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Glycans are central to information content and regulation in biological systems. These carbohydrate molecules are active either as oligo- or polysaccharides, often in the form of glycoconjugates. The monosaccharide entities are joined by glycosidic linkages and stereochemical arrangements are of utmost importance in determining conformation and flexibility of saccharides. The conformational preferences and population distributions at the glycosidic torsion angles phi and psi have been investigated for O-methyl glycosides of three disaccharides where the substitution takes place at a secondary alcohol, viz., in alpha-l-Fucp-(1 -> 3)-beta-d-Glcp-OMe, alpha-l-Fucp-(1 -> 3)-alpha-d-Galp-OMe and alpha-d-Glcp-(1 -> 4)-alpha-d-Galp-OMe, corresponding to disaccharide structural elements present in bacterial polysaccharides. Stereochemical differences at or adjacent to the glycosidic linkage were explored by solution state NMR spectroscopy using one-dimensional 1H,1H-NOESY NMR experiments to obtain transglycosidic proton-proton distances and one- and two-dimensional heteronuclear NMR experiments to obtain 3JCH transglycosidic coupling constants related to torsion angles phi and psi. Computed effective proton-proton distances from molecular dynamics (MD) simulations showed excellent agreement to experimentally derived distances for the alpha-(1 -> 3)-linked disaccharides and revealed that for the bimodal distribution at the psi torsion angle for the alpha-(1 -> 4)-linked disaccharide experiment and simulation were at variance with each other, calling for further force field developments. The MD simulations disclosed a highly intricate inter-residue hydrogen bonding pattern for the alpha-(1 -> 4)-linked disaccharide, including a nonconventional hydrogen bond between H5 ' in the glucosyl residue and O3 in the galactosyl residue, supported by a large downfield 1H NMR chemical shift displacement compared to alpha-d-Glcp-OMe. Comparison of population distribution

According to IUPAC definition, the hydrogen bond ‘is an attractive interaction usually presented as X—H Y—Z, where the electropositive hydrogen atom is located between two electronegative species X and Y.[1] The stability of hydrogen bonds varies in the range from -0.2 to -40 kcal/mol depending on the nature of the X and Y species and the geometry of the hydrogen bond. In this presentation, new modes of hydrogen bonding will be discussed. Namely, it was found that nearly 20% of all crystal structures, from Cambridge Structural Database, containing water-water or alcohol dimers, possess, so far, unusual antiparallel OH/OH interactions. The interaction energies of this type of hydrogen bonding (Figure 1.) are systematically calculated at CCSD(T)/CBS level of theory.[2] It was shown that the strength of the antiparallel interactions can be similar as the strength of classical hydrogen bonds, i.e. up to – 4.7 kcal/mol. The geometric parameters describing the antiparallel interactions were suggested, as well.

Peroxymonosulfate (PMS) as an oxidant has been extensively applied to remove organic pollutants, but the molecular interaction mechanism of PMS and organic pollutants under the electrochemical process remains unclear. This work unraveled the interaction relationship of PMS on ofloxacin (OFN) degradation by PMS-based electrochemical oxidation. The results showed that hydroxyl and sulfate radicals generated from the electrochemical reaction could effectively degrade OFN. Under the electrochemical oxidation process, 100% or 12.1 ± 2.1% of OFN was degraded within 15 min in the presence or absence of PMS, respectively. Quantum chemical calculations and molecular dynamics simulations indicated that the hydrogen bonds and van der Waals force were the primary interaction force between PMS and OFN. Besides, the PMS-OFN binding process was a stable dynamic process, and its stability was dependent on the number of hydrogen bonds generated. The structure-activity relationship suggested that OFN was transformed into short-chain intermediates with lower toxicity within 15 min. Additionally, this electrochemical system for degrading OFN retained excellent reusability and recyclability, affording high oxidation ability during successive cycles. More importantly, this electrochemical process could highly efficiently degrade various organic pollutants (4-chlorophenol, methyl orange, sulfamethoxazole, and perfluorooctanoic acid). This study provided a new possibility for the application of the electrochemical system in large-scale wastewater treatment. © 2024 American Chemical Society.

Aqueous nanodiamonds illuminated by UV light produce free solvated electrons, which may drive high-energy reduction reactions in water. However, the influence of water conformations on the excited-state electron-transfer mechanism are still under debate. In this work, we offer a theoretical study of charge-transfer states in adamantane-water structures obtained by linear-response time-dependent density-functional theory. Small water clusters with broken hydrogen bonds are found to efficiently bind the electron from adamantane. A distinction is made with respect to the nature of the water clusters: some bind the electron in a water cavity, others along a strong permanent total dipole. These two types of bound states are more strongly binding, the higher their electron affinity and their positive electrostatic potential, the latter being dominated by the energy of the lowest unoccupied molecular orbital of the isolated water clusters. Structural sampling in a thermal equilibrium at room temperature via molecular dynamics snapshots confirms under which conditions the underlying waters clusters can occur and verifies that broken hydrogen bonds in the water network close to adamantane can create traps for the solvated electron.

Unwanted ice build-up is a ubiquitous phenomenon in nature, which creates a series of catastrophic impacts on a wide range of human activities. Various anti/de-icing materials have been proposed for dealing with icing issues. Superhydrophobic anti/de-icing coatings have been widely reported since it has high efficiency and can be achieved in different ways. The surface functional groups have a significant influence on surface energy which is related to surface wettability. However, the influence of the coating surfaces functional groups on the anti-/de-icing properties is still not well studied. To investigate this influence, different groups with different hydrophilicity have been introduced to 3,3,4,4,5,5,6,6,7,7,8,8,8-Tridecafluorooctyl acrylate (TFOA) to fabricate several branch copolymer ice-phobic coatings. The anti-icing performance and the influence of group radius and interaction were studied. The acrylic acid TFOA showed a great superhydrophobic property (over 150° water contact angle), lower ice adhesion strength (<50 kPa), and lower wear depth compared with other copolymer coatings. The mechanism was studied via the molecular dynamic calculation carried out in ChemDraw software. The interaction between hydrophobic and hydrophilic groups and the steric length of the hydrophilic groups influence the surface structure and surface element distribution, further influencing the ice adhesion strength., Validerad;2024;Nivå 2;2024-06-10 (hanlid);Full text license: CC BY

Unwanted ice build-up is a ubiquitous phenomenon in nature, which creates a series of catastrophic impacts on a wide range of human activities. Various anti/de-icing materials have been proposed for dealing with icing issues. Superhydrophobic anti/de-icing coatings have been widely reported since it has high efficiency and can be achieved in different ways. The surface functional groups have a significant influence on surface energy which is related to surface wettability. However, the influence of the coating surfaces functional groups on the anti-/de-icing properties is still not well studied. To investigate this influence, different groups with different hydrophilicity have been introduced to 3,3,4,4,5,5,6,6,7,7,8,8,8-Tridecafluorooctyl acrylate (TFOA) to fabricate several branch copolymer ice-phobic coatings. The anti-icing performance and the influence of group radius and interaction were studied. The acrylic acid TFOA showed a great superhydrophobic property (over 150° water contact angle), lower ice adhesion strength (<50 kPa), and lower wear depth compared with other copolymer coatings. The mechanism was studied via the molecular dynamic calculation carried out in ChemDraw software. The interaction between hydrophobic and hydrophilic groups and the steric length of the hydrophilic groups influence the surface structure and surface element distribution, further influencing the ice adhesion strength., Validerad;2024;Nivå 2;2024-06-10 (hanlid);Full text license: CC BY

