyls having DU (8%) and DD (4%) orientations.

Measuring and modeling dynamics of regulators of G protein signaling to facilitate discovery of allosteric inhibitors of protein‐protein interactions (843.13)

Ischemic stroke morbidity and disability stem from neuronal death largely driven by glutamatergic excitotoxicity following hypoxia in brain tissue deprived of blood flow. Pharmacological inhibition of RGS4 with chemical probes significantly potentiates endogenous neuroprotection against excitotoxicity in vivo. The only known RGS4 inhibitors are unsuitable as clinical leads because they are relatively nonspecific covalent modifiers that inhibit through an uncharacterized, though putatively allosteric, mechanism. We seek to determine the structural mechanism by which current small‐molecule chemical probes allosterically inhibit RGS4. We hypothesize that inhibitors, binding to Cys148, trap a stochastically minor open conformation of RGS4 and disrupt a structurally key helical bundle to both prevent a unique conformational shift in RGS4 required to bind G‐alpha and to shift the population dynamics toward increasingly extended and unstable conformations. Structural changes in RGS proteins upon binding to inhibitory compounds measured with structural biological techniques including nuclear magnetic resonance, circular dichroism, light scattering, small‐angle X‐ray scattering, and atomistic molecular dynamics simulations support our hypothesis. Our investigations further show that RGS8, a homolog of RGS4, differs significantly in biophysical properties and we conclude that that these differences underly specificity of inhibitors for RGS4.Grant Funding Source: Supported by 5T32GM067795‐08 and pre‐doctoral fellowship from AFPE.

Searching for protein binding sites from Molecular Dynamics simulations and paramagnetic fragment-based NMR studies

Hotspot delineation on protein surfaces represents a fundamental step for targeting protein–protein interfaces. Disruptors of protein–protein interactions can be designed provided that the sterical features of binding pockets, including the transient ones, can be defined. Molecular Dynamics, MD, simulations have been used as a reliable framework for identifying transient pocket openings on the protein surface. Accessible surface area and intramolecular H-bond involvement of protein backbone amides are proposed as descriptors for characterizing binding pocket occurrence and evolution along MD trajectories. TEMPOL induced paramagnetic perturbations on 1H–15N HSQC signals of protein backbone amides have been analyzed as a fragment-based search for surface hotspots, in order to validate MD predicted pockets. This procedure has been applied to CXCL12, a small chemokine responsible for tumor progression and proliferation. From combined analysis of MD data and paramagnetic profiles, two CXCL12 sites suitable for the binding of small molecules were identified. One of these sites is the already well characterized CXCL12 region involved in the binding to CXCR4 receptor. The other one is a transient pocket predicted by Molecular Dynamics simulations, which could not be observed from static analysis of CXCL12 PDB structures. The present results indicate how TEMPOL, instrumental in identifying this transient pocket, can be a powerful tool to delineate minor conformations which can be highly relevant in dynamic discovery of antitumoral drugs.

High-resolution crystal structure of copper amine oxidase fromArthrobacter globiformis: assignment of bound diatomic molecules as O2

The crystal structure of a copper amine oxidase from Arthrobacter globiformis was determined at 1.08 Å resolution with the use of low-molecular-weight polyethylene glycol (LMW PEG; average molecular weight ∼200) as a cryoprotectant. The final crystallographic R factor and Rfree were 13.0 and 15.0%, respectively. Several molecules of LMW PEG were found to occupy cavities in the protein interior, including the active site, which resulted in a marked reduction in the overall B factor and consequently led to a subatomic resolution structure for a relatively large protein with a monomer molecular weight of ∼70,000. About 40% of the presumed H atoms were observed as clear electron densities in the Fo - Fc difference map. Multiple minor conformers were also identified for many residues. Anisotropic displacement fluctuations were evaluated in the active site, which contains a post-translationally derived quinone cofactor and a Cu atom. Furthermore, diatomic molecules, most likely to be molecular oxygen, are bound to the protein, one of which is located in a region that had previously been proposed as an entry route for the dioxygen substrate from the central cavity of the dimer interface to the active site.

