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Showing papers on "Conformational isomerism published in 1999"


Journal ArticleDOI
TL;DR: This J-based configuration analysis was applied to the stereochemical elucidation of carboxylic acid 5 derived from zooxanthellatoxin and proven to be a practical method even for natural products with complicated structures.
Abstract: A method for elucidating the relative configuration of acyclic organic compounds was developed on the basis of carbon-proton spin-coupling constants ((2,3)J(C,H)) and interproton spin-coupling constants ((3)J(H,H)). This method is based on the theory that, in acyclic systems, the conformation of adjacent asymmetric centers is represented by staggered rotamers, and their relative stereochemistry can be determined using (2,3)J(C,H) and (3)J(H,H), because the combined use of these J values enables the identification of the predominant staggered rotamer(s) out of the six possible derived from threo and erythro configurations. Detailed conformational analysis for model compounds 1-4 revealed that this method is useful in most cases for assignment of the configuration of acyclic structures occurring in natural products, in which stereogenic methine carbons are often substituted with a methyl or a hydroxy (alkoxy) group. This J-based configuration analysis was applied to the stereochemical elucidation of carboxylic acid 5 derived from zooxanthellatoxin and proven to be a practical method even for natural products with complicated structures.

644 citations


Journal ArticleDOI
TL;DR: In this article, the conformational energies of octahydro-1,3,5,7-tetranitro and DDMD were determined from high-level quantum chemistry calculations and have been used in parametrizing a classical potential function for simulations of HMX.
Abstract: The molecular geometries and conformational energies of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) and 1,3-dimethyl-1,3-dinitro methyldiamine (DDMD) and have been determined from high-level quantum chemistry calculations and have been used in parametrizing a classical potential function for simulations of HMX. Geometry optimizations for HMX and DDMD and rotational energy barrier searches for DDMD were performed at the B3LYP/6-311G** level, with subsequent single-point energy calculations at the MP2/6-311G** level. Four unique low-energy conformers were found for HMX, two whose conformational geometries correspond closely to those found in HMX polymorphs from crystallographic studies and two additional, lower energy conformers that are not seen in the crystalline phases. For DDMD, three unique low-energy conformers, and the rotational energy barriers between them, were located. In parametrizing the classical potential function for HMX, nonbonded repulsion/dispersion parameters, valence paramete...

186 citations


Journal ArticleDOI
TL;DR: The equilibrium distributions of hairpin ribozyme conformational isomers have been examined by time-resolved fluorescence resonance energy transfer and it is shown that under physiological conditions, the docking equilibrium of the natural four-way junction dramatically favors the active conformer, while those of a three-way and the two- way junction used in gene therapy applications favor the inactive conformer.
Abstract: The equilibrium distributions of hairpin ribozyme conformational isomers have been examined by time-resolved fluorescence resonance energy transfer. Ribozymes partition between active (docked) and inactive (extended) conformers, characterized by unique interdomain distance distributions, which define differences in folding free energy. The active tertiary structure is stabilized both by specific interactions between the catalytic and the substrate-binding domains and by the structure of the intervening helical junction. Under physiological conditions, the docking equilibrium of the natural four-way junction dramatically favors the active conformer, while those of a three-way and the two-way junction used in gene therapy applications favor the inactive conformer.

155 citations


Journal ArticleDOI
TL;DR: In this paper, a molecular modeling approach for the analysis of complex molecules with significant conformational freedom is described as it relates to the newly proposed humic acid building block, and a potential energy surface for various conformers of the low-energy stereoisomer has been generated.
Abstract: Multiple structural models of humic acid (HA) building blocks have been reported. In this work, the modeling is based on two structural motifs: (i) the Steelink structure and (ii) a new humic acid [TNB] building block, which incorporates more fully the results of experimental data and retro-biosynthetic analyses. Both have significant conformational freedom complicated by their stereochemistry. A molecular modeling approach for the analysis of complex molecules with significant conformational freedom is described as it relates to the newly proposed humic acid building block. A potential energy surface for various conformers of the low-energy stereoisomer has been generated. Included in this discussion is the relationship of the stereochemistry to conformation and secondary structure.

