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The dominant gas-phase conformer of [M+3H]3+ ions of the model peptide acetyl-PSSSSKSSSSKSSSSKSSSSK has been examined with ion mobility spectrometry (IMS), gas-phase hydrogen deuterium exchange (HDX), and mass spectrometry (MS) techniques. The [M+3H]3+ peptide ions are observed predominantly as a relatively compact conformer type. Upon subjecting these ions to electron transfer dissociation (ETD), the level of protection for each amino acid residue in the peptide sequence is assessed. The overall per-residue deuterium uptake is observed to be relatively more efficient for the neutral residues than for the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. In comparison, the N-terminal and C-terminal regions of the serine peptide show greater relative protection compared with interior residues. Molecular dynamics (MD) simulations have been used to generate candidate structures for collision cross section and HDX reactivity matching. Hydrogen accessibility scoring (HAS) for select structural candidates from MD simulations has been used to suggest conformer types that could contribute to the observed HDX patterns. The results are discussed with respect to recent studies employing extensive MD simulations of gas-phase structure establishment of a peptide system.ᅟ [ABSTRACT FROM AUTHOR]

Understanding the mechanisms behind amyloid protein aggregation in diseases, such as Parkinson's and Alzheimer's disease, is often hampered by the reproducibility of in vitro assays. Yet, understanding the basic mechanisms of protein misfolding is essential for the development of novel therapeutic strategies. We show here, that for the amyloid protein α-synuclein (aSyn), a protein involved in Parkinson's disease (PD), chromatographic buffers and storage conditions can significantly interfere with the overall structure of the protein and thus affect protein aggregation kinetics. We apply several biophysical and biochemical methods, including size exclusion chromatography (SEC), dynamic light scattering (DLS), and atomic force microscopy (AFM), to characterize the high molecular weight conformers formed during protein purification and storage. We further apply hydrogen/deuterium-exchange mass spectrometry (HDX-MS) to characterize the monomeric form of aSyn and reveal a thus far unknown structural component of aSyn at the C-terminus of the protein. Furthermore, lyophilizing the protein greatly affected the overall structure of this monomeric conformer. We conclude from this study that structural polymorphism may occur under different storage conditions, but knowing the structure of the majority of the protein at the start of each experiment, as well as the factors that may influence it, may pave the way to an improved understanding of the mechanism leading to aSyn pathology in PD. [ABSTRACT FROM AUTHOR]

The structure and spectral characteristics of the chimeric mixture of calixarene and pyrogallolarene (usually referred to as calix[4]tetrolarene) and its derivatives are studied employing the M06-2X-based density functional theory. Different conformers, viz., cone, partial cone, 1,2-alternate, and 1,3-alternate, were identified as the stationary point structures on their potential energy surfaces. Among these, the symmetric C4v cone conformer is found to be energetically favorable, which can be attributed to the cyclic array of hydrogen-bonding network in the calix[4]tetrolarene or its thia analogue. The substitution of methoxy groups at the upper rims of calix[4]tetrol- and thicalix[4]tetrol-arenes significantly influences the cooperative hydrogen-bonding network and conformational behavior of these hosts. The methoxy-substituted macrocycles show lowering in symmetry from C4v to C2v, engendering the pinched cone conformer to be the lowest energy structure. The enhanced solubility of the modified calix[4]tetrolarene macrocycles has been further explained from diminutive cooperative hydrogen bonding in its top rim compared to the pyrogallolarene, which is evidenced from the quantum theory of atoms in molecule and noncovalent interaction reduce density gradient method. Discernibly, the underlying cooperative hydrogen bonding emerges its signature in the characteristic vibrational patterns of the calixarene-based molecular scaffolds. The chemical shift parameters in their ¹H NMR spectra have further been characterized. [ABSTRACT FROM AUTHOR]

Density functional theory calculations allowed us to study alloxydim herbicide and to identify the most stable conformers, the factors that governs their stability, and the interconversion mechanisms among the most relevant conformers. The degradation chain involves, as a first step, the cleavage of the N-O bond and the formation of a stable intermediate difficult to characterize experimentally. The study performed also allowed us to identify the properties of this elusive intermediate and to determine that the dominant fragmentation process in the gas phase is the homolytic fragmentation. Stability of alloxydim conformers and homolytic fragments were also assessed in the water phase. Computed IR spectra were consistent with those observed experimentally. [ABSTRACT FROM AUTHOR]

Monomer-dimer equilibria of nitrosobenzene and 2-nitrosopyridine in gas phase and solution were studied by range of quantum chemical methods in an attempt to find the level of theory suitable for modeling dimerization reactions of aromatic C-nitroso compounds in general. The best agreement with the experimental standard reaction Gibbs energies was obtained with a combination of double-hybrid density functionals B2PLYP-D3, PBE0DH, and DSD-PBEB86, and basis sets of triple-ζ quality. Of all other tested functionals, global hybrid PBE0 behaved equally well, and proved to be more than adequate for at least preliminary work. Other tested methods either produced inferior results (MP2, MP4(SDQ), CCSD, G4(MP2), CBS-QBS, CBS-APNO), or were too demanding for practical use (CCSD(T)). Analysis of computationally obtained thermodynamic data reveal intricate details of these reactions. Both E- and Z-dimers have several different conformers, which all have different solvation energies. While in the gas phase the nitrosobenzene E-dimer is more stable that its Z-form, in chloroform, the Z-form is more stable. Gas-phase dimerization entropies are large and negative, so these reactions are strongly temperature dependent. In some cases, like with 2-nitrosopyridines, entropy and enthalpy terms essentially cancel each other out, allowing structural and media effects to significantly influence dimerization equilibria. [ABSTRACT FROM AUTHOR]

In this work, the study was performed with 37 gas-phase conformers of biotin and two biologically active conformers of biotin in the ligand–receptor complexes with astavidin and streptavidin. The ionization energies and photoelectron spectra of conformers were calculated by two methods: the general-R symmetry-adapted cluster-configuration interaction (general-R-SAC-CI) method and the outer-valence Green’s function (OVGF) method. The photoelectron spectrum of each conformer was calculated using basis set D95 (df,pd) for both methods. The simulated photoelectron spectra of free molecules and bioactive conformers calculated by the two methods were compared. Natural bonding orbital (NBO) calculations were also performed for the assignment of ionization bands of each conformer. NBO calculation indicated that the first to five ionization bands correspond to ionizations from orbitals localized in the two rings. The most important point about the ionization of all conformers is that the removal of an electron from the σ-bonding orbital (C–S) takes place above 10.0 eV. [ABSTRACT FROM AUTHOR]