A Comparative CEST NMR Study of Slow Conformational Dynamics of Small GTPases Complexed with GTP and GTP Analogues

The Ras superfamily of small GTPases are important intracellular signaling molecules, the functions of which are determined by the binding of guanosine nucleotides (GTP = guanosine triphosphate and GDP = guanosine diphosphate). [1] The GTP-bound (“active”) states of these enzymes are capable of interacting with specific downstream effector proteins, thus eliciting a wide range of cellular responses. [2, 3] Mutations that reduce the rate of GTP hydrolysis and thus increase the lifetime of the active GTP-bound state are frequently oncogenic and contribute to the development and metastasis of human cancers. [4] Elegant 31 P NMR studies of GTP-bound Ras showed that the enzyme interconverts between two states, a minor conformer termed state 1 and a major species designated state 2. [5–9] Similar conformational dynamics have been observed in other Ras family GTPases as well. [10–12] State 2 is generally regarded as the conformation competent for binding effector proteins, whereas state 1 exhibits significantly reduced affinity for these molecules. [5–7, 13, 14] Stabilization of the low-affinity state 1 was

Insights into the Conformation of Aminofluorene-Deoxyguanine Adduct in a DNA Polymerase Active Site

The active site conformation of the mutagenic fluoroaminofluorene-deoxyguanine adduct (dG-FAF, N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene) has been investigated in the presence of Klenow fragment of Escherichia coli DNA polymerase I (Kfexo(-)) and DNA polymerase β (pol β) using (19)F NMR, insertion assay, and surface plasmon resonance. In a single nucleotide gap, the dG-FAF adduct adopts both a major-groove- oriented and base-displaced stacked conformation, and this heterogeneity is retained upon binding pol β. The addition of a non-hydrolysable 2'-deoxycytosine-5'-[(α,β)-methyleno]triphosphate (dCMPcPP) nucleotide analog to the binary complex results in an increase of the major groove conformation of the adduct at the expense of the stacked conformation. Similar results were obtained with the addition of an incorrect dAMPcPP analog but with formation of the minor groove binding conformer. In contrast, dG-FAF adduct at the replication fork for the Kfexo(-) complex adopts a mix of the major and minor groove conformers with minimal effect upon the addition of non-hydrolysable nucleotides. For pol β, the insertion of dCTP was preferred opposite the dG-FAF adduct in a single nucleotide gap assay consistent with (19)F NMR data. Surface plasmon resonance binding kinetics revealed that pol β binds tightly with DNA in the presence of correct dCTP, but the adduct weakens binding with no nucleotide specificity. These results provide molecular insights into the DNA binding characteristics of FAF in the active site of DNA polymerases and the role of DNA structure and sequence on its coding potential.

Analysing the visible conformational substates of the FK506-binding protein FKBP12

The 1H-15N 2D NMR correlation spectrum of the widely studied FK506-binding protein FKBP12 (FK506-binding protein of 12 kDa) contains previously unreported peak doublings for at least 31 residues that arise from a minor conformational state (12% of total) which exchanges with the major conformation with a time constant of 3.0 s at 43°C. The largest differences in chemical shift occur for the 80′s loop that forms critical recognition interactions with many of the protein partners for the FKBP family. The residues exhibiting doubling extend into the adjacent strands of the β-sheet, across the active site to the α-helix and into the 50′s loop. Each of the seven proline residues adopts a trans-peptide linkage in both the major and minor conformations, indicating that this slow transition is not the result of prolyl isomerization. Many of the residues exhibiting resonance doubling also participate in conformational line-broadening transition(s) that occur ~105-fold more rapidly, proposed previously to arise from a single global process. The 1.70 Å (1 Å=0.1 nm) resolution X-ray structure of the H87V variant is strikingly similar to that of FKBP12, yet this substitution quenches the slow conformational transition throughout the protein while quenching the line-broadening transition for residues near the 80′s loop. Line-broadening was also decreased for the residues in the α-helix and 50′s loop, whereas line-broadening in the 40′s loop was unaffected. The K44V mutation selectively reduces the line-broadening in the 40′s loop, verifying that at least three distinct conformational transitions underlie the line-broadening processes of FKBP12.