137 citations


Journal ArticleDOI
TL;DR: It is demonstrated that by stretching single pectin molecules (1 --> 4-linked alpha-D-galactouronic acid polymer), the pyranose ring conformation is changed from a chair to a boat and then to an inverted chair in a clearly resolved two-step conversion.
Abstract: Atomic force microscope manipulations of single polysaccharide molecules have recently expanded con- formational chemistry to include force-driven transitions between the chair and boat conformers of the pyranose ring structure. We now expand these observations to include chair inversion, a common phenomenon in the conformational chemistry of six-membered ring molecules. We demonstrate that by stretching single pectin molecules (1 3 4-linked a-D-galactouronic acid polymer), we could change the pyr- anose ring conformation from a chair to a boat and then to an inverted chair in a clearly resolved two-step conversion: 4 C1i boati 1 C4. The two-step extension of the distance between the glycosidic oxygen atoms O1 and O4 determined by atomic force microscope manipulations is corroborated by ab initio calcu- lations of the increase in length of the residue vector O1O4 on chair inversion. We postulate that this conformational change results from the torque generated by the glycosidic bonds when a force is applied to the pectin molecule. Hence, the glycosidic bonds act as mechanical levers, driving the confor- mational transitions of the pyranose ring. When the glycosidic bonds are equatorial (e), the torque is zero, causing no conformational change. However, when the glycosidic bond is axial (a), torque is generated, causing a rotation around COC bonds and a conformational change. This hypothesis readily predicts the number of transitions observed in pyranose monomers with 1a-4a linkages (two), 1a-4e (one), and 1e-4e (none). Our results demonstrate single-molecule mechano- chemistry with the capability of resolving complex conforma- tional transitions.

133 citations


Journal ArticleDOI
TL;DR: In this paper, the enthalpy difference between the more stable cis conformer and the high-energy gauche rotamer has been determined to range from 60 ± 8 cm-1 (718 ± 96 J/mol) in liquid xenon to 81 ± 1 cm -1 (969 ± 12 J/m) in Liquid argon.
Abstract: The infrared spectra (3500−400 cm-1) of 3-fluoropropene (allyl fluoride), CH2C(H)CH2F, dissolved in liquid argon, krypton, and xenon have been recorded at various temperatures ranging from −180 to −65 °C. From these studies, the enthalpy difference between the more stable cis conformer and the high-energy gauche rotamer has been determined to range from 60 ± 8 cm-1 (718 ± 96 J/mol) in liquid xenon to 81 ± 1 cm-1 (969 ± 12 J/mol) in liquid argon. These values have been extrapolated utilizing a linear relationship between the Kirkwood function of the solvent and the enthalpy differences in the solvents to give a value of 130 ± 25 cm-1 (1.56 ± 0.30 kJ/mol) for the vapor. From the experimental enthalpy value, the gauche dihedral angle, torsional transitions for both rotamers, and better structural parameters, the potential function governing the conformational interchange has been recalculated. Ab initio calculations utilizing the 6-31G(d,p) and 6-311G(d,p) basis sets with electron correlation at the MP2 leve...

131 citations


Journal ArticleDOI
TL;DR: In this paper, a combination of resonant two-photon ionization (R2PI), resonant ion-dip infrared spectroscopy (RIDIRS), and infrared−ultraviolet (IR−UV) hole-burning spectroscopic analysis is used to characterize the hydrogen-bonding topologies.
Abstract: A combination of resonant two-photon ionization (R2PI), resonant ion-dip infrared spectroscopy (RIDIRS), and infrared−ultraviolet (IR−UV) hole-burning spectroscopy is used to characterize the hydrogen-bonding topologies of indole−(water)1,2, 1-methylindole−(water)1-3, and 3-methylindole−(water)1 clusters formed and cooled in a supersonic expansion. The combination of methods provides a means of disentangling R2PI spectra that contain contributions from more than one species in the same mass channel due either to fragmentation or to the presence of conformational isomers. Density functional theory calculations (DFT Becke3LYP/6-31+G*) of the structures, harmonic vibrational frequencies, and infrared intensities provide a basis for distinguishing which structures are observed experimentally. The clusters studied exhibit a range of solvation structures around indole. In the indole−(water)1 and 3-methylindole−(water)1 complexes, the RIDIR spectra provide a benchmark frequency shift for the N−H···OH2 H-bonds in...

