Toll-Like Receptor-9-Mediated Invasion in Breast Cancer

DTIC Science & Technology

2011-07-01

Molecular Dynamics Simulations. Theoretical structural models were obtained from molecular dynamics simulations using explicit solvation by...with AMBER by MARDIGRAS. The solution structure was then derived by coupling the resulting NMR distance restraints with a molecular dynamic ...Overlay of NMR restrained structure (red) with theoretical molecular dynamic simulated annealing structure (blue). Energetic stability of the 9-mer

The effect of co-solvent addition on Li-solvation in solvate electrolytes in Li-S batteries

NASA Astrophysics Data System (ADS)

Lau, Kah Chun; See, Kimberly A.; Wu, Heng-Liang; Shin, Minjeong; Curtiss, Larry A.; Gewirth, Andrew A.

Li?S batteries are a promising next-generation battery technology. Due to the formation of soluble polysulfides during cell operation, the electrolyte composition of the cell plays an active role in directing the formation and speciation of the soluble lithium polysulfides. Recently, new classes of electrolytes termed `solvates' that contain stoichiometric quantities of salt and solvent and form a liquid at room temperature have been explored due to their sparingly solvating properties with respect to polysulfides. The viscosity of the solvate electrolytes is understandably high limiting their viability, however, cosolvents that thought to be inert to the solvate structure itself, can be introduced to reduce viscosity and enhance diffusion. In this work, Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations are used to study the unique solvation structure of 1,1,2,2-tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether as co-solvent in solvate (MeCN)2?LiTFSI electrolyte that used in Li-S battery. The underlying design rules and implications to Li-S battery performance will be discussed. This work was supported as part of the Joint Center for Energy Storage Research, an Energy Innovation Hub funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences.

On the microscopic fluctuations driving the NMR relaxation of quadrupolar ions in water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carof, Antoine; Salanne, Mathieu; Rotenberg, Benjamin, E-mail: benjamin.rotenberg@upmc.fr

Nuclear Magnetic Resonance (NMR) relaxation is sensitive to the local structure and dynamics around the probed nuclei. The Electric Field Gradient (EFG) is the key microscopic quantity to understand the NMR relaxation of quadrupolar ions, such as {sup 7}Li{sup +}, {sup 23}Na{sup +}, {sup 25}Mg{sup 2+}, {sup 35}Cl{sup −}, {sup 39}K{sup +}, or {sup 133}Cs{sup +}. Using molecular dynamics simulations, we investigate the statistical and dynamical properties of the EFG experienced by alkaline, alkaline Earth, and chloride ions at infinite dilution in water. Specifically, we analyze the effect of the ionic charge and size on the distribution of the EFGmore » tensor and on the multi-step decay of its auto-correlation function. The main contribution to the NMR relaxation time arises from the slowest mode, with a characteristic time on the picosecond time scale. The first solvation shell of the ion plays a dominant role in the fluctuations of the EFG, all the more that the ion radius is small and its charge is large. We propose an analysis based on a simplified charge distribution around the ion, which demonstrates that the auto-correlation of the EFG, hence the NMR relaxation time, reflects primarily the collective translational motion of water molecules in the first solvation shell of the cations. Our findings provide a microscopic route to the quantitative interpretation of NMR relaxation measurements and open the way to the design of improved analytical theories for NMR relaxation for small ionic solutes, which should focus on water density fluctuations around the ion.« less

Solvation and aggregation of n,n'-dialkylimidazolium ionic liquids: a multinuclear NMR spectroscopy and molecular dynamics simulation study.

PubMed

Remsing, Richard C; Liu, Zhiwei; Sergeyev, Ivan; Moyna, Guillermo

2008-06-26

The solvation and aggregation of the ionic liquid (IL) 1-n-butyl-3-methylimidazolium chloride ([C4mim]Cl) in water and dimethylsulfoxide (DMSO) were examined by analysis of (1)H and (35/37)Cl chemical shift perturbations and molecular dynamics (MD) simulations. Evidence of aggregation of the IL n-butyl chains in aqueous environments at IL concentrations of 75-80 wt% was observed both in the NMR experiments and in the MD simulations. The studies also show that [C4mim]Cl behaves as a typical electrolyte in water, with both ions completely solvated at low concentrations. On the other hand, the data reveal that the interactions between the [C4mim](+) and Cl(-) ions strengthen as the DMSO content of the solutions increases, and IL-rich clusters persist in this solvent even at concentrations below 10 wt%. These results provide an experimentally supported atomistic explanation of the effects that these two solvents have on some of the macroscopic properties of [C4mim]Cl. The implications that these findings could have on the design of IL-based solvent systems are briefly discussed.

A deeper insight into an intriguing acetonitrile-water binary mixture: synergistic effect, dynamic Stokes shift, fluorescence correlation spectroscopy, and NMR studies.

PubMed

Koley, Somnath; Ghosh, Subhadip

2016-11-30

An insight study reveals the strong synergistic solvation behaviours from reporter dye molecules within the acetonitrile (ACN)-water (WT) binary mixture. Synergism of a binary mixture refers to some unique changes of the physical and thermodynamic properties of the solvent mixture, originating from the interactions among its cosolvents, which are absent within the pure cosolvents. Synergistic solvation of a binary mixture is likely to be fundamental for greater stabilization of an excited state solute dipole; at least to some extent greater as compared to one stabilized by any of its cosolvents alone. A dynamic Stokes shift due to the solvation of an excited dipole in the ACN-WT binary mixture is found to be highly relevant to the ground state physical properties of the solute molecule (polarity, hydrophilicity, acidity, etc.). Largely different solvation times in the ACN-WT mixture are observed from different dye molecules with widely varying polarities. However, earlier study shows that dye molecules, irrespective of their varying polarities, exhibit very similar solvation times within a pure solvent (J. Phys. Chem. B, 2014, 118, 7577-7785). On further study with fluorescence correlation spectroscopy (FCS) we observed that, unlike the translational diffusion coefficient (D t ) of a dye molecule within a pure solvent, which remains the same irrespective of the location of the dye molecule inside the solvent, a broad distribution among the D t values of a dye molecule is obtained from different locations within the ACN-WT binary mixture. Lastly our 1 H NMR study in the ACN-WT binary mixture shows the existence of strong hydrogen bond interactions among the cosolvents in the ACN-WT mixture.

Glycerol in micellar confinement with tunable rigidity

NASA Astrophysics Data System (ADS)

Lannert, Michael; Müller, Allyn; Gouirand, Emmanuel; Talluto, Vincenzo; Rosenstihl, Markus; Walther, Thomas; Stühn, Bernd; Blochowicz, Thomas; Vogel, Michael

2016-12-01

We investigate the glassy dynamics of glycerol in the confinement of a microemulsion system, which is stable on cooling down to the glass transition of its components. By changing the composition, we vary the viscosity of the matrix, while keeping the confining geometry intact, as is demonstrated by small angle X-ray scattering. By means of 2H NMR, differential scanning calorimetry, and triplet solvation dynamics we, thus, probe the dynamics of glycerol in confinements of varying rigidity. 2H NMR results show that, at higher temperatures, the dynamics of confined glycerol is unchanged compared to bulk behavior, while the reorientation of glycerol molecules becomes significantly faster than in the bulk in the deeply supercooled regime. However, comparison of different 2H NMR findings with data from calorimetry and solvation dynamics reveals that this acceleration is not due to the changed structural relaxation of glycerol, but rather due to the rotational motion of essentially rigid glycerol droplets or of aggregates of such droplets in a more fluid matrix. Thus, independent of the matrix mobility, the glycerol dynamics remains unchanged except for the smallest droplets, where an increase of Tg and, thus, a slowdown of the structural relaxation is observed even in a fluid matrix.

A Comparison of Predictive Thermo and Water Solvation Property Prediction Tools and Experimental Data for Selected Traditional Chemical Warfare Agents and Simulants II: COSMO RS and COSMOTherm

DTIC Science & Technology

2017-04-01

A COMPARISON OF PREDICTIVE THERMO AND WATER SOLVATION PROPERTY PREDICTION TOOLS AND EXPERIMENTAL DATA FOR...4. TITLE AND SUBTITLE A Comparison of Predictive Thermo and Water Solvation Property Prediction Tools and Experimental Data for Selected...1  2.  EXPERIMENTAL PROCEDURE

Effect of Hydrofluoroether Cosolvent Addition on Li Solvation in Acetonitrile-Based Solvate Electrolytes and Its Influence on S Reduction in a Li–S Battery

DOE Office of Scientific and Technical Information (OSTI.GOV)

See, Kimberly A.; Wu, Heng -Liang; Lau, Kah Chun

Li-S batteries are a promising next-generation battery technology. Due to the formation of soluble polysulfides during cell operation, the electrolyte composition of the cell plays an active role in directing the formation and speciation of the soluble lithium polysulfides. Recently, new classes of electrolytes termed "solvates" that contain stoichiometric quantities of salt and solvent and form a liquid at room temperature have been explored due to their sparingly solvating properties with respect to polysulfides. The viscosity of the solvate electrolytes is understandably high limiting their viability; however, hydrofluoroether cosolvents, thought to be inert to the solvate structure itself, can bemore » introduced to reduce viscosity and enhance diffusion. Nazar and co-workers previously reported that addition of 1,1,2,2-tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether (TTE) to the LiTFSI in acetonitrile solvate, (MeCN) 2-LiTFSI, results in enhanced capacity retention compared to the neat solvate. Here, we evaluate the effect of TTE addition on both the electrochemical behavior of the Li-S cell and the solvation structure of the (MeCN) 2-LiTFSI electrolyte. Contrary to previous suggestions, Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that TTE coordinates to Li + at the expense of MeCN coordination, thereby producing a higher content of free MeCN, a good polysulfide solvent, in the electrolyte. Furthermore, the electrolytes containing a higher free MeCN content facilitate faster polysulfide formation kinetics during the electrochemical reduction of S in a Li-S cell likely as a result of the solvation power of the free MeCN.« less

Effect of Hydrofluoroether Cosolvent Addition on Li Solvation in Acetonitrile-Based Solvate Electrolytes and Its Influence on S Reduction in a Li–S Battery

DOE PAGES

See, Kimberly A.; Wu, Heng -Liang; Lau, Kah Chun; ...

2016-11-16

Li-S batteries are a promising next-generation battery technology. Due to the formation of soluble polysulfides during cell operation, the electrolyte composition of the cell plays an active role in directing the formation and speciation of the soluble lithium polysulfides. Recently, new classes of electrolytes termed "solvates" that contain stoichiometric quantities of salt and solvent and form a liquid at room temperature have been explored due to their sparingly solvating properties with respect to polysulfides. The viscosity of the solvate electrolytes is understandably high limiting their viability; however, hydrofluoroether cosolvents, thought to be inert to the solvate structure itself, can bemore » introduced to reduce viscosity and enhance diffusion. Nazar and co-workers previously reported that addition of 1,1,2,2-tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether (TTE) to the LiTFSI in acetonitrile solvate, (MeCN) 2-LiTFSI, results in enhanced capacity retention compared to the neat solvate. Here, we evaluate the effect of TTE addition on both the electrochemical behavior of the Li-S cell and the solvation structure of the (MeCN) 2-LiTFSI electrolyte. Contrary to previous suggestions, Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that TTE coordinates to Li + at the expense of MeCN coordination, thereby producing a higher content of free MeCN, a good polysulfide solvent, in the electrolyte. Furthermore, the electrolytes containing a higher free MeCN content facilitate faster polysulfide formation kinetics during the electrochemical reduction of S in a Li-S cell likely as a result of the solvation power of the free MeCN.« less

Effect of Hydrofluoroether Cosolvent Addition on Li Solvation in Acetonitrile-Based Solvate Electrolytes and Its Influence on S Reduction in a Li-S Battery.

PubMed

See, Kimberly A; Wu, Heng-Liang; Lau, Kah Chun; Shin, Minjeong; Cheng, Lei; Balasubramanian, Mahalingam; Gallagher, Kevin G; Curtiss, Larry A; Gewirth, Andrew A

2016-12-21

Li-S batteries are a promising next-generation battery technology. Due to the formation of soluble polysulfides during cell operation, the electrolyte composition of the cell plays an active role in directing the formation and speciation of the soluble lithium polysulfides. Recently, new classes of electrolytes termed "solvates" that contain stoichiometric quantities of salt and solvent and form a liquid at room temperature have been explored due to their sparingly solvating properties with respect to polysulfides. The viscosity of the solvate electrolytes is understandably high limiting their viability; however, hydrofluoroether cosolvents, thought to be inert to the solvate structure itself, can be introduced to reduce viscosity and enhance diffusion. Nazar and co-workers previously reported that addition of 1,1,2,2-tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether (TTE) to the LiTFSI in acetonitrile solvate, (MeCN) 2 -LiTFSI, results in enhanced capacity retention compared to the neat solvate. Here, we evaluate the effect of TTE addition on both the electrochemical behavior of the Li-S cell and the solvation structure of the (MeCN) 2 -LiTFSI electrolyte. Contrary to previous suggestions, Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that TTE coordinates to Li + at the expense of MeCN coordination, thereby producing a higher content of free MeCN, a good polysulfide solvent, in the electrolyte. The electrolytes containing a higher free MeCN content facilitate faster polysulfide formation kinetics during the electrochemical reduction of S in a Li-S cell likely as a result of the solvation power of the free MeCN.

Curie-type paramagnetic NMR relaxation in the aqueous solution of Ni(II).

PubMed

Mareš, Jiří; Hanni, Matti; Lantto, Perttu; Lounila, Juhani; Vaara, Juha

2014-04-21

Ni(2+)(aq) has been used for many decades as a model system for paramagnetic nuclear magnetic resonance (pNMR) relaxation studies. More recently, its magnetic properties and also nuclear magnetic relaxation rates have been studied computationally. We have calculated electron paramagnetic resonance and NMR parameters using quantum-mechanical (QM) computation of molecular dynamics snapshots, obtained using a polarizable empirical force field. Statistical averages of hyperfine coupling, g- and zero-field splitting tensors, as well as the pNMR shielding terms, are compared to the available experimental and computational data. In accordance with our previous work, the isotropic hyperfine coupling as well as nuclear shielding values agree well with experimental measurements for the (17)O nuclei of water molecules in the first solvation shell of the nickel ion, whereas larger deviations are found for (1)H centers. We report, for the first time, the Curie-type contribution to the pNMR relaxation rate using QM calculations together with Redfield relaxation theory. The Curie relaxation mechanism is analogous to chemical shift anisotropy relaxation, well-known in diamagnetic NMR. Due to the predominance of other types of paramagnetic relaxation mechanisms for this system, it is possible to extract the Curie term only computationally. The Curie mechanism alone would result in around 16 and 20 s(-1) of relaxation rates (R1 and R2 respectively) for the (1)H nuclei of water molecules bonded to the Ni(2+) center, in a magnetic field of 11.7 T. The corresponding (17)O relaxation rates are around 33 and 38 s(-1). We also report the Curie contribution to the relaxation rate for molecules beyond the first solvation shell in a 1 M solution of Ni(2+) in water.

Preferential Solvation of an Asymmetric Redox Molecule

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, Kee Sung; Rajput, Nav Nidhi; Vijayakumar, M.

2016-12-15

The fundamental correlations between inter-molecular interactions, solvation structure and functionality of electrolytes are in many cases unknown, particularly for multi-component liquid systems. In this work, we explore such correlations by investigating the complex interplay between solubility and solvation structure for the electrolyte system comprising N-(ferrocenylmethyl)-N,N-dimethyl-N-ethylammonium bistrifluoromethylsulfonimide (Fc1N112-TFSI) dissolved in a ternary carbonate solvent mixture using combined NMR relaxation and computational analyses. Probing the evolution of the solvent-solvent, ion-solvent and ion-ion interactions with an increase in solute concentration provides a molecular level understanding of the solubility limit of the Fc1N112-TFSI system. An increase in solute con-centration leads to pronounced Fc1N112-TFSI contact-ionmore » pair formation by diminishing solvent-solvent and ion-solvent type interactions. At the solubility limit, the precipitation of solute is initiated through agglomeration of contact-ion pairs due to overlapping solvation shells.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barnes, Charles Ashley

In Chapter 2 several experimental and data analysis methods used in this thesis are described. In Chapter 3 steady-state fluorescence spectroscopy was used to determine the concentration of the efflux pump inhibitors (EPIs), pheophorbide a and pyropheophorbide a, in the feces of animals and it was found that their levels far exceed those reported to be inhibitory to efflux pumps. In Chapter 4 the solvation dynamics of 6-Propionyl-2-(N,Ndimethyl) aminonaphthalene (PRODAN) was studied in reverse micelles. The two fluorescent states of PRODAN solvate on different time scales and as such care must be exercised in solvation dynamic studies involving it andmore » its analogs. In Chapter 5 we studied the experimental and theoretical solvation dynamics of coumarin 153 (C153) in wild-type (WT) and modified myoglobins. Based on the nuclear magnetic resonance (NMR) spectroscopy and time-resolved fluorescence studies, we have concluded that it is important to thoroughly characterize the structure of a protein and probe system before comparing the theoretical and experimental results. In Chapter 6 the photophysical and spectral properties of a derivative of the medically relevant compound curcumin called cyclocurcumin was studied. Based on NMR, fluorescence, and absorption studies, the ground- and excited-states of cyclocurcumin are complicated by the existence of multiple structural isomers. In Chapter 7 the hydrolysis of cellulose by a pure form of cellulase in an ionic liquid, HEMA, and its aqueous mixtures at various temperatures were studied with the goal of increasing the cellulose to glucose conversion for biofuel production. It was found that HEMA imparts an additional stability to cellulase and can allow for faster conversion of cellulose to glucose using a pre-treatment step in comparison to only buffer.« less

Scaling Atomic Partial Charges of Carbonate Solvents for Lithium Ion Solvation and Diffusion

DOE PAGES

Chaudhari, Mangesh I.; Nair, Jijeesh R.; Pratt, Lawrence R.; ...

2016-10-21

Lithium-ion solvation and diffusion properties in ethylene carbonate (EC) and propylene carbonate (PC) were studied by molecular simulation, experiments, and electronic structure calculations. Studies carried out in water provide a reference for interpretation. Classical molecular dynamics simulation results are compared to ab initio molecular dynamics to assess nonpolarizable force field parameters for solvation structure of the carbonate solvents. Quasi-chemical theory (QCT) was adapted to take advantage of fourfold occupancy of the near-neighbor solvation structure observed in simulations and used to calculate solvation free energies. The computed free energy for transfer of Li + to PC from water, based on electronicmore » structure calculations with cluster-QCT, agrees with the experimental value. The simulation-based direct-QCT results with scaled partial charges agree with the electronic structure-based QCT values. The computed Li +/PF 6 - transference numbers of 0.35/0.65 (EC) and 0.31/0.69 (PC) agree well with NMR experimental values of 0.31/0.69 (EC) and 0.34/0.66 (PC) and similar values obtained here with impedance spectroscopy. These combined results demonstrate that solvent partial charges can be scaled in systems dominated by strong electrostatic interactions to achieve trends in ion solvation and transport properties that are comparable to ab initio and experimental results. Thus, the results support the use of scaled partial charges in simple, nonpolarizable force fields in future studies of these electrolyte solutions.« less

Characterization of Phosphate Species on Hydrated Anatase TiO2 Surfaces.

PubMed

Tielens, Frederik; Gervais, Christel; Deroy, Geraldine; Jaber, Maguy; Stievano, Lorenzo; Coelho Diogo, Cristina; Lambert, Jean-François

2016-02-02

The adsorption/interaction of KH2PO4 with solvated (100) and (101) TiO2 anatase surfaces is investigated using periodic DFT calculations in combination with GIPAW NMR calculations and experimental IR and solid state (17)O, and (31)P NMR spectroscopies. A complete and realistic model has been used to simulate the solvent by individual water molecules. The most stable adsorption configurations are characterized theoretically at the atomic scale, and experimentally supported by NMR and IR spectroscopies. It is shown that H2PO4(-) chemisorbs on the (100) and (101) anatase surfaces, preferentially via a bidentate geometry. Dimer (H3P2O7(-)) and trimer (H4P3O10(-)) adsorption models are confronted with monomer adsorption models, in order to rationalize their occurrence.

Modelling zwitterions in solution: 3-fluoro-γ-aminobutyric acid (3F-GABA).

PubMed

Cao, Jie; Bjornsson, Ragnar; Bühl, Michael; Thiel, Walter; van Mourik, Tanja

2012-01-02

The conformations and relative stabilities of folded and extended 3-fluoro-γ-aminobutyric acid (3F-GABA) conformers were studied using explicit solvation models. Geometry optimisations in the gas phase with one or two explicit water molecules favour folded and neutral structures containing intramolecular NH···O-C hydrogen bonds. With three or five explicit water molecules zwitterionic minima are obtained, with folded structures being preferred over extended conformers. The stability of folded versus extended zwitterionic conformers increases on going from a PCM continuum solvation model to the microsolvated complexes, though extended structures become less disfavoured with the inclusion of more water molecules. Full explicit solvation was studied with a hybrid quantum-mechanical/molecular-mechanical (QM/MM) scheme and molecular dynamics simulations, including more than 6000 TIP3P water molecules. According to free energies obtained from thermodynamic integration at the PM3/MM level and corrected for B3LYP/MM total energies, the fully extended conformer is more stable than folded ones by about -4.5 kJ mol(-1). B3LYP-computed (3)J(F,H) NMR spin-spin coupling constants, averaged over PM3/MM-MD trajectories, agree best with experiment for this fully extended form, in accordance with the original NMR analysis. The seeming discrepancy between static PCM calculations and experiment noted previously is now resolved. That the inexpensive semiempirical PM3 method performs so well for this archetypical zwitterion is encouraging for further QM/MM studies of biomolecular systems. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transitioning NWChem to the Next Generation of Manycore Machines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bylaska, Eric J.; Apra, E; Kowalski, Karol

The NorthWest chemistry (NWChem) modeling software is a popular molecular chemistry simulation software that was designed from the start to work on massively parallel processing supercomputers [1-3]. It contains an umbrella of modules that today includes self-consistent eld (SCF), second order Møller-Plesset perturbation theory (MP2), coupled cluster (CC), multiconguration self-consistent eld (MCSCF), selected conguration interaction (CI), tensor contraction engine (TCE) many body methods, density functional theory (DFT), time-dependent density functional theory (TDDFT), real-time time-dependent density functional theory, pseudopotential plane-wave density functional theory (PSPW), band structure (BAND), ab initio molecular dynamics (AIMD), Car-Parrinello molecular dynamics (MD), classical MD, hybrid quantum mechanicsmore » molecular mechanics (QM/MM), hybrid ab initio molecular dynamics molecular mechanics (AIMD/MM), gauge independent atomic orbital nuclear magnetic resonance (GIAO NMR), conductor like screening solvation model (COSMO), conductor-like screening solvation model based on density (COSMO-SMD), and reference interaction site model (RISM) solvation models, free energy simulations, reaction path optimization, parallel in time, among other capabilities [4]. Moreover, new capabilities continue to be added with each new release.« less

Theoretical NMR and conformational analysis of solvated oximes for organophosphates-inhibited acetylcholinesterase reactivation

NASA Astrophysics Data System (ADS)

da Silva, Jorge Alberto Valle; Modesto-Costa, Lucas; de Koning, Martijn C.; Borges, Itamar; França, Tanos Celmar Costa

2018-01-01

In this work, quaternary and non-quaternary oximes designed to bind at the peripheral site of acetylcholinesterase previously inhibited by organophosphates were investigated theoretically. Some of those oximes have a large number of degrees of freedom, thus requiring an accurate method to obtain molecular geometries. For this reason, the density functional theory (DFT) was employed to refine their molecular geometries after conformational analysis and to compare their 1H and 13C nuclear magnetic resonance (NMR) theoretical signals in gas-phase and in solvent. A good agreement with experimental data was achieved and the same theoretical approach was employed to obtain the geometries in water environment for further studies.

ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions

PubMed Central

Vitalis, Andreas; Pappu, Rohit V.

2009-01-01

A new implicit solvation model for use in Monte Carlo simulations of polypeptides is introduced. The model is termed ABSINTH for self-Assembly of Biomolecules Studied by an Implicit, Novel, and Tunable Hamiltonian. It is designed primarily for simulating conformational equilibria and oligomerization reactions of intrinsically disordered proteins in aqueous solutions. The paradigm for ABSINTH is conceptually similar to the EEF1 model of Lazaridis and Karplus (Proteins: Struct. Func. Genet., 1999, 35: 133-152). In ABSINTH, the transfer of a polypeptide solute from the gas phase into a continuum solvent is the sum of a direct mean field interaction (DMFI), and a term to model the screening of polar interactions. Polypeptide solutes are decomposed into a set of distinct solvation groups. The DMFI is a sum of contributions from each of the solvation groups, which are analogs of model compounds. Continuum-mediated screening of electrostatic interactions is achieved using a framework similar to the one used for the DMFI. Promising results are shown for a set of test cases. These include the calculation of NMR coupling constants for short peptides, the assessment of the thermal stability of two small proteins, reversible folding of both an alpha-helix and a beta-hairpin forming peptide, and the polymeric properties of intrinsically disordered polyglutamine peptides of varying lengths. The tests reveal that the computational expense for simulations with the ABSINTH implicit solvation model increase by a factor that is in the range of 2.5-5.0 with respect to gas-phase calculations. PMID:18506808

Elucidating the Solvation Structure and Dynamics of Lithium Polysulfides Resulting from Competitive Salt and Solvent Interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rajput, Nav Nidhi; Murugesan, Vijayakumar; Shin, Yongwoo

2017-04-10

Fundamental molecular level understanding of functional properties of liquid solutions provides an important basis for designing optimized electrolytes for numerous applica-tions. In particular, exhaustive knowledge of solvation structure, stability and transport properties is critical for developing stable electrolytes for fast charging and high energy density next-generation energy storage systems. Here we report the correlation between solubility, solvation structure and translational dynamics of a lithium salt (Li-TFSI) and polysulfides species using well-benchmarked classical molecular dynamics simulations combined with nuclear magnetic resonance (NMR). It is observed that the polysulfide chain length has a significant effect on the ion-ion and ion-solvent interaction asmore » well as on the diffusion coefficient of the ionic species in solution. In particular, extensive cluster formation is observed in lower order poly-sulfides (Sx2-; x≤4), whereas the longer polysulfides (Sx2-; x>4) show high solubility and slow dynamics in the solu-tion. It is observed that optimal solvent/salt ratio is essen-tial to control the solubility and conductivity as the addi-tion of Li salt increases the solubility but decreases the mo-bility of the ionic species. This work provides a coupled theoretical and experimental study of bulk solvation struc-ture and transport properties of multi-component electro-lyte systems, yielding design metrics for developing optimal electrolytes with improved stability and solubility.« less

Annual Report 2013-2014: Theoretical Studies of Nerve Agents Adsorbed on Surfaces

DTIC Science & Technology

2014-07-08

of the solvation of sarin by water are underway. The results should clarify how water affects desorption properties and the extent of solvation of...platinum activated nanocrystalline ZnO thick films. Sensors and Actuators B-Chemical 2012, 161, 372- 380. 5. Bermudez, V. M., Computational Study of...Rauk, A.; Shishkov, I. F.; Vilkov, L. V.; Koehler, K. F.; Kostyanovsky, R. G., DETERMINATION OF THE STRUCTURE AND CHIROPTICAL PROPERTIES OF THE

Using NMR Spectroscopy to Investigate the Solution Behavior of Nerve Agents and Their Binding to Acetylcholinesterase

DTIC Science & Technology

2016-01-01

USING NMR SPECTROSCOPY TO INVESTIGATE THE SOLUTION BEHAVIOR OF NERVE AGENTS AND THEIR BINDING TO...XX-01-2016 2. REPORT TYPE Final 3. DATES COVERED (From - To) Jan – Jun 2015 4. TITLE AND SUBTITLE Using NMR Spectroscopy to Investigate the...MOLECULAR MOTIONS AND NMR SPECTROSCOPY ...................................................................................................3 4. THE

Hydrolysis of Nerve Agents by Model Nucleophiles: A Computational Study

PubMed Central

Beck, Jeremy M.

2008-01-01

Density functional theory calculations were employed to study the reaction of five nerve agents with model nucleophiles, including EtX− and EtXH (X = O, S, Se) for serine, cysteine and selenocysteine, respectively. Calculations at the B3LYP/6-311++G(2d,p) level of theory predict an exothermic reaction between ethoxide and all of the nerve agents studied. As compared to EtO− as a nucleophile, these reactions become ~30 kcal/mol more endothermic for EtS−, and by ~40 kcal/mol for EtSe−. The equivalent reactions with the neutral nucleophiles (EtXH) were more endothermic. The effect of solvation on the reaction thermochemistry was determined using a polarizable continuum model simulating the dielectric constant of chloroform. While there was a large exothermic shift for reactions involving charged nucleophiles with solvation modeling, the corresponding shift was minimal for the reaction with neutral nucleophiles. PMID:18538754

Solvation behavior of carbonate-based electrolytes in sodium ion batteries.

PubMed

Cresce, Arthur V; Russell, Selena M; Borodin, Oleg; Allen, Joshua A; Schroeder, Marshall A; Dai, Michael; Peng, Jing; Gobet, Mallory P; Greenbaum, Steven G; Rogers, Reginald E; Xu, Kang

2016-12-21

Sodium ion batteries are on the cusp of being a commercially available technology. Compared to lithium ion batteries, sodium ion batteries can potentially offer an attractive dollar-per-kilowatt-hour value, though at the penalty of reduced energy density. As a materials system, sodium ion batteries present a unique opportunity to apply lessons learned in the study of electrolytes for lithium ion batteries; specifically, the behavior of the sodium ion in an organic carbonate solution and the relationship of ion solvation with electrode surface passivation. In this work the Li + and Na + -based solvates were characterized using electrospray mass spectrometry, infrared and Raman spectroscopy, 17 O, 23 Na and pulse field gradient double-stimulated-echo pulse sequence nuclear magnetic resonance (NMR), and conductivity measurements. Spectroscopic evidence demonstrate that the Li + and Na + cations share a number of similar ion-solvent interaction trends, such as a preference in the gas and liquid phase for a solvation shell rich in cyclic carbonates over linear carbonates and fluorinated carbonates. However, quite different IR spectra due to the PF 6 - anion interactions with the Na + and Li + cations were observed and were rationalized with the help of density functional theory (DFT) calculations that were also used to examine the relative free energies of solvates using cluster - continuum models. Ion-solvent distances for Na + were longer than Li + , and Na + had a greater tendency towards forming contact pairs compared to Li + in linear carbonate solvents. In tests of hard carbon Na-ion batteries, performance was not well correlated to Na + solvent preference, leading to the possibility that Na + solvent preference may play a reduced role in the passivation of anode surfaces and overall Na-ion battery performance.

Nuclear magnetic resonance studies of the solvation structures of a high-performance nonaqueous redox flow electrolyte

NASA Astrophysics Data System (ADS)

Deng, Xuchu; Hu, Mary; Wei, Xiaoliang; Wang, Wei; Mueller, Karl T.; Chen, Zhong; Hu, Jian Zhi

2016-03-01

Understanding the solvation structures of electrolytes is important for developing nonaqueous redox flow batteries that hold considerable potential for future large scale energy storage systems. The utilization of an emerging ionic-derivatived ferrocene compound, ferrocenylmethyl dimethyl ethyl ammonium bis(trifluoromethanesulfonyl)imide (Fc1N112-TFSI), has recently overcome the issue of solubility in the supporting electrolyte. In this work, 13C, 1H and 17O NMR investigations were carried out using electrolyte solutions consisting of Fc1N112-TFSI as the solute and the mixed alkyl carbonate as the solvent. It was observed that the spectra of 13C experience changes of chemical shifts while those of 17O undergo linewidth broadening, indicating interactions between solute and solvent molecules. Quantum chemistry calculations of both molecular structures and chemical shifts (13C, 1H and 17O) are performed for interpreting experimental results and for understanding the detailed solvation structures. The results indicate that Fc1N112-TFSI is dissociated at varying degrees in mixed solvent depending on concentrations. At dilute solute concentrations, most Fc1N112+ and TFSI- are fully disassociated with their own solvation shells formed by solvent molecules. At saturated concentration, Fc1N112+-TFSI- contact ion pairs are formed and the solvent molecules are preferentially interacting with the Fc rings rather than interacting with the ionic pendant arm of Fc1N112-TFSI.

In situ NMR and electrochemical quartz crystal microbalance techniques reveal the structure of the electrical double layer in supercapacitors

NASA Astrophysics Data System (ADS)

Griffin, John M.; Forse, Alexander C.; Tsai, Wan-Yu; Taberna, Pierre-Louis; Simon, Patrice; Grey, Clare P.

2015-08-01

Supercapacitors store charge through the electrosorption of ions on microporous electrodes. Despite major efforts to understand this phenomenon, a molecular-level picture of the electrical double layer in working devices is still lacking as few techniques can selectively observe the ionic species at the electrode/electrolyte interface. Here, we use in situ NMR to directly quantify the populations of anionic and cationic species within a working microporous carbon supercapacitor electrode. Our results show that charge storage mechanisms are different for positively and negatively polarized electrodes for the electrolyte tetraethylphosphonium tetrafluoroborate in acetonitrile; for positive polarization charging proceeds by exchange of the cations for anions, whereas for negative polarization, cation adsorption dominates. In situ electrochemical quartz crystal microbalance measurements support the NMR results and indicate that adsorbed ions are only partially solvated. These results provide new molecular-level insight, with the methodology offering exciting possibilities for the study of pore/ion size, desolvation and other effects on charge storage in supercapacitors.

Absolute shielding scales for Al, Ga, and In and revised nuclear magnetic dipole moments of {sup 27}Al, {sup 69}Ga, {sup 71}Ga, {sup 113}In, and {sup 115}In nuclei

DOE Office of Scientific and Technical Information (OSTI.GOV)

Antušek, A., E-mail: andrej.antusek@stuba.sk; Holka, F., E-mail: filip.holka@stuba.sk

2015-08-21

We present coupled cluster calculations of NMR shielding constants of aluminum, gallium, and indium in water-ion clusters. In addition, relativistic and dynamical corrections and the influence of the second solvation shell are evaluated. The final NMR shielding constants define new absolute shielding scales, 600.0 ± 4.1 ppm, 2044.4 ± 31.4 ppm, and 4507.7 ± 63.7 ppm for aluminum, gallium, and indium, respectively. The nuclear magnetic dipole moments for {sup 27}Al, {sup 69}Ga, {sup 71}Ga, {sup 113}In, and {sup 115}In isotopes are corrected by combining the computed shielding constants with experimental NMR frequencies. The absolute magnitude of the correction increases alongmore » the series and for indium isotopes it reaches approximately −8.0 × 10{sup −3} of the nuclear magneton.« less

Spectroscopic and structural studies of the first complex formed between salinomycin and organic amine

NASA Astrophysics Data System (ADS)

Antoszczak, Michał; Janczak, Jan; Brzezinski, Bogumił; Huczyński, Adam

2017-02-01

For the first time, the crystalline complex of salinomycin with benzylamine was obtained and its molecular structure was studied using single crystal X-ray diffraction, FT-IR, 1H NMR, 13C NMR, 2D NMR and ESI MS methods. These studies provided evidence that the proton from the carboxylic group of salinomycin (SAL) is transferred to the amine group of benzylamine (BnA) forming the host-guest complex (SAL-BnA). It was shown that the SAL-BnA complex both in solid state and in chloroform solution is stabilized by the intramolecular O-H⋯O hydrogen bonds and also by the intermolecular hydrogen bonding interactions of the carboxylate, ketone and/or hydroxyl groups of SAL with water molecules present in the investigated system. The solvated acetonitrile molecules are additionally located in the voids between the SAL-BnA complex molecules in the crystal structure, while water molecules involved in the dihydrated crystalline SAL-BnA complex partially move into the solvent upon dissolution in chloroform.

The Chemical Shift Baseline for High-Pressure NMR Spectra of Proteins.

PubMed

Frach, Roland; Kibies, Patrick; Böttcher, Saraphina; Pongratz, Tim; Strohfeldt, Steven; Kurrmann, Simon; Koehler, Joerg; Hofmann, Martin; Kremer, Werner; Kalbitzer, Hans Robert; Reiser, Oliver; Horinek, Dominik; Kast, Stefan M

2016-07-18

High-pressure (HP) NMR spectroscopy is an important method for detecting rare functional states of proteins by analyzing the pressure response of chemical shifts. However, for the analysis of the shifts it is mandatory to understand the origin of the observed pressure dependence. Here we present experimental HP NMR data on the (15) N-enriched peptide bond model, N-methylacetamide (NMA), in water, combined with quantum-chemical computations of the magnetic parameters using a pressure-sensitive solvation model. Theoretical analysis of NMA and the experimentally used internal reference standard 4,4-dimethyl-4-silapentane-1-sulfonic (DSS) reveal that a substantial part of observed shifts can be attributed to purely solvent-induced electronic polarization of the backbone. DSS is only marginally responsive to pressure changes and is therefore a reliable sensor for variations in the local magnetic field caused by pressure-induced changes of the magnetic susceptibility of the solvent. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

EFFECT OF AN ADDITIONAL HYDROPHILIC VERSUS HYDROPHOBIC COAT ON THE QUALITY OF DENTINAL SEALING PROVIDED BY TWO-STEP ETCH-AND-RINSE ADHESIVES

PubMed Central

Silva, Safira Marques de Andrade; Carrilho, Marcela Rocha de Oliveira; Marquezini, Luiz; Garcia, Fernanda Cristina Pimentel; Manso, Adriana Pigozzo; Alves, Marcelo Corrêa; de Carvalho, Ricardo Marins

2009-01-01

Objective: To test the hypothesis that the quality of the dentinal sealing provided by two-step etch-and-rinse adhesives cannot be altered by the addition of an extra layer of the respective adhesive or the application of a more hydrophobic, non-solvated resin. Material and Methods: full-crown preparations were acid-etched with phosphoric acid for 15 s and bonded with Adper Single Bond (3M ESPE), Excite DSC (Ivoclar/Vivadent) or Prime & Bond NT (Dentsply). The adhesives were used according to the manufacturers' instructions (control groups) or after application to dentin they were a) covered with an extra coat of each respective system or b) coated with a non-solvated bonding agent (Adper Scotchbond Multi-Purpose Adhesive, 3M ESPE). Fluid flow rate was measured before and after dentin surfaces were acid-etched and bonded with adhesives. Results: None of the adhesives or experimental treatments was capable to block completely the fluid transudation across the treated dentin. Application of an extra coat of the adhesive did not reduce the fluid flow rate of adhesive-bonded dentin (p>0.05). Conversely, the application of a more hydrophobic non-solvated resin resulted in significant reductions in the fluid flow rate (p<0.05) for all tested adhesives. Conclusions: The quality of the dentinal sealing provided by etch-and-rinse adhesives can be significantly improved by the application of a more hydrophobic, non-solvated bonding agent. PMID:19466248

Benchmarking of density functionals for a soft but accurate prediction and assignment of (1) H and (13)C NMR chemical shifts in organic and biological molecules.

PubMed

Benassi, Enrico

2017-01-15

A number of programs and tools that simulate 1 H and 13 C nuclear magnetic resonance (NMR) chemical shifts using empirical approaches are available. These tools are user-friendly, but they provide a very rough (and sometimes misleading) estimation of the NMR properties, especially for complex systems. Rigorous and reliable ways to predict and interpret NMR properties of simple and complex systems are available in many popular computational program packages. Nevertheless, experimentalists keep relying on these "unreliable" tools in their daily work because, to have a sufficiently high accuracy, these rigorous quantum mechanical methods need high levels of theory. An alternative, efficient, semi-empirical approach has been proposed by Bally, Rablen, Tantillo, and coworkers. This idea consists of creating linear calibrations models, on the basis of the application of different combinations of functionals and basis sets. Following this approach, the predictive capability of a wider range of popular functionals was systematically investigated and tested. The NMR chemical shifts were computed in solvated phase at density functional theory level, using 30 different functionals coupled with three different triple-ζ basis sets. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations.

PubMed

Kraus, Jodi; Gupta, Rupal; Yehl, Jenna; Lu, Manman; Case, David A; Gronenborn, Angela M; Akke, Mikael; Polenova, Tatyana

2018-03-22

Magic angle spinning NMR spectroscopy is uniquely suited to probe the structure and dynamics of insoluble proteins and protein assemblies at atomic resolution, with NMR chemical shifts containing rich information about biomolecular structure. Access to this information, however, is problematic, since accurate quantum mechanical calculation of chemical shifts in proteins remains challenging, particularly for 15 N H . Here we report on isotropic chemical shift predictions for the carbohydrate recognition domain of microcrystalline galectin-3, obtained from using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, implemented using an automated fragmentation approach, and using very high resolution (0.86 Å lactose-bound and 1.25 Å apo form) X-ray crystal structures. The resolution of the X-ray crystal structure used as an input into the AF-NMR program did not affect the accuracy of the chemical shift calculations to any significant extent. Excellent agreement between experimental and computed shifts is obtained for 13 C α , while larger scatter is observed for 15 N H chemical shifts, which are influenced to a greater extent by electrostatic interactions, hydrogen bonding, and solvation.

Quantitative measurement of regional blood flow with gadolinium diethylenetriaminepentaacetate bolus track NMR imaging in cerebral infarcts in rats: validation with the iodo[14C]antipyrine technique.

PubMed Central

Wittlich, F; Kohno, K; Mies, G; Norris, D G; Hoehn-Berlage, M

1995-01-01

NMR bolus track measurements were correlated with autoradiographically determined regional cerebral blood flow (rCBF). The NMR method is based on bolus infusion of the contrast agent gadolinium diethylenetriaminepentaacetate and high-speed T*2-sensitive NMR imaging. The first pass of the contrast agent through the image plane causes a transient decrease of the signal intensity. This time course of the signal intensity is transformed into relative concentrations of the contrast agent in each pixel. The mean transit time and relative blood flow and volume are calculated from such indicator dilution curves. We investigated whether this NMR technique correctly expresses the relative rCBF. The relative blood flow data, calculated from NMR bolus track experiments, and the absolute values of iodo[14C]antipyrine autoradiography were compared. A linear relationship was observed, indicating the proportionality of the transient NMR signal change with CBF. Excellent interindividual reproducibility of calibration constants is observed (r = 0.963). For a given NMR protocol, bolus track measurements calibrated with autoradiography after the experiment allow determination of absolute values for rCBF and regional blood volume. Images Fig. 2 Fig. 3 PMID:7892189

Anti-cancer agents based on 6-trifluoromethoxybenzimidazole derivatives and method of making

DOEpatents

Gakh, Andrei A.; Vovk, Mykhaylo V.; Mel'nychenko, Nina V.; Sukach, Volodymyr A.

2012-08-14

The present disclosure relates to novel compounds having the structural Formulas (1a,1b), stereoisomers, tautomers, racemics, prodrugs, metabolites thereof, or pharmaceutically acceptable salt and/or solvate thereof as chemotherapy agents for treating of cancer, particularly androgen-independent prostate cancer. The disclosure also relates to methods for preparing said compounds, and to pharmaceutical compositions comprising said compounds.

Anti-cancer agents based on 6-trifluoromethoxybenzimidazole derivatives and method of making

DOEpatents

Gakh, Andrei A; Vovk, Mykhaylo V; Mel& #x27; nychenko, Nina V; Sukach, Volodymyr A

2012-10-23

The present disclosure relates to novel compounds having the structural Formulas (1a,1b), stereoisomers, tautomers, racemics, prodrugs, metabolites thereof, or pharmaceutically acceptable salt and/or solvate thereof as chemotherapy agents for treating of cancer, particularly androgen-independent prostate cancer. The disclosure also relates to methods for preparing said compounds, and to pharmaceutical compositions comprising said compounds.

Correlating steric hydration forces with water dynamics through surface force and diffusion NMR measurements in a lipid–DMSO–H2O system

PubMed Central

Schrader, Alex M.; Donaldson, Stephen H.; Song, Jinsuk; Cheng, Chi-Yuan; Lee, Dong Woog; Han, Songi; Israelachvili, Jacob N.

2015-01-01

Dimethyl sulfoxide (DMSO) is a common solvent and biological additive possessing well-known utility in cellular cryoprotection and lipid membrane permeabilization, but the governing mechanisms at membrane interfaces remain poorly understood. Many studies have focused on DMSO–lipid interactions and the subsequent effects on membrane-phase behavior, but explanations often rely on qualitative notions of DMSO-induced dehydration of lipid head groups. In this work, surface forces measurements between gel-phase dipalmitoylphosphatidylcholine membranes in DMSO–water mixtures quantify the hydration- and solvation-length scales with angstrom resolution as a function of DMSO concentration from 0 mol% to 20 mol%. DMSO causes a drastic decrease in the range of the steric hydration repulsion, leading to an increase in adhesion at a much-reduced intermembrane distance. Pulsed field gradient NMR of the phosphatidylcholine (PC) head group analogs, dimethyl phosphate and tetramethylammonium ions, shows that the ion hydrodynamic radius decreases with increasing DMSO concentration up to 10 mol% DMSO. The complementary measurements indicate that, at concentrations below 10 mol%, the primary effect of DMSO is to decrease the solvated volume of the PC head group and that, from 10 mol% to 20 mol%, DMSO acts to gradually collapse head groups down onto the surface and suppress their thermal motion. This work shows a connection between surface forces, head group conformation and dynamics, and surface water diffusion, with important implications for soft matter and colloidal systems. PMID:26261313

The dynamics, structure, and conformational free energy of proline-containing antifreeze glycoprotein.

PubMed Central

Nguyen, Dat H; Colvin, Michael E; Yeh, Yin; Feeney, Robert E; Fink, William H

2002-01-01

Recent NMR studies of the solution structure of the 14-amino acid antifreeze glycoprotein AFGP-8 have concluded that the molecule lacks long-range order. The implication that an apparently unstructured molecule can still have a very precise function as a freezing inhibitor seems startling at first consideration. To gain insight into the nature of conformations and motions in AFGP-8, we have undertaken molecular dynamics simulations augmented with free energy calculations using a continuum solvation model. Starting from 10 different NMR structures, 20 ns of dynamics of AFGP were explored. The dynamics show that AFGP structure is composed of four segments, joined by very flexible pivots positioned at alanine 5, 8, and 11. The dynamics also show that the presence of prolines in this small AFGP structure facilitates the adoption of the poly-proline II structure as its overall conformation, although AFGP does adopt other conformations during the course of dynamics as well. The free energies calculated using a continuum solvation model show that the lowest free energy conformations, while being energetically equal, are drastically different in conformations. In other words, this AFGP molecule has many structurally distinct and energetically equal minima in its energy landscape. In addition, conformational, energetic, and hydrogen bond analyses suggest that the intramolecular hydrogen bonds between the N-acetyl group and the protein backbone are an important integral part of the overall stability of the AFGP molecule. The relevance of these findings to the mechanism of freezing inhibition is discussed. PMID:12023212

The dynamics, structure, and conformational free energy of proline-containing antifreeze glycoprotein.

PubMed

Nguyen, Dat H; Colvin, Michael E; Yeh, Yin; Feeney, Robert E; Fink, William H

2002-06-01

Recent NMR studies of the solution structure of the 14-amino acid antifreeze glycoprotein AFGP-8 have concluded that the molecule lacks long-range order. The implication that an apparently unstructured molecule can still have a very precise function as a freezing inhibitor seems startling at first consideration. To gain insight into the nature of conformations and motions in AFGP-8, we have undertaken molecular dynamics simulations augmented with free energy calculations using a continuum solvation model. Starting from 10 different NMR structures, 20 ns of dynamics of AFGP were explored. The dynamics show that AFGP structure is composed of four segments, joined by very flexible pivots positioned at alanine 5, 8, and 11. The dynamics also show that the presence of prolines in this small AFGP structure facilitates the adoption of the poly-proline II structure as its overall conformation, although AFGP does adopt other conformations during the course of dynamics as well. The free energies calculated using a continuum solvation model show that the lowest free energy conformations, while being energetically equal, are drastically different in conformations. In other words, this AFGP molecule has many structurally distinct and energetically equal minima in its energy landscape. In addition, conformational, energetic, and hydrogen bond analyses suggest that the intramolecular hydrogen bonds between the N-acetyl group and the protein backbone are an important integral part of the overall stability of the AFGP molecule. The relevance of these findings to the mechanism of freezing inhibition is discussed.

