Solvent Water Molecules Research Articles

Synthesis, characterization and DNA binding of four imidazo[4,5-f]1,10-phenanthroline derivatives

The synthesis and crystal structures of four imidazo[4,5- f ]1,10-phenanthroline type compounds, namely 2,6-(dimethoxypyridyl)imidazo[4,5- f ]1,10-phenanthroline monohydrate (C 20 H 17 N 5 O 3 ) 1a , (indole)imidazo[4,5- f ]1,10-phenanthroline ethanol monosolvate monohydrate (C 23 H 21 N 5 O 2 ) 2a , (benzo[b]thiophene)imidazo[4,5- f ]1,10-phenanthroline (C 21 H 12 N 4 S) 3 , and (4,5-dimethylthiophene)imidazo[4,5- f ]1,10-phenanthroline (C 19 H 14 N 4 S) 4 , are reported. The compounds were characterized in dimethyl sulfoxide- d 6 (DMSO- d 6 ) solution by 1 H and 13 C NMR spectroscopy and in the solid-state by 13 C NMR spectroscopy using the cross-polarisation magic angle spinning (CP/MAS) technique. 1 H and 13 C liquid-state NMR spectra of 1 and 2 exhibit a sharpening of peaks upon heating, suggesting the presence of two tautomeric forms of 1 and 2 , this is confirmed by the presence of two distinct signals for the N-H protons in the 1 H spectra. This tautomeric effect was not observed in 3 and 4. 1a crystallised in the triclinic space group, P 1 ¯ with one molecule and one solvent water molecule in the asymmetric unit while 2a crystallised in the monoclinic space group, P 2 1 / c, with one molecule and two solvate molecules (CH 3 CH 2 OH and H 2 O) in the asymmetric unit. 3 and 4 both crystallised in the monoclinic space group, P 2 1 / n, each with one molecule in the asymmetric unit. 4 displays a positional disorder on the 4,5-thiophene moiety in a 60:40 ratio. When a drug candidate binds to DNA via intercalation, a hypochromic effect is observed in the spectra due to stabilised π-interactions between the base pairs of the DNA structure and the drug candidate. Contrastingly, if a drug candidate binds to DNA via electrostatic attraction, a hyperchromic effect is observed. The mode of binding as well as intrinsic binding constant (K b ) of 1a – 4 are reported herein. The spectra of 1a, 2a and 4 exhibit a hypochromic effect, thus interaction via π-interactions is suggested and the spectrum of 3 exhibits a hyperchromic shift, suggesting that the mode of binding of 3 occurs via electrostatic attraction. The K b values for 1a–4 range from 1.5 × 10 3 – 1.7 × 10 4 M −1 .

Photoinduced Ligand Exchange Dynamics of a Polypyridyl Ruthenium Complex in Aqueous Solution

The understanding of photoinduced ligand exchange mechanisms in polypyridyl ruthenium(II) complexes operating in aqueous solution is of crucial importance to rationalize their photoreactivity. Herein, we demonstrate that a synergetic use of ab initio molecular dynamics simulations and static calculations, both conducted at the DFT level, can provide a full understanding of photosubstitution mechanisms of a monodentate ligand by a solvent water molecule in archetypal ruthenium complexes in explicit water. The simulations show that the photoinduced loss of a monodentate ligand generates an unreactive 16-electron species in a hitherto undescribed pentacoordinated triplet excited state that converts, via an easily accessible crossing point, to a reactive 16-electron singlet ground state, which combines with a solvent water molecule to yield the experimentally observed aqua complex in less than 10 ps. This work paves the way for the rational design of novel photoactive metal complexes relevant for biological applications.

Theory of nematic ordering driven by hydrogen bonding between rods and solvent molecules

ABSTRACT A mean-field theory is introduced to describe nematic () ordering and phase separations in aqueous low-molecular-weight liquid crystalline molecules (or short rodlike molecules). We consider a physical bonding (or a hydrogen bonding) between the rod and solvent (water) molecules. Our theory predicts that the hydrogen bonds between the unlike molecules stabilise the phase and take place novel phase separations on the temperature-concentration plane. Upon increasing the number of functional groups on the rods, capable of forming the physical bond with the solvent molecule, the stable phase region is broadened on the phase diagram. We also find a miscibility window of the phase and closed-loop coexistence curves with upper and lower critical solution temperatures near the phase.