122 citations


Journal ArticleDOI
TL;DR: In this paper, the first experimental observation of the nonionized natural amino acid valine was made using matrix-isolation IR spectroscopy and density functional theory (DFT) and ab initio calculations.
Abstract: We present results of the first experimental observation of the nonionized natural amino acid valine. The study has employed the matrix-isolation IR spectroscopy and the density functional theory (DFT) and ab initio calculations. In the calculations geometries of nine low-energy valine conformers were optimized using the DFT method with the B3LYP parametrization and the 6-31++G** basis set. Additionally, the relative energies of the conformers were calculated at the MP2/6-31++G** level. The harmonic frequencies and IR intensities were calculated for all the minima found. These data were used to separate and assign the bands of the valine conformers in the experimental spectra. We found that two valine conformers are present in the Ar matrix: one with a bifurcated NH2···OC H-bond (conformer Ia) and one with a N···H−O H-bond (conformer IIa). A trace amount of a third valine conformer with NH2···O−C H-bond (conformer IIIb) was also detected. The conformational composition of the matrix-deposited nonionized ...

120 citations


Journal ArticleDOI
TL;DR: The interactions of yeast iso-1 cytochrome c with bovine cy tochrome c oxidase were studied using cyto chrome c variants in which lysines of the binding domain were substituted by alanines, leading to the conclusion that the interprotein electron transfer rate constant is around two times higher in state B2 than in B1.
Abstract: The interactions of yeast iso-1 cytochrome c with bovine cytochrome c oxidase were studied using cytochrome c variants in which lysines of the binding domain were substituted by alanines. Resonance Raman spectra of the fully oxidized complexes of both proteins reveal structural changes of both the heme c and the hemes a and a3. The structural changes in cytochrome c are the same as those observed upon binding to phospholipid vesicles where the bound protein exists in two conformers, B1 and B2. Whereas the structure of B1 is the same as that of the unbound cytochrome c, the formation of B2 is associated with substantial alterations of the heme pocket. In cytochrome c oxidase, the structural changes in both hemes refer to more subtle perturbations of the immediate protein environment and may be a result of a conformational equilibrium involving two states. These changes are qualitatively different to those observed for cytochrome c oxidase upon poly-l-lysine binding. The resonance Raman spectra of the various cytochrome c/cytochrome c oxidase complexes were analyzed quantitatively. The spectroscopic studies were paralleled by steady-state kinetic measurements of the same protein combinations. The results of the spectra analysis and the kinetic studies were used to determine the stability of the complexes and the conformational equilibria B2/B1 for all cytochrome c variants. The complex stability decreases in the order: wild-type WT > J72K > K79A > K73A > K87A > J72A > K86A > K73A/K79A (where J is the natural trimethyl lysine). This order is not exhibited by the conformational equilibria. The electrostatic control of state B2 formation does not depend on individual intermolecular salt bridges, but on the charge distribution in a specific region of the front surface of cytochrome c that is defined by the lysyl residues at positions 72, 73 and 79. On the other hand, the conformational changes in cytochrome c oxidase were found to be independent of the identity of the bound cytochrome c variant. The maximum rate constants determined from steady-state kinetic measurements could be related to the conformational equilibria of the bound cytochrome c using a simple model that assumes that the conformational transitions are faster than product formation. Within this model, the data analysis leads to the conclusion that the interprotein electron transfer rate constant is around two times higher in state B2 than in B1. These results can be interpreted in terms of an increase of the driving force in state B2 as a result of the large negative shift of the reduction potential.

100 citations


Journal ArticleDOI
TL;DR: The conformational landscapes of 2-amino-1-phenylethanol and its 1:1 water complexes have been investigated by UV band contour, UV−UV hole-burning, and IR−UV ion dip spectroscopy, coupled with ab initio computation.
Abstract: The conformational landscapes of 2-amino-1-phenylethanol and its 1:1 water complexes have been investigated by UV band contour, UV−UV hole-burning, and IR−UV ion dip spectroscopy, coupled with ab initio computation. The two molecular conformers observed are both stabilized by an intramolecular hydrogen bond, located in the folded (gauche) OCCN side chain, which links the proton donor OH group to the terminal amino group and leads to a significant constriction of the side chain. In the dominant 1:1 water complex, the intramolecular hydrogen bond is disrupted by the first water molecule, which inserts between the OH group and the nitrogen atom, to form a cyclic H-bonded structure. The side chain expands significantly in order to accommodate the water molecule within the neighborhood of both the hydroxyl and amino groups.

