Organic Molecules In Solution Research Articles

(Invited) Fast Room-Temperature Phosphorescence of Organic Molecules: Mechanism and Molecular Design

The mechanism and molecular design for fast and efficient room-temperature phosphorescence of organic molecules in solution will be presented.

Time-Dependent Multilevel Density Functional Theory.

We present a novel three-layer approach based on multilevel density functional theory (MLDFT) and polarizable molecular mechanics to simulate the electronic excitations of chemical systems embedded in an external environment within the time-dependent DFT formalism. In our method, the electronic structure of a target system, the chromophore, is determined in the field of an embedded inactive layer, which is treated as frozen. Long-range interactions are described by employing the polarizable fluctuating charge (FQ) force field. The resulting MLDFT/FQ thus accurately describes both electrostatics (and polarization) and non-electrostatic target-environment interactions. The robustness and reliability of the approach are demonstrated by comparing our results with experimental data reported for various organic molecules in solution.

Graphene Oxide-Induced Prototropism and Enhancement of Fluorescence Yield of Organic Molecules in Solutions: Recent Advances.

Till date, humankind has mainly acknowledged the quenching phenomenon of graphene oxide (GO). From a fundamental science standpoint, the unique and dynamic prospects of graphene oxide have been showcased in a brief but concise manner. Worldwide research studies have proven that graphene oxide has tremendous potentiality in showcasing breakthroughs in the fields of both basic science and innovative applications. In this Perspective, the fact that, apart from the very common fluorescence quenching phenomenon, graphene oxide can also enhance fluorescence intensity, promote prototropism, demonstrate aggregation-induced emission, and itself exhibit photoluminescence properties in nonaqueous media has been highlighted. It draws attention to the fact regarding unveiling the unknown properties of graphene oxide that might be useful to scientific communities in upcoming years.

COSMO-RS solute partition ratios for solvent mixtures of unknown composition: Henry's law constants as descriptors for mixture sigma profiles

Henry's law constants (H) for selected probe molecules have been used as descriptors to estimate the COSMO-RS sigma profiles of solvents and solvent mixtures. Henry's law constants were calculated with COSMOtherm for small sets of probe molecules in 155 organic solvents (training set), and these constants subsequently used as descriptors to model the solvent sigma profiles with 61 multiple linear regression (MLR) equations. Subsequent input into COSMOtherm of weighted basis molecule solvent mixtures whose sigma profiles closely matched those modelled for the training set solvents allowed estimation of air-solvent and water-solvent partition ratios for solutes in solvents and solvent mixtures without input of the solvent or solvent mixture identity. The best performing model had 16 descriptors and gave both a training and test set average root-mean square error (RMSE) of 0.008 and an average relative square error (RSE) of 0.07. Partition ratios (K) were then generated for a test set of 251 additional organic solute molecules in solvent/water media where solvents were test set compounds and H constants for the same probe molecules were used as descriptors. The best performing sigma profile model yielded log K RMSE values ranging from 0.17 to 0.92. Finally, this approach was applied to several mixtures ranging from simple binary mixtures to two mixtures considered to be of unknown or variable composition, complex reaction productions or biological materials (UVCBs), namely gasoline and an essential oil mixture. Mixture/water partition ratios were estimated for 251 solutes giving log K RMSE values ranging from 0.24 to 0.88.

Optical Setup for Investigating the Hyperpolarizability of Organic Nanostructure Materials in Solutions Using Electric Field Induced Second Harmonic Generation