Water hydrogen-bonding effects on the ground and low-lying excited states of dipyridyl isomers

In this work, we examined the ground and low-lying excited states of six dipyridyl isomers (2,2′-dipyridyl, 2,3′-dipyridyl, 2,4′-dipyridyl, 3,3′-dipyridyl, 3,4′-dipyridyl, and 4,4′-dipyridyl), emphasizing the effects that solvation (water) molecules have on properties such as ground state equilibrium structures, relative energies in terms of conformations and transition states (regarding possible cis–trans interconversions), vertical excitation energies (VEs), generalized oscillator strengths (GOS), and excited state structures. Density functional theory (DFT) and its time-dependent formalism (TD-DFT) were used for determining all the ground state and excited state properties, respectively, both being employed with the CAM-B3LYP exchange–correlation functional and the cc-pVTZ basis set. In addition, effects caused by interactions with the solvent environment were probed by means of using two different approaches: i) the integral equation formalism polarizable continuum model (IEF-PCM) and ii) a composite solvation model (CSM) through the incorporation of explicit water molecules in combination with the IEF-PCM. In general, a decrease in the relative energies regarding a given cis/trans counterpart is noticed when solvation is considered independently from the model used; all the dipyridyl cis/trans isomers became (practically) isoenergetical due to dipyridyl-H2O hydrogen-bonding interactions. Moreover, the interconversion barriers were also found to be lowered due to solvation effects. For instance, the energy barrier in terms of interconversion of the trans 2,2′-dipyridyl to the cis 2,2′-dipyridyl was determined as (approximately) 67 % of the corresponding value obtained in the gas-phase. Although no major differences regarding the values of the VEs associated to a bright state are suggested from the comparison between the results obtained for a given isomer through the consideration of solvation and those corresponding determined in the gas-phase, the GOS are all increased when solvation is considered, suggesting an enhancement in the photoabsorption of all the isomers when in presence of solvent. In addition and in contrast to what was seen previously in the case of the gas-phase, 4,4′-dipyridyl presented a bright state among the five lowest-lying excited singlets (accessible at the UVC energy region), which is located at 5.49 eV (with GOS = 0.4465) at the TD-DFT/CAM-B3LYP/cc-pVTZ level of theory in water (IEF-PCM) and at 5.47 eV (with GOS = 0.5331) at the same level of theory with the CSM. Given that no significant change was noticed in the optimized structures for the excited states, it is possible to infer that all the compounds will decompose through photo decomposition (chemical reaction occurring in the excited state) rather than direct photolysis when in solution.

Crystal Structure, Spectroscopic Characterization, Antioxidant and Cytotoxic Activity of New Mg(II) and Mn(II)/Na(I) Complexes of Isoferulic Acid.

The Mg(II) and heterometallic Mn(II)/Na(I) complexes of isoferulic acid (3-hydroxy-4-methoxycinnamic acid, IFA) were synthesized and characterized by infrared spectroscopy FT-IR, FT-Raman, electronic absorption spectroscopy UV/VIS, and single-crystal X-ray diffraction. The reaction of MgCl2 with isoferulic acid in the aqueous solutions of NaOH resulted in synthesis of the complex salt of the general formula of [Mg(H2O)6]⋅(C10H9O4)2⋅6H2O. The crystal structure of this compound consists of discrete octahedral [Mg(H2O)6]2+ cations, isoferulic acid anions and solvent water molecules. The hydrated metal cations are arranged among the organic layers. The multiple hydrogen-bonding interactions established between the coordinated and lattice water molecules and the functional groups of the ligand stabilize the 3D architecture of the crystal. The use of MnCl2 instead of MgCl2 led to the formation of the Mn(II)/Na(I) complex of the general formula [Mn3Na2(C10H7O4)8(H2O)8]. The compound is a 3D coordination polymer composed of centrosymmetric pentanuclear subunits. The antioxidant activity of these compounds was evaluated by assays based on different antioxidant mechanisms of action, i.e., with •OH, DPPH• and ABTS•+ radicals as well as CUPRAC (cupric ions reducing power) and lipid peroxidation inhibition assays. The pro-oxidant property of compounds was measured as the rate of oxidation of Trolox. The Mg(II) and Mn(II)/Na(I) complexes with isoferulic acid showed higher antioxidant activity than ligand alone in DPPH (IFA, IC50 = 365.27 μM, Mg(II) IFA IC50 = 153.50 μM, Mn(II)/Na(I) IFA IC50 = 149.00 μM) and CUPRAC assays (IFA 40.92 μM of Trolox, Mg(II) IFA 87.93 μM and Mn(II)/Na(I) IFA 105.85 μM of Trolox; for compounds’ concentration 10 μM). Mg(II) IFA is a better scavenger of •OH than IFA and Mn(II)/Na(I) IFA complex. There was no distinct difference in ABTS•+ and lipid peroxidation assays between isoferulic acid and its Mg(II) complex, while Mn(II)/Na(I) complex showed lower activity than these compounds. The tested complexes displayed only slight antiproliferative activity tested in HaCaT human immortalized keratinocyte cell line within the solubility range. The Mn(II)/Na(I) IFA (16 μM in medium) caused an 87% (±5%) decrease in cell viability, the Mg salt caused a comparable, i.e., 87% (±4%) viability decrease in a concentration of 45 μM, while IFA caused this level of cell activity attenuation (87% ± 5%) at the concentration of 1582 μM (significant at α = 0.05).

