Surrounding Solvent Molecules Research Articles

Experiment-based Abraham model solute descriptors for 2‑[4-(dibutylamino)-2-hydroxybenzoyl]benzoic acid

ABSTRACT Abraham model solute descriptors for 2‑[4-(dibutylamino)-2-hydroxybenzoyl]benzoic acid were determined from the compound’s published solubility data in 10 organic solvents of varying polarity and hydrogen-bonding character. The calculated hydrogen-bond donor descriptor value, A = 0.548, suggests that intramolecular bond formation occurs between the hydrogen atom on the -OH functional group and one of the two lone pairs of electrons on the oxygen atom of the ketone functional group, >C=O, which would result in the formation of a six-membered hydrogen-bonded ring structure. A much larger A-solute descriptor would be expected if the hydrogen atoms of both the -OH and -COOH functional groups were free to engage in intermolecular H-bond formation with surrounding solvent molecules.

Computation of rate coefficients in solutions based on transition state theory combined with a heuristically corrected polarizable continuum model: intermolecular Diels-Alder reactions as case studies.

Transition state theory (TST) based on activation parameters computed using quantum mechanics calculations combined with the polarizable continuum model (QM/PCM) is a fundamental tool for investigating reaction rates in the liquid phase. In conventional QM/PCM methods, thermodynamic data and partition functions for a solute are often derived from a quasi-ideal gas treatment (IGT) widely implemented in commercially available computation packages. This approach tends to overestimate entropy because calculations of thermodynamic parameters in the liquid phase ignore hindered translational and rotational modes in real solutions. The present work formulated partition functions for more realistic solutes hindered by surrounding solvent molecules in conjunction with the basic QM/PCM concept. In addition, a configuration partition function for solute molecules at a standard concentration of 1 mol dm-3 was incorporated using a simple lattice model. The canonical partition function and thermodynamic functions were derived based on statistical thermodynamics for localized systems. Expressions for rate coefficients within TST were also derived with a consistent formalism based on the standard state selected in partition function calculations. The performance of the proposed method was assessed by predicting rate coefficients for three different Diels-Alder reactions and comparing these with experimental results. QM/PCM calculations at the G4//ωB97X-D/6-311++G(d,p)/IEF-PCM level of theory with corrections for the dispersion and repulsion energies were performed to obtain the electronic structures of stationary points on potential energy surfaces as a means of finding activation enthalpy, entropy and Gibbs energy values based on revised partition functions as well as predicting rate coefficients. The activation Gibbs energies obtained from our proposed method were lower than those obtained from the IGT method due to reasonable entropy computations. The proposed method overestimated the rate coefficients by one to two orders of magnitude compared to the experimental values, whereas the IGT method underestimated them by the same amount. This discrepancy arises because the proposed method calculates the partition function from the viewpoint of a localized system, whereas the IGT method calculates it from the viewpoint of a non-localized system. Given that actual liquids exist in a state between non-localized and localized systems, it is essential to formulate the partition function in a way that more accurately represents the liquid state.

Deep-Ultraviolet Photoexcitation of Aqueous Urea Forms Carbamic Acid/Carbamate in Less Than One Picosecond.

Urea is believed to have been essential to the synthesis of prebiotic nucleotides and thereby the RNA or DNA of the first lifeforms. Models suggesting that life began in wet-dry cycles around shallow aquatic ponds imply that reactants such as urea were exposed to deep ultraviolet irradiation from the young sun. Detrimental photodissociation of urea induced by deep UV excitation potentially challenges these models. We here follow the primary deep ultraviolet photochemistry of aqueous urea. The data show that urea is barely excited at 200 nm due to weak ultraviolet absorption. The likelihood of photodissociation is further reduced by strong intra-molecular coupling of the CN and CO stretch vibrations accompanied by an efficient dissipation of the excitation energy to the surrounding water molecules mitigated by urea-water hydrogen bonds. We find that 54±5 % of the excited urea molecules dissociate. Reactions between the photoproducts and surrounding solvent molecules form carbamic acid or the carbamate anions within 0.6 ps. The molecules that do not dissociate return to the electronic ground state in 2 ps. Interestingly, the photodissociation processes of urea in the aqueous phase is different from earlier reported reactions observed following the VUV photolysis of urea in noble gas matrices and highlight the potential influence of water on the prebiotic photochemistry.

