Anti Conformation Research Articles

The Introduction of the Radical Cascade Reaction into Polymer Chemistry: A One-Step Strategy for Synchronized Polymerization and Modification.

SummaryPolymerization and modification play central roles in polymer chemistry and are generally implemented in two steps, which suffer from the time-consuming two-step strategy and present considerable challenge for complete modification. By introducing the radical cascade reaction (RCR) into polymer chemistry, a one-step strategy is demonstrated to achieve synchronized polymerization and complete modification in situ. Attributed to the cascade feature of iron-catalyzed three-component alkene carboazidation RCR exhibiting carbon-carbon bond formation and carbon-azide bond formation with extremely high efficiency and selectivity in one step, radical cascade polymerization therefore enables the in situ synchronized polymerization through continuous carbon-carbon bond formation and complete modification through carbon-azide bond formation simultaneously. This results in a series of α, β, and γ poly(amino acid) precursors. This result not only expands the methodology library of polymerization, but also the possibility for polymer science to achieve functional polymers with tailored chemical functionality from in situ polymerization.

Molecular and structural characterization of oxidized ribonucleotide insertion into DNA by human DNA polymerase β

During oxidative stress, inflammation, or environmental exposure, ribo- and deoxyribonucleotides are oxidatively modified. 8-Oxo-7,8-dihydro-2'-guanosine (8-oxo-G) is a common oxidized nucleobase whose deoxyribonucleotide form, 8-oxo-dGTP, has been widely studied and demonstrated to be a mutagenic substrate for DNA polymerases. Guanine ribonucleotides are analogously oxidized to r8-oxo-GTP, which can constitute up to 5% of the rGTP pool. Because ribonucleotides are commonly misinserted into DNA, and 8-oxo-G causes replication errors, we were motivated to investigate how the oxidized ribonucleotide is utilized by DNA polymerases. To do this, here we employed human DNA polymerase β (pol β) and characterized r8-oxo-GTP insertion with DNA substrates containing either a templating cytosine (nonmutagenic) or adenine (mutagenic). Our results show that pol β has a diminished catalytic efficiency for r8-oxo-GTP compared with canonical deoxyribonucleotides but that r8-oxo-GTP is inserted mutagenically at a rate similar to those of other common DNA replication errors (i.e. ribonucleotide and mismatch insertions). Using FRET assays to monitor conformational changes of pol β with r8-oxo-GTP, we demonstrate impaired pol β closure that correlates with a reduced insertion efficiency. X-ray crystallographic analyses revealed that, similar to 8-oxo-dGTP, r8-oxo-GTP adopts an anti conformation opposite a templating cytosine and a syn conformation opposite adenine. However, unlike 8-oxo-dGTP, r8-oxo-GTP did not form a planar base pair with either templating base. These results suggest that r8-oxo-GTP is a potential mutagenic substrate for DNA polymerases and provide structural insights into how r8-oxo-GTP is processed by DNA polymerases.

Encapsulation-Controlled Photoisomerization of a Styryl Derivative: Stereoselective Formation of the Anti Z-Isomer in the Cucurbit[7]uril Cavity.

The photochemical isomerization of a styrylpyridinium dye (SP) bearing an unsymmetrically attached benzo-15-crown-5 ether has been studied in aqueous solution in the absence and presence of cucurbit[7]uril (CB[7]). The detailed analysis of the UV/Vis and NMR spectra showes that the isomeric composition of the photostationary mixtures of SP can be modulated by the host-guest complexation with CB[7]. It was found that steric hindrance caused by encapsulation of SP in the host cavity induces the exclusive formation of the anti conformer of Z-SP in contrast with the mixture of both anti and syn conformers obtained during photoisomerization of the dye without CB[7]. Remarkably, the displacement of anti Z-SP from CB[7] does not lead to the transformation of the anti Z-isomer into the syn Z-isomer pointing out the conformational memory of the system. The results provide an interesting example of the supramolecular stereorecognition by the achiral CB[7] host.

Structural Determinants Responsible for the Preferential Insertion of Ribonucleotides by Bacterial NHEJ PolDom.