Nitrilotris(methylenephenylphosphinic) acid (NTPAH₃) was silylated using hexamethyldisilazane to produce the tris(trimethylsilyl) derivative NTPA(SiMe₃)₃. From the latter, upon alcoholysis in chloroform, NTPAH₃ could be recovered. Thus, a new modification of that phosphinic acid formed. Meanwhile, NTPAH₃ synthesized in aqueous hydrochloric acid crystallized in the space group P3c1 with the formation of O-H···O H-bonded networks (NTPAH₃P), in chloroform crystals in the space group R3c formed (NTPAH₃M), the constituents of which are individual molecules with exclusively intramolecular O-H···O hydrogen bonds. Both solids, NTPAH₃P and NTPAH₃M, were characterized by single-crystal X-ray diffraction, multi-nuclear (¹H, ¹³C, ³¹P) solid-state NMR spectroscopy, and IR spectroscopy as well as quantum chemical calculations (both of their individual constituents as isolated molecules as well as in the periodic crystal environment). In spite of the different stabilities of their constituting molecular conformers, the different crystal packing interactions rendered the modifications of NTPAH₃P and NTPAH₃M similarly stable. In both solids, the protons of the acid are engaged in cyclic (O=P–O–H)₃ H-bond trimers. Thus, the trialkylamine N atom of this compound is not protonated. IR and ¹H NMR spectroscopy of these solids indicated stronger H-bonds in the (O=P–O–H)₃ H-bond trimers of NTPAH₃M over those in NTPAH₃P.

The excessive use and accumulation of water-soluble polymers (WSPs, known as “liquid plastics”) in the environment can pose potential risks to both ecosystems and human health, but the environmental fate of WSPs remains unclear. Here, the adsorption behavior of WSPs with different molecular weight on kaolinite (Kaol) and montmorillonite (Mt) were examined. The results showed that the adsorption of PEG and PVP on minerals were controlled by hydrogen bond and van der Waals force. The Fourier transform infrared (FTIR) spectra and two-dimensional correlation spectroscopy (2D-COS) analysis revealed that there were interactions between the Al-O and Si-O groups of the minerals and the polar O- or N-containing functional groups as well as the alkyl groups of PEG and PVP. The adsorption characteristics of WSPs were closely related to their molecular weight and the pore size of minerals. Due to the relatively large mesopore size of Kaol, both PEG and PVP were absorbed into inner spaces, for which the adsorption capacity increased with molecular weight of the polymers. For Mt, all types of PEG could enter its micropores, while PVP with larger molecular weights appeared to be confined externally, leading to a decrease in the adsorption capacity of PVP with increasing molecular weight. The findings of this study provide a theoretical basis for scientific evaluation of environmental processes of WSPs., Sanitary Engineering

Hyaluronic acid (HA) is a hydrophilic natural polysaccharide consisting of alternating monosaccharide units of glucuronic acid and N-acetyl glucosamine. In aqueous solutions the electrostatic repulsion of the carboxylate groups hampers the formation of supermolecular structures that can be partially stabilized by the addition of salt. Increased permittivity of the mixed water:organic solvents causes better compensation of the negative charge of HA chains by dissolved cations which changes their interactions with other molecules. In this study we simulate interactions of two HA chains in water:1,4-dioxane and water:tert-butanol mixed solvents with varying NaCl concentrations using molecular dynamics (MD). Anti-parallel double-helix-like duplexes are formed in NaCl-containing water:1,4-dioxane mixture and remain stable even when NaCl is removed. Parallel duplexes separate after a short time. In water:tert-butanol analogous duplexes are unstable. Stability of HA duplexes is thus determined by the solvent composition and the ability of its components to separate in the solvation shell of HA molecules, as well as by the mutual orientation of the chains.

Hydrogen bonding (HB) is vital for the phase transition and physical properties of stimuli responsive copolymers. However, the governing mechanism remains unclear. Herein, we investigated the HB dynamics in a representative thermo-responsive copolymer (PNIPAM-AM) aqueous solution. Three types of HB were identified: polymer-polymer chain (C[dbnd]O:H–N), polymer chain-water molecule (C[dbnd]O:H–O) and water-water molecules (H–O:H–O) by vibrational spectroscopy. Increasing polymer concentration, the H–O:H–O softened and C[dbnd]O:H–O stiffened, leading to the destruction of HB network in water-water clusters. Upon increasing solution temperature, C[dbnd]O:H–O softened while C[dbnd]O:H–N stiffened, resolving the dehydration and cross-linking of polymer chains. Confinement of water molecules in the “cages” (∼ tens to hundreds of micrometers) after sol-gel phase transition was visualized, disclosing the mechanism of water holding capacity of PNIPAM-AM. The correlation of molecule vibration and copolymer microscopic structure was established, contributing to the fundamental understanding of phase behavior and physical properties regulations in stimuli responsive copolymer aqueous solution. © 2024

Pharmaceutical multi-component solid forms, including salts, co-crystals and co-amorphous systems (COAMs), are used to modify the physicochemical and pharmaco-kinetic properties of these drugs. Gefitinib and two co-formers, bumetanide and furosemide, form salt hydrates in the presence of water and COAMs in the absence of water using solvent evaporation method. Molecular dynamic simulation and isolated water analysis reveal that water molecules play a multi-faceted role in stabilizing the crystalline salt hydrate systems by reducing the total energy of the system, establishing hydrogen bonds, and maintaining the crystalline 3D structures. Salt hydrates are also formed in the presence of water using liquid-assisted grinding. In the absence of water, intermolecular interactions between Gefitinib and co-formers facilitate the formation of COAMs during ball milling and quench cooling, i.e., in the absence of water. These findings provide valuable insights to the formation of salt hydrates and COAMs by controlling the presence of water.