Solid-State NMR Evidence for β-Hairpin Structure within MAX8 Designer Peptide Nanofibers

MAX8, a designer peptide known to undergo self-assembly following changes in temperature, pH, and ionic strength, has demonstrated usefulness for tissue engineering and drug delivery. It is hypothesized that the self-assembled MAX8 nanofiber structure consists of closed β-hairpins aligned into antiparallel β-sheets. Here, we report evidence from solid-state NMR spectroscopy that supports the presence of the hypothesized β-hairpin conformation within the nanofiber structure. Specifically, our 13C-13C two-dimensional exchange data indicate spatial proximity between V3 and K17, and 13C-13C dipolar coupling measurements reveal proximity between the V3 and V18 backbone carbonyls. Moreover, isotopic dilution of labeled MAX8 nanofibers did not result in a loss of the 13C-13C dipolar couplings, showing that these couplings are primarily intramolecular. NMR spectra also indicate the existence of a minor conformation, which is discussed in terms of previously hypothesized nanofiber physical cross-linking and possible nanofiber polymorphism.

Conformational Effects on the Lowest Excited States of Benzoyl-Pyrrolopyridazine: Insights from PCM Time-Dependent DFT

Time-dependent density functional theory (TD-DFT) computations and steady-state electronic spectroscopy measurements are performed on two recently synthesized pyrrolopyridazines to account for the detrimental effect of benzoyl substitution on the blue fluorescence emission. In the case of the highly fluorescent ester derivative, planar in ground state, we show that TD-DFT using the PBE0 and B3LYP hybrid functionals in the state-specific solvation approach provides an accurate description of absorption and emission properties. In benzoyl-pyrrolopyridazine, the (pretwisted) orientations of the benzoyl group and the solvent polarity are both found to modulate the nature of the lowest excited states. The first excited state has nπ* character at ground-state geometry of the main conformer (carbonyl group facing the diazine ring) in nonpolar solvents and become nearly degenerate with a ππ* state in polar solvents. The latter, lower than the nπ* state at the ground state geometry of a minor conformer, relaxes into a twisted intramolecular charge transfer. Experimental absorption and excitation spectra are consistent with the conformational-dependent picture of the lowest excited state (as derived from TD-DFT). A rather qualitative agreement in predicting the fluorescence emission wavelength is achieved in computations employing the CAM-B3LYP and BH&HLYP functionals, whereas global hybrids with low or moderate amounts of exact exchange exhibit the expected TD-DFT failure with up to 1 eV underestimated transition energies.

Mycobacterium tuberculosis MutT1 (Rv2985) and ADPRase (Rv1700) Proteins Constitute a Two-stage Mechanism of 8-Oxo-dGTP and 8-Oxo-GTP Detoxification and Adenosine to Cytidine Mutation Avoidance

Approximately one third of the world population is infected with Mycobacterium tuberculosis, the causative agent of tuberculosis. A better understanding of the pathogen biology is crucial to develop new tools/strategies to tackle its spread and treatment. In the host macrophages, the pathogen is exposed to reactive oxygen species, known to damage dGTP and GTP to 8-oxo-dGTP and 8-oxo-GTP, respectively. Incorporation of the damaged nucleotides in nucleic acids is detrimental to organisms. MutT proteins, belonging to a class of Nudix hydrolases, hydrolyze 8-oxo-G nucleoside triphosphates/diphosphates to the corresponding nucleoside monophosphates and sanitize the nucleotide pool. Mycobacteria possess several MutT proteins. However, a functional homolog of Escherichia coli MutT has not been identified. Here, we characterized MtuMutT1 and Rv1700 proteins of M. tuberculosis. Unlike other MutT proteins, MtuMutT1 converts 8-oxo-dGTP to 8-oxo-dGDP, and 8-oxo-GTP to 8-oxo-GDP. Rv1700 then converts them to the corresponding nucleoside monophosphates. This observation suggests the presence of a two-stage mechanism of 8-oxo-dGTP/8-oxo-GTP detoxification in mycobacteria. MtuMutT1 converts 8-oxo-dGTP to 8-oxo-dGDP with a Km of ∼50 μM and Vmax of ∼0.9 pmol/min per ng of protein, and Rv1700 converts 8-oxo-dGDP to 8-oxo-dGMP with a Km of ∼9.5 μM and Vmax of ∼0.04 pmol/min per ng of protein. Together, MtuMutT1 and Rv1700 offer maximal rescue to E. coli for its MutT deficiency by decreasing A to C mutations (a hallmark of MutT deficiency). We suggest that the concerted action of MtuMutT1 and Rv1700 plays a crucial role in survival of bacteria against oxidative stress.