100 citations


Journal ArticleDOI
TL;DR: The NMR, X-ray, and CD data all confirm that the steric interactions of the 5-tert-butylprolyl residue induced dipeptide 1 to adopt a type VIa beta-turn conformation.
Abstract: The influences of steric interactions on peptide geometry were studied to develop a novel means for generating type VIa β-turn mimics. (2S,5R)-5-tert-Butylproline and l-proline were respectively introduced at the C-terminal residue of N-(acetyl)dipeptide N‘-methylamides 1 and 2. The relative populations of prolyl cis- and trans-amide isomers in dipeptides 1 and 2 were measured in chloroform, DMSO, and water by proton NMR spectroscopy. Although the trans-amide isomer was favored in prolyl peptide 2, the Xaa-Pro peptide bond adopted preferably the cis-amide isomer in the case of 5-tert-butylprolyl peptide 1. Measurements of the influence of solvent and temperature on the chemical shift values for the amide proton signals of 1 in the cis-amide conformer indicated that the N‘-methylamide was engaged in a hydrogen bond with the acetamide carbonyl in a type VIa β-turn conformation. Analysis of N-(acetyl)leucyl-5-tert-butylproline N‘-methylamide (1d) in the solid state by X-ray diffraction showed the cis-amide c...

Journal ArticleDOI
TL;DR: In this article, the infrared spectrum, molecular structure, and conformations of l-tryptophan in isolated zwitterionic form have been studied by means of a recently developed infrared sampling technique and ab initio molecular orbital calculations using a nonaqueous self-consistent reaction field (SCRF).
Abstract: The infrared spectrum, molecular structure, and conformations of l-tryptophan in isolated zwitterionic form have been studied by means of a recently developed infrared sampling technique and ab initio molecular orbital calculations using a nonaqueous self-consistent reaction field (SCRF). A complete mid-IR spectrum of monomeric tryptophan in zwitterionic form was obtained in a solid solvent of KBr. SCRF calculations using KBr as the continuum at the HF/6-31G(d,p) level were performed on zwitterionic tryptophan to predict its structure and vibrational frequencies. Three possible conformers were found, and one of them was identified to be predominant in the prepared sample on the basis of spectral and energy comparisons. Good agreement in terms of both frequencies and intensities was established between the calculated and observed infrared spectra. The detailed molecular structure of the predominant conformer of zwitterionic tryptophan was predicted and discussed.

Journal ArticleDOI
TL;DR: In this paper, the energies and geometries of a series of 2-substituted-1-fluoroethanes were computed at the MP2/6-311++G**(6D)//MP2/ 6-31+G* level of theory for both the maxima and minima of the rotation about the C-C bond.
Abstract: The energies and geometries of a series of 2-substituted-1-fluoroethanes were computed at the MP2/6-311++G**(6D)//MP2/6-31+G* level of theory for both the maxima and minima of the rotation about the C–C bond. The results did not support the predictions of a hyperconjugative model, that both 1,2-difluoroethane and 1-chloro-2-fluoroethane would strongly prefer a gauche conformation, and that 1-fluoro-2-silylethane would strongly prefer an anti conformation. The existence of competing electrostatic interactions between the fluorine and the substituents at C-2 was indicated by the detailed geometries of the gauche conformers and by the calculated sensitivity of the gauche–anti energy differences to the presence of a polar solvent. However, Fourier analyses of the torsional potential energies were wholly consistent with hyperconjugative electron donation into the C–F σ* orbital contributing to the conformational preferences of these 1-fluoroethanes. Fourier analyses also showed that hyperconjugation contributes to the small variations in C–C and C–F bond lengths and in fluorine atomic charges that were computed. The torsional potential energies, variations in geometry and atomic charge, and sensitivity to solvent were all in accord with the expected ranking of hyperconjugative electron donating ability of bonds to carbon, C–Si > C–H > C–C > C–Cl > C–F.