Close-Up Look at Electronic Spectroscopic Signatures of Common Pharmaceuticals in Solution.

Simulating electronic properties and spectral signals requires robust computational approaches that need tuning with the system's peculiarities. In this paper, we test implicit and fully atomistic solvation models for the calculation of UV-vis and electronic circular dichroism (ECD) spectra of two pharmaceutically relevant molecules, namely, (2S)-captopril and (S)-naproxen, dissolved in aqueous solution. Room temperature molecular dynamics simulations reveal that these two drugs establish strong contacts with the surrounding solvent molecules via hydrogen bonds. Such specific interactions, which play a major role in the spectral response and are neglected in implicit approaches, are further characterized and quantified with natural bond orbital methods. Our calculations show that simulated spectra, and especially ECD, are in good agreement with experiments solely when conformational and configurational dynamics, mutual polarization, and solute-solvent repulsion effects are considered.

Revisiting the strain-induced softening behaviour in hydrogels.

The strain-induced softening behaviour observed in the differential modulus K(T,γ) of hydrogels is typically attributed to the breakage of internal network structures, such as the cross-links that bind the polymer chains. In this study, however, we consider a stress-strain relationship derived from a coarse-grained model to demonstrate that rupture of the network is not necessary for rubber-like gels to exhibit such behaviour. In particular, we show that, in some cases, the decrease of K(T,γ) as a function of the strain γ can be associated with the energy-related contribution to the elastic modulus that has been experimentally observed, e.g., for tetra-PEG hydrogels. Our findings suggest that the softening behaviour can be also attributed to the effective interaction between polymer chains and their surrounding solvent molecules, rather than the breakage of structural elements. We compare our theoretical expressions with experimental data determined for several hydrogels to illustrate and validate our approach.

Solvent stabilization of alkene epoxidation transition states within Ti-MFI: Interactions near and far from active sites

Kinetics of alkene epoxidation in Ti incorporated MFI (Ti-MFI) zeolites that contact liquid methanol (CH3OH) depend strongly on the bulk concentration of water ([H2O]) and the density of silanol groups ((SiOH)x) within the framework, because these species influence excess free energy contributions (Gε) that stabilize transition states for epoxidation and hydrogen peroxide derived reactive intermediates. These effects rely on hydrogen bonds among intrapore molecules that couple catalytic events to the structure of the surrounding solvent molecules. Turnover rates for 1-hexene (C6H12) epoxidation with hydrogen peroxide over Ti-MFI zeolites increase by ten-fold both when either [H2O] or (SiOH)x densities increase. Activation enthalpies and entropies of hydrophilic and hydrophobic Ti-MFI materials are similar at the lowest [H2O] (0.005 M H2O), implying solvation environments near active sites do not depend on defect density in the near-absence of H2O. However, kinetic barriers for these same Ti-MFI materials increase and diverge from one another as non-monotonic functions of [H2O] (0.005–5 M H2O), and these differences reflect stabilizing contributions from discrete solvation shells both adjacent (near) and further (or far) from active sites. The structure of these solvation shells must reorganize to accommodate H2O2 activation and formation of epoxidation transition states. Adsorption enthalpies for the epoxide product become more exothermic with larger values of [H2O] over each Ti-MFI catalyst, and the apparent activation enthalpies generally increase as epoxide adsorption enthalpies become more exothermic. Comparisons to trends previously obtained for Ti-BEA catalysts suggest the negative correlation indicates that excess contributions (Hε, Gε) impact reactive species (Ti-OOH) within the 10-membered ring pores of MFI to a greater extent than 12-membered ring pores due to distinctions among hydrogen bonding interactions among bound reactive species, spectating solvent molecules, and extended surfaces of MFI pores.

