Orientation Of OH Groups Research Articles

OH Group Orientation Leads to Organosulfate Formation at the Liquid Aerosol Surface.

Organosulfates (OSs) are well-known and ubiquitous constituents of atmospheric aerosol particles and have been used as secondary organic aerosol markers in many field studies. Hence, it is imperative to understand the formation of OS species in the atmosphere. Recently, hydroxy acids (HAs) and hydroxy acid sulfates have been extensively detected in the atmospheric environment. However, the reaction mechanism of HAs to form OSs is much less understood. In this work, we have mainly investigated the reaction of typical α-HAs, including glycolic acid (GA) and lactic acid (LA), and SO3 at the liquid aerosol surface using quantum chemistry calculations and Born-Oppenheimer molecular dynamics simulations. The OH group orientation of α-HAs at the air-water interface is found to exert a significant impact on the formation of OSs. The OH group pointing to the gas phase is obviously beneficial to the formation of OSs. Two key factors are discovered important to the reaction of α-HAs adsorbed on the liquid surface with SO3: (a) the exposure position of the active site to the gas phase and (b) the reactivity of the exposed site to the attracted SO3 molecule. Moreover, we found that the air-water interface exerts a significant influence on the physicochemical behaviors of GA and LA, especially on their OH group orientation, and thus leads to their different properties for the SO3 colliding reaction. The presented reaction mechanism provides a new feasible pathway for the production of OSs at the liquid aerosol surface, which may have important impacts on the formation of organic aerosols.

Conformation of protonated guanine nucleotides via infrared multiphoton dissociation spectroscopy: Observation of rotamers in the anti-conformation

Guanosine 5′-monophosphate (GMP) is a component in RNA, which functions as a messenger in biological systems. Infrared multiphoton dissociation (IRMPD) spectroscopy, combined with IR-laser ablation of a droplet beam, reveals that the most stable conformer of gas-phase protonated GMP has a keto form and an anti-conformation. This includes two types of rotamers with different orientations of OH groups in the sugar ring. This suggests that our own laser ablation of droplet beam method promotes conformation-selective IRMPD spectroscopy with an effective cooling system in the gas phase.

3-ALKOXY-1,5-DIARYL-4,5-DIHYDROXYIMIDAZOLIDIN-2-ONES AND 3-ALKOXY-1-ALKYL-5-ARYL-4,5-DIHYDROXYIMIDAZOLIDIN-2-ONES: SYNTHESIS AND STRUCTURE

It has been found that 4-nitrophenylglyoxal reacts with N -alkoxy- N’ -arylureas and N -alkoxy- N’ -alkylureas in acetic acid medium with the selective formation of the diastereomers of the 3-alkoxy-1,5-diaryl-4,5-dihydroxyimidazolidin-2-ones and 3-alkoxy-1-alkyl-5-aryl-4,5-dihydroxyimidazolidin-2-ones with sic -orientation of OH-groups. The X-ray structural analysis of 3-propyloxy-4 S ,5 S -dihydroxy-1-methyl-5-(4-nitrophenyl)imidazolidin-2-one and of 3- n -butyloxy-4 S ,5 S -dihydroxy-1-(4-methylphenyl)-5-(4-nitrophenyl)imidazolidin-2-one has demonstrated the structural parameters of these compounds.

SYNTHESIS AND STRUCTURE OF 3,4,5-TRIHYDROXY-5-(4-NITROPHENYL)IMIDAZOLIDIN-2-ONE

It has been found that 4-nitrophenylglyoxal reacts with N -hydroxyurea both in water and in acetic acid forming the mixture of diastereomers of 3,4,5-trihydroxy-5-(4-nitrophenyl)imidazolidin-2-one. The diastereomer with sic -orientation of OH-groups dominates. In the acetic acid medium 4-nitrophenylglyoxal reacts with 2-methylfuran selectively yielding 2-hydroxy-2-(5-methylfuran-2-yl)-1-(4-nitrophenyl)ethanone

First principles study of structural properties and electric field gradients in kaolinite

