Showing papers on "Conformational isomerism published in 2016"

Conformational Contrast of Surface-Mediated Molecular Switches Yields Ångstrom-Scale Spatial Resolution in Ultrahigh Vacuum Tip-Enhanced Raman Spectroscopy

Abstract: Tip-enhanced Raman spectroscopy (TERS) combines the ability of scanning probe microscopy (SPM) to resolve atomic-scale surface features with the single-molecule chemical sensitivity of surface-enhanced Raman spectroscopy (SERS) Here, we report additional insights into the nature of the conformational dynamics of a free-base porphyrin at room temperature adsorbed on a metal surface We have interrogated the conformational switch between two metastable surface-mediated isomers of meso-tetrakis(3,5-ditertiarybutylphenyl)-porphyrin (H2TBPP) on a Cu(111) surface At room temperature, the barrier between the porphyrin ring buckled up/down conformations of the H2TBPP-Cu(111) system is easily overcome, and a 26 A lateral resolution by simultaneous TERS and STM analysis is achieved under ultrahigh vacuum (UHV) conditions This work demonstrates the first UHV-TERS on Cu(111) and shows TERS can unambiguously distinguish the conformational differences between neighboring molecules with Angstrom-scale spatial resolu

Nonplanar Butterfly‐Shaped π‐Expanded Pyrrolopyrroles

Abstract: Large aza-analogues of curved polycyclic aromatic hydrocarbons with a double-helicene structure present unique features for molecular photonics. We present the preparation and characterization of three such structures. The synthesis of these heterocyclic nanographenes involves only a few high-yield steps that use readily available starting materials. X-ray analysis revealed that each of these new dyes has three conformational isomers: one diastereoisomer in a meso form and two enantiomers in twisted forms [(P,P)] and [(M,M)]. The low energy barriers between the conformers, however, prevent their separation by using chiral HPLC, and the NMR spectra show only one set of signals for each of these curved compounds. Density functional theory (DFT) calculations quantify the small energy difference and the small energy barriers between the chiral and meso forms, which fully supports the experimental results. Their optical absorption lacks any sensitivity to the solvent environment, whereas their fluorescence features exhibit pronounced solvatochromism. This rarely observed solvatofluorochromism of centrosymmetric molecules without either electron-withdrawing groups or -donating substituents was probed by using time-resolved spectroscopy. These studies suggest that, similar to 9,9'-bianthryl, the nonpolar locally excited state shows negligible solvatochromism, whereas the charge-transfer state is sensitive to solvent polarity.

A spectroscopic and theoretical study in the near-infrared region of low concentration aliphatic alcohols

Abstract: The near-infrared (NIR) spectra of low-concentration (5 × 10−3 M) solutions in CCl4 of basic aliphatic alcohols, methanol, ethanol, and 1-propanol were, for the first time, calculated by second-order vibrational perturbation theory computations and were compared with the corresponding experimental data. Density functional theory (DFT) using single hybrid (B3LYP) and double hybrid (B2PLYP) density functionals and their derivatives with additional empirical dispersion correction (B3LYP-D3 and B2PLYP-D, respectively) and second order Moller–Plesset perturbation theory were used in combination with selected basis sets including fairly new basis sets from the “spectroscopic” SNS family, double-ζ SNSD and triple-ζ SNST basis sets. Each time, anharmonic vibrational modes and intensities were calculated by using second-order vibrational perturbation theory. The effect of solvent cavity on the calculated results was included by the application of a self-consistent reaction field with a polarized continuum model. Ethanol and 1-propanol have conformational isomerism; following a conformational analysis, theoretical spectra of all isomers were calculated and their final predicted NIR spectra were obtained as Boltzmann-averaged spectra of resolved conformers. For ethanol and 1-propanol, the observed broadening of the overtone band of the OH stretching mode was well reflected by the differences in the position of the relevant band among conformational isomers of these alcohols; the effect of solvent on broadening was also discussed. Detailed band assignments in the experimental NIR spectra of the studied alcohols were proposed based on the calculation of potential energy distributions. The final accuracy of the predicted NIR spectra for each of the theoretical methods was estimated based on the errors in calculated frequencies of overtones and combination bands.