The catalytic active site of the Polymerization Domain (PolDom) of bacterial Ligase D is designed to promote realignments of the primer and template strands and extend mispaired 3′ ends. These features, together with the preferred use of ribonucleotides (NTPs) over deoxynucleotides (dNTPs), allow PolDom to perform efficient double strand break repair by nonhomologous end joining when only a copy of the chromosome is present and the intracellular pool of dNTPs is depleted. Here, we evaluate (i) the role of conserved histidine and serine/threonine residues in NTP insertion, and (ii) the importance in the polymerization reaction of a conserved lysine residue that interacts with the templating nucleotide. To that extent, we have analyzed the biochemical properties of variants at the corresponding His651, Ser768, and Lys606 of Pseudomonas aeruginosa PolDom (Pa-PolDom). The results show that preferential insertion of NMPs is principally due to the histidine that also contributes to the plasticity of the active site to misinsert nucleotides. Additionally, Pa-PolDom Lys606 stabilizes primer dislocations. Finally, we show that the active site of PolDom allows the efficient use of 7,8-dihydro-8-oxo-riboguanosine triphosphate (8oxoGTP) as substrate, a major nucleotide lesion that results from oxidative stress, inserting with the same efficiency both the anti and syn conformations of 8oxoGMP.

Structure of HIRAN domain of human HLTF bound to duplex DNA provides structural basis for DNA unwinding to initiate replication fork regression.

Replication fork regression is a mechanism to rescue a stalled fork by various replication stresses, such as DNA lesions. Helicase-like transcription factor, a SNF2 translocase, plays a central role in the fork regression and its N-terminal domain, HIRAN (HIP116 and Rad5 N-terminal), binds the 3'-hydroxy group of single-stranded DNA. Furthermore, HIRAN is supposed to bind double-stranded DNA (dsDNA) and involved in strand separation in the fork regression, whereas structural basis for mechanisms underlying dsDNA binding and strand separation by HIRAN are still unclear. Here, we report the crystal structure of HIRAN bound to duplex DNA. The structure reveals that HIRAN binds the 3'-hydroxy group of DNA and unexpectedly unwinds three nucleobases of the duplex. Phe-142 is involved in the dsDNA binding and the strand separation. In addition, the structure unravels the mechanism underlying sequence-independent recognition for purine bases by HIRAN, where the N-glycosidic bond adopts syn conformation. Our findings indicate direct involvement of HIRAN in the fork regression by separating of the daughter strand from the parental template.

Crystal structure, Hirshfeld surface analysis and computational study of the 1:2 co-crystal formed between N,N'-bis-(pyridin-4-ylmeth-yl)ethane-diamide and 4-chloro-benzoic acid.

The asymmetric unit of the title 1:2 co-crystal, C14H14N4O2·2C7H5ClO2, comprises two half mol-ecules of oxalamide (4 LH2), as each is disposed about a centre of inversion, and two mol-ecules of 4-chloro-benzoic acid (CBA), each in general positions. Each 4 LH2 mol-ecule has a (+)anti-periplanar conformation with the pyridin-4-yl residues lying to either side of the central, planar C2N2O2 chromophore with the dihedral angles between the respective central core and the pyridyl rings being 68.65 (3) and 86.25 (3)°, respectively, representing the major difference between the independent 4 LH2 mol-ecules. The anti conformation of the carbonyl groups enables the formation of intra-molecular amide-N-H⋯O(amide) hydrogen bonds, each completing an S(5) loop. The two independent CBA mol-ecules are similar and exhibit C6/CO2 dihedral angles of 8.06 (10) and 17.24 (8)°, indicating twisted conformations. In the crystal, two independent, three-mol-ecule aggregates are formed via carb-oxy-lic acid-O-H⋯N(pyrid-yl) hydrogen bonding. These are connected into a supra-molecular tape propagating parallel to [100] through amide-N-H⋯O(amide) hydrogen bonding between the independent aggregates and ten-membered {⋯HNC2O}2 synthons. The tapes assemble into a three-dimensional architecture through pyridyl- and methyl-ene-C-H⋯O(carbon-yl) and CBA-C-H⋯O(amide) inter-actions. As revealed by a more detailed analysis of the mol-ecular packing by calculating the Hirshfeld surfaces and computational chemistry, are the presence of attractive and dispersive Cl⋯C=O inter-actions which provide inter-action energies approximately one-quarter of those provided by the amide-N-H⋯O(amide) hydrogen bonding sustaining the supra-molecular tape.