Abraham Model Solute Descriptors for Favipiravir: Case of Tautomeric Equilibrium and Intramolecular Hydrogen-Bond Formation

Experiment-based Abraham model solute descriptors are calculated based on recently published solubility data for favipiravir dissolved in 12 chemically diverse organic mono-solvents. The calculated descriptor values indicate that favipiravir engages in intramolecular hydrogen formation that renders the hydroxyl functional group on the pyrazine ring system unable to form intermolecular hydrogen bonds with the surrounding solvent molecules. Our study further shows that the existing group contribution and machine learning methods provide rather poor estimates of the experiment-based solute descriptors of favipiravir. Poor estimation likely occurs, in part, because the methods fail to account for the intramolecular hydrogen-bonds that are believed to be formed. In the current study, it was found that the solute descriptors estimated using three different methods provided rather poor estimates of the observed solubility behavior of favipiravir, with the overall average standard errors between the experimental and predicted molar solubilities exceeding 0.40 log units.

Does a Blatter Radical Retain Its Open-Shell Character When Incorporated into Gold–Molecule–Gold Junctions?

One of the key issues for the use of organic radicals in high-performance molecular electronic, spintronic and thermoelectric devices is the retention, at room temperature, of their open-shell character when they are in contact with the metal electrodes of a junction. By means of first-principles quantum transport calculations, we have investigated the stability and the electronic transport properties of single-molecule junctions incorporating a Blatter radical (BR) with thiomethyl linker groups. Our calculations suggest that the BR can unequivocally retain its open-shell nature even when bound to gold electrodes through undercoordinated gold adatoms. Such a state cannot be destroyed by the surrounding solvent molecules and the applied bias. The calculated low-bias conductance values of junctions with BR, an oxidized BR derivative, and a closed-shell stilbene molecule are in quantitative agreement with the available experimental measurements. The small conductance of the BR can be associated with the localization of its π-type singly occupied and singly unoccupied molecular orbitals (SOMO and SUMO), leading to an asymmetrically weak electronic coupling to the two gold electrodes, even though these two orbitals lie very close to the Fermi energy. Furthermore, the nonmonotonic modulation of the junction conductance controlled by a charge gate can be used in experiments to further verify the presence of the unpaired electron. This proof may be realized in practice with an electrostatic solid-state or an electrochemical gate. Our findings deepen the current understanding of the radical–metal interfacial properties and facilitate the design of future radical-based multifunctional molecular devices.

Stepwise generation of spin-polarized radicals and their reactions in the photolysis of an oxime ester compound as studied by pulsed EPR spectroscopy

To generate spin-polarized free radicals, the photolysis of 1,2-octane-dione, 1-[4-(phenylthio)-2-(o-benzoyloxime)] (OXE01) was investigated using time-resolved electron paramagnetic resonance (TR-EPR) and pulsed EPR. This photolysis proceeds through α-cleavage of the N-O bond of OXE01 to yield iminyl and benzoyloxy radicals, the latter of which is converted to a phenyl radical by decarboxylation. The phenyl radical promptly abstracts hydrogen atoms from the surrounding solvent molecules to produce a solvent dehydrogenated radical (solvent radical). The spin polarization created in the initial OXE01 triplet excited state was preserved during these series of reactions, which enhanced EPR sensitivity. This enabled us to observe the TR-EPR spectra of the intermediate free radicals, except phenyl. The decarboxylation rate of the benzoyloxy radical was measured in various solvents by probing the free induction decay signal of the product solvent radicals using pulsed EPR. This new method for preparing free radicals with spin-polarization was applied to determine the addition reaction rate constants of the cyclohexyl radical, a solvent radical, to olefins using pulsed EPR monitoring of the electron spin echo signals of the radical.

Spatial Decay and Limits of Quantum Solute-Solvent Interactions.

Molecular excitations in the liquid-phase environment are renormalized by the surrounding solvent molecules. Herein, we employ the GW approximation to investigate the solvation effects on the ionization energy of phenol in various solvent environments. The electronic effects differ by up to 0.4 eV among the five investigated solvents. This difference depends on both the macroscopic solvent polarizability and the spatial decay of the solvation effects. The latter is probed by separating the electronic subspace and the GW correlation self-energy into fragments. The fragment correlation energy decays with increasing intermolecular distance and vanishes at ∼9 Å, and this pattern is independent of the type of solvent environment. The 9 Å cutoff defines an effective interacting volume within which the ionization energy shift per solvent molecule is proportional to the macroscopic solvent polarizability. Finally, we propose a simple model for computing the ionization energies of molecules in an arbitrary solvent environment.

Molecular Origin of Internal Friction in Intrinsically Disordered Proteins.