Octahedral Werner complexes with substituted ethylenediamine ligands: a stereochemical primer for a historic series of compounds now emerging as a modern family of catalysts

Abstract: As reported by Alfred Werner in 1911–1912, salts of the formally D3 symmetric [Co(en)3]3+ (en = ethylenediamine) trication were among the first chiral inorganic compounds to be resolved into enantiomers, the absolute configurations of which are denoted Λ (left handed helix) or Δ (right handed helix). After a >100 year dormant period during which few useful reactions of these substitution inert complexes were described, carbon substituted derivatives have recently been found to be potent catalysts for enantioselective organic synthesis. This review systematically outlines the fascinating range of stereoisomers that can arise, such as conformers associated with the five membered chelate rings (λ/δ), alignment modes of the C–C bonds with the C3 symmetry axis (lel/ob), geometric isomers (fac/mer), and configurational diastereomers (R/S) arising from carbon stereocenters. These analyses demonstrate a profound stereochemical diversity that can be applied in catalyst optimization. Efforts are made to bridge the often orthogonal nomenclature systems inorganic and organic chemists employ to describe these phenomena.

Experimental and computational evaluation of the barrier to torsional rotation in a butadiyne-linked porphyrin dimer

Abstract: The barrier to torsional rotation in a butadiyne-linked porphyrin dimer has been determined in solution using variable temperature UV-vis-NIR spectroscopy: ΔH = 5.27 ± 0.03 kJ mol−1, ΔS = 10.69 ± 0.14 J K−1 mol−1. The value of ΔH agrees well with theoretical predictions. Quantum chemical calculations (DFT) were used to predict the torsion angle dependence of the absorption spectrum, and to calculate the vibronic fine structure of the S0 → S1 absorption for the planar dimer, showing that the absorption band of the planar conformer has a vibronic component overlapping with the 〈0|0〉 absorption of the perpendicular conformer. The torsion barrier in the porphyrin dimer is higher than that of 1,4-diphenylbutadiyne (calculated ΔH = 1.1 kJ mol−1). Crystallographic bond lengths and IR vibrational frequencies confirm that there is a greater contribution of the cumulenic resonance form in butadiyne-linked porphyrin dimers than in 1,4-diphenylbutadiyne. The DFT frontier orbitals of the twisted conformer of the porphyrin dimer are helical, when calculated in the absence of symmetry. The helical character of these orbitals disappears when D2d symmetry is enforced in the 90° twisted conformer. Helical representations of the frontier orbitals can be generated by linear combinations of the more localised orbitals from a symmetry-constrained calculation but they do not indicate π-conjugation. This work provides insights into the relationship between electronic structure and conformation in alkyne-linked conjugated oligomers.

Trans-cis molecular photoswitching in interstellar space

Abstract: As many organic molecules, formic acid (HCOOH) has two conformers (trans and cis ). The energy barrier to internal conversion from trans to cis is much higher than the thermal energy available in molecular clouds. Thus, only the most stable conformer (trans ) is expected to exist in detectable amounts. We report the first interstellar detection of cis -HCOOH. Its presence in ultraviolet (UV) irradiated gas exclusively (the Orion Bar photodissociation region), with a low trans -to-cis abundance ratio of 2.8 ± 1.0, supports a photoswitching mechanism: a given conformer absorbs a stellar photon that radiatively excites the molecule to electronic states above the interconversion barrier. Subsequent fluorescent decay leaves the molecule in a different conformer form. This mechanism, which we specifically study with ab initio quantum calculations, was not considered in Space before but likely induces structural changes of a variety of interstellar molecules submitted to UV radiation.