In this study, polyvinylidene fluoride (PVDF) fibers doped with hydrated calcium nitrate were prepared using electrospinning. The samples were analyzed using scanning electron microscopy (SEM), X-ray diffraction (XRD), optical spectroscopy, X-ray photoelectron spectroscopy (XPS), Fourier transform infrared (FTIR), Raman, and photoluminescence (PL) spectroscopy. The results are complementary and confirm the presence of chemical hydrogen bonding between the polymer and the dopant. Additionally, there was a significant increase in the proportion of the electroactive polar beta phase from 72 to 86%. It was shown that hydrogen bonds acted as a transport pathway for electron capture by the conjugated salt, leading to more than a three-fold quenching of photoluminescence. Furthermore, the optical bandgap of the composite material narrowed to the range of visible light energies. For the first time, it the addition of the salt reduced the energy of the PVDF exciton by a factor of 17.3, initiating photocatalytic activity. The calcium nitrate-doped PVDF exhibited high photocatalytic activity in the degradation of methylene blue (MB) under both UV and visible light (89 and 44%, respectively). The reaction rate increased by a factor of 2.4 under UV and 3.3 under visible light during piezophotocatalysis. The catalysis experiments proved the efficiency of the membrane design and mechanisms of catalysis are suggested. This study offers insight into the nature of chemical bonds in piezopolymer composites and potential opportunities for their use.

In this study, polyvinylidene fluoride (PVDF) fibers doped with hydrated calcium nitrate were prepared using electrospinning. The samples were analyzed using scanning electron microscopy (SEM), X-ray diffraction (XRD), optical spectroscopy, X-ray photoelectron spectroscopy (XPS), Fourier transform infrared (FTIR), Raman, and photoluminescence (PL) spectroscopy. The results are complementary and confirm the presence of chemical hydrogen bonding between the polymer and the dopant. Additionally, there was a significant increase in the proportion of the electroactive polar beta phase from 72 to 86%. It was shown that hydrogen bonds acted as a transport pathway for electron capture by the conjugated salt, leading to more than a three-fold quenching of photoluminescence. Furthermore, the optical bandgap of the composite material narrowed to the range of visible light energies. For the first time, it the addition of the salt reduced the energy of the PVDF exciton by a factor of 17.3, initiating photocatalytic activity. The calcium nitrate-doped PVDF exhibited high photocatalytic activity in the degradation of methylene blue (MB) under both UV and visible light (89 and 44%, respectively). The reaction rate increased by a factor of 2.4 under UV and 3.3 under visible light during piezophotocatalysis. The catalysis experiments proved the efficiency of the membrane design and mechanisms of catalysis are suggested. This study offers insight into the nature of chemical bonds in piezopolymer composites and potential opportunities for their use.

type:Communication, A taste sensor with lipid/polymer membranes is attracting attention as a method to evaluate taste objectively. However, due to the characteristic of detecting taste by changes in membrane potential, taste sensors cannot measure non-charged bitter substances. Many foods and medicines contain non-charged bitter substances, and it is necessary to quantify these tastes with sensors. Therefore, we have been developing taste sensors to detect bitter tastes caused by non-charged substances such as caffeine. In previous studies, a sensor for detecting bitterness caused by caffeine and theobromine, theophylline, was developed, using a membrane modified with hydroxybenzoic acid (HBA) as the sensing part. The sensor was designed to form intramolecular hydrogen bonds (H-bonds) between the hydroxy group and carboxy group of HBA and to successively cause the intermolecular H-bonds between HBA and caffeine molecules to be measured. However, whether this sensing principle is correct or not cannot be confirmed from the results of taste sensor measurements. Therefore, in this study, we explored the interaction between HBA and caffeine by H^^1-nuclear magnetic resonance spectroscopy (NMR). By the H^^1 NMR detection, we confirmed that both the substances interact with each other. Furthermore, the nuclear Overhauser effect (NOE) of intermolecular spatial conformation in solution was measured, by which 2,6-dihydroxybenzoic acid (2,6-DHBA) preferably interacted with caffeine via the H-bonding and stacking configuration between aromatic rings. Identifying the binding form of 2,6-DHBA to caffeine was estimated to predict how the two substances interact.

It has been recently demonstrated that free DNA tracers have the potential in tracing water flow and contaminant transport through the vadose zone. However, whether the free DNA tracer can be used in flood irrigation area to track water flow and solute/contaminant transport is still unclear. To reveal the infiltration process and retention mechanisms of surface applied free DNA tracer through soil under flood irrigation, we tested the fate and transport behavior of surface applied free DNA tracers through packed saturated sandy soil columns with a 10 cm water head mimicking flood irrigation. From the experimental breakthrough curves and by fitting a two-site kinetic sorption model (R2 = 0.83-0.91 and NSE = 0.79-0.89), adsorption/desorption rates could be obtained and tracer retention profiles could be simulated. Together these results revealed that 1) the adsorption of free DNA was dominantly to clay particles in the soil, which took up 1.96 % by volume, but took up >97.5 % by surface area and densely cover the surface of sand particles; and 2) at a pore water pH of 8.0, excluding the 4.9 % passing through and 3.1 % degradation amount, the main retention mechanisms in the experimental soil were ligand exchange (42.0 %), Van der Waals interactions (mainly hydrogen bonds), electrostatic forces and straining (together 44.7 %), and cation bridge (5.3 %). To our knowledge, this study is the first to quantify the contribution of each of the main retention mechanisms of free synthetic DNA tracers passing through soil. Our findings could facilitate the application of free DNA tracer to trace vadose zone water flow and solute/contaminant transport under flood irrigation and other infiltration conditions.

type:Communication, A taste sensor with lipid/polymer membranes is attracting attention as a method to evaluate taste objectively. However, due to the characteristic of detecting taste by changes in membrane potential, taste sensors cannot measure non-charged bitter substances. Many foods and medicines contain non-charged bitter substances, and it is necessary to quantify these tastes with sensors. Therefore, we have been developing taste sensors to detect bitter tastes caused by non-charged substances such as caffeine. In previous studies, a sensor for detecting bitterness caused by caffeine and theobromine, theophylline, was developed, using a membrane modified with hydroxybenzoic acid (HBA) as the sensing part. The sensor was designed to form intramolecular hydrogen bonds (H-bonds) between the hydroxy group and carboxy group of HBA and to successively cause the intermolecular H-bonds between HBA and caffeine molecules to be measured. However, whether this sensing principle is correct or not cannot be confirmed from the results of taste sensor measurements. Therefore, in this study, we explored the interaction between HBA and caffeine by H^^1-nuclear magnetic resonance spectroscopy (NMR). By the H^^1 NMR detection, we confirmed that both the substances interact with each other. Furthermore, the nuclear Overhauser effect (NOE) of intermolecular spatial conformation in solution was measured, by which 2,6-dihydroxybenzoic acid (2,6-DHBA) preferably interacted with caffeine via the H-bonding and stacking configuration between aromatic rings. Identifying the binding form of 2,6-DHBA to caffeine was estimated to predict how the two substances interact.

