Chemical Reactions In Solution Research Articles

Modeling Flexible Molecules in Solution: A pKa Case Study.

Continuum solvation models have been incredibly successful for the computationally efficient study of chemical reactions in solution. However, their development and application has generally been on focused on investigations of small, rigid molecules. Additional factors must be considered when studying large, flexible and multiply ionizable species. These include whether the use of thermocycle or entirely solution-phase approaches are more appropriate for the calculation of solution-phase free energies, which metrics can be used to reliably identify the conformation(s) adopted by flexible molecules in solution, and how errors due to inaccuracies in the prediction of low energy vibrational frequencies can be avoided. Here we explore these issues using the calculation of pKas for a diverse set of amine-containing species as a case study. We show that thermocycle-based approaches should only be applied where there are relatively small structural changes between the gas- and solution-phase molecular geometries, and that these methods are generally not appropriate for conformational searching. Using gas- or solution-phase energies or gas-phase free energies can also lead to errors in the identification of the most stable molecular conformation(s). Scaling of low energy vibrational modes (i.e., use of the quasi-harmonic oscillator approximation) is helpful, however care must be taken to ensure modes that change as part of the reaction are not disregarded. Entirely solution-phase approaches to the Gibbs free energy and hence pKa calculations were found to yield accurate pKa values for the amine test set studied when each charged site is complexed with an explicit water molecule and a proton exchange scheme is applied with an appropriately chosen reference acid.

Method development of glycoprotein biomarkers for cancers.

Method development of glycoprotein biomarkers for cancers.

Rich Dynamics Underlying Solution Reactions Revealed by Sampling and Data Mining of Reactive Trajectories.

Efficient sampling in both configuration and trajectory spaces, combined with mechanism analyses via data mining, allows a systematic investigation of the thermodynamics, kinetics, and molecular-detailed dynamics of chemical reactions in solution. Through a Bayesian learning algorithm, the reaction coordinate(s) of a (retro-)Claisen rearrangement in bulk water was variationally optimized. The bond formation/breakage was found to couple with intramolecular charge separation and dipole change, and significant dynamic solvent effects manifest, leading to the “in-water” acceleration of Claisen rearrangement. In addition, the vibrational modes of the reactant and the solvation states are significantly coupled to the reaction dynamics, leading to heterogeneous and oscillatory reaction paths. The calculated reaction rate is well interpreted by the Kramers’ theory with a diffusion term accounting for solvent–solute interactions. These findings demonstrated that the reaction mechanisms can be complicated in homogeneous solutions since the solvent–solute interactions can profoundly influence the reaction dynamics and the energy transfer process.

One-step assembly of 2H-1T MoS2:Cu/reduced graphene oxide nanosheets for highly efficient hydrogen evolution

The transition metal dichagenides and their metallic 1T structure are attracting contemporary attentions for applications in high-performance devices because their peculiar optical and electrical properties. The single and few layers 1T structure is generally obtained by mechanical or chemical exfoliation. This work presents facile one-step synthesis of 2H-1T MoS2:Cu/reduced graphene oxide nanosheets. The experiment results indicated that the MoS2 and MoS2:Cu prepared by simple chemical solution reaction possessed 2H-1T structures. The reduced graphene oxide (rGO) incorporation further induced the phase transition from 2H-MoS2 to 1T-MoS2 and morphology transition from granular/nanosheet to more nanosheet. The 2H-1T structure and 2H → 1T phase transition, together with the Cu doping and interface effect between the MoS2 and rGO, remarkably enhanced the conduction and photoconduction of the nanostructures. Thus, Cu doping and rGO incorporation obviously enhanced the catalytic activity and its stability, making the MoS2:Cu/rGO nanosheet a most active and stable catalyst for hydrogen evolution. This work clearly indicates that the 1T-MoS2 nanosheets with high catalytic activity for hydrogen evolution can be easily obtained by the facile low temperature chemical method and induction of rGO.