Flexibility unleashed in acyclic monoterpenes: conformational space of citronellal revealed by broadband rotational spectroscopy

Abstract: Conformational flexibility is intrinsically related to the functionality of biomolecules. Elucidation of the potential energy surface is thus a necessary step towards understanding the mechanisms for molecular recognition such as docking of small organic molecules to larger macromolecular systems. In this work, we use broadband rotational spectroscopy in a molecular jet experiment to unravel the complex conformational space of citronellal. We observe fifteen conformations in the experimental conditions of the molecular jet, the highest number of conformers reported to date for a chiral molecule of this size using microwave spectroscopy. Studies of relative stability using different carrier gases in the supersonic expansion reveal conformational relaxation pathways that strongly favour ground-state structures with globular conformations. This study provides a blueprint of the complex conformational space of an important biosynthetic precursor and gives insights on the relation between its structure and biological functionality.

Enhancing the Sensitivity of CPMG Relaxation Dispersion to Conformational Exchange Processes by Multiple-Quantum Spectroscopy.

Abstract: A triple-quantum (1) H Carr-Purcell-Meiboom-Gill NMR relaxation dispersion experiment is presented that uses methyl group probes as reporters of conformational exchange in highly deuterated, methyl-protonated proteins. Significantly larger dispersion profiles, by as much as a factor of nine, can be obtained relative to single-quantum approaches, thus offering very significant advantages in applications involving interconverting conformers with only small changes in structure or in studies of rare states that are at very low populations. Applications to a number of protein systems are presented where the utility of the method, including its improved sensitivity to chemical exchange processes, is established.

Rational Control of Conformational Distributions and Mixed-Valence Characteristics in Diruthenium Complexes.

Abstract: The electronic characteristics of mixed-valence complexes are often inferred from the shape of the inter-valence charge transfer (IVCT) band, which usually falls in the near infrared (NIR) region, and relationships derived from Marcus-Hush theory. These analyses typically assume one single, dominant molecular conformation. The NIR spectra of the prototypical delocalised (Class III Robin–Day mixed-valence) complexes [{Ru(pp)Cp’}2(μ-C≡C−C≡C)]+ ([1]+: Cp’=Cp, pp=(PPh3)2; [2]+: Cp’=Cp, pp=dppe; [3]+: Cp’=Cp*, pp=dppe) feature a ‘two-band’ pattern, which complicates band-shape analysis using these traditional methods. In the past, the appearance of sub-bands within or near the IVCT transition has been attributed to vibronic effects or localised d-d transitions. Quantum-chemical modelling of a series of rotational conformers of [1]+–[3]+ reveals the two components that contribute to the NIR absorption band envelope to be a π-π* transition and an MLCT transition. The MLCT components only gain appreciable intensity when the orientation of the half-sandwich ruthenium ligand spheres deviates from idealised cis (Ω P−Ru−Ru−P=0°) or trans (Ω P−Ru−Ru−P=180°) conformations. The increased steric demand of the supporting ligands, together with some underlying inter-phosphine ligand T-shaped CH⋅⋅⋅π stacking interactions across the series [1]+ to [2]+ to [3]+ results in local minima biased towards such non-idealised conformations of the metal-ligand fragments (Ω P−Ru−Ru−P=33–153°). Experimentally, this is indicated by appearance of multiple bands within the IR ν˜ (C≡C) band envelopes and increasing intensity of the higher-energy MLCT transition(s) relative to the π-π* transition across the series, and the appearance of a pronounced ‘two-band’ pattern in the experimental NIR absorption envelopes. These conformational effects and the methods of analysis presented here, which combine analysis of IR and NIR spectra with quantum-chemical calculations on a range of energetically similar conformational minima, are expected to be quite general for mixed-valence systems.