In this study, polyvinylidene fluoride (PVDF) fibers doped with hydrated calcium nitrate were prepared using electrospinning. The samples were analyzed using scanning electron microscopy (SEM), X-ray diffraction (XRD), optical spectroscopy, X-ray photoelectron spectroscopy (XPS), Fourier transform infrared (FTIR), Raman, and photoluminescence (PL) spectroscopy. The results are complementary and confirm the presence of chemical hydrogen bonding between the polymer and the dopant. Additionally, there was a significant increase in the proportion of the electroactive polar beta phase from 72 to 86%. It was shown that hydrogen bonds acted as a transport pathway for electron capture by the conjugated salt, leading to more than a three-fold quenching of photoluminescence. Furthermore, the optical bandgap of the composite material narrowed to the range of visible light energies. For the first time, it the addition of the salt reduced the energy of the PVDF exciton by a factor of 17.3, initiating photocatalytic activity. The calcium nitrate-doped PVDF exhibited high photocatalytic activity in the degradation of methylene blue (MB) under both UV and visible light (89 and 44%, respectively). The reaction rate increased by a factor of 2.4 under UV and 3.3 under visible light during piezophotocatalysis. The catalysis experiments proved the efficiency of the membrane design and mechanisms of catalysis are suggested. This study offers insight into the nature of chemical bonds in piezopolymer composites and potential opportunities for their use.

In this study, polyvinylidene fluoride (PVDF) fibers doped with hydrated calcium nitrate were prepared using electrospinning. The samples were analyzed using scanning electron microscopy (SEM), X-ray diffraction (XRD), optical spectroscopy, X-ray photoelectron spectroscopy (XPS), Fourier transform infrared (FTIR), Raman, and photoluminescence (PL) spectroscopy. The results are complementary and confirm the presence of chemical hydrogen bonding between the polymer and the dopant. Additionally, there was a significant increase in the proportion of the electroactive polar beta phase from 72 to 86%. It was shown that hydrogen bonds acted as a transport pathway for electron capture by the conjugated salt, leading to more than a three-fold quenching of photoluminescence. Furthermore, the optical bandgap of the composite material narrowed to the range of visible light energies. For the first time, it the addition of the salt reduced the energy of the PVDF exciton by a factor of 17.3, initiating photocatalytic activity. The calcium nitrate-doped PVDF exhibited high photocatalytic activity in the degradation of methylene blue (MB) under both UV and visible light (89 and 44%, respectively). The reaction rate increased by a factor of 2.4 under UV and 3.3 under visible light during piezophotocatalysis. The catalysis experiments proved the efficiency of the membrane design and mechanisms of catalysis are suggested. This study offers insight into the nature of chemical bonds in piezopolymer composites and potential opportunities for their use.

Objective: The aim was to design, synthesis and investigation of possible interactions in the enzyme active site of a series of arylhydrazone derivatives for the inhibition of the FAAH enzyme.” Material and Method: Arylhydrazone derivatives were obtained through the reaction of nicotinic hydrazide or benzohydrazide with appropriate aldehyde derivatives, and the obtained crude product was recrystallized from ethanol. After elucidating chemical structures of the compounds via spectroscopic methods, the inhibitory activities against hFAAH were screened. The results were further supported with molecular modeling studies. Result and Discussion: In this study, a new series of seven arylhydrazone derivatives were screened against hFAAH. 4-phenoxyphenyl bearing derivative 5 was found to inhibit hFAAH 40 % at 10 µM which indicates that newly developed inhibitor could serve as a starting point for improving inhibitory effect of the new series. © 2023 University of Ankara. All rights reserved., Gazi Üniversitesi: 02/2020-24, The authors would like to thank Prof. Dr. Burcu Caliskan for providing her expertise in this research. This research is financially supported by Gazi University Research Project Unit (BAP: 02/2020-24).

Objective: The aim was to design, synthesis and investigation of possible interactions in the enzyme active site of a series of arylhydrazone derivatives for the inhibition of the FAAH enzyme.” Material and Method: Arylhydrazone derivatives were obtained through the reaction of nicotinic hydrazide or benzohydrazide with appropriate aldehyde derivatives, and the obtained crude product was recrystallized from ethanol. After elucidating chemical structures of the compounds via spectroscopic methods, the inhibitory activities against hFAAH were screened. The results were further supported with molecular modeling studies. Result and Discussion: In this study, a new series of seven arylhydrazone derivatives were screened against hFAAH. 4-phenoxyphenyl bearing derivative 5 was found to inhibit hFAAH 40 % at 10 µM which indicates that newly developed inhibitor could serve as a starting point for improving inhibitory effect of the new series. © 2023 University of Ankara. All rights reserved., Gazi Üniversitesi: 02/2020-24, The authors would like to thank Prof. Dr. Burcu Caliskan for providing her expertise in this research. This research is financially supported by Gazi University Research Project Unit (BAP: 02/2020-24).

In the present work, we report the synthesis, structural characterization, and computational studies of (E)-N'-((5-nitrofuran-2-yl)methylene)quinoline-8-sulfonohydrazide (QNF) as a potential antimicrobial drug candidate. To design the target molecule, we utilized a molecular hybridization technique that connects two antimicrobial pharmacophores (quinoline and 5-nitrofuran rings) with a sulfonyl hydrazone moiety. QNF was synthesized by the condensation of quinoline-8-sulfonohydrazide with 5-nitrofuran-2-carbaldehyde, and characterized by various spectral techniques including single-crystal X-ray crystallography. QNF was extensively evaluated for its antibacterial and antifungal activity. The inhibition capacity of QNF on Candida albicans filamentation and biofilm formation was further investigated. Biofilm inhibition of QNF against C. albicans was supported by molecular docking studies in the binding site of agglutinin-like sequence 3 (Als3). Drug-like profile of QNF was confirmed by in silico calculation of its significant physicochemical properties. Additionally, the optimized geometrical structure, natural bond orbital calculations, frontier molecular orbital and molecular electrostatic potential analysis of QNF were carried out using the density functional theory method at the B3LYP with 6-31+G(d,p) basis set. 1H and 13C NMR chemical shift values were performed using the gauge-invariant atomic orbital method. Structural parameters and NMR values obtained experimentally were compared with the calculated values.

The synthesis, characterization and liquid crystalline and electrochemical properties of novel triarylamines, in which the triphenylamine platform is non-symmetrically modified with a 4-(6-oxyhexyloxy)benzoic acid group, are reported. Compounds show columnar liquid crystalline behavior, as confirmed through the use of polarized optical microscopy, differential scanning calorimetry and X-ray diffraction. Electrochemical properties were measured using cyclic voltammperometry, obtaining low oxidation potentials and HOMO values that were optimum for consideration as organic semiconductors in hole transport layers. In addition, the photoredox activity of one of these derivatives in dichloromethane was studied under light irradiation. A photooxidation/assembly process under white light irradiation occurs without the assistance of hydrogen bonding amide functional groups.

Nucleophilicities N of prototype saturated and unsaturated hydrocarbons methane, ethane, cyclopropane, ethyne and ethene when acting as Lewis bases were determined from the dissociation energies D of the hydrogen-bond complexes B…HX calculated ab initio, where B is the hydrocarbon and HX is variously HF, HCl, HBr, HI, HCN, HCCH and HCP. The values of N obtained were 0.712(31), 0.736(32), 0.283(44), 2.561(73), 2.604(51) for methane, ethane, cyclopropane, ethyne and ethene, respectively. The inductive effect of the methyl group when ethyne is methylated was also investigated.