Light-Induced Radical Formation and Isomerization of an Aromatic Thiol in Solution Followed by Time-Resolved X-ray Absorption Spectroscopy at the Sulfur K-Edge

We applied time-resolved sulfur-1s absorption spectroscopy to a model aromatic thiol system as a promising method for tracking chemical reactions in solution. Sulfur-1s absorption spectroscopy allows tracking multiple sulfur species with a time resolution of ∼70 ps at synchrotron radiation facilities. Experimental transient spectra combined with high-level electronic structure theory allow identification of a radical and two thione isomers, which are generated upon illumination with 267 nm radiation. Moreover, the regioselectivity of the thione isomerization is explained by the resulting radical frontier orbitals. This work demonstrates the usefulness and potential of time-resolved sulfur-1s absorption spectroscopy for tracking multiple chemical reaction pathways and transient products of sulfur-containing molecules in solution.

Photocatalytic Activity of Reduced Graphene Oxide-SnSe Nanohybrids with Efficiency Interface Effect

Reduced graphene oxide-SnSe (rGO-SnSe) nanohybrids were synthesized with a solution chemical reaction at room temperature. The nanohybrids were characterized by various techniques for their microstructural and photocatalytic activities in photodegradation of alkaline dye malachite green in the water. The effects of rGO/SnSe ratio, initial solution pH, and H2O2 concentration on the photodegradation efficiency were studied. The SnSe nanocrystallines with nanoscale size and narrow bandgap were formed and uniformly adhered on the rGO surface. Raman analysis confirmed the reduction of GO. The experimental results indicated that the nanohybrids showed excellent sunlight-excited photocatalytic activity in degrading malachite green in the water. Significantly, the nanohybrids showed remarkable photo-Fenton-like catalytic activity. The photodegradation rates of the hybrids were greater than that of SnSe nanoparticles, increased with increasing rGO/SnSe ratio, and related to operation parameters. High photocatalytic activities were ascribed to the efficiency interface effect that was confirmed by the calculations of band energy level and photoconductivity. The TOC measurement further verified the photodegradation results. The nanoparticles and nanohybrids also showed excellent reusability.

Synthesis of MnOx/reduced graphene oxide nanocomposite as an anode electrode for lithium-ion batteries

We report the high performance of the manganese oxide/reduced graphene oxide (MnOx/rGO) nanocomposite as an anode electrode of a lithium-ion battery. The composite is synthesized by a low temperature (83°C) chemical solution reaction, and shows relatively high specific capacities (660mAhg−1) after 50 cycles. For MnOx/rGO composites, the cycling stability is increased remarkably as compared to that seen with individual MnOx, and this is due to the synergistic effects of both the components in the composite. The rGO acts as a conductive buffer layer that suppresses the volume change of MnOx, and simultaneously promotes the conductivity of MnOx. The functional groups of graphene oxide facilitate MnOx formation at low temperature, and this retains the MnOx-graphene oxide connection, thus improving the capacity and cycling stability.

Investigation of metal ion additives on the suppression of ammonia loss and CO2 absorption kinetics of aqueous ammonia-based CO2 capture

Aqueous ammonia is an attractive absorbent for the capture of CO2 from industrial flue gases. However evaporative ammonia loss limits the application of the ammonia-based CO2 capture process. The use of metal ion additives (where M(II)=Cu(II), Zn(II) and Ni(II)), has been reported previously for the effective suppression of ammonia loss in the post combustion capture of CO2. In this study, we have investigated the absorption of CO2 into various M(II)/NH3 solutions, the resulting loss of ammonia to evaporation, and have attempted to rationalise the observed effects using an extended chemical model that includes all chemical reactions in solution. The theoretical and experimental investigations suggest that complexation of ammonia by metal ions effectively reduces the concentration of free ammonia, resulting in reduced evaporative loss but also reduced reactivity towards CO2. Simple reduction of the total NH3 concentration to the same concentration of free NH3 concentration as that obtained by the addition of M(II) showed a similar reduction in the ammonia loss as well as the CO2 absorption rate. The effects on CO2 absorption capacity at 25 and 80°C, cyclic capacity and regeneration energy are also simulated and discussed.