This work reports a gauge-including projected augmented waves (GIPAW) method study of the structural and electronic properties of kaolinite (Al2Si2O5(OH)4). Different equilibrium structures were determined, and the corresponding electronic density of states and the electric field gradients (EFG) at each atomic site were calculated. The comparison of those predicted properties with measurements that come from neutron powder diffraction, single crystal synchrotron measurements, and nuclear magnetic resonance spectroscopies allowed a detailed study of the structure. In particular, the first principles calculations considered in this work cover different scales, going from the crystallographic structure to the atomic local environments, and serve as a tool to link both the structural and the hyperfine properties. This methodology predictions successfully solves a kaolinite structure in which the atomic local surroundings are consistent with the EFG measurements, thus providing answers to previous controversies between experimental studies about Al and Si local structures and the orientation of OH groups within the structure. In this sense, the GIPAW calculations support that kaolinite consists of asymmetrically distorted Si tetrahedra and Al octahedra sheets, and the interlayer OH groups are oriented nearly perpendicular to the layer.

Crucial role of the hydroxyl group orientation in Langmuir monolayers organization–The case of 7-hydroxycholesterol epimers

Oxysterols, which are products of cholesterol oxidation, are important biological molecules. For our investigations we have selected two epimers: 7α-hydroxycholesterol (7α-OH) and 7 β-hydroxycholesterol (7β-OH). Both molecules have been found to be capable of stable Langmuir monolayer formation, however, the characteristic of their monolayers were quite different. Contrary to 7β -OH, which isotherm devoid any transition, the π/A dependence for 7α-OH displayed a broad plateau. Temperature strongly affected this plateau transition – the lower the temperature, the higher the surface pressure of the transition. Such an inverse temperature dependence is uncommon for classical film-forming molecules. Film thickness results excluded multilayers as the probable cause for this plateau. Based on theoretical calculations it was possible to infer that the plateau can be attributed to the change of orientation upon film compression, from being anchored mainly with both polar groups in the pre-plateau region to that with one polar group being detached from the water surface in the post-plateau region. Differences in surface behavior of both diastereoisomers have been explained as being due to orientation of OH groups in their molecules; i.e. for 7β-OH both hydroxyl groups (at C3 and C7) are situated on the same side of the rings A and B, while for 7α-OH – on different sides, which induces the lifting off of one OH group from the water surface.

Conformational Analysis of Gentiobiose Using Genetic Algorithm Search and GIAO DFT Calculations with 13C CPMAS NMR as a Verification Method

GRAPHICAL ABSTRACTThe ALJAR03 software was implemented performing searches in the dihedral angle conformational space of disaccharides. The angles φ, ψ , and ω around glycosidic linkages, as well as the orientations of hydroxymethyl and hydroxyl groups, were considered. The energy maps were calculated using the MM+ force field. The searches were performed using a genetic algorithm (GA) combined with systematic grid search (GS). The application of a genetic algorithm-assisted grid search (GAAGS) approach yielded a significant reduction in the number of structures to be sampled in order to find the best low-energy conformation, as compared with the standard systematic grid search. Thus, time-consuming gauge-independent atomic orbital (GIAO) calculations of shielding constants can be rationalized and limited to some selected conformations. 13C CPMAS NMR chemical shifts for solid gentiobiose were measured and compared with the respective (GIAO DFT) shielding constants calculated for the crystallographic structure and for low-energy conformers. The differences in shielding are associated with the conformational effects (different arrangements of exocyclic groups) and hydrogen bonds. The best agreement (R2 = 0.99) between the experimental and calculated chemical shifts was for the XRD structure and for the best conformer (R2 = 0.98). Their geometries differ in the orientation of OH groups.