Anharmonic modeling of the conformation-specific IR spectra of ethyl, n-propyl, and n-butylbenzene

Abstract: Conformation-specific UV-IR double resonance spectra are presented for ethyl, n-propyl, and n-butylbenzene. With the aid of a local mode Hamiltonian that includes the effects of stretch-scissor Fermi resonance, the spectra can be accurately modeled for specific conformers. These molecules allow for further development of a first principles method for calculating alkyl stretch spectra. Across all chain lengths, certain dihedral patterns impart particular spectral motifs at the quadratic level. However, the anharmonic contributions are consistent from molecule to molecule and conformer to conformer. This transferability of anharmonicities allows for the Hamiltonian to be constructed from only a harmonic frequency calculation, reducing the cost of the model. The phenyl ring alters the frequencies of the CH2 stretches by about 15 cm−1 compared to their n-alkane counterparts in trans configurations. Conformational changes in the chain can lead to shifts in frequency of up to 30 cm−1.

Nucleotide Binding Preference of the Monofunctional Platinum Anticancer Agent Phenanthriplatin

Abstract: The monofunctional platinum anticancer agent phenanthriplatin generates covalent adducts with the purine bases guanine and adenine. Preferential nucleotide binding was investigated by using a polymerase stop assay and linear DNA amplification with a 163-base pair DNA double helix. Similarly to cisplatin, phenanthriplatin forms the majority of adducts at guanosine residues, but significant differences in both the number and position of platination sites emerge when comparing results for the two complexes. Notably, the monofunctional complex generates a greater number of polymerase-halting lesions at adenosine residues than does cisplatin. Studies with 9-methyladenine reveal that, under abiological conditions, phenanthriplatin binds to the N(1) or N(7) position of 9-methyladenine in approximately equimolar amounts. By contrast, comparable reactions with 9-methylguanine afforded only the N(7) -bound species. Both of the 9-methyladenine linkage isomers (N(1) and N(7) ) exist as two diastereomeric species, arising from hindered rotation of the aromatic ligands about their respective platinum-nitrogen bonds. Eyring analysis of rate constants extracted from variable-temperature NMR spectroscopic data revealed that the activation energies for ligand rotation in the N(1) -bound platinum complex and the N(7) -linkage isomers are comparable. Finally, a kinetic analysis indicated that phenanthriplatin reacts more rapidly, by a factor of eight, with 9-methylguanine than with 9-methyladenine, suggesting that the distribution of lesions formed on double-stranded DNA is kinetically controlled. In addition, implications for the potent anticancer activity of phenanthriplatin are discussed herein.

On the Stability of Cis- and Trans-2-Butene Isomers. An Insight Based on the FAMSEC, IQA, and ETS-NOCV Schemes.

Abstract: In the present account, the real space fragment attributed molecular system energy change (FAMSEC) approach, interacting quantum atoms energy decomposition scheme as well as molecular orbitals based the extended transition state scheme coupled with natural orbitals for chemical valence (ETS-NOCV) have been, for the first time, successfully used to delineate factors of importance for stability of the 2-butene conformers (cis-eq, cis-TS, trans-eq, trans-TS). Our results demonstrate that atoms of the controversial H-H contact in cis-eq (i) are involved in attractive interaction dominated by the exchange-correlation term, (ii) are weekly stabilized, (iii) show trends in several descriptors found in other typical H-bonds, and (iv) are part of most stabilized CH-HC fragment (loc-FAMSEC = -3.6 kcal/mol) with most favourably changed intrafragment interactions on trans-eq→cis-eq. Moreover, lower stability of cis-eq vs. trans-eq is linked with the entire HCCH (ethylenic) fragment which destabilized cis-eq (mol-FAMSEC, +3.9 kcal/mol) the most. Although the H-H contact can be linked with smaller, relative to trans-, rotational energy barrier in cis-2-butene, we have proven that to rationalize this phenomenon one must account for changes in interactions between various fragments that constitute the entire molecule. Importantly, we discovered a number of comparable trends in fundamental properties of equivalent molecular fragments on a methyl group rotation; for example, interaction between BP-free H-atoms in trans-eq (involving CH bonds of the methyl and ethylenic units) and BP-linked H-atoms in cis-eq. Clearly, rotational energy barrier cannot be entirely (i) rationalized by the properties of or (ii) attributed to the H-H contact in cis-eq. © 2016 Wiley Periodicals, Inc.