Plasticity or elasticity? Relating elastic moduli with secondary structural features of mixed films of polypeptides at air/fluid and fluid/solid interfaces

Viscoelastic properties of molecular assemblies formed by mixing poly (l-lysine) (PLL) and poly (l-glutamic acid) (PGA) at pH = 7.5 have been studied using Quartz crystal microbalance with dissipation (QCM-D). The inter-molecular complex between PLL and PGA arising from strong electrostatic interaction, leads to local changes in secondary structure resulting in intra-molecular complexes. ATR-FTIR analysis of the Secondary structural features of PLL, suggest an abundance of anti-parallel beta sheet that causes a significant change in the morphology of the self-assembled structures. A combination of spectroscopy, Brewster angle microscopy (BAM), Transmission electron and scanning electron microscopy show that an inverse relationship exists between the elasticity of the different PLL + PGA mixed films and the % anti parallel beta sheet conformation. The elastic moduli for the mixtures change from about 0.913 ± 0.01 GPa for pure PLL to about 0.764 ± 0.01 GPa in the mixture when PGA increases. The localized breaking and reformation of the ion pairs in the complex control their sizes and show an inverse relationship with the elastic moduli. The rheological profiles of the films, elastic moduli, together with their surface morphology from microscopy (TEM) and (SEM) confirmed their increasing propensity to self-assemble in one dimension to form tapes, colloidal particles and their composite assemblies.

2-Propionylthiophene: planar, or not planar, that is the question.

The long-standing ambiguity of the molecular planarity when an alkyl group is attached to a system with conjugated double bonds is a great challenge for both experiments and theory. This also holds true for the case of 2-propionylthiophene (2PT) where a propionyl group is attached at the second position of the planar, aromatic thiophene ring. Results from quantum chemistry at the MP2 level of theory, showing that in the two conformers syn- and anti-2PT the ethyl group of the propionyl moiety is slightly tilted out of the thiophene ring plane, conflict with those from the other methods, stating that the ethyl group is in-plane with the thiophene ring. In the microwave spectrum, both syn- and anti-2PT were observed, and their geometry parameters such as the rotational and quartic centrifugal distortion constants were precisely determined. The experimental heavy atom skeleton obtained by isotopic substitutions revealed a tiny, but non-zero tilt angle of the ethyl group out of the thiophene plane, thereby convincingly confirming the non-planarity of 2-propionylthiophene. This conclusion was further supported by the inertial defects calculated from the experimental rotational constants. Finally, splittings arising from the internal rotation of the terminal methyl group were analysed, yielding torsional barriers of 806.94(54) cm-1 and 864.5(88) cm-1 for the two observed conformers, respectively.

With complements of the ligands: an unusual S-shaped [Mn7]2 assembly from tethered calixarenes.

The reaction between MnCl2·4H2O, 2,2'-bis-p-tBu-calix[4]arene (H8L1) and 2-(hydroxymethyl)pyridine (hmpH) in a basic dmf/MeOH solution results in the formation of the complex [MnIII10MnII4(L1)3(hmp)4(μ3-O)4(μ3-OH)2(MeOH)4(dmf)6](dmf)4 (6) upon vapour diffusion of petroleum ether into the mother liquor. The crystals are in the monoclinic space group C2/c, with the asymmetric unit (ASU) comprising one half of the molecule. The structure describes a large S-shaped cluster (∼40 Å top to tail) where the unusual syn and anti conformations of the calixarene ligands results in two binding pockets each containing a [MnIII5MnII2] moiety comprised of two perpendicular, vertex-sharing [Mn4] butterflies. One butterfly possesses a [MnIII4O4] core and the second a [MnIII2MnII2O3] unit with the MnII ions in the central body positions. Magnetic susceptibility and magnetisation measurements reveal weak exchange interactions between the metal centres.