Structure and Hydrogen-Bonding Ability of Estrogens Studied in the Gas Phase

The structures of estrogens (estrone(E1), β-estradiol(E2), and estriol(E3)) and their 1:1 hydrogen-bonded (hydrated) clusters with water formed in supersonic jets have been investigated by various laser spectroscopic methods and quantum chemical calculations. In the S1-S0 electronic spectra, all three species exhibit the band origin in the 35,050-35,200 cm(-1) region. By use of ultraviolet-ultraviolet hole-burning (UV-UV HB) spectroscopy, two conformers, four conformers, and eight conformers, arising from different orientation of OH group(s) in the A-ring and D-ring, are identified for estrone, β-estradiol, and estriol, respectively. The infrared-ultraviolet double-resonance (IR-UV DR) spectra in the OH stretching vibration are observed to discriminate different conformers of the D-ring OH for β-estradiol and estriol, and it is suggested that in estriol only the intramolecular hydrogen bonded conformer exists in the jet. For the 1:1 hydrated cluster of estrogens, the S1-S0 electronic transition energies are quite different depending on whether the water molecule is bound to A-ring OH or D-ring OH. It is found that the water molecule prefers to form an H-bond to the A-ring OH for estrone and β-estradiol due to the higher acidity of phenolic OH than that of the alcoholic OH. On the other hand, in estriol the water molecule prefers to be bound to the D-ring OH due to the formation of a stable ring-structure H-bonding network with two OH groups. Thus, the substitution of one hydroxyl group to the D-ring drastically changes the hydrogen-bonding preference of estrogens.

Extreme ultraviolet photoionization of aldoses and ketoses

Gas phase monosaccharides (2-deoxyribose, ribose, arabinose, xylose, lyxose, glucose galactose, fructose, and tagatose), generated by laser desorption of solid sample pellets, are ionized with extreme ultraviolet photons (EUV, 46.9 nm, 26.44 eV). The resulting fragment ions are analyzed using a time of flight mass spectrometer. All aldoses yield identical fragment ions regardless of size, and ketoses, while also generating same ions as aldoses, yields additional features. Extensive fragmentation of the monosaccharides is the result the EUV photons ionizing various inner valence orbitals. The observed fragmentation patterns are not dependent upon hydrogen bonding structure or OH group orientation.

OPTIMUM PYROLYTIC CONDITIONS FOR FURAN DERIVATIVE FORMATION FROM POLYAMINO SUGARS

Furan derivatives were prepared by hydrolysis of glucosamine derived from polyamino sugars assisted with pyrolysis in alkaline condition. Pyrolysis was carried out with autoclaving at 15 psi/121°C/1 hour. The reaction was monitored by observing spectral characteristics at λmax 545 nm with p-dimethylaminobenzaldehyde. Alkaline hydrolysis favors the formation of furan derivatives in N-acetylglucosamine, glucosamine, hyaluronic acid, but not in dermatan sulfate and chondroitin sulfate. These results indicate –OH group orientation in the cis position at C4 of the Haworth projection formula of hexosamines may be playing a role in the formation of furans. This can be a useful method for estimation of the glucosamine in glycoprotein and urine.

Conformational analysis of o-allylphenol by density functional and IR spectroscopy methods

The two-dimensional cyclic potential energy surfaces for internal rotation of the allyl substituent and its vinyl fragment in o-allylphenol (o-APh) depending on the OH group orientation relative to the allyl substituent were constructed by a B3LYP/6-31G method. It is shown that o-APh exists in the gas phase as a mixture of eight non-planar rotamers (A, B, C, D, E, F, G, and H) and their eight optical isomers (A 1, B 1, C 1, D 1, E 1, F 1, G 1, and H 1). An intramolecular H-bond (IHB) O–H...π occurs only in four rotamers (A, B, A 1, and B 1). The content of such rotamers in the gas phase is 47.2% (as calculated by the B3LYP/cc-pVTZ method). Taking into account the solvation effect in the polarizable continuum model (PCM) for a solution of o-APh in cyclohexane decreases the total content of rotamers with an IHB (A and B) to 37.7%. The ratio of rotamers with OH groups bonded by an IHB and with free OH groups that is predicted theoretically agrees with the value measured experimentally from IR spectra of o-APH in CCl4 solution.

Conformational preferences of 2-isopropylaminoethanol in aqueous solution using the CPCM continuum solvation model

All possible conformers of 2-Isopropylaminoethanol (2-IPAE) have been optimized in aqueous solution at the DFT level of theory [B3LYP/6-311++G(d,p)] using the conductor-like polarizable continuum model (CPCM). The Gibbs energies of solvation of all conformers, as well as their components, have been computed and discussed. The differences of Δ G solv between conformers are essentially determined by the electrostatic component. The conformers exhibiting an O–H···N intramolecular H-bond predominate in the gas phase equilibrium, but in aqueous solution their contribution is greatly reduced. On the contrary, conformers with a trans orientation around the OCCN dihedral and those with a gauche OCCN but without intramolecular H-bond increase significantly their population in solution. The effect of the OH group orientation on solvation has been deeply investigated by means of scans of the Gibbs energy of solvation around the HOCC dihedral for different backbone structures. Local solvation around the polar groups has also been investigated by calculating and comparing the interaction energies of the NH and OH groups with one water molecule. The optimized monohydrates, as well as the BSSE corrected interaction energies, were obtained at the B3LYP/6-311++G(d,p) level of theory.