Mechanisms of a Cyclobutane-Fused Lactone Hydrolysis in Alkaline and Acidic Conditions.

Searching for functional polyesters with stability and degradability is important due to their potential applications in biomedical supplies, biomass fuel, and environmental protection. Recently, a cyclobutane-fused lactone (CBL) polymer was experimentally found to have superior stability and controllable degradability through hydrolysis reactions after activation by mechanical force. In order to provide a theoretical basis for developing new functional degradable polyesters, in this work, we performed a detailed quantum chemical study of the alkaline and acidic hydrolysis of CBL using dispersion-corrected density functional theory (DFT-D3) and mixed implicit/explicit solvent models. Various possible hydrolysis mechanisms were found: BAC2 and BAL2 in the alkaline condition and AAC2, AAL2, and AAL1 in the acidic condition. Our calculations indicated that CBL favors the BAC2 and AAC2 mechanisms in alkaline and acidic conditions, respectively. In addition, we found that incorporating explicit water solvent molecules is highly necessary because of their strong hydrogen-bonding with reactant/intermediate/product molecules.

Crystal structure of di-aqua-(3,14-diethyl-2,6,13,17-tetra-aza-tri-cyclo-[16.4.0.07,12]docosa-ne)copper(II) (3,14-diethyl-2,6,13,17-tetra-aza-tri-cyclo[16.4.0.07,12]docosa-ne)copper(II) tetra-bromide dihydrate, [Cu(C22H44N4)(H2O)2][Cu(C22H44N4)]Br4·2H2O.

The crystal structure of the new double CuII complex salt, [Cu(L)(H2O)2][Cu(L)]Br4·2H2O (L = 3,14-diethyl-2,6,13,17-tetra-aza-tri-cyclo-[16.4.0.07,12]docosane, C22H44N4) has been determined using synchrotron radiation. The asymmetric unit contains one half of a [Cu(L)(H2O)2]2+ cation, one half of a [Cu(L)]2+ cation (both completed by crystallographic inversion symmetry), two bromide anions and one water solvent mol-ecule. The CuII atom in the first complex exists in a tetra-gonally distorted octa-hedral environment with the four N atoms of the macrocyclic ligand in equatorial and two aqua ligands in axial positions, whereas the CuII atom in the second complex exists in a square-planar environment defined by the four nitro-gen atoms of the macrocyclic ligand. The two macrocyclic rings adopt the most stable trans-III configuration with normal Cu-N bond lengths from 2.016 (3) to 2.055 (3) Å and an axial Cu-O bond length of 2.658 (4) Å. The crystal structure is stabilized by inter-molecular hydrogen bonds involving the macrocycle N-H or C-H groups and the O-H groups of water mol-ecules as donor groups, and the O atoms of water mol-ecules and bromide anions as acceptor groups, giving rise to a one-dimensional network extending parallel to [100].