Journal ArticleDOI
TL;DR: In this paper, the effect of solvent on the ground state free energy differences of enol conformers of 2-(2'-hydroxyphenyl)benzimidazole and its keto tautomer has been examined by means of Monte Carlo simulations and continuum model calculations.
Abstract: The effect of the solvent on the ground state free energy differences of three enol conformers of 2-(2‘-hydroxyphenyl)benzimidazole and its keto tautomer has been examined by means of Monte Carlo simulations and continuum model calculations. In agreement with the experimental data, calculations show that the trans enol and keto forms are stabilized by polar solvents, leading to a conformational and tautomeric equilibrium with the closed cis enol conformer in water, the only single species in apolar solvents. Monte Carlo simulations have also been used to examine the influence of the solvent on the absorption band of the closed cis enol structure and the fluorescence band of the keto form generated by photoinduced intramolecular proton transfer. In concordance with the experimental spectra, absorption and fluorescence band maxima for the closed cis enol and keto forms, respectively, are found to be blue-shifted with increasing polarity and hydrogen bonding capacity of the solvent.

Patent
05 Aug 1999
TL;DR: In this paper, a method of separating ions having the same mass to charge ratio but different ion mobility characteristics, based on the ion focussing principles of high field asymmetric waveform ion mobility spectrometry, was proposed.
Abstract: The present invention relates to a method of separating ions having the same mass to charge ratio but different ion mobility characteristics, based on the ion focussing principles of high field asymmetric waveform ion mobility spectrometry. Isomers including gas-phase molecular anions of the amino acids leucine and isoleucine are separable by the method of the present invention. Identification of different conformers of ions at the same charge state, including conformers present at certain charge states of the protein bovine ubiquitin, is also possible using the method of the present invention.

Journal ArticleDOI
TL;DR: A close agreement is seen between the chi1 populations calculated from the experimental coupling constant data and predictions from the statistical model for a random coil that uses the chi2 torsion angle distributions in a data base of native protein structures.

Journal ArticleDOI
TL;DR: In this article, the molar rotations for an indoline and an azetidine, as well as for menthol and menthone, were calculated using ab inito methods and compared to the experimental values.
Abstract: The ability to compute and to interpret optical rotation angles of chiral molecules is of great value in assigning relative and absolute stereochemistry. The molar rotations for an indoline and an azetidine, as well as for menthol and menthone, were calculated using ab inito methods and compared to the experimental values. In one case the calculated rotation angle allowed the assignment of the absolute configuration of a heterocycle of unknown stereochemistry. The critical importance of Boltzmann averaging of conformers for reliable prediction of the optical rotation angle was established. Comparisons between static-field and time-dependent methods were made pointing to the limits and validity of the methods as electronic resonance is approached. A protocol analogous to population analysis was used to analyze atomic contributions to the rotation angle in specific conformers. The combination of atomic contribution maps and conformational analysis may provide an indirect tool to assist in three-dimensional structure determination.

Journal ArticleDOI
TL;DR: The role of alkaline metal cations in the synthesis and in determining the conformer distribution of tetrakis((ethoxycarbonyl)methoxy)tetrathiacalix[4]arene obtained by treatment of tetrathiaalix 1 in acetone by ethyl bromoacetate in the presence of M2CO3 was systematically investigated.

Journal ArticleDOI
TL;DR: In this article, the structures of 2-phenylethanol and its 1:1 water complexes have been investigated by UV-UV hole burning and IR-UV ion-dip spectroscopy, coupled with ab initio computation.

Journal ArticleDOI
TL;DR: In this article, a trans (T) and two gauche (G1 and G2) conformers were identified for protonated dopamine in the gas phase upon ab initio calculations up to QCISD(T)/6-31G* and MP2/6-311++G**.
Abstract: A trans (T) and two gauche (G1 and G2) conformers have been identified for protonated dopamine in the gas phase upon ab initio calculations up to the QCISD(T)/6-31G*//HF/6-31G* and MP2/6-311++G**//MP2/6-311++G** levels and based on B3LYP/6-31G* optimizations in DFT. Free energy differences at 298 K and 1 atm were calculated to be 3.2−5.6 kcal/mol between T and G1, and about 0 kcal/mol between the G2 and G1 conformers. The OH groups are nearly coplanar with the benzene ring and form an O−H···O−H intramolecular hydrogen bond in their most stable arrangement. Using the free energy perturbation method through Monte Carlo simulations, relative solvation free energies were evaluated in aqueous solution at T = 310 K and 1 atm. Ab initio/Monte Carlo torsional potential curves were calculated along pathways where small rotations about the C(ring)−Cβ and Cβ−Cα axes were allowed. No stable rotamers but the gas-phase optimized structures were identified. The T − G1 and G2 − G1 relative solvation free energies were ca...