Protein folding and dynamics are controlled by an interplay of thermal and viscosity effects. The effect of viscous drag through the solvent molecules is described by the classic Kramers theory in the high friction limit, which considers the dampening of the reactant molecules in the solution and quantifies the dependence of the reaction rate on the frictional drag. In addition to the external energy dissipation originating from the surrounding solvent molecules, there is an additional mode of internal energy dissipative force operative within the polypeptide chain reflecting the internal resistance of the chain to its conformational alterations. This dry, solvent-independent intrinsic frictional drag is termed internal friction. In the case of natively folded proteins, the physical origin of internal friction is primarily attributed to the intrachain interactions or other nonnative interactions in their compact states. However, the molecular origin of internal friction in intrinsically disordered proteins (IDPs) remains elusive.In this Account, we address this fundamental issue: what are the principal drivers of viscosity-independent (dry) friction in highly solvated, expanded, conformationally flexible, rapidly fluctuating IDPs that do not possess persistent intrachain interactions? IDPs exhibit diffusive conformational dynamics that is predominantly dominated by the segmental motion of the backbone arising due to the dihedral rotations in the Ramachandran Φ-Ψ space. The physical origin of friction in a complex biopolymeric system such as IDPs can be described by classic polymer models, namely, Rouse/Zimm models with internal friction. These one-dimensional models do not invoke torsional fluctuation components. Kuhn's classic description includes the connection between internal friction and microscopic dihedral hopping. Based on our time-resolved fluorescence anisotropy results, we describe that the sequence-dependent, collective, short-range backbone dihedral rotations govern localized internal friction in an archetypal IDP, namely, α-synuclein. The highly sensitive, residue-specific fluorescence depolarization kinetics offers a potent methodology to characterize and quantify the directional decorrelation engendered due to the short-range dihedral relaxation of the polypeptide backbone in the dihedral space. We utilized this characteristic relaxation time scale as our dynamic readout to quantify the site-specific frictional component. Our linear viscosity-dependent model of torsional relaxation time scale furnished a finite nonzero time constant at the zero solvent viscosity representing the solvent-independent internal friction. These results unveil the effect of the degree of dihedral restraining parameter on the internal friction component by showing that a restrained proline residue imparts higher torsional stiffness in the chain segments and, therefore, exhibits higher internal friction. This Account sheds light on the molecular underpinning of the sequence-specific internal friction in IDPs and will be of interest to unmask the role of internal friction in a diverse range of biomolecular processes involving binding-induced folding, allosteric interaction, protein misfolding and aggregation, and biomolecular condensation via phase separation.

Impact of Solvent-Solute Hydrogen Bonding on Ultrafast Electron Transfer in a Trimetallic Iron-Ruthenium Complex

