Solvent Water Molecules Research Articles

Semisynthesis and absolute configuration of a novel rearranged 19,20-δ-lactone (9βH)-pimarane diterpene.

Annonalide (3β,20-epoxy-3α,16-dihydroxy-15-oxo-7-pimaren-19,6β-olide, C20H26O6, 1) is the major (9βH)-pimarane diterpene isolated from tubers of Cassimirella ampla, and it exhibits cytotoxic properties upon interaction with ctDNA. We have prepared new derivatives of 1 by modification of the (9βH)-pimarane backbone and report here the semisynthesis and absolute configuration of a novel rearranged 19,20-δ-lactone (9βH)-pimarane. Our approach was the reduction of the carbonyl groups of 1 with sodium borohydride, at positions C15 (no stereoselectivity) and C3 (stereoselective reduction), followed by rearrangement of the 6,19-γ-lactone ring into the six-membered 19,20-δ-lactone ring in 4a (3β,6β,16-trihydroxy-7-pimaren-19,20β-olide monohydrate, C20H30O6·H2O). The absolute structure of the new compound, 4a, was determined unambiguously with a Flack parameter x of -0.01 (11), supporting the stereochemistry assignment of 1 redetermined here. Besides the changes in the pattern of covalent bonds caused by reduction and lactone rearrangement, the conformation of one of the three fused cyclohexane rings is profoundly different in 4a, adopting a chair conformation instead of the boat shape found in 1. Furthermore, the intramolecular hydrogen bond present in 1 is lost in new compound 4a, due to hydrogen bonding between the 3-OH group and the solvent water molecule.

Ni(II) Complex of N2O3 Donor Unsymmetrical Ligand and Its Use for the Synthesis of NiII-MnII Complexes of Diverse Nuclearity: Structures, Magnetic Properties, and Catalytic Oxidase Activities.

A new mononuclear Ni(II) complex [NiL] (1) of an unsymmetrically dicondensed N2O3 donor ligand, H2L ( N-α-methylsalicylidene- N'-3-methoxysalicylidene-1,3-propanediamine), has been synthesized. Complex 1 on reaction with Mn(ClO4)2·6H2O and NaN3 in different molar ratios yielded three novel heterometallic NiII-MnII complexes, [(NiL)2Mn(N3)](ClO4) (2), [(NiL)2Mn2(N3)2(μ1,1-N3)2(CH3OH)2] (3), and [{(NiL)2Mn}2(μ1,3-N3)(H2O)]·(CH3OH),(ClO4)3 (4). The single crystal structure analyses show a trinuclear NiII2MnII structure for complex 2 and a tetranuclear NiII2MnII2 structure where two dinuclear NiIIMnII units are connected via μ1,1-azido and phenoxido bridges for complex 3. Complex 4 possesses a hexanuclear structure where two trinuclear NiII2MnII units are connected via a μ1,3-azido bridge. The temperature-dependent dc molar magnetic susceptibility measurements reveal that complexes 3 and 4 are antiferromagnetically coupled with the exchange coupling constants ( J) of -4.97, -0.14, -0.55 cm-1 for 3 and -3.94 cm-1 for 4. All complexes 2-4 show biomimetic catalytic oxidase activities. For catecholase like activity, the turnover numbers ( Kcat) are 768, 1985, and 2309 h-1 for complexes 2-4, respectively, whereas for phenoxazinone synthase like activity, the turnover numbers are 3240, 3360, and 13 248 h-1 for complexes 2-4, respectively. This difference in catalytic efficiencies is attributed to the variations in structures of the complexes and formation of active NiII-MnII species in solution during catalysis. The mass spectral analyses suggest the probable intermediate formation and cyclic voltammetry measurement suggest the reduction of Ni(II) to Ni(I) during catalytic reaction. The very high catalytic efficiencies for aerial dioxygen activation of all these heterometallic complexes as well as the highest activity of 4 is attributed to the coordinatively unsaturated penta-coordinated geometry or hexa-coordinated geometry with a solvent water molecule around Mn(II).

Lanthanide-benzophenone-3,3'-disulfonyl-4,4'-dicarboxylate Frameworks: Temperature and 1-Hydroxypyren Luminescence Sensing and Proton Conduction.