Journal ArticleDOI
TL;DR: In this paper, the rotational spectra of 18O-glycine and all monodeutero and dideutero isotopically substituted species of the conformer of glycine which has the most intense microwave spectrum, gly(2) were derived and the derived spectroscopic data made possible the first complete gas phase structural determination of an aminoacid.

Journal ArticleDOI
TL;DR: In this paper, infrared−ultraviolet double-resonance spectroscopy has been applied to discriminate rotamers of jet-cooled aryl alcohol homologues, φ-(CH2)nOH, where φ represents phenyl group and n = 1, 2, and 3 correspond to benzyl, phenethyl and 3-phenylpropyl alcohols, respectively.
Abstract: Infrared−ultraviolet double-resonance spectroscopy has been applied to discriminate rotamers of jet-cooled aryl alcohol homologues, φ-(CH2)nOH, where φ represents phenyl group and n = 1, 2, and 3 correspond to benzyl, phenethyl, and 3-phenylpropyl alcohols, respectively. Experimental results indicate that different OH stretching frequencies are associated with different rotamers and that the ability of intramolecular hydrogen bonding with the benzene π-electron decreases with an increase in alkyl chain length. In each aryl alcohol, the most prominent species in jets corresponds to the non-hydrogen-bonded rotamer having higher OH stretching frequency.

Journal ArticleDOI
TL;DR: A comprehensive conformational map for two nucleoside-5',3'-diphosphates and for a truncated dinucleotide derived from a grid search of all potential conformers using hard sphere steric exclusion criteria to define allowed conformers is presented.

Journal ArticleDOI
TL;DR: In this article, a concerted molecular orbital and vibrational spectroscopic approach was used to investigate conformational isomerism in isolated and liquid 2-aminoethanol molecules using the extended 6-31G* basis set at the HF-SCF ab initio level.

Journal ArticleDOI
TL;DR: In this paper, the vibrational spectra of two ribonucleosides containing pyrimidine bases were analyzed in the solid state at low temperature by neutron inelastic scattering (NIS) and in an aqueous solution at room temperature by Raman scattering and Fourier transform infrared absorption (FT-IR).
Abstract: Vibrational spectra of two ribonucleosides containing pyrimidine bases, i.e., uridine and cytidine, were analyzed in the solid state at low temperature by neutron inelastic scattering (NIS) and in an aqueous solution at room temperature by Raman scattering and Fourier transform infrared absorption (FT-IR). Analysis of all these experimental spectra, measured on both native and deuterated (on labile hydrogens) species, allows a complete set of information on the vibrational modes arising from the base residues and ribose to be obtained. To interpret the vibrational spectra, a harmonic force field has been estimated for isolated ribonucleosides at the Hartree-Fock (HF) and density functional theory (DFT) levels. All these calculations have been performed by means of the Becke-Lee-Yang-Parr (B3LYP) local exchange and correlation functional (for DFT calculations) and the split valence basis sets, 631G (*) , including nonstandard polarization functions on heavy atoms (for DFT and HF calculations). The lowest energy conformers of these ribonucleosides, i.e., C3′-endo/ anti and C2′-endo/anti have been used in the vibrational mode calculations, where C3′-endo and C2′-endo refer to the N-type and S-type ribose puckering, respectively, and anti designates the orientation of base with respect to the sugar. The absence of any imaginary frequencies in the vibrational calculations confirms that the optimized geometry of the ribonucleosides well corresponds to their local mimima. The addition of the zero-point vibrational energy (ZPVE) to the electronic energy does not, however, change the energy order of the conformers. In both ribonucleosides, the C3′-endo/anti conformer has a lower energy than the C2′-endo/ anti one. It has been shown that NIS intensities calculated at the DFT/B3LYP/631G (*) level account more accurately for the characteristics of the experimental spectra. Therefore, the assignment of the observed vibrational modes has been extensively discussed in this paper on the basis of the results calculated by means of the DFT method. On the other hand, comparison between observed and calculated NIS spectra of native and deuterated species can give insight on the effect of intermolecular hydrogen bonding in the solid phase. Finally, the calculated results seem to be able to interpret the Raman marker shifts observed upon the A-Z helix transitions of poly- and oligonucleotides (C3′-endo/anti to C2′-endo/anti conformational transition of the cytosine residue), as well as those related to the UUCG tetraloop hairpin, involving C2′-endo/anti uridine and cytidine residues found in the middle positions of this highly stable tetraloop.