Peptoid polymers are often crystalline in the solid-state as examined by X-ray scattering, but thus far, there has been no attempt to identify a common structural motif among them. In order to probe the relationship between molecular structure and crystal structure, we synthesized and analyzed a series of crystalline peptoid copolymers, systematically varying peptoid side-chain length (S) and main-chain length (N). We also examined X-ray scattering data from 18 previously reported peptoid polymers. In all peptoids, we found that the unit cell dimensions, a, b, and c, are simple functions of S and N: a (À) = 4.55, b (À) = [2.98]N + 0.35, and c (À) = [1.86]S + 5.5. These relationships, which apply to both bulk crystals and self-assembled nanosheets in water, indicate that the molecules adopt extended, planar conformations. Furthermore, we performed molecular dynamics simulations (MD) of peptoid polymer lattices, which indicate that all backbone amides adopt the cis conformation. This is a surprising conclusion, because previous studies on isolated molecules indicated an energetic preference for the trans conformer. This study demonstrates that when packed into supramolecular lattices or crystals, peptoid polymers prefer to adopt a regular, extended, all-cis secondary structure. [ABSTRACT FROM AUTHOR]

Both the role of the absolute configuration and the tendency of a chiral monomer to promote a certain helical scaffold in a poly(phenylacetylene) (PPA) have been evaluated to study the communication between two chiral monomers within a copolymer chain. Nineteen different PPA copolymer series -- 47 helical copolymers altogether -- were prepared to explore the existence of a chiral-to-chiral communication mechanism. From the data obtained, we found that communication between two different chiral monomers emerges when both exhibit two special features: (a) a different conformational composition -- one must exist in a single low-energy conformation ("chiral Sergeant") and the other must present two conformers ("chiral Soldier") -- and (b) the induction of a similar scaffold in the PPA, either cis-cisoidal or cis-transoidal. In the selected systems, the chiral Soldier includes the 4-ethynylanilide (para position) of either (R)- or (S)-2-methoxy-2-phenylacetic acid pendants characterized by their conformational flexibility (equilibrium between synperiplanar and antiperiplanar conformations). The chiral Sergeant contains the same chiral groups but linked to the backbone in meta position [3-ethynylanilide of (R)- or (S)-2-methoxy-2-phenylacetic acid] and is selected on the basis of its restricted antiperiplanar conformation. Incorporation of a very small amount (1%) of the Sergeant into a chain composed of just the Soldier transforms the originally axially racemic chain into a helix with strong sense preference (either M or P) that is determined by the absolute configuration of the Soldier. [ABSTRACT FROM AUTHOR]

The rotational spectrum of acrylic sulfuric anhydride (CH2═CHCOOSO2OH, AcrSA) has been observed using pulsed-nozzle Fourier transform microwave spectroscopy. The species was produced from the reaction between acrylic acid and sulfur trioxide in a supersonic jet. Spectroscopic constants are reported for both the s-cis- and s-trans-AcrSA conformers of the parent and monodeuterated (OD) isotopologues. Geometries were optimized for both conformers using M06-2X/6-311++G(3df,3pd) methods. Single-point energy calculations at the M06-2X geometries were calculated using the CCSD(T)/complete basis set method with double and triple extrapolation [CBS(D-T)]. Further calculations indicate that the anhydride results from a π2 + π2 + σ2 cycloaddition reaction within the acrylic acid-SO3 complex. Because the C═O double bond of the acrylic acid migrates from one of the COOH oxygens to the other during the reaction, the s-cis form of acrylic acid leads to the s-trans form of the anhydride and vice versa. With zero-point energy corrections applied to the CCSD(T) energies, the s-cis and s-trans forms of CH2═CHCOOSO2OH are 19.0 and 18.8 kcal/mol lower in energy than that of SO3 + their corresponding CH2═CHCOOH precursor conformation. The zero-point-corrected transition state energies for formation of the s-trans and s-cis anhydrides are 0.22 and 0.33 kcal/mol lower than those of the complexes of SO3 with s-cis and s-trans acrylic acid, respectively, indicating that the reaction is essentially barrierless. This system adds to a growing body of examples demonstrating that carboxylic acids readily add to SO3 in the gas phase to produce the corresponding carboxylic sulfuric anhydride. [ABSTRACT FROM AUTHOR]

In this study, we demonstrate the ability of polarization-difference Raman spectroscopy (PDRS) to detect dissolved free water molecules in a n-octacosane (n-C28H58) liquid-rich phase, and thus to determine its solubility, at temperatures and pressures relevant to the Fischer-Tropsch synthesis. Our results for the pure alkane reveal thermal decomposition above a temperature of 500 K as well as an increase of gauche conformers of the alkane chains with an increase in temperature. For binary homogeneous mixtures, raw spectra obtained from two different polarization scattering geometries did not show a relevant signal in the OH stretching frequency range. In contrast, isotropic spectra obtained from the PDRS technique reveal a narrow and tiny peak associated with the dangling OH bonds. Over the complete range of temperatures and pressures, no signature of hydrogen-bonded water molecules was observed in the isotropic Raman scattering intensities. A thorough investigation covering a large range of temperatures and pressures using PDRS signals showed that the higher the fraction of gauche conformers of hydrocarbon, the higher the solubility of water. The proportion of gauche and trans conformers was found to be water-concentration-independent, and the intensity of the OH-dangling peak increased linearly with increasing the vapor partial pressure of water. Therefore, we established a relation between a relevant intensity ratio and the concentration of water obtained from SAFT calculations. Contrary to the results from relevant literature, the calibration factor was found to be temperature-independent between 424 and 572 K. The isotropic Raman scattering intensities are corrected in order to provide a better representation of the vibrational density of states. The influence of correction of the isotropic scattering intensities on the solubility measurements as well as on the analysis of the molecular arrangement is discussed. [ABSTRACT FROM AUTHOR]

Calix[n]triazoles are developed as new derivatives in the calixarene family. Calixtriazole compounds 2-4 are synthesized using an iterative convergent strategy including an inter-/intramolecular copper(I)-catalyzed azide-alkyne cycloaddition reaction. Solid-state structures are clearly refined to give 1,2-alternate and partial cone conformations for calix[4]triazole and calix[5]triazole, respectively. Theoretical studies based on density functional theory (DFT) calculations indicated that intermolecular interactions are crucial in determining the conformers of the crystals, and the most stable conformers of calix[4]triazole, calix[5]triazole, and calix[6]triazole in the monomeric forms are 1,3-alternate, 1,3-alternate, and 1,3,5-alternate, respectively. [ABSTRACT FROM AUTHOR]

Isopropyl cyanide was recently detected in space as the first branched alkyl compound. Its abundance with respect to n-propyl cyanide in the Galactic center source Sagittarius B2(N2) is about 0.4. Astrochemical model calculations suggest that for the heavier homologue butyl cyanide the branched isomers dominate over the unbranched n-butyl cyanide and that 2-cyanobutane is the most abundant isomer. We have studied the rotational spectrum of 2-cyanobutane between 2 and 24 GHz using Fourier transform microwave spectroscopy and between 36 and 402 GHz employing (sub)millimeter absorption spectroscopy. Transitions of the lowest energy conformer were identified easily. Its rotational spectrum is very rich, and the quantum numbers J and Ka reach values of 111 and 73, respectively. This wealth of data yielded rotational and centrifugal distortion parameters up to tenth order, diagonal and one off-diagonal 14N nuclear quadrupole coupling parameters, and one nuclear spin-rotation coupling parameter. We have also carried out quantum chemical calculations in part to facilitate the assignments. The molecule 2-cyanobutane was not found in the present ALMA data of Sagittarius B2(N2), but it may be found in the more sensitive data that have been completed very recently in the ALMA Cycle 4. [ABSTRACT FROM AUTHOR]