Solution NMR Refinement of a Metal Ion Bound Protein Using Metal Ion Inclusive Restrained Molecular Dynamics Methods

PubMed Central

Chakravorty, Dhruva K.; Wang, Bing; Lee, Chul Won; Guerra, Alfredo J.; Giedroc, David P.; Merz, Kenneth M.

2013-01-01

Correctly calculating the structure of metal coordination sites in a protein during the process of nuclear magnetic resonance (NMR) structure determination and refinement continues to be a challenging task. In this study, we present an accurate and convenient means by which to include metal ions in the NMR structure determination process using molecular dynamics (MD) constrained by NMR-derived data to obtain a realistic and physically viable description of the metal binding site(s). This method provides the framework to accurately portray the metal ions and its binding residues in a pseudo-bond or dummy-cation like approach, and is validated by quantum mechanical/molecular mechanical (QM/MM) MD calculations constrained by NMR-derived data. To illustrate this approach, we refine the zinc coordination complex structure of the zinc sensing transcriptional repressor protein Staphylococcus aureus CzrA, generating over 130 ns of MD and QM/MM MD NMR-data compliant sampling. In addition to refining the first coordination shell structure of the Zn(II) ion, this protocol benefits from being performed in a periodically replicated solvation environment including long-range electrostatics. We determine that unrestrained (not based on NMR data) MD simulations correlated to the NMR data in a time-averaged ensemble. The accurate solution structure ensemble of the metal-bound protein accurately describes the role of conformational dynamics in allosteric regulation of DNA binding by zinc and serves to validate our previous unrestrained MD simulations of CzrA. This methodology has potentially broad applicability in the structure determination of metal ion bound proteins, protein folding and metal template protein-design studies. PMID:23609042

In search of a viable reaction pathway in the chelation of a metallo-protein

NASA Astrophysics Data System (ADS)

Rose, Frisco; Hodak, Miroslav; Bernholc, Jerry

2010-03-01

Misfolded metallo-proteins are potential causal agents in the onset of neuro-degenerative diseases, such as Alzheimer's and Parkinson's Diseases (PD). Experimental results involving metal chelation have shown significant promise in symptom reduction and misfolding reversal. We explore, through atomistic simulations, potential reaction pathways for the chelation of Cu^2+ from the metal binding site in our representation of a partially misfolded α-synuclein, the protein implicated in PD. Our ab initio simulations use Density Functional Theory (DFT) and nudged elastic band to obtain the minimized energy coordinates of this reaction. Our simulations include ab initio water at the interaction site and in its first solvation shells, while the remainder is fully solvated with orbital-free DFT water representation [1]. Our ongoing studies of viable chelation agents include nicotine, caffeine and other potential reagents, we will review the best case agents in this presentation. [4pt] [1] Hodak M, Lu W, Bernholc J. Hybrid ab initio Kohn-Sham density functional theory/frozen-density orbital-free density functional theory simulation method suitable for biological systems. J. Chem. Phys. 2008 Jan;128(1):014101-9.

GIAO-DFT calculation of 15 N NMR chemical shifts of Schiff bases: Accuracy factors and protonation effects.

PubMed

Semenov, Valentin A; Samultsev, Dmitry O; Krivdin, Leonid B

2018-02-09

15 N NMR chemical shifts in the representative series of Schiff bases together with their protonated forms have been calculated at the density functional theory level in comparison with available experiment. A number of functionals and basis sets have been tested in terms of a better agreement with experiment. Complimentary to gas phase results, 2 solvation models, namely, a classical Tomasi's polarizable continuum model (PCM) and that in combination with an explicit inclusion of one molecule of solvent into calculation space to form supermolecule 1:1 (SM + PCM), were examined. Best results are achieved with PCM and SM + PCM models resulting in mean absolute errors of calculated 15 N NMR chemical shifts in the whole series of neutral and protonated Schiff bases of accordingly 5.2 and 5.8 ppm as compared with 15.2 ppm in gas phase for the range of about 200 ppm. Noticeable protonation effects (exceeding 100 ppm) in protonated Schiff bases are rationalized in terms of a general natural bond orbital approach. Copyright © 2018 John Wiley & Sons, Ltd.

Probing hydrogen bond networks in half-sandwich Ru(II) building blocks by a combined 1H DQ CRAMPS solid-state NMR, XRPD, and DFT approach.

PubMed

Chierotti, Michele R; Gobetto, Roberto; Nervi, Carlo; Bacchi, Alessia; Pelagatti, Paolo; Colombo, Valentina; Sironi, Angelo

2014-01-06

The hydrogen bond network of three polymorphs (1α, 1β, and 1γ) and one solvate form (1·H2O) arising from the hydration-dehydration process of the Ru(II) complex [(p-cymene)Ru(κN-INA)Cl2] (where INA is isonicotinic acid), has been ascertained by means of one-dimensional (1D) and two-dimensional (2D) double quantum (1)H CRAMPS (Combined Rotation and Multiple Pulses Sequences) and (13)C CPMAS solid-state NMR experiments. The resolution improvement provided by homonuclear decoupling pulse sequences, with respect to fast MAS experiments, has been highlighted. The solid-state structure of 1γ has been fully characterized by combining X-ray powder diffraction (XRPD), solid-state NMR, and periodic plane-wave first-principles calculations. None of the forms show the expected supramolecular cyclic dimerization of the carboxylic functions of INA, because of the presence of Cl atoms as strong hydrogen bond (HB) acceptors. The hydration-dehydration process of the complex has been discussed in terms of structure and HB rearrangements.

Antiviral agents of plant origin. III. Scopadulin, a novel tetracyclic diterpene from Scoparia dulcis L.

PubMed

Hayashi, T; Kawasaki, M; Miwa, Y; Taga, T; Morita, N

1990-04-01

The structure and stereochemistry of scopadulin, a novel aphidicolane-type diterpene isolated from Scoparia dulcis L. have been established from spectral data and single-crystal X-ray analysis of its acetone solvate.

Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model

NASA Astrophysics Data System (ADS)

Bordner, Andrew J.; Zorman, Barry; Abagyan, Ruben

2011-10-01

Membrane proteins comprise a significant fraction of the proteomes of sequenced organisms and are the targets of approximately half of marketed drugs. However, in spite of their prevalence and biomedical importance, relatively few experimental structures are available due to technical challenges. Computational simulations can potentially address this deficit by providing structural models of membrane proteins. Solvation within the spatially heterogeneous membrane/solvent environment provides a major component of the energetics driving protein folding and association within the membrane. We have developed an implicit solvation model for membranes that is both computationally efficient and accurate enough to enable molecular mechanics predictions for the folding and association of peptides within the membrane. We derived the new atomic solvation model parameters using an unbiased fitting procedure to experimental data and have applied it to diverse problems in order to test its accuracy and to gain insight into membrane protein folding. First, we predicted the positions and orientations of peptides and complexes within the lipid bilayer and compared the simulation results with solid-state NMR structures. Additionally, we performed folding simulations for a series of host-guest peptides with varying propensities to form alpha helices in a hydrophobic environment and compared the structures with experimental measurements. We were also able to successfully predict the structures of amphipathic peptides as well as the structures for dimeric complexes of short hexapeptides that have experimentally characterized propensities to form beta sheets within the membrane. Finally, we compared calculated relative transfer energies with data from experiments measuring the effects of mutations on the free energies of translocon-mediated insertion of proteins into lipid bilayers and of combined folding and membrane insertion of a beta barrel protein.

Investigation of fluorocarbon blowing agents in insulating polymer foams by 19F NMR imaging.

PubMed

Fyfe, C A; Mei, Z; Grondey, H

1996-01-01

Currently, there is no reliable and readily accessible technique with which the distribution and diffusion of blowing agents in rigid insulating foams can be detected and monitored. In this paper, we demonstrate that 19F NMR microscopic imaging together with 19F solid-state MAS NMR spectroscopy is ideally suited for such measurements and yield quantitatively reliable information that will be critical to the development and fabrication of optimized insulating materials with alternative blowing agents. Polystyrene (PS) and polyurethane (PU) foam samples were investigated with the objective of determining quantitatively the amount of blowing agents in the gaseous phase and dissolved in the polymer phase, and to determine and monitor the distribution of the blowing agents in aged foams as a function of time and temperature. The concentrations of the gaseous blowing agents in the cells and dissolved in the solid were simultaneously and quantitatively measured by 19F MAS NMR spectroscopy. An unfaced 1-yr-old PS foam filled with CH3CF2Cl has about 13% of total HCFCs dissolved in the solid; while there is about 24% of HCFCs in the solid of a faced 3-mos-old PU foam filled with CH3CCl2F. The data from 19F NMR imaging demonstrate that the distributions of the blowing agents in an aged foam are quite uniform around the center part (2 cm away from any edge) of a foam board; however, a gradient in blowing agent concentration was found as a function of distance from the initial factory cut edge. The effective diffusion coefficients of the blowing agents can be directly calculated from the imaging data. Quantitative diffusion constants and activation barriers were determined. Additionally, a foam treated with a second blowing agent was monitored with chemical shift selective imaging and the diffusion of the second gas into the foam and the out-diffusion of the original gas were determined.

Synergic application of spectroscopic and theoretical methods to the chlorogenic acid structure elucidation

NASA Astrophysics Data System (ADS)

Marković, Svetlana; Tošović, Jelena; Dimitrić Marković, Jasmina M.

2016-07-01

Although chlorogenic acid (5-O-caffeoylquinic acid, 5CQA) is a dietary polyphenol known for its pharmacological and nutritional properties, its structural features have not been completely elucidated. This is the first study whose aim is to contribute to clarification of the 5CQA structure by comparing the experimental and simulated IR, Raman, 1H NMR, 13C NMR, and UV spectra. For this purpose, a comprehensive conformational analysis of 5CQA was performed to reveal its most stable conformations in the gas-state and solution (DMSO and methanol). The lowest-energy conformers were used to predict the spectra at two levels of theory: B3LYP-D3/and M06-2X/6-311+G(d,p) in combination with the CPCM solvation model. Both methods provide very good agreement between all experimental and simulated spectra, thus indicating correct arrangement of the atoms in the 5CQA molecule. The quinic moiety is characterized with directed hydrogen bonds, where the carboxylic hydrogen is not oriented towards the carbonyl oxygen of the carboxylic group, but towards the oxygen of the proximate hydroxyl group. In the gas-state the lowest-energy conformers are characterized with the O4sbnd H4 ⋯ O9‧ hydrogen bond, whereas in the solvated state the structures with the O4sbnd H4 ⋯ O10‧ hydrogen bond prevail. Knowing the fine structural details, i.e. the proper conformation of 5CQA, provides a solid base for all further investigations related to this compound.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deng, Xuchu; Hu, Mary; Wei, Xiaoliang

Understanding the solvation structures of electrolytes is important for developing nonaqueous redox flow batteries that hold considerable potential for future large scale energy storage systems. The utilization of an emerging ionic-derivative ferrocene compounds, ferrocenylmethyl dimethyl ethyl ammonium bis (triflyoromethanesulfonyl)imide (Fc1N112-TFSI), has recently overcome the issue of solubility in the supporting electrolyte. In this work, 13C1H and 17O NMR investigations were carried out using solvent. It was observed that the spectra of 13C experience changes of chemical shifts while those of 17O undergo line width broadening, indicating interactions between solute and solvent molecules

Synthesis, structural and spectral characterization of a novel NLO crystal N,N‧-diphenylguanidinium picrate: diacetone solvate

NASA Astrophysics Data System (ADS)

Shanmugavadivu, T.; Dhandapani, M.; Naveen, S.; Lokanath, N. K.

2017-09-01

An organic NLO active material N,N‧-diphenylguanidinium picrate: diacetone solvate (C13H14N3+. C6H2N3O7-. 2C3H6O) (DPGPD) was synthesized and single crystals were grown by slow evaporation-solution growth technique at room temperature. DPGPD crystallizes in monoclinic crystal system with noncentrosymmetric space group, Cc confirmed by single crystal X-ray diffraction analysis. The presence of various functional groups was identified from FT-IR spectral analysis and the proton transfer during the formation of compound was confirmed by NMR spectroscopic techniques. The thermal stability was investigated by TG/DTA analyses. Optical transmittance was measured by UV-Vis-NIR spectroscopy and band gap energy was calculated. Photoluminescence spectrum was used to explore its applicability towards laser diodes. Dielectric property of the material was ascertained at different temperatures and it is found that the grown crystal has higher dielectric constant in low frequencies. Photoconductivity study revealed that DPGPD exhibits positive photoconductivity. SHG property was found to be 0.6 times higher than that of KDP.

Calculating Water Thermodynamics in the Binding Site of Proteins - Applications of WaterMap to Drug Discovery.

PubMed

Cappel, Daniel; Sherman, Woody; Beuming, Thijs

2017-01-01

The ability to accurately characterize the solvation properties (water locations and thermodynamics) of biomolecules is of great importance to drug discovery. While crystallography, NMR, and other experimental techniques can assist in determining the structure of water networks in proteins and protein-ligand complexes, most water molecules are not fully resolved and accurately placed. Furthermore, understanding the energetic effects of solvation and desolvation on binding requires an analysis of the thermodynamic properties of solvent involved in the interaction between ligands and proteins. WaterMap is a molecular dynamics-based computational method that uses statistical mechanics to describe the thermodynamic properties (entropy, enthalpy, and free energy) of water molecules at the surface of proteins. This method can be used to assess the solvent contributions to ligand binding affinity and to guide lead optimization. In this review, we provide a comprehensive summary of published uses of WaterMap, including applications to lead optimization, virtual screening, selectivity analysis, ligand pose prediction, and druggability assessment. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Relativistic Zeroth-Order Regular Approximation Combined with Nonhybrid and Hybrid Density Functional Theory: Performance for NMR Indirect Nuclear Spin-Spin Coupling in Heavy Metal Compounds.

PubMed

Moncho, Salvador; Autschbach, Jochen

2010-01-12

A benchmark study for relativistic density functional calculations of NMR spin-spin coupling constants has been performed. The test set contained 47 complexes with heavy metal atoms (W, Pt, Hg, Tl, Pb) with a total of 88 coupling constants involving one or two heavy metal atoms. One-, two-, three-, and four-bond spin-spin couplings have been computed at different levels of theory (nonhybrid vs hybrid DFT, scalar vs two-component relativistic). The computational model was based on geometries fully optimized at the BP/TZP scalar relativistic zeroth-order regular approximation (ZORA) and the conductor-like screening model (COSMO) to include solvent effects. The NMR computations also employed the continuum solvent model. Computations in the gas phase were performed in order to assess the importance of the solvation model. The relative median deviations between various computational models and experiment were found to range between 13% and 21%, with the highest-level computational model (hybrid density functional computations including scalar plus spin-orbit relativistic effects, the COSMO solvent model, and a Gaussian finite-nucleus model) performing best.

Using low-field NMR to infer the physical properties of glassy oligosaccharide/water mixtures.

PubMed

Aeberhardt, Kasia; Bui, Quang D; Normand, Valéry

2007-03-01

Low-field NMR (LF-NMR) is usually used as an analytical technique, for instance, to determine water and oil contents. For this application, no attempt is made to understand the physical origin of the data. Here we build a physical model to explain the five fit parameters of the conventional free induction decay (FID) for glassy oligosaccharide/water mixtures. The amplitudes of the signals from low-mobility and high-mobility protons correspond to the density of oligosaccharide protons and water protons, respectively. The relaxation time of the high-mobility protons is described using a statistical model for the probability that oligosaccharide hydroxyl groups form multiple hydrogen bonds. The variation of energy of the hydrogen bond is calculated from the average bond distance and the average angle contribution. Applying the model to experimental data shows that hydrogen atoms screen the water oxygen atoms when two water molecules solvate a single hydroxyl group. Furthermore, the relaxation time of the oligosaccharide protons is independent of its molecular weight and the water content. Finally, inversion of the FID using the inverse Laplace transform gives the continuous spectrum of relaxation times, which is a fingerprint of the oligosaccharide.

Producing >60,000-fold room-temperature 89Y NMR signal enhancement

NASA Astrophysics Data System (ADS)

Lumata, Lloyd; Jindal, Ashish; Merritt, Matthew; Malloy, Craig; Sherry, A. Dean; Kovacs, Zoltan

2011-03-01

89 Y in chelated form is potentially valuable in medical imaging because its chemical shift is sensitive to local factors in tumors such as pH. However, 89 Y has a low gyromagnetic ratio γn thus its NMR signal is hampered by low thermal polarization. Here we show that we can enhance the room-temperature NMR signal of 89 Y up to 65,000 times the thermal signal, which corresponds to 10 % nuclear polarization, via fast dissolution dynamic nuclear polarization (DNP). The relatively long spin-lattice relaxation time T1 (~ 500 s) of 89 Y translates to a long polarization lifetime. The 89 Y NMR enhancement is optimized by varying the glassing matrices and paramagnetic agents as well as doping the samples with a gadolinium relaxation agent. Co-polarization of 89 Y-DOTA with a 13 C sample shows that both nuclear spin species acquire the same spin temperature Ts , consistent with thermal mixing mechanism of DNP. The high room-temperature NMR signal enhancement places 89 Y, one of the most challenging nuclei to detect by NMR, in the list of viable magnetic resonance imaging (MRI) agents when hyperpolarized under optimized conditions. This work is supported in part by the National Institutes of Health grant numbers 1R21EB009147-01 and RR02584.

Nuclear magnetic resonance study of Gd-based nanoparticles to tag boron compounds in boron neutron capture therapy

NASA Astrophysics Data System (ADS)

Corti, M.; Bonora, M.; Borsa, F.; Bortolussi, S.; Protti, N.; Santoro, D.; Stella, S.; Altieri, S.; Zonta, C.; Clerici, A. M.; Cansolino, L.; Ferrari, C.; Dionigi, P.; Porta, A.; Zanoni, G.; Vidari, G.

2011-04-01

We report the investigation of new organic complexes containing a magnetic moment (Gd-based molecular nanomagnets), which can serve the double purpose of acting as boron neutron capture therapy (BNCT) agents, and at the same time act as contrast agents to detect the molecule in the tissue by a proton magnetic resonance imaging (MRI). We also explore the possibility of monitoring the concentration of the BNCT agent directly via proton and boron NMR relaxation. The absorption of 10B-enriched molecules inside tumoral liver tissues has been shown by NMR measurements and confirmed by α spectroscopy. A new molecular Gd-tagged nanomagnet and BNCT agent (GdBPA) has been synthesized and characterized measuring its relaxivity R1 between 10 kHz and 66 MHz, and its use as a contrast agent in MRI has been demonstrated. The NMR-based evidence of the absorption of GdBPA into living tumoral cells is also shown.

Nuclear Magnetic Resonance Technology for Medical Studies.

ERIC Educational Resources Information Center

Budinger, Thomas F.; Lauterbur, Paul C.

1984-01-01

Reports on the status of nuclear magnetic resonance (NMR) from theoretical and clinical perspectives, reviewing NMR theory and relaxation parameters relevant to NMR imaging. Also reviews literature related to modern imaging strategies, signal-to-noise ratio, contrast agents, in vivo spectroscopy, spectroscopic imaging, clinical applications, and…

Evidence for cis Amide Bonds in Peptoid Nanosheets.

PubMed

Hudson, Benjamin C; Battigelli, Alessia; Connolly, Michael D; Edison, John; Spencer, Ryan K; Whitelam, Stephen; Zuckermann, Ronald N; Paravastu, Anant K

2018-05-17

Peptoid nanosheets are supramolecular protein-mimetic materials that form from amphiphilic polypeptoids with aromatic and ionic side chains. Nanosheets have been studied at the nanometer scale, but the molecular structure has been difficult to probe. We report the use of 13 C- 13 C dipolar recoupling solid-state NMR measurements to reveal the configuration of backbone amide bonds selected by 13 C isotopic labeling of adjacent α-carbons. Measurements on the same molecules in the amorphous state and in nanosheets revealed that amide bonds in the center of the amino block of peptoid (NaeNpe) 7 -(NceNpe) 7 (B28) favor the trans configuration in the amorphous state and the cis configuration in the nanosheet. This unexpected result contrasts with previous NMR and theoretical studies of short solvated peptoids. Furthermore, examination of the amide bond at the junction of the two charged blocks within B28 revealed a mixture of both cis and trans configurational states, consistent with the previously predicted brickwork-like intermolecular organization.

Synthesis, crystal structure, and spectral studies of 10-(2-Benzothiazolylazo)-9-phenanthrol

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davydov, V. V.; Sokol, V. I.; Polyanskaya, N. A.

2012-03-15

10-(2-Benzothiazolylazo)-9-phenanthrol (L) is prepared by a reaction of 2-hydrazinobenzothiazol with 9,10-phenanthrenequinone. The crystal and molecular structure of the L{center_dot}CHCl{sub 3} solvate is determined by X-ray diffraction. The data of the X-ray diffraction study, as well as IR, {sup 1}H NMR, and electronic absorption spectra, indicate that in the crystal state and solutions the L molecule exists in the form of a quinohydrazone tautomer (b) (s-trans, cis) stabilized by the intramolecular N{sub 2}-HN{sub 2} Horizontal-Ellipsis O1 hydrogen bond. The 'mobile' H atom is located at the N2 atom of the azo group. The benzothiazolyl and phenanthrenequinone fragments are nearly coplanar. Spectroscopicmore » criteria for the state of L in various media are determined based on the data of IR, {sup 1}H NMR, and electronic absorption spectroscopy and the results of the Pariser-Parr-Pople quantum-chemical calculations.« less

Polymorphs of Theophylline Characterized by DNP Enhanced Solid-State NMR

PubMed Central

2015-01-01

We show how dynamic nuclear polarization (DNP) enhanced solid-state NMR spectroscopy can be used to characterize polymorphs and solvates of organic solids. We applied DNP to three polymorphs and one hydrated form of the asthma drug molecule theophylline. For some forms of theophylline, sample grinding and impregnation with the radical-containing solution, which are necessary to prepare the samples for DNP, were found to induce polymorphic transitions or desolvation between some forms. We present protocols for sample preparation for solid-state magic-angle spinning (MAS) DNP experiments that avoid the polymorphic phase transitions in theophylline. These protocols include cryogrinding, grinding under inert atmosphere, and the appropriate choice of the impregnating liquid. By applying these procedures, we subsequently demonstrate that two-dimensional correlation experiments, such as 1H–13C and 1H–15N HETCOR or 13C–13C INADEQUATE, can be obtained at natural isotopic abundance in reasonable times, thus enabling more advanced structural characterization of polymorphs. PMID:26393368

1H NMR analysis of complexation of hydrotropic agents nicotinamide and caffeine with aromatic biologically active molecules in aqueous solution

NASA Astrophysics Data System (ADS)

Lantushenko, Anastasia O.; Mukhina, Yulia V.; Veselkov, Kyrill A.; Davies, David B.; Veselkov, Alexei N.

2004-07-01

NMR spectroscopy has been used to elucidate the molecular mechanism of solubilization action of hydrotropic agents nicotinamide (NA) and caffeine (CAF). Hetero-association of NA with riboflavine-mononucleotide (FMN) and CAF with low soluble in aqueous solution synthetic analogue of antibiotic actinomycin D, actinocyl-bis-(3-dimethylaminopropyl) amine (Actill), has been investigated by 500 MHz 1H NMR spectroscopy. Concentration and temperature dependences of proton chemical shifts have been analysed in terms of a statistical-thermodynamic model of indefinite self- and heteroassociation of aromatic molecules. The obtained results enable to conclude that NA-FMN and CAF-Actill intermolecular complexes are mainly stabilized by the stacking interactions of the aromatic chromophores. Hetero-association of the investigated molecules plays an important role in solubilization of aromatic drugs by hydrotropic agents nicotinamide and caffeine.

Investigating the Hydrolysis Reactions of a Chemical Warfare Agent Surrogate. A Systematic Study using 1H, 13C, 17O, 19F, 31P, and 35Cl NMR Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alam, Todd M.; Wilson, Brendan W.

2015-07-24

During the summer of 2015, I participated in the DHS HS-STEM fellowship at Sandia National Laboratories (SNL, NM) under the supervision of Dr. Todd M. Alam in his Nuclear Magnetic Resonance (NMR) Spectroscopy research group. While with the group, my main project involved pursing various hydrolysis reactions with Diethyl Chlorophosphate (DECP), a surrogate for the agent Sarin (GB). Specifically, I performed different hydrolysis reactions, monitored and tracked the different phosphorous containing species using phosphorous ( 31P) NMR spectroscopy. With the data collected, I performed kinetics studies mapping the rates of DECP hydrolysis. I also used the NMR of different nucleimore » such as 1H, 13C, 17O, and 35Cl to help understand the complexity of the reactions that take place. Finally, my last task at SNL was to work with Insensitive Nuclei Enhanced by Polarization Transfer (INEPT) NMR Spectroscopy optimizing conditions for 19F- 31P filtering NMR experiments.« less

Demetalation of Fe, Mn, and Cu chelates and complexes: application to the NMR analysis of micronutrient fertilizers.

PubMed

López-Rayo, Sandra; Lucena, Juan J; Laghi, Luca; Cremonini, Mauro A

2011-12-28

The application of nuclear magnetic resonance (NMR) for the quality control of fertilizers based on Fe(3+), Mn(2+), and Cu(2+) chelates and complexes is precluded by the strong paramagnetism of metals. Recently, a method based on the use of ferrocyanide has been described to remove iron from commercial iron chelates based on the o,o-EDDHA [ethylenediamine-N,N'bis(2-hydroxyphenylacetic)acid] chelating agent for their analysis and quantification by NMR. The present work extended that procedure to other paramagnetic ions, manganese and copper, and other chelating, EDTA (ethylenediaminetetraacetic acid), IDHA [N-(1,2-dicarboxyethyl)-d,l-aspartic acid], and complexing agents, gluconate and heptagluconate. Results showed that the removal of the paramagnetic ions was complete, allowing us to obtain (1)H NMR spectra characterized by narrow peaks. The quantification of the ligands by NMR and high-performance liquid chromatography showed that their complete recovery was granted. The NMR analysis enabled detection and quantification of unknown impurities without the need of pure compounds as internal standards.

Adapting Poisson-Boltzmann to the self-consistent mean field theory: Application to protein side-chain modeling

NASA Astrophysics Data System (ADS)

Koehl, Patrice; Orland, Henri; Delarue, Marc

2011-08-01

We present an extension of the self-consistent mean field theory for protein side-chain modeling in which solvation effects are included based on the Poisson-Boltzmann (PB) theory. In this approach, the protein is represented with multiple copies of its side chains. Each copy is assigned a weight that is refined iteratively based on the mean field energy generated by the rest of the protein, until self-consistency is reached. At each cycle, the variational free energy of the multi-copy system is computed; this free energy includes the internal energy of the protein that accounts for vdW and electrostatics interactions and a solvation free energy term that is computed using the PB equation. The method converges in only a few cycles and takes only minutes of central processing unit time on a commodity personal computer. The predicted conformation of each residue is then set to be its copy with the highest weight after convergence. We have tested this method on a database of hundred highly refined NMR structures to circumvent the problems of crystal packing inherent to x-ray structures. The use of the PB-derived solvation free energy significantly improves prediction accuracy for surface side chains. For example, the prediction accuracies for χ1 for surface cysteine, serine, and threonine residues improve from 68%, 35%, and 43% to 80%, 53%, and 57%, respectively. A comparison with other side-chain prediction algorithms demonstrates that our approach is consistently better in predicting the conformations of exposed side chains.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deng, Xuchu; Hu, Mary Y.; Wei, Xiaoliang

Understanding the solvation structures of electrolytes should prove conducive for the development of nonaqueous redox flow batteries that hold considerable potential for future large scale energy storage systems. The utilization of an emerging ionic-derivatived ferrocene compound, ferrocenylmethyl dimethyl ethyl ammonium bis(trifluoromethanesulfonyl)imide (Fc1N112-TFSI), has recently overcome the issue of solubility in the supporting electrolyte. In this work, 13C, 1H and 17O NMR investigations were carried out using electrolyte solutions consisting of Fc1N112-TFSI as the solute and the mixed alkyl carbonate as the solvent. It was observed that the spectra of 13C experience changes of chemical shifts while those of 17O undergomore » linewidth broadening, indicating interactions between solute and solvent molecules. Quantum chemistry calculations of both molecular structures and chemical shifts (13C, 1H and 17O) are performed for interpreting experimental results and of understanding the detailed solvation structures and molecular dynamics. The results indicate that Fc1N112-TFSI is dissociated at varying degrees in mixed solvent depending on concentrations. Solvent molecules encircle Fc1N112 and TFSI respectively as solvation shells, rapidly exchanging with both bulk solvent and TFSI. Additionally, the solvent with high dielectric constant is more capable of dissociating Fc1N112-TFSI molecules compared with those with low dielectric constant. At saturated concentration, contact ion pairs are formed and the solvent molecules are interacting with the Fc rings rather than interacting with the ionic pendant arm of Fc1N112-TFSI. These studies will contribute to the development of nonaqueous electrolytes of storage systems.« less

Structure of dimethylphenyl betaine hydrochloride studied by X-ray diffraction, DFT calculation, NMR and FTIR spectra

NASA Astrophysics Data System (ADS)

Szafran, M.; Katrusiak, A.; Dega-Szafran, Z.; Kowalczyk, I.

2013-01-01

The structure of dimethylphenyl betaine hydrochloride (1) has been studied by X-ray diffraction, DFT calculations, NMR and FTIR spectra. The crystals are monoclinic, space group P21/c. In the crystal, the Cl- anion is connected with protonated betaine through the O-H⋯Cl- hydrogen bond of 2.943(2) Å. The structures in the gas phase (2) and water solution (3) have been optimized by the B3LYP/6-311++G(d,p) approach and the geometrical results have been compared with the X-ray data of 1. The FTIR spectrum of the solid compound is consistent with the X-ray results. The probable assignments of the anharmonic experimental vibrational frequencies of the investigated chloride (1) based on the calculated harmonic frequencies in water solution (3) are proposed. The correlations between the experimental 1H and 13C NMR chemical shifts (δexp) of 1 in D2O and the magnetic isotropic shielding constants (σcalc) calculated by the GIAO/B3LYP/6-311G++(d,p) approach, using the screening solvation model (COSMO), δexp = a + b σcalc, for optimized molecule 3 in water solution are linear and correctly reproduce the experimental chemical shifts.

Comparative Investigation of the Ionicity of Aprotic and Protic Ionic Liquids in Molecular Solvents by using Conductometry and NMR Spectroscopy.

PubMed

Thawarkar, Sachin; Khupse, Nageshwar D; Kumar, Anil

2016-04-04

Electrical conductivity (σ), viscosity (η), and self-diffusion coefficient (D) measurements of binary mixtures of aprotic and protic imidazolium-based ionic liquids with water, dimethyl sulfoxide, and ethylene glycol were measured from 293.15 to 323.15 K. The temperature dependence study reveals typical Arrhenius behavior. The ionicities of aprotic ionic liquids were observed to be higher than those of protic ionic liquids in these solvents. The aprotic ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate, [bmIm][BF4 ], displays 100 % ionicity in both water and ethylene glycol. The protic ionic liquids in both water and ethylene glycol are classed as good ionic candidates, whereas in DMSO they are classed as having a poor ionic nature. The solvation dynamics of the ionic species of the ionic liquids are illustrated on the basis of the (1) H NMR chemical shifts of the ionic liquids. The self-diffusion coefficients D of the cation and anion of [HmIm][CH3 COO] in D2 O and in [D6 ]DMSO are determined by using (1) H nuclei with pulsed field gradient spin-echo NMR spectroscopy. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spectral analysis, vibrational assignments, NBO analysis, NMR, UV-Vis, hyperpolarizability analysis of 2-aminofluorene by density functional theory.

PubMed

Jone Pradeepa, S; Sundaraganesan, N

2014-05-05

In this present investigation, the collective experimental and theoretical study on molecular structure, vibrational analysis and NBO analysis has been reported for 2-aminofluorene. FT-IR spectrum was recorded in the range 4000-400 cm(-1). FT-Raman spectrum was recorded in the range 4000-50 cm(-1). The molecular geometry, vibrational spectra, and natural bond orbital analysis (NBO) were calculated for 2-aminofluorene using Density Functional Theory (DFT) based on B3LYP/6-31G(d,p) model chemistry. (13)C and (1)H NMR chemical shifts of 2-aminofluorene were calculated using GIAO method. The computed vibrational and NMR spectra were compared with the experimental results. The total energy distribution (TED) was derived to deepen the understanding of different modes of vibrations contributed by respective wavenumber. The experimental UV-Vis spectra was recorded in the region of 400-200 nm and correlated with simulated spectra by suitably solvated B3LYP/6-31G(d,p) model. The HOMO-LUMO energies were measured with time dependent DFT approach. The nonlinearity of the title compound was confirmed by hyperpolarizabilty examination. Using theoretical calculation Molecular Electrostatic Potential (MEP) was investigated. Copyright © 2014 Elsevier B.V. All rights reserved.

Impact of various lipophilic substituents on ruthenium(II), rhodium(III) and iridium(III) salicylaldimine-based complexes: synthesis, in vitro cytotoxicity studies and DNA interactions.

PubMed

Cassells, Irwin; Stringer, Tameryn; Hutton, Alan T; Prince, Sharon; Smith, Gregory S

2018-05-30

A series of bidentate salicylaldimine ligands was prepared and reacted with either [RuCl(µ-Cl)(p-cymene)] 2 , [RhCl(µ-Cl)(Cp*)] 2 or [IrCl(µ-Cl)(Cp*)] 2 . All of the compounds were characterised using an array of spectroscopic and analytical techniques, namely, nuclear magnetic resonance (NMR) spectroscopy, infrared (IR) spectroscopy and mass spectrometry. Single crystal X-ray diffraction (XRD) was used to confirm the bidentate coordination mode of the salicylaldimine ligand to the metal centre. The platinum group metal (PGM) complexes were screened against the MCF7 breast cancer cell line. The ruthenium and iridium salicylaldimine complexes showed comparable or greater cytotoxicity than cisplatin against the MCF7 cancer cells, as well as greater cytotoxicity than their rhodium counterparts. Three of the salicylaldimine complexes showed potent activity in the range 18-21 µM. Two of these complexes had a greater affinity for cancerous cells than for CHO non-cancerous cells (SI > 4). Preliminary mechanistic studies suggest that the ruthenium complexes undergo solvation prior to 5'-GMP binding, whereas the iridium complexes were inert to the solvation process.

Synthesis, thermal analyses, characterization and biological evaluation of new enrofloxacin vanadium(V) solvates(L) (L = An, DMF, Py, Et3N and o-Tol)

NASA Astrophysics Data System (ADS)

Zordok, Wael A.; Sadeek, Sadeek A.

2016-09-01

Five metal complexes of antibacterial agent enrofloxacin with vanadium(V) in the presence of aniline, pyridine, orthotolidine and triethylamine as nitrogen donor molecules and dimethylformamide as oxygen donor molecule have been prepared and characterized with physicochemical and diverse spectroscopic techniques (IR, UV-Vis. and 1H NMR spectroscopes) as well as thermal analysis. The deprotonated enrofloxacin complexes of V(V) were isolated as solids with the general formulas; [VO(Enr)2DMF]Cl·5H2O, [VO(Enr)2An]Cl·2H2O, [VO(Enr)2o-Tol]Cl·H2O, [VO(Enr)2Py]Cl·4H2O and [VO(Enr)2Et3N]Cl·6H2O. The prepared complexes are formed with a metal to ligand ratios as 1:2:1 for all complexes. The lowest energy model structure of each complex has been proposed by using the density functional theory (DFT) at the B3LYP/CEP-31G level of theory. The energy barrier for the pyridine complex greater than others complexes while, Et3N complex has lower value. The ligand and their metal complexes were also evaluated for their antibacterial activity against three Gram (+ve) and three Gram (-ve) microorganisms.

Dynamic NMR of Intramolecular Exchange Processes in EDTA Complexes of Sc[superscript 3+], Y[superscript 3+], and La[superscript 3+

ERIC Educational Resources Information Center

Ba, Yong; Han, Steven; Ni, Lily; Su, Tony; Garcia, Andres

2006-01-01

Dynamic NMR makes use of the effect of chemical exchanges on NMR spectra to study kinetics and thermodynamics. An advanced physical chemistry lab experiment was developed to study the intramolecular exchange processes of EDTA (the disodium salt of ethylenediaminetetraacetic acid) metal complexes. EDTA is an important chelating agent, used in…

Structural characterization of chemical warfare agent degradation products in decontamination solutions with proton band-selective (1)H-(31)P NMR spectroscopy.

PubMed

Koskela, Harri; Hakala, Ullastiina; Vanninen, Paula

2010-06-15

Decontamination solutions, which are usually composed of strong alkaline chemicals, are used for efficient detoxification of chemical warfare agents (CWAs). The analysis of CWA degradation products directly in decontamination solutions is challenging due to the nature of the matrix. Furthermore, occasionally an unforeseen degradation pathway can result in degradation products which could be eluded to in standard analyses. Here, we present the results of the application of proton band-selective (1)H-(31)P NMR spectroscopy, i.e., band-selective 1D (1)H-(31)P heteronuclear single quantum coherence (HSQC) and band-selective 2D (1)H-(31)P HSQC-total correlation spectroscopy (TOCSY), for ester side chain characterization of organophosphorus nerve agent degradation products in decontamination solutions. The viability of the approach is demonstrated with a test mixture of typical degradation products of nerve agents sarin, soman, and VX. The proton band-selective (1)H-(31)P NMR spectroscopy is also applied in characterization of unusual degradation products of VX in GDS 2000 solution.

Dynamic Nuclear Polarization NMR in Human Cells Using Fluorescent Polarizing Agents.

PubMed

Albert, Brice J; Gao, Chukun; Sesti, Erika L; Saliba, Edward P; Alaniva, Nicholas; Scott, Faith J; Sigurdsson, Snorri Th; Barnes, Alexander B

2018-06-20

Solid-state nuclear magnetic resonance (NMR) enables atomic resolution characterization of molecular structure and dynamics within complex heterogeneous samples, but it is typically insensitive. Dynamic nuclear polarization (DNP) increases NMR signal intensity by orders of magnitude and can be performed in combination with magic angle spinning (MAS) for sensitive, high-resolution spectroscopy. Here we report MAS DNP experiments, for the first time, within intact human cells with >40-fold DNP enhancement and a sample temperature below 6 K. In addition to cryogenic MAS results below 6 K, we also show in-cell DNP enhancements of 57-fold at 90 K. In-cell DNP is demonstrated using biradicals and sterically-shielded monoradicals as polarizing agents. A novel trimodal polarizing agent is introduced for DNP, which contains a nitroxide biradical, a targeting peptide for cell penetration, and a fluorophore for subcellular localization with confocal microscopy. The fluorescent polarizing agent provides in-cell DNP enhancements of 63-fold at a concentration of 2.7 mM. These experiments pave the way for structural characterization of biomolecules in an endogenous cellular context.

NMR-Fragment Based Virtual Screening: A Brief Overview.

PubMed

Singh, Meenakshi; Tam, Benjamin; Akabayov, Barak

2018-01-25

Fragment-based drug discovery (FBDD) using NMR has become a central approach over the last twenty years for development of small molecule inhibitors against biological macromolecules, to control a variety of cellular processes. Yet, several considerations should be taken into account for obtaining a therapeutically relevant agent. In this review, we aim to list the considerations that make NMR fragment screening a successful process for yielding potent inhibitors. Factors that may govern the competence of NMR in fragment based drug discovery are discussed, as well as later steps that involve optimization of hits obtained by NMR-FBDD.

New insights into the coordination chemistry of Schiff bases derived from amino acids: Planar [Ni4] complexes with tyrosine side-chains

NASA Astrophysics Data System (ADS)

Muche, Simon; Hołyńska, Małgorzata

2017-08-01

Structure and properties of a rare metal complex of the chiral Schiff base ligand derived from ortho-vanillin and L-tyrosine are presented. This study is a continuation of research on ligands containing biologically compatible moieties. The ligand is also fully characterized in form of a sodium salt, in particular in solution, for the first time. The metal complex contains a unique bowl-shaped [Ni4] core. Its structure is investigated both in solution (ESI-MS, NMR) and in solid state (X-ray diffraction studies). Under certain conditions the complex can be isolated as crystalline DMF solvate which is studied in solid state.

Comparison of experimental and DFT-calculated NMR chemical shifts of 2-amino and 2-hydroxyl substituted phenyl benzimidazoles, benzoxazoles and benzothiazoles in four solvents using the IEF-PCM solvation model.

PubMed

Pierens, Gregory K; Venkatachalam, T K; Reutens, David C

2016-04-01

A comparative study of experimental and calculated NMR chemical shifts of six compounds comprising 2-amino and 2-hydroxy phenyl benzoxazoles/benzothiazoles/benzimidazoles in four solvents is reported. The benzimidazoles showed interesting spectral characteristics, which are discussed. The proton and carbon chemical shifts were similar for all solvents. The largest chemical shift deviations were observed in benzene. The chemical shifts were calculated with density functional theory using a suite of four functionals and basis set combinations. The calculated chemical shifts revealed a good match to the experimentally observed values in most of the solvents. The mean absolute error was used as the primary metric. The use of an additional metric is suggested, which is based on the order of chemical shifts. The DP4 probability measures were also used to compare the experimental and calculated chemical shifts for each compound in the four solvents. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Solution-state structure and affinities of cyclodextrin: Fentanyl complexes by nuclear magnetic resonance spectroscopy and molecular dynamics simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mayer, Brian P.; Kennedy, Daniel J.; Lau, Edmond Y.

Cyclodextrins (CDs) are investigated for their ability to form inclusion complexes with the analgesic fentanyl and three similar molecules: acetylfentanyl, thiofentanyl, and acetylthiofentanyl. Stoichiometry, binding strength, and complex structure are revealed through nuclear magnetic resonance (NMR) techniques and discussed in terms of molecular dynamics (MD) simulations. It was found that β-cyclodextrin is generally capable of forming the strongest complexes with the fentanyl panel. Two-dimensional NMR data and computational chemical calculations are used to derive solution-state structures of the complexes. Binding of the fentanyls to the CDs occurs at the amide phenyl ring, leaving the majority of the molecule solvated bymore » water, an observation common to all four fentanyls. This finding suggests a universal binding behavior, as the vast majority of previously synthesized fentanyl analogues contain this structural moiety. Furthermore, this baseline study serves as the most complete work on CD:fentanyl complexes to date and provides the insights into strategies for producing future generations of designer cyclodextrins capable of stronger and more selective complexation of fentanyl and its analogues.« less

Solution-state structure and affinities of cyclodextrin: Fentanyl complexes by nuclear magnetic resonance spectroscopy and molecular dynamics simulation

DOE PAGES

Mayer, Brian P.; Kennedy, Daniel J.; Lau, Edmond Y.; ...

2016-02-04

Cyclodextrins (CDs) are investigated for their ability to form inclusion complexes with the analgesic fentanyl and three similar molecules: acetylfentanyl, thiofentanyl, and acetylthiofentanyl. Stoichiometry, binding strength, and complex structure are revealed through nuclear magnetic resonance (NMR) techniques and discussed in terms of molecular dynamics (MD) simulations. It was found that β-cyclodextrin is generally capable of forming the strongest complexes with the fentanyl panel. Two-dimensional NMR data and computational chemical calculations are used to derive solution-state structures of the complexes. Binding of the fentanyls to the CDs occurs at the amide phenyl ring, leaving the majority of the molecule solvated bymore » water, an observation common to all four fentanyls. This finding suggests a universal binding behavior, as the vast majority of previously synthesized fentanyl analogues contain this structural moiety. Furthermore, this baseline study serves as the most complete work on CD:fentanyl complexes to date and provides the insights into strategies for producing future generations of designer cyclodextrins capable of stronger and more selective complexation of fentanyl and its analogues.« less

Reduced native state stability in crowded cellular environment due to protein-protein interactions.

PubMed

Harada, Ryuhei; Tochio, Naoya; Kigawa, Takanori; Sugita, Yuji; Feig, Michael

2013-03-06

The effect of cellular crowding environments on protein structure and stability is a key issue in molecular and cellular biology. The classical view of crowding emphasizes the volume exclusion effect that generally favors compact, native states. Here, results from molecular dynamics simulations and NMR experiments show that protein crowders may destabilize native states via protein-protein interactions. In the model system considered here, mixtures of villin head piece and protein G at high concentrations, villin structures become increasingly destabilized upon increasing crowder concentrations. The denatured states observed in the simulation involve partial unfolding as well as more subtle conformational shifts. The unfolded states remain overall compact and only partially overlap with unfolded ensembles at high temperature and in the presence of urea. NMR measurements on the same systems confirm structural changes upon crowding based on changes of chemical shifts relative to dilute conditions. An analysis of protein-protein interactions and energetic aspects suggests the importance of enthalpic and solvation contributions to the crowding free energies that challenge an entropic-centered view of crowding effects.

Spirocyclic character of ixazomib citrate revealed by comprehensive XRD, NMR and DFT study

NASA Astrophysics Data System (ADS)

Skorepova, Eliska; Čerňa, Igor; Vlasáková, Růžena; Zvoníček, Vít; Tkadlecová, Marcela; Dušek, Michal

2017-11-01

Ixazomib citrate is a very recently approved anti-cancer drug. Until now, to the best of our knowledge, no one has been able to solve any crystal structures of this compound. In this work, we present the crystal structures of two isostructural solvates of ixazomib citrate. In all currently available literature, the molecule is characterized as containing a single optically active carbon atom and a borate cycle formed when ixazomib is reacted with citric acid to form a stabilized ixazomib citrate that can be administered orally. However, the crystal structures revealed that none of the up-to-date presented structural formulas of ixazomib citrate are fully accurate. In addition to the citrate ring, another 5-membered ring is formed. These two rings are connected by the boron atom, making this compound a spirocyclic borate. By spirocyclization, the boron atom becomes tetrahedral and therefore optically active. In the crystal structures, ixazomib citrate was found to be in forms of two RR and RS stereoisomers. The results are supported by solid-state and solution NMR and DFT quantum mechanical calculations.

Folding of the 25 residue Abeta(12-36) peptide in TFE/water: temperature-dependent transition from a funneled free-energy landscape to a rugged one.

PubMed

Kamiya, Narutoshi; Mitomo, Daisuke; Shea, Joan-Emma; Higo, Junichi

2007-05-17

The free-energy landscape of the Alzheimer beta-amyloid peptide Abeta(12-36) in a 40% (v/v) 2,2,2-trifluoroethanol (TFE)/water solution was determined by using multicanonical molecular dynamics simulations. Simulations using this enhanced conformational sampling technique were initiated from a random unfolded polypeptide conformation. Our simulations reliably folded the peptide to the experimental NMR structure, which consists of two linked helices. The shape of the free energy landscape for folding was found to be strongly dependent on temperature: Above 325 K, the overall shape was funnel-like, with the bottom of the funnel coinciding exactly with the NMR structure. Below 325 K, on the other hand, the landscape became increasingly rugged, with the emergence of new conformational clusters connected by low free-energy pathways. Finally, our simulations reveal that water and TFE solvate the polypeptide in different ways: The hydrogen bond formation between TFE and Abeta was enhanced with decreasing temperature, while that between water and Abeta was depressed.