Photocatalysis of novel reduced graphene oxide-CoSe nanocomposites with efficient interface-induced effect

In this work, reduced graphene oxide–CoSe (rGO–CoSe) nanocomposites were synthesized with chemical solution reaction and characterized by X-ray diffraction, scanning electron microscopy, Raman spectroscopy, Fourier transform infrared spectroscopy, UV–vis spectroscopy, and photodegradation of toxicity malachite green in the water. The effects of rGO/CoSe ratio, initial solution pH, and H2O2 concentration on the photodegradation effeciency were studied. The nanocomposites showed excellent sunlight-excited photocatalytic activity to toxicity malachite green in the water. The photodegradation rate increased with increasing rGO/CoSe ratio and initial solution pH. Significantly, remarkable Fenton-like photocatalytic activity enhanced with increasing rGO/CoSe ratio and H2O2 concentration was observed. The photodegradation rate constant, k obs, was determined under pseudo-first order conditions. The interface-induced mechanism on enhanced photocatalysis with rGO/CoSe was suggested.

Control of Reactivity and Regioselectivity for On-Surface Dehydrogenative Aryl-Aryl Bond Formation.

Regioselectivity is of fundamental importance in chemical synthesis. Although many concepts for site-selective reactions are well established for solution chemistry, it is not a priori clear whether they can easily be transferred to reactions taking place on a metal surface. A metal will fix the chemical potential of the electrons and perturb the electronic states of the reactants because of hybridization. Additionally, techniques to characterize chemical reactions in solution are generally not applicable to on-surface reactions. Only recent developments in resolving chemical structures by atomic force microscopy (AFM) and scanning tunneling microscopy (STM) paved the way for identifying individual reaction products on surfaces. Here we exploit a combined STM/AFM technique to demonstrate the on-surface formation of complex molecular architectures built up from a heteroaromatic precursor, the tetracyclic pyrazino[2,3-f][4,7]phenanthroline (pap) molecule. Selective intermolecular aryl-aryl coupling via dehydrogenative C-H activation occurs on Au(111) upon thermal annealing under ultrahigh vacuum (UHV) conditions. A full atomistic description of the different reaction products based on an unambiguous discrimination between pyrazine and pyridine moieties is presented. Our work not only elucidates that ortho-hydrogen atoms of the pyrazine rings are preferentially activated over their pyridine equivalents, but also sheds new light onto the participation of substrate atoms in metal-organic coordination bonding during covalent C-C bond formation.

In situ solution chemical reaction deposition of Bi2S3 quantum dots on mesoscopic TiO2 films for application in quantum dot sensitised solar cells

Bi2S3 quantum dot (QD) modified mesoscopic TiO2 films were prepared by in situ solution chemical reaction deposition, using ethylene glycol monomethylether and ethanol as solvent of cationic precursor solution and anionic precursor solution respectively. Ultraviolet–visible–near infrared absorption spectra reveal that the Bi2S3 QDs extends the range of the photo response of the TiO2 films to the visible region. A maximum conversion effciency of 0·615%, with short circuit current density of 2·940 mA cm− 2 and open circuit voltage of 505 mV, was obtained after five deposition cycles under illumination at 1000 W m− 2. These results indicate that the Bi2S3 has a potential application in the field of QD sensitised solar cell.

In-situ solution chemical reaction deposition of Bi2S3 quantum dots on mesoscopic TiO2 films for application in quantum-dot-sensitized solar cells

ABSTRACTBi2S3 quantum dots modified mesoscopic TiO2 films were prepared by in-situ solution chemical reaction deposition, using ethylene glycol monomethylether (EGME) and ethanol as solvent of Cationic precursor solution and anionic precursor solution respectively. UV-vis-NIR absorption spectra reveal that the Bi2S3 QDs extends the range of the photo response of the TiO2 films to visible region. A maximum conversion efficiency of 0.205% was obtained after five deposition cycles under illumination at 1000 W/m2. These results indicate that the Bi2S3 has potential application in the field of QDSSC.