Transition metal complexes (TMCs) are widely used as light absorbers and catalysts for photochemical energy conversion processes such as photocatalytic reactions in liquid environments. Of particular interest are TMCs which incorporate multiple bridged metal centres because they represent a step towards more complex supramolecular assemblies that can ultimately enable control of the charge flow in solution-based photo-redox processes. However, the development of design guidelines for such molecular assemblies is impeded by an incomplete understanding of the coupling between their electronic and nuclear dynamics, including the interplay of TMCs with their liquid environment upon photoexcitation. Probing the involved processes requires high spatial sensitivity towards electronic motion and the ability to capture atomic motion on ultrafast timescales – a combination which is not readily available for optical transient spectroscopic techniques.X-ray free electron lasers (XFELs) have revolutionized the field of ultrafast science in recent years. XFELs generate tuneable and extremely bright X-ray pulses with a typical pulse duration of <30 fs, which are well-suited as an element-specific probe of ultrafast electronic and atomic motion in molecules and materials.1,2 Applied to TMCs, XFEL probes are sensitive to the local electronic structure in such molecular systems as well as to intra- and inter-molecular structural reorganization at an atomic level.3 In this talk, I will present work on the interaction of a linear trimetallic cyanide-bridged iron-ruthenium complex (FeRuFe) with its solvent environment, carried out using the LCLS XFEL facility at SLAC National Accelerator Laboratory. The focus of this study lies on elucidating how photoinduced intramolecular electron transfer processes in FeRuFe are affected by hydrogen bonding interactions between its cyanide ligands and the surrounding solvent molecules. In water, such solvent-solute hydrogen bonding interactions are stronger for Fe(II) than Fe(III), leading to substantial changes in solute-solvent interactions upon photoinduced electron transfer between metal centres.The experiment is performed in a pump-probe geometry on a liquid jet, where a visible/near-infrared pump induces a metal-to-metal charge transfer (MMCT) between Ru and Fe which is followed by an ultrafast back-electron transfer (BET). The excited state dynamics are monitored using hard X-ray pulses as a function of time delay between the laser pump and the X-ray probe pulses. To resolve and correlate electronic and structural dynamics upon MMCT excitation, we simultaneously perform ultrafast Fe Kβ X-ray emission spectroscopy (XES) and X-ray solution scattering (XSS) measurements, where XES is sensitive to the oxidation and spin state of the Fe centres and XSS provides information on atomic motion in solute and solvent, as demonstrated in previous work on a similar system.4 To evaluate the effect of solute-solvent hydrogen bonding interactions on the electron transfer dynamics, we perform measurements in a series of solvents with different hydrogen bonding properties, including water, methanol, and acetonitrile. We find that the BET increases as a function of decreasing hydrogen bonding ability of the solvent, and that distinct signatures of solvation dynamics are present in the scattering data. The resulting molecular level understanding of solvent reorganization coupled to electron transfer demonstrates that the strength and type of solute-solvent interactions are a central factor in determining the outcome of photoinduced charge transfer processes in TMCs.References Bergmann, U. et al. Using X-ray free-electron lasers for spectroscopy of molecular catalysts and metalloenzymes. Nat. Rev. Phys. 3, 264–282 (2021).Schoenlein, R. et al. Recent advances in ultrafast X-ray sources. Philos. Trans. R. Soc. Math. Phys. Eng. Sci. 377, 20180384 (2019).Gaffney, K. J. Capturing photochemical and photophysical transformations in iron complexes with ultrafast X-ray spectroscopy and scattering. Chem. Sci. 12, 8010–8025 (2021).Biasin, E. et al. Direct observation of coherent femtosecond solvent reorganization coupled to intramolecular electron transfer. Nat. Chem. 13, 343–349 (2021).

Interactions of CO2 Anion Radicals with Electrolyte Environments from First-Principles Simulations.

Successful transformation of carbon dioxide (CO2) into value-added products is of great interest, as it contributes in part to the circular carbon economy. Understanding chemical interactions that stabilize crucial reaction intermediates of CO2 is important, and in this contribution, we employ atom centered density matrix propagation (ADMP) molecular dynamics simulations to investigate interactions between CO2– anion radicals with surrounding solvent molecules and electrolyte cations in both aqueous and nonaqueous environments. We show how different cations and solvents affect the stability of the CO2– anion radical by examining its angle and distance to a coordinating cation in molecular dynamics simulations. We identify that the strength of CO2– interactions can be tailored through choosing an appropriate cation and solvent combination. We anticipate that this fundamental understanding of cation/solvent interactions can facilitate the optimization of a chemical pathway that results from selective stabilization of a crucial reaction intermediate.

Optimization of LIB Electrolyte and Exploration of Novel Compounds via the Molecular Dynamics Method

Due to great interest in the development of electric vehicles and other applications, improving the performances of lithium-ion batteries (LIBs) is crucial. Specifically, components of electrolytes for LIBs should be adequately chosen from hundreds of thousands of candidate compounds. In this study, we aimed to evaluate some physical properties expected for combinations of molecules for electrolytes by microscopic simulations. That is, the viscosity, ionic conductivity, degree of dissociation, diffusion coefficient, and conformation of each molecule were analyzed via molecular dynamics (MD) simulations. We aimed to understand how molecular-sized structures and properties collaboratively affect the behavior of electrolytes. The practical models of molecules we used were ethylene carbonate (EC), fluoroethylene carbonate (FEC), propylene carbonate (PC), butylene carbonate (BC), γ-butyrolactone (GBL), γ-valerolactone (GVL), dimethyl carbonate (DMC), ethyl-methyl carbonate (EMC), diethyl carbonate (DEC), and lithium hexafluorophosphate (LiPF6). Many molecular systems of electrolytes were simulated, in which one molar LiPF6 was mixed into a single or combined solvent. It was found that small solvent molecules diffused with relative ease, and they contributed to the higher ionic conductivity of electrolytes. It was clarified that the diffusion coefficient of lithium (Li) ions is greatly affected by the surrounding solvent molecules. We can conclude that high-permittivity solvents can be selectively coordinated around Li ions, and Li salts are sufficiently dissociated, even when there is only a small content of high-permittivity solvent. Thus, we can confirm solely by MD simulation that one of the better candidates for solvent molecules, formamide (F), will exhibit higher performance than the current solvents.

