Hydrogen-bonding Solvents Research Articles

Hydrogen bond and surface stress relaxation by aldehydic and formic acidic molecular solvation

Solvation of aldehydes and formic acids has an important impact to health care because these additives can damage DNA and denature proteins causing cancers with the mechanism behind remaining great challenge. From the perspective of solvent hydrogen bond (O:HO or HB with “:” being the electron lone pair of oxygen) transition from the mode of the ordinary water to the hydrating states, we examined the solvation bonding dynamics and the solute capabilities of O:HO bond and surface stress transition using differential Raman spectroscopy and contact angle detection. Results suggest that besides the short-range O:H van der Waals (vdW) bond, the H↔H and O:⇔:O repulsive intermolecular interactions, and the molecular dipolar polarization play important roles in disrupting the solution network and surface stress. Observations may infer the manner of DNA fragmentation by aldehyde and formic acid disruption.

Polymorph Control by Investigating the Effects of Solvent and Supersaturation on Clopidogrel Hydrogen Sulfate in Reactive Crystallization

Reactive crystallization and polymorphic transformation of clopidogrel hydrogen sulfate (CHS) in nine pure solvents were studied at 313.15 K. It is found that thermodynamically stable polymorphic form tends to be obtained in solvents with higher solubility of CHS and the conversion rates from form I to form II are also mainly increased with increasing solubility. The solvent hydrogen bond donor ability is essential for determining the solvent effects on solubility and polymorphic formation of CHS. Besides, the reactive crystallization of CHS at different supersaturations in 2-propanol and 2-butanol was monitored online by using ATR-FTIR and FBRM with a calibration-based approach. The results indicate the nucleation induction period is the kinetic-determining stage and supersaturation is a direct factor to determine the polymorphic formation of CHS: form II was obtained with s under 18 while form I was produced when s increases above 21.

The anti-frozen attribute of sugar solutions

Low-temperature Raman spectroscopy revealed that sugar solvation depresses the critical temperature for homogeneous ice nucleation (TN) whose depression extent follows the order of: trehalose>glucose>fructose at the same concentration and the extent of TN depression for a specific sugar is proportional to its concentration. We attribute the TN depression to the O:H vibration mode redshift induced by the solute dipolar polarization and distortion of the solvent hydrogen bond (O:HO or HB with “:” being the electron lone air of oxygen). The O:H phonon redshift lowers the Debye temperature of the O:H specific heat and disperses the quasisolid-phase boundary and the associated TN.

(Invited) Superconformal Film Growth:Impact of Additives and Deposition on Hydrophilicity

State of the art manufacturing of semiconductor devices involves electrodeposition of copper for device wiring and more recently for through-silicon-vias (TSVs). The process depends on the use of electrolyte additives that affect the local deposition rate thereby resulting in superconformal, or bottom–up “superfilling” of trenches and vias. Quantitative descriptions based on mass balance analysis of the additives and their effect on the local deposition rate have been shown to be effective for describing Damascene feature filling (CEAC, Curvature Enhanced Coverage Mechanism) and larger scale TSV filling (S_NDR, S-shaped negative differential resistance models). Despite the success of these processes much remains to be known concerning the detailed molecular nature of the competitive co-adsorption processes involved in both the suppression and acceleration of the metal deposition reaction. Accordingly, the application of in situ surface science tools such as in situ STM and SEIRAS towards a better understanding of the additive interaction will also be detailed. These studies show that the addition of Cl- to an acidified CuSO4 electrolyte displaces co-adsorbed SO4 2--water species from the Cu surface. The rapidly formed ordered halide overlayer disrupts the adjacent solvent hydrogen bond network to create a hydrophobic interface that facilitates co-adsorption of polyethers, such as poly(ethylene glycol) (PEG), polyoxamers (EPE), polyoxamines (TET), that are known to block the Cu deposition reaction by limiting access of Cu2+ aq to the underlying metal surface. When challenged by bis-(3-sodium sulfopropyl disulfide) (SPS), or mercaptopropane sulfonate (MPS), competitive disulfide/thiol adsorption leads to disruption and displacement of the polymer suppressor. The disulfide/thiol head group tethers SPS/MPS to the surface, via Cu adatoms or defects in the Cl- covered surface, while the SO3 - terminal group makes the interface hydrophilic which accounts for its anti-suppressor action. The potential dependence of competitive SPS adsorption and its dependence on the strength of polyether adsorption were measured.