Journal ArticleDOI
TL;DR: It is proposed that the cone conformers act as anion hosts due to a combination of positive charge as well as apolarity and size of the cavity, as deduced from (1)H NMR studies.
Abstract: The open “molecular box” [(en)Pt(UH-N1,N3)]4(NO3)4 (with en = 1,2-diaminoethane, UH = uracil monoanion) resembles calix[4]arenes in its structure and solution dynamics. It adopts a 1,3-alternate conformation in the solid-state (1a), but in solution and after deprotonation to [(en)Pt(U-N1,N3)]4, a second major species (cone conformer (1b-4H+)) occurs. 1b-4H+ acts as an efficient ligand for additional metal ions through the oxo-surface formed by the four O2 exocyclic atoms of the uracil nucleobases. As shown here, 1b-4H+ can incorporate a single metal ion only, giving rise to the formation of species of type {[(en)PtU]4M}(X)n with M = ZnII (2a), BeII (3) (not isolated in the solid state), and LaIII (4); X = NO3, SO4/2; n = 2, 3. In addition, both the protonated species of the cone conformer (1b, pH 2−4) and compounds 2a (at pH 3−8) and 3 (at pH 3−5) act as hosts for organic anions in water, as deduced from 1H NMR studies. It is proposed that the cone conformers act as anion hosts due to a combination of pos...

Journal ArticleDOI
TL;DR: In this paper, the energy difference between the two most stable conformers of calix[4]arene (cone and partial-cone) is 10 kcal mol-1 at the BLYP/6-31G** level with the geometries optimized at BLYP /6- 31G*.
Abstract: Density functional theory results for the structure and conformational equilibrium of four calix[4]arene conformers are reported. The results are compared with experiment, force field, and semiempirical molecular orbital calculations. The energy difference between the two most stable conformers of calix[4]arene (cone and partial-cone) is 10 kcal mol-1 at the BLYP/6-31G** level with the geometries optimized at BLYP/6-31G*. For the most stable conformer, results for the protonated structure are also reported. Electrostatic potential surfaces for the cone calix[4]arene and the corresponding tetra-O−H-depleted structure have been calculated. It is suggested that their representation may be of relevance to understand the known ability of calix[n]arene systems to form complexes with charged species in host−guest chemistry.

Journal ArticleDOI
TL;DR: In this article, a 6-31G* basis set was used to perform MP2 and DFT abinitio calculations on the vibrational spectra of dimethyl carbonate.
Abstract: Infrared (4000–50 cm-1) spectra of the vapor, the amorphous and crystalline solid phase, and Raman spectra (4000–50 cm-1) of the vapor, liquid and crystalline solid phases of dimethyl carbonate have been recorded, and assignments are proposed. MP2 and DFT abinitio calculations were carried out using a 6-31G** basis set. The calculations show that the compound can occur as the cis–cis, cis–trans and near-trans–near-trans conformers, with the cis–cis being the global minimum. Vibrational frequencies and solvation free enthalpies were predicted on the DFT level of theory. Both cis–cis and cis–trans conformers were identified in the vibrational spectra of all fluid phases. The enthalpy difference between them was determined to be 8.0(4) kJ mol-1 in the pure liquid phase and 13.6(9) kJ mol-1 in the vapor phase.

Journal ArticleDOI
TL;DR: In this article, the crystal and molecular structure of two 3-(2-benzyloxy-6-hydroxyphenyl)-5-styryl pyrazoles were determined by X-ray analysis.

Journal ArticleDOI
TL;DR: In this paper, a novel tetraethylether of thiacalix[4]arene by means of NMR spectroscopy is presented. But the authors do not describe the structure of the tetraETHylether.