Novel electro self-assembled DNA nanospheres as a drug delivery system for atenolol

We describe new method for preparing DNA nanospheres for a self-assembled atenolol@DNA (core/shell) drug delivery system. In this paper, we propose the electrochemical transformation of an alkaline polyelectrolyte solution of DNA into DNA nanospheres. We successfully electrosynthesized DNA nanospheres that were stable for at least 2 months at 4 °C. UV–visible spectra of the prepared nanospheres revealed a peak ranging from 372 to 392 nm depending on the DNA concentration and from 361 to 398.3 nm depending on the electrospherization time. This result, confirmed with size distribution curves worked out from transmission electron microscopy (TEM) images, showed that increasing electrospherization time (6, 12 and 24 h) induces an increase in the average size of DNA nanospheres (48, 65.5 and 117 nm, respectively). In addition, the average size of DNA nanospheres becomes larger (37.8, 48 and 76.5 nm) with increasing DNA concentration (0.05, 0.1 and 0.2 wt%, respectively). Also, the affinity of DNA chains for the surrounding solvent molecules changed from favorable to bad with concomitant extreme reduction in the zeta potential from −31 mV to −17 mV. Principally, the attractive and hydrophobic interactions tend to compact the DNA chain into a globule, as confirmed by Fourier transform infrared spectroscopy (FTIR) and TEM. To advance possible applications, we successfully electro self-assembled an atenolol@DNA drug delivery system. Our findings showed that electrospherization as a cost–benefit technique could be effectively employed for sustained drug release. This delivery system achieved a high entrapment efficiency of 68.03 ± 2.7% and a moderate drug-loading efficiency of 3.73%. The FTIR spectra verified the absence of any chemical interaction between the drug and the DNA during the electrospherization process. X-ray diffraction analysis indicated noteworthy lessening in atenolol crystallinity. The present findings could aid the effectiveness of electrospherized DNA for use in various other pharmaceutical and biomedical applications.

Origin of the material dependence of temperature coefficient of redox potential in conjugated polymers

The thermal coefficient α (=d V/d T) of the redox potential (V) is an important physical parameter for thermal energy harvesting. To clarify the microscopic origin of α in conjugated polymers, we compared α and the physical quantity obtained by a quantum chemistry calculation in typical polymers with small monomer molecular weight. We observed a strong correlation between α and the number (N active) of the active atom, which is defined as the atom whose variation of the Mulliken charge (Δq) at the oxidation process is beyond a threshold (Δq th). We interpreted the material dependence of α in terms of N active, because active atoms have a significant effect on the configuration entropy of the surrounding solvent molecules.

Abiraterone and D4, 3-keto Abiraterone binding to CYP17A1, a structural comparison study by molecular dynamic simulation

The importance of computer-aided drug design and development is clear nowadays. These approaches smooth the way of designing some efficient candidates based on drugs in use. At this place, we studied the mechanism of D4-abiraterone (D4A), the active metabolite of Abiraterone (Abi), binding to CYP17A1 compared with Abi. The molecular dynamics simulation results reveal that the metabolite, which lacks the key 3β-OH group, has a varied H-bond forming pattern. The critical H-bond between 3β-OH of Abi with Asn_202 turns to 3 Keto-O of D4A with Arg_239 in the substrate-binding site. This interaction causes a remarkable distance of 0.63 nm between D4A nitrogen and Fe in heme, which reduces its 17,20 lyase selectivity. The D4A keto moiety presents an immense number of H-bond with surrounding solvent molecules compared with the Abi hydroxyl group. As a result, D4A develops a weaker H-bond network with the enzyme. Otherwise, the heterocyclic nature of inhibitors helps for noticeable van der Waals interaction formation with CYP17A1. However, Abi stabilized position in the binding site helps more van der Waals interactions deposition than D4A. These results convinced the importance of the conserved H-bond for acquiring the proper position by the substrate or inhibitor in the binding site.