Prediction of functionally significant single nucleotide polymorphisms in PTEN tumor suppressor gene: An in silico approach.

The phosphatase and tensin homolog (PTEN) gene plays a crucial role in signal transduction by negatively regulating the PI3K signaling pathway. It is the most frequent mutated gene in many human-related cancers. Considering its critical role, a functional analysis of missense mutations of PTEN gene was undertaken in this study. Thirty five nonsynonymous single nucleotide polymorphisms (nsSNPs) within the coding region of the PTEN gene were selected for our in silico investigation, and five nsSNPs (G129E, C124R, D252G, H61D, and R130G) were found to be deleterious based on combinatorial predictions of different computational tools. Moreover, molecular dynamics (MD) simulation was performed to investigate the conformational variation between native and all the five mutant PTEN proteins having predicted deleterious nsSNPs. The results of MD simulation of all mutant models illustrated variation in structural attributes such as root-mean-square deviation, root-mean-square fluctuation, radius of gyration, and total energy; which depicts the structural stability of PTEN protein. Furthermore, mutant PTEN protein structures also showed a significant variation in the solvent accessible surface area and hydrogen bond frequencies from the native PTEN structure. In conclusion, results of this study have established the deleterious effect of the all the five predicted nsSNPs on the PTEN protein structure. Thus, results of the current study can pave a new platform to sort out nsSNPs that can be undertaken for the confirmation of their phenotype and their correlation with diseased status in case of control studies.

Influence of hydrogen bonds on the colloidal and fluorescent properties of detonation nanodiamonds in water, methanol and ethanol

ABSTRACTThis paper presents the results of research of influence of hydrogen bonds with different strength on fluorescence and colloidal properties of detonation nanodiamonds with surface carboxylic groups in the solvents. It is established that the colloidal properties of detonation nanodiamonds are almost independent on hydrogen bonds strength in water, methanol and ethanol. The fluorescent properties of detonation nanodiamonds are dependent on the type of solvent: the more intensive fluorescent properties correspond to weaker hydrogen bonds in solvents.

Position-Specific 13C Fractionation during Liquid-Vapor Transition Correlated to the Strength of Intermolecular Interaction in the Liquid Phase.

The relationship between the strength of the intermolecular interaction in liquid and the position-specific 13C fractionation observed during distillation was investigated. A range of molecules showing different intermolecular interactions in terms of mode and intensity were incorporated in the study. Although it had previously been suggested that during evaporation the diffusive 13C isotope effect in the thin liquid layer interfaced with vapor is not position-specific, herein we show that this is not the case. In particular, the position-specific effect was demonstrated for a series of alcohols. Our hypothesis is that intermolecular interactions in the liquid phase are the source of position-specific 13C fractionation observed on the molecule. A clear trend is observed between the 13C isotope effect of the carbon bearing the heteroatom of chemical function and the relative permittivity, the solvent hydrogen bond acidity, and the solvent hydrogen bond basicity, while only a weak trend was observed when using the 13C content of the whole molecule. Furthermore, two families of products appeared when using the hydrogen bond acidity parameter for the correlation by distinguishing H-acceptor and H-donor molecules from those H-acceptors only. This strongly reinforces the hypothesis of an important role of the 13C positioned close to the interaction center.

Spectroscopic characterisation and structural modelling of new hydrogen-bonded charge transfer complex between picric acid and 3-aminoquinoline

ABSTRACTNew charge transfer hydrogen-bonded (HBCT) complex between the electron donor 3-aminoquinoline with the electron acceptor picric acid has been synthesised and characterised experimentally and theoretically using a variety of physicochemical techniques. The experimental work included the use of UV–vis, IR and 1H NMR studies to characterise the complex in different hydrogen-bonded solvents. The studied reaction proceeded based on 1:1 stoichiometric ratio and the stability constant recorded high values. The solid complex was prepared and characterised by elemental analysis that confirmed its formation in 1:1. Both IR and NMR studies supported the existence of proton and charge transfers in the formed complex. In complemented with experimental results, molecular modelling using DFT using 31–6G(d,p) basis set was carried out in the gas phase where the existence of both charge and hydrogen transfers was reconfirmed in the obtained complex in full consistency with experimental results.