Photoexcitation Dynamics of NO-Bound Ferric Myoglobin Investigated by Femtosecond Vibrational Spectroscopy

Femtosecond vibrational spectroscopy was used to investigate the photoexcitation dynamics of NO-bound ferric myoglobin (Mb(III)NO) in D2O solution at 294 K after excitation with a 575 nm pulse. The stretching mode of NO in Mb(III)NO consists of a major band at 1922 cm(-1) (97.7%) and a minor band at 1902 cm(-1) (2.3%), suggesting that Mb(III)NO in room temperature solution has two conformational substates. The time-resolved spectra show small but significant new absorption features at the lower-energy side of the main band (1920-1800 cm(-1)). One new absorption feature in the region of 1920-1880 cm(-1) exhibits the (15)NO isotope shift (37 cm(-1)) the same as that of the NO band in the ground electronic state of Mb(III)NO. This absorption shifts toward higher energy and narrows with a time constant of 2.4 ps, indicating that it evolves with rapid electronic and thermal relaxation of the photoexcited Mb(III)NO without photodeligation of the NO from the heme. Absorption features assigned to proteins undergoing thermal relaxation without NO deligation add up to 14 ± 1% of the total bleach, implying that the photolysis quantum yield of Mb(III)NO with a Q-band excitation is ≤0.86 ± 0.01. The remaining absorption bands peaked near 1867, 1845, and 1815 cm(-1), each showing the (15)NO isotope shift the same as that of the free NO radical (33 cm(-1)), were assigned to the vibrational band of the photodeligated NO, the NO band of Mb(III)NO in an intermediate electronic state with low-spin Fe(III)-NO(radical) character (denoted as the R state), and the NO band of the vibrationally excited NO in the R state, respectively. A kinetics model successfully reproducing the time-dependent intensity changes of the transient bands suggests that every rebound NO forms the R state that eventually relaxes into the ground electronic state nonexponentially. Most of the photodissociated NO undergoes fast geminate recombination (GR), and the rebinding kinetics depends on the conformation of the protein. GR of NO to Mb(III) in the major conformation shows highly nonexponential kinetics described by a stretched exponential function, exp(-(t/290 ps)(0.44). The NO rebinding to Mb(III) in the minor conformation is exponential, exp(-t/1.8 ns), suggesting that the distal histidine, the interaction of which dictates the conformation of Mb(III)NO, participates in mediating the binding of NO to Mb(III). In Mb(III)NO, the elusive low-spin Fe(III)-NO(radical) state, proposed in electronic structure calculations, indeed exists at >12 kJ/mol above the ground state and takes part in the bond formation of Fe(III)-NO, suggesting that it plays a significant role in the function of NO-bound ferric protein. Time-resolved vibrational spectra with high sensitivity reveal rich photophysical and photochemical processes of photoexcited Mb(III)NO.

Generation of Silk Fibroin Nanoparticles via Solution-Enhanced Dispersion by Supercritical CO2

A solution-enhanced dispersion by supercritical CO2 (SEDS) was employed to prepare silk fibroin (SF) nanoparticles. The results of 24 full factorial experiment indicated that SF nanoparticles with particle size (PS) from 52.5 to 102.3 nm and particle size distribution (PSD) from 0.32 to 0.66 can be fabricated successfully. Moreover, reducing precipitation pressure or increasing concentration of SF solution, flow rate of SF solution, or precipitation temperature can increase PS and PSD of SF nanoparticles. The nanoparticle formation mechanism was elucidated through the formation and growth of SF nuclei in the gaseous miscible phase evolved from initial droplets generated by liquid–liquid phase split. Mass transfer between supercritical CO2 and SF solution superimposed on supersaturation was the most important process parameter affecting nanoparticle formation. Furthermore, Fourier transform infrared spectroscopy and X-ray powder diffraction analysis revealed that SF nanoparticles exhibited predominant random coil and α-helix structure with minor β-sheet conformation.