Raman optical activity (ROA) spectroscopy combined with quantum-chemical simulations is a sensitive method to determine the absolute configuration and conformation of chiral molecules in solutions. However, the precision of this approach varies for different systems. In the present study, the reliability and numerical stability of decomposing experimental spectra into calculated subspectra is tested on the Ala-Ala dipeptide. Molecular dynamics (MD) snapshots of Ala-Ala/water clusters are averaged to account for solvent effects and molecular flexibility. Multiple experiments with protonated, zwitterionic, and deprotonated dipeptide forms and natural and d2- and d8-isotopically labeled dipeptides are used to verify the results and estimate the overall accuracy. Although the precision is still limited by experimental noise and computational error, a very close match between the observed and theoretical spectral shapes has been achieved. This enabled quantitative determination of conformer populations with a typical dispersion of 10%. The spectroscopy also demonstrated how the conformation depends on pH. The ROA results were more consistent than the Raman ones. Typically, the ROA analysis was more resistant to artifacts in the experiment, such as incomplete baseline subtraction. Conformer ratios predicted by MD agree fairly but not fully with the experimental ones. This indicates minor deficiencies in the Amber force field, particularly for the protonated dipeptide. Overall, the combination of ROA experiment and computational chemistry appears to be a robust tool providing deep insight into molecular structure. [ABSTRACT FROM AUTHOR]

We investigate the peptide AcPheAla5LysH+, a model system for studying helix formation in the gas phase, in order to fully understand the forces that stabilize the helical structure. In particular, we address the question of whether the local fixation of the positive charge at the peptide's C-terminus is a prerequisite for forming helices by replacing the protonated C-terminal Lys residue by Ala and a sodium cation. The combination of gas-phase vibrational spectroscopy of cryogenically cooled ions with molecular simulations based on density-functional theory (DFT) allows for detailed structure elucidation. For sodiated AcPheAla6, we find globular rather than helical structures, as the mobile positive charge strongly interacts with the peptide backbone and disrupts secondary structure formation. Interestingly, the global minimum structure from simulation is not present in the experiment. We interpret that this is due to high barriers involved in rearranging the peptide-cation interaction that ultimately result in kinetically trapped structures being observed in the experiment. [ABSTRACT FROM AUTHOR]

The ability of the COSMO-RS method to predict the relative stability of different conformers of the same species in solution was evaluated by comparing computational results with experimental conformer data for 105 molecules from 20 literature sources. The solvents CDCl3, CD2Cl2, benzene, toluene, ethyl ether, tetrahydrofuran, acetone, dimethylformamide, DMSO (and DMSO-d6), water, and ethanol were used (dictated by the solvents used in the literature). In the case of 16 molecules the quantitative conformer abundances were also available and were compared with the data from computations. The results show that although COSMO-RS reproduces the conformer abundances only very approximately, the most stable conformer is determined correctly in 103 cases out of 105. This result validates the use of COSMO-RS in a number of applications (distribution coefficients, vapor pressures, solubilities, etc.) where the most stable conformer of a molecule can be different in different phases and accounting for this difference is important for obtaining meaningful results. [ABSTRACT FROM AUTHOR]

Two enantiomers of 2-methyl-N-(1-thien-2-ylethyl)propane-2-sulfonamide (TSA) were synthesized, and their VCD, ROA, IR, and Raman spectra were registered. The solved (S)-TSA X-ray structure shows a disorder connected to the presence of two TSA conformers differing by a slight rotation of the thiophene ring. Two molecules in the unit cell of the monoclinic P21 crystal form a net of NH···OS and C*H···OS hydrogen bonds. Out of a series of computational levels tested to interpret the spectra, the B3LYP functional combined with the def2TZVP basis set satisfactorily reproduces the experimental VCD and ROA spectra. To simulate the VCD spectra of TSA enantiomers in KBr pellets, dimers and tetramers, with two different positions of the thiophene ring, were considered. The VCD spectra measured in CDCl3 are completely different from those taken in KBr due to the conformational freedom of TSA in chloroform. Seven TSA conformers fall into two groups of opposite configurations at the pyramidal N atom forming the additional stereogenic center. However, the barriers between conformers in each group are lower than the energy of thermal motions at 300 K. Thus, all conformers, but the most stable in each group, are likely to be metastable states. The calculated IR, VCD, Raman, and ROA spectra of the conformers depend not only on the type of stereogenic N atom but also on the thiophene ring rotation. Yet, they are likely to coexist because of low barriers between them. Three approaches were tested to reproduce the chiroptical spectra in solution using PCM and hybrid solvation models. As a consequence, it was found that a model in which all conformers contribute to the spectra with equal population factors seems to best reproduce the experimental data. Such a result suggests that in a dissolved state in 300 K TSA occurs in a very shallow potential well and all of its conformers coexist. [ABSTRACT FROM AUTHOR]

Enantiopure alleno-acetylenic cage (AAC) receptors with a resorcin[4]arene scaffold, from which four homochiral alleno-acetylenes converge to shape a cavity closed by a four-fold OH-hydrogen-bonding array, form a highly ordered porous network in the solid state. They enable the complexation and co-crystallization of otherwise non-crystalline small molecules. This paper analyzes the axial conformers of monohalo- and (±)-trans-1,2-dihalocyclohexanes, bound in the interior cavity of the AACs, on the atomic level in the solid state and in solution, accompanied by accurate calculations. The dihedral angles ϑa,a (X-C(1)-C(2)-X/H) of the axial/diaxial conformers deviate substantially from 180°, down to 144°, accompanied by strong flattening of the ring dihedral angles. Structure optimization of the isolated guest molecules demonstrates that the non-covalent interactions with the host hardly affect the dihedral angles, validating that the host is an ideal means to study the elusive axial/diaxial conformers. X-ray co-crystal structures of AACs further allowed for a detailed investigation, both experimentally and theoretically, on the interplay between space occupancy, guest conformation, and chiral recognition based purely on dispersion forces and weak C--X···π (X = Cl, Br, I) and C--X···||| (acetylene) contacts (X = Cl, Br). The theoretical analysis of the non-covalent interactions between host and guest confirmed the high shape complementarity with fully enveloping dispersive interactions between the binding partners, rationalizing the high degree of enantioselectivity in the previously communicated complexation of (±)-trans-1,2-dimethylcyclohexane. This study also showed that (±)-trans-1,2-dihalocyclohexanes (X = Cl, Br) engage in significant halogen bonding (XB) interactions C--X···||| with the hosts. Slow host-guest exchange on the NMR time scale enabled the characterization of the encapsulated guests in solution, demonstrating that the complexes have identical geometries to those seen in the solid state, with the guests bound in axial/diaxial conformations. [ABSTRACT FROM AUTHOR]