Theoretical study of the spectroscopic and nonlinear optical properties of trans- and cis-4-hydroxyazobenzene.

We investigate the molecular structure, vibrational and electronic absorption spectra, and electronic hyperpolarizabilities of trans and cis isomers of 4-hydroxyazobenzene (HOAB) via density functional theory. Results show that the azo dye exhibits a high third-order nonlinear optical response and good optical transparency. Both the basis set and the functional are important influences on the results obtained when calculating the absorption spectrum and NLO response. We also study the effect of the solvent on the electronic absorption spectrum to assess the ability of the functional to reproduce the experimental spectrum in combination with a suitable solvent model. Our calculations show that the SMD model of Truhlar et al. handles the electrostatic and the non-electrostatic effects of hydrogen-bonding solvents on the absorption spectrum better than the traditional polarizable continuum model does. In addition, our results indicate that the dye trans-HOAB exhibits a high second hyperpolarizability and excellent optical transparency. Also, although the second hyperpolarizability of cis-HOAB is much lower than that of trans-HOAB, it is non-negligible when calculating the optical nonlinearity of HOAB under an optical pump. We also examine the effect of frequency dispersion on second harmonic generation. This study provides the basis for further research on the spectroscopic and nonlinear optical properties of novel azo dyes and other π-conjugated compounds.

Direct use of allylic alcohols and allylic amines in palladium-catalyzed allylic amination.

Allylic alcohols and allylic amines were directly utilized in a Pd-catalyzed hydrogen-bond-activated allylic amination under mild reaction conditions in the absence of any additives. The cooperative action of a Pd-catalyst and a hydrogen-bonding solvent is most likely responsible for its high reactivity. The catalytic system is compatible with a variety of functional groups and can be used to prepare a wide range of linear allylic amines in good to excellent yields. Furthermore, this methodology can be easily applied to the one-step synthesis of two drugs, cinnarizine and naftifine, on a gram scale.

Conformational change in the association of a heterocyclic urea derivative forming two intramolecular hydrogen bonds in polar solvent

Competition of two urea moieties for the same counterpart including change of conformation upon binding in polar solvent.

Ultrafast X-ray measurements of the glass-like, high-frequency stiffness of aqueous solutions.

The ultrafast dynamics of the domains surrounding solutes in aqueous solution were measured using laser-generating GHz phonons inside of 30 mM ferrocyanide solutions and the resulting molecular motions of the solutes and their hydrogen-bonded solvation shells were detected using ultrafast X-ray absorption spectroscopy (UXAS). The measurements of the phonon dynamics around the solutes showed that the domains had a glass-like stiffness on a timescale of tens of picoseconds.

Symmetry and dynamics of FHF− anion in vacuum, in CD2Cl2 and in CCl4. Ab initio MD study of fluctuating solvent–solute hydrogen and halogen bonds

FHF- anion is a classic example of a central-symmetric strongly hydrogen bonded system that has been intensively investigated both experimentally and theoretically. In this paper we focus on solvent effects on symmetry, structure and dynamics of the anion. The FHF- anion is studied in vacuum, dissolved in CH2Cl2 and dissolved in CCl4 by ab initio molecular dynamics simulations. We show that CH2Cl2 molecules form CHF hydrogen bonds with lone pairs of fluorine atoms, while CCl4 molecules form halogen bonds. These specific non-covalent solvent-solute interactions are cooperatively coupled to the FHF- hydrogen bonds. The fluctuation of solvent molecules' positions is the driving force changing the FHF- hydrogen bond geometry. Most of the time, the anion is solvated asymmetrically, which leads to the asymmetric bridging particle position, though the time-averaged D∞h symmetry is retained. Interestingly, this transient asymmetrization of FHF- is more pronounced in CCl4, than in CH2Cl2. We show that the 1H and 19F NMR chemicals shifts react sensitively to the changes of anion's geometry and the limiting chemical shifts of free solvated FH and F- are strongly solvent-dependent.