Crystal structure, sorption properties, and electronic structure of flexible MOF, (Ni-4,4′azopyridine)[Ni(CN)4

The flexible metal organic framework (MOF) compound, Ni(L)[Ni(CN)4], (L = 4,4′azopyridine (C10N4H8), nicknamed AzoPyr) is a 3D porous material that adopts the Hofmann-type structure. This paper reports our synthesis of Ni-AzoPyr and its structural, bonding, and sorption characterization. The red monoclinic crystals (with space group P2/n) were found to be multiple twins with three main components related by twin laws. The lattice parameters are a = 7.102 (3) Å, b = 14.154 (4) Å, c = 25.655 (10) Å, β = 92.575 (12)°, and V = 2577 (2) Å3. Ni-AzoPyr adopts a pillared structure with layers defined by the 2-D Ni [Ni(CN)4]n nets and AzoPyr ligands as pillars linking between 6-fold coordinated Ni3 sites. An additional AzoPyr ligand was found to cross link between the 6-fold Ni1 sites to the open ends of the four-fold Ni2 sites. This arrangement results in a 5-fold pseudo square-pyramid for Ni2 and a significantly long Ni2–N distance of 2.436 (11) Å. Density functional theory (DFT) calculations show that almost all states in the conduction band minimum (CBM) are occupied by the 6-fold coordinated Ni site, indicating little to no electrons are conducted at the 5-fold coordinated Ni site. Water molecules were found to be entrapped in the cavities of the structure. In addition to the gating adsorption feature of Ni-AzoPyr, using computational approach, we found that in the absence of water molecules, the pores were found to have a local diameter of 5.8 Å with a maximum number of 15.5 CO2 molecules per unit cell. The inclusion of disordered water solvent molecules gives rise to the formula of Ni(AzoPyr)[Ni(CN)4]·0.8H2O, or C19H12N10Ni2·0.8(H2O).

Water-Mediated Oxidation of Guanine by a Repair Enzyme: Simulation Using the ABEEM Polarizable Force Field.

The recognition mechanism of oxidative damage in organisms has long been a research hotspot. Water is an important medium in the recognition process, but its specific role remains unknown. There is a need to develop a suitable force field that can adequately describe the electrostatic, hydrogen bond, and other interactions among the molecules in the complex system of the repair enzyme and oxidized base. The developing ABEEM polarizable force field (PFF) has been used to simulate the repaired enzyme hOGG1 and oxidized DNA (PDB ID: 1EBM) in a biological environment, and the corresponding results are better than those of the fixed-charge force fields OPLS/AA and AMBER OL15. 8-Oxo-G is recognized by Gln315 of hOGG1 mainly through hydrogen bonds mediated by continuous exchange of 2 water molecules. Phe319 and Cys253 are stacked on both sides of the π planes of bases to form sandwich structures. The charge polarization effect gives an important signal to drive the exchange of water molecules and maintains the recognition of oxidation bases by enzymes. The mediated main water molecule A and mediated auxiliary water molecule B together pull Gln315 to recognize 8-oxo-G by hydrogen bond interactions. Then, the charge polarization signal of solvent water molecule C with a large absolute charge causes the absolute charge of O atoms in water molecule A or B to increase by approximately 0.2 e, and water molecule A or B leaves Gln315 and 8-oxo-G. The other water molecule and water molecule C synergistically recognize 8-oxo-G with Gln315. Even though the water molecules between Gln315 and 8-oxo-G are removed, the MD simulation results show that water molecules appear between Gln315 and 8-oxo-G in a very short time (<2 ps). The dwell time of each water molecule is approximately 60 ps. The radial distribution function and dwell time support the correctness of the above mechanism. These polarization effects and hydrogen bonding interactions cannot be simulated by a fixed-charge force field.

Active Site Hydrogen Bonding Induced in Cytochrome P450cam by Effector Putidaredoxin.

Cytochrome P450s are diverse and powerful catalysts that can activate molecular oxygen to oxidize a wide variety of substrates. Catalysis relies on effective uptake of two electrons and two protons. For cytochrome P450cam, an archetypal member of the superfamily, the second electron must be supplied by the redox partner putidaredoxin (Pdx). Pdx also plays an effector role beyond electron transfer, but after decades the mechanism remains under investigation. We applied infrared spectroscopy to heme-ligated CN- to examine the influence of Pdx binding. The results indicate that Pdx induces the population of a conformation wherein the CN- ligand forms a strong hydrogen bond to a solvent water molecule, experimentally corroborating the formation of a proposed proton delivery network. Further, characterization of T252A P450cam implicates the side chain of Thr252 in regulating the population equilibrium of hydrogen-bonded states within the P450cam/Pdx complex, which could underlie its role in directing activated oxygen toward product formation and preventing reaction uncoupling through peroxide release.

Crystal structure of di-aqua-(3,14-diethyl-2,6,13,17-tetra-aza-tri-cyclo-[16.4.0.07,12]docosa-ne)copper(II) dichloride tetra-hydrate.