39 In-silico study of the arrangement of the snRNPs within the native spliceosome

The elaborate process of transforming the information coded in the DNA to protein molecules is performed by several large and intricate molecular machines: RNA polymerase II transcribes the coded genes to pre-mRNAs, the spliceosome processes the pre-mRNAs, eliminating noncoding introns and producing functional mRNAs, and the ribosome translates the genetic code embedded in the mRNAs and catalyzes the synthesis of proteins. The spliceosome is a huge mega-Dalton ribonucleoprotein (RNP) assembly. Electron microscopy structures of the native spliceosome and of several spliceosomal subcomplexes, such as the spliceosomal U snRNPs, are available but the spatial arrangement of the latter within the native spliceosome is not known. We developed fitEM2EM computational tools (Frankenstein et al., 2008), that match and dock low resolution structures. Next, we represented each spliceosomal subcomplex by an ensemble of normal-modes conformers and designed a new “conformer selection” procedure that efficiently fitted the thousands of conformers into the native spliceosome envelope. Despite the low resolution limitations, we obtained only one model that complies with the available biochemical data. Our model localizes the five small nuclear RNPs (snRNPs), mostly within the large subunit of the native spliceosome, requiring only minor conformation changes. The remaining free volume presumably accommodates additional spliceosomal components. Moreover, the ample free volume suggests that structural modulations of the snRNPs can be tolerated while keeping the integrity of the spliceosome assembly. The constituents of the active core of the spliceosome are juxtaposed in our model, forming a continuous surface deep within the large spliceosomal cavity. This cavity emerges as the site of mRNA binding and splicing; its depth provides a sheltered environment for the splicing reaction (Frankenstein et al., 2012). To experimentally localize U snRNPs within the native spliceosome and validate the model, we use gold nanoclusters of 1.5 nm in diameter, covalently attached to antisense oligodeoxynucleotides, each complementary to one of the spliceosomal U snRNAs.

38 A network of interactions within the supraspliceosome

Pre-mRNA splicing of RNA polymerase II transcripts is executed in the cell nucleus within a huge (21 MDa) and highly dynamic RNP machine – the supraspliceosome. Supraspliceosomes harbor all five spliceosomal U snRNPs, as well as protein splicing factors, and they are functional in splicing. Supraspliceosomes also harbor other components of pre-mRNA processing, such as the RNA-editing enzymes ADAR1 and ADAR2, cap-binding proteins, and 3’-end processing components. The supraspliceosome is composed of four native spliceosomes, each resembling the spliceosome assembled in vitro, and they are connected by the pre-mRNA (Sperling et al., 2008). The structure of the native spliceosome, at a resolution of 20 Å, was determined by cryo-EM (Azubel et al., 2004). A unique spatial arrangement of the spliceosomal U snRNPs within the native spliceosome emerged from in silico studies (Frankenstein et al., 2012). The model localizes the five U snRNPs mostly within the large subunit of the native spliceosome, requiring only minor conformation changes, and the components of the active core of the spliceosome are found sheltered deep within the large spliceosomal cavity. We use gold-tagged probes and cryo-EM to experimentally confirm this model. The supraspliceosome structure likely provides a platform for regulation of RNA-processing activities (e.g. alternative splicing). Indeed, all the phosphorylated splicing regulators SR proteins are predominantly found associated with supraspliceosomes. Furthermore, both the constitutively and alternatively spliced mRNAs of tested endogenous human Pol II transcripts are predominantly found in supraspliceosomes, and changes in alternative splicing occur within them (Sebbag-Sznajder et al., 2012). These findings substantiate the role of the supraspliceosome as the nuclear pre-mRNA processing machine.

High-Precision FRET to Analyze the Architecture and Heterogeneity of RNA Junctions

Like for many other non-coding RNAs, helical four-way and three-way junctions (4WJs and 3WJs) are an essential structural motif of the for functional RNA structures. Using FRET restrained high-precision structural modeling as a hybrid tool we resolve the structures of three coexisting conformers of a fully Watson-Crick base paired RNA4WJ based on the hairpin ribozyme. 51 different FRET-pairs were measured using single-molecule multi-parameter fluorescence detection (smMFD). For each dataset, the single-molecule approach allowed for the simultaneous extraction of three distances (and their corresponding errors) belonging to one major FRET state and two minor states. Distinct Mg2+-affinities were used for the assignment of the two minor states to the corresponding conformers. Rigid body models for the major and both minor conformers were obtained by docking rigid ds A-RNA helices explicitly taking into account dye position distributions. The three rigid body models were refined by all-atom MD simulations and coarse-grained RNA folding using FRET-restraints. A cluster analysis gives confidence levels for the proposed ensemble of models, and the precision was assessed via bootstrapping. The achieved precisions are significantly better than the uncertainty of the dye position with respect to the macromolecule. The structure of the 4WJ was compared with FRET restrained structures of related RNA 3WJs, where one stem was removed. The types of 3WJs were studied: (I) without bulges, (II) with a small bulge (two unpaired nucleotides) and (III) with larger bulge (5 unpaired nucleotides). In conclusion the overall geometry of the RNA helices depends drastically on the junction type.[1] Sisamakis, E., et al.; Methods in Enzymology 475, 455-514 (2010)[2] Sindbert, S., et al.; J. Am. Chem. Soc. 133, 2463-2480 (2011)[3] Kalinin, S. et al. Nat. Methods in press