Efficient Computational Research Protocol to Survey Free Energy Surface for Solution Chemical Reaction in the QM/MM Framework: The FEG-ER Methodology and Its Application to Isomerization Reaction of Glycine in Aqueous Solution.

In solution chemical reaction, we often need to consider a multidimensional free energy (FE) surface (FES) which is analogous to a Born-Oppenheimer potential energy surface. To survey the FES, an efficient computational research protocol is proposed within the QM/MM framework; (i) we first obtain some stable states (or transition states) involved by optimizing their structures on the FES, in a stepwise fashion, finally using the free energy gradient (FEG) method, and then (ii) we directly obtain the FE differences among any arbitrary states on the FES, efficiently by employing the QM/MM method with energy representation (ER), i.e., the QM/MM-ER method. To validate the calculation accuracy and efficiency, we applied the above FEG-ER methodology to a typical isomerization reaction of glycine in aqueous solution, and reproduced quite satisfactorily the experimental value of the reaction FE. Further, it was found that the structural relaxation of the solute in the QM/MM force field is not negligible to estimate correctly the FES. We believe that the present research protocol should become prevailing as one computational strategy and will play promising and important roles in solution chemistry toward solution reaction ergodography.

Volumetric Properties of Alkali Salt in Aqueous 1-Butyl-3-Methylimidazolium Tetrafluoroborate at Various Temperatures

Volumetric characterstics of multiple electrolytic solutions in a wide range of solute concentrations and solutions temperatutre are of fundamental importance for the understanding of numerous physicochemical processes occurring in various brances of the chemical industry as well as in the natural envirnoment. In a view of importance of NaCl as primary salts in seawater and most of other natural water, accurate thermophysical data is crucial for understanding industrial and natural processes [1]. Ionic interaction plays an important role in chemical reactions in solutions [2]. In fact, the effect of the addition of salts in aquous solutions of ILs is very complex, primarily because a large number of different types of intermolecular interactions come into play between the ion and water, ion and IL, and IL and water. From a thermodynamic perspective, the solvation of ionic species in the ILs is much more favored than in conventional solvents. This is one of the key advantages of using ILs in separations involving ionic species.

Enzymatic Kinetic Isotope Effects from Path-Integral Free Energy Perturbation Theory.

Path-integral free energy perturbation (PI-FEP) theory is presented to directly determine the ratio of quantum mechanical partition functions of different isotopologs in a single simulation. Furthermore, a double averaging strategy is used to carry out the practical simulation, separating the quantum mechanical path integral exactly into two separate calculations, one corresponding to a classical molecular dynamics simulation of the centroid coordinates, and another involving free-particle path-integral sampling over the classical, centroid positions. An integrated centroid path-integral free energy perturbation and umbrella sampling (PI-FEP/UM, or simply, PI-FEP) method along with bisection sampling was summarized, which provides an accurate and fast convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. The PI-FEP method is illustrated by a number of applications, to highlight the computational precision and accuracy, the rule of geometrical mean in kinetic isotope effects, enhanced nuclear quantum effects in enzyme catalysis, and protein dynamics on temperature dependence of kinetic isotope effects.

QM/MM Protocol for Direct Molecular Dynamics of Chemical Reactions in Solution: The Water-Accelerated Diels-Alder Reaction.

We describe a solvent-perturbed transition state (SPTS) sampling scheme for simulating chemical reaction dynamics in condensed phase. The method, adapted from Truhlar and Gao's ensemble-averaged variational transition state theory, includes the effect of instantaneous solvent configuration on the potential energy surface of the reacting system (RS) and allows initial conditions for the RS to be sampled quasiclassically by TS normal mode sampling. We use a QM/MM model with direct dynamics, in which QM forces of the RS are computed at each trajectory point. The SPTS scheme is applied to the acceleration of the Diels-Alder reaction of cyclopentadiene (CP) + methyl vinyl ketone (MVK) in water. We explored the effect of the number of SPTS and of solvent box size on the distribution of bond lengths in the TS. Statistical sampling of the sampling was achieved when distribution of forming bond lengths converged. We describe the region enclosing the partial bond lengths as the transition zone. Transition zones in the gas phase, SMD implicit solvent, QM/MM, and QM/MM+QM (3 water molecules treated by QM) vary according to the ability of the medium to stabilize zwitterionic structures. Mean time gaps between formation of C-C bonds vary from 11 fs for gas phase to 25 fs for QM/MM+QM. Mean H-bond lengths to O(carbonyl) in QM/MM+QM are 0.14 Å smaller at the TS than in MVK reactant, and the mean O(carbonyl)-H(water)-O(water) angle of H-bonds at the TS is 10° larger than in MVK reactant.