The benzophenone-3,3'-disulfonyl-4,4'-dicarboxylic acid (H4-BODSDC) ligand and compounds, {(H3O)[Ln(BODSDC)(H2O)2]} n (Ln = Tb(1), Eu(2), and Gd(3)), were synthesized and structurally characterized. The lanthanide centers are bridged by the carboxylate groups of BODSDC4- ligands to give a one-dimensional (1D) chain. The 1D chains are connected by the BODSDC4- ligands to yield a three-dimensional (3D) structure featuring 1D channels. The lanthanide ions are efficiently sensitized by the BODSDC4- ligand with an appropriate triplet excited state to generate characteristic Tb(III) and Eu(III) emissions in Tb(1) and Eu(2), respectively. Thus the binary compound, {(H3O)[Tb0.93Eu0.07(BODSDC)(H2O)2]} n (abbreviated as Tb0.93Eu0.07-BODSDC), was achieved for use as a ratiometric temperature sensor. The ratio values of Tb(III) emission at 544 nm ( ITb) and Eu(III) emission at 616 nm ( IEu) for Tb0.93Eu0.07-BODSDC linearly vary with temperature over a wide range, which indicates that the Tb0.93Eu0.07-BODSDC is a thermometer for ratiometric fluorescence sensing of temperature. Additionally, Tb(1) is a fluorescent probe for detecting 1-hydroxypyrene (1-HP) by luminescence quenching. The uncoordinated sulfonate oxygens exposed on the channel surfaces serve as the binding sites for 1-HP. Finally, the enrichment of the solvent water molecules in the channels decorated by high-density hydrophilic sulfonate groups resulted in a high proton conductivity for Tb(1).

Crystal structure and Hirshfeld surface analysis of 2,4-di-amino-6-methyl-1,3,5-triazin-1-ium tri-chloro-acetate monohydrate.

The asymmetric unit of the title mol-ecular salt, C4H8N5+·C2Cl3O2-·H2O, coomprises a 2,4-di-amino-6-methyl-1,3,5-triazin-1-ium cation, a tri-chloro-acetate anion and a water mol-ecule of solvation. The protonated N atom of the cation forms a hydrogen bond with a carboxyl O atom of the anion, which also acts as a hydrogen-atom acceptor with the water mol-ecule. The cations form centrosymmetric dimeric units through R22(8) N-H⋯N bond pairs and are extended into zigzag chains along the c-axis direction, also through similar cyclic R22(8) dual N-H⋯N hydrogen-bonding inter-actions. The water mol-ecule acts as a dual acceptor forming N-H⋯O hydrogen bonds between the amine groups of the cations, forming cyclic R23(8) motifs. The second H atom of the water mol-ecule also acts as a donor in an O-H⋯O hydrogen bond with the second carboxyl O atom, linking the chains along the b-axis direction. These interactions give rise to an overall three-dimensional supra-molecular structure. A Hirshfeld surface analysis was employed in order to study the inter-molecular inter-actions.

Molecular dynamics simulation of N-octyl-N-quaternized chitosan derivatives as a drug carrier

The dynamic amphiphilic behavior of N-octyl-N-quaternized chitosan derivatives in aqueous solution is investigated using molecular dynamics (MD) simulations. It is found that quaternization decreases the intra-chain hydrogen bond formation which leads to reduced rigidity of the chitosan backbone. The effect of octyl substitution is much less pronounced. Analysis of hydrogen bonding reveals the presence of a hydrogen bond within the quaternized glucosamine unit, which causes the distortion of the usual chair conformation. Also, H-bond formation with the solvent water molecules was found to stabilize the intra-chain HO3-O5 hydrogen bond. Additionally, an aqueous solution containing the 10%-N-octyl-50%-N-quaternized chitosan derivative (1O5QCS) and the anti-cancer drug 10-hydroxycamptothecin (10-HCPT) was also investigated using MD simulations. It was found that van der Waals and electrostatic forces have virtually equal contributions to the nonbonded interactions responsible for complexation. Furthermore, H-bond formation between drug and drug carrier contributes to lactone ring stability and subsequent bioavailability.