Solvation Dynamics in Different Phases of the Lyotropic Liquid Crystalline System.

PubMed

Roy, Bibhisan; Satpathi, Sagar; Gavvala, Krishna; Koninti, Raj Kumar; Hazra, Partha

2015-09-03

Reverse hexagonal (HII) liquid crystalline material based on glycerol monooleate (GMO) is considered as a potential carrier for drugs and other important biomolecules due to its thermotropic phase change and excellent morphology. In this work, the dynamics of encapsulated water, which plays important role in stabilization and formation of reverse hexagonal mesophase, has been investigated by time dependent Stokes shift method using Coumarin-343 as a solvation probe. The formation of the reverse hexagonal mesophase (HII) and transformation to the L2 phase have been monitored using small-angle X-ray scattering and polarized light microscopy experiments. REES studies suggest the existence of different polar regions in both HII and L2 systems. The solvation dynamics study inside the reverse hexagonal (HII) phase reveals the existence of two different types of water molecules exhibiting dynamics on a 120-900 ps time scale. The estimated diffusion coefficients of both types of water molecules obtained from the observed dynamics are in good agreement with the measured diffusion coefficient collected from the NMR study. The calculated activation energy is found to be 2.05 kcal/mol, which is associated with coupled rotational-translational water relaxation dynamics upon the transition from "bound" to "quasi-free" state. The observed ∼2 ns faster dynamics of the L2 phase compared to the HII phase may be associated with both the phase transformation as well as thermotropic effect on the relaxation process. Microviscosities calculated from time-resolved anisotropy studies infer that the interface is almost ∼22 times higher viscous than the central part of the cylinder. Overall, our results reveal the unique dynamical features of water inside the cylinder of reverse hexagonal and inverse micellar phases.

How well do force fields capture the strength of salt bridges in proteins?

PubMed Central

Ahmed, Mustapha Carab; Papaleo, Elena

2018-01-01

Salt bridges form between pairs of ionisable residues in close proximity and are important interactions in proteins. While salt bridges are known to be important both for protein stability, recognition and regulation, we still do not have fully accurate predictive models to assess the energetic contributions of salt bridges. Molecular dynamics simulation is one technique that may be used study the complex relationship between structure, solvation and energetics of salt bridges, but the accuracy of such simulations depends on the force field used. We have used NMR data on the B1 domain of protein G (GB1) to benchmark molecular dynamics simulations. Using enhanced sampling simulations, we calculated the free energy of forming a salt bridge for three possible lysine-carboxylate ionic interactions in GB1. The NMR experiments showed that these interactions are either not formed, or only very weakly formed, in solution. In contrast, we show that the stability of the salt bridges is overestimated, to different extents, in simulations of GB1 using seven out of eight commonly used combinations of fixed charge force fields and water models. We also find that the Amber ff15ipq force field gives rise to weaker salt bridges in good agreement with the NMR experiments. We conclude that many force fields appear to overstabilize these ionic interactions, and that further work may be needed to refine our ability to model quantitatively the stability of salt bridges through simulations. We also suggest that comparisons between NMR experiments and simulations will play a crucial role in furthering our understanding of this important interaction.

Structural Characterization of Methanol Substituted Lanthanum Halides

PubMed Central

Boyle, Timothy J.; Ottley, Leigh Anna M.; Alam, Todd M.; Rodriguez, Mark A.; Yang, Pin; Mcintyre, Sarah K.

2010-01-01

The first study into the alcohol solvation of lanthanum halide [LaX3] derivatives as a means to lower the processing temperature for the production of the LaBr3 scintillators was undertaken using methanol (MeOH). Initially the de-hydration of {[La(µ-Br)(H2O)7](Br)2}2 (1) was investigated through the simple room temperature dissolution of 1 in MeOH. The mixed solvate monomeric [La(H2O)7(MeOH)2](Br)3 (2) compound was isolated where the La metal center retains its original 9-coordination through the binding of two additional MeOH solvents but necessitates the transfer of the innersphere Br to the outersphere. In an attempt to in situ dry the reaction mixture of 1 in MeOH over CaH2, crystals of [Ca(MeOH)6](Br)2 (3) were isolated. Compound 1 dissolved in MeOH at reflux temperatures led to the isolation of an unusual arrangement identified as the salt derivative {[LaBr2.75•5.25(MeOH)]+0.25 [LaBr3.25•4.75(MeOH)]−0.25} (4). The fully substituted species was ultimately isolated through the dissolution of dried LaBr3 in MeOH forming the 8-coordinated [LaBr3(MeOH)5] (5) complex. It was determined that the concentration of the crystallization solution directed the structure isolated (4 concentrated; 5 dilute) The other LaX3 derivatives were isolated as [(MeOH)4(Cl)2La(µ-Cl)]2 (6) and [La(MeOH)9](I)3•MeOH (7). Beryllium Dome XRD analysis indicated that the bulk material for 5 appear to have multiple solvated species, 6 is consistent with the single crystal, and 7 was too broad to elucidate structural aspects. Multinuclear NMR (139La) indicated that these compounds do not retain their structure in MeOD. TGA/DTA data revealed that the de-solvation temperatures of the MeOH derivatives 4 – 6 were slightly higher in comparison to their hydrated counterparts. PMID:20514349

Unscrambling micro-solvation of -COOH and -NH groups in neat dimethyl sulfoxide: insights from 1H-NMR spectroscopy and computational studies.

PubMed

Takis, Panteleimon G; Papavasileiou, Konstantinos D; Peristeras, Loukas D; Boulougouris, Georgios C; Melissas, Vasilios S; Troganis, Anastassios N

2017-05-31

Dimethyl sulfoxide (DMSO) has a significant, multi-faceted role in medicine, pharmacy, and biology as well as in biophysical chemistry and catalysis. Its physical properties and impact on biomolecular structures still attract major scientific interest, especially the interactions of DMSO with biomolecular functional groups. In the present study, we shed light on the "isolated" carboxylic (-COOH) and amide (-NH) interactions in neat DMSO via 1 H NMR studies along with extensive theoretical approaches, i.e. molecular dynamics (MD) simulations, density functional theory (DFT), and ab initio calculations, applied on model compounds (i.e. acetic and benzoic acid, ethyl acetamidocyanoacetate). Both experimental and theoretical results show excellent agreement, thereby permitting the calculation of the association constants between the studied compounds and DMSO molecules. Our coupled MD simulations, DFT and ab initio calculations, and NMR spectroscopy results indicated that complex formation is entropically driven and DMSO molecules undergo multiple strong interactions with the studied molecules, particularly with the -COOH groups. The combined experimental and theoretical techniques unraveled the interactions of DMSO with the most abundant functional groups of peptides (i.e. peptide bonds, side chain and terminal carboxyl groups) in high detail, providing significant insights on the underlying thermodynamics driving these interactions. Moreover, the developed methodology for the analysis of the simulation results could serve as a template for future thermodynamic and kinetic studies of similar systems.

The conformational stability, solvation and the assignments of the experimental infrared, Raman, 1H and 13C NMR spectra of the local anesthetic drug lidocaine

NASA Astrophysics Data System (ADS)

Badawi, Hassan M.; Förner, Wolfgang; Ali, Shaikh A.

2015-05-01

The structure, vibrational and 1H and 13C NMR spectra of the local anesthetic drug lidocaine were investigated by the B3LYP/6-311G∗∗ calculations. The molecule was predicted to have the non-planar cis (NCCN ∼ 0°) structures being about 2-6 kcal/mol lower in energy than the corresponding trans (NCCN ∼ 180°) forms. The calculated NCCN (9.6°) and CNCC (-132.2°) torsional angles were in a good qualitative agreement with the reported X-ray angles (3.1 and 13.0°, -102.67 and -77.9°, respectively, for H-bonded dimers). The Gibbs energy of solution of lidocaine in formamide, water, dimethylsulfoxide, acetonitrile, methanol, ethanol and chloroform solutions was estimated at the B3LYP level. The predicted affinity of lidocaine toward the alcohols, acetonitrile and chloroform solutions was in excellent agreement with the reported experimental solubility of the drug in organic solvents. The analysis of the observed vibrational spectra is consistent with the presence of lidocaine in only one conformation at room temperature. The 1H and 13C NMR spectra of lidocaine were interpreted by experimental and DFT calculated chemical shifts of the drug. The RMSD between experimental and theoretical 1H and 13C chemical shifts for lidocaine is 0.47 and 8.26 ppm, respectively.

Synthesis, characterization and computational studies of 3-{(E)-[(2-hydroxyphenyl)imino]methyl}benzene-1,2-diol and molecular structure of its zwitterionic form

NASA Astrophysics Data System (ADS)

Ezeorah, Julius Chigozie; Ossai, Valentine; Obasi, Lawrence Nnamdi; Elzagheid, Mohamed I.; Rhyman, Lydia; Lutter, Michael; Jurkschat, Klaus; Dege, Necmi; Ramasami, Ponnadurai

2018-01-01

The Schiff base 3-{(E)-[(2-hydroxyphenyl)imino]methyl}benzene-1,2-diol was synthesized by the condensation of 2,3-dihydroxybenzaldehyde and 2-aminophenol in water at room temperature. The crystal was grown using two solvents (dry methanol and 60% methanol). The compound was characterized using elemental microanalysis, IR, NMR, UV spectroscopies and single-crystal X-ray diffraction crystallography. The X-ray structure reveals that the Schiff base crystallizes as a methanol solvate in dry methanol with triclinic crystal system, space group P-1 and Z = 2 in the unit cell and as a non-methanol solvate in 60% methanol with triclinic crystal system, space group P-1 and Z = 4 in the unit cell. The compound showed absorption bands at 272, 389, 473 and 602 nm in DMSO. These bands were assigned as π → π ∗, n → π∗ and n-σ∗ transitions. The 473 and 602 nm bands in DMSO reveal that the compound exists in tautomeric forms. The presence of N-H, C-O and Cdbnd N stretching vibrations in the IR spectrum indicates that the compound is zwitterionic in the solid state. This study was supplemented using density functional theory method.

Solvation Effect on Complexation of Alkali Metal Cations by a Calix[4]arene Ketone Derivative.

PubMed

Požar, Josip; Nikšić-Franjić, Ivana; Cvetnić, Marija; Leko, Katarina; Cindro, Nikola; Pičuljan, Katarina; Borilović, Ivana; Frkanec, Leo; Tomišić, Vladislav

2017-09-14

The medium effect on the complexation of alkali metal cations with a calix[4]arene ketone derivative (L) was systematically examined in methanol, ethanol, N-methylformamide, N,N-dimethylformamide, dimethyl sulfoxide, and acetonitrile. In all solvents the binding of Na + cation by L was rather efficient, whereas the complexation of other alkali metal cations was observed only in methanol and acetonitrile. Complexation reactions were enthalpically controlled, while ligand dissolution was endothermic in all cases. A notable influence of the solvent on NaL + complex stability could be mainly attributed to the differences in complexation entropies. The higher NaL + stability in comparison to complexes with other alkali metal cations in acetonitrile was predominantly due to a more favorable complexation enthalpy. The 1 H NMR investigations revealed a relatively low affinity of the calixarene sodium complex for inclusion of the solvent molecule in the calixarene hydrophobic cavity, with the exception of acetonitrile. Differences in complex stabilities in the explored solvents, apart from N,N-dimethylformamide and acetonitrile, could be mostly explained by taking into account solely the cation and complex solvation. A considerable solvent effect on the complexation equilibria was proven to be due to an interesting interplay between the transfer enthalpies and entropies of the reactants and the complexes formed.

Preparation and physicochemical characterization of 5 niclosamide solvates and 1 hemisolvate.

PubMed

van Tonder, Elsa C; Mahlatji, Mabatane D; Malan, Sarel F; Liebenberg, Wilna; Caira, Mino R; Song, Mingna; de Villiers, Melgardt M

2004-02-23

The purpose of the study was to characterize the physicochemical, structural, and spectral properties of the 1:1 niclosamide and methanol, diethyl ether, dimethyl sulfoxide, N,N' dimethylformamide, and tetrahydrofuran solvates and the 2:1 niclosamide and tetraethylene glycol hemisolvate prepared by recrystallization from these organic solvents. Structural, spectral, and thermal analysis results confirmed the presence of the solvents and differences in the structural properties of these solvates. In addition, differences in the activation energy of desolvation, batch solution calorimetry, and the aqueous solubility at 25 degrees C, 24 hours, showed the stability of the solvates to be in the order: anhydrate > diethyl ether solvate > tetraethylene glycol hemisolvate > methanol solvate > dimethyl sulfoxide solvate > N,N' dimethylformamide solvate. The intrinsic and powder dissolution rates of the solvates were in the order: anhydrate > diethyl ether solvate > tetraethylene glycol hemisolvate > N,N' dimethylformamide solvate > methanol solvate > dimethyl sulfoxide solvate. Although these nonaqueous solvates had higher solubility and dissolution rates than the monohydrous forms, they were unstable in aqueous media and rapidly transformed to one of the monohydrous forms.

Diastereoselective reactions in glycine templates containing an ent-ardeemin fragment.

PubMed

Martín-Santamaría, Sonsoles; Corzo-Suárez, Raúl; Avendaño, Carmen; Espada, Modesta; Gago, Federico; García-Granda, Santiago; Rzepa, Henry S

2002-04-05

Self-consistent reaction field solvation models derived from SCF-MO calculations are shown to be reliable in modeling the diastereoselectivity of the reactions of the anion and cation derived from (4S)-2,4-dimethyl-2,4-dihydro-1H-pyrazino[2,1-b]quinazoline-3,6-dione (1) at C(1) with electrophiles and nucleophiles, respectively. The found anti/syn ratio of compound 8, which is a seco-ent-ardeemin analogue obtained by alkylation of 1 with gramine methiodide, confirms this computational model. A close similarity between the calculated geometry of the piperazine ring in the anti isomers of 1,2,4-trialkyl derivatives and that deduced from their (1)H NMR (solution) and X-ray data has been also established.

Two Compartmentalized Inner Receptors for the Tetramethylammonium Guest within a Keplerate-Type Capsule.

PubMed

Watfa, Nancy; Haouas, Mohamed; Floquet, Sébastien; Hijazi, Akram; Naoufal, Daoud; Taulelle, Francis; Cadot, Emmanuel

2016-09-19

The host-guest interactions between the spherical porous Keplerate anion, [Mo132O372(CH3CO2)30(H2O)72](42-) (abbreviated {Mo132}) and the tetramethylammonium cation have been investigated extensively by one- and two-dimensional (EXSY, ROESY, and DOSY) and variable-temperature NMR. Evidence of two inner receptor sites specific for a NMe4(+) guest appears consistent with a quite striking compartmentalization phenomenon. ROESY NMR analyses showed that both sites exhibit a close spatial proximity with the hanging inner acetate groups, while a quantitative EXSY study revealed that these two sites are differentiated by their exchange rates. These NMR data support the hypothesis that these two inner sites could be delimited by the hanging inner acetate groups forming triangular (S1) or pentagonal (S2) hydrophobic pockets on the inner side of the capsule wall. Furthermore, the stability constants associated with the trapping process of the NMe4(+) guest on both the S1 and S2 sites have been determined, showing that the stability constant of the S1 sites decreases significantly as the concentration of the capsule increases gradually, while that of the S2 sites remains nearly unaffected. Such an observation has been interpreted as a result of the plugging process of the {Mo9O9} pores by the counterions NH4(+), which causes unfavorable electrostatic interactions for the NMe4(+) coordination on the proximal S1 site. Finally, the thermodynamic parameters of the NMe4(+) transfer from the solvated situation to the interior of the capsule were estimated from variable-temperature NMR experiments that provide the split of the global process into two successive events corresponding to the plugging and transfer across the inorganic shell.

51V solid-state NMR and density functional theory studies of vanadium environments in V(V)O2 dipicolinic acid complexes

NASA Astrophysics Data System (ADS)

Bolte, Stephanie E.; Ooms, Kristopher J.; Polenova, Tatyana; Baruah, Bharat; Crans, Debbie C.; Smee, Jason J.

2008-02-01

V51 solid-state NMR and density functional theory (DFT) investigations are reported for a series of pentacoordinate dioxovanadium(V)-dipicolinate [V(V )O2-dipicolinate] and heptacoordinate aquahydroxylamidooxovanadium(V)-dipicolinate [V(V)O-dipicolinate] complexes. These compounds are of interest because of their potency as phosphatase inhibitors as well as their insulin enhancing properties and potential for the treatment of diabetes. Experimental solid-state NMR results show that the electric field gradient tensors in the V(V )O2-dipicolinate derivatives are affected significantly by substitution on the dipicolinate ring and range from 5.8to8.3MHz. The chemical shift anisotropies show less dramatic variations with respect to the ligand changes and range between -550 and -600ppm. To gain insights on the origins of the NMR parameters, DFT calculations were conducted for an extensive series of the V(V )O2- and V(V)O-dipicolinate complexes. To assess the level of theory required for the accurate calculation of the V51 NMR parameters, different functionals, basis sets, and structural models were explored in the DFT study. It is shown that the original x-ray crystallographic geometries, including all counterions and solvation water molecules within 5Å of the vanadium, lead to the most accurate results. The choice of the functional and the basis set at a high level of theory has a relatively minor impact on the outcome of the chemical shift anisotropy calculations; however, the use of large basis sets is necessary for accurate calculations of the quadrupole coupling constants for several compounds of the V(V )O2 series. These studies demonstrate that even though the vanadium compounds under investigations exhibit distorted trigonal bipyramidal coordination geometry, they have a "perfect" trigonal bipyramidal electronic environment. This observation could potentially explain why vanadate and vanadium(V) adducts are often recognized as potent transition state analogs.

On-line high-performance liquid chromatography-ultraviolet-nuclear magnetic resonance method of the markers of nerve agents for verification of the Chemical Weapons Convention.

PubMed

Mazumder, Avik; Gupta, Hemendra K; Garg, Prabhat; Jain, Rajeev; Dubey, Devendra K

2009-07-03

This paper details an on-flow liquid chromatography-ultraviolet-nuclear magnetic resonance (LC-UV-NMR) method for the retrospective detection and identification of alkyl alkylphosphonic acids (AAPAs) and alkylphosphonic acids (APAs), the markers of the toxic nerve agents for verification of the Chemical Weapons Convention (CWC). Initially, the LC-UV-NMR parameters were optimized for benzyl derivatives of the APAs and AAPAs. The optimized parameters include stationary phase C(18), mobile phase methanol:water 78:22 (v/v), UV detection at 268nm and (1)H NMR acquisition conditions. The protocol described herein allowed the detection of analytes through acquisition of high quality NMR spectra from the aqueous solution of the APAs and AAPAs with high concentrations of interfering background chemicals which have been removed by preceding sample preparation. The reported standard deviation for the quantification is related to the UV detector which showed relative standard deviations (RSDs) for quantification within +/-1.1%, while lower limit of detection upto 16mug (in mug absolute) for the NMR detector. Finally the developed LC-UV-NMR method was applied to identify the APAs and AAPAs in real water samples, consequent to solid phase extraction and derivatization. The method is fast (total experiment time approximately 2h), sensitive, rugged and efficient.

Method and apparatus for low temperature destruction of halogenated hydrocarbons

DOEpatents

Reagen, William Kevin; Janikowski, Stuart Kevin

1999-01-01

A method and apparatus for decomposing halogenated hydrocarbons are provided. The halogenated hydrocarbon is mixed with solvating agents and maintained in a predetermined atmosphere and at a predetermined temperature. The mixture is contacted with recyclable reactive material for chemically reacting with the recyclable material to create dehalogenated hydrocarbons and halogenated inorganic compounds. A feature of the invention is that the process enables low temperature destruction of halogenated hydrocarbons.

Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method

NASA Astrophysics Data System (ADS)

Jézéquel, Tangi; Silvestre, Virginie; Dinis, Katy; Giraudeau, Patrick; Akoka, Serge

2018-04-01

Isotope ratio monitoring by 13C NMR spectrometry (irm-13C NMR) provides the complete 13C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of 13C natural abundance values (50‰), irm-13C NMR requires a 1‰ accuracy and thus highly quantitative analysis by 13C NMR. Until now, the conventional strategy to determine the position-specific abundance xi relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and 13C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform 13C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative 1H NMR pulse sequence (named DWET) with a 13C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T1, which forms a serious limitation for irm-13C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T1 variations. Their performance is evaluated on the determination of the 13C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm-13C NMR since it is now possible to perform isotopic analysis with high relaxing agent concentrations, leading to a strong reduction of the overall experiment time.

Anti-cancer agents based on 4-(hetero)Ary1-1,2,5-oxadiazol-3-yl Amino derivatives and a method of making

DOEpatents

Gakh, Andrei A.; Krasavin, Mikhail; Karapetian, Ruben; Rufanov, Konstantin A.; Konstantinov, Igor; Godovykh, Elena; Soldatkina, Olga; Sosnov, Andrey V.

2013-01-29

The present disclosure relates to novel compounds that can be used as anti-cancer agents in the prostate cancer therapy. ##STR00001## In particular, the invention relates N-substituted derivatives of 4-(hetero)aryl-1,2,5-oxadiazol-3-yl amines having the structural Formula (I) and (II), stereoisomers, tautomers, racemics, prodrugs, metabolites thereof, or pharmaceutically acceptable salt and/or solvate thereof. Meaning of R1 and R2 in the Formula (I) and (II) are defined in claim 1. The invention also relates to methods for preparing said compounds, and to pharmaceutical compositions comprising said compounds.

The development of ultrashort acting neuromuscular relaxant tropane derivatives.

PubMed

Gyermek, Laszlo; Lee, Chingmuh

2009-03-01

There is a need for neuromuscular relaxant (NMR) agents that are of the "nondepolarizing type" and produce rapidly developing and short-lasting skeletal muscle relaxation in anesthesiology. Many efforts have been directed to produce such agents. Our research focused on the design, synthesis, and evaluation of numerous "bisquaternary" derivatives of the cyclic aminoalkanes: tropane and granatane. Through systematic "steric structure-activity relationship" studies, we arrived at some new bisquaternary tropine and granatanol diesters, which in laboratory studies appeared to be the fastest and shortest acting NMRs recognized so far. Their ultrashort duration action-mechanism was, however, linked to the formation of nephrotoxic metabolites, precluding further development. Even so, we believe that the scientific information gained from more than a thousand such agents, will be useful toward developing the "ideal," ultrashort-acting NMR that could be clinically successful without the use of "reversing" agents, at least until "new biotechnology" may solve all problematic aspects of "transient" muscle relaxation.

Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide.

PubMed

Oktaviani, Nur Alia; Risør, Michael W; Lee, Young-Ho; Megens, Rik P; de Jong, Djurre H; Otten, Renee; Scheek, Ruud M; Enghild, Jan J; Nielsen, Niels Chr; Ikegami, Takahisa; Mulder, Frans A A

2015-06-01

Co-solute paramagnetic relaxation enhancement (PRE) is an attractive way to speed up data acquisition in NMR spectroscopy by shortening the T 1 relaxation time of the nucleus of interest and thus the necessary recycle delay. Here, we present the rationale to utilize high-spin iron(III) as the optimal transition metal for this purpose and characterize the properties of its neutral chelate form Fe(DO3A) as a suitable PRE agent. Fe(DO3A) effectively reduces the T 1 values across the entire sequence of the intrinsically disordered protein α-synuclein with negligible impact on line width. The agent is better suited than currently used alternatives, shows no specific interaction with the polypeptide chain and, due to its high relaxivity, is effective at low concentrations and in 'proton-less' NMR experiments. By using Fe(DO3A) we were able to complete the backbone resonance assignment of a highly fibrillogenic peptide from α1-antitrypsin by acquiring the necessary suite of multidimensional NMR datasets in 3 h.

Rational design and synthesis of an orally bioavailable peptide guided by NMR amide temperature coefficients

PubMed Central

Wang, Conan K.; Northfield, Susan E.; Colless, Barbara; Chaousis, Stephanie; Hamernig, Ingrid; Lohman, Rink-Jan; Nielsen, Daniel S.; Schroeder, Christina I.; Liras, Spiros; Price, David A.; Fairlie, David P.; Craik, David J.

2014-01-01

Enhancing the oral bioavailability of peptide drug leads is a major challenge in drug design. As such, methods to address this challenge are highly sought after by the pharmaceutical industry. Here, we propose a strategy to identify appropriate amides for N-methylation using temperature coefficients measured by NMR to identify exposed amides in cyclic peptides. N-methylation effectively caps these amides, modifying the overall solvation properties of the peptides and making them more membrane permeable. The approach for identifying sites for N-methylation is a rapid alternative to the elucidation of 3D structures of peptide drug leads, which has been a commonly used structure-guided approach in the past. Five leucine-rich peptide scaffolds are reported with selectively designed N-methylated derivatives. In vitro membrane permeability was assessed by parallel artificial membrane permeability assay and Caco-2 assay. The most promising N-methylated peptide was then tested in vivo. Here we report a novel peptide (15), which displayed an oral bioavailability of 33% in a rat model, thus validating the design approach. We show that this approach can also be used to explain the notable increase in oral bioavailability of a somatostatin analog. PMID:25416591

Delamination mechanism study of large size waste printed circuit boards by using dimethylacetamide.

PubMed

Verma, Himanshu Ranjan; Singh, Kamalesh K; Mankhand, Tilak Raj

2017-07-01

Present work investigates the recycling of waste printed circuit boards (PCBs) by cracking of its multi-layered structure by using dimethylacetamide (DMA). The study shows that cracking and separation of layers of PCBs increases as the temperature increases; and decreases as the surface area of PCBs increases. After separation of layers, the used solvent was analyzed by proton and carbon nuclear magnetic resonance spectroscopy (NMR) to understand the dissolution phenomenon of resin. Further, NMR and Fourier transform infrared spectroscopy analysis of DMA sample after 1h, 2h, 3h, 4h and 8h of reaction with PCBs at 433K and PCB:DMA ratio (wt/vol) of 3:10 has been carried out to investigate the mechanism of dissolution of resin. These studies revealed that hydroxyl group of PCBs polymeric chain participates in hydrogen bonding with parent carbonyl group of DMA molecule that results in the solvation of resin. Possible chemical reaction based on the above finding has been discussed. Using this technique, separation of the metallic fraction without application of any energy intensive mechanical pre-processing is possible. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dispersion of Rod-like Particles of Nafion in Salt-Free Water/1-Propanol and Water/Ethanol Solutions.

PubMed

Yamaguchi, Makoto; Matsunaga, Takuro; Amemiya, Kazuki; Ohira, Akihiro; Hasegawa, Naoki; Shinohara, Kazuhiko; Ando, Masaki; Yoshida, Toshihiko

2014-12-26

The dispersion of perfluorinated sulfonic acid ionomers in catalyst inks is an important factor controlling the performance of catalyst layers in membrane electrode assemblies of proton exchange membrane fuel cells (PEMFCs). The effect of water/alcohol composition on the dispersion of H-Nafion in water/1-propanol and water/ethanol solutions was studied by dynamic light scattering (DLS), small-angle X-ray scattering (SAXS), and (19)F nuclear magnetic resonance ((19)F NMR) spectroscopy. Hydrodynamic radii calculated from DLS decay profiles and the radii and interparticle distance of rod-like particles derived from SAXS profiles showed almost the same dependence on alcohol concentration. 1-Propanol was more effective than ethanol to induce changes in the characteristic lengths of the rod-like particles. The motional narrowing in the (19)F NMR spectra by addition of 1-propanol indicates selective solvation of the rod-like particles. We suppose this might have decreased their radii and induced their elongation, which eventually led to extension of the ordered regions as observed in the hydrodynamic radii. Our study helps to clarify the dispersion of Nafion in aqueous alcohol solutions, which has implications for the performance of PEMFCs.

Rational design and synthesis of an orally bioavailable peptide guided by NMR amide temperature coefficients.

PubMed

Wang, Conan K; Northfield, Susan E; Colless, Barbara; Chaousis, Stephanie; Hamernig, Ingrid; Lohman, Rink-Jan; Nielsen, Daniel S; Schroeder, Christina I; Liras, Spiros; Price, David A; Fairlie, David P; Craik, David J

2014-12-09

Enhancing the oral bioavailability of peptide drug leads is a major challenge in drug design. As such, methods to address this challenge are highly sought after by the pharmaceutical industry. Here, we propose a strategy to identify appropriate amides for N-methylation using temperature coefficients measured by NMR to identify exposed amides in cyclic peptides. N-methylation effectively caps these amides, modifying the overall solvation properties of the peptides and making them more membrane permeable. The approach for identifying sites for N-methylation is a rapid alternative to the elucidation of 3D structures of peptide drug leads, which has been a commonly used structure-guided approach in the past. Five leucine-rich peptide scaffolds are reported with selectively designed N-methylated derivatives. In vitro membrane permeability was assessed by parallel artificial membrane permeability assay and Caco-2 assay. The most promising N-methylated peptide was then tested in vivo. Here we report a novel peptide (15), which displayed an oral bioavailability of 33% in a rat model, thus validating the design approach. We show that this approach can also be used to explain the notable increase in oral bioavailability of a somatostatin analog.

X-ray diffraction and infrared spectroscopy of N,N-dimethylformamide and dimethyl sulfoxide solvatomorphs of betulonic acid.

PubMed

Boryczka, Stanisław; Jastrzebska, Maria; Bębenek, Ewa; Kusz, Joachim; Zubko, Maciej; Kadela, Monika; Michalik, Ewa

2012-12-01

X-ray diffraction and infrared spectroscopy measurements for the N,N-dimethylformamide (DMF) and dimethyl sulfoxide (DMSO) solvatomorphs of betulonic acid (BA) were investigated. BA [3-oxolup-20(29)-en-28-oic acid, C(30)H(46)O(3)] exhibits a wide spectrum of biological activities and is considered to be a promising natural agent for the treatment of various cancer diseases. BA as a noncrystalline substance was obtained by oxidation of betulin. Crystal structures and the spectral data allowed analysis of hydrogen bonding (H-bonding), molecular conformation, and crystal packing differences in the solvatomorphs. Crystals of BA solvates were grown from the DMF-acetone (1:10, v/v) and DMSO-water (9:1, v/v) solutions. BA-DMF (1:1) solvate crystallizes in the monoclinic P2(1) space group, Z = 2. The unit cell parameters are as follows: cell lengths a = 13.2458(5) Å, b = 6.6501(2) Å, c = 17.9766(7) Å, and β = 110.513(4)°. BA-DMSO (1:1) solvate crystallizes in the orthorhombic P2(1)2(1)2(1) (Z = 4) space group with the following unit cell parameters: a = 6.6484(4) Å, b = 13.3279(8) Å, and c = 32.6821(19) Å. Conformational analysis of the six-membered rings, cyclopentane ring, and isopropenyl group showed differences in comparison with other betulin derivatives examined earlier. For both solvates, the intermolecular packing arrangement was governed mainly by H-bonds. The shortest H-bonds with D···A distances of 2.604 and 2.657 Å, and almost linear DH···A connection occurred between OH of carboxylic group of BA and oxygen atoms from O=C and O=S groups of DMF and DMSO, respectively. Copyright © 2012 Wiley Periodicals, Inc.

Self-doped molecular composite battery electrolytes

DOEpatents

Harrup, Mason K.; Wertsching, Alan K.; Stewart, Frederick F.

2003-04-08

This invention is in solid polymer-based electrolytes for battery applications. It uses molecular composite technology, coupled with unique preparation techniques to render a self-doped, stabilized electrolyte material suitable for inclusion in both primary and secondary batteries. In particular, a salt is incorporated in a nano-composite material formed by the in situ catalyzed condensation of a ceramic precursor in the presence of a solvated polymer material, utilizing a condensation agent comprised of at least one cation amenable to SPE applications. As such, the counterion in the condensation agent used in the formation of the molecular composite is already present as the electrolyte matrix develops. This procedure effectively decouples the cation loading levels required for maximum ionic conductivity from electrolyte physical properties associated with condensation agent loading levels by utilizing the inverse relationship discovered between condensation agent loading and the time domain of the aging step.

Preferential solvation of lithium cations and impacts on oxygen reduction in lithium–air batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Dong; Qu, Deyu; Yang, Xiao -Qing

2015-09-16

The solvation of Li⁺ with eleven non-aqueous solvents commonly used as the electrolytes for Li batteries were studied. The solvation preferences of different solvents were compared by means of electrospray mass spectrometry and collision-induced dissociation. The relative strength of the solvent for the solvation of Li⁺ was determined. The Lewis acidity of the solvated Li⁺ cations was determined by the preferential solvation of the solvent in the solvation shell. The kinetics of the catalytic disproportionation of the O₂⁻ depends on the relative Lewis acidity of the solvated Li⁺ ion. The impact of the solvated Li⁺ cation on the O₂ redoxmore » reaction was also investigated.« less

NMR structural studies of the supramolecular adducts between a liver cytosolic bile acid binding protein and gadolinium(III)-chelates bearing bile acids residues: molecular determinants of the binding of a hepatospecific magnetic resonance imaging contrast agent.

PubMed

Assfalg, Michael; Gianolio, Eliana; Zanzoni, Serena; Tomaselli, Simona; Russo, Vito Lo; Cabella, Claudia; Ragona, Laura; Aime, Silvio; Molinari, Henriette

2007-11-01

The binding affinities of a selected series of Gd(III) chelates bearing bile acid residues, potential hepatospecific MRI contrast agents, to a liver cytosolic bile acid transporter, have been determined through relaxivity measurements. The Ln(III) complexes of compound 1 were selected for further NMR structural analysis aimed at assessing the molecular determinants of binding. A number of NMR experiments have been carried out on the bile acid-like adduct, using both diamagnetic Y(III) and paramagnetic Gd(III) complexes, bound to a liver bile acid binding protein. The identified protein "hot spots" defined a single binding site located at the protein portal region. The presented findings will serve in a medicinal chemistry approach for the design of hepatocytes-selective gadolinium chelates for liver malignancies detection.

On the Basicity of 8-Phenylsulfanyl Quipazine Derivatives: New Potential Serotonergic Agents.

PubMed

Pieńko, T; Taciak, P P; Mazurek, A P

2015-07-09

A protonation state of serotonergic ligands plays a crucial role in their pharmacological activity. In this research, the basicity of 8-phenylsulfanyl quipazine derivatives as new potential serotonergic agents was studied. The most favorable protonation sites were determined in the gas and aqueous phases. In water, a solvation effect promoting the protonation of the N3 atom overcomes a positive charge delocalization phenomenon favoring a N1 atom protonation. The most stable conformations of neutral and protonated molecules in gas and water were found. It was demonstrated that a diprotonation reaction may occur. The most favorable among the diprotonated structures is the molecule with the N1 and N3 atoms protonated. A calculation of the pKa and pKa2 in water of a set of monosubstituted 8-phenylsulfanyl quipazine derivatives was performed using B3LYP/6-31G(d) and the SMD continuum solvation model. Enthalpic and entropic contributions to the pKa and pKa2 in gas and water were separated for a rationalization of a substituent effect on values of the pKa and pKa2. The relationship of the proton affinity and the solvation enthalpy in water with some reactivity descriptors, such as the Fukui function, the molecular electrostatic potential (MEP), and the global softness, was investigated. The order of the pKa values is the most controlled by the entropy. The diprotonation reaction, despite having an unfavorable enthalpy in water, is driven entropically. Final state effects in the diprotonated species were analyzed with the triadic formula. Results of a calculation of the theoretical basicity of the 8-phenylsulfanyl quipazines indicate that they should be monoprotonated on the N3 atom in the CNS environment. Diprotonation of the studied compounds may occur in very acidic body fluids such as the gastric juice.

Structure and stability of hexa-aqua V(III) cations in vanadium redox flow battery electrolytes.

PubMed

Vijayakumar, M; Li, Liyu; Nie, Zimin; Yang, Zhenguo; Hu, JianZhi

2012-08-07

The vanadium(III) cation structure in mixed acid based electrolyte solution from vanadium redox flow batteries is studied by (17)O and (35/37)Cl nuclear magnetic resonance (NMR) spectroscopy, electronic spectroscopy and density functional theory (DFT) based computational modelling. Both computational and experimental results reveal that the V(III) species can complex with counter anions (sulfate/chlorine) depending on the composition of its solvation sphere. By analyzing the powder precipitate it was found that the formation of sulfate complexed V(III) species is the crucial process in the precipitation reaction. The precipitation occurs through nucleation of neutral species formed through deprotonation and ion-pair formation process. However, the powder precipitate shows a multiphase nature which warrants multiple reaction pathways for precipitation reaction.

Solvent and structural effects on the spectral shifts of 5-(substituted phenylazo)-3-cyano-6-hydroxy-1-(2-hydroxyethyl)-4-methyl-2-pyridones

NASA Astrophysics Data System (ADS)

Mirković, Jelena M.; Božić, Bojan Đ.; Mutavdžić, Dragosav R.; Ušćumlić, Gordana S.; Mijin, Dušan Ž.

2014-11-01

Spectral properties, solvatochromism and azo-hydrazone tautomerism of ten 5-(substituted phenylazo)-3-cyano-6-hydroxy-1-(2-hydroxyethyl)-4-methyl-2-pyridones in twenty-two solvents are investigated. For quantitative evaluation of the solvent effects on the UV-vis absorption maxima, the principles of the linear solvation energy relationships are used, i.e. models proposed by Kamlet-Taft and Catalán. Linear free energy relationships are applied to the UV-vis absorption spectra and correlation of absorption frequencies with Hammett substituent constants are performed. Furthermore, the influence of the electronic nature of the substituents on 1H and 13C NMR shifts is investigated by simple and extended Hammett equations, as well as by Swain-Lupton equation.

Solution NMR spectroscopy of food polysaccharides

USDA-ARS?s Scientific Manuscript database

Many polysaccharides are allowed for direct food use, where they serve a number of useful functions. In addition to possibly being a source of calories, a food polysaccharide may be a dietary fiber, bulking agent, crystallization inhibitor, thickener, encapsulant, gelling agent, foam and emulsion s...

Dissolution DNP-NMR spectroscopy using galvinoxyl as a polarizing agent

NASA Astrophysics Data System (ADS)

Lumata, Lloyd L.; Merritt, Matthew E.; Malloy, Craig R.; Sherry, A. Dean; van Tol, Johan; Song, Likai; Kovacs, Zoltan

2013-02-01

The goal of this work was to test feasibility of using galvinoxyl (2,6-di-tert-butyl-α-(3,5-di-tert-butyl-4-oxo-2,5-cyclohexadien-1-ylidene)-p-tolyloxy) as a polarizing agent for dissolution dynamic nuclear polarization (DNP) NMR spectroscopy. We have found that galvinoxyl is reasonably soluble in ethyl acetate, chloroform, or acetone and the solutions formed good glasses when mixed together or with other solvents such as dimethyl sulfoxide. W-band electron spin resonance (ESR) measurements revealed that galvinoxyl has an ESR linewidth D intermediate between that of carbon-centered free radical trityl OX063 and the nitroxide-based 4-oxo-TEMPO, thus the DNP with galvinoxyl for nuclei with low gyromagnetic ratio γ such as 13C and 15N is expected to proceed predominantly via the thermal mixing process. The optimum radical concentration that would afford the highest 13C nuclear polarization (approximately 6% for [1-13C]ethyl acetate) at 3.35 T and 1.4 K was found to be around 40 mM. After dissolution, large liquid-state NMR enhancements were achieved for a number of 13C and 15N compounds with long spin-lattice relaxation time T1. In addition, the hydrophobic galvinoxyl free radical can be easily filtered out from the dissolution liquid when water is used as the solvent. These results indicate that galvinoxyl can be considered as an easily available free radical polarizing agent for routine dissolution DNP-NMR spectroscopy.

Real-time tracking of dissociation of hyperpolarized 89Y-DTPA: a model for degradation of open-chain Gd3+ MRI contrast agents

NASA Astrophysics Data System (ADS)

Ferguson, Sarah; Niedbalski, Peter; Parish, Christopher; Kiswandhi, Andhika; Kovacs, Zoltan; Lumata, Lloyd

Gadolinium (Gd) complexes are widely used relaxation-based clinical contrast agents in magnetic resonance imaging (MRI). Gd-based MRI contrast agents with open-chain ligand such as Gd-DTPA, commercially known as magnevist, are less stable compared to Gd complexes with macrocyclic ligands such as GdDOTA (Dotarem). The dissociation of Gd-DPTA into Gd ion and DTPA ligand under certain biological conditions such as high zinc levels can potentially cause kidney damage. Since Gd is paramagnetic, direct NMR detection of the Gd-DTPA dissociation is quite challenging due to ultra-short relaxation times. In this work, we have investigated Y-DTPA as a model for Gd-DPTA dissociation under high zinc content solutions. Using dissolution dynamic nuclear polarization (DNP), the 89Y NMR signal is amplified by several thousand-fold. Due to the the relatively long T1 relaxation time of 89Y which translates to hyperpolarization lifetime of several minutes, the dissociation of Y-DTPA can be tracked in real-time by hyperpolarized 89Y NMR spectroscopy. Dissociation kinetic rates and implications on the degradation of open-chain Gd3+ MRI contrast agents will be discussed. This work was supported by the U.S. Department of Defense Award Number W81XWH-14-1-0048 and by the Robert A. Welch Foundation research Grant Number AT-1877.

Effects of Electronic-State-Dependent Solute Polarizability: Application to Solute-Pump/Solvent-Probe Spectra.

PubMed

Sun, Xiang; Ladanyi, Branka M; Stratt, Richard M

2015-07-23

Experimental studies of solvation dynamics in liquids invariably ask how changing a solute from its electronic ground state to an electronically excited state affects a solution's dynamics. With traditional time-dependent-fluorescence experiments, that means looking for the dynamical consequences of the concomitant change in solute-solvent potential energy. But if one follows the shift in the dynamics through its effects on the macroscopic polarizability, as recent solute-pump/solvent-probe spectra do, there is another effect of the electronic excitation that should be considered: the jump in the solute's own polarizability. We examine the spectroscopic consequences of this solute polarizability change in the classic example of the solvation dye coumarin 153 dissolved in acetonitrile. After demonstrating that standard quantum chemical methods can be used to construct accurate multisite models for the polarizabilities of ground- and excited-state solvation dyes, we show via simulation that this polarizability change acts as a contrast agent, significantly enhancing the observable differences in optical-Kerr spectra between ground- and excited-state solutions. A comparison of our results with experimental solute-pump/solvent-probe spectra supports our interpretation and modeling of this spectroscopy. We predict, in particular, that solute-pump/solvent-probe spectra should be sensitive to changes in both the solvent dynamics near the solute and the electronic-state-dependence of the solute's own rotational dynamics.

On the nature of the solvated electron in ice Ih.

PubMed

de Koning, Maurice; Fazzio, Adalberto; da Silva, Antônio José Roque; Antonelli, Alex

2016-02-14

The water-solvated excess electron (EE) is a key chemical agent whose hallmark signature, its asymmetric optical absorption spectrum, continues to be a topic of debate. While nearly all investigation has focused on the liquid-water solvent, the fact that the crystalline-water solvated EE shows a very similar visible absorption pattern has remained largely unexplored. Here, we present spin-polarized density-functional theory calculations subject to periodic boundary conditions of the interplay between an EE and a number of intrinsic lattice defects in ice Ih. Our results show that the optical absorption signatures in the presence of three unsaturated hydrogen bonds (HB) are very similar to those observed experimentally. Its low-energy side can be attributed to transitions between the EE ground state and a single localized excited level, in a picture that is different from that for the liquid solvent, where this portion has been associated with hydrogen-like s → p excitations. The blue tail, on the other hand, relates to transitions between the EE ground state and delocalized excited states, which is in line with the bound-to-continuum transition interpretations for the EE in liquid water. Finally, we find that, depending on the number of dangling HBs participating in the EE trap, its charge density may spontaneously break the spin degeneracy through exchange interactions with the surrounding electrons, displaying the many-electron quantum nature of the EE problem in ice Ih.

Natural Optical Activity of Chiral Epoxides: the Influence of Structure and Environment on the Intrinsic Chiroptical Response

NASA Astrophysics Data System (ADS)

Lemler, Paul M.; Craft, Clayton L.; Vaccaro, Patrick

2017-06-01

Chiral epoxides built upon nominally rigid frameworks that incorporate aryl substituents have been shown to provide versatile backbones for asymmetric syntheses designed to generate novel pharmaceutical and catalytic agents. The ubiquity of these species has motivated the present studies of their intrinsic (solvent-free) circular birefringence (CB), the measurement of which serves as a benchmark for quantum-chemical predictions of non-resonant chiroptical behavior and as a beachhead for understanding the often-pronounced mediation of such properties by environmental perturbations (e.g., solvation). The optical rotatory dispersion (or wavelength-resolved CB) of (R)-styrene oxide (R-SO) and (S,S)-phenylpropylene oxide (S-PPO) have been interrogated under ambient solvated and isolated conditions, where the latter efforts exploited the ultrasensitive techniques of cavity ring-down polarimetry. Both of the targeted systems display marked solvation effects as evinced by changes the magnitude and (in the case of R-SO) the sign of the extracted specific optical rotation, with the anomalously large response evoked from S-PPO distinguishing it from other members of the epoxide family. Linear-response calculations of dispersive optical activity have been performed at both density-functional and coupled-cluster levels of theory to unravel the structural and electronic origins of experimental findings, thereby suggesting the possible involvement of hindered torsional motion along dihedral coordinates adjoining phenyl and epoxide moieties.

Low Cost, High-Throughput 3-D Pulmonary Imager Using Hyperpolarized Contrast Agents and Low-Field MRI

DTIC Science & Technology

2017-10-01

capacitive matching element (see Figs. S3 and S4, SI). The solenoid was constructed with 170 windings using 28 AWG gauge magnet wire with a measured...10.1002/9780470034590.emrstm0491. (59) Minard, K. R.; Wind , R. A. Solenoidal microcoil designPart II: Optimizing winding parameters for maximum...TiO2 catalyst to an NMR tube containing 0.5 mL of acetone-d6. The position of the NMR tube inside the NMR spinner turbine was adjusted for the

Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method.

PubMed

Jézéquel, Tangi; Silvestre, Virginie; Dinis, Katy; Giraudeau, Patrick; Akoka, Serge

2018-04-01

Isotope ratio monitoring by 13 C NMR spectrometry (irm- 13 C NMR) provides the complete 13 C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of 13 C natural abundance values (50‰), irm- 13 C NMR requires a 1‰ accuracy and thus highly quantitative analysis by 13 C NMR. Until now, the conventional strategy to determine the position-specific abundance x i relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and 13 C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform 13 C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative 1 H NMR pulse sequence (named DWET) with a 13 C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T 1 , which forms a serious limitation for irm- 13 C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T 1 variations. Their performance is evaluated on the determination of the 13 C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm- 13 C NMR since it is now possible to perform isotopic analysis with high relaxing agent concentrations, leading to a strong reduction of the overall experiment time. Copyright © 2018 Elsevier Inc. All rights reserved.

A new glycation product ‘norpronyl-lysine,’ and direct characterization of cross linking and other glycation adducts: NMR of model compounds and collagen

PubMed Central

Bullock, Peter T. B.; Reid, David G.; Ying Chow, W.; Lau, Wendy P. W.; Duer, Melinda J.