The Structure and Torsional Dynamics of Two Methyl Groups in 2-Acetyl-5-methylfuran as Observed by Microwave Spectroscopy.

Abstract: The molecular-beam Fourier transform microwave spectrum of 2-acetyl-5-methylfuran is recorded in the frequency range 2-26.5 GHz. Quantum chemical calculations calculate two conformers with trans or cis configuration of the acetyl group, both of which are assigned in the experimental spectrum. All rotational transitions split into quintets due to the internal rotations of two nonequivalent methyl groups. By using the program XIAM, the experimental spectra can be simulated with standard deviations within the measurement accuracy, and yield well-determined rotational and internal rotation parameters, inter alia the V3 potentials. Whereas the V3 barrier height of the ring-methyl rotor does not change for the two conformers, that of the acetyl-methyl rotor differs by about 100 cm-1 . The predicted values from quantum chemistry are only on the correct order of magnitude.

Gas-Phase Folding of a Prototypical Protonated Pentapeptide: Spectroscopic Evidence for Formation of a Charge-Stabilized β-Hairpin

Abstract: Ultraviolet and infrared-ultraviolet (IR-UV) double-resonance photofragment spectroscopy has been carried out in a tandem mass spectrometer to determine the three-dimensional structure of cryogenically cooled protonated C-terminally methyl esterified leucine enkephalin [YGGFL-OMe+H]+. By comparing the experimental IR spectrum of the dominant conformer with the predictions of DFT M05-2X/6-31+G(d) calculations, a backbone structure was assigned that is analogous to that previously assigned by our group for the unmodified peptide [Burke, N.L.; et al. Int. J. Mass Spectrom. 2015, 378, 196], despite the loss of a C-terminal OH binding site that was thought to play an important role in its stabilization. Both structures are characterized by a type II′ β-turn around Gly3-Phe4 and a γ-turn around Gly2, providing spectroscopic evidence for the formation of a β-hairpin hydrogen bonding pattern. Rather than disrupting the peptide backbone structure, the protonated N-terminus serves to stabilize the β-hairpin by posi...

Travelling-wave ion mobility and negative ion fragmentation of high-mannose N-glycans

Abstract: The isomeric structure of high-mannose N-glycans can significantly impact biological recognition events. Here, the utility of travelling-wave ion mobility mass spectrometry for isomer separation of high-mannose N-glycans is investigated. Negative ion fragmentation using collision-induced dissociation gave more informative spectra than positive ion spectra with mass-different fragment ions characterizing many of the isomers. Isomer separation by ion mobility in both ionization modes was generally limited, with the arrival time distributions (ATD) often showing little sign of isomers. However, isomers could be partially resolved by plotting extracted fragment ATDs of the diagnostic fragment ions from the negative ion spectra, and the fragmentation spectra of the isomers could be extracted by using ions from limited areas of the ATD peak. In some cases, asymmetric ATDs were observed, but no isomers could be detected by fragmentation. In these cases, it was assumed that conformers or anomers were being separated. Collision cross sections of the isomers in positive and negative fragmentation mode were estimated from travelling-wave ion mobility mass spectrometry data using dextran glycans as calibrant. More complete collision cross section data were achieved in negative ion mode by utilizing the diagnostic fragment ions. Examples of isomer separations are shown for N-glycans released from the well-characterized glycoproteins chicken ovalbumin, porcine thyroglobulin and gp120 from the human immunodeficiency virus. In addition to the cross-sectional data, details of the negative ion collision-induced dissociation spectra of all resolved isomers are discussed.