Switching On/Off the Intramolecular Hydrogen Bonding of 2-Methoxyphenol Conformers: An NMR Study

Intramolecular hydrogen bonding of 2-methoxyphenol (2-MP, guaiacol) is studied using NMR spectroscopy combined with quantum mechanical density functional theory (DFT) calculations. The hydrogen bonding of OH⋯O and HO⋯H is switched on in the conformers of anti–syn (AS, 99.64% dominance) and anti–gauche (AG), respectively, with respect to the anti–anti (AA) conformer (without either such hydrogen bonding interactions). It confirms that the 13C and 1H NMR chemical shift of AS dominates the measured NMR spectra, as the AS conformer reproduces the measurements in CDCl3 solvent (RMSD of 1.86ppm for 13C NMR and of 0.27ppm for 1H NMR). The chemical shift of hydroxyl H(1) at 5.66 pm is identified as the fingerprint of the OH(1)⋯OCH3 hydrogen bonding in AS, as it exhibits a significant deshielding from H(1) of AA (4.24ppm) and H(1) of AG (4.38ppm) without such OH(1)⋯OCH3 hydrogen bonding. The AG conformer (C1 point group symmetry) possesses a less strong hydrogen bonding of HO⋯HCH2O, with the methoxyl group out of the aromatic phenol plane. The substituent effect of AG due to the resonance interaction of methoxyl being out of plane in a concentrated solution shifts the ortho- and para-aromatic carbons, C(3)/C(5), of the AG to ~125.05/125.44ppm from the corresponding carbons in AS at 108.81/121.60ppm. The hydrogen bonding exhibits inwards reduction of IR frequency regions of AS and AG from AA. Finally, energy decomposition analysis (EDA) indicates that there is a steric energy of 45.01kcal mol−1 between the AS and AG when different intramolecular hydrogen bonding is switched on.

Structure of an Unusual Tetracyclic Deoxyguanosine Adduct: Implications for Frameshift Mutagenicity of ortho-Cyano Nitroanilines.

Nitroaromatic compounds represent a major class of industrial chemicals that are also found in nature. Polycyclic derivatives are regarded as potent mutagens and carcinogens following bioactivation to produce nitrenium electrophiles that covalently modify DNA to afford N-linked C8-2'-deoxyguanosine (C8-dG) lesions that can induce frameshift mutations, especially in CpG repeat sequences. In contrast, their monocyclic counterparts typically exhibit weak mutagenicity or a lack thereof, despite also undergoing bioactivation to afford N-linked C8-dG adducts. Recently, it has been reported that cyano substitution can greatly increase the mutagenicity of nitroaniline derivatives that are components of azo dyes. The basis of this "cyano effect" may be rooted in the formation of a novel polycyclic adduct arising from initial formation of the N-linked C8-dG adduct followed by a cyclization process involving N7 of dG and the ortho-CN group of the attached C8-aryl moiety to generate a quinazolinimine ring as part of a fused tetracyclic C8,N7-dG adduct structure. The present work structurally characterizes this novel cyclic adduct using a combination of optical spectroscopies, NMR analysis, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations. Our data indicate that this highly fluorescent cyclic adduct adopts the promutagenic syn conformation and can stabilize the slipped mutagenic intermediate (SMI) within the CpG repeat of the NarI sequence, which is a hotspot for frameshift mutagenesis mediated by polycyclic N-linked C8-dG adducts. In contrast, the open para-CN (4-aminobenzontrile-derived) N-linked C8-dG adduct is less likely to disrupt the canonical B-form. Together, our results provide a rationale for the potent mutagenicity of cyano-substituted nitroaniline derivatives recently reported in frameshift-sensitive tester strains.

Dark-Binding Process Relevant to Preventing Photosensitized Oxidation: Conformation-Dependent Light and Dark Mechanisms by a Dual-Functioning Diketone.

Few photosensitizers function in both light and dark processes as they usually have no function when the lights are turned off. We hypothesized that light and dark mechanisms in an α-diketone will be decoupled by dihedral rotation in a conformation-dependent binding process. Successful decoupling of these two functions is now shown. Namely, anti- and syn-skewed conformations of 4,4′-dimethylbenzil promote photosensitized alkoxy radical production, whereas the syn conformation promotes a binding shutoff reaction with trimethyl phosphite. Less rotation of the diketone is better suited to the photosensitizing function since phosphite binding arises through the syn conformer of lower stability. The dual function seen here with the α-diketone is generally not available to sensitizers of limited conformational flexibility, such as porphyrins, phthalocyanines, and fullerenes.

NMR Chemical Exchange Measurements Reveal That N6-Methyladenosine Slows RNA Annealing.