Excited state ultrafast conformational reorganization is recognized as an important phenomenon that facilitates light-induced functions of many molecular systems. This report describes the femtosecond and picosecond conformational relaxation dynamics of middle-ring and terminal ring twisted conformers of the acetylene π-conjugated system bis(phenylethynyl)benzene, a model system for molecular wires. Through excitation wavelength dependent, femtosecond-transient absorption measurements, we found that the middle-ring and terminal ring twisted conformers relax at femtosecond (400-600 fs) and picosecond (20-24 ps) time scales, respectively. Actinic pumping into the red flank of the absorption spectrum leads to excitation of primarily planar conformers, and results in very different excited state dynamics. In addition, ultrafast Raman loss spectroscopic studies revealed the vibrational mode dependent relaxation dynamics for different excitation wavelengths. To corroborate our experimental findings, DFT and time-dependent DFT calculations were carried out. The Franck-Condon simulation indicated that the vibronic structure observed in the electronic absorption and the fluorescence spectra are due to progressions and combinations of several vibrational modes corresponding to the phenyl ring and the acetylenic groups. Furthermore, the middle ring torsional rotation matches the room-temperature electronic absorption, in stark contrast to the terminal ring torsional rotation. Finally, we show that the middle-ring twisted conformer undergoes femtosecond torsional planarization dynamic, whereas the terminal rings relax on a few tens of picosecond time scale. [ABSTRACT FROM AUTHOR]

The significance of the heteroatom in influencing the acidity and binding affinity of the C(2)–H donor in five-membered heterocyclic rings is explored. The water clusters of benzoxazole (BOX) are studied in a supersonic jet by IR–UV double resonance spectroscopy and compared with those of benzimidazole (BIM) and its N-methyl derivative (MBIM). Two conformers are identified for the monohydrated cluster, both of which are O–H···N bound and differ in their orientation with respect to the intermolecular hydrogen bond. IR spectroscopy of the doubly hydrated cluster shows the presence of an intensity enhanced C(2)–H (carbon atom between the heteroatoms in the five-membered ring) stretching mode in addition to two red-shifted bound OH stretches, indicating that the water molecules form a hydrogen-bonded bridge encompassing the N acceptor and the weakly activated C(2)–H bond in oxazole. Comparison of the topological parameters of electron density, natural bond orbital analyses, and computed binding energies of the analogous hydrated structures of BOX, BIM, and MBIM indicates that the C(2)–H bond in the former is a more potent H-bond donor. [ABSTRACT FROM AUTHOR]

Conformers of carboxyl radical (HOCO) have been studied by IR spectroscopy in argon and nitrogen matrices. In an argon matrix, only the lower-energy conformer trans-HOCO is observed, whereas both cis and trans conformers are found for deuterated carboxyl radical DOCO. In a nitrogen matrix, both conformers of HOCO and DOCO isotopologues can be prepared, indicating strong stabilization of the higher-energy cis conformer by a nitrogen matrix. Selective vibrational excitation promotes the trans-to-cis and cis-to-trans conversions of DOCO in an argon matrix and HOCO and DOCO in a nitrogen matrix, which is the first conformational photoswitching of an open-shell species. In a nitrogen matrix, the cis-to-trans and trans-to-cis conversions of HOCO is also found upon broadband IR light of the spectrometer, and the ratio of the quantum yields of these processes is about 3.3. The photoswitching peculiarities are in agreement with the available theoretical energy barriers. The higher-energy cis conformer decays to the lower-energy trans conformer via hydrogen-atom tunneling through the torsional barrier, which is also a unique observation for an open-shell species. The tunneling mechanism of the cis-to-trans switching is supported by the low-temperature limit of the reaction rate and by the H/D kinetic isotope effect. Our results suggest a large difference in the H/D kinetic isotope effects in nitrogen and argon matrices (∼5 and >100, respectively). The stabilizing effect on cis-DOCO by a nitrogen matrix (by 2 orders of magnitude versus an argon matrix) is much smaller than that on cis-HOCO (estimated to be >104). [ABSTRACT FROM AUTHOR]

The ground-state rotational spectrum of propene-3-d1, CH2...CHCH2D, was measured by Fourier transform microwave spectroscopy. Transitions were assigned for the two conformers, one with the D atom in the symmetry plane (S) and the other with the D atom out of the plane (A). The energy difference between the two conformers was calculated to be 6.5 cm-1, the S conformer having lower energy. The quadrupole hyperfine structure due to deuterium was resolved and analyzed for both conformers. The experimental quadrupole coupling and the centrifugal distortion constants compared favorably to their ab initio counterparts. Ground-state rotational constants for the S conformer are 40582.157(9), 9067.024(1), and 7766.0165(12) MHz. Ground-state rotational constants for the A conformer are 43403.75(3), 8658.961(2), and 7718.247(2) MHz. For the A conformer, a small tunneling splitting (19 MHz) due to internal rotation was observed and analyzed. Using the new rotational constants of this work as well as those previously determined for the 13C species and for some deuterium-substituted species from the literature, a new semiexperimental equilibrium structure was determined and its high accuracy was confirmed. The difficulty in obtaining accurate coordinates for the out-of-plane hydrogen atom is discussed. [ABSTRACT FROM AUTHOR]

Intrinsic fluctuations of a protein enable it to sample a large repertoire of conformers including the open and closed forms. These distinct forms of the protein called conformational substates pre-exist together in equilibrium as an ensemble independent from its ligands. The role of ligand might be simply to alter the equilibrium toward the most appropriate form for binding. Normal mode analysis is proved to be useful in identifying the directions of conformational changes between substates. In this study, we demonstrate that the ratios of normalized weights of a few normal modes driving the protein between its substates can give insights about the ratios of kinetic conversion rates of the substates, although a direct relation between the eigenvalues and kinetic conversion rates or populations of each substate could not be observed. The correlation between the normalized mode weight ratios and the kinetic rate ratios is around 83% on a set of 11 non-enzyme proteins and around 59% on a set of 17 enzymes. The results are suggestive that mode motions carry intrinsic relations with thermodynamics and kinetics of the proteins. [ABSTRACT FROM AUTHOR]

The design of innovative combustion processes relies on a comprehensive understanding of biodiesel oxidation kinetics. The present study aims at unraveling the reaction mechanism involved in the epoxidation of a realistic biodiesel surrogate, methyl trans-3-hexenoate, by hydroperoxy radicals using a bottom-up theoretical kinetics methodology. The obtained rate constants are in good agreement with experimental data for alkene epoxidation by HO2. The impact of temperature and pressure on epoxidation pathways involving H-bonded and non-H-bonded conformers was assessed. The obtained rate constant was finally implemented into a state-of-the-art detailed combustion mechanism, resulting in fairly good agreement with engine experiments. [ABSTRACT FROM AUTHOR]