A multi target approach to control chemical reactions in their inhomogeneous solvent environment

Shaped laser pulses offer a powerful tool to manipulate molecular quantum systems. Their application to chemical reactions in solution is a promising concept to redesign chemical synthesis. Along this road, theoretical developments to include the solvent surrounding are necessary. An appropriate theoretical treatment is helpful to understand the underlying mechanisms. In our approach we simulate the solvent by randomly selected snapshots from molecular dynamics trajectories. We use multi target optimal control theory to optimize pulses for the various arrangements of explicit solvent molecules simultaneously. This constitutes a major challenge for the control algorithm, as the solvent configurations introduce a large inhomogeneity to the potential surfaces. We investigate how the algorithm handles the new challenges and how well the controllability of the system is preserved with increasing complexity. Additionally, we introduce a way to statistically estimate the efficiency of the optimized laser pulses in the complete thermodynamical ensemble.

Intermediates in the cation reactions in solution probed by an in situ surface enhanced Raman scattering method.

For chemical reactions in liquid state, such as catalysis, understanding of dynamical changes is conducive to practical applications. Solvation of copper salts in aqueous solution has implications for life, the environment, and industry. In an ongoing research, the question arises that why the color of aqueous CuCl2 solution changes with solution concentration? In this work, we have developed a convenient and efficient in situ surface enhanced Raman scattering technique to probe the presence of many intermediates, some of them are responsible for color change, in crystallization of aqueous copper chloride solution. The versatility of the novel technique was confirmed in the identification of five intermediates states in the transition from CdS to MoS2 nanowires in solution. The facile in situ method is expected to be widely applicable in probing intermediate states in a variety of chemical reactions in solution.

The influence of the "cage effect" on the mechanism of reversible bimolecular multistage chemical reactions in solutions.

Manifestations of the "cage effect" at the encounters of reactants are theoretically treated by the example of multistage reactions in liquid solutions including bimolecular exchange reactions as elementary stages. It is shown that consistent consideration of quasi-stationary kinetics of multistage reactions (possible only in the framework of the encounter theory) for reactions proceeding near reactants contact can be made on the basis of the concepts of a "cage complex." Though mathematically such a consideration is more complicated, it is more clear from the standpoint of chemical notions. It is established that the presence of the "cage effect" leads to some important effects not inherent in reactions in gases or those in solutions proceeding in the kinetic regime, such as the appearance of new transition channels of reactant transformation that cannot be caused by elementary event of chemical conversion for the given mechanism of reaction. This results in that, for example, rate constant values of multistage reaction defined by standard kinetic equations of formal chemical kinetics from experimentally measured kinetics can differ essentially from real values of these constants.

Preparation of PbS Quantum Dots on TiO2 Porous Film by an In-Situ Process for Solar Cells Application

PbS QDs with size of 7–9 nm were deposited by an in-situ room temperature solution chemical reaction process using lead nitrate cationic resource in a form of solid precursor film and ammonium sulfide as an anionic reaction solution. The TiO2 film with PbS QDs deposited by the in-situ method was used to fabricate QDs-sensitized solar cells. The power conversation efficiency of the as prepared solar cells improved by increasing cycle numbers. For 7 deposition cycles of PbS QDs, the PbS/TiO2 device shows an open-circuit voltage (Voc) of 538 mV, a short-circuit current density (Jsc) of 0.145 mA, fill factor (FF) of 0.416 and a power conversion efficiency (η) of 0.163%.