Solid‐state NMR studies and DFT calculations of flavonoids: baicalein, baicalin and wogonoside

Three flavonoids of pharmaceutical importance-baicalein, baicalin, and wogonoside-were isolated from a Chinese medicinal plant Scutellaria baicalensis Georgi and studied by 13C NMR in solution and solid state. Two-dimensional (2D) NMR spectroscopy in the liquid phase and dipolar dephasing (DD) experiments in magic-angle spinning (MAS) spectra enabled the assignment of 13C resonances. The cross-polarization (CP) time constants T(CH) and relaxation times T(H) (1rho) were obtained from the variable-contact time experiments. The principal elements of the 13C chemical shift tensor were determined in the spectra recorded under slow sample spinning (2 kHz) using phase-adjusted spinning sideband (PASS)-2D NMR technique, and were verified by density functional theory gauge-independent atomic orbital (DFT GIAO) calculations of shielding constants. Analysis of the 13C delta(ii) and comparison with shielding parameters calculated for different conformers of compounds 1-3 enabled the selection of the most reliable geometry in the solid phase. In all three compounds, an intramolecular hydrogen bond C5--OH...=C4 is formed; the existence of baicalein and baicalin with 'anticlockwise' orientation of OH groups is more probable.

Competitive H-bonds in vacuo and in aqueous solution for N-protonated adrenaline and its monohydrated complexes

The conformational landscape of the N-protonated form of adrenaline (epinephrine in the U.S.) has been considered at both the B3LYP/6-31G* and 6-311++G** levels, with full geometry optimization in the gas phase and in aqueous solution, using the integral equation formalism for the polarizable continuum model (IEF-PCM). All stable orientations of the two catecholic hydroxy groups as well as the interconversion pathways between them have been taken into account. The dependence of the potential energy profile for the −[NH 2CH 3] + group rotation on the catechol ring and side-chain OH group orientation has been also examined. B3LYP/6-31G* stationary points have been confirmed with frequency calculations (at 310 K and 1 atm) allowing thermal corrections and IR spectra to be evaluated. Basis set effects do not alter the relative stability of the various forms that is maintained also when MP2 correlation corrections are included. The role of the internal structures either embedding in aqueous solution the conformers kept rigid at their in vacuo geometries or allowing the structure to relax has been examined at the IEF-PCM/B3LYP/6-31G* and 6-311++G** levels and compared to the IEF-PCM/MP2/6-31G* results. In vacuo the G1 conformers are favored with respect to the T and G2 ones, while in water the stability ordering changes, T becoming significantly more stable than both gauche forms. This occurs even for the gas-phase structures, including or not thermal corrections. The addition of a single water molecule to N-protonated adrenaline caused the intramolecular H-bond within the side chain to weaken till formation of two H-bonds with water. This fact, coupled to the strain relaxation, further stabilized the G1 and T conformers. The maximum intensity of the IR spectra increases in solution, especially for monohydrated adducts, where a significant red shift in the vibration of the NH involved in a H-bond to the water O is found.

Conformational Study of Tyramine and Its Water Clusters by Laser Spectroscopy

Tyramine and its monohydrated clusters have been investigated by several laser spectroscopic methods in a pulsed molecular beam. The conformational structures and their effects on hydration have been revealed by resonant two-photon ionization (R2PI), UV-UV ion-dip, and ab initio calculations. UV rotational band contour spectra of the S1 <-- S0 origin bands enabled determination of ethylamine side chain conformations for all seven stable conformers of tyramine. When coexpanding tyramine with a mixture of Ar and water vapor, we have found two kinds of conformational effects on hydration. One is sensitive to conformation of the ethylamine chain and the other to the orientation of the OH group, particularly in the most stable pair of conformers. UV-UV ion-dip spectra detected seven stable conformers of the monohydrated clusters, of which hydrogen-bonding structures, spectral shifts, and origin band intensity distributions are well explained by considering tyramine as a hybrid of phenylethylamine (PEA) and phenol. Monohydration of the most stable gauche conformer pair (cis and trans) of tyramine leads to more detailed conformational assignments regarding the orientation of the phenolic OH group. Cyclic hydrogen-bonding linkage formed in the monohydrated cluster pair is found to be sensitive to the orientation of the phenolic OH group. One of the cluster pair, in which tyramine has the gauche-cis conformation, is more stabilized by the cyclic hydrogen bonding and its origin band intensity becomes stronger than that of the other.