Recent NMR studies of the exchangeable protons of GAGs in aqueous solution, including those of the amide, sulfamate, and hydroxyl moieties, have demonstrated potential for the detection of intramolecular hydrogen bonds providing insights into secondary structure preferences. GAG amide protons are observable by NMR over wide pH and temperature ranges; however, specific solution conditions are required to reduce the exchange rate of the sulfamate and hydroxyl protons and allow their detection by NMR. Building on the vast body of knowledge on detection of hydrogen bonds in peptides and proteins, a variety of methods can be used to identify hydrogen bonds in GAGs including temperature coefficient measurements, evaluation of chemical shift differences between oligo- and monosaccharides, and relative exchange rates measured through line shape analysis and EXSY spectra. Emerging strategies to allow direct detection of hydrogen bonds through heteronuclear couplings offer promise for the future. Molecular dynamic simulations are important in this effort both to predict and confirm hydrogen bond donors and acceptors.

Hyaluronic acid (HA) is a natural polysaccharide present in the connective tissues of vertebrates, often used in the cosmetics and pharmaceutical industries. HA is a strongly hydrophilic macromolecule forming highly swollen random coils in aqueous solutions. Although some authors reported the secondary and tertiary structures of HA chain, others brought convincing evidence contradicting this hypothesis. This study aims at investigation of the stability and dynamics of the temporary duplex HA structures at different NaCl concentrations by molecular dynamics (MD) simulations. The tendency to duplex formation grows with NaCl concentration reaching its maximum at 0.6 M. This profile is a result of two counteracting NaCl-concentration dependent phenomena, the growing electrostatic-repulsion screening on one side and the disturbance of hydrogen-bonds formation on the other side. Although the weak intermolecular attraction cannot lead to long-lived secondary and tertiary structures, it may influence the properties of large HA macromolecules and concentrated HA solutions.

Soft polymer actuators have myriad applications and have therefore gained considerable attention in recent years. However, it remains challenging to prepare soft actuators with predefined shapes. Here, a bilayer polymer actuator with a (re)programmable shape is prepared from a microporous anisotropic polypropylene scaffold and a thin, pH-responsive liquid crystalline network (LCN) layer. The hydrogen bonds between dimerized benzoic acid derivatives in the LCN can be disrupted by an alkaline treatment, resulting in a pH-responsive LCN hydrogel layer. The pH-responsive actuation is governed by both the anisotropic mechanical properties of the scaffold and the cross-link density of the LCN hydrogel. Ca2+ ions can be used to chemically cross-link the actuator resulting in an initial programmed shape. The shape fixing can be reversed by removing the Ca2+ ions with an ethylenediaminetetraacetic acid (EDTA) solution. The shape fixing can be performed locally, resulting in pH-responsive actuators with three-dimensional initial configurations of choice., Soft polymer actuators have myriad applications and have therefore gained considerable attention in recent years. However, it remains challenging to prepare soft actuators with predefined shapes. Here, a bilayer polymer actuator with a (re)programmable shape is prepared from a microporous anisotropic polypropylene scaffold and a thin, pH-responsive liquid crystalline network (LCN) layer. The hydrogen bonds between dimerized benzoic acid derivatives in the LCN can be disrupted by an alkaline treatment, resulting in a pH-responsive LCN hydrogel layer. The pH-responsive actuation is governed by both the anisotropic mechanical properties of the scaffold and the cross-link density of the LCN hydrogel. Ca2+ ions can be used to chemically cross-link the actuator resulting in an initial programmed shape. The shape fixing can be reversed by removing the Ca2+ ions with an ethylenediaminetetraacetic acid (EDTA) solution. The shape fixing can be performed locally, resulting in pH-responsive actuators with three-dimensional initial configurations of choice.

Understanding the performance of individual ions in salt solutions and the consequence of ionic hydration on hydrogen bonding network distortion, surface stress, and solution viscosity remains great challenge. We show herein findings pertained to alkali halide YX solutions using differential phonon spectroscopy (X = Cl, Br, I; Y = Li, Na, K, Rb, Cs): (i) an ion occupies eccentrically the tetrahedrally-coordinated interstitial of water to form a (±:4H2O:6H2O) hydration cell without bonding to H2O molecules; (ii) ionic polarization shortens and stiffens the H-O bond while does the O:H nonbond contrastingly; (iii) the screening of the hydrating water dipoles limits the cation hydration cell to be size invariant while the inter-anion repulsion reduces its hydration volume by weakening the anionic long-range electric field when the ionic separation shrinks; and (iv) the polarization of cation and anion dictates respectively the linear and the nonlinear part of Jones-Dale's viscosity and surface stress. Findings would provide profound impact to the understanding and deep engineering of water, ice, and aqueous solutions.

An atomic-scale mechanism of T Cell Receptor (TCR) mechanosensing of peptides in the binding groove of the peptide-major histocompatibility complex (pMHC) may inform the design of novel TCRs for immunotherapies. Using steered molecular dynamics simulations, our study demonstrates that mutations to peptides in the binding groove of the pMHC - which are known to discretely alter the T cell response to an antigen - alter the MHC conformation at equilibrium. This subsequently impacts the overall strength (duration and length) of the TCR-pMHC bond under constant load. Moreover, physiochemical features of the TCR-pMHC dynamic bond strength, such as hydrogen bonds and Lennard-Jones contacts, correlate with the immunogenic response elicited by the specific peptide in the MHC groove. Thus, formation of transient TCR-pMHC bonds is characteristic of immunogenic peptides, and steered molecular dynamics simulations can be used in the overall design strategy of TCRs for immunotherapies.

Background: The SARS-CoV-2 main protease (Mpro) is an attractive target in the COVID-19 drug development process. It catalyzes the polyprotein's translation from viral RNA and specifies a particular cleavage site. Due to the absence of identical cleavage specificity in human cell proteases, targeting Mpro with chemical compounds can obstruct the replication of the virus. Methods: To explore the potential binding mechanisms of 1,2,3-triazole scaffolds in comparison to co-crystallized inhibitors 11a and 11b towards Mpro, we herein utilized molecular dynamics and enhanced sampling simulation studies. Results and conclusion: All the 1,2,3-triazole scaffolds interacted with catalytic residues (Cys145 and His41) and binding pocket residues of Mpro involving Met165, Glu166, Ser144, Gln189, His163, and Met49. Furthermore, the adequate binding free energy and potential mean force of the topmost compound 3h was comparable to the experimental inhibitors 11a and 11b of Mpro. Overall, the current analysis could be beneficial in developing the SARS-CoV-2 Mpro potential inhibitors. © 2022 Elsevier Ltd

Recent NMR studies of the exchangeable protons of GAGs in aqueous solution, including those of the amide, sulfamate, and hydroxyl moieties, have demonstrated potential for the detection of intramolecular hydrogen bonds providing insights into secondary structure preferences. GAG amide protons are observable by NMR over wide pH and temperature ranges; however, specific solution conditions are required to reduce the exchange rate of the sulfamate and hydroxyl protons and allow their detection by NMR. Building on the vast body of knowledge on detection of hydrogen bonds in peptides and proteins, a variety of methods can be used to identify hydrogen bonds in GAGs including temperature coefficient measurements, evaluation of chemical shift differences between oligo- and monosaccharides, and relative exchange rates measured through line shape analysis and EXSY spectra. Emerging strategies to allow direct detection of hydrogen bonds through heteronuclear couplings offer promise for the future. Molecular dynamic simulations are important in this effort both to predict and confirm hydrogen bond donors and acceptors.