Abstract: In this paper, an optical setup for electric field-induced second-harmonic generation (EFISH) at 1.9 μm experiment was arranged and used to investigate and determine the hyperpolarizability of some nanostructure organic components in two different solutions. First, a laser beam at 1.9 μm was generated by pumping a hydrogen Raman cell pressurized to 55 bar with 10 Hz Q-switched Nd: YAG nanosecond laser operating at λ = 1.064 μm. Next, the generated laser beam was aligned with all optical components within the assembly. The final step was to optimize the beam’s power and polarization at the center of the EFSH cell. Different nanostructure organic samples in solutions were prepared with nearly the same standard concentration of about 5 mmol/L to be investigated under the optimized system. Two solvents were used in this work, dichloromethane, or DCM (CH2Cl2), and chloroform, or trichloromethane (CHCl3). First, the harmonic order hyperpolarizability of five organic molecules in solutions with different chemical components such as quinolinium groups and organic boron complexes (supplied by the Chemistry Department at Catania University, Italy) were experimentally investigated experimentally. Only component (2-(2-[5′-(N,N-dimethylamino)-(2,2′-bithiophen)-5-yl]vinyl)-1-methyquinolin-1-ium iodide) in chloroform showed a significant difference in Maker fringes amplitude of the applied electrical field in comparison with fringes of its pure solvent. The value ofμfor this component has been calculated as 1320 x 10-48 esu. This value indicates that the component is a suitable candidate for use in second-harmonic generation imaging for biological applications. Keywords: Electric field-induced second-harmonic generation (EFISH), Harmonic light, Organic materials, hyperpolarizability. PACS: Nonlinear optics, 42.65.-k, Electric fields, instrumentation for measurement, 07.50.-e, Organic-inorganic hybrid nanostructures, 81.07.Pr, Organic materials optical materials, 42.70.Jk

3D Chiral Micro-Pinwheels Based on Rolling-Up Kirigami Technology.

Expanding micro-/nanostructures into 3Dones results not only in boosting structural integration level with compact geometry but also enhancing a device's complexity and functionality. Herein, a synergetic 3D micro-/nanoshape transformation is proposed by combining kirigami and rolling-up techniques, or rolling-up kirigami, for the first time. As an example, micro-pinwheels with multiple flabella are patterned on pre-stressed bilayer membranes and rolled up into 3D structures. The flabella are designed when they are patterned on a 2Dthin film, facilitating the integration of micro-/nanoelement and other functionalization processes during 2D patterning, which is typically much easier than post-shaping an as-fabricated 3D structure by removing redundant materials or 3D printing. The dynamic rolling-up process is simulated using elastic mechanics with a movable releasing boundary. Mutual competition and cooperation among flabella are observed during the whole release process. More importantly, the mutual conversion between translation and rotation offers a reliable platform for developing parallel microrobots and adaptive 3D micro-antennas. Additionally, 3D chiral micro-pinwheel arrays integrated into a microfluidic chip are successfully applied to detect organic molecules in solution using a terahertz apparatus. With an extra actuation, active micro-pinwheels can potentially serve as a base to functionalize 3D kirigami as tunable devices.

Residual Dipolar Coupling Based Conformational Analysis Allows the Configurational Assessment of Steroids with up to Eight Stereocenters.

Residual dipolar couplings (RDCs) induced by anisotropic media have been proved as a powerful tool for the structure elucidation of organic molecules in solution in nuclear magnetic resonance (NMR) based analysis. The value of dipolar couplings to solve complex conformational and configurational problems represents indeed an appealing analytical tool for the pharmaceutical industry particularly focusing on the stereochemistry characterization of NCEs since the early phase of the drug development process. In our work, RDCs were used for the conformational and configurational study of synthetic steroids with multiple stereocenters - prednisone and beclomethasone dipropionate (BDP) -. For both molecules the correct relative configuration was identified among all the possible diastereoisomers (32 and 128 respectively) arising from the compounds stereogenic carbons. Only for prednisone the use of additional experimental data (i. e. rOes) was necessary to resolve the right stereochemical structure.

Identifying Conformational Isomers of Organic Molecules in Solution via Unsupervised Clustering.

We present a systematic approach for the identification of statistically relevant conformational macrostates of organic molecules from molecular dynamics trajectories. The approach applies to molecules characterized by an arbitrary number of torsional degrees of freedom and enables the transferability of the macrostates definition across different environments. We formulate a dissimilarity measure between molecular configurations that incorporates information on the characteristic energetic cost associated with transitions along all relevant torsional degrees of freedom. Such metric is employed to perform unsupervised clustering of molecular configurations based on the Fast Search and Find of Density Peaks algorithm. We apply this method to investigate the equilibrium conformational ensemble of Sildenafil, a conformationally complex pharmaceutical compound, in different environments including the crystal bulk, the gas phase, and three different solvents (acetonitrile, 1-butanol, and toluene). We demonstrate that while Sildenafil can adopt more than 100 metastable conformational configurations, only 12 are significantly populated across all of the environments investigated. Despite the complexity of the conformational space, we find that the most abundant conformers in solution are the closest to the conformers found in the most common Sildenafil crystal phase.