Structural studies of methyl brevifolincarboxylate in solid state by means of NMR spectroscopy and DFT calculations

Methyl brevifolincarboxylate isolated from the herb of Potentilla argentea L. (Rosaceae) is a representative of the naturally occurring polyphenols. The compound is of pharmaceutical interest mainly because of its antiviral and antioxidant properties. 13C NMR spectra were recorded for solution and solid phase. 13C CPMAS spectra were assigned by comparison with solution data, dipolar dephasing and short contact time experiments. The correctness of assignments was verified by GIAO DFT calculations of shielding constants. The differences between the solution and solid state chemical shift values were explained in terms of orientation of OH groups and intramolecular hydrogen bonds. The splitting of the C1 O resonance shows that there exists a polymorphism in the solid phase, which might be due to the formation of intramolecular hydrogen bond involving carbonyl or methoxy oxygen (i.e. C10 OH⋯O C or C10 OH⋯OCH 3).

Effects of substrate structure and composition on the structure, dynamics, and energetics of water at mineral surfaces: A molecular dynamics modeling study

Molecular dynamics computer simulations of the molecular structure, diffusive dynamics and hydration energetics of water adsorbed on (0 0 1) surfaces of brucite Mg(OH) 2, gibbsite Al(OH) 3, hydrotalcite Mg 2Al(OH) 6Cl · 2H 2O, muscovite KAl 2(Si 3Al)O 10(OH) 2, and talc Mg 3Si 4O 10(OH) 2 provide new insight into the relationships between the substrate structure and composition and the molecular-scale structure and properties of the interfacial water. For the three hydroxide phases studied here, the differences in the structural charge on the octahedral sheet, cation occupancies and distributions, and the orientations of OH groups all affect the surface water structure. The density profiles of water molecules perpendicular to the surface are very similar, due to the prevalent importance of H-bonding between the surface and the water and to their similar layered crystal structures. However, the predominant orientations of the surface water molecules and the detailed two-dimensional near-surface structure are quite different. The atomic density profiles and other structural characteristics of water at the two sheet silicate surfaces are very different, because the talc (0 0 1) surface is hydrophobic whereas the muscovite (0 0 1) surface is hydrophilic. At the hydrophilic and electrostatically neutral brucite and gibbsite (0 0 1) surfaces, both donating and accepting H-bonds from the H 2O molecules are important for the development of a continuous hydrogen bonding network across the interfacial region. For the hydrophilic but charged hydrotalcite and muscovite (0 0 1) surfaces, only accepting or donating H-bonds from the water molecules contribute to the formation of the H-bonding network at the negatively and positively charged interfaces, respectively. For the hydrophobic talc (0 0 1) surface, H-bonds between water molecules and the surface sites are very weak, and the H-bonds among H 2O molecules dominate the interfacial H-bonding network. For all the systems studied, the orientation of the interfacial water molecules in the first few layers is influenced by both the substrate surface charge and the ability by the surfaces to facilitate H-bond formation. The first layer of water molecules at all surfaces is well ordered in the xy plane (parallel to the surface) and the atomic density distributions reflect the substrate crystal structure. The enhanced ordering of water molecules at the interfaces indicates reduced orientational and translational entropy. In thin films, water molecules are more mobile parallel to the surface than perpendicular to it due to spatial constraints. At neutral, hydrophilic substrates, single-monolayer surface coverage stabilizes the adsorbed water molecules and results in a minimum of the surface hydration energy. In contrast, at the charged and hydrophilic muscovite surface, the hydration energy increases monotonically with increasing water coverage over the range of coverages studied. At the neutral and hydrophobic talc surface, the adsorption of H 2O is unfavorable at all surface coverages, and the hydration energy decreases monotonically with increasing coverage.