2014-01-01

NMR is ideal for characterizing non-enzymatic protein glycation, including AGEs (advanced glycation endproducts) underlying tissue pathologies in diabetes and ageing. Ribose, R5P (ribose-5-phosphate) and ADPR (ADP-ribose), could be significant and underinvestigated biological glycating agents especially in chronic inflammation. Using [U-13C]ribose we have identified a novel glycoxidation adduct, 5-deoxy-5-desmethylpronyl-lysine, ‘norpronyl-lysine’, as well as numerous free ketones, acids and amino group reaction products. Glycation by R5P and ADPR proceeds rapidly with R5P generating a brown precipitate with PLL (poly-L-lysine) within hours. ssNMR (solid-state NMR) 13C–13C COSY identifies several crosslinking adducts such as the newly identified norpronyl-lysine, in situ, from the glycating reaction of 13C5-ribose with collagen. The same adducts are also identifiable after reaction of collagen with R5P. We also demonstrate for the first time bio-amine (spermidine, N-acetyl lysine, PLL) catalysed ribose 2-epimerization to arabinose at physiological pH. This work raises the prospect of advancing understanding of the mechanisms and consequences of glycation in actual tissues, in vitro or even ex vivo, using NMR isotope-labelled glycating agents, without analyses requiring chemical or enzymatic degradations, or prior assumptions about glycation products. PMID:27919030

NMR Hyperpolarization Techniques for Biomedicine

PubMed Central

Nikolaou, Panayiotis; Goodson, Boyd M.

2015-01-01

Recent developments in NMR hyperpolarization have enabled a wide array of new in vivo molecular imaging modalities—ranging from functional imaging of the lungs to metabolic imaging of cancer. This Concept article explores selected advances in methods for the preparation and use of hyperpolarized contrast agents, many of which are already at or near the phase of their clinical validation in patients. PMID:25470566

Introductory Chemistry: A Molar Relaxivity Experiment in the High School Classroom.

PubMed

Dawsey, Anna C; Hathaway, Kathryn L; Kim, Susie; Williams, Travis J

2013-07-09

Dotarem and Magnevist, two clinically available magnetic resonance imaging (MRI) contrast agents, were assessed in a high school science classroom with respect to which is the better contrast agent. Magnevist, the more efficacious contrast agent, has negative side effects because its gadolinium center can escape from its ligand. However, Dotarem, though a less efficacious contrast agent, is a safer drug choice. After the experiment, students are confronted with the FDA warning on Magnevist, which enabled a discussion of drug efficacy versus safety. We describe a laboratory experiment in which NMR spin lattice relaxation rate measurements are used to quantify the relaxivities of the active ingredients of Dotarem and Magnevist. The spin lattice relaxation rate gives the average amount of time it takes the excited nucleus to relax back to the original state. Students learn by constructing molar relaxivity curves based on inversion recovery data sets that Magnevist is more relaxive than Dotarem. This experiment is suitable for any analytical chemistry laboratory with access to NMR.

Solvation structure of the halides from x-ray absorption spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Antalek, Matthew; Hedman, Britt; Sarangi, Ritimukta, E-mail: ritis@slac.stanford.edu

2016-07-28

Three-dimensional models for the aqueous solvation structures of chloride, bromide, and iodide are reported. K-edge extended X-ray absorption fine structure (EXAFS) and Minuit X-ray absorption near edge (MXAN) analyses found well-defined single shell solvation spheres for bromide and iodide. However, dissolved chloride proved structurally distinct, with two solvation shells needed to explain its strikingly different X-ray absorption near edge structure (XANES) spectrum. Final solvation models were as follows: iodide, 8 water molecules at 3.60 ± 0.13 Å and bromide, 8 water molecules at 3.40 ± 0.14 Å, while chloride solvation included 7 water molecules at 3.15 ± 0.10 Å, andmore » a second shell of 7 water molecules at 4.14 ± 0.30 Å. Each of the three derived solvation shells is approximately uniformly disposed about the halides, with no global asymmetry. Time-dependent density functional theory calculations simulating the chloride XANES spectra following from alternative solvation spheres revealed surprising sensitivity of the electronic state to 6-, 7-, or 8-coordination, implying a strongly bounded phase space for the correct structure during an MXAN fit. MXAN analysis further showed that the asymmetric solvation predicted from molecular dynamics simulations using halide polarization can play no significant part in bulk solvation. Classical molecular dynamics used to explore chloride solvation found a 7-water solvation shell at 3.12 (−0.04/+0.3) Å, supporting the experimental result. These experiments provide the first fully three-dimensional structures presenting to atomic resolution the aqueous solvation spheres of the larger halide ions.« less

Quantification of terpene trilactones in Ginkgo biloba with a 1H NMR method.

PubMed

Liang, Tingfu; Miyakawa, Takuya; Yang, Jinwei; Ishikawa, Tsutomu; Tanokura, Masaru

2018-06-01

Ginkgo biloba L. has been used as a herbal medicine in the traditional treatment of insufficient blood flow, memory deficits, and cerebral insufficiency. The terpene trilactone components, the bioactive agents of Ginkgo biloba L., have also been reported to exhibit useful functionality such as anti-inflammatory and neuroprotective effects. Therefore, in the present research, we attempted to analyze quantitatively the terpene trilactone components in Ginkgo biloba leaf extract, with quantitative 1 H NMR (qNMR) and obtained almost identical results to data reported using HPLC. Application of the qNMR method for the analysis of the terpene trilactone contents in commercial Ginkgo extract products, such as soft gel capsules and tablets, produced the same levels noted in package labels. Thus, qNMR is an alternative method for quantification of the terpene trilactone components in commercial Ginkgo extract products.

Examination of the formation process of pre-solvated and solvated electron in n-alcohol using femtosecond pulse radiolysis

NASA Astrophysics Data System (ADS)

Toigawa, Tomohiro; Gohdo, Masao; Norizawa, Kimihiro; Kondoh, Takafumi; Kan, Koichi; Yang, Jinfeng; Yoshida, Yoichi

2016-06-01

The formation process of pre-solvated and solvated electron in methanol (MeOH), ethanol (EtOH), n-butanol (BuOH), and n-octanol (OcOH) were investigated using a fs-pulse radiolysis technique by observing the pre-solvated electron at 1400 nm. The formation time constants of the pre-solvated electrons were determined to be 1.2, 2.2, 3.1, and 6.3 ps for MeOH, EtOH, BuOH, and OcOH, respectively. The formation time constants of the solvated electrons were determined to be 6.7, 13.6, 22.2, and 32.9 ps for MeOH, EtOH, BuOH, and OcOH, respectively. The formation dynamics and structure of the pre-solvated and solvated electrons in n-alcohols were discussed based on relation between the obtained time constant and dielectric relaxation time constant from the view point of kinetics. The observed formation time constants of the solvated electrons seemed to be strongly correlated with the second component of the dielectric relaxation time constants, which are related to single molecule motion. On the other hand, the observed formation time constants of the pre-solvated electrons seemed to be strongly correlated with the third component of the dielectric relaxation time constants, which are related to dynamics of hydrogen bonds.

Ap4A is not an efficient Zn(II) binding agent. A concerted potentiometric, calorimetric and NMR study.

PubMed

Wszelaka-Rylik, Małgorzata; Witkiewicz-Kucharczyk, Aleksandra; Wójcik, Jacek; Bal, Wojciech

2007-05-01

Diadenosine 5',5''-P(1)P(4) tetraphosphate (Ap(4)A) has been considered as an intracellular partner for Zn(II). We applied potentiometry, ITC and NMR to study protonation equilibria of Ap(4)A and Zn(II) complexation by this dinucleotide. The values of binding constants obtained by these three techniques under various experimental conditions coherently demonstrated that Ap(4)A binds Zn(II) weakly, with an apparent binding constant of ca. 10(4) at neutral pH. Such a low stability of Zn(II) complexes with Ap(4)A excludes a possibility for interactions between these two agents in vivo.

Outer-sphere interaction of aluminum and gallium solvates with competitive anions in 1,2-propanediol solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petrosyants, S.P.; Buslaeva, E.R.

1986-04-01

The interaction of aluminum and gallium solvates with ..pi..-acid ligand in 1,2-propanediol solutions has been investigated. The formation of associates of hexacoordinate aluminum solvates depends on the solvation of the anions in the bulk of the solution or on the faces of the solvento complexes. In the case of gallium the association of the solvates with the anions is determined by two factors: the existence of a configurational equilibrium for the solvento complexes and the preferential solvation of the competitive ..pi..-acid ligands.

Estimation of Solvation Quantities from Experimental Thermodynamic Data: Development of the Comprehensive CompSol Databank for Pure and Mixed Solutes

NASA Astrophysics Data System (ADS)

Moine, Edouard; Privat, Romain; Sirjean, Baptiste; Jaubert, Jean-Noël

2017-09-01

The Gibbs energy of solvation measures the affinity of a solute for its solvent and is thus a key property for the selection of an appropriate solvent for a chemical synthesis or a separation process. More fundamentally, Gibbs energies of solvation are choice data for developing and benchmarking molecular models predicting solvation effects. The Comprehensive Solvation—CompSol—database was developed with the ambition to propose very large sets of new experimental solvation chemical-potential, solvation entropy, and solvation enthalpy data of pure and mixed components, covering extended temperature ranges. For mixed compounds, the solvation quantities were generated in infinite-dilution conditions by combining experimental values of pure-component and binary-mixture thermodynamic properties. Three types of binary-mixture properties were considered: partition coefficients, activity coefficients at infinite dilution, and Henry's-law constants. A rigorous methodology was implemented with the aim to select data at appropriate conditions of temperature, pressure, and concentration for the estimation of solvation data. Finally, our comprehensive CompSol database contains 21 671 data associated with 1969 pure species and 70 062 data associated with 14 102 binary mixtures (including 760 solvation data related to the ionic-liquid class of solvents). On the basis of the very large amount of experimental data contained in the CompSol database, it is finally discussed how solvation energies are influenced by hydrogen-bonding association effects.

Determination of NIST-Traceable Quantitative Weight Percentage Purity for G Agent Standards

DTIC Science & Technology

Nuclear magnetic resonance (NMR) with phosphorus -31 detection is described to determine the weight percent purity of feedstock samples of agents GA...and GD in a way that is National Institute of Standards and Technology (NIST)-traceable. A Precision and Accuracy test is described.

Solid-state structure of a Li/F carbenoid: pentafluoroethyllithium.

PubMed

Waerder, Benedikt; Steinhauer, Simon; Neumann, Beate; Stammler, Hans-Georg; Mix, Andreas; Vishnevskiy, Yury V; Hoge, Berthold; Mitzel, Norbert W

2014-10-20

Lithium carbenoids are versatile compounds for synthesis owing to their intriguing ambiphilic behavior. Although this class of compounds has been known for several years, few solid-state structures exist because of their high reactivity and often low thermal stability. Using cryo X-ray techniques, we were now able to elucidate the first solid-state structure of a Li/F alkyl carbenoid, pentafluoroethyllithium (LiC2F5), finally yielding a prototype for investigating structure-reactivity relationships for this class of molecules. The compound forms a diethyl ether-solvated dimer bridged by a rare C-F-Li link. Complementary NMR spectroscopy studies in solution show dynamic processes and indicate rapid exchange of starting material and product. Theoretical investigations help to understand the formation of the observed unusual structural motif. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spectroscopic and structural investigation of 2,5-dicarboxy-1-methylpyridinium inner salt

NASA Astrophysics Data System (ADS)

Barczyński, P.; Komasa, A.; Katrusiak, A.; Dega-Szafran, Z.; Nowaczyk, Ł.; Ratajczak-Sitarz, M.; Szafran, M.

2014-03-01

The structure of 2,5-dicarboxy-1-methylpyridinium inner salt (1), has been studied by X-ray diffraction, B3LYP/6-311G(d,p) calculations, FTIR, Raman and NMR spectroscopy. The molecules are linked by short intermolecular and asymmetric Osbnd H⋯O hydrogen bonds of 2.486(2) Å between carboxyl and carboxylate groups of neighboring molecules into infinite chains. The hydrogen bonds in the molecules optimized by the B3LYP/6-311G(d,p) approach in trimer (2) and dimer (3) are slightly longer than in the crystal. The FTIR spectrum of the investigated inner salt is dominated by a broad and intense absorption in the 1500-800 cm-1 region attributed to the νas(OHO) and γ(OHO) vibrations of the strong hydrogen bond. In the Raman spectrum the broad absorption is absent. Linear correlations, δexp = a + b σcalc between the experimental 1H and 13C NMR chemical shifts (δexp) of the investigated inner salt in D2O and the calculated magnetic isotropic shielding constants (σcalc) for the optimized monomer (4a) solvated in water are reported. The pKa value for 1 of 2.31 ± 0.02 was determined by the potentiometric titration.

Solvation effects on chemical shifts by embedded cluster integral equation theory.

PubMed

Frach, Roland; Kast, Stefan M

2014-12-11

The accurate computational prediction of nuclear magnetic resonance (NMR) parameters like chemical shifts represents a challenge if the species studied is immersed in strongly polarizing environments such as water. Common approaches to treating a solvent in the form of, e.g., the polarizable continuum model (PCM) ignore strong directional interactions such as H-bonds to the solvent which can have substantial impact on magnetic shieldings. We here present a computational methodology that accounts for atomic-level solvent effects on NMR parameters by extending the embedded cluster reference interaction site model (EC-RISM) integral equation theory to the prediction of chemical shifts of N-methylacetamide (NMA) in aqueous solution. We examine the influence of various so-called closure approximations of the underlying three-dimensional RISM theory as well as the impact of basis set size and different treatment of electrostatic solute-solvent interactions. We find considerable and systematic improvement over reference PCM and gas phase calculations. A smaller basis set in combination with a simple point charge model already yields good performance which can be further improved by employing exact electrostatic quantum-mechanical solute-solvent interaction energies. A larger basis set benefits more significantly from exact over point charge electrostatics, which can be related to differences of the solvent's charge distribution.

KECSA-Movable Type Implicit Solvation Model (KMTISM)

PubMed Central

2015-01-01

Computation of the solvation free energy for chemical and biological processes has long been of significant interest. The key challenges to effective solvation modeling center on the choice of potential function and configurational sampling. Herein, an energy sampling approach termed the “Movable Type” (MT) method, and a statistical energy function for solvation modeling, “Knowledge-based and Empirical Combined Scoring Algorithm” (KECSA) are developed and utilized to create an implicit solvation model: KECSA-Movable Type Implicit Solvation Model (KMTISM) suitable for the study of chemical and biological systems. KMTISM is an implicit solvation model, but the MT method performs energy sampling at the atom pairwise level. For a specific molecular system, the MT method collects energies from prebuilt databases for the requisite atom pairs at all relevant distance ranges, which by its very construction encodes all possible molecular configurations simultaneously. Unlike traditional statistical energy functions, KECSA converts structural statistical information into categorized atom pairwise interaction energies as a function of the radial distance instead of a mean force energy function. Within the implicit solvent model approximation, aqueous solvation free energies are then obtained from the NVT ensemble partition function generated by the MT method. Validation is performed against several subsets selected from the Minnesota Solvation Database v2012. Results are compared with several solvation free energy calculation methods, including a one-to-one comparison against two commonly used classical implicit solvation models: MM-GBSA and MM-PBSA. Comparison against a quantum mechanics based polarizable continuum model is also discussed (Cramer and Truhlar’s Solvation Model 12). PMID:25691832

Structures in solutions from joint experimental-computational analysis: applications to cyclic molecules and studies of noncovalent interactions.

PubMed

Aliev, Abil E; Mia, Zakirin A; Khaneja, Harmeet S; King, Frank D

2012-01-26

The potential of an approach combining nuclear magnetic resonance (NMR) spectroscopy, molecular dynamics (MD) simulations, and quantum mechanical (QM) calculations for full structural characterizations in solution is assessed using cyclic organic compounds, namely, benzazocinone derivatives 1-3 with fused five- and eight-membered aliphatic rings, camphoric anhydride 4, and bullvalene 5. Various MD simulations were considered, using force field and semiempirical QM treatments, implicit and explicit solvation, and high-temperature MD calculations for selecting plausible molecular geometries for subsequent QM geometry optimizations using mainly B3LYP, M062X, and MP2 methods. The QM-predicted values of NMR parameters were compared to their experimental values for verification of the final structures derived from the MD/QM analysis. From these comparisons, initial estimates of quality thresholds (calculated as rms deviations) were 0.7-0.9 Hz for (3)J(HH) couplings, 0.07-0.11 Å for interproton distances, 0.05-0.08 ppm for (1)H chemical shifts, and 1.0-2.1 ppm for (13)C chemical shifts. The obtained results suggest that the accuracy of the MD analysis in predicting geometries and relative conformational energies is not critical and that the final geometry refinements of the structures selected from the MD simulations using QM methods are sufficient for correcting for the expected inaccuracy of the MD analysis. A unique example of C(sp(3))-H···N(sp(3)) intramolecular noncovalent interaction is also identified using the NMR/MD/QM and the natural bond orbital analyses. As the NMR/MD/QM approach relies on the final QM geometry optimization, comparisons of geometric characteristics predicted by different QM methods and those from X-ray and neutron diffraction measurements were undertaken using rigid and flexible cyclic systems. The joint analysis shows that intermolecular noncovalent interactions present in the solid state alter molecular geometries significantly compared to the geometries of isolated molecules from QM calculations.

Ultralow field NMR spectrometer with an atomic magnetometer near room temperature

NASA Astrophysics Data System (ADS)

Liu, Guobin; Li, Xiaofeng; Sun, Xianping; Feng, Jiwen; Ye, Chaohui; Zhou, Xin

2013-12-01

We present a Cs atomic magnetometer with a sensitivity of 150 fT/Hz1/2 operating near room temperature. The nuclear magnetic resonance (NMR) signal of 125 μL tap water was detected at an ultralow magnetic field down to 47 nT, with the signal-to-noise ratio (SNR) of the NMR signal approaching 50 after eight averages. Relaxivity experiments with a Gd(DTPA) contrast agent in zero field were performed, in order to show the magnetometer's ability to measure spin-lattice relaxation time with high accuracy. This demonstrates the feasibility of an ultralow field NMR spectrometer based on a Cs atomic magnetometer, which has a low working temperature, short data acquisition time and high sensitivity. This kind of NMR spectrometer has great potential in applications such as chemical analysis and magnetic relaxometry detection in ultralow or zero fields.

NMR spectroscopy of Group 13 metal ions: biologically relevant aspects.

PubMed

André, J P; Mäcke, H R

2003-12-01

In spite of the fact that Group 13 metal ions (Al(3+), Ga(3+), In(3+) and Tl(+/3+)) show no main biological role, they are NMR-active nuclides which can be used in magnetic resonance spectroscopy of biologically relevant systems. The fact that these metal ions are quadrupolar (with the exception of thallium) means that they are particularly sensitive to ligand type and coordination geometry. The line width of the NMR signals of their complexes shows a strong dependence on the symmetry of coordination, which constitutes an effective tool in the elucidation of structures. Here we report published NMR studies of this family of elements, applied to systems of biological importance. Special emphasis is given to binding studies of these cations to biological molecules, such as proteins, and to chelating agents of radiopharmaceutical interest. The possibility of in vivo NMR studies is also stressed, with extension to (27)Al-based MRI (magnetic resonance imaging) experiments.

Building solids inside nano-space: from confined amorphous through confined solvate to confined 'metastable' polymorph.

PubMed

Nartowski, K P; Tedder, J; Braun, D E; Fábián, L; Khimyak, Y Z

2015-10-14

The nanocrystallisation of complex molecules inside mesoporous hosts and control over the resulting structure is a significant challenge. To date the largest organic molecule crystallised inside the nano-pores is a known pharmaceutical intermediate - ROY (259.3 g mol(-1)). In this work we demonstrate smart manipulation of the phase of a larger confined pharmaceutical - indomethacin (IMC, 357.8 g mol(-1)), a substance with known conformational flexibility and complex polymorphic behaviour. We show the detailed structural analysis and the control of solid state transformations of encapsulated molecules inside the pores of mesoscopic cellular foam (MCF, pore size ca. 29 nm) and controlled pore glass (CPG, pore size ca. 55 nm). Starting from confined amorphous IMC we drive crystallisation into a confined methanol solvate, which upon vacuum drying leads to the stabilised rare form V of IMC inside the MCF host. In contrast to the pure form, encapsulated form V does not transform into a more stable polymorph upon heating. The size of the constraining pores and the drug concentration within the pores determine whether the amorphous state of the drug is stabilised or it recrystallises into confined nanocrystals. The work presents, in a critical manner, an application of complementary techniques (DSC, PXRD, solid-state NMR, N2 adsorption) to confirm unambiguously the phase transitions under confinement and offers a comprehensive strategy towards the formation and control of nano-crystalline encapsulated organic solids.

Solvation thermodynamics and the physical-chemical meaning of the constant in Abraham solvation equations.

PubMed

van Noort, Paul C M

2012-04-01

Abraham solvation equations find widespread use in environmental chemistry. Until now, the intercept in these equations was determined by fitting experimental data. To simplify the determination of the coefficients in Abraham solvation equations, this study derives theoretical expressions for the value of the intercept for various partition processes. To that end, a modification of the description of the Ben-Naim standard state into the van der Waals volume is proposed. Differences between predicted and fitted values of the Abraham solvation equation intercept for the enthalpy of solvation, the entropy of solvation, solvent-water partitioning, air-solvent partitioning, partitioning into micelles, partitioning into lipid membranes and lipids, and chromatographic retention indices are comparable to experimental uncertainties in these values. Copyright © 2011 Elsevier Ltd. All rights reserved.

Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuffel, Anna; Czapiewski, Dariusz; Zielkiewicz, Jan, E-mail: jaz@chem.pg.gda.pl

2015-10-07

The dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties of solvation water of ice around its two crystallographic planes: basal and prism. Three main conclusions are inferred from our investigations. The first one is that the solvation shell of CfAFP does not seem to be particularlymore » far-ranged, at least not beyond what is usually observed for proteins that do not interact with ice. Therefore, it does not appear to us that the antifreeze activity is enhanced by a long-ranged retardation of water mobility. Also the correlation between the collective mobility of water and the collective mobility of protein atoms highly resembles the one measured for the protein that does not interact with ice. Our second conclusion is that the dynamical properties of solvation water of CfAFP are non-uniform. The dynamics of solvation water of ice-binding plane is, in some respects, different from the dynamics of solvation water of the two remaining planes. The feature that distinguishes the dynamics of solvation water of the three planes is the activation energy of diffusion process. The third conclusion is that—from the three analyzed solvation shells of CfAFP—the dynamical properties of solvation water of the ice-binding plane resemble the most the properties of solvation water of ice; note, however, that these properties still clearly differ from the dynamic properties of solvation water of ice.« less

Metabonomics of Pig Blood Plasma Following Whole Body Exposure to Low Levels of Gb Vapor

DTIC Science & Technology

2005-10-01

METABONOMICS OF PIG BLOOD PLASMA FOLLOWING WHOLE BODY EXPOSURE TO LOW LEVELS OF GB VAPOR Vicky L. H. Bevilacqua▲, Terrence G...of chemometrics and NMR will yield metabonomics data useful for establishing biochemical markers for agent exposure. Ideally, such markers would...associated with environmental change, a field recently referred to as " metabonomics ." High field nuclear magnetic resonance (NMR) has emerged as a

NMR hyperpolarization techniques for biomedicine.

PubMed

Nikolaou, Panayiotis; Goodson, Boyd M; Chekmenev, Eduard Y

2015-02-16

Recent developments in NMR hyperpolarization have enabled a wide array of new in vivo molecular imaging modalities, ranging from functional imaging of the lungs to metabolic imaging of cancer. This Concept article explores selected advances in methods for the preparation and use of hyperpolarized contrast agents, many of which are already at or near the phase of their clinical validation in patients. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thermodynamic-ensemble independence of solvation free energy.

PubMed

Chong, Song-Ho; Ham, Sihyun

2015-02-10

Solvation free energy is the fundamental thermodynamic quantity in solution chemistry. Recently, it has been suggested that the partial molar volume correction is necessary to convert the solvation free energy determined in different thermodynamic ensembles. Here, we demonstrate ensemble-independence of the solvation free energy on general thermodynamic grounds. Theoretical estimates of the solvation free energy based on the canonical or grand-canonical ensemble are pertinent to experiments carried out under constant pressure without any conversion.

Explicitly Representing the Solvation Shell in Continuum Solvent Calculations

PubMed Central

Svendsen, Hallvard F.; Merz, Kenneth M.

2009-01-01

A method is presented to explicitly represent the first solvation shell in continuum solvation calculations. Initial solvation shell geometries were generated with classical molecular dynamics simulations. Clusters consisting of solute and 5 solvent molecules were fully relaxed in quantum mechanical calculations. The free energy of solvation of the solute was calculated from the free energy of formation of the cluster and the solvation free energy of the cluster calculated with continuum solvation models. The method has been implemented with two continuum solvation models, a Poisson-Boltzmann model and the IEF-PCM model. Calculations were carried out for a set of 60 ionic species. Implemented with the Poisson-Boltzmann model the method gave an unsigned average error of 2.1 kcal/mol and a RMSD of 2.6 kcal/mol for anions, for cations the unsigned average error was 2.8 kcal/mol and the RMSD 3.9 kcal/mol. Similar results were obtained with the IEF-PCM model. PMID:19425558

Single-Ion Solvation Free Energies and the Normal Hydrogen Electrode Potential in Methanol, Acetonitrile, and Dimethyl Sulfoxide

PubMed Central

Kelly, Casey P.; Cramer, Christopher J.; Truhlar, Donald G.

2008-01-01

The division of thermodynamic solvation free energies of electrolytes into ionic constituents is conventionally accomplished by using the single-ion solvation free energy of one reference ion, conventionally the proton, to set the single-ion scales. Thus the determination of the free energy of solvation of the proton in various solvents is a fundamental issue of central importance in solution chemistry. In the present article, relative solvation free energies of ions and ion-solvent clusters in methanol, acetonitrile, and dimethyl sulfoxide (DMSO) have been determined using a combination of experimental and theoretical gas-phase free energies of formation, solution-phase reduction potentials and acid dissociation constants, and gas-phase clustering free energies. Applying the cluster pair approximation to differences between these relative solvation free energies leads to values of −263.5, −260.2, and −273.3 kcal/mol for the absolute solvation free energy of the proton in methanol, acetonitrile, and DMSO, respectively. The final absolute proton solvation free energies are used to assign absolute values for the normal hydrogen electrode potential and the solvation free energies of other single ions in the above solvents. PMID:17214493

A unified perspective on preferential solvation and adsorption based on inhomogeneous solvation theory

NASA Astrophysics Data System (ADS)

Shimizu, Seishi; Matubayasi, Nobuyuki

2018-02-01

How cosolvents affects solvation has been revealed through the independent determination of solute-solvent and solute-cosolvent interactions guaranteed by the phase rule. Based on the first principles of inhomogeneous solvation theory, we present here a general matrix theory encompassing both preferential solvation and surface adsorption. The central role of the stability conditions, that govern how many excess numbers (surface excesses) are independently determinable, have been clarified from the first principles. The advantage of the inhomogeneous approach has been demonstrated to be in its ease in treating solvation and adsorption in a unified manner, while its disadvantage, for example in membrane dialysis experiments, can be overcome by the inhomogeneous-homogeneous conversion.

Agents Within our Midst

DTIC Science & Technology

2012-03-14

agents; and the development of bio -monitoring protocols for civilian and service personnel during a chemical attack. These efforts have resulted in greater...produced by staphylococcal bacteria that is and is classified as a CDC select agent which has the potential to be used as a biological weapon .1...NMR chemical shift perturbation titrations with Fab (fragment, antigen binding regions) domains of 20B1, 14G8, and 6D3 using deuterated (2H) SEB

Solubility enhancement of a bisnaphthalimide tumoricidal agent, DMP 840, through complexation.

PubMed

Raghavan, K S; Nemeth, G A; Gray, D B; Hussain, M A

1996-10-01

The purpose of this research was to enhance the aqueous solubility of DMP 840 by complexation with water-soluble and nontoxic agents, and to understand the nature of the interactions involved in complex formation using nuclear magnetic resonance (1H-NMR). The solubility of DMP 840 in water, saline, acetate buffers, and cosolvent mixtures was determined by high-performance liquid chromatography, and the effect of nicotinamide and pyridoxine concentrations on the solubility of DMP 840 was examined by the phase solubility method. 1H-NMR spectra were acquired in deuterated acetate buffer at 400 MHz on a Varian Unity-400 spectrometer. The aqueous solubility of DMP 840 was sensitive to the presence of chloride and acetate anions in solution, and did not improve in the presence of cosolvents. The use of the nontoxic and water-soluble complex-forming agents nicotinamide and pyridoxine, however, resulted in a linear increase in the aqueous solubility of DMP 840 with both ligands. The solubilization appears to be due to formation of 1:1 complexes between DMP 840 and the bioorganic ligands. The complexation constants were 15.57 M-1 for the DMP 840:nicotinamide complex and 13.36 M-1 for the DMP 840:pyridoxine complex. The NMR results indicate that the interaction is a result of vertical or plane-to-plane stacking and the complexation constants were in agreement with that obtained by phase solubility. The results suggest that the aqueous solubility of a poorly water soluble drug substance such as DMP 840 can be significantly enhanced by its complexation with water-soluble and nontoxic agents.

Exploring Applications of Covalent Organic Frameworks: Homogeneous Reticulation of Radicals for Dynamic Nuclear Polarization.

PubMed

Cao, Wei; Wang, Wei David; Xu, Hai-Sen; Sergeyev, Ivan V; Struppe, Jochem; Wang, Xiaoling; Mentink-Vigier, Frederic; Gan, Zhehong; Xiao, Ming-Xing; Wang, Lu-Yao; Chen, Guo-Peng; Ding, San-Yuan; Bai, Shi; Wang, Wei

2018-06-06

Rapid progress has been witnessed in the past decade in the fields of covalent organic frameworks (COFs) and dynamic nuclear polarization (DNP). In this contribution, we bridge these two fields by constructing radical-embedded COFs as promising DNP agents. Via polarization transfer from unpaired electrons to nuclei, DNP realizes significant enhancement of NMR signal intensities. One of the crucial issues in DNP is to screen for suitable radicals to act as efficient polarizing agents, the basic criteria for which are homogeneous distribution and fixed orientation of unpaired electrons. We therefore envisioned that the crystalline and porous structures of COFs, if evenly embedded with radicals, may work as a new "crystalline sponge" for DNP experiments. As a proof of concept, we constructed a series of proxyl-radical-embedded COFs (denoted as PR( x)-COFs) and successfully applied them to achieve substantial DNP enhancement. Benefiting from the bottom-up and multivariate synthetic strategies, proxyl radicals have been covalently reticulated, homogeneously distributed, and rigidly embedded into the crystalline and mesoporous frameworks with adjustable concentration ( x%). Excellent performance of PR( x)-COFs has been observed for DNP 1 H, 13 C, and 15 N solid-state NMR enhancements. This contribution not only realizes the direct construction of radical COFs from radical monomers, but also explores the new application of COFs as DNP polarizing agents. Given that many radical COFs can therefore be rationally designed and facilely constructed with well-defined composition, distribution, and pore size, we expect that our effort will pave the way for utilizing radical COFs as standard polarizing agents in DNP NMR experiments.

Ligand solvation in molecular docking.

PubMed

Shoichet, B K; Leach, A R; Kuntz, I D

1999-01-01

Solvation plays an important role in ligand-protein association and has a strong impact on comparisons of binding energies for dissimilar molecules. When databases of such molecules are screened for complementarity to receptors of known structure, as often occurs in structure-based inhibitor discovery, failure to consider ligand solvation often leads to putative ligands that are too highly charged or too large. To correct for the different charge states and sizes of the ligands, we calculated electrostatic and non-polar solvation free energies for molecules in a widely used molecular database, the Available Chemicals Directory (ACD). A modified Born equation treatment was used to calculate the electrostatic component of ligand solvation. The non-polar component of ligand solvation was calculated based on the surface area of the ligand and parameters derived from the hydration energies of apolar ligands. These solvation energies were subtracted from the ligand-receptor interaction energies. We tested the usefulness of these corrections by screening the ACD for molecules that complemented three proteins of known structure, using a molecular docking program. Correcting for ligand solvation improved the rankings of known ligands and discriminated against molecules with inappropriate charge states and sizes.

Lithium ion solvation and diffusion in bulk organic electrolytes from first-principles and classical reactive molecular dynamics.

PubMed

Ong, Mitchell T; Verners, Osvalds; Draeger, Erik W; van Duin, Adri C T; Lordi, Vincenzo; Pask, John E

2015-01-29

Lithium-ion battery performance is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact both the solvation and diffusivity of Li ions. In this work, we used first-principles molecular dynamics to examine the solvation and diffusion of Li ions in the bulk organic solvents ethylene carbonate (EC), ethyl methyl carbonate (EMC), and a mixture of EC and EMC. We found that Li ions are solvated by either carbonyl or ether oxygen atoms of the solvents and sometimes by the PF6(-) anion. Li(+) prefers a tetrahedrally coordinated first solvation shell regardless of which species are involved, with the specific preferred solvation structure dependent on the organic solvent. In addition, we calculated Li diffusion coefficients in each electrolyte, finding slightly larger diffusivities in the linear carbonate EMC compared to the cyclic carbonate EC. The magnitude of the diffusion coefficient correlates with the strength of Li(+) solvation. Corresponding analysis for the PF6(-) anion shows greater diffusivity associated with a weakly bound, poorly defined first solvation shell. These results can be used to aid in the design of new electrolytes to improve Li-ion battery performance.

Cluster-continuum quasichemical theory calculation of the lithium ion solvation in water, acetonitrile and dimethyl sulfoxide: an absolute single-ion solvation free energy scale.

PubMed

Carvalho, Nathalia F; Pliego, Josefredo R

2015-10-28

Absolute single-ion solvation free energy is a very useful property for understanding solution phase chemistry. The real solvation free energy of an ion depends on its interaction with the solvent molecules and on the net potential inside the solute cavity. The tetraphenyl arsonium-tetraphenyl borate (TATB) assumption as well as the cluster-continuum quasichemical theory (CC-QCT) approach for Li(+) solvation allows access to a solvation scale excluding the net potential. We have determined this free energy scale investigating the solvation of the lithium ion in water (H2O), acetonitrile (CH3CN) and dimethyl sulfoxide (DMSO) solvents via the CC-QCT approach. Our calculations at the MP2 and MP4 levels with basis sets up to the QZVPP+diff quality, and including solvation of the clusters and solvent molecules by the dielectric continuum SMD method, predict the solvation free energy of Li(+) as -116.1, -120.6 and -123.6 kcal mol(-1) in H2O, CH3CN and DMSO solvents, respectively (1 mol L(-1) standard state). These values are compatible with the solvation free energy of the proton of -253.4, -253.2 and -261.1 kcal mol(-1) in H2O, CH3CN and DMSO solvents, respectively. Deviations from the experimental TATB scale are only 1.3 kcal mol(-1) in H2O and 1.8 kcal mol(-1) in DMSO solvents. However, in the case of CH3CN, the deviation reaches a value of 9.2 kcal mol(-1). The present study suggests that the experimental TATB scale is inconsistent for CH3CN. A total of 125 values of the solvation free energy of ions in these three solvents were obtained. These new data should be useful for the development of theoretical solvation models.

The Thermodynamics of Anion Complexation to Nonpolar Pockets.

PubMed

Sullivan, Matthew R; Yao, Wei; Tang, Du; Ashbaugh, Henry S; Gibb, Bruce C

2018-02-08

The interactions between nonpolar surfaces and polarizable anions lie in a gray area between the hydrophobic and Hofmeister effects. To assess the affinity of these interactions, NMR and ITC were used to probe the thermodynamics of eight anions binding to four different hosts whose pockets each consist primarily of hydrocarbon. Two classes of host were examined: cavitands and cyclodextrins. For all hosts, anion affinity was found to follow the Hofmeister series, with associations ranging from 1.6-5.7 kcal mol -1 . Despite the fact that cavitand hosts 1 and 2 possess intrinsic negative electrostatic fields, it was determined that these more enveloping hosts generally bound anions more strongly. The observation that the four hosts each possess specific anion affinities that cannot be readily explained by their structures, points to the importance of counter cations and the solvation of the "empty" hosts, free guests, and host-guest complexes, in defining the affinity.

Transitioning NWChem to the Next Generation of Manycore Machines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bylaska, Eric J.; Apra, Edoardo; Kowalski, Karol

The NorthWest Chemistry (NWChem) modeling software is a popular molecular chemistry simulation software that was designed from the start to work on massively parallel processing supercomputers[6, 28, 49]. It contains an umbrella of modules that today includes Self Consistent Field (SCF), second order Mller-Plesset perturbation theory (MP2), Coupled Cluster, multi-conguration selfconsistent eld (MCSCF), selected conguration interaction (CI), tensor contraction engine (TCE) many body methods, density functional theory (DFT), time-dependent density functional theory (TDDFT), real time time-dependent density functional theory, pseudopotential plane-wave density functional theory (PSPW), band structure (BAND), ab initio molecular dynamics, Car-Parrinello molecular dynamics, classical molecular dynamics (MD), QM/MM,more » AIMD/MM, GIAO NMR, COSMO, COSMO-SMD, and RISM solvation models, free energy simulations, reaction path optimization, parallel in time, among other capabilities[ 22]. Moreover new capabilities continue to be added with each new release.« less

Neutral six-coordinate bis(dithiocarbamato)silicon(iv) complexes with an SiCl2S4 skeleton.

PubMed

Baus, Johannes A; Tacke, Reinhold

2017-07-11

Treatment of SiCl 4 with lithium dithiocarbamates of the formula type Li[R 2 NCS 2 ] (R = Ph, iPr) in a molar ratio of 1 : 2 afforded the respective six-coordinate silicon(iv) complexes [Ph 2 NCS 2 ] 2 SiCl 2 (3) and [iPr 2 NCS 2 ] 2 SiCl 2 (4), which were isolated as the solvates 3·MeCN and 4·MeCN. Compounds 3·MeCN and 4·MeCN were structurally characterised by single-crystal X-ray diffraction and multinuclear NMR spectroscopic studies in the solid state and in solution. In this study, dithiocarbamato ligands were implemented in silicon coordination chemistry for the first time. Compounds 3 and 4 represent the first six-coordinate silicon(iv) complexes with an SiCl 2 S 4 skeleton.

Induced Polarization Influences the Fundamental Forces in DNA Base Flipping

PubMed Central

2015-01-01

Base flipping in DNA is an important process involved in genomic repair and epigenetic control of gene expression. The driving forces for these processes are not fully understood, especially in the context of the underlying dynamics of the DNA and solvent effects. We studied double-stranded DNA oligomers that have been previously characterized by imino proton exchange NMR using both additive and polarizable force fields. Our results highlight the importance of induced polarization on the base flipping process, yielding near-quantitative agreement with experimental measurements of the equilibrium between the base-paired and flipped states. Further, these simulations allow us to quantify for the first time the energetic implications of polarization on the flipping pathway. Free energy barriers to base flipping are reduced by changes in dipole moments of both the flipped bases that favor solvation of the bases in the open state and water molecules adjacent to the flipping base. PMID:24976900

Magnetization transfer from laser-polarized xenon to protons located in the hydrophobic cavity of the wheat nonspecific lipid transfer protein

PubMed Central

Landon, Céline; Berthault, Patrick; Vovelle, Françoise; Desvaux, Hervé

2001-01-01

Nonspecific lipid transfer protein from wheat is studied by liquid-state NMR in the presence of xenon. The gas–protein interaction is indicated by the dependence of the protein proton chemical shifts on the xenon pressure and formally confirmed by the first observation of magnetization transfer from laser-polarized xenon to the protein protons. Twenty-six heteronuclear nOes have allowed the characterization of four interaction sites inside the wheat ns-LTP cavity. Their locations are in agreement with the variations of the chemical shifts under xenon pressure and with solvation simulations. The richness of the information obtained by the noble gas with a nuclear polarization multiplied by ∼12,000 makes this approach based on dipolar cross-relaxation with laser-polarized xenon promising for probing protein hydrophobic pockets at ambient pressure. PMID:11274467

Free energy of solvated salt bridges: a simulation and experimental study.

PubMed

White, Andrew D; Keefe, Andrew J; Ella-Menye, Jean-Rene; Nowinski, Ann K; Shao, Qing; Pfaendtner, Jim; Jiang, Shaoyi

2013-06-20

Charged amino acids are the most common on surfaces of proteins and understanding the interactions between these charged amino acids, salt bridging, is crucial for understanding protein-protein interactions. Previous simulations have been limited to implicit solvent or fixed binding geometry due to the sampling required for converged free energies. Using well-tempered metadynamics, we have calculated salt bridge free energy surfaces in water and confirmed the results with NMR experiments. The simulations give binding free energies, quantitative ranking of salt bridging strength, and insights into the hydration of the salt bridges. The arginine-aspartate salt bridge was found to be the weakest and arginine-glutamate the strongest, showing that arginine can discriminate between aspartate and glutamate, whereas the salt bridges with lysine are indistinguishable in their free energy. The salt bridging hydration is found to be complementary to salt bridge orientation with arginine having specific orientations.

Some heterocyclic azo dyes derived from thiazolyl derivatives; synthesis; substituent effects and solvatochromic studies

NASA Astrophysics Data System (ADS)

Yazdanbakhsh, M. R.; Mohammadi, A.; Abbasnia, M.

2010-12-01

A series of azo disperse dyes were synthesized by coupling reaction of N, N-diethylaniline, 2-anilinoethanol and N-phenyl-2,2'-iminodiethanol with diazotized aminothiazolyl derivatives as diazo components. These dyes have been prepared in good yields, and were characterized by UV-Vis, FT-IR and 1H NMR spectroscopic techniques. The effects of solvent polarity and various pH on dyes in the visible absorption spectra were evaluated. All dyes exhibit an excellent correlation coefficient ( r > 0.92) for the linear solvation energy relationship with π* values calculated by Kamlet et al. The influence of the pH on the dyes with electron-donating group implied that these dyes exist in acid-base equilibrium in acidic environment. The effect of substituents of both coupler and diazo component on the color of dyes was investigated as well.

Synthesis, structure and cytotoxic activity of acetylenic derivatives of betulonic and betulinic acids

NASA Astrophysics Data System (ADS)

Bębenek, Ewa; Chrobak, Elwira; Wietrzyk, Joanna; Kadela, Monika; Chrobak, Artur; Kusz, Joachim; Książek, Maria; Jastrzębska, Maria; Boryczka, Stanisław

2016-02-01

A series of acetylenic derivatives of betulonic and betulinic acids has been synthesized and characterized by 1H and 13C NMR, IR and MS spectroscopy. The structure of propargyl betulonate 4 and propargyl betulinate-DMF solvate 8A was solved by X-ray diffraction. Thermal properties were examined using a DSC technique. The resulting alkynyl derivatives, as well as betulin 1 and betulinic acid 3, were evaluated in vitro for their cytotoxic activity against human T47D breast cancer, CCRF/CEM leukemia, SW707 colorectal, murine P388 leukemia and BALB3T3 normal fibroblasts cell lines. Several of the obtained compounds have a favorable cytotoxic profile than betulin 1. Propargyl betulinate 8 was the most active derivative, being up to 3-fold more potent than betulin 1 against the human leukemia (CCRF/CEM) cell line, with an IC50 value of 3.9 μg/mL.

Proceedings of the U.S. Army Chemical Research, Development and Engineering Center Scientific Conference on Chemical Defense Research Held in Aberdeen Proving Ground, Maryland on 14-17 November 1989

DTIC Science & Technology

1990-08-01

to react in a similar electrochemical manner to the agent 2,21- dichlorodiethylsulfide (Mustard gas or HD). As a simulant for the nerve agents ...attack which may permit effective discrimination of pesticides from nerve agents in a chemical agent detector. Table 1 shows the results of film badge...amount of CASARM agent ( GA , GB, HD or VX) was placed into a 5 mm O.D. Pyrex NMR tube and 1.0 ml of the decontaminating solution was added. The tube was

Preparation of cerium halide solvate complexes

DOEpatents

Vasudevan, Kalyan V; Smith, Nickolaus A; Gordon, John C; McKigney, Edward A; Muenchaussen, Ross E

2013-08-06

Crystals of a solvated cerium(III) halide solvate complex resulted from a process of forming a paste of a cerium(III) halide in an ionic liquid, adding a solvent to the paste, removing any undissolved solid, and then cooling the liquid phase. Diffusing a solvent vapor into the liquid phase also resulted in crystals of a solvated cerium(III) halide complex.

Difference rule-a new thermodynamic principle: prediction of standard thermodynamic data for inorganic solvates.

PubMed

Jenkins, H Donald Brooke; Glasser, Leslie

2004-12-08

We present a quite general thermodynamic "difference" rule, derived from thermochemical first principles, quantifying the difference between the standard thermodynamic properties, P, of a solid n-solvate (or n-hydrate), n-S, containing n molecules of solvate, S (water or other) and the corresponding solid parent (unsolvated) salt: [P[n-solvate] - P[parent

Chemical structures and characteristics of animal manures and composts during composting and assessment of maturity indices

PubMed Central

Huang, Jieying; Yu, Zixuan; Gao, Hongjian; Yan, Xiaoming; Chang, Jiang; Wang, Chengming; Hu, Jingwei

2017-01-01

Changes in physicochemical characteristics, chemical structures and maturity of swine, cattle and chicken manures and composts during 70-day composting without addition of bulking agents were investigated. Physicochemical characteristics were measured by routine analyses and chemical structures by solid-state 13C NMR and FT-IR. Three manures were of distinct properties. Their changes in physicochemical characteristics, chemical structures, and maturity were different not only from each other but also from those with addition of bulking agents during composting. Aromaticity in chicken manure composts decreased at first, and then increased whereas that in cattle and swine manure composts increased. Enhanced ammonia volatilization occurred without addition of bulking agents. NMR structural information indicated that cattle and chicken composts were relatively stable at day 36 and 56, respectively, but swine manure composts were not mature up to day 70. Finally, the days required for three manures to reach the threshold values of different maturity indices were different. PMID:28604783

Emerging New Strategies for Successful Metabolite Identification in Metabolomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bingol, Ahmet K.; Bruschweiler-Li, Lei; Li, Dawei

2016-02-26

NMR is a very powerful tool for the identification of known and unknown (or unnamed) metabolites in complex mixtures as encountered in metabolomics. Known compounds can be reliably identified using 2D NMR methods, such as 13C-1H HSQC, for which powerful web servers with databases are available for semi-automated analysis. For the identification of unknown compounds, new combinations of NMR with MS have been developed recently that make synergistic use of the mutual strengths of the two techniques. The use of chemical additives to the NMR tube, such as reactive agents, paramagnetic ions, or charged silica nanoparticles, permit the identification ofmore » metabolites with specific physical chemical properties. In the following sections, we give an overview of some of the recent advances in metabolite identification and discuss remaining challenges.« less

Bis(2,3,5,6-tetra-2-pyridyl­pyrazine-κ3 N 2,N 1,N 6)nickel(II) dithio­cyanate dihydrate

PubMed Central

De la Pinta, Noelia; Fidalgo, M. Luz; Ezpeleta, José M.; Cortés, Roberto; Madariaga, Gotzon

2011-01-01

In the title compound, [Ni(C24H16N6)2](NCS)2·2H2O, the central NiII ion is octahedrally coordinated by six N atoms of two tridentate 2,3,5,6-tetra-2-pyridyl­pyrazine ligands (tppz). Two thio­cyanate anions act as counter-ions and two water mol­ecules act as solvation agents. O—H⋯N hydrogen bonds are observed in the crystral structure. PMID:21522540

A Comparison of QSAR Based Thermo and Water Solvation Property Prediction Tools and Experimental Data for Selected Traditional Chemical Warfare Agents and Simulants

DTIC Science & Technology

2014-07-01

Labs uses parameterized Hammett -type equations to describe 1500 possible combinations of more than 650 ionizable functional groups. The change in...of the form ⋯ , ⋯ Equation (1) where Ypred is the predicted property, c0 is a constant, c1 to cn are coefficients from the...regression to the training set of measurements, X1 to Xn represent molecular or fragment or field-based descriptors, and the final term in Equation 1

Lithium Ion Solvation and Diffusion in Bulk Organic Electrolytes from First-Principles and Classical Reactive Molecular Dynamics

DOE PAGES

Ong, Mitchell T.; Verners, Osvalds; Draeger, Erik W.; ...