Molecular polarizability anisotropy of liquid water revealed by terahertz-induced transient orientation

Reaction pathways of biochemical processes are influenced by the dissipative electrostatic interaction of the reagents with solvent water molecules. The simulation of these interactions requires a parametrization of the permanent and induced dipole moments. However, the underlying molecular polarizability of water and its dependence on ions are partially unknown. Here, we apply intense terahertz pulses to liquid water, whose oscillations match the timescale of orientational relaxation. Using a combination of terahertz pump / optical probe experiments, molecular dynamics simulations, and a Langevin dynamics model, we demonstrate a transient orientation of their dipole moments, not possible by optical excitation. The resulting birefringence reveals that the polarizability of water is lower along its dipole moment than the average value perpendicular to it. This anisotropy, also observed in heavy water and alcohols, increases with the concentration of sodium iodide dissolved in water. Our results enable a more accurate parametrization and a benchmarking of existing and future water models.

Lanthanide-Based Porous Coordination Polymers: Syntheses, Slow Relaxation of Magnetization, and Magnetocaloric Effect.

Two lanthanide-containing structurally analogous porous coordination polymers (PCPs) have been isolated with the general molecular formula [Ln2(L1)2(H2O)4(ox)] n.4 nH2O (where L1 = fumarate, ox = oxalate; Ln = Dy (1), Gd (2)). Thermogravimetric analysis (TGA) and TG-MS measurements performed on 1 and 2 suggest that not only the solvated water molecules in the crystal lattice but also the four coordinated water molecules on the respective lanthanides in 1 and 2 are removed upon activation. Due to the removal of the waters, 1 and 2 lost their crystallinity and became amorphous, as confirmed by powder X-ray diffraction (PXRD). We propose the molecular formula [Ln2(L1)2(ox)] n for the amorphous phase of 1 and 2 (where Ln = Dy (1'), Gd (2')) on the basis of XANES, EXAFS, and other experimental investigations. Magnetization relaxation dynamics probed on 1 and 1' reveal two different relaxation processes with effective energy barriers of 53.5 and 7.0 cm-1 for 1 and 45.1 and 6.4 cm-1 for 1', which have been rationalized by detailed ab initio calculations. For the isotropic lanthanide complexes 2 and 2', magnetocaloric effect (MCE) efficiency was estimated through detailed magnetization measurements. We have estimated -Δ S m values of 52.48 and 41.62 J kg1- K-1 for 2' and 2, respectively, which are one of the largest values reported for an extended structure. In addition, a 26% increase in -Δ Sm value in 2' in comparison to 2 is achieved by simply removing the passively contributing (for MCE) solvated water molecule in the lattice and coordinated water molecules.

Monitoring Coil-Globule Transitions of Thermoresponsive Polymers by Using NMR Solvent Relaxation.

Thermoresponsive polymers exhibit coil-globule transition in aqueous solution where the polymer undergoes transition from the coil-like morphology to a globular form with the change of temperature. Such transitions also reflect changes in the solvent dynamics captured by various spectroscopic methods. In this work, we construct a phenomenological model to capture the dynamics of the NMR relaxation of water molecules of an aqueous solution of thermoresponsive polymers that are known to form hydrogen bonds with the solvent water molecules. The model relies on the behavior of the polymer-solvent hydrogen bonds and the sharing of rotational kinetic energy of water molecules in the vicinity of the polymer chain and the bulk. This is shown to provide a direct estimate of the fractional change of the polymer-water hydrogen bonds across lower critical solution temperature from NMR relaxation data of solvent water along with a reliable estimate of the transition temperature. In addition, it also provides a measure of the dispersion of the strengths of these hydrogen bonds. We exemplify the validity of this model by successfully fitting the experimental data to show that the extracted parameters provide significant insights into the role played by the hydrogen bonds in the process. The possible extension of this model to solvents that form no hydrogen bonds with the polymers is also discussed.

Impact of the Ligand Flexibility and Solvent on the O-O Bond Formation Step in a Highly Active Ruthenium Water Oxidation Catalyst.