Unveiling the novel characteristics of IGPD polymer and inhibitors binding affinities using 12-6-4 LJ-type nonbonded Mn2+ model

The metalloenzyme imidazole glycerophosphate dehydratase (IGPD) (EC 4.2.1.19) is essential in the histidine biosynthesis pathway in prokaryotes and eukaryotes, hence it has been identified as an attractive target with a majority of inhibitor studies focused on the development of broad-spectrum herbicides and bacteriostatic agent. However, due to the lack of work in structural biology, the reported inhibitors developed slowly with poor selectivity and diversity. To reveal the inhibitors binding affinities in ions centers of IGPD, we built point charge models based on a 12-6-4 type Lennard-Jones (LJ) potential, while combined DFT analyses, molecular docking and molecular dynamics (MD) simulations. This work introduced the interaction with surrounding solvent molecules and revealed a few undiscovered structural and kinetic characterizations of IGPD Mn2+ ions centers and ligand binding path, which revised some previous inexact assumptions inferred from crystal structures information. In addition, we also compared the dynamic binding characteristics of five IGPD inhibitors, and found that hydrogen bond interaction, spatial position and coordination stability with two Mn2+ ions can lead to the difference in potency. Overall, this work firstly unraveled the dynamic characteristics of IGPD polymer systems in explicit solvent and also provided a reference for the theoretical work of Mn2+-containing metalloenzyme, contributing for further target development.

Fluorimetric detection of distinct lyotropic anion interactions on nanoscopic surfaces

The molecular structure, stability and function of proteins, nucleic acids, and many other colloidal entities including nanomaterials depend greatly on their highly specific response towards surrounding solvent molecules and inorganic ions. In order to earn an unambiguous mechanistic insight into the origin of these effects, water-soluble fluorescent carbon nanomaterials having amide groups in a hydrophobic microenvironment were successfully employed as the model colloidal system in this research study. Quantum dots with acidic functionalities were first of all prepared using a simple carbon precursor. Subsequently, chemical modification of carbon quantum dots (CQDs) was carried out with isopropylamine to impart protein-like amide richness to the nanoparticle surface. Moreover, the prepared CQDs were found to be highly fluorescent. Fluorescence intensity, interestingly, showed unique modulation patterns on incubation with different types of anions. Lipophilic chaotropic anions such as I−, SCN−, and Br− showed concentration-dependent fluorescence quenching whereas hydrophilic kosmotropic anions like SO42− had almost no impact on the nanomaterial fluorescence. This striking observation in the case of chaotropic anions can be correlated to their strong partitioning affinity for the amide groups on the nanomaterial surface. High charge density anions like sulphate, on the other hand, are mostly excluded from the colloidal interfaces. The current study emphasizes the fact that the functional groups available on the surface of macromolecules as well as anion's inherent thermodynamic parameters in a solvent play a pivotal role in the observed anion specificity.

Highly efficient triplet-triplet annihilation upconversion in high viscosity phthalate ester media

Movement of molecules are always affected by the surrounding solvent molecules, so solvents have an essential effect in triplet-triplet annihilation (TTA) upconversion. In this article, the TTA upconversion system with Diiodo-BODIPY (MBDP-2I) as sensitizer and perylene as acceptor in six solvents of differing viscosity were investigated (toluene, 1,4-dioxane and four high viscosity phthalate ester solvents DMP, DBP, DNOP and DOP). The upconversion efficiency was positively correlated with the solvent viscosity. Among the six solvents, the highest upconversion quantum efficiency of 9.59% was observed in high viscosity DOP (η = 72.4 mPa s), almost 1.5 times higher than that in 1,4-dioxane (η = 3.2 mPa s, ΦUC = 6.36%). The efficient upconversion was attributed to the long-lived triplet excited states of MBDP-2I, efficient fluorescence quantum yield of perylene and efficient TTA in high viscosity phthalate esters solvents. The mechanism underlying the highly efficient TTA upconversion in the high viscosity phthalate esters solvents was investigated by solvent cage effect. In addition, significant room temperature phosphorescence of MBDP-2I at 765 nm was observed in the viscous phthalate esters solvents.