2014-12-19

We report that lithium-ion battery performance is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact both the solvation and diffusivity of Li ions. In this work, we used first-principles molecular dynamics to examine the solvation and diffusion of Li ions in the bulk organic solvents ethylene carbonate (EC), ethyl methyl carbonate (EMC), and a mixture of EC and EMC. We found that Li ions are solvated by either carbonyl or ether oxygen atoms of the solvents and sometimes by the PF more » $$\\bar{6}$$ anion. Li + prefers a tetrahedrally coordinated first solvation shell regardless of which species are involved, with the specific preferred solvation structure dependent on the organic solvent. In addition, we calculated Li diffusion coefficients in each electrolyte, finding slightly larger diffusivities in the linear carbonate EMC compared to the cyclic carbonate EC. The magnitude of the diffusion coefficient correlates with the strength of Li + solvation. Corresponding analysis for the PF $$\\bar{6}$$ anion shows greater diffusivity associated with a weakly bound, poorly defined first solvation shell. In conclusion, these results can be used to aid in the design of new electrolytes to improve Li-ion battery performance.« less

Absolute single-ion solvation free energy scale in methanol determined by the lithium cluster-continuum approach.

PubMed

Pliego, Josefredo R; Miguel, Elizabeth L M

2013-05-02

Absolute solvation free energy of the lithium cation in methanol was calculated by the cluster-continuum quasichemical theory of solvation. Clusters with up to five methanol molecules were investigated using X3LYP, MP2, and MP4 methods with DZVP, 6-311+G(2df,2p), TZVPP+diff, and QZVPP+diff basis sets and including the cluster solvation through the PCM and SMD continuum models. Our calculations have determined a value of -118.1 kcal mol(-1) for the solvation free energy of the lithium, in close agreement with a value of -116.6 kcal mol(-1) consistent with the TATB assumption. Using data of solvation and transfer free energy of a pair of ions, electrode potentials and pKa, we have obtained the solvation free energy of 25 ions in methanol. Our analysis leads to a value of -253.6 kcal mol(-1) for the solvation free energy of the proton, which can be compared with the value of -263.5 kcal mol(-1) obtained by Kelly et al. using the cluster pair approximation. Considering that this difference is due to the methanol surface potential, we have estimated that it corresponds to -0.429 V.

Teaching Ionic Solvation Structure with a Monte Carlo Liquid Simulation Program

NASA Astrophysics Data System (ADS)

Serrano, Agostinho; Santos, Flávia M. T.; Greca, Ileana M.

2004-09-01

It is shown how basic aspects of ionic solvation structure, a fundamental topic for understanding different concepts and levels of representations of chemical structure and transformation, can be taught with the help of a Monte Carlo simulation package for molecular liquids. By performing a pair distribution function analysis of the solvation of Na + , Cl , and Ar in water, it is shown that it is feasible to explain the differences in solvation for these differently charged solutes. Visual representations of the solvated ions can also be employed to help the teaching activity. This may serve as an introduction to the study of solvation structure in chemistry undergraduate courses. The advantages of using tested, up-to-date scientific simulation programs as the fundamental bricks in the construction of virtual laboratories is also discussed.

Solid-state NMR as an effective method of polymorphic analysis: solid dosage forms of clopidogrel hydrogensulfate.

PubMed

Pindelska, Edyta; Szeleszczuk, Lukasz; Pisklak, Dariusz Maciej; Mazurek, Andrzej; Kolodziejski, Waclaw

2015-01-01

Clopidogrel hydrogensulfate (HSCL) is an antiplatelet agent, one of top-selling drugs in the world. In this paper, we have described a rapid and convenient method of verification which polymorph of HSCL is present in its final solid dosage form. Our methodology based on solid-state NMR spectroscopy and ab initio gauge-including projector-augmented wave calculations of NMR shielding constants is appropriate for currently available commercial solid dosage forms of HSCL. Furthermore, such structural characterization can assist with the development of new pharmaceutical products containing HSCL and also be useful in the identification of counterfeit drugs. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

A fast method for the determination of fractional contributions to solvation in proteins

PubMed Central

Talavera, David; Morreale, Antonio; Meyer, Tim; Hospital, Adam; Ferrer-Costa, Carles; Gelpi, Josep Lluis; de la Cruz, Xavier; Soliva, Robert; Luque, F. Javier; Orozco, Modesto

2006-01-01

A fast method for the calculation of residue contributions to protein solvation is presented. The approach uses the exposed polar and apolar surface of protein residues and has been parametrized from the fractional contributions to solvation determined from linear response theory coupled to molecular dynamics simulations. Application of the method to a large subset of proteins taken from the Protein Data Bank allowed us to compute the expected fractional solvation of residues. This information is used to discuss when a residue or a group of residues presents an uncommon solvation profile. PMID:17001031

Effects of solvent concentration and composition on protein dynamics: 13C MAS NMR studies of elastin in glycerol-water mixtures.

PubMed

Demuth, Dominik; Haase, Nils; Malzacher, Daniel; Vogel, Michael

2015-08-01

We use (13)C CP MAS NMR to investigate the dependence of elastin dynamics on the concentration and composition of the solvent at various temperatures. For elastin in pure glycerol, line-shape analysis shows that larger-scale fluctuations of the protein backbone require a minimum glycerol concentration of ~0.6 g/g at ambient temperature, while smaller-scale fluctuations are activated at lower solvation levels of ~0.2 g/g. Immersing elastin in various glycerol-water mixtures, we observe at room temperature that the protein mobility is higher for lower glycerol fractions in the solvent and, thus, lower solvent viscosity. When decreasing the temperature, the elastin spectra approach the line shape for the rigid protein at 245 K for all studied samples, indicating that the protein ceases to be mobile on the experimental time scale of ~10(-5) s. Our findings yield evidence for a strong coupling between elastin fluctuations and solvent dynamics and, hence, such interaction is not restricted to the case of protein-water mixtures. Spectral resolution of different carbon species reveals that the protein-solvent couplings can, however, be different for side chain and backbone units. We discuss these results against the background of the slaving model for protein dynamics. Copyright © 2015 Elsevier B.V. All rights reserved.

Conformational analyses of 2,3-dihydroxypropanoic acid as a function of solvent and ionization state as determined by NMR spectroscopy.

PubMed

Drake, Michael D; Harsha, Alex K; Terterov, Sergei; Roberts, John D

2006-03-01

Vicinal (1)H--(1)H coupling constants were used to determine the conformational preferences of 2,3-dihydroxypropanoic acid (1) (DL-glyceric acid) in various solvents and its different carboxyl ionization states. The stereospecific assignments of J(12) and J(13) were confirmed through the point-group substitution of the C-3 hydrogen with deuterium, yielding rac-(2SR,3RS)-[3-(2)H]-1, and the observation of only J(13) in the (1)H NMR spectra. While hydrogen bonding and steric strain may be expected to drive the conformational equilibrium, their role is overshadowed by a profound gauche effect between the vicinal hydroxyl groups that mimics other substituted ethanes, such as 1,2-ethanediol and 1,2-difluoroethane. At low pH, the conformational equilibrium is heavily weighted toward the gauche-hydroxyl rotamers with a range of 81% in DMSO-d(6) to 92% in tert-butyl alcohol-d(10). At high pH, the equilibrium exhibits a larger dependence upon the polarity and solvating capability of the medium, although the gauche effect still dominates in D(2)O, 1,4-dioxane-d(8), methanol-d(4), and ethanol-d(6) (96, 89, 85, and 83% gauche-hydroxyls respectively). The observed preference for the gauche-hydroxyl rotamers is believed to stem primarily from hyperconjugative sigma(C--H) --> sigma*(C--OH) interactions.

SABRE hyperpolarization enables high-sensitivity 1H and 13C benchtop NMR spectroscopy.

PubMed

Richardson, Peter M; Parrott, Andrew J; Semenova, Olga; Nordon, Alison; Duckett, Simon B; Halse, Meghan E

2018-06-19

Benchtop NMR spectrometers operating with low magnetic fields of 1-2 T at sub-ppm resolution show great promise as analytical platforms that can be used outside the traditional laboratory environment for industrial process monitoring. One current limitation that reduces the uptake of benchtop NMR is associated with the detection fields' reduced sensitivity. Here we demonstrate how para-hydrogen (p-H2) based signal amplification by reversible exchange (SABRE), a simple to achieve hyperpolarization technique, enhances agent detectability within the environment of a benchtop (1 T) NMR spectrometer so that informative 1H and 13C NMR spectra can be readily recorded for low-concentration analytes. SABRE-derived 1H NMR signal enhancements of up to 17 000-fold, corresponding to 1H polarization levels of P = 5.9%, were achieved for 26 mM pyridine in d4-methanol in a matter of seconds. Comparable enhancement levels can be achieved in both deuterated and protio solvents but now the SABRE-enhanced analyte signals dominate due to the comparatively weak thermally-polarized solvent response. The SABRE approach also enables the acquisition of 13C NMR spectra of analytes at natural isotopic abundance in a single scan as evidenced by hyperpolarized 13C NMR spectra of tens of millimolar concentrations of 4-methylpyridine. Now the associated signal enhancement factors are up to 45 500 fold (P = 4.0%) and achieved in just 15 s. Integration of an automated SABRE polarization system with the benchtop NMR spectrometer framework produces renewable and reproducible NMR signal enhancements that can be exploited for the collection of multi-dimensional NMR spectra, exemplified here by a SABRE-enhanced 2D COSY NMR spectrum.

Ionomer Design, Synthesis and Characterization for Ion-Conducting Energy Materials

NASA Astrophysics Data System (ADS)

Colby, Ralph H.

2013-03-01

For ionic actuators and battery separators, it is vital to utilize single-ion conductors that avoid the detrimental polarization of other ions; the commonly studied dual-ion conductors simply will not be used in the next generation of materials for these applications. Ab initio quantum chemistry calculations at 0 K in vacuum characterize ion interactions and ion solvation by various functional groups, allowing identification of constituents with weak interactions to be incorporated in ionomers for facile ion transport. Simple ideas for estimating the ion interactions and solvation at practical temperatures and dielectric constants are presented that indicate the rank ordering observed at 0 K in vacuum should be preserved. Hence, such ab initio calculations are useful for screening the plethora of combinations of polymer-ion, counterion and polar functional groups, to decide which are worthy of synthesis for new ionomers. Single-ion conducting ionomers are synthesized based on these calculations, with low glass transition temperatures (facile dynamics) to prepare ion-conducting membranes for ionic actuators and battery separators. Characterization by X-ray scattering, dielectric spectroscopy, NMR and linear viscoelasticity collectively develop a coherent picture of ionic aggregation and both counterion and polymer dynamics. Examples are shown of how ab initio calculations can be used to understand experimental observations of dielectric constant, glass transition temperature and conductivity of polymerized ionic liquids with counterions being either lithium, sodium, fluoride, hydroxide (for batteries) or bulky ionic liquids (for ionic actuators). This work was supported by the Department of Energy under Grant BES-DE-FG02-07ER46409.

Differential geometry based solvation model. III. Quantum formulation

PubMed Central

Chen, Zhan; Wei, Guo-Wei

2011-01-01

Solvation is of fundamental importance to biomolecular systems. Implicit solvent models, particularly those based on the Poisson-Boltzmann equation for electrostatic analysis, are established approaches for solvation analysis. However, ad hoc solvent-solute interfaces are commonly used in the implicit solvent theory. Recently, we have introduced differential geometry based solvation models which allow the solvent-solute interface to be determined by the variation of a total free energy functional. Atomic fixed partial charges (point charges) are used in our earlier models, which depends on existing molecular mechanical force field software packages for partial charge assignments. As most force field models are parameterized for a certain class of molecules or materials, the use of partial charges limits the accuracy and applicability of our earlier models. Moreover, fixed partial charges do not account for the charge rearrangement during the solvation process. The present work proposes a differential geometry based multiscale solvation model which makes use of the electron density computed directly from the quantum mechanical principle. To this end, we construct a new multiscale total energy functional which consists of not only polar and nonpolar solvation contributions, but also the electronic kinetic and potential energies. By using the Euler-Lagrange variation, we derive a system of three coupled governing equations, i.e., the generalized Poisson-Boltzmann equation for the electrostatic potential, the generalized Laplace-Beltrami equation for the solvent-solute boundary, and the Kohn-Sham equations for the electronic structure. We develop an iterative procedure to solve three coupled equations and to minimize the solvation free energy. The present multiscale model is numerically validated for its stability, consistency and accuracy, and is applied to a few sets of molecules, including a case which is difficult for existing solvation models. Comparison is made to many other classic and quantum models. By using experimental data, we show that the present quantum formulation of our differential geometry based multiscale solvation model improves the prediction of our earlier models, and outperforms some explicit solvation model. PMID:22112067

O2-dependent Aliphatic Carbon-carbon Bond Cleavage Reactivity in a Ni(II) Enolate Complex Having a Hydrogen Bond Donor Microenvironment; Comparison with a Hydrophobic Analog

PubMed Central

Grubel, Katarzyna; Fuller, Amy L.; Chambers, Bonnie M.; Arif, Atta M.; Berreau, Lisa M.

2010-01-01

A mononuclear Ni(II) complex having an acireductone type ligand, and supported by the bnpapa (N,N-bis((6-neopentylamino-2-pyridyl)methyl-N-((2-pyridyl)methyl)amine ligand, [(bnpapa)Ni(PhC(O)C(OH)C(O)Ph)]ClO4 (14), has been prepared and characterized by elemental analysis, 1H NMR, FTIR, and UV-vis. To gain insight into the 1H NMR features of 14, the air stable analog complexes [(bnpapa)Ni(CH3C(O)CHC(O)CH3)]ClO4 (16) and [(bnpapa)Ni(ONHC(O)CH3)]ClO4 (17) were prepared and characterized by X-ray crystallography, 1H NMR, FTIR, UV-vis, mass spectrometry, and solution conductivity measurements. Compounds 16 and 17 are 1:1 electrolyte species in CH3CN. 1H and 2H NMR studies of 14, 16, and 17 and deuterated analogs revealed that the complexes having six-membered chelate rings for the exogenous ligand (14 and 16) do not have a plane of symmetry within the solvated cation and thus exhibit more complicated 1H NMR spectra. Compound 17, as well as other simple Ni(II) complexes of the bnpapa ligand (e.g. [(bnpapa)Ni(ClO4)(CH3CN)]ClO4 (18) and [(bnpapaNi)2(μ-Cl)2](ClO4)2 (19)), exhibit 1H NMR spectra consistent with the presence of a plane of symmetry within the cation. Treatment of [(bnpapa)Ni(PhC(O)C(OH)C(O)Ph)]ClO4 (14) with O2 results in aliphatic carbon-carbon bond cleavage within the acireductone-type ligand and the formation of [(bnpapa)Ni(O2CPh)]ClO4 (9), benzoic acid, benzil, and CO. Use of 18O2 in the reaction gives high levels of incorporation (>80%) of one labeled oxygen atom into 9 and benzoic acid. The product mixture and level of 18O incorporation in this reaction is different than that exhibited by the analog supported the hydrophobic 6-Ph2TPA ligand, [(6-Ph2TPA)Ni(PhC(O)C(OH)C(O)Ph)]ClO4 (2). We propose that this difference is due to variations in the reactivity of bnpapa- and 6-Ph2TPA-ligated Ni(II) complexes with triketone and/or peroxide species produced in the reaction pathway. PMID:20039645

Towards MRI microarrays.

PubMed

Hall, Andrew; Mundell, Victoria J; Blanco-Andujar, Cristina; Bencsik, Martin; McHale, Glen; Newton, Michael I; Cave, Gareth W V

2010-04-14

Superparamagnetic iron oxide nanometre scale particles have been utilised as contrast agents to image staked target binding oligonucleotide arrays using MRI to correlate the signal intensity and T(2)* relaxation times in different NMR fluids.

The solvation of ions in acetonitrile and acetone. II. Monte Carlo simulations using polarizable solvent models

NASA Astrophysics Data System (ADS)

Fischer, R.; Richardi, J.; Fries, P. H.; Krienke, H.

2002-11-01

Structural properties and energies of solvation are simulated for alkali and halide ions. The solvation structure is discussed in terms of various site-site distribution functions, of solvation numbers, and of orientational correlation functions of the solvent molecules around the ions. The solvent polarizability has notable effects which cannot be intuitively predicted. In particular, it is necessary to reproduce the experimental solvation numbers of small ions. The changes of solvation properties are investigated along the alkali and halide series. By comparing the solvation of ions in acetone to that in acetonitrile, it is shown that the spatial correlations among the solvent molecules around an ion result in a strong screening of the ion-solvent direct intermolecular potential and are essential to understand the changes in the solvation structures and energies between different solvents. The solvation properties derived from the simulations are compared to earlier predictions of the hypernetted chain (HNC) approximation of the molecular Ornstein-Zernike (MOZ) theory [J. Richardi, P. H. Fries, and H. Krienke, J. Chem. Phys. 108, 4079 (1998)]. The MOZ(HNC) formalism gives an overall qualitatively correct picture of the solvation and its various unexpected findings are corroborated. For the larger ions, its predictions become quantitative. The MOZ approach allows to calculate solvent-solvent and ion-solvent potentials of mean force, which shed light on the 3D labile molecular and ionic architectures in the solution. These potentials of mean force convey a unique information which is necessary to fully interpret the angle-averaged structural functions computed from the simulations. Finally, simulations of solutions at finite concentrations show that the solvent-solvent and ion-solvent spatial correlations at infinite dilution are marginally altered by the introduction of fair amounts of ions.

How to study picosecond solvation dynamics using fluorescent probes with small Stokes shifts

NASA Astrophysics Data System (ADS)

Silori, Yogita; Dey, Shivalee; De, Arijit K.

2018-02-01

Xanthene dyes have wide ranging applications as fluorescent probes in analytical, biochemical and medical contexts. Being cationic/anionic in nature, the solvation dynamics of xanthene dyes confined within a negatively/positively charged interface are very interesting. Unfortunately, the floppy structure and small Stokes shift render any xanthene dye unsuitable for use as a solvation probe. Using di-sodium fluorescein, we present our work on the picosecond solvation dynamics of bulk and confined water (at pH = 9.2). We also propose a new methodology for studying picosecond solvation dynamics using any fluorescent dye with a small Stokes shift. We discuss how scattering contributions can be effectively removed, and propose an alternative way of defining zero time of solvation. Finally, we demonstrate the tuning location of the probe within confinement.

Heterogeneous Microtesla SABRE Enhancement of 15 N NMR Signals.

PubMed

Kovtunov, Kirill V; Kovtunova, Larisa M; Gemeinhardt, Max E; Bukhtiyarov, Andrey V; Gesiorski, Jonathan; Bukhtiyarov, Valerii I; Chekmenev, Eduard Y; Koptyug, Igor V; Goodson, Boyd M

2017-08-21

The hyperpolarization of heteronuclei via signal amplification by reversible exchange (SABRE) was investigated under conditions of heterogeneous catalysis and microtesla magnetic fields. Immobilization of [IrCl(COD)(IMes)], [IMes=1,3-bis(2,4,6-trimethylphenyl), imidazole-2-ylidene; COD=cyclooctadiene] catalyst onto silica particles modified with amine linkers engenders an effective heterogeneous SABRE (HET-SABRE) catalyst that was used to demonstrate a circa 100-fold enhancement of 15 N NMR signals in 15 N-pyridine at 9.4 T following parahydrogen bubbling within a magnetic shield. No 15 N NMR enhancement was observed from the supernatant liquid following catalyst separation, which along with XPS characterization supports the fact that the effects result from SABRE under heterogeneous catalytic conditions. The technique can be developed further for producing catalyst-free agents via SABRE with hyperpolarized heteronuclear spins, and thus is promising for biomedical NMR and MRI applications. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Intercalation complex of proflavine with DNA: Structure and dynamics by solid-state NMR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Pei; Juang, Chilong; Harbison, G.S.

1990-07-06

The structure of the complex formed between the intercalating agent proflavine and fibrous native DNA was studied by one- and two-dimensional high-resolution solid-state nuclear magnetic resonance (NMR). Carbon-13-labeled proflavine was used to show that the drug is stacked with the aromatic ring plane perpendicular to the fiber axis and that it is essentially immobile. Natural abundance carbon-13 NMR of the DNA itself shows that proflavine binding does not change the puckering of the deoxyribose ring. However, phosphorus-31 NMR spectra show profound changes in the orientation of the phosphodiester grouping on proflavine binding, with some of the phosphodiesters tilting almost parallelmore » to the helix axis, and a second set almost perpendicular. The first group to the phosphodiesters probably spans the intercalation sites, whereas the tilting of the second set likely compensates for the unwinding of the DNA by the intercalator.« less

Production and NMR signal optimization of hyperpolarized 13C-labeled amino acids

NASA Astrophysics Data System (ADS)

Parish, Christopher; Niedbalski, Peter; Ferguson, Sarah; Kiswandhi, Andhika; Lumata, Lloyd

Amino acids are targeted nutrients for consumption by cancers to sustain their rapid growth and proliferation. 13C-enriched amino acids are important metabolic tracers for cancer diagnostics using nuclear magnetic resonance (NMR) spectroscopy. Despite this diagnostic potential, 13C NMR of amino acids however is hampered by the inherently low NMR sensitivity of the 13C nuclei. In this work, we have employed a physics technique known as dynamic nuclear polarization (DNP) to enhance the NMR signals of 13C-enriched amino acids. DNP works by transferring the high polarization of electrons to the nuclear spins via microwave irradiation at low temperature and high magnetic field. Using a fast dissolution method in which the frozen polarized samples are dissolved rapidly with superheated water, injectable solutions of 13C-amino acids with highly enhanced NMR signals (by at least 5,000-fold) were produced at room temperature. Factors that affect the NMR signal enhancement levels such as the choice of free radical polarizing agents and sample preparation will be discussed along with the thermal mixing physics model of DNP. The authors would like to acknowledge the support by US Dept of Defense Award No. W81XWH-14-1-0048 and Robert A. Welch Foundation Grant No. AT-1877.

Using 2H labelling to improve the NMR detectability of pyridine and its derivatives by SABRE

PubMed Central

Norcott, Philip; Burns, Michael J.; Rayner, Peter J.; Mewis, Ryan E.

2018-01-01

By introducing a range of 2H labels into pyridine and the para‐substituted agents, methyl isonicotinate and isonicotinamide, we significantly improve their NMR detectability in conjunction with the signal amplification by reversible exchange process. We describe how the rates of T 1 relaxation for the remaining 1H nuclei are increased and show how this leads to a concomitant increase in the level of 1H and 13C hyperpolarization that can ultimately be detected. PMID:29274294

Theory of competitive solvation of polymers by two solvents and entropy-enthalpy compensation in the solvation free energy upon dilution with the second solvent.

PubMed

Dudowicz, Jacek; Freed, Karl F; Douglas, Jack F

2015-06-07

We develop a statistical mechanical lattice theory for polymer solvation by a pair of relatively low molar mass solvents that compete for binding to the polymer backbone. A theory for the equilibrium mixture of solvated polymer clusters {AiBCj} and free unassociated molecules A, B, and C is formulated in the spirit of Flory-Huggins mean-field approximation. This theoretical framework enables us to derive expressions for the boundaries for phase stability (spinodals) and other basic properties of these polymer solutions: the internal energy U, entropy S, specific heat CV, extent of solvation Φsolv, average degree of solvation 〈Nsolv〉, and second osmotic virial coefficient B2 as functions of temperature and the composition of the mixture. Our theory predicts many new phenomena, but the current paper applies the theory to describe the entropy-enthalpy compensation in the free energy of polymer solvation, a phenomenon observed for many years without theoretical explanation and with significant relevance to liquid chromatography and other polymer separation methods.

Relative complexation energies for Li(+) ion in solution: molecular level solvation versus polarizable continuum model study.

PubMed

Eilmes, Andrzej; Kubisiak, Piotr

2010-01-21

Relative complexation energies for the lithium cation in acetonitrile and diethyl ether have been studied. Quantum-chemical calculations explicitly describing the solvation of Li(+) have been performed based on structures obtained from molecular dynamics simulations. The effect of an increasing number of solvent molecules beyond the first solvation shell has been found to consist in reduction of the differences in complexation energies for different coordination numbers. Explicit-solvation data have served as a benchmark to the results of polarizable continuum model (PCM) calculations. It has been demonstrated that the PCM approach can yield relative complexation energies comparable to the predictions based on molecular-level solvation, but at significantly lower computational cost. The best agreement between the explicit-solvation and the PCM results has been obtained when the van der Waals surface was adopted to build the molecular cavity.

Comparative assessment of computational methods for the determination of solvation free energies in alcohol-based molecules.

PubMed

Martins, Silvia A; Sousa, Sergio F

2013-06-05

The determination of differences in solvation free energies between related drug molecules remains an important challenge in computational drug optimization, when fast and accurate calculation of differences in binding free energy are required. In this study, we have evaluated the performance of five commonly used polarized continuum model (PCM) methodologies in the determination of solvation free energies for 53 typical alcohol and alkane small molecules. In addition, the performance of these PCM methods, of a thermodynamic integration (TI) protocol and of the Poisson-Boltzmann (PB) and generalized Born (GB) methods, were tested in the determination of solvation free energies changes for 28 common alkane-alcohol transformations, by the substitution of an hydrogen atom for a hydroxyl substituent. The results show that the solvation model D (SMD) performs better among the PCM-based approaches in estimating solvation free energies for alcohol molecules, and solvation free energy changes for alkane-alcohol transformations, with an average error below 1 kcal/mol for both quantities. However, for the determination of solvation free energy changes on alkane-alcohol transformation, PB and TI yielded better results. TI was particularly accurate in the treatment of hydroxyl groups additions to aromatic rings (0.53 kcal/mol), a common transformation when optimizing drug-binding in computer-aided drug design. Copyright © 2013 Wiley Periodicals, Inc.

MTS-MD of Biomolecules Steered with 3D-RISM-KH Mean Solvation Forces Accelerated with Generalized Solvation Force Extrapolation.

PubMed

Omelyan, Igor; Kovalenko, Andriy

2015-04-14

We developed a generalized solvation force extrapolation (GSFE) approach to speed up multiple time step molecular dynamics (MTS-MD) of biomolecules steered with mean solvation forces obtained from the 3D-RISM-KH molecular theory of solvation (three-dimensional reference interaction site model with the Kovalenko-Hirata closure). GSFE is based on a set of techniques including the non-Eckart-like transformation of coordinate space separately for each solute atom, extension of the force-coordinate pair basis set followed by selection of the best subset, balancing the normal equations by modified least-squares minimization of deviations, and incremental increase of outer time step in motion integration. Mean solvation forces acting on the biomolecule atoms in conformations at successive inner time steps are extrapolated using a relatively small number of best (closest) solute atomic coordinates and corresponding mean solvation forces obtained at previous outer time steps by converging the 3D-RISM-KH integral equations. The MTS-MD evolution steered with GSFE of 3D-RISM-KH mean solvation forces is efficiently stabilized with our optimized isokinetic Nosé-Hoover chain (OIN) thermostat. We validated the hybrid MTS-MD/OIN/GSFE/3D-RISM-KH integrator on solvated organic and biomolecules of different stiffness and complexity: asphaltene dimer in toluene solvent, hydrated alanine dipeptide, miniprotein 1L2Y, and protein G. The GSFE accuracy and the OIN efficiency allowed us to enlarge outer time steps up to huge values of 1-4 ps while accurately reproducing conformational properties. Quasidynamics steered with 3D-RISM-KH mean solvation forces achieves time scale compression of conformational changes coupled with solvent exchange, resulting in further significant acceleration of protein conformational sampling with respect to real time dynamics. Overall, this provided a 50- to 1000-fold effective speedup of conformational sampling for these systems, compared to conventional MD with explicit solvent. We have been able to fold the miniprotein from a fully denatured, extended state in about 60 ns of quasidynamics steered with 3D-RISM-KH mean solvation forces, compared to the average physical folding time of 4-9 μs observed in experiment.

Chemical analysis of bleach and hydroxide-based solutions after decontamination of the chemical warfare agent O-ethyl S-2-diisopropylaminoethyl methylphosphonothiolate (VX).

PubMed

Hopkins, F B; Gravett, M R; Self, A J; Wang, M; Chua, Hoe-Chee; Hoe-Chee, C; Lee, H S Nancy; Sim, N Lee Hoi; Jones, J T A; Timperley, C M; Riches, J R

2014-08-01

Detailed chemical analysis of solutions used to decontaminate chemical warfare agents can be used to support verification and forensic attribution. Decontamination solutions are amongst the most difficult matrices for chemical analysis because of their corrosive and potentially emulsion-based nature. Consequently, there are relatively few publications that report their detailed chemical analysis. This paper describes the application of modern analytical techniques to the analysis of decontamination solutions following decontamination of the chemical warfare agent O-ethyl S-2-diisopropylaminoethyl methylphosphonothiolate (VX). We confirm the formation of N,N-diisopropylformamide and N,N-diisopropylamine following decontamination of VX with hypochlorite-based solution, whereas they were not detected in extracts of hydroxide-based decontamination solutions by nuclear magnetic resonance (NMR) spectroscopy or gas chromatography-mass spectrometry. We report the electron ionisation and chemical ionisation mass spectroscopic details, retention indices, and NMR spectra of N,N-diisopropylformamide and N,N-diisopropylamine, as well as analytical methods suitable for their analysis and identification in solvent extracts and decontamination residues.

Breaking the polar-nonpolar division in solvation free energy prediction.

PubMed

Wang, Bao; Wang, Chengzhang; Wu, Kedi; Wei, Guo-Wei

2018-02-05

Implicit solvent models divide solvation free energies into polar and nonpolar additive contributions, whereas polar and nonpolar interactions are inseparable and nonadditive. We present a feature functional theory (FFT) framework to break this ad hoc division. The essential ideas of FFT are as follows: (i) representability assumption: there exists a microscopic feature vector that can uniquely characterize and distinguish one molecule from another; (ii) feature-function relationship assumption: the macroscopic features, including solvation free energy, of a molecule is a functional of microscopic feature vectors; and (iii) similarity assumption: molecules with similar microscopic features have similar macroscopic properties, such as solvation free energies. Based on these assumptions, solvation free energy prediction is carried out in the following protocol. First, we construct a molecular microscopic feature vector that is efficient in characterizing the solvation process using quantum mechanics and Poisson-Boltzmann theory. Microscopic feature vectors are combined with macroscopic features, that is, physical observable, to form extended feature vectors. Additionally, we partition a solvation dataset into queries according to molecular compositions. Moreover, for each target molecule, we adopt a machine learning algorithm for its nearest neighbor search, based on the selected microscopic feature vectors. Finally, from the extended feature vectors of obtained nearest neighbors, we construct a functional of solvation free energy, which is employed to predict the solvation free energy of the target molecule. The proposed FFT model has been extensively validated via a large dataset of 668 molecules. The leave-one-out test gives an optimal root-mean-square error (RMSE) of 1.05 kcal/mol. FFT predictions of SAMPL0, SAMPL1, SAMPL2, SAMPL3, and SAMPL4 challenge sets deliver the RMSEs of 0.61, 1.86, 1.64, 0.86, and 1.14 kcal/mol, respectively. Using a test set of 94 molecules and its associated training set, the present approach was carefully compared with a classic solvation model based on weighted solvent accessible surface area. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

On the solvation of hydronium by carbon dioxide: Structural and infrared spectroscopic study of (H3O+)(CO2)n

NASA Astrophysics Data System (ADS)

Yang, Jianpeng; Kong, Xiangtao; Jiang, Ling

2018-02-01

Hydronium (H3O+) is the smallest member of protonated water. In this work, we use quantum chemical calculations to explore the solvation of H3O+ by adding one CO2 molecule at a time. The effect of stepwise solvation on infrared spectroscopy, structure, and energetics has been systematically studied. It has been found that the first solvation shell of H3O+ is completed at n = 6. Besides the hydrogen-bond interaction, the CCO2-OCO2 intermolecular interaction is also responsible for the stabilization of the larger clusters. The transfer of the proton from H3O+ onto CO2 with the formation of the OCOH+ moiety is not observed in the early stage of solvation process. Calculated IR spectra suggest that vibrational frequencies of H-bonded Osbnd H stretching would afford a sensitive probe for exploring the early stage solvation of hydronium by carbon dioxide. IR spectra for the (H3O+)(CO2)n (n = 1-7) clusters could be measured by the infrared photodissociation spectroscopic technique and thus provide a vivid physical picture about how carbon dioxide solvates the hydronium.

Crystallization of toxic glycol solvates of rifampin from glycerin and propylene glycol contaminated with ethylene glycol or diethylene glycol.

PubMed

de Villiers, Melgardt M; Caira, Mino R; Li, Jinjing; Strydom, Schalk J; Bourne, Susan A; Liebenberg, Wilna

2011-06-06

This study was initiated when it was suspected that syringe blockage experienced upon administration of a compounded rifampin suspension was caused by the recrystallization of toxic glycol solvates of the drug. Single crystal X-ray structure analysis, powder X-ray diffraction, thermal analysis and gas chromatography were used to identify the ethylene glycol in the solvate crystals recovered from the suspension. Controlled crystallization and solubility studies were used to determine the ease with which toxic glycol solvates crystallized from glycerin and propylene glycol contaminated with either ethylene or diethylene glycol. The single crystal structures of two distinct ethylene glycol solvates of rifampin were solved while thermal analysis, GC analysis and solubility studies confirmed that diethylene glycol solvates of the drug also crystallized. Controlled crystallization studies showed that crystallization of the rifampin solvates from glycerin and propylene glycol depended on the level of contamination and changes in the solubility of the drug in the contaminated solvents. Although the exact source of the ethylene glycol found in the compounded rifampin suspension is not known, the results of this study show how important it is to ensure that the drug and excipients comply with pharmacopeial or FDA standards.

Synergistic behavior of glycine betaine-urea mixture: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Kumar, Narendra; Kishore, Nand

2013-09-01

Glycine betaine (GB) is one of the most important osmolyte which is known to stabilize proteins as well as counteract the denaturing effect of urea. There have been many studies indicating protein stabilization and counteraction of the effect of urea by GB. However, the exact mechanism of counteraction is still debated and is of important research interest. In this study, distribution functions, hydrogen bonds, and energetics were analysed to understand different interactions between GB and urea, and their solvation properties in presence of each other. The results show that in the GB-urea mixture, GB acted as a stronger osmolyte and urea became a weaker denaturing agent than its individual counterparts. The increase in the solvation of urea and GB in GB-urea mixture and their mutual interactions through hydrogen bonding and coulombic energy resulted in more involvement of GB and urea with solvent as well as with themselves. This might result in the increase of the exclusion of GB from protein surface and decrease in the protein-urea interactions in the mixture. This synergistic behavior might be the prime reason for the counteraction of denaturing effect of urea by GB.

Rationalization of the solvation effects on the AtO+ ground-state change.

PubMed

Ayed, Tahra; Réal, Florent; Montavon, Gilles; Galland, Nicolas

2013-09-12

(211)At radionuclide is of considerable interest as a radiotherapeutic agent for targeted alpha therapy in nuclear medicine, but major obstacles remain because the basic chemistry of astatine (At) is not well understood. The AtO(+) cationic form might be currently used for (211)At-labeling protocols in aqueous solution and has proved to readily react with inorganic/organic ligands. But AtO(+) reactivity must be hindered at first glance by spin restriction quantum rules: the ground state of the free cation has a dominant triplet character. Investigating AtO(+) clustered with an increasing number of water molecules and using various flavors of relativistic quantum methods, we found that AtO(+) adopts in solution a Kramers restricted closed-shell configuration resembling a scalar-relativistic singlet. The ground-state change was traced back to strong interactions, namely, attractive electrostatic interactions and charge transfer, with water molecules of the first solvation shell that lift up the degeneracy of the frontier π* molecular orbitals (MOs). This peculiarity brings an alternative explanation to the highly variable reproducibility reported for some astatine reactions: depending on the production protocols (with distillation in gas-phase or "wet chemistry" extraction), (211)At may or may not readily react.

Hydrophobic Solvation: Aqueous Methane Solutions

ERIC Educational Resources Information Center

Konrod, Oliver; Lankau, Timm

2007-01-01

A basic introduction to concept of a solvation shell around an apolar solute as well as its detection is presented. The hydrophobic solvation of toluene is found to be a good teaching example which connects macroscopic, phenomenological thermodynamic results with an atomistic point of view.

Development of an 19F NMR method for the analysis of fluorinated acids in environmental water samples.

PubMed

Ellis, D A; Martin, J W; Muir, D C; Mabury, S A

2000-02-15

This investigation was carried out to evaluate 19F NMR as an analytical tool for the measurement of trifluoroacetic acid (TFA) and other fluorinated acids in the aquatic environment. A method based upon strong anionic exchange (SAX) chromatography was also optimized for the concentration of the fluoro acids prior to NMR analysis. Extraction of the analyte from the SAX column was carried out directly in the NMR solvent in the presence of the strong organic base, DBU. The method allowed the analysis of the acid without any prior cleanup steps being involved. Optimal NMR sensitivity based upon T1 relaxation times was investigated for seven fluorinated compounds in four different NMR solvents. The use of the relaxation agent chromium acetylacetonate, Cr(acac)3, within these solvent systems was also evaluated. Results show that the optimal NMR solvent differs for each fluorinated analyte. Cr(acac)3 was shown to have pronounced effects on the limits of detection of the analyte. Generally, the optimal sensitivity condition appears to be methanol-d4/2M DBU in the presence of 4 mg/mL of Cr-(acac)3. The method was validated through spike and recovery for five fluoro acids from environmentally relevant waters. Results are presented for the analysis of TFA in Toronto rainwater, which ranged from < 16 to 850 ng/L. The NMR results were confirmed by GC-MS selected-ion monitoring of the fluoroanalide derivative.

Role of Dispersive Fluorous Interaction in the Solvation Dynamics of the Perfluoro Group Containing Molecules.

PubMed

Mondal, Saptarsi; Chaterjee, Soumit; Halder, Ritaban; Jana, Biman; Singh, Prashant Chandra

2017-08-17

Perfluoro group containing molecules possess an important self-aggregation property through the fluorous (F···F) interaction which makes them useful for diverse applications such as medicinal chemistry, separation techniques, polymer technology, and biology. In this article, we have investigated the solvation dynamics of coumarin-153 (C153) and coumarin-6H (C6H) in ethanol (ETH), 2-fluoroethanol (MFE), and 2,2,2-trifluoroethanol (TFE) using the femtosecond upconversion technique and molecular dynamics (MD) simulation to understand the role of fluorous interaction between the solute and solvent molecules in the solvation dynamics of perfluoro group containing molecules. The femtosecond upconversion data show that the time scales of solvation dynamics of C6H in ETH, MFE, and TFE are approximately the same whereas the solvation dynamics of C153 in TFE is slow as compared to that of ETH and MFE. It has also been observed that the time scale of solvation dynamics of C6H in ETH and MFE is higher than that of C153 in the same solvents. MD simulation results show a qualitative agreement with the experimental data in terms of the time scale of the slow components of the solvation for all the systems. The experimental and simulation studies combined lead to the conclusion that the solvation dynamics of C6H in all solvents as well as C153 in ETH and MFE is mostly governed by the charge distribution of ester moieties (C═O and O) of dye molecules whereas the solvation of C153 in TFE is predominantly due to the dispersive fluorous interaction (F···F) between the perfluoro groups of the C153 and solvent molecules.

Biomolecular electrostatics and solvation: a computational perspective

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G.

2012-11-01

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. Thismore » review discusses the solvation of biomolecules with a computational biophysics view towards describing the phenomenon. While our main focus lies on the computational aspect of the models, we summarize the common characteristics of biomolecular solvation (e.g., solvent structure, polarization, ion binding, and nonpolar behavior) in order to provide reasonable backgrounds to understand the solvation models.« less

Biomolecular electrostatics and solvation: a computational perspective

PubMed Central

Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G.; Schnieders, Michael J.; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A.

2012-01-01

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view towards describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g., solvent structure, polarization, ion binding, and nonpolar behavior) in order to provide a background to understand the different types of solvation models. PMID:23217364

Biomolecular electrostatics and solvation: a computational perspective.

PubMed

Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G; Schnieders, Michael J; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A

2012-11-01

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.

Readily Made Solvated Electrons

ERIC Educational Resources Information Center

Ibanez, Jorge G.; Guerra-Millan, Francisco J.; Hugerat, Muhamad; Vazquez-Olavarrieta, Jorge L.; Basheer, Ahmad; Abu-Much, Riam

2011-01-01

The existence of solvated electrons has been known for a long time. Key methods for their production (i.e., photoionization of reducing ions, water radiolysis, and the reaction between H[middle dot] and OH[superscript -]) are unsuitable for most school laboratories. We describe a simple experiment to produce liquid ammonia and solvated electrons…

Solvated Electrons in Organic Chemistry Laboratory

ERIC Educational Resources Information Center

Ilich, Predrag-Peter; McCormick, Kathleen R.; Atkins, Adam D.; Mell, Geoffrey J.; Flaherty, Timothy J.; Bruck, Martin J.; Goodrich, Heather A.; Hefel, Aaron L.; Juranic, Nenad; Seleem, Suzanne

2010-01-01

A novel experiment is described in which solvated electrons in liquid ammonia reduce a benzyl alcohol carbon without affecting the aromatic ring. The reductive activity of solvated electrons can be partially or completely quenched through the addition of electron scavengers to the reaction mixture. The effectiveness of these scavengers was found…

How High Pressure Unifies Solvation Processes in Liquid Chromatography.

PubMed

Bocian, Szymon; Škrinjar, Tea; Bolanca, Tomislav; Buszewski, Bogusław

2017-11-01

A series of core-shell-based stationary phases of varying surface chemistry were subjected to solvent adsorption investigation under ultra-HPLC conditions. Acetonitrile and water excess isotherms were measured using a minor disturbance method. It was observed that adsorption of organic solvent is unified under high pressure. Preferential solvation due to specific interactions between the stationary phases and solvent molecules was limited. The obtained results showed that the solvation process is almost independent of surface chemistry, in contrast to HPLC conditions in which specific interactions differentiate solvation processes.

Atomic decomposition of the protein solvation free energy and its application to amyloid-beta protein in water

NASA Astrophysics Data System (ADS)

Chong, Song-Ho; Ham, Sihyun

2011-07-01

We report the development of an atomic decomposition method of the protein solvation free energy in water, which ascribes global change in the solvation free energy to local changes in protein conformation as well as in hydration structure. So far, empirical decomposition analyses based on simple continuum solvation models have prevailed in the study of protein-protein interactions, protein-ligand interactions, as well as in developing scoring functions for computer-aided drug design. However, the use of continuum solvation model suffers serious drawbacks since it yields the protein free energy landscape which is quite different from that of the explicit solvent model and since it does not properly account for the non-polar hydrophobic effects which play a crucial role in biological processes in water. Herein, we develop an exact and general decomposition method of the solvation free energy that overcomes these hindrances. We then apply this method to elucidate the molecular origin for the solvation free energy change upon the conformational transitions of 42-residue amyloid-beta protein (Aβ42) in water, whose aggregation has been implicated as a primary cause of Alzheimer's disease. We address why Aβ42 protein exhibits a great propensity to aggregate when transferred from organic phase to aqueous phase.

Anisotropic solvent model of the lipid bilayer. 1. Parameterization of long-range electrostatics and first solvation shell effects.

PubMed

Lomize, Andrei L; Pogozheva, Irina D; Mosberg, Henry I

2011-04-25

A new implicit solvation model was developed for calculating free energies of transfer of molecules from water to any solvent with defined bulk properties. The transfer energy was calculated as a sum of the first solvation shell energy and the long-range electrostatic contribution. The first term was proportional to solvent accessible surface area and solvation parameters (σ(i)) for different atom types. The electrostatic term was computed as a product of group dipole moments and dipolar solvation parameter (η) for neutral molecules or using a modified Born equation for ions. The regression coefficients in linear dependencies of solvation parameters σ(i) and η on dielectric constant, solvatochromic polarizability parameter π*, and hydrogen-bonding donor and acceptor capacities of solvents were optimized using 1269 experimental transfer energies from 19 organic solvents to water. The root-mean-square errors for neutral compounds and ions were 0.82 and 1.61 kcal/mol, respectively. Quantification of energy components demonstrates the dominant roles of hydrophobic effect for nonpolar atoms and of hydrogen-bonding for polar atoms. The estimated first solvation shell energy outweighs the long-range electrostatics for most compounds including ions. The simplicity and computational efficiency of the model allows its application for modeling of macromolecules in anisotropic environments, such as biological membranes.

Weighted-density functionals for cavity formation and dispersion energies in continuum solvation models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sundararaman, Ravishankar; Gunceler, Deniz; Arias, T. A.

2014-10-07

Continuum solvation models enable efficient first principles calculations of chemical reactions in solution, but require extensive parametrization and fitting for each solvent and class of solute systems. Here, we examine the assumptions of continuum solvation models in detail and replace empirical terms with physical models in order to construct a minimally-empirical solvation model. Specifically, we derive solvent radii from the nonlocal dielectric response of the solvent from ab initio calculations, construct a closed-form and parameter-free weighted-density approximation for the free energy of the cavity formation, and employ a pair-potential approximation for the dispersion energy. We show that the resulting modelmore » with a single solvent-independent parameter: the electron density threshold (n c), and a single solvent-dependent parameter: the dispersion scale factor (s 6), reproduces solvation energies of organic molecules in water, chloroform, and carbon tetrachloride with RMS errors of 1.1, 0.6 and 0.5 kcal/mol, respectively. We additionally show that fitting the solvent-dependent s 6 parameter to the solvation energy of a single non-polar molecule does not substantially increase these errors. Parametrization of this model for other solvents, therefore, requires minimal effort and is possible without extensive databases of experimental solvation free energies.« less

Weighted-density functionals for cavity formation and dispersion energies in continuum solvation models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sundararaman, Ravishankar; Gunceler, Deniz; Arias, T. A.

2014-10-07

Continuum solvation models enable efficient first principles calculations of chemical reactions in solution, but require extensive parametrization and fitting for each solvent and class of solute systems. Here, we examine the assumptions of continuum solvation models in detail and replace empirical terms with physical models in order to construct a minimally-empirical solvation model. Specifically, we derive solvent radii from the nonlocal dielectric response of the solvent from ab initio calculations, construct a closed-form and parameter-free weighted-density approximation for the free energy of the cavity formation, and employ a pair-potential approximation for the dispersion energy. We show that the resulting modelmore » with a single solvent-independent parameter: the electron density threshold (n{sub c}), and a single solvent-dependent parameter: the dispersion scale factor (s{sub 6}), reproduces solvation energies of organic molecules in water, chloroform, and carbon tetrachloride with RMS errors of 1.1, 0.6 and 0.5 kcal/mol, respectively. We additionally show that fitting the solvent-dependent s{sub 6} parameter to the solvation energy of a single non-polar molecule does not substantially increase these errors. Parametrization of this model for other solvents, therefore, requires minimal effort and is possible without extensive databases of experimental solvation free energies.« less

Solvation thermodynamics of amino acid side chains on a short peptide backbone

NASA Astrophysics Data System (ADS)

Hajari, Timir; van der Vegt, Nico F. A.

2015-04-01

The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment. A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone. To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvation free energies of nonpolar and polar side chains attached to a short peptide backbone. The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone. We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected. This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution. We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar side chain cavities in bulk water, in agreement with earlier work in the literature on analysis of cavity fluctuations at nonpolar molecular surfaces. The cavity and dispersion interaction contributions correlate quite well with the solvent accessible surface area of the nonpolar side chains attached to the backbone. This correlation however is weak for the overall solvation free energies owing to the fact that the cavity and dispersion free energy contributions are almost exactly cancelling each other.

Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water.

PubMed

Paschek, Dietmar; Nymeyer, Hugh; García, Angel E

2007-03-01

We simulate the folding/unfolding equilibrium of the 20-residue miniprotein Trp-cage. We use replica exchange molecular dynamics simulations of the AMBER94 atomic detail model of the protein explicitly solvated by water, starting from a completely unfolded configuration. We employ a total of 40 replicas, covering the temperature range between 280 and 538 K. Individual simulation lengths of 100 ns sum up to a total simulation time of about 4 micros. Without any bias, we observe the folding of the protein into the native state with an unfolding-transition temperature of about 440 K. The native state is characterized by a distribution of root mean square distances (RMSD) from the NMR data that peaks at 1.8A, and is as low as 0.4A. We show that equilibration times of about 40 ns are required to yield convergence. A folded configuration in the entire extended ensemble is found to have a lifetime of about 31 ns. In a clamp-like motion, the Trp-cage opens up during thermal denaturation. In line with fluorescence quenching experiments, the Trp-residue sidechain gets hydrated when the protein opens up, roughly doubling the number of water molecules in the first solvation shell. We find the helical propensity of the helical domain of Trp-cage rather well preserved even at very high temperatures. In the folded state, we can identify states with one and two buried internal water molecules interconnecting parts of the Trp-cage molecule by hydrogen bonds. The loss of hydrogen bonds of these buried water molecules in the folded state with increasing temperature is likely to destabilize the folded state at elevated temperatures.

Structurally characterized 1,1,3,3-tetramethylguanidine solvated magnesium aryloxide complexes: [Mg(mu-OEt)(DBP)(H-TMG)]2, [Mg(mu-OBc)(DBP)(H-TMG)]2, [Mg(mu-TMBA)(DBP)(H-TMG)]2, [Mg(mu-DPP)(DBP)(H-TMG)]2, [Mg(BMP)2(H-TMG)2], [Mg(O-2,6-Ph2C6H3)2 (H-TMG)2].

PubMed

Monegan, Jessie D; Bunge, Scott D

2009-04-06

The synthesis and structural characterization of several 1,1,3,3-tetramethylguanidine (H-TMG) solvated magnesium aryloxide complexes are reported. Bu(2)Mg was successfully reacted with H-TMG, HOC(6)H(3)(CMe(3))(2)-2,6 (H-DBP), and either ethanol, a carboxylic acid, or diphenyl phosphate in a 1:1 ratio to yield the corresponding [Mg(mu-L)(DBP)(H-TMG)](2) where L = OCH(2)CH(3) (OEt, 1), O(2)CC(CH(3))(3) (OBc, 2), O(2)C(C(6)H(2)-2,4,6-(CH(3))(3)) (TMBA, 3), or O(2)P(OC(6)H(5))(2) (DPP, 4). Bu(2)Mg was also reacted with two equivalents of H-TMG and HOC(6)H(3)(CMe(3))-2-(CH(3))-6 (BMP) or HO-2,6-Ph(2)C(6)H(3) to yield [Mg(BMP)(2)(H-TMG)(2)] (5) and [Mg(O-2,6-Ph(2)C(6)H(3))(2)(H-TMG)(2)] (6). Compounds 1-6 were characterized by single-crystal X-ray diffraction. Polymerization of l- and rac-lactide with 1 was found to generate polylactide (PLA). A discussion concerning the relevance of compounds 2 - 4 to the structure of Mg-activated phosphatase enzymes is also provided. The bulk powders for all complexes were found to be in agreement with the crystal structures based on elemental analyses, FT-IR spectroscopy, and (1)H, (13)C and (31)P NMR studies.

1,1,3,3-Tetramethylguanidine solvated lanthanide aryloxides: pre-catalysts for intramolecular hydroalkoxylation.

PubMed

Janini, Thomas E; Rakosi, Robert; Durr, Christopher B; Bertke, Jeffrey A; Bunge, Scott D

2009-12-21

The synthesis and structural characterization of six 1,1,3,3-tetramethylguanidine (H-TMG) solvated lanthanide aryloxide complexes are reported. Ln[N{Si(CH3)3}2]3 (Ln = Nd, La) was reacted with two equivalents of both H-TMG and HOAr {HOAr = HOC6H2(CMe3)2-2,6 (H-DBP) or HOC6H2(CMe3)2-2,6-CH3-4 (H-4MeDBP)} and one equivelent of ethanol (HOEt) to yield the corresponding [Nd(H-TMG)2(4MeDBP)2(OEt)] (1) and [La(H-TMG)2(DBP)2(OEt)] (2). Compounds 1 and 2 were further reacted with 4-pentyn-1-ol {HO(CH2)3C[triple bond]CH} to isolate [Nd(H-TMG)2(4MeDBP)2{O(CH2)3C[triple bond]CH}] (3) and [La(H-TMG)2(DBP)2{O(CH2)3C[triple bond]CH}] (4), respectively. Three equivalents of HOAr and one equivalent of H-TMG were additionally reacted with Ln[N{Si(CH3)3}2]3 to generate [Nd(4MeDBP)3(H-TMG)] (5) and [La(DBP)3(H-TMG)] (6). In order to examine the formation of 1-6, the interaction of H-TMG and HOAr was further examined in solution and the hydrogen bonded complexes (H-TMG:HOAr), 7 and 8, were isolated. Upon successful isolation of 1-6, the utility of 1, 2, 4 and 5 as pre-catalysts for the intramolecular hydroalkoxylation of 4-pentyn-1-ol was investigated. The bulk powders for all complexes were found to be in agreement with the crystal structures based on elemental analyses, FT-IR spectroscopy, and 1H and 13C NMR investigations.

Crown Ether Complexes of Alkali-Metal Chlorides from SO2.

PubMed

Reuter, Kirsten; Rudel, Stefan S; Buchner, Magnus R; Kraus, Florian; von Hänisch, Carsten

2017-07-18

The structures of alkali-metal chloride SO 2 solvates (Li-Cs) in conjunction with 12-crown-4 or 1,2-disila-12-crown-4 show strong discrepancies, despite the structural similarity of the ligands. Both types of crown ethers form 1:1 complexes with LiCl to give [Li(1,2-disila-12-crown-4)(SO 2 Cl)] (1) and [Li(12-crown-4)Cl]⋅4 SO 2 (2). However, 1,2-disila-12-crown-4 proved unable to coordinate cations too large for the cavity diameter, for example, by the formation of sandwich-type complexes. As a result, 12-crown-4 reacts exclusively with the heavier alkali-metal chlorides NaCl, KCl and RbCl. Compounds [Na(12-crown-4) 2 ]Cl⋅4 SO 2 (3) and [M(12-crown-4) 2 (SO 2 )]Cl⋅4 SO 2 (4: M=K; 5: M=Rb) all showed S-coordination to the chloride ions through four SO 2 molecules. Compounds 4 and 5 additionally exhibit the first crystallographically confirmed non-bridging O,O'-coordination mode of SO 2 . Unexpectedly, the disila-crown ether supports the dissolution of RbCl and CsCl in the solvent and gives the homoleptic SO 2 -solvated alkali-metal chlorides [MCl⋅3 SO 2 ] (6: M=Rb; 7: M=Cs), which incorporate bridging μ-O,O'-coordinating moieties and the unprecedented side-on O,O'-coordination mode. All compounds were characterised by single-crystal X-ray diffraction. The crown ether complexes were additionally studied by using NMR spectroscopy, and the presence of SO 2 at ambient temperature was revealed by IR spectroscopy of the neat compounds. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Application of High-Resolution Magic-Angle Spinning NMR Spectroscopy to Define the Cell Uptake of MRI Contrast Agents

NASA Astrophysics Data System (ADS)

Calabi, Luisella; Alfieri, Goffredo; Biondi, Luca; De Miranda, Mario; Paleari, Lino; Ghelli, Stefano

2002-06-01

A new method, based on proton high-resolution magic-angle spinning ( 1H HR-MAS) NMR spectroscopy, has been employed to study the cell uptake of magnetic resonance imaging contrast agents (MRI-CAs). The method was tested on human red blood cells (HRBC) and white blood cells (HWBC) by using three gadolinium complexes, widely used in diagnostics, Gd-BOPTA, Gd-DTPA, and Gd-DOTA, and the analogous complexes obtained by replacing Gd(III) with Dy(III), Nd(III), and Tb(III) (i.e., complexes isostructural to the ones of gadolinium but acting as shift agents). The method is based on the evaluation of the magnetic effects, line broadening, or induced lanthanide shift (LIS) caused by these complexes on NMR signals of intra- and extracellular water. Since magnetic effects are directly linked to permeability, this method is direct. In all the tests, these magnetic effects were detected for the extracellular water signal only, providing a direct proof that these complexes are not able to cross the cell membrane. Line broadening effects (i.e., the use of gadolinium complexes) only allow qualitative evaluations. On the contrary, LIS effects can be measured with high precision and they can be related to the concentration of the paramagnetic species in the cellular compartments. This is possible because the HR-MAS technique provides the complete elimination of bulk magnetic susceptibility (BMS) shift and the differentiation of extra- and intracellular water signals. Thus with this method, the rapid quantification of the MRI-CA amount inside and outside the cells is actually feasible.

Synthesis, spectroscopic and theoretical studies of ethyl (2E)-3-amino-2-({[(4-benzoyl-1,5-diphenyl-1H-pyrazol-3-yl)carbonyl]amino}carbonothioyl)but-2-enoate butanol solvate

NASA Astrophysics Data System (ADS)

Koca, İrfan; Sert, Yusuf; Gümüş, Mehmet; Kani, İbrahim; Çırak, Çağrı

2014-01-01

We have synthesized ethyl (2E)-3-amino-2-({[(4-benzoyl-1,5-diphenyl-1H-pyrazol-3-yl)carbonyl]amino}carbonothioyl)but-2-enoate (2) by the reaction of 4-benzoyl-1,5-diphenyl-1H-pyrazole-3-carbonyl chloride (1), ammonium thiocyanate and ethyl 3-aminobut-2-enoate and then characterized by elemental analyses, IR, Raman, 1H NMR, 13C NMR and X-ray diffraction methods. The experimental and theoretical vibrational spectra of 2 were investigated. The experimental FT-IR (4000-400 cm-1) and Laser-Raman spectra (4000-100 cm-1) of the molecule in the solid phase were recorded. Theoretical vibrational frequencies and geometric parameters (bond lengths, bond angles) were calculated using Ab Initio Hartree Fock (HF), Density Functional Theory (B3LYP) methods with 6-311++G(d,p) basis set by Gaussian 09W program. The computed values of frequencies are scaled using a suitable scale factor to yield good coherence with the observed values. The assignments of the vibrational frequencies were performed by potential energy distribution (PED) analysis by using VEDA 4 program. The theoretical optimized geometric parameters and vibrational frequencies were compared with the corresponding experimental X-ray diffraction data, and they were seen to be in a good agreement with each other. Also, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies were calculated.

Proof of Concept Studies Directed Towards Designed Molecular Wires: Property-Driven Synthesis of Air and Moisture-Stable Polystannanes.

PubMed

Pau, Jeffrey; Lough, Alan J; Wylie, R Stephen; Gossage, Robert A; Foucher, Daniel A

2017-10-12

Polystannanes with azobenzene moieties designed to protect the Sn-Sn backbone from light- and moisture-induced degradation are described. The azo-stannyl precursor 3 (70 %) is converted in good yields (88-91 %) to the mono- (4), and dichlorostannanes (5), by sequential chlorination, followed by further reduction of 5 to the dihydride (6) using NaBH 4 (78 %). All stannanes were characterised by NMR ( 1 H, 13 C, 119 Sn) spectroscopy and HRMS; in addition, 3, 4 and 5 were structurally elucidated using X-ray diffraction analysis. Metal-free dehydrocoupling of 6 at RT leads exclusively to homopolymer (7-i) displaying an initial solution 119 Sn NMR signal (δ=-196 ppm) that migrates to -235 ppm after 10 days (7-f). In contrast, metal-catalyzed dehydrocoupling of 6 in toluene at RT leads directly 7-f. Random co-polymers formed from 6 and (nBu) 2 SnH 2 at 4:1 (8 a) and 1:1 (8 b) ratios were compared to the alternating polystannane (9) prepared by the reaction of 6 with (nBu) 2 Sn(NEt 2 ) 2 . DFT calculations of 3-6 indicate that hypercoordination at Sn is influenced by substituents and by solvation. Homopolymer 7 was found to have unprecedented moisture and light stability in the solid state for >6 months. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

NMR shielding and a thermodynamic study of the effect of environmental exposure to petrochemical solvent on DPPC, an important component of lung surfactant

NASA Astrophysics Data System (ADS)

Monajjemi, M.; Afsharnezhad, S.; Jaafari, M. R.; Abdolahi, T.; Nikosade, A.; Monajemi, H.

2007-12-01

The chemical and petrochemical industries are the major air polluters. Millions of workers are exposed to toxic chemicals on the job, and it is becoming more toxic, causing much damage to respiratory system, today. One of the main components of lung alveoli is a surfactant. DPPC (Dipalmitolphosphatidylcholine) is the predominant lipid component in the lung surfactant, which is responsible for lowering surface tension in alveoli. In this article, we used an approximate model and ab initio computations to describe interactions between DPPC and some chemical solvents, such as benzene, toluene, heptane, acetone, chloroform, ether, and ethanol, which cause lung injuries and lead to respiratory distress such as ARDS. The effect of these solvents on the conformation and disordering of the DPPC head group was investigated by calculations at the Hatree-Fock level using the 6-31G basis set with the Onsager continuum solvation, GAIO, and frequency models. The simulation model was confirmed by accurate NMR measurements as concerns conformational energy. Water can be the most suitable solvent for DPPC. Furthermore, this study shows that ethanol has the most destructive effect on the conformation and lipid disorder of the DPPC head group of the lung surfactant in our model. Our finding will be useful for detecting the dysfunction of DPPC in the lung surfactant caused by acute or chronic exposures to air toxics from petrochemical organic solvent emission source and chronic alcohol consumption, which may lead to ARDS.

Anti-cancer agents based on N-acyl-2, 3-dihydro-1H-pyrrolo[2,3-b] quinoline derivatives and a method of making

DOEpatents

Gakh, Andrei; Krasavin, Mikhail; Karapetian, Ruben; Rufanov, Konstantin A; Konstantinov, Igor; Godovykh, Elena; Soldatkina, Olga; Sosnov, Andrey V

2013-04-16

The present disclosure relates to novel compounds that can be used as anti-cancer agents in the prostate cancer therapy. In particular, the invention relates to N-acyl derivatives of 2,3-dihydro-1H-pyrrolo[2,3-b]quinolines having the structural Formula (I), ##STR00001## stereoisomers, tautomers, racemics, prodrugs, metabolites thereof, or pharmaceutically acceptable salt and/or solvate thereof. The meaning of R1 is independently selected from H; C1-C6 Alkyl, cyclo-Alkyl or iso-Alkyl substituents; R2 is selected from C1-C6 Alkyl, cyclo-Alkyl or iso-Alkyl; substituted or non-substituted, fused or non-fused to substituted or non-substituted aromatic ring, aryl or heteroaryl groups. The invention also relates to methods for preparing said compounds, and to pharmaceutical compositions comprising said compounds.

Synthesis, Characterization and Reactivity of a Hexane-Soluble Silver Salt

ERIC Educational Resources Information Center

Stockland, Robert A. Jr.; Wilson, Brian D.; Goodman, Caton C.; Giese, Barret J.; Shrimp, Frederick L., II

2007-01-01

The connectivity of a hexane-soluble silver salt is established by using NMR spectroscopy to describe the synthesis, characterization and reactivity of the salt. The results found hexane-soluble silver to be an effective transfer agent.

Synthesis, thermogravimetric, spectroscopic and theoretical characterization of copper(II) complex with 4-chloro-2-nitrobenzenosulfonamide

NASA Astrophysics Data System (ADS)

Camí, G.; Chacón Villalba, E.; Di Santi, Y.; Colinas, P.; Estiu, G.; Soria, D. B.

2011-05-01

4-Chloro-2-nitrobenzenesulfonamide (ClNbsa) was purified and characterized. A new copper(II) complex, [Cu(ClNbsa) 2(NH 3) 2], has been prepared using the sulfonamide as ligand. The thermal behavior of both, the ligand and the Cu(II) complex, was investigated by thermogravimetric analyses (TG) and differential thermal analysis (DT), and the electronic characteristics analyzed by UV-VIS, FTIR, Raman and 1H NMR spectroscopies. The experimental IR, Raman and UV-VIS spectra have been assigned on the basis of DFT calculations at the B3LYP level of theory using the standard (6-31 + G ∗∗) basis set. The geometries have been fully optimized in vacuum and in modeled dimethylsulfoxide (DMSO) solvent, using for the latter a continuum solvation model that reproduced the experimental conditions of the UV-VIS spectroscopy. The theoretical results converged to stable conformations for the free sulfonamide and for the complex, suggesting for the latter a distorted square planar geometry in both environments.

Synthesis, electronic structure and spectral fluorescent properties of vinylogous merocyanines derived from 1,3-dialkyl-benzimidazole and malononitrile

NASA Astrophysics Data System (ADS)

Kulinich, Andrii V.; Mikitenko, Elena K.; Ishchenko, Alexander A.

2017-01-01

A vinylogous series of merocyanines were synthesized with 1,3-dibutyl-benzimidazole and malononitrile residues as the donor and acceptor terminal groups. These dyes do not comprise carbonyl groups, which are prone to the strong specific solvation by polar solvents up to hydrogen bond formation, and nevertheless they possess distinct reversed solvatochromism, i.e. their molecules have very high dipolarity. At that, they are soluble in a wide range of solvents from n-hexane to ethanol and do not aggregate readily. They were studied thoroughly by UV/Vis, fluorescence, IR, and NMR spectroscopy methods. Their structure and spectral properties in the ground and excited fluorescent states were modelled at the DFT level both in vacuum and in solvents of various polarities by using the PCM solvent field simulation. The calculations were performed using several hybrid functionals (B3LYP, CAM-B3LYP, and wB97XD) and the split-valence 6-31G (d,p) basis set.

The impact of surface area, volume, curvature, and Lennard-Jones potential to solvation modeling.

PubMed

Nguyen, Duc D; Wei, Guo-Wei

2017-01-05

This article explores the impact of surface area, volume, curvature, and Lennard-Jones (LJ) potential on solvation free energy predictions. Rigidity surfaces are utilized to generate robust analytical expressions for maximum, minimum, mean, and Gaussian curvatures of solvent-solute interfaces, and define a generalized Poisson-Boltzmann (GPB) equation with a smooth dielectric profile. Extensive correlation analysis is performed to examine the linear dependence of surface area, surface enclosed volume, maximum curvature, minimum curvature, mean curvature, and Gaussian curvature for solvation modeling. It is found that surface area and surfaces enclosed volumes are highly correlated to each other's, and poorly correlated to various curvatures for six test sets of molecules. Different curvatures are weakly correlated to each other for six test sets of molecules, but are strongly correlated to each other within each test set of molecules. Based on correlation analysis, we construct twenty six nontrivial nonpolar solvation models. Our numerical results reveal that the LJ potential plays a vital role in nonpolar solvation modeling, especially for molecules involving strong van der Waals interactions. It is found that curvatures are at least as important as surface area or surface enclosed volume in nonpolar solvation modeling. In conjugation with the GPB model, various curvature-based nonpolar solvation models are shown to offer some of the best solvation free energy predictions for a wide range of test sets. For example, root mean square errors from a model constituting surface area, volume, mean curvature, and LJ potential are less than 0.42 kcal/mol for all test sets. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Modulation of the aggregation properties of sodium deoxycholate in presence of hydrophilic imidazolium based ionic liquid: water dynamics study to probe the structural alteration of the aggregates.

PubMed

Kundu, Niloy; Banik, Debasis; Roy, Arpita; Kuchlyan, Jagannath; Sarkar, Nilmoni

2015-10-14

In this article, we have investigated the effect of a hydrophilic ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim]-BF4), on the aggregation properties of a biological surfactant, sodium deoxycholate (NaDC), in water. In solution, unlike conventional surfactants it shows stepwise aggregation and the effect of the conventional ionic liquid on the aggregation properties is rather interesting. We have observed concentration dependent dual role of the ionic liquid; at their low concentration, the aggregated structure of NaDC reorganizes itself into an elongated rod like structure. However, the aggregated network is disintegrated into small aggregates upon further addition of ionic liquid. TEM (Transmission Electron Microscopy), SEM (Scanning Electron Microscopy) and FLIM (Fluorescence Lifetime Imaging Microscopy) images also confirmed the structural alteration of NaDC upon varying the concentration of the ionic liquid. The proton NMR data indicate that hydrophobic as well as electrostatic interaction is solely responsible for such structural adaptation of NaDC in the presence of an ionic liquid. The host-guest interaction inside the aggregates is monitored using Coumarin-153 (C-153) and the location of C-153 is probed by varying the excitation wavelength from 375 nm to 440 nm and the two binding sites of the aggregates are affected in a different fashion in the presence of ionic liquid. Excitation in the blue region selects the fluorophores which preferably bind to the buried region of the aggregates, whereas 440 nm excitation corresponds to the guest molecules which are exposed to the solvent molecules. The average solvation time of C-153 is increased in the presence of 1.68 wt% [bmim]-BF4 at λexc = 440 nm i.e. the probe molecules relocate themselves to a more restricted region. However, the average solvation time became 2.6 times faster in the presence of 11.2 wt% [bmim]-BF4, which corresponds to a more polar and exposed region. The time resolved anisotropy measurements and polarity determined by pyrene also supported our results in addition to solvation dynamics measurements. In summary, ionic liquids can modulate the host-guest interaction of bile salt aggregates, which can be used as nanocarriers for drug delivery.

Benzene derivatives produced by Fusarium graminearum - Short communication.

PubMed

Ntushelo, Khayalethu; Setshedi, Itumeleng

2015-06-01

Using NMR spectroscopy benzene derivatives were detected in mycelia of Fusarium graminearum, a pathogen of wheat and maize. In previous studies F. graminearum was found to cause cancer to humans and benzene derivatives were detected in breath of cancer sufferers. Surprisingly, no study found benzene derivatives to be the cancerous agents in F. graminearum. In this study we detected benzene derivatives in F. graminearum and propose to study their role as cancer agents.

Structure of solvates of o-hydroxybenzoic acid in supercritical CO2-cosolvent media, according to molecular dynamics data

NASA Astrophysics Data System (ADS)

Petrenko, V. E.; Antipova, M. L.; Gurina, D. L.

2015-03-01

Three-component supercritical carbon dioxide-cosolvent (methanol, ethanol, water)- o-hydroxybenzoic acid ( o-HBA) mixtures at a density of 0.7 g/cm3 and temperatures of 318 and 348 K are simulated by means of molecular dynamics. The solvate structures are investigated. It is shown that the solvation mechanism of o-HBA (particularly the o-HBA molecule forming a stable solvate complex with one molecule of a cosolvent via a hydrogen bond through the carboxyl group) does not depend on the temperature or the cosolvent. It is noted that the form of the cosolvent in a supercritical fluid varies: alcohols are distributed in the bulk in the form of monomers and hydrogen-bonded dimers, and water molecules tend to form microclusters along with chained and spatially branched structures by means of hydrogen bonds. It is established that the local molar fraction of cosolvent around the solvate complexes grows. It is concluded that the solvation of o-HBA is determined by the behavior of cosolvent in media of supercritical CO2.

Long-ranged contributions to solvation free energies from theory and short-ranged models

PubMed Central

Remsing, Richard C.; Liu, Shule; Weeks, John D.

2016-01-01

Long-standing problems associated with long-ranged electrostatic interactions have plagued theory and simulation alike. Traditional lattice sum (Ewald-like) treatments of Coulomb interactions add significant overhead to computer simulations and can produce artifacts from spurious interactions between simulation cell images. These subtle issues become particularly apparent when estimating thermodynamic quantities, such as free energies of solvation in charged and polar systems, to which long-ranged Coulomb interactions typically make a large contribution. In this paper, we develop a framework for determining very accurate solvation free energies of systems with long-ranged interactions from models that interact with purely short-ranged potentials. Our approach is generally applicable and can be combined with existing computational and theoretical techniques for estimating solvation thermodynamics. We demonstrate the utility of our approach by examining the hydration thermodynamics of hydrophobic and ionic solutes and the solvation of a large, highly charged colloid that exhibits overcharging, a complex nonlinear electrostatic phenomenon whereby counterions from the solvent effectively overscreen and locally invert the integrated charge of the solvated object. PMID:26929375

Functionalized multimodal ZnO@Gd2O3 nanosystems to use as perspective contrast agent for MRI

NASA Astrophysics Data System (ADS)

Babayevska, Nataliya; Florczak, Patryk; Woźniak-Budych, Marta; Jarek, Marcin; Nowaczyk, Grzegorz; Zalewski, Tomasz; Jurga, Stefan

2017-05-01

The main aim of this research was the synthesis of the multimodal hybrid ZnO@Gd2O3 nanostructures as prospective contrast agent for Magnetic Resonance Imaging (MRI) for bio-medical applications. The nanoparticles surface was functionalized by organosilicon compounds (OSC) then, by folic acid (FA) as targeting agent and doxorubicin (Dox) as chemotherapeutic agent. Doxorubicin and folic acid were attached to the nanoparticles surface by amino groups as well as due to attractive physical interactions. The morphology and crystallography of the nanostructures were studied by HRTEM and SAXS techniques. After ZnO nanoparticles surface modification by Gd3+ and annealing at 900 °C, ZnO@Gd2O3 nanostructures are polydispersed with size 30-100 nm. NMR (Nuclear Magnetic Resonance) studies of ZnO@Gd2O3 were performed on fractionated particles with size up to 50 nm. Fourier transform infrared spectroscopy (FTIR), UV-vis spectroscopy, zeta-potential measurements and energy dispersive X-ray analysis (EDX) showed that functional groups have been effectively bonded onto the nanoparticles surface. The high adsorption capacity of folic acid (up to 20%) and doxorubicin (up to 40%) on nanoparticles was reached upon 15 min of adsorption process in a temperature-dependent manner. The nuclear magnetic resonance (NMR) relaxation measurements confirmed that the obtained ZnO@Gd2O3 nanostructures could be good contrast agents, useful for magnetic resonance imaging.

Anion Solvation in Carbonate-Based Electrolytes

DOE PAGES

von Wald Cresce, Arthur; Gobet, Mallory; Borodin, Oleg; ...

2015-11-16

The correlation between Li + solvation and interphasial chemistry on anodes firmly established in Li-ion batteries, the effect of cation–solvent interaction has gone beyond bulk thermodynamic and transport properties and become an essential element that determines the reversibility of electrochemistry and kinetics of Li-ion intercalation chemistries. Now, most studies are dedicated to the solvation of Li +, and the solvation of anions in carbonate-based electrolytes and its possible effect on the electrochemical stability of such electrolytes remains little understood. Moreover, as a mirror effort to prior Li + solvation studies, this work focuses on the interactions between carbonate-based solvents andmore » two anions (hexafluorophosphate, PF 6–, and tetrafluoroborate, BF 4–) that are most frequently used in Li-ion batteries. The possible correlation between such interaction and the interphasial chemistry on cathode surface is also explored.« less

Rates and mechanism of fluoride and water exchange in UO(2)F(5)(3-) and [UO(2)F(4)(H(2)O)](2-) studied by NMR spectroscopy and wave function based methods.

PubMed

Vallet, Valérie; Wahlgren, Ulf; Szabó, Zoltán; Grenthe, Ingmar

2002-10-21

The reaction mechanism for the exchange of fluoride in UO(2)F(5)(3-) and UO(2)F(4)(H(2)O)(2-) has been investigated experimentally using (19)F NMR spectroscopy at -5 degrees C, by studying the line broadening of the free fluoride, UO(2)F(4)(2-)(aq) and UO(2)F(5)(3-), and theoretically using quantum chemical methods to calculate the activation energy for different pathways. The new experimental data allowed us to make a more detailed study of chemical equilibria and exchange mechanisms than in previous studies. From the integrals of the different individual peaks in the new NMR spectra, we obtained the stepwise stability constant K(5) = 0.60 +/- 0.05 M(-1) for UO(2)F(5)(3-). The theoretical results indicate that the fluoride exchange pathway of lowest activation energy, 71 kJ/mol, in UO(2)F(5)(3-) is water assisted. The pure dissociative pathway has an activation energy of 75 kJ/mol, while the associative mechanism can be excluded as there is no stable UO(2)F(6)(4-) intermediate. The quantum chemical calculations have been made at the SCF/MP2 levels, using a conductor-like polarizable continuum model (CPCM) to describe the solvent. The effects of different model assumptions on the activation energy have been studied. The activation energy is not strongly dependent on the cavity size or on interactions between the complex and Na(+) counterions. However, the solvation of the complex and the leaving fluoride results in substantial changes in the activation energy. The mechanism for water exchange in UO(2)F(4)(H(2)O)(2-) has also been studied. We could eliminate the associative mechanism, the dissociative mechanism had the lowest activation energy, 39 kJ/mol, while the interchange mechanism has an activation energy that is approximately 50 kJ/mol higher.

A comparison of the solvation structure and dynamics of the lithium ion in linear organic carbonates with different alkyl chain lengths.

PubMed

Fulfer, K D; Kuroda, D G

2017-09-20

The structure and dynamics of electrolytes composed of lithium hexafluorophosphate (LiPF 6 ) in dimethyl carbonate, ethyl methyl carbonate, and diethyl carbonate were investigated using a combination of linear and two-dimensional infrared spectroscopies. The solutions studied here have a LiPF 6 concentration of X(LiPF 6 ) = 0.09, which is typically found in commercial lithium ion batteries. This study focuses on comparing the differences in the solvation shell structure and dynamics produced by linear organic carbonates of different alkyl chain lengths. The IR experiments show that either linear carbonate forms a tetrahedral solvation shell (coordination number of 4) around the lithium ion irrespective of whether the solvation shell has anions in close proximity to the carbonates. Moreover, analysis of the absorption cross sections via FTIR and DFT computations reveals a distortion in the angle formed by Li + -O[double bond, length as m-dash]C which decreases from the expected 180° when the alkyl chains of the carbonate are lengthened. In addition, our findings also reveal that, likely due to its asymmetric structure, ethyl methyl carbonate has a significantly more distorted tetrahedral lithium ion solvation shell than either of the other two investigated carbonates. IR photon echo studies further demonstrate that the motions of the solvation shell have a time scale of a few picoseconds for all three linear carbonates. Interestingly, a slowdown of the in place-motions of the first solvation shell is observed when the carbonate has a longer alkyl chain length irrespective of the symmetry. In addition, vibrational energy transfer with a time scale of tens of picoseconds is observed between strongly coupled modes arising from the solvation shell structure of the Li + which corroborates the modeling of these solvation shells in terms of highly coupled vibrational states. Results of this study provide new insights into the molecular structure and dynamics of the lithium ion electrolyte components as a function of solvent structure.

Modeling ultrafast solvated electronic dynamics using time-dependent density functional theory and polarizable continuum model.

PubMed

Liang, Wenkel; Chapman, Craig T; Ding, Feizhi; Li, Xiaosong

2012-03-01

A first-principles solvated electronic dynamics method is introduced. Solvent electronic degrees of freedom are coupled to the time-dependent electronic density of a solute molecule by means of the implicit reaction field method, and the entire electronic system is propagated in time. This real-time time-dependent approach, incorporating the polarizable continuum solvation model, is shown to be very effective in describing the dynamical solvation effect in the charge transfer process and yields a consistent absorption spectrum in comparison to the conventional linear response results in solution. © 2012 American Chemical Society

Differential geometry based solvation model II: Lagrangian formulation.

PubMed

Chen, Zhan; Baker, Nathan A; Wei, G W

2011-12-01

Solvation is an elementary process in nature and is of paramount importance to more sophisticated chemical, biological and biomolecular processes. The understanding of solvation is an essential prerequisite for the quantitative description and analysis of biomolecular systems. This work presents a Lagrangian formulation of our differential geometry based solvation models. The Lagrangian representation of biomolecular surfaces has a few utilities/advantages. First, it provides an essential basis for biomolecular visualization, surface electrostatic potential map and visual perception of biomolecules. Additionally, it is consistent with the conventional setting of implicit solvent theories and thus, many existing theoretical algorithms and computational software packages can be directly employed. Finally, the Lagrangian representation does not need to resort to artificially enlarged van der Waals radii as often required by the Eulerian representation in solvation analysis. The main goal of the present work is to analyze the connection, similarity and difference between the Eulerian and Lagrangian formalisms of the solvation model. Such analysis is important to the understanding of the differential geometry based solvation model. The present model extends the scaled particle theory of nonpolar solvation model with a solvent-solute interaction potential. The nonpolar solvation model is completed with a Poisson-Boltzmann (PB) theory based polar solvation model. The differential geometry theory of surfaces is employed to provide a natural description of solvent-solute interfaces. The optimization of the total free energy functional, which encompasses the polar and nonpolar contributions, leads to coupled potential driven geometric flow and PB equations. Due to the development of singularities and nonsmooth manifolds in the Lagrangian representation, the resulting potential-driven geometric flow equation is embedded into the Eulerian representation for the purpose of computation, thanks to the equivalence of the Laplace-Beltrami operator in the two representations. The coupled partial differential equations (PDEs) are solved with an iterative procedure to reach a steady state, which delivers desired solvent-solute interface and electrostatic potential for problems of interest. These quantities are utilized to evaluate the solvation free energies and protein-protein binding affinities. A number of computational methods and algorithms are described for the interconversion of Lagrangian and Eulerian representations, and for the solution of the coupled PDE system. The proposed approaches have been extensively validated. We also verify that the mean curvature flow indeed gives rise to the minimal molecular surface and the proposed variational procedure indeed offers minimal total free energy. Solvation analysis and applications are considered for a set of 17 small compounds and a set of 23 proteins. The salt effect on protein-protein binding affinity is investigated with two protein complexes by using the present model. Numerical results are compared to the experimental measurements and to those obtained by using other theoretical methods in the literature. © Springer-Verlag 2011

Differential geometry based solvation model II: Lagrangian formulation

PubMed Central

Chen, Zhan; Baker, Nathan A.; Wei, G. W.

2010-01-01

Solvation is an elementary process in nature and is of paramount importance to more sophisticated chemical, biological and biomolecular processes. The understanding of solvation is an essential prerequisite for the quantitative description and analysis of biomolecular systems. This work presents a Lagrangian formulation of our differential geometry based solvation model. The Lagrangian representation of biomolecular surfaces has a few utilities/advantages. First, it provides an essential basis for biomolecular visualization, surface electrostatic potential map and visual perception of biomolecules. Additionally, it is consistent with the conventional setting of implicit solvent theories and thus, many existing theoretical algorithms and computational software packages can be directly employed. Finally, the Lagrangian representation does not need to resort to artificially enlarged van der Waals radii as often required by the Eulerian representation in solvation analysis. The main goal of the present work is to analyze the connection, similarity and difference between the Eulerian and Lagrangian formalisms of the solvation model. Such analysis is important to the understanding of the differential geometry based solvation model. The present model extends the scaled particle theory (SPT) of nonpolar solvation model with a solvent-solute interaction potential. The nonpolar solvation model is completed with a Poisson-Boltzmann (PB) theory based polar solvation model. The differential geometry theory of surfaces is employed to provide a natural description of solvent-solute interfaces. The minimization of the total free energy functional, which encompasses the polar and nonpolar contributions, leads to coupled potential driven geometric flow and Poisson-Boltzmann equations. Due to the development of singularities and nonsmooth manifolds in the Lagrangian representation, the resulting potential-driven geometric flow equation is embedded into the Eulerian representation for the purpose of computation, thanks to the equivalence of the Laplace-Beltrami operator in the two representations. The coupled partial differential equations (PDEs) are solved with an iterative procedure to reach a steady state, which delivers desired solvent-solute interface and electrostatic potential for problems of interest. These quantities are utilized to evaluate the solvation free energies and protein-protein binding affinities. A number of computational methods and algorithms are described for the interconversion of Lagrangian and Eulerian representations, and for the solution of the coupled PDE system. The proposed approaches have been extensively validated. We also verify that the mean curvature flow indeed gives rise to the minimal molecular surface (MMS) and the proposed variational procedure indeed offers minimal total free energy. Solvation analysis and applications are considered for a set of 17 small compounds and a set of 23 proteins. The salt effect on protein-protein binding affinity is investigated with two protein complexes by using the present model. Numerical results are compared to the experimental measurements and to those obtained by using other theoretical methods in the literature. PMID:21279359

Effect of unsaturation on the absorption of ethane and ethylene in imidazolium-based ionic liquids.

PubMed

Moura, Leila; Mishra, Manas; Bernales, Varinia; Fuentealba, Patricio; Padua, Agilio A H; Santini, Catherine C; Costa Gomes, Margarida F

2013-06-20

The influence of the presence of imidazolium side chain unsaturation on the solubility of ethane and ethylene was studied in three ionic liquids: 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)amide-saturated alkyl side-chain in the cation; 1-methyl-3-(buten-3-yl)imidazolium bis(trifluorosulfonyl)imide-double bond in the side-chain of the cation; and 1-methyl-3-benzylimidazolium bis(trifluorosulfonyl)imide-benzyl group in the side-chain of the cation. The solubility of both gases decreases when the side-chain of the cations is functionalized with an unsaturated group. This can be explained by a less favorable enthalpy of solvation. The difference of solubility between ethane and ethylene can be explained from a balance of enthalpic and entropic factors: for the ionic liquid with the saturated alkyl side-chain and the benzyl-substituted side-chain, it is the favorable entropy of solvation that explains the larger ethylene solubility, whereas in the case of the saturated side-chain, it is the more favorable enthalpy of solvation. Molecular simulation allowed the identification of the mechanisms of solvation and the preferential solvation sites for each gas in the different ionic liquids. Simulations have shown that the entropy of solvation is more favorable when the presence of the gas weakens the cation-anion interactions or when the gas can be solvated near different sites of the ionic liquid.

Niclosamide methanol solvate and niclosamide hydrate: structure, solvent inclusion mode and implications for properties.

PubMed

Harriss, Bethany I; Wilson, Claire; Radosavljevic Evans, Ivana

2014-08-01

Structural studies have been carried out of two solid forms of niclosamide [5-chloro-N-(2-chloro-4-nitrophenyl)-2-hydroxybenzamide, NCL], a widely used anthelmintic drug, namely niclosamide methanol monosolvate, C13H8Cl2N2O4·CH3OH or NCL·MeOH, and niclosamide monohydrate, denoted HA. The structure of the methanol solvate obtained from single-crystal X-ray diffraction is reported for the first time, elucidating the key host-guest hydrogen-bonding interactions which lead to solvate formation. The essentially planar NCL host molecules interact via π-stacking and pack in a herringbone-type arrangement, giving rise to channels along the crystallographic a axis in which the methanol guest molecules are located. The methanol and NCL molecules interact via short O-H...O hydrogen bonds. Laboratory powder X-ray diffraction (PXRD) measurements reveal that the initially phase-pure NCL·MeOH solvate readily transforms into NCL monohydrate within hours under ambient conditions. PXRD further suggests that the NCL monohydrate, HA, is isostructural with the NCL·MeOH solvate. This is consistent with the facile transformation of the methanol solvate into the hydrate when stored in air. The crystal packing and the topology of guest-molecule inclusion are compared with those of other NCL solvates for which the crystal structures are known, giving a consistent picture which correlates well with known experimentally observed desolvation properties.

Tuned range separated hybrid functionals for solvated low bandgap oligomers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Queiroz, Thiago B. de, E-mail: thiago.branquinho-de-queiroz@uni-bayreuth.de; Kümmel, Stephan

2015-07-21

The description of charge transfer excitations has long been a challenge to time dependent density functional theory. The recently developed concept of “optimally tuned range separated hybrid (OT-RSH) functionals” has proven to describe charge transfer excitations accurately in many cases. However, describing solvated or embedded systems is yet a challenge. This challenge is not only computational but also conceptual, because the tuning requires identifying a specific orbital, typically the highest occupied one of the molecule under study. For solvated molecules, this orbital may be delocalized over the solvent. We here demonstrate that one way of overcoming this problem is tomore » use a locally projected self-consistent field diagonalization on an absolutely localized molecular orbital expansion. We employ this approach to determine ionization energies and the optical gap of solvated oligothiophenes, i.e., paradigm low gap systems that are of relevance in organic electronics. Dioxane solvent molecules are explicitly represented in our calculations, and the ambiguities of straightforward parameter tuning in solution are elucidated. We show that a consistent estimate of the optimal range separated parameter (ω) at the limit of bulk solvation can be obtained by gradually extending the solvated system. In particular, ω is influenced by the solvent beyond the first coordination sphere. For determining ionization energies, a considerable number of solvent molecules on the first solvation shell must be taken into account. We demonstrate that accurately calculating optical gaps of solvated systems using OT-RSH can be done in three steps: (i) including the chemical environment when determining the range-separation parameter, (ii) taking into account the screening due to the solvent, and (iii) using realistic molecular geometries.« less

Zero-point energy effects in anion solvation shells.

PubMed

Habershon, Scott

2014-05-21

By comparing classical and quantum-mechanical (path-integral-based) molecular simulations of solvated halide anions X(-) [X = F, Cl, Br and I], we identify an ion-specific quantum contribution to anion-water hydrogen-bond dynamics; this effect has not been identified in previous simulation studies. For anions such as fluoride, which strongly bind water molecules in the first solvation shell, quantum simulations exhibit hydrogen-bond dynamics nearly 40% faster than the corresponding classical results, whereas those anions which form a weakly bound solvation shell, such as iodide, exhibit a quantum effect of around 10%. This observation can be rationalized by considering the different zero-point energy (ZPE) of the water vibrational modes in the first solvation shell; for strongly binding anions, the ZPE of bound water molecules is larger, giving rise to faster dynamics in quantum simulations. These results are consistent with experimental investigations of anion-bound water vibrational and reorientational motion.

Implicit solvation model for density-functional study of nanocrystal surfaces and reaction pathways

NASA Astrophysics Data System (ADS)

Mathew, Kiran; Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Arias, T. A.; Hennig, Richard G.

2014-02-01

Solid-liquid interfaces are at the heart of many modern-day technologies and provide a challenge to many materials simulation methods. A realistic first-principles computational study of such systems entails the inclusion of solvent effects. In this work, we implement an implicit solvation model that has a firm theoretical foundation into the widely used density-functional code Vienna ab initio Software Package. The implicit solvation model follows the framework of joint density functional theory. We describe the framework, our algorithm and implementation, and benchmarks for small molecular systems. We apply the solvation model to study the surface energies of different facets of semiconducting and metallic nanocrystals and the SN2 reaction pathway. We find that solvation reduces the surface energies of the nanocrystals, especially for the semiconducting ones and increases the energy barrier of the SN2 reaction.

Decontamination of 2-chloroethyl ethylsulfide using titanate nanoscrolls

NASA Astrophysics Data System (ADS)

Kleinhammes, Alfred; Wagner, George W.; Kulkarni, Harsha; Jia, Yuanyuan; Zhang, Qi; Qin, Lu-Chang; Wu, Yue

2005-08-01

Titanate nanoscrolls, a recently discovered variant of TiO 2 nanocrystals, are tested as reactive sorbent for chemical warfare agent (CWA) decontamination. The large surface area of the uncapped tubules provides the desired rapid absorption of the contaminant while water molecules, intrinsic constituents of titanate nanoscrolls, provide the necessary chemistry for hydrolytic reaction. In this study the decomposition of 2-chloroethyl ethylsulfide (CEES), a simulant for the CWA mustard, was monitored using 13C NMR. The NMR spectra reveal reaction products as expected from the hydrolysis of CEES. This demonstrates that titanate nanoscrolls could potentially be employed as a decontaminant for CWAs.

Using 2 H labelling to improve the NMR detectability of pyridine and its derivatives by SABRE.

PubMed

Norcott, Philip; Burns, Michael J; Rayner, Peter J; Mewis, Ryan E; Duckett, Simon B

2018-07-01

By introducing a range of 2 H labels into pyridine and the para-substituted agents, methyl isonicotinate and isonicotinamide, we significantly improve their NMR detectability in conjunction with the signal amplification by reversible exchange process. We describe how the rates of T 1 relaxation for the remaining 1 H nuclei are increased and show how this leads to a concomitant increase in the level of 1 H and 13 C hyperpolarization that can ultimately be detected. © 2017 The Authors. Magnetic Resonance in Chemistry published by John Wiley & Sons Ltd.

In Vitro Evaluation of Gd(3+)-Anionic Linear Globular Dendrimer-Monoclonal Antibody: Potential Magnetic Resonance Imaging Contrast Agents for Prostate Cancer Cell Imaging.

PubMed

Mirzaei, Mehdi; Mehravi, Bita; Ardestani, Mehdi Shafiee; Ziaee, Seyed Amir Mohsen; Pourghasem, Peyman

2015-12-01

Early stage prostate cancer diagnosis is of high global interest. Magnetic resonance imaging (MRI) is a non-invasive modality for early cancer diagnosis, in particular for prostate cancer detection. The research aim is to synthesize a nanodendrimer and its conjugate with C595 monoclonal antibody (mAb C595), against prostate cancer, followed by its chelating with Gd(3+). Anti-MUC-1 mAb C595 was conjugated to an anionic linear globular dendrimer (ALGDG2). The polyethylene glycol core and citric acid shell were synthesized followed by loading with Gd(3+) to make novel contrast agents for functional MRI. The in vitro behavior and MRI parameters of the nanoconjugate were investigated performing several studies such as cell toxicity and TNF-alpha evaluations. The investigation of magnetic resonance imaging parameters indicated how well nanoconjugate performs in (1)H-NMR and (17)O-NMR in vitro. Results showed a potential specific MRI activity by improving the swelling responses cell binding. The MTT (2-(4,5-dimethyl-2-thiazolyl)-3,5-diphenyl-2H-tetrazolium bromide) assay demonstrated that this contrast agent had significant cytotoxicity on prostate cancer cells. These results showed that Gd(3+)-ALGDG2-C595 is a potential prostate molecular imaging agent and could be considered as an ideal functional nanoprobe. Additionally, further investigations by clinical trials are in the pipeline.

Hydration property of globular proteins: An analysis of solvation free energy by energy representation method

NASA Astrophysics Data System (ADS)

Saito, Hiroaki; Matubayasi, Nobuyuki; Nishikawa, Kiyoshi; Nagao, Hidemi

2010-09-01

Molecular dynamics simulations and solvation free energy calculations of five globular proteins (BPTI, RNase A, Lysozyme, β-lactoglobulin A, and α-chymotrypsinogen A) have been carried out to elucidate the hydration properties. Solvation free energies of the proteins with explicit solvent were estimated by energy representation (ER) method. The calculated solvation free energies were correlated with the solvent accessible surface area of hydrophilic portion, being consistent with the hydrophilic property of the proteins. These results showed that the ER method should be a powerful tool for estimating the hydration property of proteins, showing a progress of the free energy calculation with explicit solvent.

Improving accuracy of electrochemical capacitance and solvation energetics in first-principles calculations

NASA Astrophysics Data System (ADS)

Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Schwarz, Kathleen A.