By advanced molecular dynamics simulations, we show that for a highly active ruthenium-based water oxidation catalyst the dangling carboxylate group of the catalyst plays an important role in the crucial O–O bond formation step. The interplay of the flexible group and solvent molecules facilitates two possible pathways: a direct pathway with a single solvent water molecule or a mediated pathway involving two solvent water molecules, which have similar activation barriers. Our results provide an example for which a realistic molecular dynamics approach, incorporating an explicit description of the solvent, is required to reveal the full complexity of an important catalytic reaction in aqueous solvent.

Short Azapeptides of Folded Structures in Aqueous Solutions.

Building folded short peptides that are driven by the intramolecular hydrogen bonding in aqueous solutions remains challenging because of their highly competitive intermolecular hydrogen-bonding interactions with water solvent molecules that would have favored the extended conformations. Here, we show folded β-turn structures in acyl amino acid-based N-amidothioureas, the nonclassic azapeptides, in aqueous solutions, as well as in solid-state and organic solvents, by X-ray crystal structures, DFT calculations, 1D and 2D NMR spectra, and absorption and CD spectra. The achiral phenylthiourea chromophore acts as a CD reporter for the β-turn structure that communicates the chirality of the amino acid residue to the achiral thiourea moiety and the relative intensity of the intramolecular hydrogen bond that stabilizes the turn structure. The amidothiourea moiety represents a versatile structural framework for folded short peptides in aqueous environments.

A Novel 2d Zinc(II) Coordination Polymer Based on 2,2'-bipyridine-4,4'-dicarboxylic Acid: Synthesis, Crystal Structure and Photoluminescence Property

Graphical Abstract: A new two dimensional 2,2′-bipyridine-4,4′-dicarboxylate Zn(II) coordination polymer was obtained by hydrothermal synthesis and characterized by IR spectrum and single-crystal X-ray diffraction. The crystal lattice hosts the N,N-dimethylformamide and water solvent molecules. The new material reveals blue-orange luminescence upon excitation with ultraviolet light.

Two tris(oxalato)ferrate(III) hybrid salts with pyridinium derivative isomers as counter cations: synthesis, crystal structures, thermal analyses, and magnetic properties

Two organic–inorganic hybrid salts, tris(2-amino-4,6-dimethylpyridinium) tris(oxalato)ferrate(III), (C7H11N2)3[Fe(C2O4)3] (1), and tris(4-dimethylaminopyridinium) tris(oxalato)ferrate(III) tetrahydrate, (C7H11N2)3[Fe(C2O4)3]·4H2O (2), have been synthesized and characterized by elemental and thermal analyses, IR spectroscopy, single-crystal X-ray diffraction, and SQUID magnetometry. Compounds 1 and 2 crystallize in triclinic P-1 and monoclinic C2/c space groups, respectively. Each compound contains the anionic complex [Fe(C2O4)3]3- in which the central metal is six-coordinate in a slightly distorted octahedron defined by three chelating oxalate(2-) ligands. The two substituted pyridinium cations are isomers. However, due to the great steric hindrance provided by the bulky cation, 2-amino-4,6-dimethylpyridinium, only the 4-dimethylaminopyridinium cation, the smallest of this series, led to formation of 2 with enough vacant spaces to be occupied by four solvent water molecules. In the crystals, cations and anions are connected via hydrogen-bonds of the types N–H⋯O in 1 and N–H⋯O and O–H⋯O in 2, with π–π stacking interactions between the pyridine rings stabilizing the 3-D framework. The thermal studies confirmed the anhydrous character of salt 1 and the presence of water molecules in salt 2. The magnetic susceptibility measurements in the 2–300 K temperature range revealed weak antiferromagnetic coupling in the two salts.

Accessing the Vibrational Signatures of Amino Acid Ions Embedded in Water Clusters.