Benzene dimer is a prototype to study intermolecular interactions between aromatic systems. Owing to the weak interactions between the molecules within the dimer, several conformational geometries are nearly isoenergetic and thus coexist even at low temperatures. Furthermore, standard spectroscopies are unable to distinguish between them. In this work, we study the electronic relaxation processes following inner-valence ionization of benzene and the lowest conformers of benzene dimer. We show that the kinetic energy distributions of the secondary electrons emitted via two autoionization mechanisms, namely, the Auger and the intermolecular coulombic decay (ICD) effects, provide a means to probe the conformers of benzene dimer. The proposed spectroscopy opens the way to a better characterization of weakly bound molecular clusters. [ABSTRACT FROM AUTHOR]

Based on a small test system, (R)-CH(OH)(OO·)CH2CHO, we have developed a cost-effective approach to the practical implementation of multiconformer transition state theory for peroxy radical hydrogen shift reactions at atmospherically relevant temperatures. While conformer searching is crucial for accurate reaction rates, an energy cutoff can be used to significantly reduce the computational cost with little loss of accuracy. For the reaction barrier, high-level calculations are needed, but the highest level of electronic structure theory is not necessary for the relative energy between conformers. Improving the approach to both transition state theory and electronic structure theory decreases the calculated reaction rate significantly, so low-level calculations can be used to rule out slow reactions. Further computational time can be saved by approximating the tunneling coefficients for each transition state by only that of the lowest-energy transition state. Finally, we test and validate our approach using higher-level theoretical values for our test system and existing experimental results for additional peroxy radical hydrogen shift reactions in three slightly larger systems. [ABSTRACT FROM AUTHOR]

Exploration of interfacial hydration networks of zwitterion and nonionized trialanine has been performed using DFT-M062X quantum chemical computations explicitly considering up to 41 water molecules. The step-by-step water molecules peptide surrounding, carried out for unfolded extended (β), polyproline II (PPII) conformations reveals the crucial importance of explicit solvent effects in stabilizing the zwitterion form and the left-handed PPII-helix ubiquitously found at room temperature for short polyalanines. Hydration effects are much greater for the ionized form of the peptide; thus, the zwitterion is about 10 kcal mol-1 more stable than the nonionized form. For the β → PPII transformation, the two components of free Gibbs energy act in the opposite direction; thus, it is favored by enthalpy but not by entropy. These findings agree with experimental data that report an equilibrium between these conformers modulated by temperature. Thermodynamic functions of the four conformers (β-β, β-PPII, PPII−β, and PPII-PPII) for zwitterion trialanine are similar to those derived for the protonated one (Ala3H+); therefore, the peptidic conformation is independent of the pH of the solution. Rather, it reflects the high propensity of alanine toward PPII helix. The enthalpic preference of the PPII has electrostatic origin and it is owing to a more favorable interaction of dipole of each peptidic residue with water dipole of H-bonded molecules. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The microwave spectra of two conformers of N,N-diethylpropionamide were recorded using a molecular beam Fourier transform microwave spectrometer operating in the frequency range 2-26.5 GHz. Hyperfine splittings arising from the 14N quadrupole coupling effect were observed and analyzed. Fits using a rigid rotor model with centrifugal distortion correction and first-order perturbation approach for the quadrupole coupling yielded highly accurate molecular parameters and standard deviations within the measurement accuracy for both conformers. Complementary quantum chemical calculations were carried out for a conformational analysis, theoretical values of the spectroscopic constants, and the 14N nuclear quadrupole coupling constants. [ABSTRACT FROM AUTHOR]

Because of both experimental and computational challenges, protonated tryptophan has remained the last aromatic amino acid for which the intrinsic structures of low-energy conformers have not been unambiguously solved. The IR-IR-UV hole-burning spectroscopy technique has been applied to overcome the limitations of the commonly used IR-UV double resonance technique and to measure conformer-specific vibrational spectra of TrpH+, cooled to T = 10 K. Anharmonic ab initio vibrational spectroscopy simulations unambiguously assign the dominant conformers to the two lowest-energy geometries from benchmark coupled-cluster structure computations. The match between experimental and ab initio spectra provides an unbiased validation of the calculated structures of the two experimentally observed conformers of this benchmark ion. Furthermore, the vibrational spectra provide conformer-specific signatures of the stabilizing interactions, including hydrogen bonding and an intramolecular cation-π interaction. [ABSTRACT FROM AUTHOR]

The rotational spectra of four conformers (At, Ag, Et, Eg) of the tertiary alcohol 1-methylcyclohexanol were assigned by pulsed jet Fourier transform microwave spectroscopy. The transitions of two gauche conformers were split in two separated component lines, but it was not possiblefrom the available measured transitionsto accurately determine their vibrational ΔE0+0- ground-state splittings, respectively. In addition, the rotational spectra of the four OD deuterated isotopologues were measured and assigned. For the gauche species of this isotopologue we were able to determine the tunneling splittings, ΔE0+0-(Ag, OD) = 15.581(5) GHz and ΔE0+0-(Eg, OD) = 18.17(3) GHz, respectively. From these splittings the inversion barriers for Ag and Eg were determined, by using a flexible model, to be B2(Ag) = 356(10) and B2(Eg) = 320(10) cm-1, respectively. [ABSTRACT FROM AUTHOR]

The microwave spectrum of 2-propynylhydrazine (HCCCH2NHNH2) was investigated in the 23-124 GHz spectral interval. The spectra of two conformers denoted I and II were assigned. I is the lower-energy form, and relative intensity measurements yielded an internal energy difference of 3.0(4) kJ/mol between I and II. The spectra of the ground and five vibrationally excited states were assigned for I, whereas only the spectrum of the ground vibrational state was assigned for II. Both I and II are each stabilized simultaneously by two intramolecular hydrogen bonds. The first of these hydrogen bonds is formed between the hydrogen atom of the −NH- part of the hydrazino group, and the second internal hydrogen bond is formed between one of the hydrogen atoms of the −NH2 part. The π-electrons of the triple bond is thus shared by these two hydrogen atoms. The shortest contact between a hydrogen atom of the hydrazino group and the π-electrons of the ethynyl group is found in lower-energy conformer I. The conformational properties of 2-propynylhydrazine were explored by MP2/cc-pVTZ and CCSD/cc-pVQZ calculations. The CCSD method predicts that seven rotameric forms exist for this compound. Five of these rotamers are stabilized by internal hydrogen bonding. The simultaneous sharing of the π-electrons of the triple bond by two hydrogen atoms occurs only in Conformers I and II, which are predicted to be the two forms with the lowest energies, with I 2.52 kJ/mol lower in energy than II. The effective rotational constants of the ground vibrational states of I and II were predicted by a combination of MP2 and CCSD calculations, whereas centrifugal distortion constants and vibration-rotation constants were calculated by the MP2 method. The theoretical spectroscopic constants are compared with the experimental counterparts. It is concluded that more refined calculations are necessary to obtain complete agreement. [ABSTRACT FROM AUTHOR]