Thermal imidization process of polyimide film: Interplay between solvent evaporation and imidization

The thermal imidization process of 1,2,4,5-benzenetetracaboxylic (PMDA)/4,4’-diamnodiphenyl ether (4,4′-ODA) solutions in N-methyl-2-pyrrolidone (NMP) from polyimide (PI) precursor, poly (amic acid) (PAA), was systematically investigated through a series of characterization methods, such as Fourier transform infrared spectroscopy (FT-IR), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and dynamic mechanical analysis (DMA). At the low-temperature drying stage, mechanical properties and Tg of polymer films were increased as a result of solvent removal. TGA method was used to quantitatively monitor the evaporations of hydrogen-bonded solvents on PAA and of the dehydration during the imidization reaction that occurred above 150 °C. During the imidization stage, the interplay between the solvent evaporation and the imidization was the key factor that determined the enhancement of the mechanical properties and Tg. The degree of imidization approached 94% when the temperature was increased to 250 °C. A “complete” imidization was achieved by annealing between 350 and 400 °C. The enhancement in the mechanical properties of final PI films may result from the increased Tg and the crystallized structure formed during the annealing stage.

Conformational studies of new pseudotripeptide with pyrazine amidoxime motif and simplified analogs using IR, NMR spectroscopy, and molecular dynamic simulations

Solution structures of new pyrazine-based pseudotripeptide with amidoxime function and simplified pseudodipeptide analogs were determined by a combination of IR and NMR spectroscopic studies and molecular dynamic simulations using explicit chloroform as a solvent. It was found that proline-phenylalanine dipeptide residue and amidoxime moiety in o-position are essential for intramolecular hydrogen bonding including a seven-membered γ-turn formation. In addition, a cis/trans equilibrium study was present for prolyl amides in polar solvents (D2O and DMSO). A phenylalanine substituent was found to exhibit profound effect on thermodynamic parameters in prolyl peptides. The presence of intramolecular hydrogen bonds dramatically increases the amount of trans isomer in non-hydrogen-bonding CHCl3 and significantly favor cis isomer in hydrogen-bonding solvents such as DMSO and D2O. All molecules are not cytotoxic therefore they can be further studied in relation to potent biological activities.

Confinement effects on micellar systems with a hydrogen-bonding solvent.

Space confinement greatly influences the properties of liquids, such as their viscosity and capillary critical point. For aqueous solutions of amphiphiles, this effect is extended to the mobility and micellization properties of these molecules, changing important characteristics of micellar solutions such as the critical micelle concentration (CMC). In the present work, we use a lattice Monte Carlo model, which allows for orientational freedom and hydrogen-bond formation for the water molecules, to investigate confinement effects on a solution of surfactants limited by two parallel walls perpendicular to one of the Cartesian axes. This configuration aims to reproduce a small pore, and walls with a hydrophilic or hydrophobic character are studied. We find that, for hydrophilic walls, there is an increase in the value of the CMC for small pores, caused by space confinement effects and also by the interactions of the amphiphile polar heads with the walls. Micelles are able to adhere to the walls as a whole, and their shape shows little change compared to micelles in the bulk solution. Hydrophobic walls show a more dramatic effect on the properties of the solution, arising mainly from the strong adsorption of the amphiphile tails on the walls, driven by the hydrophobic effect. The process of adsorption of amphiphiles with increasing concentration shows a behavior very similar to the one observed in experiments and simulations of such systems. Micelles adsorbed to the hydrophobic walls also show significant changes in their moments of inertia compared to the bulk ones, which is attributed to the formation of half-micelles that have their tails attached to the walls and the polar heads facing the solution. We extend our analysis to the change in the hydrogen-bonding properties of the solvent caused by the confinement, and how that is directly related to the number of free amphiphiles in our system for different pore sizes. Finally, we test different surfactant sizes and how they affect the micellar shape for different concentrations.