We present an infrared predissociation (IRPD) study of microsolvated GlyH+(H2O) n and GlyH+(D2O) n clusters, formed inside of a cryogenic ion trap via condensation of H2O or D2O onto the protonated glycine ions. The resulting IRPD spectra, showing characteristic O-H and O-D stretches, indicate that H/D exchange reactions are quenched when the ion trap is held at 80 K, minimizing the presence of isotopomers. Comparisons of GlyH+(H2O) n and GlyH+(D2O) n spectra clearly highlight and distinguish the vibrational signatures of the water solvent molecules from those of the core GlyH+ ion, allowing for quick assessment of solvation structures. Without the aid of calculations, we can already infer solvation motifs and the presence of multiple conformations. The use of a cryogenic ion trap to cluster solvent molecules around ions of interest and control H/D exchange reactions is broadly applicable and should be extendable to studies of more complex peptidic ions in large solvated clusters.

Spectroscopic Evidence of Size-Dependent Buffering of Interfacial pH By Cation Hydrolysis during CO2 Electroreduction

The nature of the electrolyte cation is known to affect the Faradaic efficiency and selectivity of CO2 electroreduction. Singh et al. (J. Am. Chem. Soc. 2016, 138, 13006–13012) recently attributed this effect to the buffering ability of cation hydrolysis at the electrical double layer. According to them, the pKa of hydrolysis decreases close to the cathode due to the polarization of the solvation water molecules between the cation’s positive charge and the negative charge on the electrode surface. We have tested this hypothesis experimentally, by probing the pH at the gold-electrolyte interface in situ using ATR-SEIRAS. The ratio between the integrated intensity of the CO2 and HCO3 - bands, which has to be inversely proportional to the pH, provided a means to determining the pH change in-situ during the electroreduction of CO2. Our results confirm that the magnitude of the pH increase at the interface follows the trend Li+ > Na+ > K+ > Cs+, adding strong experimental support to Singh’s et al.’s hypothesis. We show, however, that the pH buffering effect was overestimated by Singh et al., their overestimation being larger the larger the cation. Figure 1

A simple and effective solution to the constrained QM/MM simulations.

It is a promising extension of the quantum mechanical/molecular mechanical (QM/MM) approach to incorporate the solvent molecules surrounding the QM solute into the QM region to ensure the adequate description of the electronic polarization of the solute. However, the solvent molecules in the QM region inevitably diffuse into the MM bulk during the QM/MM simulation. In this article, we developed a simple and efficient method, referred to as the "boundary constraint with correction (BCC)," to prevent the diffusion of the solvent water molecules by means of a constraint potential. The point of the BCC method is to compensate the error in a statistical property due to the bias potential by adding a correction term obtained through a set of QM/MM simulations. The BCC method is designed so that the effect of the bias potential completely vanishes when the QM solvent is identical with the MM solvent. Furthermore, the desirable conditions, that is, the continuities of energy and force and the conservations of energy and momentum, are fulfilled in principle. We applied the QM/MM-BCC method to a hydronium ion(H3O+) in aqueous solution to construct the radial distribution function (RDF) of the solvent around the solute. It was demonstrated that the correction term fairly compensated the error and led the RDF in good agreement with the result given by an ab initio molecular dynamics simulation.

Formation of the unprecedented trinuclear [NiCu2(CN)8]4− complex anion within the crystal structure of [Ni(5,5′-dmbpy)3]2[NiCu2(CN)8]·6H2O

From an aqueous-ethanolic solution of CuCl2, 5,5′-dmbpy (5,5′-dmbpy = 5,5′-dimethyl-2,2′-bipyridine) and K2[Ni(CN)4], a novel Cu/Ni heterobimetallic complex [Ni(5,5′-dmbpy)3]2[NiCu2(CN)8]·6H2O was isolated and characterized. Its ionic crystal structure contains the unprecedented Cu(I)/Ni(II,D4h) complex anion [Cu2Ni(CN)8]4−, along with the rarely structurally characterized [Ni(5,5′-dmbpy)3]2+ complex cation and water solvate molecules. The anions and water molecules are linked by hydrogen bonds, yielding a 1D supramolecular structure. Magnetic measurements performed down to 1.8 K revealed a Curie behavior between 15 and 300 K, while a small zero field splitting effect can be seen below 15 K.

Microhydration of 2-Naphthol at Ground, First Excited Triplet, and First Excited Singlet States: A Case Study on Photo Acids.