2018-04-01

Reliable first-principles calculations of electrochemical processes require accurate prediction of the interfacial capacitance, a challenge for current computationally efficient continuum solvation methodologies. We develop a model for the double layer of a metallic electrode that reproduces the features of the experimental capacitance of Ag(100) in a non-adsorbing, aqueous electrolyte, including a broad hump in the capacitance near the potential of zero charge and a dip in the capacitance under conditions of low ionic strength. Using this model, we identify the necessary characteristics of a solvation model suitable for first-principles electrochemistry of metal surfaces in non-adsorbing, aqueous electrolytes: dielectric and ionic nonlinearity, and a dielectric-only region at the interface. The dielectric nonlinearity, caused by the saturation of dipole rotational response in water, creates the capacitance hump, while ionic nonlinearity, caused by the compactness of the diffuse layer, generates the capacitance dip seen at low ionic strength. We show that none of the previously developed solvation models simultaneously meet all these criteria. We design the nonlinear electrochemical soft-sphere solvation model which both captures the capacitance features observed experimentally and serves as a general-purpose continuum solvation model.

"Martinizing" the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins.

PubMed

Ricci, Clarisse G; Li, Bo; Cheng, Li-Tien; Dzubiella, Joachim; McCammon, J Andrew

2017-07-13

Solvation is a fundamental driving force in many biological processes including biomolecular recognition and self-assembly, not to mention protein folding, dynamics, and function. The variational implicit solvent method (VISM) is a theoretical tool currently developed and optimized to estimate solvation free energies for systems of very complex topology, such as biomolecules. VISM's theoretical framework makes it unique because it couples hydrophobic, van der Waals, and electrostatic interactions as a functional of the solvation interface. By minimizing this functional, VISM produces the solvation interface as an output of the theory. In this work, we push VISM to larger scale applications by combining it with coarse-grained solute Hamiltonians adapted from the MARTINI framework, a well-established mesoscale force field for modeling large-scale biomolecule assemblies. We show how MARTINI-VISM ( M VISM) compares with atomistic VISM ( A VISM) for a small set of proteins differing in size, shape, and charge distribution. We also demonstrate M VISM's suitability to study the solvation properties of an interesting encounter complex, barnase-barstar. The promising results suggest that coarse-graining the protein with the MARTINI force field is indeed a valuable step to broaden VISM's and MARTINI's applications in the near future.

Performance of the SMD and SM8 models for predicting solvation free energy of neutral solutes in methanol, dimethyl sulfoxide and acetonitrile.

PubMed

Zanith, Caroline C; Pliego, Josefredo R

2015-03-01

The continuum solvation models SMD and SM8 were developed using 2,346 solvation free energy values for 318 neutral molecules in 91 solvents as reference. However, no solvation data of neutral solutes in methanol was used in the parametrization, while only few solvation free energy values of solutes in dimethyl sulfoxide and acetonitrile were used. In this report, we have tested the performance of the models for these important solvents. Taking data from literature, we have generated solvation free energy, enthalpy and entropy values for 37 solutes in methanol, 21 solutes in dimethyl sulfoxide and 19 solutes in acetonitrile. Both SMD and SM8 models have presented a good performance in methanol and acetonitrile, with mean unsigned error equal or less than 0.66 and 0.55 kcal mol(-1) in methanol and acetonitrile, respectively. However, the correlation is worse in dimethyl sulfoxide, where the SMD and SM8 methods present mean unsigned error of 1.02 and 0.95 kcal mol(-1), respectively. Our results point out the SMx family of models need be improved for dimethyl sulfoxide solvent.

Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

DOE PAGES

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.; ...

2017-07-26

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. In this paper, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation and isolate the effects of charge and cavitation, comparing tomore » the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. Finally, this suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.« less

Standard electrode potential, Tafel equation, and the solvation thermodynamics.

PubMed

Matyushov, Dmitry V

2009-06-21

Equilibrium in the electronic subsystem across the solution-metal interface is considered to connect the standard electrode potential to the statistics of localized electronic states in solution. We argue that a correct derivation of the Nernst equation for the electrode potential requires a careful separation of the relevant time scales. An equation for the standard metal potential is derived linking it to the thermodynamics of solvation. The Anderson-Newns model for electronic delocalization between the solution and the electrode is combined with a bilinear model of solute-solvent coupling introducing nonlinear solvation into the theory of heterogeneous electron transfer. We therefore are capable of addressing the question of how nonlinear solvation affects electrochemical observables. The transfer coefficient of electrode kinetics is shown to be equal to the derivative of the free energy, or generalized force, required to shift the unoccupied electronic level in the bulk. The transfer coefficient thus directly quantifies the extent of nonlinear solvation of the redox couple. The current model allows the transfer coefficient to deviate from the value of 0.5 of the linear solvation models at zero electrode overpotential. The electrode current curves become asymmetric in respect to the change in the sign of the electrode overpotential.

A salient effect of density on the dynamics of nonaqueous electrolytes.

PubMed

Han, Sungho

2017-04-24

The mobility and solvation of lithium ions in electrolytes are crucial for the performance and safety of lithium ion batteries. It has been known that a single type of solvent cannot satisfy the requirements of both mobility and solvation simultaneously for electrolytes. Therefore, complex solvent mixtures have been used to optimize both properties. Here we present the effects of density on the dynamics and solvation of organic liquid electrolytes via extensive molecular dynamics simulations. Our study finds that a small variation in density can induce a significant effect on the mobility of electrolytes but does not influence the solvation structure of a lithium ion. It turns out that an adjustment of the density of electrolytes could provide a more effective way to enhance mobility than a control of the solvent mixture ratio of electrolytes. Our study reveals that the density change of electrolytes mainly affects the residence time of solvents in the first solvation shell of a lithium ion rather than the structural change of the solvation sheath. Finally, our results suggest an intriguing point for understanding and designing electrolytes of lithium ion batteries for better performance and safety.

Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. In this paper, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation and isolate the effects of charge and cavitation, comparing tomore » the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. Finally, this suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.« less

Solvated dissipative electro-elastic network model of hydrated proteins

NASA Astrophysics Data System (ADS)

Martin, Daniel

2013-03-01

Elastic network models coarse grain proteins into a network of residue beads connected by springs. We add dissipative dynamics to this mechanical system by applying overdamped Langevin equations of motion to normal-mode vibrations of the network. In addition, the network is made heterogeneous and softened at the protein surface by accounting for hydration of the ionized residues. Solvation changes the network Hessian in two ways. Diagonal solvation terms soften the spring constants and off-diagonal dipole-dipole terms correlate displacements of the ionized residues. The model is used to formulate the response functions of the electrostatic potential and electric field appearing in theories of redox reactions and spectroscopy. We also formulate the dielectric response of the protein and find that solvation of the surface ionized residues leads to a slow relaxation peak in the dielectric loss spectrum, about two orders of magnitude slower than the main peak of protein relaxation. Finally, the solvated network is used to formulate the allosteric response of the protein to ion binding. The global thermodynamics of ion binding is not strongly affected by the network solvation, but it dramatically enhances conformational changes in response to placing a charge at the a the active site.

Solvated dissipative electro-elastic network model of hydrated proteins

NASA Astrophysics Data System (ADS)

Martin, Daniel R.; Matyushov, Dmitry V.

2012-10-01

Elastic network models coarse grain proteins into a network of residue beads connected by springs. We add dissipative dynamics to this mechanical system by applying overdamped Langevin equations of motion to normal-mode vibrations of the network. In addition, the network is made heterogeneous and softened at the protein surface by accounting for hydration of the ionized residues. Solvation changes the network Hessian in two ways. Diagonal solvation terms soften the spring constants and off-diagonal dipole-dipole terms correlate displacements of the ionized residues. The model is used to formulate the response functions of the electrostatic potential and electric field appearing in theories of redox reactions and spectroscopy. We also formulate the dielectric response of the protein and find that solvation of the surface ionized residues leads to a slow relaxation peak in the dielectric loss spectrum, about two orders of magnitude slower than the main peak of protein relaxation. Finally, the solvated network is used to formulate the allosteric response of the protein to ion binding. The global thermodynamics of ion binding is not strongly affected by the network solvation, but it dramatically enhances conformational changes in response to placing a charge at the active site of the protein.

Hydrophilic Solvation Dominates the Terahertz Fingerprint of Amino Acids in Water.

PubMed

Esser, Alexander; Forbert, Harald; Sebastiani, Federico; Schwaab, Gerhard; Havenith, Martina; Marx, Dominik

2018-02-01

Spectroscopy in the terahertz frequency regime is a sensitive tool to probe solvation-induced effects in aqueous solutions. Yet, a systematic understanding of spectral lineshapes as a result of distinct solvation contributions remains terra incognita. We demonstrate that modularization of amino acids in terms of functional groups allows us to compute their distinct contributions to the total terahertz response. Introducing the molecular cross-correlation analysis method provides unique access to these site-specific contributions. Equivalent groups in different amino acids lead to look-alike spectral contributions, whereas side chains cause characteristic but additive complexities. Specifically, hydrophilic solvation of the zwitterionic groups in valine and glycine leads to similar terahertz responses which are fully decoupled from the side chain. The terahertz response due to H-bonding within the large hydrophobic solvation shell of valine turns out to be nearly indistinguishable from that in bulk water in direct comparison to the changes imposed by the charged functional groups that form strong H-bonds with their hydration shells. Thus, the hydrophilic groups and their solvation shells dominate the terahertz absorption difference, while on the same intensity scale, the influence of hydrophobic water can be neglected.

A salient effect of density on the dynamics of nonaqueous electrolytes

NASA Astrophysics Data System (ADS)

Han, Sungho

2017-04-01

The mobility and solvation of lithium ions in electrolytes are crucial for the performance and safety of lithium ion batteries. It has been known that a single type of solvent cannot satisfy the requirements of both mobility and solvation simultaneously for electrolytes. Therefore, complex solvent mixtures have been used to optimize both properties. Here we present the effects of density on the dynamics and solvation of organic liquid electrolytes via extensive molecular dynamics simulations. Our study finds that a small variation in density can induce a significant effect on the mobility of electrolytes but does not influence the solvation structure of a lithium ion. It turns out that an adjustment of the density of electrolytes could provide a more effective way to enhance mobility than a control of the solvent mixture ratio of electrolytes. Our study reveals that the density change of electrolytes mainly affects the residence time of solvents in the first solvation shell of a lithium ion rather than the structural change of the solvation sheath. Finally, our results suggest an intriguing point for understanding and designing electrolytes of lithium ion batteries for better performance and safety.

Protons in non-ionic aqueous reverse micelles.

PubMed

Rodriguez, Javier; Martí, Jordi; Guàrdia, Elvira; Laria, Daniel

2007-05-03

Using molecular dynamics techniques, we investigate the solvation of an excess proton within an aqueous reverse micelle in vacuo, with the neutral surfactant diethylene glycol monodecyl ether [CH3(CH2)11(OC2H4)2OH]. The simulation experiments were performed using a multistate empirical valence bond Hamiltonian model. Our results show that the stable solvation environments for the excess proton are located in the water-surfactant interface and that its first solvation shell is composed exclusively by water molecules. The relative prevalence of Eigen- versus Zundel-like solvation structures is investigated; compared to bulk results, Zundel-like structures in micelles become somewhat more stable. Characteristic times for the proton translocation jumps have been computed using population relaxation time correlation functions. The micellar rate for proton transfer is approximately 40x smaller than that found in bulk water at ambient conditions. Differences in the computed rates are examined in terms of the hydrogen-bond connectivity involving the first solvation shell of the excess charge with the rest of the micellar environment. Simulation results would indicate that proton transfers are correlated with rare episodes during which the HB connectivity between the first and second solvation shells suffers profound modifications.

Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

NASA Astrophysics Data System (ADS)

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.; Mundy, Chistopher J.

2017-10-01

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. Here, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation and isolate the effects of charge and cavitation, comparing to the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. This suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.

Performance of the SMD and SM8 models for predicting solvation free energy of neutral solutes in methanol, dimethyl sulfoxide and acetonitrile

NASA Astrophysics Data System (ADS)

Zanith, Caroline C.; Pliego, Josefredo R.

2015-03-01

The continuum solvation models SMD and SM8 were developed using 2,346 solvation free energy values for 318 neutral molecules in 91 solvents as reference. However, no solvation data of neutral solutes in methanol was used in the parametrization, while only few solvation free energy values of solutes in dimethyl sulfoxide and acetonitrile were used. In this report, we have tested the performance of the models for these important solvents. Taking data from literature, we have generated solvation free energy, enthalpy and entropy values for 37 solutes in methanol, 21 solutes in dimethyl sulfoxide and 19 solutes in acetonitrile. Both SMD and SM8 models have presented a good performance in methanol and acetonitrile, with mean unsigned error equal or less than 0.66 and 0.55 kcal mol-1 in methanol and acetonitrile, respectively. However, the correlation is worse in dimethyl sulfoxide, where the SMD and SM8 methods present mean unsigned error of 1.02 and 0.95 kcal mol-1, respectively. Our results point out the SMx family of models need be improved for dimethyl sulfoxide solvent.

Solvent effects on the crystal growth structure and morphology of the pharmaceutical dirithromycin

NASA Astrophysics Data System (ADS)

Wang, Yuan; Liang, Zuozhong

2017-12-01

Solvent effects on the crystal structure and morphology of pharmaceutical dirithromycin molecules were systematically investigated using both experimental crystallization and theoretical simulation. Dirithromycin is one of the new generation of macrolide antibiotics with two polymorphic forms (Form I and Form II) and many solvate forms. Herein, six solvates of the dirithromycin, including acetonitrile, acetonitrile/water, acetone, 1-propanol, N,N-dimethylformamide (DMF) and cyclohexane, were studied. Experimentally, we crystallized the dirithromycin molecules in different solvents by the solvent evaporating method and measured the crystal structures with the X-ray diffraction (XRD). We compared these crystal structures of dirithromycin solvates and analyzed the solvent property-determined structure evolution. The solvents have a strong interaction with the dirithromycin molecule due to the formation of inter-molecular interactions (such as the hydrogen bonding and close contacts (sum of vdW radii)). Theoretically, we calculated the ideal crystal habit based on the solvated structures with the attachment growth (AE) model. The predicted morphologies and aspect ratios of dirithromycin solvates agree well with the experimental results. This work could be helpful to better understand the structure and morphology evolution of solvates controlled by solvents and guide the crystallization of active pharmaceutical ingredients in the pharmaceutical industry.

Solvation thermodynamics of amino acid side chains on a short peptide backbone

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hajari, Timir; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de

The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment. A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone. To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvationmore » free energies of nonpolar and polar side chains attached to a short peptide backbone. The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone. We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected. This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution. We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar side chain cavities in bulk water, in agreement with earlier work in the literature on analysis of cavity fluctuations at nonpolar molecular surfaces. The cavity and dispersion interaction contributions correlate quite well with the solvent accessible surface area of the nonpolar side chains attached to the backbone. This correlation however is weak for the overall solvation free energies owing to the fact that the cavity and dispersion free energy contributions are almost exactly cancelling each other.« less

Association Thermodynamics and Conformational Stability of β-Sheet Amyloid β(17-42) Oligomers: Effects of E22Q (Dutch) Mutation and Charge Neutralization

PubMed Central

Blinov, Nikolay; Dorosh, Lyudmyla; Wishart, David; Kovalenko, Andriy

2010-01-01

Amyloid fibrils are associated with many neurodegenerative diseases. It was found that amyloidogenic oligomers, not mature fibrils, are neurotoxic agents related to these diseases. Molecular mechanisms of infectivity, pathways of aggregation, and molecular structure of these oligomers remain elusive. Here, we use all-atom molecular dynamics, molecular mechanics combined with solvation analysis by statistical-mechanical, three-dimensional molecular theory of solvation (also known as 3D-RISM-KH) in a new MM-3D-RISM-KH method to study conformational stability, and association thermodynamics of small wild-type Aβ17–42 oligomers with different protonation states of Glu22, as well the E22Q (Dutch) mutants. The association free energy of small β-sheet oligomers shows near-linear trend with the dimers being thermodynamically more stable relative to the larger constructs. The linear (within statistical uncertainty) dependence of the association free energy on complex size is a consequence of the unilateral stacking of monomers in the β-sheet oligomers. The charge reduction of the wild-type Aβ17–42 oligomers upon protonation of the solvent-exposed Glu22 at acidic conditions results in lowering the association free energy compared to the wild-type oligomers at neutral pH and the E22Q mutants. The neutralization of the peptides because of the E22Q mutation only marginally affects the association free energy, with the reduction of the direct electrostatic interactions mostly compensated by the unfavorable electrostatic solvation effects. For the wild-type oligomers at acidic conditions such compensation is not complete, and the electrostatic interactions, along with the gas-phase nonpolar energetic and the overall entropic effects, contribute to the lowering of the association free energy. The differences in the association thermodynamics between the wild-type Aβ17–42 oligomers at neutral pH and the Dutch mutants, on the one hand, and the Aβ17–42 oligomers with protonated Glu22, on the other, may be explained by destabilization of the inter- and intrapeptide salt bridges between Asp23 and Lys28. Peculiarities in the conformational stability and the association thermodynamics for the different models of the Aβ17–42 oligomers are rationalized based on the analysis of the local physical interactions and the microscopic solvation structure. PMID:20338850

Solution equilibrium behind the room-temperature synthesis of nanocrystalline titanium dioxide

NASA Astrophysics Data System (ADS)

Seisenbaeva, Gulaim A.; Daniel, Geoffrey; Nedelec, Jean-Marie; Kessler, Vadim G.

2013-03-01

Formation of nanocrystalline and monodisperse TiO2 from a water soluble and stable precursor, ammonium oxo-lactato-titanate, (NH4)8Ti4O4(Lactate)8.4H2O, often referred to as TiBALDH or TALH, is demonstrated to be due to a coordination equilibrium. This compound, individual in the solid state, exists in solution in equilibrium with ammonium tris-lactato-titanate, (NH4)2Ti(Lactate)3 and uniform crystalline TiO2 nanoparticles (anatase) stabilized by surface-capping with lactate ligands. This equilibrium can be shifted towards nano-TiO2via application of a less polar solvent like methanol or ethanol, dilution of the solution, introduction of salts or raising the temperature, and reverted on addition of polar and strongly solvating media such as dimethyl sulfoxide, according to NMR. Aggregation and precipitation of the particles were followed by DLS and could be achieved by a decrease in their surface charge by adsorption of strongly hydrogen-bonding cations, e.g. in solutions of ammonia, ethanolamine or amino acid arginine or by addition of ethanol. The observed equilibrium may be involved in formation of nano-titania on the surface of plant roots exerting chelating organic carboxylate ligands and thus potentially influencing plant interactions.Formation of nanocrystalline and monodisperse TiO2 from a water soluble and stable precursor, ammonium oxo-lactato-titanate, (NH4)8Ti4O4(Lactate)8.4H2O, often referred to as TiBALDH or TALH, is demonstrated to be due to a coordination equilibrium. This compound, individual in the solid state, exists in solution in equilibrium with ammonium tris-lactato-titanate, (NH4)2Ti(Lactate)3 and uniform crystalline TiO2 nanoparticles (anatase) stabilized by surface-capping with lactate ligands. This equilibrium can be shifted towards nano-TiO2via application of a less polar solvent like methanol or ethanol, dilution of the solution, introduction of salts or raising the temperature, and reverted on addition of polar and strongly solvating media such as dimethyl sulfoxide, according to NMR. Aggregation and precipitation of the particles were followed by DLS and could be achieved by a decrease in their surface charge by adsorption of strongly hydrogen-bonding cations, e.g. in solutions of ammonia, ethanolamine or amino acid arginine or by addition of ethanol. The observed equilibrium may be involved in formation of nano-titania on the surface of plant roots exerting chelating organic carboxylate ligands and thus potentially influencing plant interactions. Electronic supplementary information (ESI) available: Crystallographic data in cif and table format, detailed description of hydrogen bonding in (NH4)2[Ti(l-Lactate)3].3H2O, additional TEM images, DLS data on particle size in solutions and NanoSight data on particle size distribution, photos of produced TiO2 colloids, details of NMR experiments and a real-time movie demonstrating the equilibrium leading to TiO2 formation and re-dissolution in pH-neutral ammonium lactate solutions. CCDC 915222. For ESI and crystallographic data in CIF or other electronic format. see DOI: 10.1039/c3nr34068f

Correlation of the antimicrobial activity of salicylaldehydes with broadening of the NMR signal of the hydroxyl proton. Possible involvement of proton exchange processes in the antimicrobial activity.

PubMed

Elo, Hannu; Kuure, Matti; Pelttari, Eila

2015-03-06

Certain substituted salicylaldehydes are potent antibacterial and antifungal agents and some of them merit consideration as potential chemotherapeutic agents against Candida infections, but their mechanism of action has remained obscure. We report here a distinct correlation between broadening of the NMR signal of the hydroxyl proton of salicylaldehydes and their activity against several types of bacteria and fungi. When proton NMR spectra of the compounds were determined using hexadeuterodimethylsulfoxide as solvent and the height of the OH proton signal was measured, using the signal of the aldehyde proton as an internal standard, it was discovered that a prerequisite of potent antimicrobial activity is that the proton signal is either unobservable or relatively very low, i.e. that it is extremely broadened. Thus, none of the congeners whose OH proton signal was high were potent antimicrobial agents. Some congeners that gave a very low OH signal were, however, essentially inactive against the microbes, indicating that although drastic broadening of the OH signal appears to be a prerequisite, also other (so far unknown) factors are needed for high antimicrobial activity. Because broadening of the hydroxyl proton signal is related to the speed of the proton exchange process(es) involving that proton, proton exchange may be involved in the mechanism of action of the compounds. Further studies are needed to analyze the relative importance of different factors (such as electronic effects, strength of the internal hydrogen bond, co-planarity of the ring and the formyl group) that determine the rates of those processes. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Reactivity between biphenyl and precursor of solvated electrons in tetrahydrofuran measured by picosecond pulse radiolysis in near-ultraviolet, visible, and infrared.

PubMed

Saeki, Akinori; Kozawa, Takahiro; Ohnishi, Yuko; Tagawa, Seiichi

2007-02-22

The initial decrease of solvated electrons in tetrahydrofuran (THF) upon addition of biphenyl was investigated by picosecond pulse radiolysis. Transient absorption spectra derived from the biphenyl radical anion (centered at 408 and 655 nm) and solvated electrons of THF (infrared) were successfully measured in the wavelength region from 400 to 900 nm by the extension of a femtosecond continuum probe light to near-ultraviolet using a second harmonic generation of Ti:sapphire laser and a CaF2 plate. From the analysis of kinetic traces at 1300 nm considering the overlap of primary solvated electrons and partial biphenyl radical anion, C37, which is defined by the solute concentration to reduce the initial yield of solvated electrons to 1/e, was found to be 87 +/- 3 mM. The rate constant of solvated electrons with biphenyl was determined as 5.8 +/- 0.3 x 10(10) M(-1) s(-1). We demonstrate that the kinetic traces at both 408 nm mainly due to biphenyl radical anion and 1300 nm mainly due to solvated electrons are reproduced with high accuracy and consistency by a simple kinetic analysis. Much higher concentrations of biphenyl (up to 2 M) were examined, showing further increase of the initial yield of biphenyl radical anion accompanying a fast decay component. This observation is discussed in terms of geminate ion recombination, scavenging, delayed geminate ion recombination, and direct ionization of biphenyl at high concentration.

Investigation of rubidium(I) ion solvation in liquid ammonia using QMCF-MD simulation and NBO analysis of first solvation shell structure.

PubMed

Hidayat, Yuniawan; Armunanto, Ria; Pranowo, Harno Dwi

2018-04-27

Rb(I) ion solvation in liquid ammonia has been studied by an ab initio quantum mechanical charge field molecular dynamics simulation, and the first solvation shell structure has been analyzed using natural bond orbital. The simulation was performed for an ion and 593 ammonia molecules in a box with a length of 29.03 Å corresponding to a liquid ammonia density of 0.69 g/mL at 235.16 K. The quantum mechanical calculation was carried out for atomic interactions in the radius of 6.4 Å from the ion using LANL2DZ ECP and DZP (Dunning) basis sets for Rb(I) ion and ammonia respectively. The trajectories of the simulation were analyzed in terms of radial, angular, and coordination number distribution functions, vibration, and mean residence time (MRT). Two solvation shell regions are observed for the Rb(I)-N as well as the Rb(I)-H. The maximum distance of Rb(I)-N in the first solvation shell is in accordance with experimental data where a coordination number of 8 is favorable. A non-single coordination number of the first and second shell indicates dynamic solvation structure. It is confirmed by frequent exchange ligand processes observed within a simulation time of 15 ps. The low stabilization energy of donor acceptor ion-ligand interaction with a small Wiberg bond index affirms that the Rb(I)-NH 3 interaction is weak electrostatically.

MAS-NMR investigations of the crystallization behaviour of lithium aluminum silicate (LAS) glasses containing P 2O 5 and TiO 2 nucleants

NASA Astrophysics Data System (ADS)

Ananthanarayanan, A.; Kothiyal, G. P.; Montagne, L.; Revel, B.

2010-06-01

Lithium aluminum silicate (LAS) glass of composition (mol%) 20.4Li 2O-4.0Al 2O 3-68.6SiO 2-3.0K 2O-2.6B 2O 3-0.5P 2O 5-0.9TiO 2 was prepared by melt quenching. The glass was then nucleated and crystallized based on differential thermal analysis (DTA) data and was characterized by 29Si, 31P, 11B and 27Al MAS-NMR. XRD and 29Si NMR showed that lithium metasilicate (Li 2SiO 3) is the first phase to c form followed by cristobalite (SiO 2) and lithium disilicate (Li 2Si 2O 5). 29Si MAS-NMR revealed a change in the network structure already for the glasses nucleated at 550 °C. Since crystalline Li 3PO 4, as observed by 31P MAS-NMR, forms concurrently with the silicate phases, we conclude that crystalline Li 3PO 4 does not act as a nucleating agent for lithium silicate phases. Moreover, 31P NMR indicates the formation of M-PO 4 ( M=B, Al or Ti) complexes. The presence of BO 3 and BO 4 structural units in all the glass/glass-ceramic samples is revealed through 11B MAS-NMR. B remains in the residual glass and the crystallization of silicate phases causes a reduction in the number of alkali ions available for charge compensation. As a result, the number of trigonally coordinated B (BO 3) increases at the expense of tetrahedrally coordinated B (BO 4). The 27Al MAS-NMR spectra indicate the presence of tetrahedrally coordinated Al species, which are only slightly perturbed by the crystallization.

Chemical synthesis of 9(Z)-octadecenamide and its hypolipidemic effect: a bioactive agent found in the essential oil of mountain celery seeds.

PubMed

Cheng, Ming-Ching; Ker, Yaw-Bee; Yu, Tung-Hsi; Lin, Li-Yun; Peng, Robert Y; Peng, Chiung-Huei

2010-02-10

The unusual hypolipidemic activity of the methanolic fractionate of the essential oil (EOM) obtained from the mountain celery seed was previously reported. The most enriched 9(Z)-octadecenamide (oleamide) was speculated to be responsible for the relevant bioactivity. Chemically syntheized oleamide (CSO) yielded 85.1% with a purity of 98.6% when identified by RP-HPLC, FTIR, HREIMS, (1)H NMR, and (13)C NMR. CSO was tested for its antioxidative and hypolipidemic bioactivities. Results indicated CSO was potently hypolipidemic with regard to serum TG, TC, LDL-C, LDL-C/HDL-C, and hepatic TG (p < 0.05), but not for serum HDL-C and hepatic TC. In addition, CSO exhibited only poor antioxidative activity, implicating the possibility that the hypolipidemic and antioxidative bioactivity of original EOM was due to another coexisting constituent, probably gamma-selinene. Conclusively, oleamide is a potent hypolipidemic agent as regarding its effects on decreasing serum TG, TC, LDL-C and hepatic TG.

Molecular modelling and synthesis of spiroimidazolidine-2,4-diones with dual activities as hypoglycemic agents and selective inhibitors of aldose reductase.

PubMed

Salem, Manar G; Abdel Aziz, Yasmine M; Elewa, Marwa; Elshihawy, Hosam A; Said, Mohamed M

2018-05-02

Novel derivatives of spiroimidazolidinedione were synthesized and evaluated as hypoglycemic agents through binding to sulfonylurea receptor 1 (SUR1) in pancreatic beta-cells. Their selectivity index was calculated against both aldehyde reductase (ALR1) and aldose reductase (ALR2). Aldehyde reductase is a key enzyme in the polyol pathway that is involved in the etiology of the secondary diabetic complications. All structures were confirmed by microanalysis and by IR, 1 H NMR, 13 C NMR and EI-MS spectroscopy. The investigated compounds were subjected to molecular docking and an in silico prediction study to determine their free energy of binding (ΔG) values and predict their physicochemical properties and drug-likeness scores. Compound 1'-(5-chlorothiophene-2-ylsulfonyl)spiro[cyclohexane-1,5'-imidazolidine]-2',4'-dione showed IC 50 0.47 µM and 79% reduction in blood glucose level with a selectivity index 127 for ALR2. Copyright © 2018 Elsevier Inc. All rights reserved.

Temperature dependence of proton NMR relaxation times at earth's magnetic field

NASA Astrophysics Data System (ADS)

Niedbalski, Peter; Kiswandhi, Andhika; Parish, Christopher; Ferguson, Sarah; Cervantes, Eduardo; Oomen, Anisha; Krishnan, Anagha; Goyal, Aayush; Lumata, Lloyd

The theoretical description of relaxation processes for protons, well established and experimentally verified at conventional nuclear magnetic resonance (NMR) fields, has remained untested at low fields despite significant advances in low field NMR technology. In this study, proton spin-lattice relaxation (T1) times in pure water and water doped with varying concentrations of the paramagnetic agent copper chloride have been measured from 6 to 92oC at earth's magnetic field (1700 Hz). Results show a linear increase of T1 with temperature for each of the samples studied. Increasing the concentration of the copper chloride greatly reduced T1 and reduced dependence on temperature. The consistency of the results with theory is an important confirmation of past results, while the ability of an ultra-low field NMR system to do contrast-enhanced magnetic resonance imaging (MRI) is promising for future applicability to low-cost medical imaging and chemical identification. This work is supported by US Dept of Defense Award No. W81XWH-14-1-0048 and the Robert A. Welch Foundation Grant No. AT-1877.

Simple 1H NMR spectroscopic method for assay of salts of the contrast agent diatrizoate in commercial solutions.

PubMed

Hanna, G M; Lau-Cam, C A

1996-01-01

A simple, accurate, and specific 1H NMR spectroscopic method was developed for the assay of diatrizoate meglumine or the combination diatrizoate meglumine and diatrizoate sodium in commercial solutions for injection. A mixture of injectable solution and sodium acetate, the internal standard, was diluted with D2O and the 1H NMR spectrum of the solution was obtained. Two approaches were used to calculate the drug content, based on the integral values for the -N-CO-CH3 protons of diatrizoic acid at 2.23 ppm, and -N-CH3 protons of meglumine at 2.73 ppm, and the CH3-CO-protons of sodium acetate at 1.9 ppm. Recoveries (mean +/- standard deviation) of diatrizoic acid and meglumine from 10 synthetic mixtures of various amounts of these compounds with a fixed amount of internal standard were 100.3 +/- 0.55% and 100.1 +/- 0.98%, respectively. In addition to providing a direct means of simultaneously assaying diatrizoic acid and meglumine, the proposed NMR method can also be used to identify diatrizoate meglumine and each of its molecular components.

Solvent signal suppression for high-resolution MAS-DNP

NASA Astrophysics Data System (ADS)

Lee, Daniel; Chaudhari, Sachin R.; De Paëpe, Gaël

2017-05-01

Dynamic nuclear polarization (DNP) has become a powerful tool to substantially increase the sensitivity of high-field magic angle spinning (MAS) solid-state NMR experiments. The addition of dissolved hyperpolarizing agents usually results in the presence of solvent signals that can overlap and obscure those of interest from the analyte. Here, two methods are proposed to suppress DNP solvent signals: a Forced Echo Dephasing experiment (FEDex) and TRAnsfer of Populations in DOuble Resonance Echo Dephasing (TRAPDORED) NMR. These methods reintroduce a heteronuclear dipolar interaction that is specific to the solvent, thereby forcing a dephasing of recoupled solvent spins and leaving acquired NMR spectra free of associated resonance overlap with the analyte. The potency of these methods is demonstrated on sample types common to MAS-DNP experiments, namely a frozen solution (of L-proline) and a powdered solid (progesterone), both containing deuterated glycerol as a DNP solvent. The proposed methods are efficient, simple to implement, compatible with other NMR experiments, and extendable past spectral editing for just DNP solvents. The sensitivity gains from MAS-DNP in conjunction with FEDex or TRAPDORED then permits rapid and uninterrupted sample analysis.

Neosordarin and hydroxysordarin, two new antifungal agents from Sordaria araneosa.

PubMed

Davoli, Paolo; Engel, Günther; Werle, Andreas; Sterner, Olov; Anke, Timm

2002-04-01

Two novel antifungal agents belonging to the sordarin family have been isolated from fermentations of Sordaria araneosa by bioassay-guided purification and their structures elucidated by NMR techniques. Neosordarin (1) is closely related to the recently discovered hypoxysordarin (2), with only small differences on the aliphatic side chain acylating the hydroxyl in the 3'-position of the sordarose moiety. Hydroxysordarin (3) closely resembles sordarin (4), the only slight difference being the replacement of sordarose with altrose as the sugar unit.

Spectrum of Slow and Super-Slow (Picosecond to Nanosecond) Water Dynamics around Organic and Biological Solutes.

PubMed

Ramakrishnan, Gopakumar; González-Jiménez, Mario; Lapthorn, Adrian J; Wynne, Klaas

2017-07-06

Water dynamics in the solvation shell of solutes plays a very important role in the interaction of biomolecules and in chemical reaction dynamics. However, a selective spectroscopic study of the solvation shell is difficult because of the interference of the solute dynamics. Here we report on the observation of heavily slowed down water dynamics in the solvation shell of different solutes by measuring the low-frequency spectrum of solvation water, free from the contribution of the solute. A slowdown factor of ∼50 is observed even for relatively low concentrations of the solute. We go on to show that the effect can be generalized to different solutes including proteins.

Evidence for Reduced Hydrogen-Bond Cooperativity in Ionic Solvation Shells from Isotope-Dependent Dielectric Relaxation

NASA Astrophysics Data System (ADS)

Cota, Roberto; Ottosson, Niklas; Bakker, Huib J.; Woutersen, Sander

2018-05-01

We find that the reduction in dielectric response (depolarization) of water caused by solvated ions is different for H2O and D2O . This isotope dependence allows us to reliably determine the kinetic contribution to the depolarization, which is found to be significantly smaller than predicted by existing theory. The discrepancy can be explained from a reduced hydrogen-bond cooperativity in the solvation shell: we obtain quantitative agreement between theory and experiment by reducing the Kirkwood correlation factor of the solvating water from 2.7 (the bulk value) to ˜1.6 for NaCl and ˜1 (corresponding to completely uncorrelated motion of water molecules) for CsCl.

Tannin fingerprinting in vegetable tanned leather by solid state NMR spectroscopy and comparison with leathers tanned by other processes.

PubMed

Romer, Frederik H; Underwood, Andrew P; Senekal, Nadine D; Bonnet, Susan L; Duer, Melinda J; Reid, David G; van der Westhuizen, Jan H

2011-01-28

Solid state ¹³C-NMR spectra of pure tannin powders from four different sources--mimosa, quebracho, chestnut and tara--are readily distinguishable from each other, both in pure commercial powder form, and in leather which they have been used to tan. Groups of signals indicative of the source, and type (condensed vs. hydrolyzable) of tannin used in the manufacture are well resolved in the spectra of the finished leathers. These fingerprints are compared with those arising from leathers tanned with other common tanning agents. Paramagnetic chromium (III) tanning causes widespread but selective disappearance of signals from the spectrum of leather collagen, including resonances from acidic aspartyl and glutamyl residues, likely bound to Cr (III) structures. Aluminium (III) and glutaraldehyde tanning both cause considerable leather collagen signal sharpening suggesting some increase in molecular structural ordering. The ²⁷Al-NMR signal from the former material is consistent with an octahedral coordination by oxygen ligands. Solid state NMR thus provides easily recognisable reagent specific spectral fingerprints of the products of vegetable and some other common tanning processes. Because spectra are related to molecular properties, NMR is potentially a powerful tool in leather process enhancement and quality or provenance assurance.

Decomposition of adsorbed VX on activated carbons studied by {sup 31}P MAS NMR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ishay Columbus; Daniel Waysbort; Liora Shmueli

2006-06-15

The fate of the persistent OP nerve agent O-ethyl S-(2-(diisopropylamino)ethyl) methylphosphonothioate (VX) on granular activated carbons that are used for gas filtration was studied by means of 31P magic angle spinning (MAS) NMR spectroscopy. Four types of activated carbon were used, including coal-based BPL. VX as vapor or liquid was adsorbed on carbon granules, and MAS NMR spectra were recorded periodically. The results show that at least 90% of the adsorbed VX decomposes within 20 days or less to the nontoxic ethyl methylphosphonic acid (EMPA) and bis(S-2-diisopropylaminoethane) ((DES){sub 2}). Decomposition occurred irrespective of the phase from which VX was loaded,more » the presence of metal impregnation on the carbon surface, and the water content of the carbon. Theoretical and practical aspects of the degradation are discussed. 17 refs., 6 figs., 3 tabs.« less

Evaluation of saffron (Crocus sativus L.) adulteration with plant adulterants by (1)H NMR metabolite fingerprinting.

PubMed

Petrakis, Eleftherios A; Cagliani, Laura R; Polissiou, Moschos G; Consonni, Roberto

2015-04-15

In the present work, a preliminary study for the detection of adulterated saffron and the identification of the adulterant used by means of (1)H NMR and chemometrics is reported. Authentic Greek saffron and four typical plant-derived materials utilised as bulking agents in saffron, i.e., Crocus sativus stamens, safflower, turmeric, and gardenia were investigated. A two-step approach, relied on the application of both OPLS-DA and O2PLS-DA models to the (1)H NMR data, was adopted to perform authentication and prediction of authentic and adulterated saffron. Taking into account the deficiency of established methodologies to detect saffron adulteration with plant adulterants, the method developed resulted reliable in assessing the type of adulteration and could be viable for dealing with extensive saffron frauds at a minimum level of 20% (w/w). Copyright © 2014 Elsevier Ltd. All rights reserved.

Computational analysis of the solvation of coffee ingredients in aqueous ionic liquid mixtures.

PubMed

Zeindlhofer, Veronika; Khlan, Diana; Bica, Katharina; Schröder, Christian

2017-01-13

In this paper, we investigate the solvation of coffee ingredients including caffeine, gallic acid as representative for phenolic compounds and quercetin as representative for flavonoids in aqueous mixtures of the ionic liquid 1-ethyl-3-methylimidazolium acetate [C 2 mim][OAc] at various concentrations. Due to the anisotropy of the solutes we show that classical Kirkwood-Buff theory is not appropriate to study solvation effects with increasing ionic liquid content. However, excess coordination numbers as well as the mean residence time of solvent molecules at the surface of the solutes can be determined by Voronoi tessellation. Since the volume of the hydration shells is also available by this method, solvation free energies will be discussed as a function of the ionic liquid concentration to yield a physical meaningful picture of solvation for the anisotropic solutes. Hydrogen bonding capabilities of the solutes and their relevance for experimental extraction yields from spent coffee grounds are also discussed.

Elucidating Solvation Structures for Rational Design of Multivalent Electrolytes-A Review.

PubMed

Rajput, Nav Nidhi; Seguin, Trevor J; Wood, Brandon M; Qu, Xiaohui; Persson, Kristin A

2018-04-26

Fundamental molecular-level understanding of functional properties of liquid solutions provides an important basis for designing optimized electrolytes for numerous applications. In particular, exhaustive knowledge of solvation structure, stability, and transport properties is critical for developing stable electrolytes for fast-charging and high-energy-density next-generation energy storage systems. Accordingly, there is growing interest in the rational design of electrolytes for beyond lithium-ion systems by tuning the molecular-level interactions of solvate species present in the electrolytes. Here we present a review of the solvation structure of multivalent electrolytes and its impact on the electrochemical performance of these batteries. A direct correlation between solvate species present in the solution and macroscopic properties of electrolytes is sparse for multivalent electrolytes and contradictory results have been reported in the literature. This review aims to illustrate the current understanding, compare results, and highlight future needs and directions to enable the deep understanding needed for the rational design of improved multivalent electrolytes.

Stabilization of Quinapril by Incorporating Hydrogen Bonding Interactions

PubMed Central

Roy, B. N.; Singh, G. P.; Godbole, H. M.; Nehate, S. P.

2009-01-01

In the present study stability of various known solvates of quinapril hydrochloride has been compared with nitromethane solvate. Nitromethane solvate was found to be more stable compared to other known solvates. Single crystal X-ray diffraction analysis of quinapril nitromethane solvate shows intermolecular hydrogen bonding between quinapril molecule and nitromethane. Stabilization of quinapril by forming strong hydrogen bonding network as in case of co-crystals was further studied by forming co-crystal with tris(hydroxymethyl)amino methane. Quinapril free base forms a stable salt with tris(hydroxymethyl)amino methane not reported earlier. Quinapril tris(hydroxymethyl)amino methane salt found to be stable even at 80° for 72 h i.e. hardly any formation of diketopiperazine and diacid impurity. As expected single crystal X-ray diffraction analysis reveals tris(hydroxymethyl)amino methane salt of quinapril shows complex hydrogen bonding network between the two entities along with ionic bond. The properties of this stable salt - stable in solid as well as solution phase, might lead to an alternate highly stable formulation. PMID:20502545

Extrapolating Single Organic Ion Solvation Thermochemistry from Simulated Water Nanodroplets.

PubMed

Coles, Jonathan P; Houriez, Céline; Meot-Ner Mautner, Michael; Masella, Michel

2016-09-08

We compute the ion/water interaction energies of methylated ammonium cations and alkylated carboxylate anions solvated in large nanodroplets of 10 000 water molecules using 10 ns molecular dynamics simulations and an all-atom polarizable force-field approach. Together with our earlier results concerning the solvation of these organic ions in nanodroplets whose molecular sizes range from 50 to 1000, these new data allow us to discuss the reliability of extrapolating absolute single-ion bulk solvation energies from small ion/water droplets using common power-law functions of cluster size. We show that reliable estimates of these energies can be extrapolated from a small data set comprising the results of three droplets whose sizes are between 100 and 1000 using a basic power-law function of droplet size. This agrees with an earlier conclusion drawn from a model built within the mean spherical framework and paves the road toward a theoretical protocol to systematically compute the solvation energies of complex organic ions.

Communication: Free-energy analysis of hydration effect on protein with explicit solvent: Equilibrium fluctuation of cytochrome c

NASA Astrophysics Data System (ADS)

Karino, Yasuhito; Matubayasi, Nobuyuki

2011-01-01

The relationship between the protein conformation and the hydration effect is investigated for the equilibrium fluctuation of cytochrome c. To elucidate the hydration effect with explicit solvent, the solvation free energy of the protein immersed in water was calculated using the molecular dynamics simulation coupled with the method of energy representation. The variations of the protein intramolecular energy and the solvation free energy are found to compensate each other in the course of equilibrium structural fluctuation. The roles of the attractive and repulsive components in the protein-water interaction are further examined for the solvation free energy. The attractive component represented as the average sum of protein-water interaction energy is dominated by the electrostatic effect and is correlated to the solvation free energy through the linear-response-type relationship. No correlation with the (total) solvation free energy is seen, on the other hand, for the repulsive component expressed as the excluded-volume effect.

Ultrafast Decay of the Solvated Electron in a Neat Polar Solvent: The Unusual Case of Propylene Carbonate.

PubMed

Le Caër, Sophie; Ortiz, Daniel; Marignier, Jean-Louis; Schmidhammer, Uli; Belloni, Jacqueline; Mostafavi, Mehran

2016-01-07

The behavior of carbonates is critical for a detailed understanding of aging phenomena in Li-ion batteries. Here we study the first reaction stages of propylene carbonate (PC), a cyclical carbonate, by picosecond pulse radiolysis. An absorption band with a maximum around 1360 nm is observed at 20 ps after the electron pulse and is shifted to 1310 nm after 50 ps. This band presents the features of a solvated electron absorption band, the solvation lasting up to 50 ps. Surprisingly, in this polar solvent, the solvated electron follows an ultrafast decay and disappears with a half time of 360 ps. This is attributed to the formation of a radical anion PC(-•). The yield of the solvated electron is low, suggesting that the radical anions are mainly directly produced from presolvated electrons. These results demonstrate that the initial electron transfers mechanisms are strongly different in linear compared with cyclical carbonates.

Electron solvation and localization at interfaces

NASA Astrophysics Data System (ADS)

Harris, Charles B.; Szymanski, Paul; Garrett-Roe, Sean; Miller, Andre D.; Gaffney, Kelly J.; Liu, Simon H.; Bezel, Ilya

2003-12-01

Two-photon photoemission of thiolate/Ag(111), nitrile/Ag(111), and alcohol/Ag(111) interfaces elucidates electron solvation and localization in two dimensions. For low coverages of thiolates on Ag(111), the occupied (HOMO) and unoccupied (LUMO) electronic states of the sulfer-silver bond are localized due to the lattice gas structure of the adsorbate. As the coverage saturates and the adsorbate-adsorbate nearest neighbor distance decreases, the HOMO and LUMO delocalize across many adsorbate molecules. Alcohol- and nitrile-covered Ag(111) surfaces solvate excess image potential state (IPS) electrons. In the case of alcohol-covered surfaces, this solvation is due to a shift in the local workfunction of the surface. For two-monolayer coverages of nitriles/Ag(111), localization accompanies solvation of the IPS. The size of the localized electron can be estimated by Fourier transformation of the wavefunction from momentum- to position-space. The IPS electron localizes to 15 +/- 4 angstroms full-width at half maximum in the plane of the surface, i.e., to a single lattice site.

Solvation and Dynamics of Sodium and Potassium in Ethylene Carbonate from ab Initio Molecular Dynamics Simulations

DOE PAGES

Pham, Tuan Anh; Kweon, Kyoung E.; Samanta, Amit; ...

2017-09-18

The development of sodium and potassium batteries offers a promising way to meet the scaling and cost challenges of energy storage. However, compared to Li +, several intrinsic properties of Na + and K +, including their solvation and dynamics in typical organic electrolytes utilized in battery applications, are less well-understood. Here in this paper, we report a systematic investigation of Na + and K + in ethylene carbonate (EC) using first-principles molecular dynamics simulations. Our simulations reveal significant differences in the solvation structure and dynamical properties of Na + and K + compared to Li +. We find that,more » in contrast to Li + which exhibits a well-defined first solvation shell, the larger Na+ and K+ ions show more disordered and flexible solvation structures. These differences in solvation were found to significantly influence the ion dynamics, leading to larger diffusion coefficients of Na + and K + compared to Li +. Our simulations also reveal a clear and interesting analog in the behavior of the ions in EC and aqueous environments, particularly in the specific ion effects on the solvent dynamics. Lastly, this work provides fundamental understanding of the intrinsic properties of Na + and K + in organic electrolytes, which may ultimately influence the intercalation mechanism at the electrode–electrolyte interface and therefore battery performance, lifetime, and safety.« less

Solvatochromism and preferential solvation of 1,4-dihydroxy-2,3-dimethyl-9,10-anthraquinone by UV-vis absorption and laser-induced fluorescence measurements

NASA Astrophysics Data System (ADS)

Sasirekha, V.; Vanelle, P.; Terme, T.; Ramakrishnan, V.