Continuum Crystallization Model Derived from Pharmaceutical Crystallization Mechanisms.

The crystallization mechanisms of organic molecules in solution are not well-understood. The mechanistic scenarios where crystalline order evolves directly from the molecularly dissolved state (“classical”) and from initially formed amorphous intermediates (“nonclassical”) are suggested and debated. Here, we studied crystallization mechanisms of two widely used analgesics, ibuprofen (IbuH) and etoricoxib (ETO), using direct cryogenic transmission electron microscopy (cryo-TEM) imaging. In the IbuH case, parallel crystallization pathways involved diverse phases of high and low density, in which the instantaneous formation of final crystalline order was observed. ETO crystallization started from well-defined round-shaped amorphous intermediates that gradually evolved into crystals. This mechanistic diversity is rationalized by introducing a continuum crystallization paradigm: order evolution depends on ordering in the initially formed intermediates and efficiency of molecular rearrangements within them, and there is a continuum of states related to the initial order and rearrangement rates. This model provides a unified view of crystallization mechanisms, encompassing classical and nonclassical pictures.

The contribution of aqueous catechol-silica complexes to silicification during carbonate diagenesis

Pore-filling and carbonate-replacing silica is exceedingly common in carbonates, but the fundamental geochemical mechanisms that drive these silicification reactions during diagenesis remain poorly understood. An existing model has proposed that carbonate silicification proceeds through an interface-coupled dissolution-precipitation reaction, but it lacks a mechanism that enables pore fluids to reach the requisite level of supersaturation with respect to silica to allow nucleation and growth. Here, we present a sequence of batch experiments ranging in duration from 7 to 49 days designed to test the hypothesis that these reactions are facilitated by the formation and destruction of organo-silica complexes during diagenesis. Our results illustrate that the stability of organo-silica complexes is dependent upon the concentration of organic molecules in solution, as well as pH, salinity, and solution redox state. Together, these results allow us to present the following scheme for organo-silica complex mediation of silicification reactions: Firstly, the breakdown of organic matter in the presence of siliceous material creates organo-silica complexes, leading to silica-enriched pore fluids, a process which is enhanced by the anoxic conditions accompanying sediment burial. Then, as environmental conditions evolve (fO2, salinity, light, fCO2, pH…), the stability of the organo-silica complexes diminishes, and the organo-silica complexes break down. Simultaneously, the pore fluids become intensely silica-supersaturated, in direct proportion to the amount of organic material remaining in solution. The resulting supersaturation drives carbonate silicification via the precipitation of silica minerals, a process which is aided by the presence of silica “nuclei” (such as sponge spicules). This study contributes new data and a conceptual model that will aid in the ongoing quest to understand carbonate silicification reactions and their potential applications in hydrocarbon exploitation and geologic CO2 storage. Moreover, it helps to explain the common association between silica precipitates and organic mineral in the sedimentary rock record.

Crystallization of Small Organic Molecules in a Polymer Matrix: Multistep Mechanism Enables Structural Control.

The widely employed crystallization of organic molecules in solution is not well understood and is difficult to control. Employing polymers as crystallization media may allow enhanced control via temperature-induced regulation of polymer dynamics. Crystallization of a small organic molecule (perylene diimide) is investigated in polymer matrices (polystyrene) that enable the mechanistic study and control over order evolution. The crystallization is induced by heating above the glass transition temperature of the polymer, and quenched by cooling, leading to stabilization of crystallization intermediates. The mechanistic studies include direct imaging by electron microscopy, revealing a complex self-assembly process starting from amorphous aggregates that densify and transform into an unstable crystalline phase of N ,N'-bis(2,6-dimethylphenyl)perylene-3,4,9,10-tetracarboxylic diimide (DMP-PDI), followed by a conversion into a more stable crystalline form. Stabilization of crystallization intermediates at room temperature provides diverse structures based on a single molecular component. These findings have implications for the rational design of organic crystalline materials.

Generation of Tautomers Using Micro-p Ka's.