Characterization of Two Distinct Amorphous Forms of Valsartan by Solid-State NMR

Abstract: Valsartan (VAL) is an antihypertensive drug marketed in an amorphous form. Amorphous materials can have different physicochemical properties depending on preparation method, thermal history, etc., but the nature of such materials is difficult to study by diffraction techniques. This study characterizes two different amorphous forms of valsartan (AR and AM) using solid-state NMR (SSNMR) as a primary investigation tool, supported by solution-state NMR, FT-IR, TMDSC, and dissolution tests. The two forms are found to be clearly distinct, with a significantly higher level of structural arrangement in the AR form, as observed in (13)C, (15)N, and (1)H SSNMR. (13)C and (15)N NMR indicates that the fully amorphous material (AM) contains an approximately equal ratio of cis-trans conformers about the amide bond, whereas the AR form exists mainly as one conformer, with minor conformational "defects". (1)H ultrafast MAS NMR shows significant differences in the hydrogen bonding involving the tetrazole and acid hydrogens between the two materials, while (15)N NMR shows that both forms exist as a 1,2,3,4-tetrazole tautomer. NMR relaxation times show subtle differences in local and bulk molecular mobility, which can be connected with the glass transition, the stability of the glassy material, and its response to aging. Counterintuitively the fully amorphous material is found to have a significantly lower dissolution rate than the apparently more ordered AR material.

Water-Induced Structural Changes in Crown Ethers from Broadband Rotational Spectroscopy.

Abstract: The complexes of 12-crown-4 ether (12C4) with water, generated in a supersonic jet, have been studied using broadband Fourier transform microwave spectroscopy. Three 1:1 and one 1:2 clusters have been observed and their structures unambiguously identified through the observation of isotopologue spectra. The structures of the clusters are based on networks of O–H···O and C–H···O hydrogen bonds. The most abundant 1:1 cluster is formed from the most stable S4 symmetry conformer of 12C4, even though it is not the energetically favored water complex. Interestingly, the structures of the most stable water cluster and the other remaining observed 1:1 and 1:2 complexes are formed from the second or the fifth most abundant conformers of 12C4. This shows the existence of a mechanism that changes the conformation of 12C4 so that the host–guest interactions can be maximized, even for a “soft” ligand like water.

Effect of Conformers on Free Energies of Atmospheric Complexes

Abstract: In this article we show how to calculate free energies for atmospherically relevant complexes when multiple conformers and/or isomers are present. We explain why the thermal averaging methods used in several published works are incorrect. On the basis of our two sample cases, the sulfuric acid–pinic acid complex and the (H2SO4)3(NH3)3(H2O)4 cluster, we provide numerical evidence that the use of these incorrect formulas can result in errors larger than 1 kcal/mol. We recommend that if vibrational frequencies and thus Gibbs free energies of the individual conformers are unavailable, one should not attempt to correct for the presence of multiple conformers and instead use only the global minimum conformers for both reactants and products. On the contrary, if the free energies for the conformers are calculated for both reactants and products, their effect can be accounted for by the statistical mechanical methods presented in this article.

Fourier-transform microwave spectroscopy of a halogen substituted Criegee intermediate ClCHOO.

Abstract: Pure rotational spectra of the chloro-substituted Criegee intermediate (ClCHOO) were observed by Fourier-transform microwave spectroscopy. Two conformers (syn and anti) of the isolated molecule were identified from the rotational spectra of the parent and 37Cl and 13C isotopologues detected in natural abundance. Rotational constants, centrifugal distortion constants, and all components of the nuclear quadrupole coupling tensor were determined for both conformers. Structural features of the molecule have been rationalized with supporting ab initio calculations and the natural bond orbital analysis, which suggest that the conformational preferences are driven by hyperconjugative effects.

Probing the Methyl Torsional Barriers of the E and Z Isomers of Butadienyl Acetate by Microwave Spectroscopy.

Abstract: The Fourier transform microwave spectra of the E and Z isomers of butadienyl acetate were measured in the frequency range from 2 to 26.5 GHz under molecular-jet conditions. The most stable conformer of each isomer, in which all heavy atoms are located in a symmetry plane, was identified after analyzing the spectrum by comparison with the results from quantum-chemical calculations. The barriers to internal rotation of the acetyl methyl group were found to be 149.1822(20) and 150.2128(48) cm(-1) for the E and Z isomers, respectively, which are similar to that of vinyl acetate. A comparison between two theoretical approaches treating internal rotation, the rho axis method and combined axis method, was also performed. The influence of the alkyl R chain on the methyl torsional barriers in CH3 -COOR acetates was explored.