The importance of preferential solvation of the CN ligands in electron- and proton-transfers observed for cis–[Ru(CN) 2(bpy) 2] under ion bombardment

Liquid secondary ion mass spectrometry (LSIMS) mass spectra of cis-[Ru(CN) 2(bpy) 2] with a strong hydrogen-bonding-induced solvatochromism were measured using 3-nitrobenzyl alcohol (NBA) (oxidizing agent) and glycerol (reducing agent), and mixtures of these solvents. The formation of M + (oxidized molecule) correlated closely to the extent of preferential solvation by NBA (preferential solvation-shell) around the cyanide ligands as observed from changes in the energy of the maximum metal-to-ligand charge transfer absorption. (M + H) + is caused mainly by the preferential orientation of OH groups with protons in the NBA molecules toward the cyanide ligands in the disrupted region of the solvent structure as observed from the variation in the peak position of the stretching vibration of (OH) in the solvents. Large decreases in (M + 2H) + and (M + 3H) + (reduced molecules) resulted from the large decrease in the interaction between the cyanide ligands and glycerol owing to the preferential solvation by NBA. The LSIMS mass spectra clearly showed the electron- and proton-transfer processes along with the change in the hydrogen-bonding interaction between the acceptor (NBA and glycerol) and donor (the cyanide ligands), and in the solvent structure of the preferential solvation-shell. These results indicate that the composition of solvent molecules around the cyanide ligands at the surface of the solvents in LSIMS still holds the composition in the preferential solvation around the ligands in the primary solvation-shell.

Interplay of intra‐ and intermolecular H‐bonds for the addition of a water molecule to the neutral and N‐protonated forms of noradrenaline

AbstractThe conformational flexibility of noradrenaline in its N‐protonated and neutral forms was considered at the Hartree–Fock (HF)/6‐31G* level, taking into account the orientation of the two hydroxy groups located on the catechol ring and the interconversion pathways between their stable arrangements. The difference in stability among the various forms of N‐protonated noradrenaline was maintained including either more diffuse functions on the heteroatoms or Møller–Plesset second order (MP2) correlation corrections. The embedding in aqueous solution, in the polarizable continuum model framework, of the conformers kept rigid at their in vacuo geometries favored the T conformers with respect to the G ones at the HF level (for neutral noradrenaline at the MP2 level as well). The addition of a single water molecule to noradrenaline (either N‐protonated or not) caused the intramolecular H‐bond within the side chain to weaken until formation of one or two intermolecular H‐bonds with water. This fact, coupled to the intramolecular H‐bond strain relaxation, further stabilized the G1 and T conformers. Continuum solvation of the hydrated clusters of neutral noradrenaline favored significantly the Twater adducts at the HF level, but only slightly at the MP2 level, because of their large energy gap in vacuo with respect to G1water, even enhanced by MP2 geometry optimizations. The dependence of the potential energy profile for the NH2 group rotation on the catechol ring and side chain OH group orientation was examined in noradrenaline and compared to the trend shown by dopamine. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

DFT theoretical, spectroscopic and X-ray diffraction studies on 4-methyl-2 ′-hydroxy-4 ′-alkyloxyazobenzenes

Liquid crystalline 4-methyl-2 ′-hydroxy-4 ′-alkyloxyazobenzenes containing chelate O–H ⋯ N hydrogen bonds and alkyl chains with 1–12 carbon atoms were studied by using IR spectra, X-ray diffraction and DFT calculations. The results showed that in condensed phases dimeric species can be formed with antiparallel orientation of OH groups that presents an example of interaction traditionally treated as bifurcated hydrogen bonds. The experimentally determined structure of single molecules is in excellent agreement with predicted theoretically. There is also relatively good agreement with respect to dimers. The results based on IR spectra for various derivatives including parent compounds without OH groups and deuterated samples and calculations of frequencies and intensities allowed to analyse the dynamics of investigated molecules and contribution of coordinates of particular atoms to observed modes. Of particular interest were modes into which the δ(OH) and γ(OH) vibrations contributed. A minor influence of dimerization and alkyl-chain length on IR spectra was discussed.