Solutions of organic molecules containing one or more heterocycles with conjugated bonds may exist as a mixture of tautomers, but typically only a few of them are significantly populated even though the potential number grows combinatorially with the number of protonation and deprotonation sites. Generating the most stable tautomers from a given input structure is an important and challenging task, and numerous algorithms to tackle it have been proposed in the literature. This work describes a novel approach for tautomer prediction that involves the combined use of molecular mechanics, semiempirical quantum chemistry, and density functional theory. The key idea in our method is to identify the protonation and deprotonation sites using estimated micro-p Ka's for every atom in the molecule as well as in its nearest protonated and deprotonated forms. To generate tautomers in a systematic way with minimal bias, we then consider the full set of tautomers that arise from the combinatorial distribution of all such mobile protons among all protonatable sites, with efficient postprocessing to screen away high-energy species. To estimate the micro-p Ka's, we present a new method designed for the current task, but we emphasize that any alternative method can be used in conjunction with our basic algorithm. Our approach is therefore grounded in the computational prediction of physical properties in aqueous solution, in contrast to other approaches that may rely on the use of hard-coded rules of proton distribution, previously observed tautomerization patterns from a known chemical space, or human input. We present examples of the application of our algorithm to organic and drug-like molecules, with a focus on novel structures where traditional methods are expected to perform worse.

Absolute Nonlinear Refractive Index Spectra Determination of Organic Molecules in Solutions.

It has been a great challenge to measure the spectrum of pure bound-electronic third-order nonlinear refraction ( n2) of organic chromophores in solutions because of the spurious contribution from the solvent and cuvette walls. In order to circumvent this problem, we present here a new method to obtain a highly accurate absolute n2 value of organic molecules in solutions with a self-referenced nonlinear ellipse rotation (NER) technique. As a proof of concept, we measured n2 spectra of two well-known chromophores, rhodamines B and 6G dissolved in methanol, in the range from ∼600 to 1200 nm. Our results pointed out that these two dyes present similar dispersion curves with strong negative nonlinearities near the one-photon absorption band and small positive values at long wavelengths. Furthermore, the negative signal of the dyes can be strong enough to cancel and even invert the positive nonlinear refraction of the solvent (methanol) as the solution's concentration increases. To understand the n2 spectrum and its connection to molecular properties of organic chromophores, we employed the sum-over-states (SOS) approach within the few-energy-level model and observed an excellent agreement between the experimental and theoretical spectra. In this way, we believe that, employing our NER technique and the SOS model, it is possible to determine both experimentally and theoretically the absolute magnitude and spectra of pure electronic n2 for a large variety of other organic molecules.

Time-resolved photoelectron spectroscopy of organic molecules in aqueous solutions

We use time-resolved photoelectron spectroscopy with wavelength-selected XUV femtosecond pulses to study photoinduced dynamics of organic molecules in solutions at millimolar concentrations. Upon electronic excitation we observe relaxation processes, such as excited state intramolecular proton transfer and trans-cis isomerization.

Rationalising crystal nucleation of organic molecules in solution using artificial neural networks

Artificial neural network modelling is used to analyse and predict primary nucleation based on various physicochemical solute and solvent parameters.

Generation of twisted nanowires with achiral organic amphiphilic copper complexes.

Drying under solvent atmosphere (DUSA) was investigated as an experimental technique to generate self-assembled nanowires and needles from solutions of organic molecules under controlled conditions. Experimental observations of twisted nanowires are reported. These twisted nanowires were obtained by drying of solutions of achiral molecules under solvent controlled atmospheres: achiral, amphiphilic copper complexes were dissolved in an achiral solvent and these solutions were dried under controlled conditions. Two structurally related copper complexes were investigated. Microscopic investigations of the resulting nanowires revealed, and scanning electron microscopy confirmed: self-assembled twisted ribbons could be selectively obtained from one of these compounds. This behavior could be explained by comparing the ratio of the size of the head group and the overall length of the molecules. The occurrence of chiral filaments and chiral phases of nanosegregated filaments are rare in achiral compounds. The occurance of such twisted filaments is thought to be related to symmetry-breaking during a phase transition from liquid crystalline or lyotropic liquid crystalline phases to a nanosegregated phase. In the reported experiments, the concentration of a solution was gradually increased until crystallization occurred. The results clearly show how DUSA can be applied to investigate the capability of achiral substances to yield twisted filaments. Moreover, the investigated compounds had high-enough charge carrier mobilities, such that the twisted filaments obtained are candidates for self-assembled, intrinsically coiled nano-inductivities.