N6-Methyladenosine (m6A) is an abundant epitranscriptomic modification that plays important roles in many aspects of RNA metabolism. While m6A is thought to mainly function by recruiting reader proteins to specific RNA sites, the modification can also reshape RNA-protein and RNA-RNA interactions by altering RNA structure mainly by destabilizing base pairing. Little is known about how m6A and other epitranscriptomic modifications might affect the kinetic rates of RNA folding and other conformational transitions that are also important for cellular activity. Here, we used NMR R1ρ relaxation dispersion and chemical exchange saturation transfer to noninvasively and site-specifically measure nucleic acid hybridization kinetics. The methodology was validated on two DNA duplexes and then applied to examine how a single m6A alters the hybridization kinetics in two RNA duplexes. The results show that m6A minimally impacts the rate constant for duplex dissociation, changing koff by ∼1-fold but significantly slows the rate of duplex annealing, decreasing kon by ∼7-fold. A reduction in the annealing rate was observed robustly for two different sequence contexts at different temperatures, both in the presence and absence of Mg2+. We propose that rotation of the N6-methyl group from the preferred syn conformation in the unpaired nucleotide to the energetically disfavored anti conformation required for Watson-Crick pairing is responsible for the reduced annealing rate. The results help explain why in mRNA m6A slows down tRNA selection and more generally suggest that m6A may exert cellular functions by reshaping the kinetics of RNA conformational transitions.

Sugar Puckering Drives G-Quadruplex Refolding: Implications for V-Shaped Loops.

A DNA G‐quadruplex adopting a (3+1) hybrid structure was modified in two adjacent syn positions of the antiparallel strand with anti‐favoring 2′‐deoxy‐2′‐fluoro‐riboguanosine (FrG) analogues. The two substitutions promoted a structural rearrangement to a topology with the 5′‐terminal G residue located in the central tetrad and the two modified residues linked by a V‐shaped zero‐nucleotide loop. Strikingly, whereas a sugar pucker in the preferred north domain is found for both modified nucleotides, the FrG analogue preceding the V‐loop is forced to adopt the unfavored syn conformation in the new quadruplex fold. Apparently, a preferred C3′‐endo sugar pucker within the V‐loop architecture outweighs the propensity of the FrG analogue to adopt an anti glycosidic conformation. Refolding into a V‐loop topology is likewise observed for a sequence modified at corresponding positions with two riboguanosine substitutions. In contrast, 2′‐F‐arabinoguanosine analogues with their favored south‐east sugar conformation do not support formation of the V‐loop topology. Examination of known G‐quadruplexes with a V‐shaped loop highlights the critical role of the sugar conformation for this distinct structural motif.

Small Molecule Rescue and Glycosidic Conformational Analysis of the Twister Ribozyme.

The number of self-cleaving ribozymes has increased sharply in recent years, giving rise to elaborations of the four known ribozyme catalytic strategies, α, β, γ, and δ. One such extension is utilized by the twister ribozyme, which is hypothesized to conduct δ, or general acid catalysis, via N3 of the syn adenine +1 nucleobase indirectly via buffer catalysis at biological pH and directly at lower pH. Herein, we test the δ catalysis role of A1 via chemical rescue and the catalytic relevance of the syn orientation of the nucleobase by conformational analysis. Using inhibited twister ribozyme variants with A1(N3) deaza or A1 abasic modifications, we observe >100-fold chemical rescue effects in the presence of protonatable biological small molecules such as imidazole and histidine, similar to observed rescue values previously reported for C75U/C76Δ in the HDV ribozyme. Brønsted plots for the twister variants support a model in which small molecules rescue catalytic activity via a proton transfer mechanism, suggesting that A1 in the wild type is involved in proton transfer, most likely general acid catalysis. Additionally, through glycosidic conformational analysis in an appropriate background that accommodates the bromine atom, we observe that an 8BrA1-modified twister ribozyme is up to 10-fold faster than a nonmodified A1 ribozyme, supporting crystallographic data that show that A1 is syn when conducting proton transfer. Overall, this study provides functional evidence that the nucleotide immediately downstream of the cleavage site participates directly or indirectly in general acid-base catalysis in the twister ribozyme while occupying the syn conformation.