The crystal structure of the novel hydrated CuII salt, [Cu(L)(H2O)2]Cl2·4H2O (L = 3,14-diethyl-2,6,13,17-tetra-aza-tri-cyclo-[16.4.0.07,12]docosane, C22H44N4) has been determined using synchrotron radiation. The asymmetric unit contains one half of the [Cu(L)(H2O)2]2+ cation (completed by crystallographic inversion symmetry), one chloride anion and two lattice water mol-ecules. The copper(II) atom exists in a tetra-gonally distorted octa-hedral environment with the four N atoms of the macrocyclic ligand in equatorial and two O atoms from water mol-ecules in axial positions. The latter exhibit a long axial Cu-O bond length of 2.7866 (16) Å due to the Jahn-Teller distortion. The macrocyclic ring adopts a stable trans-III conformation with typical Cu-N bond lengths of 2.0240 (11) and 2.0441 (3) Å. The complex is stabilized by hydrogen bonds formed between the O atoms of coordinated water mol-ecules and the NH groups as donors, and chloride anions as acceptors. The chloride anions are further connected to the lattice water solvent molecules through O-H⋯Cl hydrogen bonds, giving rise to a three-dimensional network structure.

Interactive Regulation between Aliphatic Hydroxylation and Aromatic Hydroxylation of Thaxtomin D in TxtC: A Theoretical Investigation.

TxtC is an unusual bifunctional cytochrome P450 that is able to perform sequential aliphatic and aromatic hydroxylation of the diketopiperazine substrate thaxtomin D in two distinct sites to produce thaxtomin A. Though the X-ray structure of TxtC complexed with thaxtomin D revealed a binding mode for its aromatic hydroxylation, the preferential hydroxylation site is aliphatic C14. It is thus intriguing to unravel how TxtC accomplishes such two-step catalytic hydroxylation on distinct aliphatic and aromatic carbons and why the aliphatic site is preferred in the hydroxylation step. In this work, by employing molecular docking and molecular dynamics (MD) simulation, we revealed that thaxtomin D could adopt two different conformations in the TxtC active site, which were equal in energy with either the aromatic C20-H or aliphatic C14-H pointing toward the active Cpd I oxyferryl moiety. Further ONIOM calculations indicated that the energy barrier for the rate-limiting hydroxylation step on the aliphatic C14 site was 9.6 kcal/mol more favorable than that on the aromatic C20 site. The hydroxyl group on the monohydroxylated intermediate thaxtomin B C14 site formed hydrogen bonds with Ser280 and Thr385, which induced the l-Phe moiety to rotate around the Cβ-Cγ bond of the 4-nitrotryptophan moiety. Thus, it adopted an energetically favorable conformation with aromatic C20 adjacent to the oxyferryl moiety. In addition, the hydroxyl group induced solvent water molecules to enter the active site, which propelled thaxtomin B toward the heme plane and resulted in heme distortion. Based on this geometrical layout, the rate-limiting aromatic hydroxylation energy barrier decreased to 15.4 kcal/mol, which was comparable to that of the thaxtomin D aliphatic hydroxylation process. Our calculations indicated that heme distortion lowered the energy level of the lowest Cpd I α-vacant orbital, which promoted electron transfer in the rate-limiting thaxtomin B aromatic hydroxylation step in TxtC.

Different cation-anion interaction mechanisms of diamino protic ionic liquids: A density functional theory study

Diamino protic ionic liquids (DPILs) possess a wide application prospect in the field of gas separation and absorption. In this work, two kinds of DPILs, dimethylethylenediamine 4-fluorophenolate ([DMEDAH][4-F-PhO]) and dimethylethylenediamine acetate ([DMEDAH][OAc]) were selected to investigate the microstructure properties and interaction mechanism of [DMEDAH]+ cations with different [4-F-PhO]-/[OAc]- anions by density functional theory (DFT) method. The stable configurations were determined at B3LYP/6-311+G (d, p) level, and the effects of solvent water molecules on the structure were investigated. Based on this, the different interaction mechanisms and the structural/charges parameters were revealed.