An atomic-scale mechanism of T Cell Receptor (TCR) mechanosensing of peptides in the binding groove of the peptide-major histocompatibility complex (pMHC) may inform the design of novel TCRs for immunotherapies. Using steered molecular dynamics simulations, our study demonstrates that mutations to peptides in the binding groove of the pMHC - which are known to discretely alter the T cell response to an antigen - alter the MHC conformation at equilibrium. This subsequently impacts the overall strength (duration and length) of the TCR-pMHC bond under constant load. Moreover, physiochemical features of the TCR-pMHC dynamic bond strength, such as hydrogen bonds and Lennard-Jones contacts, correlate with the immunogenic response elicited by the specific peptide in the MHC groove. Thus, formation of transient TCR-pMHC bonds is characteristic of immunogenic peptides, and steered molecular dynamics simulations can be used in the overall design strategy of TCRs for immunotherapies.

A series of 26 hydrogen-bonded complexes between Br- and halogen, oxygen and sulfur hydrogen-bond (HB) donors is investigated at the M06-2X/6-311 +G(2df,2p) level of theory. Analysis using a model in which Br- is replaced by a point charge shows that the interaction energy (Delta E-Int) of the complexes is accurately reproduced by the scaled interaction energy with the point charge (Delta E-Int(PC)). This is demonstrated by Delta E-Int = 0.86 Delta E-Int(PC) with a correlation coefficient, R-2=0.999. The only outlier is (Br-H-Br)(-), which generally is classified as a strong charge-transfer complex with covalent character rather than a HB complex. Delta E-Int(PC) can be divided rigorously into an electrostatic contribution (Delta E-ES(PC)) and a polarization contribution (Delta E-pol(PC)).Within the set of HB complexes investigated, the former varies between -7.2 and -32.7 kcal mol(-1), whereas the latter varies between -1.6 and -11.5 kcal mol(-1). Compared to our previous study of halogen-bonded (XB) complexes between Br and C-Br XB donors, the electrostatic contribution is generally stronger and the polarization contribution is generally weaker in the HB complexes. However, for both types of bonding, the variation in interaction strength can be reproduced accurately without invoking a charge-transfer term. For the Br-center dot center dot center dot HF complex, the importance of charge penetration on the variation of the interaction energy with intermolecular distance is investigated. It is shown that the repulsive character of Delta E-Int at short distances in this complex to a large extent can be attributed to charge penetration., QC 20220920

ATP-sensitive potassium (KATP) channels couple the intracellular ATP concentration to insulin secretion. KATP channel activity is inhibited by ATP binding to the Kir6.2 tetramer and activated by phosphatidylinositol 4,5-bisphosphate (PIP2). Here, we use molecular dynamics simulation, electrophysiology and fluorescence spectroscopy to show that ATP and PIP2 occupy different binding pockets that share a single amino acid residue, K39. When both ligands are present, simulations suggest that K39 shows a greater preference to co-ordinate with PIP2 than with ATP. They also predict that a neonatal diabetes mutation at K39 (K39R) increases the number of hydrogen bonds formed between K39 and PIP2, potentially accounting for the reduced ATP inhibition observed in electrophysiological experiments. Our work suggests that PIP2 and ATP interact allosterically to regulate KATP channel activity. (Figure presented.). Key points: The KATP channel is activated by the binding of phosphatidylinositol 4,5-bisphosphate (PIP2) lipids and inactivated by the binding of ATP. K39 has the potential to bind to both PIP2 and ATP. A mutation to this residue (K39R) results in neonatal diabetes. This study uses patch-clamp fluorometry, electrophysiology and molecular dynamics simulation. We show that PIP2 competes with ATP for K39, and this reduces channel inhibition by ATP. We show that K39R increases channel affinity to PIP2 by increasing the number of hydrogen bonds with PIP2, when compared with the wild-type K39. This therefore decreases KATP channel inhibition by ATP., QC 20230524

This is the accepted version of the following article:Chen X., Huang R.K., Takahashi K., et al. A Proton Conductive Porous Framework of an 18-Crown-6-Ether Derivative Networked by Rigid Hydrogen Bonding Modules. Angewandte Chemie - International Edition 61, e202211686 (2022), which has been published in final form at https://doi.org/10.1002/anie.202211686. This article may be used for non-commercialpurposes in accordance with the Wiley Self-ArchivingPolicy [https://authorservices.wiley.com/author-resources/Journal-Authors/licensing/self-archiving.html], A rigid hydrogen-bonded organic framework (HOF) was constructed from a C3-symmetric hexatopic carboxylic acid with a hydrophilic 18-crown-6-ether (18C6) component. Despite the flexible macrocyclic structure with many conformations, the derivative with three 4,4’-dicarboxy-o-terphenyl moieties in the periphery yielded a rigid layered porous framework through directional intermolecular hydrogen bonding. Interestingly, the HOF possesses 1D channels with bottleneck composed of 18C6 rings. The HOF shows proton conductivity (1.12×10−7 S cm−1) through Grotthuss mechanism (Ea=0.27 eV) under 98 %RH. The present unique water channel structure provides an inspiration to create molecular porous materials.

This work describes the rich self-assembly behavior obtained by grafting a pyrazole-derived platform at the focal point of poly(benzyl ether) dendrons. Liquid crystals and supergels made out of fibers are obtained by supramolecular organization of non-discoid entities, and they notably increment the photoluminescence in these aggregated states (Aggregation-Induced Emission, AIE). The novel focal point, which is derived from 3,5-dimethyl-4-phenyl-1H-pyrazole, shows great tendency to arrange both wedge-shaped or cone-shaped dendrons in columnar arrangements by the formation of supramolecular polymers by hydrogen-bonding following the cylinder model. Two different linkers, amide or ether groups, connecting with the pyrazole-based apex are investigated, obtaining similar mesomorphic behavior, but different luminescent properties. A combined study of NMR, IR and X-ray diffraction allows establishing analogies between the fiber mesoscopic organization and the columnar organization in the liquid crystalline phase.