Molecular interactions of 2-naphthol (nap) with water molecules are studied at the ground, first excited triplet and first excited singlet states, applying DFT and TD-DFT methods. The minimum energy structure of hydrated clusters of 2-naphthol up to four water molecules are selected from several possible input geometries. It is observed that the minimum energy conformer of the tetra-hydrate of 2-naphthol has proton transfer occurring from nap to solvent water molecules, in its first excited singlet state. This is however not observed in case of its ground or first excited triplet state. It is consistent with the fact that the pKa of nap in the first excited singlet state is very much lower compared to the ground and first excited triplet state. This is also reflected in the O-H potential energy profile of tetrahydrate of nap, obtained by performing a rigid potential energy scan of the dissociating O-H bond of nap at ground, first excited triplet and first excited singlet states. Frequency of O-H stretching vibration of 2-napthol and its hydrated clusters in the ground (S0) as well as in the first excited singlet (S1) state are calculated and compared with the available experimental data. The performance of macroscopic solvation model is also examined in the ground and these excited states.

Crystal structure of 8-(4-methyl-phen-yl)-2'-de-oxy-adenosine hemihydrate.

In the asymmetric unit, equalling the unit cell (triclinic, P1, Z = 1), two mol-ecules of the title compound, 8-(4-methyl-phen-yl)-d-2'-de-oxy-adenosine, C17H19N5O3, are present, with distinct conformations of the two sugar moieties, together with one solvent water mol-ecule. All three ribose O atoms are involved in hydrogen bonding and the crystal packing is largely determined by hydrogen-bonding or hydrogen-heteroatom inter-actions (O-H⋯O, O-H⋯N, N-H⋯O, C-H⋯O and C-H⋯N) with one independent mol-ecule directly linked to four neighbouring mol-ecules and the other mol-ecule directly linked to six neighbouring mol-ecules. The two independent mol-ecules of the asymmetric unit display three weak intra-molecular C-H-to-heteroatom contacts, two of which are very similar despite the different conformations of the deoxyribosyl moieties. The aromatic ring systems of both mol-ecules are in proximity to each other and somehow aligned, though not coplanar. The absolute structures of the two mol-ecules were assumed with reference to the reactant 8-bromo-d-2'-de-oxy-adenosine as they could not be determined crystallographically.

Syntheses, Crystal Structures, and Properties of Two d10 Metal Complexes Based on Ferrocenyl Ligands Bearing Pyrazolyl Pyridine Substituents

Two new complexes, namely, [Cd2(L1)2(NCS)4(DMF)2] · 4H2O (I) and {[Zn3(L2)4(SO4)3(H2O)8] · 3DMF · 6H2O} n (II) have been synthesized through self-assembly of Cd(II) or Zn(II) salts with ferrocenyl ligands bearing pyrazolyl pyridine substituents. The two compounds were characterized by IR spectra, element analysis, X-ray powder diffraction, single-crystal X-ray diffraction (СIF files CCDC nos. 949526 (I), 949527 (II)), and thermogravimetric analysis. Complex I crystallizes in the monocline space group P21/c and exhibits a discrete dinuclear structure. The adjacent dinuclear molecules are packed into a 1D linear chain through the hydrogen-bond interactions. Complex II is a neutral one-dimensional infinite zigzag coordination chain. The 3D packing diagram of II contains two types of voids and the solvated DMF and water molecules filled them and stabilized by the hydrogen bonds. In addition, the redox properties of both complexes I and II have also been investigated.

Ultrafast Charge Transfer Processes Accompanying KLL Auger Decay in Aqueous KCl Solution.

X-ray photoelectron and KLL Auger spectra were measured for the K^{+} and Cl^{-} ions in aqueous KCl solution. While the XPS spectra of these ions have similar structures, both exhibiting only weak satellites near the main line, the Auger spectra differ dramatically. Contrary to the chloride case, a very strong extra peak was found in the Auger spectrum of K^{+} at the low kinetic energy side of the ^{1}D state. Using the equivalent core model and abinitio calculations this spectral feature was assigned to electron transfer processes from solvent water molecules to the solvated cation. The observed charge transfer processes are suggested to play an important role in charge redistribution following single and multiple core-hole creation in atoms and molecules placed into environment.