<p>Vitamin K1 As A Potential Molecule For Reducing Single-Walled Carbon Nanotubes-Stimulated α-Synuclein Structural Changes And Cytotoxicity</p>

AimsDifferent kinds of vitamins can be used as promising candidates to mitigate the structural changes of proteins and associated cytotoxicity stimulated by NPs. Therefore, the structural changes of α-syn molecules and their associated cytotoxicity in the presence of SWCNTs either alone or co-incubated with vitamin K1 were studied by spectroscopic, bioinformatical, and cellular assays.MethodsIntrinsic and ThT fluorescence, CD, and Congo red absorption spectroscopic approaches as well as TEM investigation, molecular docking, and molecular dynamics were used to explore the protective effect of vitamin K1 on the structural changes of α-syn induced by SWCNTs. The cytotoxicity of α-syn/SWCNTs co-incubated with vitamin K1 against SH-SY5Y cells was also carried out by MTT, LDH, and caspase-3 assays.ResultsFluorescence spectroscopy showed that vitamin K1 has a significant effect in reducing SWCNT-induced fluorescence quenching and aggregation of α- syn. CD, Congo red adsorption, and TEM investigations determined that co-incubation of α- syn with vitamin K1 inhibited the propensity of α-syn into the structural changes and amorphous aggregation in the presence of SWCNT. Docking studies determined the occupation of preferred docked site of SWCNT by vitamin K1 on α- syn conformation. A molecular dynamics study also showed that vitamin K1 reduced the structural changes of α- syn induced by SWCNT. Cellular data exhibited that the cytotoxicity of α- syn co-incubated with vitamin K1 in the presence of SWCNTs is less than the outcomes obtained in the absence of the vitamin K1.ConclusionIt may be concluded that vitamin K1 decreases the propensity of α- syn aggregation in the presence of SWCNTs and induction of cytotoxicity.

Promutagenicity of 8-Chloroguanine, A Major Inflammation-Induced Halogenated DNA Lesion.

Chronic inflammation is closely associated with cancer development. One possible mechanism for inflammation-induced carcinogenesis is DNA damage caused by reactive halogen species, such as hypochlorous acid, which is released by myeloperoxidase to kill pathogens. Hypochlorous acid can attack genomic DNA to produce 8-chloro-2′-deoxyguanosine (ClG) as a major lesion. It has been postulated that ClG promotes mutagenic replication using its syn conformer; yet, the structural basis for ClG-induced mutagenesis is unknown. We obtained crystal structures and kinetics data for nucleotide incorporation past a templating ClG using human DNA polymerase β (polβ) as a model enzyme for high-fidelity DNA polymerases. The structures showed that ClG formed base pairs with incoming dCTP and dGTP using its anti and syn conformers, respectively. Kinetic studies showed that polβ incorporated dGTP only 15-fold less efficiently than dCTP, suggesting that replication across ClG is promutagenic. Two hydrogen bonds between syn-ClG and anti-dGTP and a water-mediated hydrogen bond appeared to facilitate mutagenic replication opposite the major halogenated guanine lesion. These results suggest that ClG in DNA promotes G to C transversion mutations by forming Hoogsteen base pairing between syn-ClG and anti-G during DNA synthesis.

Quantitative Assessment of the Conformational Heterogeneity in Amylose across Force Fields.

The inherent flexibility and conformational heterogeneity of a carbohydrate pose a challenge for its modeling and sampling by the existing classical force field. This work quantitatively assesses the quality of four popular carbohydrate force fields (CHARMM36, GLYCAM06, OPLS-AA, GROMOS53A6CARBO_R) against their ability to accurately model the conformational landscape of a dodecamer of single-stranded amylose, the key constituent of starch. While past NMR and X-ray studies have hinted at evidence of a helical structure of amylose and its spontaneous helix-coil transition, it remains to be seen how existing force fields fare against modeling its structural transition. Toward this end, we perform a multimicrosecond long extensive molecular dynamics simulation of dodecamer of a single-stranded amylose chain in explicit water in each of the four force fields and assess these force fields' ability to model relative structural transitions via analyzing the radius of gyration, glycosidic linkage orientation, and pyranose ring puckering of the amylose. In particular, the simulations show that while GLYCAM06 and CHARMM36 force fields predict a significant helix-coil transition in the amylose, GROMOS53A6CARBO_R and OPLS-AA majorly favor extended conformation. The Markov State Model (MSM), built using the simulation trajectories, for each force field, provides a comparative quantification of the population of key macrostates of amylose and elucidates an underlying network of pathways of their mutual interconversion. The macrostates obtained from MSM revealed that metastable helixlike and semicoil intermediate conformations are more probable for CHARMM36, whereas elongated or helixlike conformations are more probable in OPLS-AA and GROMOS53A6CARBO_R. GLYCAM06 showed significant probability for both helix and coil conformations along with intermediate conformations. We find that the differences in the conformations across force fields are governed by differences in the kinetics of glycosidic linkages and pyranose ring pucker conformers. All four force fields share one common point that the majority of α(1 → 4) glycosidic linkages preferred syn conformation, which is found to be energetically more favorable than anti. However, except for GROMOS53A6CARBO_R, all other force fields predicted non-negligible minor anti conformation. The multimicrosecond long simulations on the single-chain amylose, in combination with MSM, described here, suggest that sampling of α(1 → 4) linked oligosacharides on microsecond time scales enable quantitative predictions of helix-coil, glycosidic linkage, and pyranose ring exchange kinetics. These exchange kinetics have otherwise remained inaccessible to quantification by experiments or nanosecond time scale simulations which might have hindered the comparison of the possibility of helix-coil exchange across different force fields on equal footing.