N-Methylmorpholine-N-oxide (NMMO) is the solvent of choice in the lyocell process because of the interesting biodegradable, non-toxic and non-ecotoxic features that the full recovery of NMMO provides to the process. NMMO is used in its monohydrate form (1NMMO:1H2O) and cellulose dissolution occurs via hydrogen bond (HBs) formation between the oxygen at the oxide group (as the HB acceptor, HBA) and the hydroxyl groups of the cellulosic units (as the HB donor, HBD). Interestingly, HO is a serious competitor for NMMO to form HBs with cellulose so the number of HO-cellulose-HBs should be kept under control. Addition of co-solvents has become a common practice and the challenge is studying the capability of this additional co-solvent to balance the NMMO-cellulose-HBs versus HO-cellulose-HBs and thus modify the solvent capabilities of the resulting ternary mixture. Herein, we prepared ternary mixtures by addition of the respective equivalents of HO and DMSO (e.g., 1:0.5, 1:1 and 0.5:1) to anhydrous NMMO to obtain 1NMMO:1HO:0.5DMSO, 1NMMO:1HO:1DMSO and 1NMMO:0.5HO:1DMSO. We correlated the solvent capability with the HB formed among the components in the different three ternary mixtures. 1NMMO:0.5HO:1DMSO controlled the number of HO-cellulose-HBs better than the other two mixtures and this helped to maintain the resulting cellulose solution in the liquid form at room temperature.

Soft polymer actuators have myriad applications and have therefore gained considerable attention in recent years. However, it remains challenging to prepare soft actuators with predefined shapes. Here, a bilayer polymer actuator with a (re)programmable shape is prepared from a microporous anisotropic polypropylene scaffold and a thin, pH-responsive liquid crystalline network (LCN) layer. The hydrogen bonds between dimerized benzoic acid derivatives in the LCN can be disrupted by an alkaline treatment, resulting in a pH-responsive LCN hydrogel layer. The pH-responsive actuation is governed by both the anisotropic mechanical properties of the scaffold and the cross-link density of the LCN hydrogel. Ca2+ ions can be used to chemically cross-link the actuator resulting in an initial programmed shape. The shape fixing can be reversed by removing the Ca2+ ions with an ethylenediaminetetraacetic acid (EDTA) solution. The shape fixing can be performed locally, resulting in pH-responsive actuators with three-dimensional initial configurations of choice., Soft polymer actuators have myriad applications and have therefore gained considerable attention in recent years. However, it remains challenging to prepare soft actuators with predefined shapes. Here, a bilayer polymer actuator with a (re)programmable shape is prepared from a microporous anisotropic polypropylene scaffold and a thin, pH-responsive liquid crystalline network (LCN) layer. The hydrogen bonds between dimerized benzoic acid derivatives in the LCN can be disrupted by an alkaline treatment, resulting in a pH-responsive LCN hydrogel layer. The pH-responsive actuation is governed by both the anisotropic mechanical properties of the scaffold and the cross-link density of the LCN hydrogel. Ca2+ ions can be used to chemically cross-link the actuator resulting in an initial programmed shape. The shape fixing can be reversed by removing the Ca2+ ions with an ethylenediaminetetraacetic acid (EDTA) solution. The shape fixing can be performed locally, resulting in pH-responsive actuators with three-dimensional initial configurations of choice.

Hyaluronic acid (HA) is a natural polysaccharide present in the connective tissues of vertebrates, often used in the cosmetics and pharmaceutical industries. HA is a strongly hydrophilic macromolecule forming highly swollen random coils in aqueous solutions. Although some authors reported the secondary and tertiary structures of HA chain, others brought convincing evidence contradicting this hypothesis. This study aims at investigation of the stability and dynamics of the temporary duplex HA structures at different NaCl concentrations by molecular dynamics (MD) simulations. The tendency to duplex formation grows with NaCl concentration reaching its maximum at 0.6 M. This profile is a result of two counteracting NaCl-concentration dependent phenomena, the growing electrostatic-repulsion screening on one side and the disturbance of hydrogen-bonds formation on the other side. Although the weak intermolecular attraction cannot lead to long-lived secondary and tertiary structures, it may influence the properties of large HA macromolecules and concentrated HA solutions.

Interface dipoles formed at an electrolyte/electrode interface have been widely studied and interpreted using the "double dipole step" model, where the dipole vector is determined by the size and/or range of motion of the charged ions. Some electron transport materials (ETMs) with lone pairs of electrons on heteroatoms exhibit a similar interfacial behavior. However, the origin of the dipoles in such materials has not yet been explored in great depth. Herein, we systematically investigate the influence of the lone pair of electrons on the interface dipole through three pyridine derivatives B2-B4PyMPM. Experiments show that different positions of nitrogen atoms in the three materials give rise to different hydrogen bonds and molecular orientations, thereby affecting the areal density and direction of the lone pair of electrons. The interface dipoles of the three materials predicted by the "double dipole step" model are in good agreement with the ultraviolet photoelectron spectroscopy results both in spin-coated and vacuum-deposited films. These findings help to better understand the ETMs/electrode interfacial behaviors and provide new guidelines for the molecular design of the interlayer., Funding agencies: The Swedish Research Council (project grants no. 2016-05498, 2016-05990, and 2020-04538), The Swedish Government Strategic Research Area in Materials Science on Functional Materials at Linköping University (Faculty Grant SFO Mat LiU no. 2009 00971), The Open Fund of the State Key Laboratory of Luminescent Materials and Devices (South China University of Technology)

In this work, graphene oxide–based tablets (GO-Tabs) were prepared by applying a thin layer of functionalized GO on a polyethylene substrate. The GO was functionalized with amine groups (–NH2) by poly(ethylene glycol)bis(3-aminopropyl) terminated (GO-NH2-PEG-NH2). The functionalized GO-Tabs were used for the extraction of ritonavir (RTV) in human saliva samples. RTV in plasma and saliva samples was analyzed using LC–MS/MS. Gradient LC system with MS/MS in the positive-ion mode [electrospray ionization (ESI+)] was used. The transitions m/z 721 → 269.0 and m/z 614 → 421 were used for RTV and the internal standard indinavir, respectively. This study determined the human immunodeficiency virus protease inhibitor RTV in human saliva samples using functionalized GO-Tab and LC–MS/MS, and the method was validated. The standard calibration curve for plasma and saliva samples was constructed from 5.0 to 2000 nmol L−1. The limit of detection was 0.1 nmol L−1, and the limit of quantification was 5.0 nmol L−1 in both plasma and saliva matrices. The intra- and inter-assay precision values were found to be between 1.5 and 5.8%, and the accuracy values ranged from 88.0 to 108% utilizing saliva and plasma samples. The extraction recovery was more than 80%, and the presented functionalized GO-Tabs could be reused for more than 10 extractions without deterioration in recovery., QC 20220314