Structure analysis of substrate catalyst complexes in mixtures with ultrafast two-dimensional infrared spectroscopy

The understanding of reaction mechanisms requires structure elucidation of short-lived intermediates, even in the presence of other, similar structures. Here we show that polarization dependent two-dimensional infrared spectroscopy is a powerful method to determine the structure of molecules that participate in fast equilibria, in a regime where standard techniques such as nuclear magnetic resonance spectroscopy are beyond their limits. Using catalyst-substrate complexes in a Lewis acid catalyzed enantioselective Diels-Alder reaction as an example we present two methods that allow the resolution of molecular structure in mixtures even when the spectroscopic signals partially overlap. The structures of N-crotonyloxazolidin-2-one, a reactant carrying the Evans auxiliary, and its complex with the Lewis acid SnCl(4) were determined in a mixture as used under the typical reaction conditions. In addition to the chelate that mainly forms, three additional substrate-catalyst complexes were detected and could be tentatively assigned. Observation of minor complex conformers suggests a rationale for the observed diastereoselectivity of the reaction using SnCl(4) as compared to other Lewis acids. Knowledge about additional species may lead to a better understanding of the different selectivities for various Lewis acids and allow reaction optimization.

Spatial structure of cyclosporin A and insight into its flexibility

The molecule of immunosuppressant drug cyclosporin A (CsA) exhibits different properties when dissolved in different media. In apolar solvents it is stabilized by intramolecular hydrogen bonds, but there also exist some less populated conformations. Existence of minor forms is clearly seen from 1H NMR spectra.Using nuclear Overhauser effect (NOE) spectroscopy and analysis of residual dipolar couplings, we obtained data on the molecular structure of the dominant conformers. Based on these data, the spatial structure of the main conformer of cyclosporin in chloroform was determined by molecular dynamics simulation. The kinetics of exchange between the major and minor forms was also studied. Energy barrier (ΔG‡) between the two states is 81±2kJ/mol. The conformation of CsA in complex with sodium dodecyl sulphate micelles was determined from NOE data.Use of independent structural data improves the reliability of the simulated results. The structure of the minor forms, which exist in organic solvents and also in micellar solution, cannot be assessed by means of nuclear magnetic resonance. Spectroscopic and thermodynamic parameters, however, point to their certain properties. In particular, the minor conformer of CsA in chloroform differs from the main one by a peptide bond (in cis- rather than trans-conformation) in the region of residues from 4 to 7.

Molecular structure of 4-hidroxy-3-(3-methyl-2-butenyl) acetophenone, a plant antifungal, by X-ray diffraction, DFT calculation, and NMR and FTIR spectroscopy

The molecular structure of two mixed and closely related conformers of the title compound, C13H16O2, found in the solid with unequal occupancies has been determined by X-ray diffraction methods. The substance crystallizes in the monoclinic Pca21 space group with a=17.279(2), b=5.1716(7), c=12.549(2)Å, and Z=4 molecules per unit cell. The structure was solved from 1314 reflections with I>2σ(I) and refined to an agreement R1-factor of 0.049. The minor conformer (34.7%) is nearly mirror-related to and extensively overlapped with the major one. The skeleton of the 4-hydroxyacetophenone molecular fragment and the prenyl group, (CH2)(CH)C(CH3)2, pendant arm attached to it are both planar and perpendicular to each other. A strong intermolecular OH⋯O bond links neighboring molecules in the lattice to produce a polymeric structure. The conformational structures of the compound in the gas phase have been calculated by the DFT method and the geometrical results have been compared with the X-ray data. These data allow a complete assignment of vibration modes in the solid state FTIR and Raman spectra. The calculated 1H and 13C chemicals shifts are in good agreement with the corresponding experimental NMR spectra of the compound in solution.