Energetic contribution to both acidity and conformational stability in peptide models

Abstract: The acidity of N-acyl amino acids is dependent upon the rotameric state of the amide bond. In this work we systematically investigated the acidity difference of the rotamers (ΔpKa) in the frames of various acetylated amino acids. Our results indicated a mutual interaction of two carbonyl groups of an attractive type. We observed conservative ΔpKas for acyclic amino acids (2.2–3.0 kJ mol−1), whereas in the case of alicyclic amino acids, the experimental values revealed a strong dependency on the structural context (1.5–4.4 kJ mol−1). In homologous amino acids (α-, β-, γ-, etc.), the strength of the attraction decays in an exponential fashion. Furthermore, the interaction can accumulate through a chain of amide bonds in a cascade fashion, as demonstrated by an Ac-Pro-Pro dipeptide. As a result, we demonstrate that ΔpKa is an experimental parameter to estimate increments in the carbonyl–carbonyl alignment, as determined by the amino acid or peptidyl context. This parameter is also important in understanding the roles of amino acids in both protein folding and translation in biological systems as well as their evolutionary appearance in the genetic code.

Aromatic embedding wins over classical hydrogen bonding - a multi-spectroscopic approach for the diphenyl ether-methanol complex.

Abstract: Dispersion interactions are omnipresent in intermolecular interactions, but their respective contributions are difficult to predict. Aromatic ethers offer competing docking sites for alcohols: the ether oxygen as a well known hydrogen bond acceptor, but also the aromatic π system. The interaction with two aromatic moieties in diphenyl ether can tip the balance towards π binding. We use a multi-spectroscopic approach to study the molecular recognition, the structure and internal dynamics of the diphenyl ether-methanol complex, employing infrared, infrared-ultraviolet and microwave spectroscopy. We find that the conformer with the hydroxy group of the alcohol binding to one aromatic π cloud and being coordinated by an aromatic C-H bond of the other phenyl group is preferred. Depending on the expansion conditions in the supersonic jet, we observe a second conformer, which exhibits a hydrogen bond to the ether oxygen and is higher in energy.

A zeolitic imidazolate framework with conformational variety: conformational polymorphs versus frameworks with static conformational disorder

Abstract: We show via structural considerations and DFT calculations that for a zeolitic imidazolate framework (ZIF) with sodalite (SOD) topology, [Zn(dcim)2]-SOD (dcim = 4,5-dichloroimidazolate), structural models of an infinite number of hypothetical conformational polymorphs with distinct linker orientations can be generated, which can be interconverted most likely only via reconstructive structural transitions. The relative total energies suggest that some of those polymorphs might be synthetically accessible. Efforts in that direction led to the synthesis of new trigonal 1 and previously known cubic 2 with improved crystallinity. According to structural analyses based on powder X-ray diffraction (PXRD) methods supported by NMR spectroscopy, 1 is the most stable of the theoretically predicted SOD-type framework conformers (isostructural to ZIF-7), whereas 2, at variance to a recent proposal, is a SOD-type material with a high degree of orientational disorder of the dcim linker units. The statistics of the linker orientations in 2 is close to that in 1, indicating that the disorder in 2 is not random. Rather crystals of 2 are likely twins consisting of nanoscopic domains of trigonal 1 that are deformed to a cubic metric, with linker disorder being located in the domain interfaces. As structural differences appear to be more related to characteristics of the real as opposed to the ideal crystal structures, we propose to not consider 1 and 2 as true conformational polymorphs. Systematic investigations of solvent mixtures led to the discovery of intermediate materials of 1 and 2. The PXRD patterns and SEM images indicate that they belong to a complete series of structural intermediates. Differences in the Ar adsorption/desorption behaviours reveal that 1, in contrast to 2, is a flexible ZIF framework.

Observation of a Dynamic G-Tetrad Flip in Intramolecular G-Quadruplexes.