Interface dipoles formed at an electrolyte/electrode interface have been widely studied and interpreted using the "double dipole step" model, where the dipole vector is determined by the size and/or range of motion of the charged ions. Some electron transport materials (ETMs) with lone pairs of electrons on heteroatoms exhibit a similar interfacial behavior. However, the origin of the dipoles in such materials has not yet been explored in great depth. Herein, we systematically investigate the influence of the lone pair of electrons on the interface dipole through three pyridine derivatives B2-B4PyMPM. Experiments show that different positions of nitrogen atoms in the three materials give rise to different hydrogen bonds and molecular orientations, thereby affecting the areal density and direction of the lone pair of electrons. The interface dipoles of the three materials predicted by the "double dipole step" model are in good agreement with the ultraviolet photoelectron spectroscopy results both in spin-coated and vacuum-deposited films. These findings help to better understand the ETMs/electrode interfacial behaviors and provide new guidelines for the molecular design of the interlayer., Funding agencies: The Swedish Research Council (project grants no. 2016-05498, 2016-05990, and 2020-04538), The Swedish Government Strategic Research Area in Materials Science on Functional Materials at Linköping University (Faculty Grant SFO Mat LiU no. 2009 00971), The Open Fund of the State Key Laboratory of Luminescent Materials and Devices (South China University of Technology)

Interface dipoles formed at an electrolyte/electrode interface have been widely studied and interpreted using the "double dipole step" model, where the dipole vector is determined by the size and/or range of motion of the charged ions. Some electron transport materials (ETMs) with lone pairs of electrons on heteroatoms exhibit a similar interfacial behavior. However, the origin of the dipoles in such materials has not yet been explored in great depth. Herein, we systematically investigate the influence of the lone pair of electrons on the interface dipole through three pyridine derivatives B2-B4PyMPM. Experiments show that different positions of nitrogen atoms in the three materials give rise to different hydrogen bonds and molecular orientations, thereby affecting the areal density and direction of the lone pair of electrons. The interface dipoles of the three materials predicted by the "double dipole step" model are in good agreement with the ultraviolet photoelectron spectroscopy results both in spin-coated and vacuum-deposited films. These findings help to better understand the ETMs/electrode interfacial behaviors and provide new guidelines for the molecular design of the interlayer., Funding agencies: The Swedish Research Council (project grants no. 2016-05498, 2016-05990, and 2020-04538), The Swedish Government Strategic Research Area in Materials Science on Functional Materials at Linköping University (Faculty Grant SFO Mat LiU no. 2009 00971), The Open Fund of the State Key Laboratory of Luminescent Materials and Devices (South China University of Technology)

A random walk on the PES for (MeSH)4 clusters produced 50 structural isomers held together by hydrogenbonding networks according to calculations performed at the B3LYP/6-311++G* * andMP2/6-311++G* * levels. The geometric motifs observed are somewhat similar to those encountered for the methanol tetramer, but the interactions responsible for cluster stabilization are quite different in origin. Cluster stabilization is not related to the number of hydrogen bonds. Two distinct, well-defined types of hydrogen bonds scattered over a wide range of distances are predicted. © Springer-Verlag Berlin Heidelberg 2012.

In this paper we report the geometries and properties of 38 distinct geometrical motifs located on the B3LYP/6-31+G(d), MP2/6-311++G(d, p) potential energy surfaces of the water heptamer. Binding energies of up to 45 kcal/mol are calculated. All motifs fall within 10 kcal/mol of the most stable conformation, with at least 13 structural patterns located no more than 3 kcal/mol above, leading to a very complex potential energy surface, populated by a multitude of motifs each one allowing large numbers of conformations. Cluster stability does not seem to be correlated with the number of hydrogen bonds. Compact structures are energetically favored by electronic energies with zero-point energy corrections, while more open structures are preferred when temperature and entropy are accounted for. The molecular interactions holding the clusters as discrete units lead to large binding energies but are not strong enough to cause significant changes in the geometries of the interacting monomers. Our results indicate that bonding in the water heptamers can be considered as largely non-shared interactions with contributions from intermediate character of increasing covalency. © 2013 AIP Publishing LLC.

In this paper we report the geometries and properties of 40 structural isomers located on the MP2/6-311++G** PES of the carbonic acid dimer. All six possible combinations of carbonic acid monomers were considered. The dimers are divided into six geometrical motifs. Our data suggests that combinations of anti-anti monomers do not necessarily lead to larger stabilization energies in the formation of the dimers. MP2 underestimates the relative binding energies with respect to CCSD(T) by as much as 3.2 kcal mol-1. At least 3 different dimers which may contribute to the stability of carbonic acid are predicted to have significant populations. Binding energy is only directly related to relative stability when comparing dimers formed from the same monomers. Overall stabilization is mainly dictated by attractive electrostatic interactions via cooperative polarization by virtue of the spatial arrangement of the dipole moment components along the polar bonds. Shorter O…H bond distances and larger bond orders predicted for the hydrogen bonds directed towards carbonyl groups make for stronger hydrogen bonding than in O…H bonds directed towards hydroxyl groups. © the Owner Societies.

In this paper, we report the geometries and properties of the structural isomers obtained from a random walk of the potential energy surface (PES) of the methanol tetramer. Thirty-three structures were obtained after B3LYP/6-31+g* optimization of 94 candidate structures generated from a stochastic search of the PM3 conformational space. The random search was carried out using a recently proposed modified Metropolis acceptance test in the simulated annealing (SA) procedure. Corrections for the basis set superposition error (BSSE) show improvements on the binding energies of the clusters in an average of approximately 2.0 kcal/mol, while geometries are predicted to be less sensitive to BSSE corrections. MP2/aug-cc-pvdz calculations on representative structures did not change the geometries but predicted better binding energies. Highly correlated CCSD(T) energies were calculated on the B3LYP and MP2 stationary points and used to establish relative stabilities. We report several new conformations and group the structures into six distinct geometrical motifs. Only the cyclic tetramers with four primary hydrogen bonds in the same plane are predicted to have significant populations. Secondary hydrogen bonds, those for which the donated proton comes from an alkyl group, lead to a rich conformational space.

The adsorption of Cr(VI) on biochars can be suppressed by coexisting anions, but the roles of O-containing functional groups and in particular N-containing functional groups are unclear. In this study, we combined spectroscopic and molecular simulation approaches to investigate the selective adsorption of Cr(VI) on the O-rich (PB, UB1) and N-rich (UB3, UB5) biochars under strong competition of anions. The elemental analysis and pyrolysis-gas chromatography/mass spectrometry indicated that the structures of PB and UB1 were similar, and so were the UB3 and UB5. Quantification of functional groups showed that for UB1, 75.3% of Cr(VI) removal was attributed to O-containing groups, while 53.3–72.7% of that was mediated by N-containing groups in UB3 and UB5. X-ray photoelectron spectra and density functional theory calculations confirmed that for O-rich biochars, surface complexation and strong H-bonds between carboxyl/hydroxyl and HCrO4– improved Cr(VI) removal in the presence of anions, while for N-rich biochars, Cr(VI) adsorption was depressed by coexisting anions in the order of Cl–>NO3– >SO42– because of the weaker H-bond between protonated amino groups and HCrO4–. This study presents a novel approach for quantitative, molecular-level evaluation of the roles of biochar functional groups in the Cr(VI) removal from complex environmental systems.