Cd(II)/Fe(III) heterobimetallic complexes with dien and cyanido ligands as precursors of ferrite-type oxides: Syntheses, crystal structures, thermal properties and identification of the oxides

From the aqueous systems Cd(II) – dien – [Fe(CN)6]3-, where dien is 1,4,7-triazaheptane, two novel ionic complexes [Cd(dien)2]3[Fe(CN)6]2·3H2O (1) and NH4[Bu4N][Cd(dien)2]2[Fe(CN)6]2 (2) were prepared and characterized by spectroscopic (IR and UV–VIS) and EDX method. Both complexes 1 and 2 exhibit ionic crystal structures built up of [Cd(dien)2]2+ and [Fe(CN)6]3- complex ions; the respective crystals structures comprise water solvate molecules in 1 and, additional ammonium and tetrabutylammonium cations in 2. In both crystal structures the supramolecular structures are formed by extensive hydrogen bonding systems. The thermal decompositions of both complexes under dynamic conditions were studied on air. The solid residues 1R and 2R were identified by X-ray powder diffractometry as mixture of oxides formed of ferrite CdFe2O4 and CdO for 1R and iron hydroxide oxide, Fe1.833(OH)0.5O2.5 for 2R. Examination of the solid residues by SEM and EDX analyses has confirmed homogeneity of products, and for R2 discrete particles were observed.

Hands-On Model of the Principle of Isotope Dilution Analysis for Use in an Interactive Teaching and Learning Classroom Exercise

A simple hands-on model for illustrating the concept of isotope dilution analysis (IDA) has been devised. The model consists of two sets of beads of different sizes, with one set representing atoms of the analyte and the other set representing solvent water molecules. Phase separation is mimicked by sieving the beads, and the results are detected according to the color of the analyte beads. In this paper, the following three IDA methods are illustrated using the model: (1) direct IDA, (2) substoichiometric IDA, and (3) IDA-assisted neutron activation analysis. The model was demonstrated for a small group of graduate students with previous knowledge of nuclear chemistry, and the response from an inquiry held after the demonstration was good. It is suggested that the model can be used in a dry chemistry laboratory exercise to demonstrate the methodological differences between the different IDA methods, without the need for costly radioisotopes or irradiation facilities. It can also be used as a tool for engaging students in meta-modeling activities.

Peptide Hydrolysis by Metal (Oxa)cyclen Complexes: Revisiting the Mechanism and Assessing Ligand Effects.

The mechanism responsible for peptide bond hydrolysis by Co(III) and Cu(II) complexes with (oxa)cyclen ligands has been revisited by means of computational tools. We propose that the mechanism starts by substrate coordination and an outer-sphere attack on the amide C atom of a solvent water molecule assisted by the metal hydroxo moiety as a general base, which occurs through six-membered ring transition states. This new mechanism represents a more likely scenario than the previously proposed mechanisms that involved an inner-sphere nucleophilic attack through more strained four-membered rings transition states. The corresponding computed overall free-energy barrier of 25.2 kcal mol-1 for hydrolysis of the peptide bond in Phe-Ala by a cobalt(III) oxacyclen catalyst (1) is consistent with the experimental values obtained from rate constants. Also, we assessed the influence of the nature of the ligand throughout a systematic replacement of N by O atoms in the (oxa)cyclen ligand. Increasing the number of coordinating O atoms accelerates the reaction by increasing the Lewis acidity of the metal ion. On the other hand, the higher reactivity observed for the copper(II) oxacyclen catalyst with respect to the analogous Co(III) complex can be attributed to the larger Brönsted basicity of the copper(II) hydroxo ligand. Ultimately, the detailed understanding of the ligand and metal nature effects allowed us to identify the double role of the metal hydroxo complexes as Lewis acids and Brönsted bases and to rationalize the observed reactivity trends.

Proton transfer in bulk water using the full adaptive QM/MM method: integration of solute- and solvent-adaptive approaches.

The quantum mechanical/molecular mechanical (QM/MM) method is a hybrid molecular simulation technique that increases the accessibility of local electronic structures of large systems. The technique combines the benefit of accuracy found in the QM method and that of cost efficiency found in the MM method. However, it is difficult to directly apply the QM/MM method to the dynamics of solution systems, particularly for proton transfer. As explained in the Grotthuss mechanism, proton transfer is a structural interconversion between hydronium ions and solvent water molecules. Hence, when the QM/MM method is applied, an adaptive treatment, namely on-the-fly revisions on molecular definitions, is required for both the solute and solvent. Although several solvent-adaptive methods have been proposed, a full adaptive framework, which is an approach that also considers adaptation for solutes, remains untapped. In this paper, we propose a new numerical expression for the coordinates of the excess proton and its control algorithm. Furthermore, we confirm that this method can stably and accurately simulate proton transfer dynamics in bulk water.