Abstract: A MYC sequence forming an intramolecular G-quadruplex with a parallel topology was modified by the incorporation of 8-bromoguanosine (BrG) analogues in one of its outer G-tetrads. The propensity of the BrG analogues to adopt a syn glycosidic torsion angle results in an exceptional monomolecular quadruplex conformation featuring a complete flip of one tetrad while keeping a parallel orientation of all G-tracts as shown by circular dichroism and nuclear magnetic resonance spectroscopic studies. When substituting three of the four G-tetrad residues with BrG analogues, two coexisting quadruplex conformational isomers with an all-syn and all-anti outer G-quartet are approximately equally populated in solution. A dynamic interconversion of the two quadruplexes with an exchange rate (kex) of 0.2 s–1 is demonstrated through the observation of exchange crosspeaks in rotating frame Overhauser effect spectroscopy and nuclear Overhauser effect spectroscopy experiments at 50 °C. The kinetic properties suggest disrupti...

The molecular structure of phenetole studied by microwave spectroscopy and quantum chemical calculations

Abstract: A pulsed molecular beam Fourier transform microwave spectrometer operating in the frequency range 2–26.5 GHz was used to measure the spectrum of phenetole (ethyl phenyl ether or ethoxybenzene, C6H5OC2H5). The conformational landscape is completely determined by the orientations of the phenyl ring and the ethyl group. A two-dimensional potential energy surface was calculated at the MP2/6-311++G(d,p) level of theory. Two conformers were found: the trans conformer has a Cs symmetry, and the gauche conformer has the ethyl group tilted out of the phenyl plane by about 70°. Totally, 186 rotational transitions were assigned to the more stable planar trans conformer, and fitted using a semi-rigid rotor model to measure accuracy. Highly accurate rotational and centrifugal distortion constants were determined. Several method and basis set combinations were applied to check for convergence and to compare with the experimentally deduced molecular parameters.

Conformational distortion of α-phenylethyl amine in cryogenic matrices - a matrix isolation VCD study.

Abstract: The chiral amine α-phenylethyl amine (PEA) was isolated in cryogenic matrices and investigated using vibrational circular dichroism (VCD) and infrared spectroscopy. The potential energy surface (PES) of PEA features five different conformers connected by relatively low conformational transition states. Based on the IR spectra, it could be confirmed that all conformational energy barriers are passed at a deposition temperature of 20 K, and that only the global minimum conformation of PEA is populated in both argon and nitrogen matrices. However, differences in the calculated and experimental VCD spectra indicate deviations from the minimum structure by perturbation of the phenyl ring as well as of the amine orientation. The degree of the perturbation is found to also depend on the choice of the host gas, which shows the subtle influence of the environment on the conformational distortion of PEA.

Evolutionary Conserved Positions Define Protein Conformational Diversity

Abstract: Conformational diversity of the native state plays a central role in modulating protein function. The selection paradigm sustains that different ligands shift the conformational equilibrium through their binding to highest-affinity conformers. Intramolecular vibrational dynamics associated to each conformation should guarantee conformational transitions, which due to its importance, could possibly be associated with evolutionary conserved traits. Normal mode analysis, based on a coarse-grained model of the protein, can provide the required information to explore these features. Herein, we present a novel procedure to identify key positions sustaining the conformational diversity associated to ligand binding. The method is applied to an adequate refined dataset of 188 paired protein structures in their bound and unbound forms. Firstly, normal modes most involved in the conformational change are selected according to their corresponding overlap with structural distortions introduced by ligand binding. The subspace defined by these modes is used to analyze the effect of simulated point mutations on preserving the conformational diversity of the protein. We find a negative correlation between the effects of mutations on these normal mode subspaces associated to ligand-binding and position-specific evolutionary conservations obtained from multiple sequence-structure alignments. Positions whose mutations are found to alter the most these subspaces are defined as key positions, that is, dynamically important residues that mediate the ligand-binding conformational change. These positions are shown to be evolutionary conserved, mostly buried aliphatic residues localized in regular structural regions of the protein like β-sheets and α-helix.