In nature, the folding of oligomers and polymers is used to generate complex three-dimensional structures, yielding macromolecules with diverse functions in catalysis, recognition, transport, and charge- and energy-transfer. Over the past 20--30 years, chemists have sought to replicate this strategy by developing new foldamers: oligomers that fold into well-defined secondary structures in solution. A wide array of abiotic foldamers have been developed, ranging from non-natural peptides to aromatics. The ortho-phenylenes represent a recent addition to the family of aromatic foldamers. Despite their structural simplicity (chains of benzenes connected at the ortho positions), it was not until 2010 that systematic studies of o-phenylenes showed that they reliably fold into helices in solution (and in the solid state). This conformational behavior is of fundamental interest: o-Arylene and o-heteroarylene structures are found embedded within many other systems, part of an emerging interest in sterically congested polyphenylenes. Further, o-phenylenes are increasingly straightforward to synthesize because of continuing developments in arene--arene coupling, the Asao--Yamamoto benzannulation, and benzyne polymerization. In this Account, we discuss the folding of o-phenylenes with emphasis on features that make them unique among aromatic foldamers. Interconversion between their different backbone conformers is slow on the NMR time scale around room temperature. The 1H NMR spectra of oligomers can therefore be deconvoluted to give sets of chemical shifts for different folding states. The chemical shifts are both highly sensitive to conformation and readily predicted using ab initio methods, affording critical information about the conformational distribution. The picture that emerges is that o-phenylenes fold into helices with offset stacking between every third repeat unit. In general, misfolding occurs primarily at the oligomer termini (i.e., "frayed ends"). Because of their structural simplicity, the folding can be described by straightforward models. The overall population can be divided into two enantiomeric pools, with racemization and misfolding as two distinct processes. Examination of substituent effects on folding reveals that the determinant of the relative stability of different conformers is (offset) aromatic stacking interactions parallel to the helical axis. That is, the folding of o-phenylenes is analogous to that of α-helices, with aromatic stacking in place of hydrogen bonding. The folding propensity can be tuned using well-known substituent effects on aromatic stacking, with moderate electron-withdrawing substituents giving nearly perfect folding. The combination of a simple folding mechanism and readily characterized conformational populations makes o-phenylenes attractive structural motifs for incorporation into more-complex architectures, an important part of the next phase of foldamer research. [ABSTRACT FROM AUTHOR]

The coexistence of two conformers in perfluoropropanoyl fluoride, CF3CF2C(O)F, differing in the CC-CF dihedral angle (gauche 85(10)% and anti 15(10)%), has been determined by means of gas-phase electron diffraction (GED). Quantum-chemical calculations performed at the MP2 and B3LYP approximations and cc-pVTZ basis sets reproduce the experimental values with confidence. By contrast, FTIR spectra give no clear evidence for the anti-conformer in the gas phase. Information on this less abundant but stable rotamer is obtained from matrix-isolation/FTIR spectroscopy and liquid Raman spectroscopy. In situ crystallization and single-crystal X-ray diffraction (XRD) data reveal the presence of solely the gauche-conformation in the solid state. A set of intermolecular interactions including C=O...C=O, C-F...F-C, and F...C=O is detected. The nature of bonding and the relative stabilities of gauche- and anti-conformers are explored using natural bond orbitals. [ABSTRACT FROM AUTHOR]

Shape-persistent macrocycles are attractive functional targets for synthesis, molecular recognition, and hierarchical self-assembly. Such macrocycles are noncollapsible and geometrically well-defined, and they are traditionally characterized by having repeat units and low conformational flexibility. Here, we find it necessary to refine these ideas in the face of highly flexible yet shape-persistent macrocycles. A molecule is shape-persistent if it has a small change in shape when perturbed by external stimuli (e.g., heat, light, and redox chemistry). In support of this idea, we provide the first examination of the relationships between a macrocycle's shape persistence, its conformational space, and the resulting functions. We do this with a star-shaped macrocycle called cyanostar that is flexible as well as being shape-persistent. We employed molecular dynamics (MD), density functional theory (DFT), and NMR experiments. Considering a thermal bath as a stimulus, we found a single macrocycle has 332 accessible conformers with olefins undergoing rapid interconversion by up-down and in-out motions on short time scales (0.2 ns). These many interconverting conformations classify single cyanostars as flexible. To determine and confirm that cyanostars are shape-persistent, we show that they have a high 87% shape similarity across these conformations. To further test the idea, we use the binding of diglyme to the single macrocycle as guest-induced stimulation. This guest has almost no effect on the conformational space. However, formation of a 2:1 sandwich complex involving two macrocycles enhances rigidity and dramatically shifts the conformer distribution toward perfect bowls. Overall, the present study expands the scope of shape-persistent macrocycles to include flexible macrocycles if, and only if, their conformers have similar shapes. [ABSTRACT FROM AUTHOR]

High field asymmetric waveform ion mobility spectrometry (FAIMS), also known as differential ion mobility spectrometry, is emerging as a tool for biomolecular analysis. In this article, the benefits and limitations of FAIMS for protein analysis are discussed. The principles and mechanisms of FAIMS separation of ions are described, and the differences between FAIMS and conventional ion mobility spectrometry are detailed. Protein analysis is considered from both the top-down (intact proteins) and the bottom-up (proteolytic peptides) perspective. The roles of FAIMS in the analysis of complex mixtures of multiple intact proteins and in the analysis of multiple conformers of a single protein are assessed. Similarly, the application of FAIMS in proteomics and targeted analysis of peptides are considered. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

A detailed Raman study has been carried out on the ionic liquid 1-butyl-1-methylpyrrolidinium bis(trifluoromethanesulfonyl)imide (PYR14-TFSI) over a wide pressure (0-8 GPa) and temperature (100-300 K) range. The explored thermodynamic region allowed us to study the evolution of the system across different solid and liquid phases. Calculated Raman spectra remarkably helped in the spectral data analysis. In particular, the pressure behavior of the most intense Raman peak and the shape analysis of the ruby fluorescence (used as a local pressure gauge) allowed us to identify a liquid-solid transition around 2.2 GPa at T = 300 K. The low-frequency Raman signal as well as the absence of remarkable spectral shape modifications on crossing the above threshold and the comparison with the spectra of the crystalline phase suggest a glassy nature of the high-pressure phase. A detailed analysis of the pressure dependence of the relative concentration of two conformers of TFSI allowed us to obtain an estimate of the volume variation between trans-TFSI and the smaller cis-TFSI, which is the favored configuration on applying the pressure. Finally, the combined use of both visual inspection and Raman spectroscopy confirmed the peculiar sequence of phase transitions observed as a function of temperature at ambient pressure and the different spectral/morphological characteristics of the two crystalline phases. [ABSTRACT FROM AUTHOR]

Recently an X-ray crystallographic structure of a single-domain antibody was reported with the protein chain trapped in a rare homodimeric form. One of the conformers appears to exhibit a misfolded region, and thus presumably the configurational stability is less favorable. To investigate whether simulation methods can detect any difference between the conformers and buttress the notion that one conformation is trapped on a pathway that incurs lower activation energy to unfold, adaptive temperature-based replica exchange simulations were applied to each chain to model conformational transitions. Simulation results found that the observed crystallographic difference between the two chains in the complementarity determining region CDR2 induces a stark distinction in conformational populations on the energy landscape. An appraisal of the energetic difference between the CDR2 conformations at 300 K revealed a localized order-disorder free-energy transition of roughly equivalent to two peptide hydrogen bonds in solution. It was also found that interconversion between the conformers is slower than the rate to unfold and that near an unfolding transition temperature one conformer retained a greater fraction of native-like contacts and energy over a longer time span before fully populating the denatured state, thus verifying the coexistence of a metastable conformation in the crystallographic assembly. [ABSTRACT FROM AUTHOR]