The Fluorine gauche Effect and a Comparison with Other Halogens in 2‐Halofluoroethanes and 2‐Haloethanols

While the gauche effect in 1,2‐difluoroethane is widely known as being due to hyperconjugative interactions between σCH electron‐donating orbitals and σ*CF electron‐accepting orbitals, the corresponding 1,2‐dichloro, 1,2‐dibromo, and 1,2‐diiodo derivatives are preferentially in the anti conformation. 2‐Halofluoroethanes (F‐CH2‐CH2‐X) combine a small halogen (fluorine) and a vicinal low‐lying energy antibonding orbital (σ*CX) that activates a stabilizing antiperiplanar σCH → σ*CX electron delocalization, which can induce the gauche effect. On the other hand, σCX orbitals are good electron donors to σ*CF, that would favor an “anti effect”, in addition to traditional interpretations based on steric and electrostatic repulsion. Therefore, a balance of steric, dipolar and hyperconjugative effects drive the conformational equilibrium of these compounds – hyperconjugation was found to explain the gauche effect in some cases, whilst Lewis‐type interactions determine the anti preference in others. The gauche effect takes place in a polar solvent, but not for 1‐fluoro‐2‐iodoethane. According to NMR three‐bond spin‐spin coupling constants, the gauche population increases when fluorine is replaced by a hydroxyl group (except for 2‐fluoroethanol relative to 1,2‐difluoroethane), but this is not primarily due to intramolecular hydrogen bond.

Interplay between Conformation and Crystal Packing in Aryl Propargyl Ethers: Structural and Spectroscopic Properties of 2‐(prop‐2‐yn‐1‐yloxy)acene Derivatives

AbstractThe 2‐(prop‐2‐yn‐1‐yloxy)naphthalene (compound I) and 1‐nitro‐2‐(prop‐2‐yn‐1‐yloxy)benzene (compound II) were prepared in excellent yields by the reaction of propargyl bromide with 2‐naphthol and 2‐nitrophenol, respectively. Structural and conformational properties of both compounds have been analyzed using a combined approach including single‐crystal X‐ray diffraction and quantum chemical calculations. Two forms are found to be stable and nearly isoenergetic conformers, depending on the mutual orientation of the C≡C triple bond and the O–C single bond of the prop‐2‐yn‐1‐yloxy group. The gauche conformation is the most stable form for the vacuum isolated species, with the anti conformation higher in energy by 1.00 and 1.89 kcal/mol computed at the M06‐2X/6‐311++G(d,p) level of approximation, for I and II, respectively. The gauche form is observed in the crystal of I but the nearly planar anti conformation is adopted in the crystalline phase of compound II. The occurrence of C–H⋅⋅⋅π and C–H⋅⋅⋅O intermolecular interactions involving the acidic ‐C≡C–H hydrogen donor and ‐C≡C‐ and ‐OCH2– acceptors is discussed. Furthermore, vibrational features of the prop‐2‐yn‐1‐yloxy moiety are analyzed by infrared and Raman spectroscopy. The UV‐Vis spectrum shows the presence of well‐defined absorption at ca. 280 and 320 nm assigned to the π→π* transitions in the naphtyl/benzyl and prop‐2‐yn‐1‐yloxy groups, respectively.