Hydrogen bond-induced abrupt spin crossover behaviour in 1-D cobalt(II) complexes - the key role of solvate water molecules.

The magnetic properties and structural aspects of the 1-D cobalt(ii) complexes, [Co(pyterpy)Cl2]·2H2O (1·2H2O; pyterpy = 4'-(4'''-pyridyl)-2,2':6',2''-terpyridine) and [Co(pyethyterpy)Cl2]·2H2O (2·2H2O; pyethyterpy = 4'-((4'''-pyridyl)ethynyl)-2,2':6',2''-terpyridine) are reported. In each complex the central cobalt(ii) ion displays an octahedral coordination environment composed of three nitrogen donors from the terpyridine moiety, a nitrogen donor from a pyridyl group and two chloride ligands which occupy the axial sites. 1·2H2O exhibits abrupt spin-crossover (SCO) behaviour (T1/2↓ = 218 K; T1/2↑ = 227 K) along with a thermal hysteresis loop, while 2·2H2O and the dehydrated species 1 and 2 exhibit high-spin (HS) states at 2-300 K as well as field-induced single-molecule magnet (SMM) behaviour attributed to the presence of magnetic anisotropic HS cobalt(ii) species (S = 3/2). 1·2H2O exhibited reversible desorption/resorption of its two water molecules, revealing reversible switching between SCO and SMM behaviour triggered by the dehydration/rehydration processes. Single crystal X-ray structural analyses revealed that 1·2H2O crystalizes in the orthorhombic space group Pcca while 2 and 2·2H2O crystallize in the monoclinic space group P2/n. Each of the 1-D chains formed by 1·2H2O in the solid state are bridged by hydrogen bonds between water molecules and chloride groups to form a 2-D layered structure. The water molecules bridging 1-D chains in 1·2H2O interact with the chloride ligands occupying the axial positions, complementing the effect of Jahn-Teller distortion and contributing to the abrupt SCO behaviour and associated stabilization of the LS state.

Hydrogenation of Cinnamaldehyde by Water‐Soluble Ruthenium(II) Phosphine Complexes: A DFT Study on the Selectivity and Viability of trans‐Dihydride Pathways

AbstractApart from the important trans‐dihydrido‐transition metal catalysts containing polydentate phosphine, diamine or pincer‐type ligands, the catalytic role of trans‐dihydride complexes with monodentate ligands is generally neglected given their inferior thermodynamic stability compared to the cis isomers. This way however, a mechanistic investigation about selectivity loses important details as more prominent catalysts provide multiple competing pathways towards the desired product. Here, we used the hydrogenation of cinnamaldehyde as model reaction to gain theoretical insight about whether the water soluble ruthenium trans‐dihydride complexes, trans‐[Ru(II)H2P3L] (P=PPh3 in the model, monosulfonated PPh3 (mtppms) in experiments, L=H2O or P), are, indeed, feasible catalytic species as suggested on the basis of experimental investigations. After evaluating numerous catalytic cycles, we found that the consideration of thermodynamically accessible trans‐dihydrides provides two viable competing reaction channels. The key feature of the mechanisms is the inclusion of explicit solvent (water) molecules, which allows the separation of substrate hydrogenation from the rate determining catalyst regeneration, where the H−H activation occurs. We found that the former determines the selectivity towards carbonyl hydrogenation through the more favorable hydride transfer to the carbonyl carbon.

Water-mediated formation of hydride derivates from flexible Pd-salan complexes: A DFT study

The formation of hydride derivatives of sulfonated palladium(II) salan (hydrogenated salen) complexes was studied with DFT methods. The non-hydrolytic property, chirality, and flexibility lead to a significant difference compared to salen derivatives. We made a detailed computational study to understand the relevance of the flexibility in contrast to the rigid salen complex. Two main pathways were investigated: one of them was a direct monohydride formation where the oxygen of the phenolate group was substituted by a hydrogen molecule followed by a proton transfer. Another was an indirect monohydride formation involving the substitution of phenolate arm by a solvent water molecule in the first step and subsequent reaction with H2 in the second. We focused on weak interactions among the Pd-complex and water molecules. Trigonal, square, and diamond motifs of H-bond networks were found around the oxygen atom of the phenolate arm which is crucial during the proton transfer step, however, substitution steps prefer chain type motifs.