The conformational analysis of push-pull enaminones using FTIR and NMR spectroscopy, and quantum chemical calculations. VI. β−N−Methyl-aminovinyl trifluoromethyl ketone and α−methyl−β−N−methylaminovinyl trifluoromethyl ketone

X-Ray analysis, NMR and IR Fourier spectra of two enaminoketones 4-(N-methylamino)-1,1,1-trifluorobut-3-en-2-one F3CCOCHCHNH(CH3) (1) 4-(N-methylamino)-1,1,1-trifluoro-3-methylbut-3-en-2-one F3CCOC(CH3)CHNH(CH3) (2) were studied in solid state and solutions. It was shown that the substitution of proton at α-position of vinyl moiety with methyl group changes significantly electronic and spatial structure of enaminoketone. In solid state enaminoketone 1 is found to be exclusively as Z-s-Z-ap isomer with intramolecular hydrogen bond. At the same time molecules of enaminoketone 2 have E-s-E-ap stereoisomeric structure forming dimers due to intermolecular NH⋯OC hydrogen bonds. Exposure of Ar-matrix isolated 1 to UV-radiation results in appearance of various E forms with free methylamino- and hydroxy groups. The same effect was observed for 2 in solutions in CCl4 under addition of polar HMPA or DMSO during spontaneous E ⇌ Z isomerization. For enaminoketone 1 under similar conditions we observed reverse process of Z ⇌ E isomerization, E stereoisomeric forms with hydroxy group being trace quantity only.Study of solvent influence on FTIR spectra revealed that introduction of methyl group as substituent at α-position of vinyl moiety increases electron population of CO double bond. Consequently, in contrast with enaminoketone 1 where the main contribution to the ν˜ (CO) band shift to lower wavenumbers in all three stereoisomeric structures makes solvent polarity/polarizability term (π*), influence of solvent's hydrogen bond acceptor (HBA) basicity (β) on ν˜ (CO) band shift of 2 predominates in the E-s-Z-ap and Z-s-Z-ap isomers. Similarly to enaminoketone 1, negative shift of the ν˜ (CC) band to lower wavenumbers occurs due to hydrogen bond formation between π system of vinyl moiety and hydrogen bond donor solvents in all stereoisomeric forms of enaminoketone 2.

Catalysis of Heterocyclic Azadiene Cycloaddition Reactions by Solvent Hydrogen Bonding: Concise Total Synthesis of Methoxatin.

Although it has been examined for decades, no general approach to catalysis of the inverse electron demand Diels-Alder reactions of heterocyclic azadienes has been introduced. Typically, additives such as Lewis acids lead to nonproductive consumption of the electron-rich dienophiles without productive activation of the electron-deficient heterocyclic azadienes. Herein, we report the first general method for catalysis of such cycloaddition reactions by using solvent hydrogen bonding of non-nucleophilic perfluoroalcohols, including hexafluoroisopropanol (HFIP) and trifluoroethanol (TFE), to activate the electron-deficient heterocyclic azadienes. Its use in promoting the cycloaddition of 1,2,3-triazine 4 with enamine 3 as the key step of a concise total synthesis of methoxatin is described.

Molecular Conductance through a Quadruple‐Hydrogen‐Bond‐Bridged Supramolecular Junction

AbstractA series of self‐complementary ureido pyrimidinedione (UPy) derivatives modified with different aurophilic anchoring groups were synthesized. Their electron transport properties through the quadruple hydrogen bonds in apolar solvent were probed employing the scanning tunneling microscopy break junction (STMBJ) technique. The molecule terminated with a thiol shows the optimal electron transport properties, with a statistical conductance value that approaches 10−3 G0. The 1H NMR spectra and control experiments verify the formation of quadruple hydrogen bonds, which can be effectively modulated by the polarity of the solvent environment. These findings provide a new design strategy for supramolecular circuit elements in molecular electronics.

Molecular Conductance through a Quadruple-Hydrogen-Bond-Bridged Supramolecular Junction.

A series of self-complementary ureido pyrimidinedione (UPy) derivatives modified with different aurophilic anchoring groups were synthesized. Their electron transport properties through the quadruple hydrogen bonds in apolar solvent were probed employing the scanning tunneling microscopy break junction (STMBJ) technique. The molecule terminated with a thiol shows the optimal electron transport properties, with a statistical conductance value that approaches 10(-3) G0 . The (1) H NMR spectra and control experiments verify the formation of quadruple hydrogen bonds, which can be effectively modulated by the polarity of the solvent environment. These findings provide a new design strategy for supramolecular circuit elements in molecular electronics.