Carbon-carbon bond is one of the most ubiquitous molecular building blocks for natural and man-made materials. Rotational isomerization is fundamentally important for understanding the structure and reactivity of chemical and biological molecules. Reported herein is the first demonstration that a single C-C bond does not rotate in water. The two distal C-S bonds in both 1,2-ethanedithiolate (-S-CH2-CH2-S-, 1,2-EDT2-) and 2,3-butanedithiolate (2,3-BuDT2-) are exclusively in the trans conformer with reference to their respective center single C-C bond. In contrast, both trans and gauche conformers are observed in neutral 1,2-ethanedithiol (1,2-EDT) and 2, 3-butanedithiol (2,3-BuDT). The insight from this work should be important for understanding the charge effect on the molecular conformation in aqueous solutions. [ABSTRACT FROM AUTHOR]

The structural preference of [7]circulene is analyzed by taking into account vibronic interactions. DFT calculations reveal that pseudo-Jahn-Teller effects cause the D7h-symmetry structure to relax to C2- and Cs-symmetry structures, which are both ca. 9 kcal/mol lower in energy than the D7h structure. In energy terms, the C2-symmetry structure is 0.05 kcal/mol lower than that of the Cs-symmetry. The active vibrations are attributed to low-frequency puckering modes that are coupled with π-σ excitation states. The optical activities of the C2-symmetry structure were simulated by configuration interaction calculations, and the simulated CD/ORD spectra were reasonable and consistent with the experimental data. The optical rotatory strengths obeyed the helix rule; that is, the left-handed helix shows negative Cotton effects through the antisymmetric excited states. The calculated spectra will serve as a foundation for further investigation of optical activities of negatively curved structures. [ABSTRACT FROM AUTHOR]

Novel poly(l-lysine)-block-poly(l-proline) (PLL-b-PLP)-basedmaterials with all PLPhelical conformers, i.e., PLP II and the rare PLP I are here reported.Electrostatic supramolecular complexation of the adjacent cationicPLL with anionic molecules bearing DNA analogue H-bonding functionalities,such as deoxyguanosine monophosphate (dGMP), preserves the extendedPLP II helix, and the complexed molecule is locked and held in positionby orthogonal shape-persistent hydrogen-bonded dGMP ribbons and theirextended π-stacking. The branched anionic surfactant dodecylbenzenesulfonicacid (DBSA) on the other hand, introduces periodicity frustrationand interlayer plasticization, leading to a reversed mutarotationto the more compact PLP I helix by complexation, without externalstimuli, and is here reported for the first time. We foresee thatour findings can be used as a platform for novel molecularly adaptivefunctional materials, and could possibly give insight in many proline-relatedtransmembrane biological functions. [ABSTRACT FROM AUTHOR]

A crucial step in the mechanism for oxygen evolution in the Photosystem II complex resides in the transition from the S2 state to the S3 state of Kok–Joliot’s cycle, in which an additional water molecule binds to the cluster. On the basis of computational chemistry calculations on Photosystem II models, we propose a reorganization mechanism involving a hydroxyl (W2) and a μ2-oxo bridge (O5) that is able to link the closed cubane S2B intermediate conformer to the S3 open cubane structure. This mechanism can reconcile the apparent conflict between recently reported water exchange and electron paramagnetic resonance experiments, and theoretical studies. [ABSTRACT FROM AUTHOR]

Gas-phase infrared measurements ofdiacetone diperoxide (DADP)indicate a chair conformation with less than 5% of the predicted twistconformer. Vibrational frequencies are very similar to those previouslymeasured in the solid state. Solution NMR measurements using 2D exchangespectroscopy (EXSY) also set a very low maximum limit on the equilibriumpopulation of the twist conformer, with a room-temperature free-energydifference in excess of 14.5 kJ/mol. These experimental results arein accord with high-level quantum calculations incorporating fullthermochemistry and solvation effects, which indicate a free-energydifference in the range of 14.7–17.5 kJ/mol in polar solvents. [ABSTRACT FROM AUTHOR]

A molecular seesaw balance 1·MeI has been developedto measure pyridinium−π interactions. This balance adoptstwo distinct conformers, Aand B, whichare stabilized by a cation−π interaction and a π–πinteraction, respectively. The conformer ratio was determined on thebasis of the averaged 3Jcoupling constantsfor H1–C–C–H2 and the corresponding boundary Jvalues for conformers Aand B. The effects of the solvent and the counteranion on the ΔGvalues were investigated using this molecular balance.Thermodynamic parameters obtained from a van’t Hoff plot helpedus to better understand the solvent and counteranion effects. [ABSTRACT FROM AUTHOR]

Microwavespectra for a higher-energy conformer of cyclopropanecarboxylicacid (CPCA) were measured using a Flygare–Balle-type pulsed-beamFourier transform microwave spectrometer. The rotational constants(in megahertz) and centrifugal distortion constants (in kilohertz)for this higher-energy conformer are A= 7452.3132(57), B= 2789.8602(43), C= 2415.0725(40), DJ= 0.29(53), and DJK= 2.5(12). Differences between rotationalconstants for this excited-state conformation and the ground stateare primarily due to the acidic OH bond moving from a position cisrelative to the cyclopropyl group about the C1–C9bond to the more stable trans conformation. Calculationsindicate that the relative abundance of the higher-energy state shouldbe 15% to 17% at room temperature, but the observed relative abundancefor the supersonic expansion conditions is about 1%. The measurementsof rotational transitions for the trans form of CPCA were extendedto include all of the unique 13C singly substituted positions.These measurements, along with previously measured transitions ofthe parent and −OD isotopologues, were used to determine abest-fit gas-phase structure. [ABSTRACT FROM AUTHOR]

Quantumchemical calculations have been carried out to investigatethe gas-phase structure, stability, and decomposition of the two simplestalkanediols, methanediol and 1,1-ethanediol, in the presence of variouscatalysts. Three different conformers for monomeric alkanediols namely cis, trans, and trans′were considered. The calculations reveal that alkanediols may existnot only as monomers but also as dimers that have high binding energiesof 7–11 kcal/mol due to hydrogen bonding among the oxygenatefunctionalities. Some of these dimers have high dipole moments and,thus, may be more easily detected experimentally than the monomersof alkanediols. For the decomposition of alkanediols, the calculationsdominantly favor dehydration over dehydrogenation. The relativelylow barrier for the decomposition of 1,1-ethanediol suggests thatthe structure of an alkanediol plays a role in its decomposition.Though the dehydration of alkanediols with or without water catalystinvolves large barriers, organic and inorganic acids, the hydroperoxylradical catalytically influences the reaction to such an extent thatthe dehydration reaction either involves significantly reduced barriersor essentially becomes barrierless. Considering that alkanediols containhydroxyl groups and their dimers have high binding energies, the gas-phasedehydration may be self-driven. Because acids are present in significantamounts in the troposphere, results suggest that diol dehydrationmay be facile under atmospheric conditions. [ABSTRACT FROM AUTHOR]