A Combined Experimental and Theoretical Study on the Activity and Selectivity of the Electrocatalytic Hydrogenation of Aldehydes

A detailed mechanistic study of the electrochemical hydrogenation of aldehydes is presented toward the goal of identifying how organic molecules in solution behave at the interface with charged surfaces and what is the best manner to convert them. Specifically, this study focuses on designing an electrocatalytic route for ambient-temperature postpyrolysis treatment of bio-oil. Aldehyde reductions are needed to convert biomass into fuels or chemicals. A combined experimental and computational approach is taken toward catalyst design to provide testable hypotheses regarding catalyst composition, activity, and selectivity. Electrochemical hydrogenation mechanisms for benzaldehyde and pentanal reduction are found to proceed by a coupled proton–electron transfer process. Initial results show that Au, Ag, Cu, and C catalysts exhibit the highest conversion to alcohol products. These catalysts are suitable because they show high cathodic onset potentials for H2 formation and low cathodic onset potentials for orga...

The influence of flexibility on the spectroscopic properties for organic molecules in solution: A theoretical study applied to A3R polypeptide

Here we reported the impact of flexibility of solvent effects on the optical absorption, nuclear magnetic resonance (NMR) and electrical properties of A3R, a tetrapeptide compound derived from peptide bonds in the α-helix form of 3-alanines and one arginine, in aqueous environment. The in-water A3R configurations were generated by S-MM/QM and MD procedures and also using the PCM model. We have used the ASEC approach with 100 uncorrelated settings obtained from Monte Carlo simulation to achieve the convergence of the dipole moment for each in-water geometry in all steps between MC and QM calculations. The converged values of μ for A3R-MD geometries present increments between 69 and 392% in comparison with the gas phase value. Our results for optical absorption demonstrate the possibility of absorption in large range, with strong dependence of the geometric conformation of the A3R molecule. Our findings corroborate both the importance of the solute polarization and the geometric flexibility in the analyzed properties. Spectroscopic results obtained experimentally for the σ(13C) indicates that our A3R-MD geometry calculations are consistent with the adopted model.

A Capture-SELEX Strategy for Multiplexed Selection of RNA Aptamers Against Small Molecules.

In vitro selection of aptamers that recognize small organic molecules has proven difficult, in part due to the challenge of immobilizing small molecules on solid supports for SELEX (Systematic Evolution of Ligands by Exponential Enrichment). This study describes the implementation of RNA Capture-SELEX, a selection strategy that uses an RNA library to yield ligand-responsive RNA aptamers targeting small organic molecules in solution. To demonstrate the power of this method we selected several aptamers with specificity towards either the natural sweetener rebaudioside A or the food-coloring agent carminic acid. In addition, Bio-layer interferometry is used to screen clonal libraries of aptamer candidates and is used to interrogate aptamer affinity. The RNA-based Capture-SELEX strategy described here simplifies selection of RNA aptamers against small molecules by avoiding ligand immobilization, while also allowing selection against multiple candidate targets in a single experiment. This makes RNA Capture-SELEX particularly attractive for accelerated development of RNA aptamers targeting small metabolites for incorporation into synthetic riboswitches and for analytical biosensors.

Solute clustering in undersaturated solutions - systematic dependence on time, temperature and concentration.

Molecular clustering and solvent-solute interactions in isopropanol solutions of fenoxycarb have been thoroughly and systematically investigated by dynamic light scattering, small-angle X-ray scattering, and nanoparticle tracking, supported by infrared spectroscopy and molecular dynamics simulations. The existence of molecular aggregates, clusters, ranging in size up to almost a micrometre is clearly recorded at undersaturated as well as supersaturated conditions by all three analysis techniques. The results systematically reveal that the cluster size increases with solute concentration and time at stagnant conditions. For most concentrations the time scale of cluster growth is of the order of days. In undersaturated solutions the size appears to eventually reach a maximum value, higher the higher the concentration. Below a certain concentration threshold clusters are significantly smaller. Clusters are found to be smaller in solutions pre-heated at a higher temperature, which offers a possible explanation for the so-called "history of solution" effect. The cluster distribution is influenced by filtration through membranes with a pore size of 0.1 μm, offering an alternative explanation for the "foreign particle-catalysed nucleation" effect. At moderate concentrations larger clusters appear to be sheared into smaller ones, but the original size distribution is rapidly re-established. At higher concentrations, although still well below solubility, the cluster size as well as solute concentration are strongly affected, suggesting that larger clusters contain at least a core of more organized molecules not able to pass through the filter.