The conformers of a-serine were investigated by matrix-isolation IR spectroscopy combined with NIR laser irradiation. This method, aided by 2D correlation analysis, enabled unambiguously grouping the spectral lines to individual conformers. On the basis of comparison of at least nine experimentally observed vibrational transitions of each conformer with empirically scaled (SQM) and anharmonic (GVPT2) computed IR spectra, six conformers were identified. In addition, the presence of at least one more conformer in Ar matrix was proved, and a short-lived conformer with a half-life of (3.7 ± 0.5) × 10³ s in N2 matrix was generated by NIR irradiation. The analysis of the NIR laser-induced conversions revealed that the excitation of the stretching overtone of both the side chain and the carboxylic OH groups can effectively promote conformational changes, but remarkably different paths were observed for the two kinds of excitations. [ABSTRACT FROM AUTHOR]

We measure UV photodissociation (UVPD)spectra of cold benzo-15-crown-5(B15C5) and benzo-18-crown-6 (B18C6) complexes with divalent ions(M2+= Ca2+, Sr2+, Ba2+, and Mn2+), solvated with an H2O or a CH3OH molecule: M2+·B15C5·H2O,M2+·B15C5·CH3OH, M2+·B18C6·H2O, and M2+·B18C6·CH3OH. Allthe species show a number of sharp vibronic bands in the 36600–37600cm–1region, which can be attributed to electronictransitions of the B18C6 or B15C5 component. Conformer-specific IRspectra of these complexes are also obtained by IR-UV double-resonancespectroscopy in the OH stretching region. All the IR-UV spectra ofthe H2O complexes show IR bands at ∼3610 and ∼3690cm–1; these bands can be assigned to the symmetricand asymmetric OH stretching vibrations of the H2O component.The CH3OH complexes also show the stretching vibrationof the OH group at ∼3630 cm–1. The H2O and the CH3OH components are directly bondedto the M2+ion through the M2+···Obond in all the complexes, but a small difference in the conformationresults in a noticeable difference in the OH stretching frequency,which enables us to determine the number of conformers. For Ca2+, Sr2+, and Mn2+, the number of conformersfor the B18C6 complexes is in the range of 2–5, which is clearlylarger than complexes with B15C5 (1 or 2). However, for Ba2+the number of conformers with B18C6 (1 or 2) is almost the sameas that with B15C5. This is probably because the Ba2+ionis too large to be located in the cavity center of either B15C5 andB18C6, which provides an open site at the Ba2+ion suitablefor solvation with H2O or CH3OH. The more conformationsa complex can take, the more entropically favored it is at nonzerotemperatures. Hence, the larger number of conformations suggests higherstability of the complexes under solvated conditions, leading to ahigher degree of ion encapsulation in solution. [ABSTRACT FROM AUTHOR]

A new divergent ligand, N,N′-bis(4-carboxyphenylmethylene)ethane-1,2-diamine(H4L1), has beenprepared in high yield and used to generate two copper(II) coordinationpolymer materials, poly-[Cu(H2L1)(OH2)]·H2O (1) and poly-[Cu(H2L1)(OH2)]·H2O·DMF (2). Both networks possess (4,4) sheettopologies and have almost identical compositions and coordinationmodes. The only major difference between the compounds lies with theconformation of the chelating ethylenediamine cores; compound 1adopts a trans-(R,R/S,S) conformation, whilecompound 2exhibits a cis-(R,S) conformation. This seemingly small differencearising from variation in synthetic conditions influences the extendedstructures of each network through hydrogen bonding interactions,resulting in the formation of a close packed 2-fold 2D → 2Dparallel interpenetrated network for 1, while the extended,non-interpenetrated structure of 2contains aligned one-dimensionalsolvent channels. After solvent exchange and evacuation, compound 2was found to adsorb approximately 35 cm3(STP)/gof CO2at atmospheric pressure at 273 K, with a zero-loadingenthalpy of adsorption of −33 kJ/mol, while adsorbing onlyminimal quantities of N2. These findings are a rare exampleof conformer-dependent porosity in otherwise geometrically similarframeworks and highlight the importance of understanding weak andfluxional secondary interactions in framework and ligand design. [ABSTRACT FROM AUTHOR]

The per-residue, gas-phase hydrogen deuterium exchange (HDX) kinetics for individual amino acid residues on selected ion conformer types of the model peptide KKDDDDDIIKIIK have been examined using ion mobility spectrometry (IMS) and HDX-tandem mass spectrometry (MS/MS) techniques. The [M + 4H] ions exhibit two major conformer types with collision cross sections of 418 Å and 446 Å; the [M + 3H] ions also yield two different conformer types having collision cross sections of 340 Å and 367 Å. Kinetics plots of HDX for individual amino acid residues reveal fast- and slow-exchanging hydrogens. The contributions of each amino acid residue to the overall conformer type rate constant have been estimated. For this peptide, N- and C-terminal K residues exhibit the greatest contributions for all ion conformer types. Interior D and I residues show decreased contributions. Several charge state trends are observed. On average, the D residues of the [M + 3H] ions show faster HDX rate contributions compared with [M + 4H] ions. In contrast the interior I8 and I9 residues show increased accessibility to exchange for the more elongated [M + 4H] ion conformer type. The contribution of each residue to the overall uptake rate showed a good correlation with a residue hydrogen accessibility score model calculated using a distance from charge site and initial incorporation site for nominal structures obtained from molecular dynamic simulations (MDS). [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

The S1(1ππ*)state of the (dominant) syn-conformer of 2-chlorophenol(2-ClPhOH) in the gas phasehas a subpicosecond lifetime, whereas the corresponding S1states of 3- and 4-ClPhOH have lifetimes that are, respectively,∼2 and ∼3-orders of magnitude longer. A range of experimentaltechniques–electronic spectroscopy, ultrafast time-resolvedphotoion and photoelectron spectroscopies, H Rydberg atom photofragmenttranslational spectroscopy, velocity map imaging, and time-resolvedFourier transform infrared emission spectroscopy–as well aselectronic structure calculations (of key regions of the multidimensionalground (S0) state potential energy surface (PES) and selectedcuts through the first few excited singlet PESs) have been used inthe quest to explain these striking differences in excited state lifetime.The intramolecular O–H···Cl hydrogen bond specificto syn-2-ClPhOH is key. It encourages partial chargetransfer and preferential stabilization of the diabatic 1πσ* potential (relative to that of the 1ππ*state) upon stretching the C–Cl bond, with the result thatinitial C–Cl bond extension on the adiabatic S1PESoffers an essentially barrierless internal conversion pathway viaregions of conical intersection with the S0PES. Intramolecularhydrogen bonding is thus seen to facilitate the type of heterolyticdissociation more typically encountered in solution studies. [ABSTRACT FROM AUTHOR]