2008-12-01

Solvation characteristics of 1,4-dihydroxy-2,3-dimethyl-9,10-anthraquinone ( 1) in pure and binary solvent mixtures have been studied by UV-vis absorption spectroscopy and laser-induced fluorescence techniques. The binary solvent mixtures used as CCl 4 (tetrachloromethane)-DMF ( N, N-dimethylformamide), AN (acetonitrile)-DMSO (dimethylsulfoxide), CHCl 3 (chloroform)-DMSO, CHCl 3-MeOH (methanol), and MeOH-DMSO. The longest wavelength band of 1 has been studied in pure solvents as well as in binary solvent mixtures as a function of the bulk mole fraction. The Vis absorption band maxima show an unusual blue shift with increasing solvent polarity. The emission maxima of 1 show changes with varying the pure solvents and the composition in the case of binary solvent mixtures. Non-ideal solvation characteristics are observed in all binary solvent mixtures. It has been observed that the quantity [ ν-(Xν+Xν)] serves as a measure of the extent of preferential solvation, where ν˜ and X are the position of band maximum in wavenumbers (cm -1) and the bulk mole fraction values, respectively. The preferential solvation parameters local mole fraction ( X2L), solvation index ( δs2), and exchange constant ( k12) are evaluated.

Preferential solvation and solvation shell composition of free base and protonated 5, 10, 15, 20-tetrakis(4-sulfonatophenyl)porphyrin in aqueous organic mixed solvents

NASA Astrophysics Data System (ADS)

Farajtabar, Ali; Jaberi, Fatemeh; Gharib, Farrokh

2011-12-01

The solvatochromic properties of the free base and the protonated 5, 10, 15, 20-tetrakis(4-sulfonatophenyl)porphyrin (TPPS) were studied in pure water, methanol, ethanol (protic solvents), dimethylsulfoxide, DMSO, (non-protic solvent), and their corresponding aqueous-organic binary mixed solvents. The correlation of the empirical solvent polarity scale ( ET) values of TPPS with composition of the solvents was analyzed by the solvent exchange model of Bosch and Roses to clarify the preferential solvation of the probe dyes in the binary mixed solvents. The solvation shell composition and the synergistic effects in preferential solvation of the solute dyes were investigated in terms of both solvent-solvent and solute-solvent interactions and also, the local mole fraction of each solvent composition was calculated in cybotactic region of the probe. The effective mole fraction variation may provide significant physico-chemical insights in the microscopic and molecular level of interactions between TPPS species and the solvent components and therefore, can be used to interpret the solvent effect on kinetics and thermodynamics of TPPS. The obtained results from the preferential solvation and solvent-solvent interactions have been successfully applied to explain the variation of equilibrium behavior of protonation of TPPS occurring in aqueous organic mixed solvents of methanol, ethanol and DMSO.

“Martinizing” the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins

PubMed Central

2017-01-01

Solvation is a fundamental driving force in many biological processes including biomolecular recognition and self-assembly, not to mention protein folding, dynamics, and function. The variational implicit solvent method (VISM) is a theoretical tool currently developed and optimized to estimate solvation free energies for systems of very complex topology, such as biomolecules. VISM’s theoretical framework makes it unique because it couples hydrophobic, van der Waals, and electrostatic interactions as a functional of the solvation interface. By minimizing this functional, VISM produces the solvation interface as an output of the theory. In this work, we push VISM to larger scale applications by combining it with coarse-grained solute Hamiltonians adapted from the MARTINI framework, a well-established mesoscale force field for modeling large-scale biomolecule assemblies. We show how MARTINI-VISM (MVISM) compares with atomistic VISM (AVISM) for a small set of proteins differing in size, shape, and charge distribution. We also demonstrate MVISM’s suitability to study the solvation properties of an interesting encounter complex, barnase–barstar. The promising results suggest that coarse-graining the protein with the MARTINI force field is indeed a valuable step to broaden VISM’s and MARTINI’s applications in the near future. PMID:28613904

Solvent-Induced Shift of Spectral Lines in Polar–Polarizable Solvents

DOE PAGES

Matyushov, Dmitry V.; Newton, Marshall D.

2017-03-09

Solvent-induced shift of optical transition lines is traditionally described by the Lippert- McRae equation given in terms of the Onsager theory for dipole solvation. It splits the overall shift into the equilibrium solvation by induced dipoles and the reaction field by the permanent dipoles in equilibrium with the chromophore in the ground state. Here we have reconsidered this classical problem from the perspective of microscopic solvation theories. A microscopic solvation functional is derived and continuum solvation is consistently introduced by taking the limit of zero wavevector in the reciprocal-space solvation susceptibility functions. We show that the phenomenological expression for themore » reaction field of permanent dipoles in the Lippert-McRae equation is not consistent with the microscopic theory. The main deficiency of the Lippert- McRae equation equation is the use of additivity of the response by permanent and induced dipoles of the liquid. An alternative closed-form equation for the spectral shift is derived. Its continuum limit allows a new, non-additive functionality for the solvent-induced shift in terms of the high-frequency and static dielectric constants. Finally, the main qualitative outcome of the theory is a significantly weaker dependence of the spectral shift on the polarizability of the solvent than predicted by the Lippert-McRae formula.« less

Combined Quantum Chemical/Raman Spectroscopic Analyses of Li+ Cation Solvation: Cyclic Carbonate Solvents - Ethylene Carbonate and Propylene Earbonate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allen, Joshua L.; Borodin, Oleg; Seo, D. M.

2014-12-01

Combined computational/Raman spectroscopic analyses of ethylene carbonate (EC) and propylene carbonate (PC) solvation interactions with lithium salts are reported. It is proposed that previously reported Raman analyses of (EC)n-LiX mixtures have utilized faulty assumptions. In the present studies, density functional theory (DFT) calculations have provided corrections in terms of both the scaling factors for the solvent's Raman band intensity variations and information about band overlap. By accounting for these factors, the solvation numbers obtained from two different EC solvent bands are in excellent agreement with one another. The same analysis for PC, however, was found to be quite challenging. Commerciallymore » available PC is a racemic mixture of (S)- and (R)-PC isomers. Based upon the quantum chemistry calculations, each of these solvent isomers may exist as multiple conformers due to a low energy barrier for ring inversion, making deconvolution of the Raman bands daunting and inherently prone to significant error. Thus, Raman spectroscopy is able to accurately determine the extent of the EC...Li+ cation solvation interactions using the provided methodology, but a similar analysis of PC...Li+ cation solvation results in a significant underestimation of the actual solvation numbers.« less

Solvent-Induced Shift of Spectral Lines in Polar-Polarizable Solvents.

PubMed

Matyushov, Dmitry V; Newton, Marshall D

2017-03-23

Solvent-induced shift of optical transition lines is traditionally described by the Lippert-McRae equation given in terms of the Onsager theory for dipole solvation. It splits the overall shift into the equilibrium solvation by induced dipoles and the reaction field by the permanent dipoles in equilibrium with the chromophore in the ground state. We have reconsidered this classical problem from the perspective of microscopic solvation theories. A microscopic solvation functional is derived, and continuum solvation is consistently introduced by taking the limit of zero wavevector in the reciprocal-space solvation susceptibility functions. We show that the phenomenological expression for the reaction field of permanent dipoles in the Lippert-McRae equation is not consistent with the microscopic theory. The main deficiency of the Lippert-McRae equation is the use of additivity of the response by permanent and induced dipoles of the liquid. An alternative closed-form equation for the spectral shift is derived. Its continuum limit allows a new, nonadditive functionality for the solvent-induced shift in terms of the high-frequency and static dielectric constants. The main qualitative outcome of the theory is a significantly weaker dependence of the spectral shift on the polarizability of the solvent than predicted by the Lippert-McRae formula.

Strength order and nature of the π-hole bond of cyanuric chloride and 1,3,5-triazine with halide.

PubMed

Wang, Hui; Li, Chen; Wang, Weizhou; Jin, Wei Jun

2015-08-28

The (13)C NMR chemical shift moving upfield indicates the main model of π-holeX(-) bond between cyanuric chloride/1,3,5-triazine (3ClN/3N), which possess both the π-hole and σ-hole, and X(-). (13)C NMR and UV absorption titration in acetonitrile confirmed that the bonding abilities of 3ClN/3N with X(-) follow the order I(-) > Br(-) > Cl(-), which is apparently the order of the charge transfer ability of halide to 3ClN/3N. Chemical calculations showed that the bonding abilities in solution were essentially consistent with those obtained by titration experiments. However, the results in the gas phase were the reverse, i.e., π-holeCl(-) > π-holeBr(-) > π-holeI(-) in bonding energy, which obeys the order of electrostatic interaction. In fact, the π-hole bond and σ-hole bond compete with solvation and possible anion-hydrogen bond between a solvent molecule and a halide in solution. An explanation is that the apparent charge transfer order of π-/σ-holeI(-) > π-/σ-holeBr(-) > π-/σ-holeCl(-) occurs for weak π-hole bonds and σ-hole bonds, whereas the order of electrostatic attraction of π-/σ-holeCl(-) > π-/σ-holeBr(-) > π-/σ-holeI(-) is valid for strong bonds. It can be concluded by combining energy decomposition analysis and natural bond orbital analysis that the π-holeX(-) bond and σ-holeX(-) bond are electrostatically attractive in nature regardless of whether the order is I(-) > Br(-) > Cl(-) or the reverse.

Proton transfer in a short hydrogen bond caused by solvation shell fluctuations: an ab initio MD and NMR/UV study of an (OHO)(-) bonded system.

PubMed

Pylaeva, Svetlana; Allolio, Christoph; Koeppe, Benjamin; Denisov, Gleb S; Limbach, Hans-Heinrich; Sebastiani, Daniel; Tolstoy, Peter M

2015-02-14

We present a joint experimental and quantum chemical study on the influence of solvent dynamics on the protonation equilibrium in a strongly hydrogen bonded phenol-acetate complex in CD2Cl2. Particular attention is given to the correlation of the proton position distribution with the internal conformation of the complex itself and with fluctuations of the aprotic solvent. Specifically, we have focused on a complex formed by 4-nitrophenol and tetraalkylammonium-acetate in CD2Cl2. Experimentally we have used combined low-temperature (1)H and (13)C NMR and UV-vis spectroscopy and showed that a very strong OHO hydrogen bond is formed with proton tautomerism (PhOH···(-)OAc and PhO(-)···HOAc forms, both strongly hydrogen bonded). Computationally, we have employed ab initio molecular dynamics (70 and 71 solvent molecules, with and without the presence of a counter-cation, respectively). We demonstrate that the relative motion of the counter-cation and the "free" carbonyl group of the acid plays the major role in the OHO bond geometry and causes proton "jumps", i.e. interconversion of PhOH···(-)OAc and PhO(-)···HOAc tautomers. Weak H-bonds between CH(CD) groups of the solvent and the oxygen atom of carbonyl stabilize the PhOH···(-)OAc type of structures. Breaking of CH···O bonds shifts the equilibrium towards PhO(-)···HOAc form.

Vibrational and electronic investigations, NLO, FMO analysis on a hetarylazoindole disperse dye by density functional theory

NASA Astrophysics Data System (ADS)

Çatıkkaş, Berna; Aktan, Ebru; Yalçın, Ergin

2016-08-01

This work deals with the optimized molecular structure, vibrational spectra, nonlinear optic (NLO) and frontier molecule orbital (FMO) properties of 1-Methyl-2-phenyl-3-(1,3,4-thiadiazol-2-yldiazenyl)-1H-indole (MPI) by quantum chemical calculations. The Fourier transform infrared (FT-MIR and FT-FIR) and Raman spectra of 1-Methyl-2-phenyl-3-(1,3,4-thiadiazol-2-yldiazenyl)-1H-indole (MPI) were recorded in the region (4000-400 cm-1 and 400-30 cm-1) and (3200-92 cm-1), respectively. The analysis and complete vibrational assignments of the fundamental modes of the MPI molecule were carried out by using the observed FT-IR and FT-Raman data and calculated Total Energy Distribution (TED) according to Scaled Quantum Mechanics procedure. The calculated geometrical parameters of the MPI molecule are in agreement with the obtained values from XRD studies. On the other hand, the difference between the scaled and observed wavenumber values of the most of the fundamentals are very small. 1H NMR and 13C NMR chemical shift values, and energy gap between LUMO-HOMO and molecular electrostatic potential (MEP) were investigated by using density functional theory (B3LYP) methods. UV/Visible spectra and λ maximum absorption values, the oscillator strengths in the chloroform, methanol and DMSO solvation in combination with different basis sets were calculated by using the time-dependent density functional theory (TD-DFT). Additionally, the predicted nonlinear optical (NLO) properties of the MPI are quite greater than that of urea at the B3LYP/6-31++G(d,p) level.

Synthesis, spectroscopic and theoretical studies of ethyl (2E)-3-amino-2-({[(4-benzoyl-1,5-diphenyl-1H-pyrazol-3-yl)carbonyl]amino}carbonothioyl)but-2-enoate butanol solvate.

PubMed

Koca, İrfan; Sert, Yusuf; Gümüş, Mehmet; Kani, İbrahim; Çırak, Çağrı

2014-01-24

We have synthesized ethyl (2E)-3-amino-2-({[(4-benzoyl-1,5-diphenyl-1H-pyrazol-3-yl)carbonyl]amino}carbonothioyl)but-2-enoate (2) by the reaction of 4-benzoyl-1,5-diphenyl-1H-pyrazole-3-carbonyl chloride (1), ammonium thiocyanate and ethyl 3-aminobut-2-enoate and then characterized by elemental analyses, IR, Raman, (1)H NMR, (13)C NMR and X-ray diffraction methods. The experimental and theoretical vibrational spectra of 2 were investigated. The experimental FT-IR (4000-400 cm(-1)) and Laser-Raman spectra (4000-100 cm(-1)) of the molecule in the solid phase were recorded. Theoretical vibrational frequencies and geometric parameters (bond lengths, bond angles) were calculated using Ab Initio Hartree Fock (HF), Density Functional Theory (B3LYP) methods with 6-311++G(d,p) basis set by Gaussian 09W program. The computed values of frequencies are scaled using a suitable scale factor to yield good coherence with the observed values. The assignments of the vibrational frequencies were performed by potential energy distribution (PED) analysis by using VEDA 4 program. The theoretical optimized geometric parameters and vibrational frequencies were compared with the corresponding experimental X-ray diffraction data, and they were seen to be in a good agreement with each other. Also, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies were calculated. Copyright © 2013 Elsevier B.V. All rights reserved.

Understanding the influence of capillary waves on solvation at the liquid-vapor interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rane, Kaustubh, E-mail: rane@csi.tu-darmstadt.de; Vegt, Nico F. A. van der

2016-03-21

This work investigates the question if surface capillary waves (CWs) affect interfacial solvation thermodynamic properties that determine the propensity of small molecules toward the liquid-vapor interface. We focus on (1) the evaluation of these properties from molecular simulations in a practical manner and (2) understanding them from the perspective of theories in solvation thermodynamics, especially solvent reorganization effects. Concerning the former objective, we propose a computational method that exploits the relationship between an external field acting on the liquid-vapor interface and the magnitude of CWs. The system considered contains the solvent, an externally applied field (f) and the solute moleculemore » fixed at a particular location. The magnitude of f is selected to induce changes in CWs. The difference between the solvation free energies computed in the presence and in the absence of f is then shown to quantify the contribution of CWs to interfacial solvation. We describe the implementation of this method in the canonical ensemble by using a Lennard-Jones solvent and a non-ionic solute. Results are shown for three types of solutes that differ in the nature of short-ranged repulsive (hard-core) interactions. Overall, we observe that CWs have a negligible or very small effect on the interfacial solvation free energy of a solute molecule fixed near the liquid-vapor interface for the above systems. We also explain how the effects of pinning or dampening of CWs caused by a fixed solute are effectively compensated and do not contribute to the solvation free energy.« less

Phenolic Polymer Solvation in Water and Ethylene Glycol, I: Molecular Dynamics Simulations

NASA Technical Reports Server (NTRS)

Bucholz, Eric W.; Haskins, Justin B.; Monk, Joshua D.; Bauschlicher, Charles W.; Lawson, John W.

2017-01-01

Interactions between pre-cured phenolic polymer chains and a solvent have a significant impact on the structure and properties of the final post-cured phenolic resin. Developing an understanding of the nature of these interactions is important and will aid in the selection of the proper solvent that will lead to the desired final product. Here, we investigate the role of phenolic chain structure and solvent type on the overall solvation performance of the system through molecular dynamics simulations. Two types of solvents are considered, ethylene glycol (EGL) and H2O. In addition, three phenolic chain structures were considered including two novolac-type chains with either an ortho-ortho (OON) or ortho-para (OPN) backbone network and a resole-type (RES) chain with an ortho-ortho network. Each system is characterized through structural analysis of the solvation shell and hydrogen bonding environment as well as through quantification of the solvation free energy along with partitioned interaction energies between specific molecular species. The combination of the simulations and analyses indicate that EGL provides a larger solvation free energy than H2O due to more energetically favorable hydrophilic interactions as well as favorable hydrophobic interactions between CH element groups. In addition, phenolic chain structure significantly impacts solvation performance with OON having limited intermolecular hydrogen bond formations while OPN and RES interact more favorably with the solvent molecules. The results suggest that a resole-type phenolic chain with an ortho-para network should have the best solvation performance in EGL, H2O, and other similar solvents.

Phenolic Polymer Solvation in Water and Ethylene Glycol, I: Molecular Dynamics Simulations.

PubMed

Bucholz, Eric W; Haskins, Justin B; Monk, Joshua D; Bauschlicher, Charles W; Lawson, John W

2017-04-06

Interactions between pre-cured phenolic polymer chains and a solvent have a significant impact on the structure and properties of the final postcured phenolic resin. Developing an understanding of the nature of these interactions is important and will aid in the selection of the proper solvent that will lead to the desired final product. Here, we investigate the role of the phenolic chain structure and the solvent type on the overall solvation performance of the system through molecular dynamics simulations. Two types of solvents are considered: ethylene glycol (EGL) and H 2 O. In addition, three phenolic chain structures are considered, including two novolac-type chains with either an ortho-ortho (OON) or an ortho-para (OPN) backbone network and a resole-type (RES) chain with an ortho-ortho network. Each system is characterized through a structural analysis of the solvation shell and the hydrogen-bonding environment as well as through a quantification of the solvation free energy along with partitioned interaction energies between specific molecular species. The combination of simulations and the analyses indicate that EGL provides a higher solvation free energy than H 2 O due to more energetically favorable hydrophilic interactions as well as favorable hydrophobic interactions between CH element groups. In addition, the phenolic chain structure significantly affects the solvation performance, with OON having limited intermolecular hydrogen-bond formations, while OPN and RES interact more favorably with the solvent molecules. The results suggest that a resole-type phenolic chain with an ortho-para network should have the best solvation performance in EGL, H 2 O, and other similar solvents.

Method for nuclear magnetic resonance imaging using deuterum as a contrast agent

DOEpatents

Kehayias, Joseph J.; Joel, Darrel D.; Adams, William H.; Stein, Harry L.

1990-01-01

A method for in vivo NMR imaging of the blood vessels and organs of a patient characterized by using a dark dye-like imaging substance consisting essentially of a stable, high-purity concentration of D.sub.2 O in a solution with water.

Determination of Benzalkonium Chloride in Commercial Disinfectant Formulations by Quantitative NMR Spectroscopy

DTIC Science & Technology

2012-11-01

disinfectant solutions containing benzalkonium chloride (BAC); a molluscicide and antifouling chemical. In order to determine the efficacy of this...formulations. The methods and results presented herein will be used in a separate study to assess the efficacy of BACs as antifouling agents under

Development of a methodology to compute solvation free energies on the basis of the theory of energy representation for solutions represented with a polarizable force field.

PubMed

Suzuoka, Daiki; Takahashi, Hideaki; Ishiyama, Tatsuya; Morita, Akihiro

2012-12-07

We have developed a method of molecular simulations utilizing a polarizable force field in combination with the theory of energy representation (ER) for the purpose of establishing an efficient and accurate methodology to compute solvation free energies. The standard version of the ER method is, however, based on the assumption that the solute-solvent interaction is pairwise additive for its construction. A crucial step in the present method is to introduce an intermediate state in the solvation process to treat separately the many-body interaction associated with the polarizable model. The intermediate state is chosen so that the solute-solvent interaction can be formally written in the pairwise form, though the solvent molecules are interacting with each other with polarizable charges dependent on the solvent configuration. It is, then, possible to extract the free energy contribution δμ due to the many-body interaction between solute and solvent from the total solvation free energy Δμ. It is shown that the free energy δμ can be computed by an extension of the recent development implemented in quantum mechanical∕molecular mechanical simulations. To assess the numerical robustness of the approach, we computed the solvation free energies of a water and a methanol molecule in water solvent, where two paths for the solvation processes were examined by introducing different intermediate states. The solvation free energies of a water molecule associated with the two paths were obtained as -5.3 and -5.8 kcal∕mol. Those of a methanol molecule were determined as -3.5 and -3.7 kcal∕mol. These results of the ER simulations were also compared with those computed by a numerically exact approach. It was demonstrated that the present approach produces the solvation free energies in comparable accuracies to simulations of thermodynamic integration (TI) method within a tenth of computational time used for the TI simulations.

Molecular basis for competitive solvation of the Burkholderia cepacia lipase by sorbitol and urea.

PubMed

Oliveira, Ivan P; Martínez, Leandro

2016-08-21

Increasing the stability of proteins is important for their application in industrial processes. In the intracellular environment many small molecules, called osmolytes, contribute to protein stabilization under physical or chemical stress. Understanding the nature of the interactions of these osmolytes with proteins can help the design of solvents and mutations to increase protein stability in extracellular media. One of the most common stabilizing osmolyes is sorbitol and one of the most common chemical denaturants is urea. In this work, we use molecular dynamics simulations to obtain a detailed picture of the solvation of the Burkholderia cepacia lipase (BCL) in the presence of the protecting osmolyte sorbitol and of the urea denaturant. We show that both sorbitol and urea compete with water for interactions with the protein surface. Overall, sorbitol promotes the organization of water in the first solvation shell and displaces water from the second solvation shell, while urea causes opposite effects. These effects are, however, highly heterogeneous among residue types. For instance, the depletion of water from the first protein solvation shell by urea can be traced down essentially to the side chain of negatively charged residues. The organization of water in the first solvation shell promoted by sorbitol occurs at polar (but not charged) residues, where the urea effect is minor. By contrast, sorbitol depletes water from the second solvation shell of polar residues, while urea promotes water organization at the same distances. The interactions of urea with negatively charged residues are insensitive to the presence of sorbitol. This osmolyte removes water and urea particularly from the second solvation shell of polar and non-polar residues. In summary, we provide a comprehensive description of the diversity of protein-solvent interactions, which can guide further investigations on the stability of proteins in non-conventional media, and assist solvent and protein design.

Thin Metallic Films From Solvated Metal Atoms

NASA Astrophysics Data System (ADS)

Trivino, Galo C.; Klabunde, Kenneth J.; Dale, Brock

1988-02-01

Metals were evaporated under vacuum and the metal atoms solvated by excess organic solvents at low temperature. Upon warming stable colloidal metal particles were formed by controlled metal atom clustering. The particles were stabilized toward flocculation by solvation and electrostatic effects. Upon solvent removal the colloidal particles grew to form thin films that were metallic in appearance, but showed higher resistivities than pure metallic films. Gold, palladium, platinium, and especially indium are discussed.

Analysis of biomolecular solvation sites by 3D-RISM theory.

PubMed

Sindhikara, Daniel J; Hirata, Fumio

2013-06-06

We derive, implement, and apply equilibrium solvation site analysis for biomolecules. Our method utilizes 3D-RISM calculations to quickly obtain equilibrium solvent distributions without either necessity of simulation or limits of solvent sampling. Our analysis of these distributions extracts highest likelihood poses of solvent as well as localized entropies, enthalpies, and solvation free energies. We demonstrate our method on a structure of HIV-1 protease where excellent structural and thermodynamic data are available for comparison. Our results, obtained within minutes, show systematic agreement with available experimental data. Further, our results are in good agreement with established simulation-based solvent analysis methods. This method can be used not only for visual analysis of active site solvation but also for virtual screening methods and experimental refinement.

Revisiting structure and dynamics of preferential solvation of K(I) ion in aqueous ammonia using QMCF-MD simulation

NASA Astrophysics Data System (ADS)

Hidayat, Yuniawan; Pranowo, Harno Dwi; Armunanto, Ria

2018-05-01

Structure and dynamics of preferential solvation of K(I) ion in aqueous ammonia have been reinvestigated using ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) simulation. The average coordination number of the first solvation consists of 2 ammonia and 4 waters. The mean residence time is less than 2 ps confirming the rapid mobility of ligands. The distance evolution data shows the frequent of ligand exchanges. The second solvation shell shows a more labile structure. The NBO analysis of the first shell structure emphasizes that interaction of K(I)-H2O is stronger than K(I)-NH3. The Wiberg bond confirms a weak electrostatic of ion-ligand interaction.

Decomposition of total solvation energy into core, side-chains and water contributions: Role of cross correlations and protein conformational fluctuations in dynamics of hydration layer

NASA Astrophysics Data System (ADS)

Mondal, Sayantan; Mukherjee, Saumyak; Bagchi, Biman

2017-09-01

Dynamical coupling between water and amino acid side-chain residues in solvation dynamics is investigated by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on protein surface. Such differently placed residues are found to exhibit different timescales of relaxation. The total solvation response measured by the probe is decomposed in terms of its interactions with (i) protein core, (ii) side-chain and (iii) water. Significant anti cross-correlation among these contributions are observed. When the motion of the protein side-chains is quenched, solvation either becomes faster or slower depending on the location of the probe.

The Generalized Born solvation model: What is it?

NASA Astrophysics Data System (ADS)

Onufriev, Alexey

2004-03-01

Implicit solvation models provide, for many applications, an effective way of describing the electrostatic effects of aqueous solvation. Here we outline the main approximations behind the popular Generalized Born solvation model. We show how its accuracy, relative to the Poisson-Boltzmann treatment, can be significantly improved in a computationally inexpensive manner to make the model useful in the studies of large-scale conformational transitions at the atomic level. The improved model is tested in a molecular dynamics simulation of folding of a 46-residue (three helix bundle) protein. Starting from an extended structure at 450K, the protein folds to the lowest energy conformation within 6 ns of simulation time, and the predicted structure differs from the native one by 2.4 A (backbone RMSD).

Design, synthesis, biological assessment and molecular docking studies of new 2-aminoimidazole-quinoxaline hybrids as potential anticancer agents

NASA Astrophysics Data System (ADS)

Ghanbarimasir, Zahra; Bekhradnia, Ahmadreza; Morteza-Semnani, Katayoun; Rafiei, Alireza; Razzaghi-Asl, Nima; Kardan, Mostafa

2018-04-01

In a search for novel antiproliferative agents, a series of quinoxaline derivatives containing 2-aminoimidazole (8a-8x) were designed and synthesized. The structures of synthesized compounds were confirmed by IR, 1H NMR, 13C NMR, Mass Spectroscopy and analyzed using HSQC, COSY, ROESY, HMBC techniques. The anticancer activity of all derivatives were evaluated for colon cancer and breast cancer cell lines by the MTT assay and acridine orange/ethidium bromide double staining method. The anti-cancer effect in human colon cancer (HCT-116) and breast cancer (MCF-7) cell lines exhibited that compounds 8a, 8s, 8t, 8w, 8x appeared as potent antiproliferative agents and especially inhibited the human colon cancer cell proliferation with percentage of inhibition by over 50%. The most active compound was (E)-4-phenyl-1-((quinoxalin-2-ylmethylene)amino)-1H-imidazol-2-amine (8a) with the highest inhibition for MCF-7 (83.3%) and HCT-116 (70%) cell lines after 48 and 24 h, respectively. Molecular docking studies of these derivatives within c-kit active site as a validated target might be suggested them as appropriate candidates for further efforts toward more potent anticancer compounds.

Synthesis of Thymoquinone derivatives and its activity analysis: In-silico approach

NASA Astrophysics Data System (ADS)

Ulfa, Siti Mariyah; Sholikhah, Shoimatus; Utomo, Edi Priyo

2017-03-01

Thymoquinone derivatives which synthesized in this research is bromoalkylquinones with alkyl chain consist of seven carbons (C7) and ten carbons (C10). The synthesis was carried out by oxidation of 2,3-dimethylhydroquinone followed by alkylation using reflux for 1.5 hours. The alkylation products were successfully characterized as 5-(7-bromoheptyl)-2,3-dimethyl-1,4-benzoquinone (C7) and 5-(10-bromodecyl)-2,3-dimethyl-1,4-benzoquinone (C10) in 31.93 and 16.89%, respectively. These compounds were fully characterized using FT-IR, 1H-NMR and 13C-NMR. Thus, the activity of C7 and C10 was analyzed by in silico approach with molecular docking using macromolecule model extracted from Protein Data Bank (PDB). Macromolecules used in this research is mitochondrial translocator protein (TSPO) as an antioxidant receptor, glycogen phosphorylase (GPA) as antidiabetic receptor and phosphatase tensin homolog (PTEN) as an anticancer agent. The result showed that C7 and C10 has a very good activity as antioxidant and antidiabetic agents with IC50 2.03 and 1.02 ppm (TSPO) and 16.98 and 14.88 ppm (GPA) compared with Thymoquinone. While the activity of C7 and C10 against PTEN gave the IC50 23.13 and 18.31 ppm showed a good candidate for an anticancer agent.

Serum metabonomic analysis of protective effects of Curcuma aromatica oil on renal fibrosis rats.

PubMed

Zhao, Liangcai; Zhang, Haiyan; Yang, Yunjun; Zheng, Yongquan; Dong, Minjian; Wang, Yaqiang; Bai, Guanghui; Ye, Xinjian; Yan, Zhihan; Gao, Hongchang

2014-01-01

Curcuma aromatica oil is a traditional herbal medicine demonstrating protective and anti-fibrosis activities in renal fibrosis patients. However, study of its mechanism of action is challenged by its multiple components and multiple targets that its active agent acts on. Nuclear magnetic resonance (NMR)-based metabonomics combined with clinical chemistry and histopathology examination were performed to evaluate intervening effects of Curcuma aromatica oil on renal interstitial fibrosis rats induced by unilateral ureteral obstruction. The metabolite levels were compared based on integral values of serum 1H NMR spectra from rats on 3, 7, 14, and 28 days after the medicine administration. Time trajectory analysis demonstrated that metabolic profiles of the agent-treated rats were restored to control levels after 7 days of dosage. The results confirmed that the agent would be an effective anti-fibrosis medicine in a time-dependent manner, especially in early renal fibrosis stage. Targeted metabolite analysis showed that the medicine could lower levels of lipid, acetoacetate, glucose, phosphorylcholine/choline, trimethylamine oxide and raise levels of pyruvate, glycine in the serum of the rats. Serum clinical chemistry and kidney histopathology examination dovetailed well with the metabonomics data. The results substantiated that Curcuma aromatica oil administration can ameliorate renal fibrosis symptoms by inhibiting some metabolic pathways, including lipids metabolism, glycolysis and methylamine metabolism, which are dominating targets of the agent working in vivo. This study further strengthens the novel analytical approach for evaluating the effect of traditional herbal medicine and elucidating its molecular mechanism.

Fluoro-alcohol phase modifiers and process for cesium solvent extraction

DOEpatents

Bonnesen, Peter V.; Moyer, Bruce A.; Sachleben, Richard A.

2003-05-20

The invention relates to a class of phenoxy fluoro-alcohols, their preparation, and their use as phase modifiers and solvating agents in a solvent composition for the extraction of cesium from alkaline solutions. These phenoxy fluoro-alcohols comply with the formula: ##STR1## in which n=2 to 4; X represents a hydrogen or a fluorine atom, and R.sup.2 -R.sup.6 are hydrogen or alkyl substituents. These phenoxy fluoro-alcohol phase modifiers are a necessary component to a robust solvent composition and process useful for the removal of radioactive cesium from alkaline nuclear waste streams. The fluoro-alcohols can also be used in solvents designed to extract other cesium from acidic or neutral solutions.

Resorcinol-formaldehyde reactions in dilute solution observed by carbon-13 NMR spectroscopy

Treesearch

Alfred W. Christiansen

2000-01-01

A recently discovered coupling agent, hydroxymethylated resorcinol (HMR), based on resorcinol-formaldehyde, can greatly enhance wood-to-epoxy resin bond durability in exterior applications. However, for HMR to be most effective, it needs to be prepared a few hours before it is applied to the...

Computer Modeling and Research in the Classroom

ERIC Educational Resources Information Center

Ramos, Maria Joao; Fernandes, Pedro Alexandrino

2005-01-01

We report on a computational chemistry course for undergraduate students that successfully incorporated a research project on the design of new contrast agents for magnetic resonance imaging and shift reagents for in vivo NMR. Course outcomes were positive: students were quite motivated during the whole year--they learned what was required of…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Maoyuan; Besford, Quinn Alexander; Mulvaney, Thomas

The entropy of hydrophobic solvation has been explained as the result of ordered solvation structures, of hydrogen bonds, of the small size of the water molecule, of dispersion forces, and of solvent density fluctuations. We report a new approach to the calculation of the entropy of hydrophobic solvation, along with tests of and comparisons to several other methods. The methods are assessed in the light of the available thermodynamic and spectroscopic information on the effects of temperature on hydrophobic solvation. Five model hydrophobes in SPC/E water give benchmark solvation entropies via Widom’s test-particle insertion method, and other methods and modelsmore » are tested against these particle-insertion results. Entropies associated with distributions of tetrahedral order, of electric field, and of solvent dipole orientations are examined. We find these contributions are small compared to the benchmark particle-insertion entropy. Competitive with or better than other theories in accuracy, but with no free parameters, is the new estimate of the entropy contributed by correlations between dipole moments. Dipole correlations account for most of the hydrophobic solvation entropy for all models studied and capture the distinctive temperature dependence seen in thermodynamic and spectroscopic experiments. Entropies based on pair and many-body correlations in number density approach the correct magnitudes but fail to describe temperature and size dependences, respectively. Hydrogen-bond definitions and free energies that best reproduce entropies from simulations are reported, but it is difficult to choose one hydrogen bond model that fits a variety of experiments. The use of information theory, scaled-particle theory, and related methods is discussed briefly. Our results provide a test of the Frank-Evans hypothesis that the negative solvation entropy is due to structured water near the solute, complement the spectroscopic detection of that solvation structure by identifying the structural feature responsible for the entropy change, and point to a possible explanation for the observed dependence on length scale. Our key results are that the hydrophobic effect, i.e. the signature, temperature-dependent, solvation entropy of nonpolar molecules in water, is largely due to a dispersion force arising from correlations between rotating permanent dipole moments, that the strength of this force depends on the Kirkwood g-factor, and that the strength of this force may be obtained exactly without simulation.« less

Ionic size effects to molecular solvation energy and to ion current across a channel resulted from the nonuniform size-modified PNP equations.

PubMed

Qiao, Yu; Tu, Bin; Lu, Benzhuo

2014-05-07

Ionic finite size can impose considerable effects to both the equilibrium and non-equilibrium properties of a solvated molecular system, such as the solvation energy, ionic concentration, and transport in a channel. As discussed in our former work [B. Lu and Y. C. Zhou, Biophys. J. 100, 2475 (2011)], a class of size-modified Poisson-Boltzmann (PB)/Poisson-Nernst-Planck (PNP) models can be uniformly studied through the general nonuniform size-modified PNP (SMPNP) equations deduced from the extended free energy functional of Borukhov et al. [I. Borukhov, D. Andelman, and H. Orland, Phys. Rev. Lett. 79, 435 (1997)] This work focuses on the nonuniform size effects to molecular solvation energy and to ion current across a channel for real biomolecular systems. The main contributions are: (1) we prove that for solvation energy calculation with nonuniform size effects (through equilibrium SMPNP simulation), there exists a simplified approximation formulation which is the same as the widely used one in PB community. This approximate form avoids integration over the whole domain and makes energy calculations convenient. (2) Numerical calculations show that ionic size effects tend to negate the solvation effects, which indicates that a higher molecular solvation energy (lower absolute value) is to be predicted when ionic size effects are considered. For both calculations on a protein and a DNA fragment systems in a 0.5M 1:1 ionic solution, a difference about 10 kcal/mol in solvation energies is found between the PB and the SMPNP predictions. Moreover, it is observed that the solvation energy decreases as ionic strength increases, which behavior is similar as those predicted by the traditional PB equation (without size effect) and by the uniform size-modified Poisson-Boltzmann equation. (3) Nonequilibrium SMPNP simulations of ion permeation through a gramicidin A channel show that the ionic size effects lead to reduced ion current inside the channel compared with the results without considering size effects. As a component of the current, the drift term is the main contribution to the total current. The ionic size effects to the total current almost come through the drift term, and have little influence on the diffusion terms in SMPNP.

SISGR: Linking Ion Solvation and Lithium Battery Electrolyte Properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trulove, Paul C.; Foley, Matthew P.

2012-09-30

The solvation and phase behavior of the model battery electrolyte salt lithium trifluoromethanesulfonate (LiCF 3SO 3) in commonly used organic solvents; ethylene carbonate (EC), gamma-butyrolactone (GBL), and propylene carbonate (PC) was explored. Data from differential scanning calorimetry (DSC), Raman spectroscopy, and X-ray diffraction were correlated to provide insight into the solvation states present within a sample mixture. Data from DSC analyses allowed the construction of phase diagrams for each solvent system. Raman spectroscopy enabled the determination of specific solvation states present within a solvent-salt mixture, and X-ray diffraction data provided exact information concerning the structure of a solvates that couldmore » be isolated Thermal analysis of the various solvent-salt mixtures revealed the phase behavior of the model electrolytes was strongly dependent on solvent symmetry. The point groups of the solvents were (in order from high to low symmetry): C2V for EC, CS for GBL, and C1 for PC(R). The low symmetry solvents exhibited a crystallinity gap that increased as solvent symmetry decreased; no gap was observed for EC-LiTf, while a crystallinity gap was observed spanning 0.15 to 0.3 mole fraction for GBL-LiTf, and 0.1 to 0.33 mole fraction for PC(R)-LiTf mixtures. Raman analysis demonstrated the dominance of aggregated species in almost all solvent compositions. The AGG and CIP solvates represent the majority of the species in solutions for the more concentrated mixtures, and only in very dilute compositions does the SSIP solvate exist in significant amounts. Thus, the poor charge transport characteristics of CIP and AGG account for the low conductivity and transport properties of LiTf and explain why is a poor choice as a source of Li + ions in a Li-ion battery.« less

The road not taken: Applications of fluorescence spectroscopy and electronic structure theory to systems of materials and biological relevance

NASA Astrophysics Data System (ADS)

Carlson, Philip Joseph

Applications of Fluorescence Spectroscopy and Electronic Structure Theory to Systems of Materials and Biological Relevance. The photophysics of curcumin was studied in micelles and the solvation dynamics were probed. The high-energy ionic liquid HEATN was also studied using the fragment molecular orbital method. The solvation dynamics of the HEATN system were determined. This marks the first study of the solvation dynamics in a triazolium ionic liquid system.

Phase-Equilibria and Nanostructure Formation in Charged Rigid-Rod Polymers and Carbon Nanotubes

DTIC Science & Technology

2002-11-10

or liquid crystalline) and the crystalline polymer state. The form-I crystal solvate, identi- fied as a cocrystal of the protonated polymer and the...dissolution temperature, below 100 °C.12,13 The form-II crystal solvate, considered a polymer-solvent cocrystal in which the polymer is deprotonated,11,12...solvate that is a cocrystal of protonated PBZT and PPA anions. As previously mentioned, the fact that these two extreme cases result in similar

Calculating pKa values for substituted phenols and hydration energies for other compounds with the first-order Fuzzy-Border continuum solvation model

PubMed Central

Sharma, Ity; Kaminski, George A.

2012-01-01

We have computed pKa values for eleven substituted phenol compounds using the continuum Fuzzy-Border (FB) solvation model. Hydration energies for 40 other compounds, including alkanes, alkenes, alkynes, ketones, amines, alcohols, ethers, aromatics, amides, heterocycles, thiols, sulfides and acids have been calculated. The overall average unsigned error in the calculated acidity constant values was equal to 0.41 pH units and the average error in the solvation energies was 0.076 kcal/mol. We have also reproduced pKa values of propanoic and butanoic acids within ca. 0.1 pH units from the experimental values by fitting the solvation parameters for carboxylate ion carbon and oxygen atoms. The FB model combines two distinguishing features. First, it limits the amount of noise which is common in numerical treatment of continuum solvation models by using fixed-position grid points. Second, it employs either second- or first-order approximation for the solvent polarization, depending on a particular implementation. These approximations are similar to those used for solute and explicit solvent fast polarization treatment which we developed previously. This article describes results of employing the first-order technique. This approximation places the presented methodology between the Generalized Born and Poisson-Boltzmann continuum solvation models with respect to their accuracy of reproducing the many-body effects in modeling a continuum solvent. PMID:22815192

Understanding Lithium Solvation and Diffusion through Topological Analysis of First-Principles Molecular Dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhatia, Harsh; Gyulassy, Attila; Ong, Mitchell

2016-09-27

The performance of lithium-ion batteries is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact, both, the solvation and diffusivity of Li ions. In this work, we present our application of the topological techniques to extract and predict such behavior in the data generated by the first-principles molecular dynamics simulation of Li ions in an important organic solvent -ethylene carbonate. More specifically, we use the scalar topology of the electron charge density field tomore » analyze the evolution of the solvation structures. This allows us to derive a parameter-free bond definition for lithium-oxygen bonds, to provide a quantitative measure for bond strength, and to understand the regions of influence of each atom in the simulation. This has provided new insights into how and under what conditions certain bonds may form and break. As a result, we can identify and, more importantly, predict, unstable configurations in solvation structures. This can be very useful in understanding when small changes to the atoms' movements can cause significantly different bond structures to evolve. Ultimately, this promises to allow scientists to explore lithium ion solvation and diffusion more systematically, with the aim of new insights and potentially accelerating the calculations themselves.« less

Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

PubMed Central

Ricci, Clarisse Gravina; Li, Bo; Cheng, Li-Tien; Dzubiella, Joachim; McCammon, J. Andrew

2018-01-01

Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the solvent can turn out to be too expensive in large biomolecular systems, most implicit solvent methods fail to capture “dewetting” effects and heterogeneous hydration by relying on a pre-established (i.e., guessed) solvation interface. Here we focus on the Variational Implicit Solvent Method, an implicit solvent method that adds water “plasticity” back to the picture by formulating the solvation free energy as a functional of all possible solvation interfaces. We survey VISM's applications to the problem of molecular recognition and report some of the most recent efforts to tailor VISM for more challenging scenarios, with the ultimate goal of including thermal fluctuations into the framework. The advances reported herein pave the way to make VISM a uniquely successful approach to characterize complex solvation properties in the recognition and binding of large-scale biomolecular complexes. PMID:29484300

Influence of temperature and molecular structure on ionic liquid solvation layers.

PubMed

Wakeham, Deborah; Hayes, Robert; Warr, Gregory G; Atkin, Rob

2009-04-30

Atomic force microscopy (AFM) force profiling is used to investigate the structure of adsorbed and solvation layers formed on a mica surface by various room temperature ionic liquids (ILs) ethylammonium nitrate (EAN), ethanolammonium nitrate (EtAN), ethylammonium formate (EAF), propylammonium formate (PAF), ethylmethylammonium formate (EMAF), and dimethylethylammonium formate (DMEAF). At least seven layers are observed for EAN at 14 degrees C (melting point 13 degrees C), decreasing as the temperature is increased to 30 degrees C due to thermal energy disrupting solvophobic forces that lead to segregation of cation alkyl tails from the charged ammonium and nitrate moieties. The number and properties of the solvation layers can also be controlled by introducing an alcohol moiety to the cation's alkyl tail (EtAN), or by replacing the nitrate anion with formate (EAF and PAF), even leading to the detection of distinct cation and anion sublayers. Substitution of primary by secondary or tertiary ammonium cations reduces the number of solvation layers formed, and also weakens the cation layer adsorbed onto mica. The observed solvation and adsorbed layer structures are discussed in terms of the intermolecular cohesive forces within the ILs.

Computational analysis of the solvation of coffee ingredients in aqueous ionic liquid mixtures† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6ra24736a Click here for additional data file.

PubMed Central

Zeindlhofer, Veronika; Khlan, Diana; Bica, Katharina

2017-01-01

In this paper, we investigate the solvation of coffee ingredients including caffeine, gallic acid as representative for phenolic compounds and quercetin as representative for flavonoids in aqueous mixtures of the ionic liquid 1-ethyl-3-methylimidazolium acetate [C2mim][OAc] at various concentrations. Due to the anisotropy of the solutes we show that classical Kirkwood–Buff theory is not appropriate to study solvation effects with increasing ionic liquid content. However, excess coordination numbers as well as the mean residence time of solvent molecules at the surface of the solutes can be determined by Voronoi tessellation. Since the volume of the hydration shells is also available by this method, solvation free energies will be discussed as a function of the ionic liquid concentration to yield a physical meaningful picture of solvation for the anisotropic solutes. Hydrogen bonding capabilities of the solutes and their relevance for experimental extraction yields from spent coffee grounds are also discussed. PMID:28496974

Strong Stretching of Poly(ethylene glycol) Brushes Mediated by Ionic Liquid Solvation.

PubMed

Han, Mengwei; Espinosa-Marzal, Rosa M

2017-09-07

We have measured forces between mica surfaces coated with a poly(ethylene glycol) (PEG) brush solvated by a vacuum-dry ionic liquid, 1-ethyl-3-methyl imidazolium bis(trifluoromethylsulfonyl)imide, with a surface forces apparatus. At high grafting density, the solvation mediated by the ionic liquid causes the brush to stretch twice as much as in water. Modeling of the steric repulsion indicates that PEG behaves as a polyelectrolyte; the hydrogen bonding between ethylene glycol and the imidazolium cation seems to effectively charge the polymer brush, which justifies the strong stretching. Importantly, under strong polymer compression, solvation layers are squeezed out at a higher rate than for the neat ionic liquid. We propose that the thermal fluctuations of the PEG chains, larger in the brush than in the mushroom configuration, maintain the fluidity of the ionic liquid under strong compression, in contrast to the solid-like squeezing-out behavior of the neat ionic liquid. This is the first experimental study of the behavior of a polymer brush solvated by an ionic liquid under nanoconfinement.

Atomic Radius and Charge Parameter Uncertainty in Biomolecular Solvation Energy Calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Xiu; Lei, Huan; Gao, Peiyuan

Atomic radii and charges are two major parameters used in implicit solvent electrostatics and energy calculations. The optimization problem for charges and radii is under-determined, leading to uncertainty in the values of these parameters and in the results of solvation energy calculations using these parameters. This paper presents a method for quantifying this uncertainty in solvation energies using surrogate models based on generalized polynomial chaos (gPC) expansions. There are relatively few atom types used to specify radii parameters in implicit solvation calculations; therefore, surrogate models for these low-dimensional spaces could be constructed using least-squares fitting. However, there are many moremore » types of atomic charges; therefore, construction of surrogate models for the charge parameter space required compressed sensing combined with an iterative rotation method to enhance problem sparsity. We present results for the uncertainty in small molecule solvation energies based on these approaches. Additionally, we explore the correlation between uncertainties due to radii and charges which motivates the need for future work in uncertainty quantification methods for high-dimensional parameter spaces.« less

Highly Stable Lithium Metal Batteries Enabled by Regulating the Solvation of Lithium Ions in Nonaqueous Electrolytes.

PubMed

Zhang, Xue-Qiang; Chen, Xiang; Cheng, Xin-Bing; Li, Bo-Quan; Shen, Xin; Yan, Chong; Huang, Jia-Qi; Zhang, Qiang

2018-05-04

Safe and rechargeable lithium metal batteries have been difficult to achieve because of the formation of lithium dendrites. Herein an emerging electrolyte based on a simple solvation strategy is proposed for highly stable lithium metal anodes in both coin and pouch cells. Fluoroethylene carbonate (FEC) and lithium nitrate (LiNO 3 ) were concurrently introduced into an electrolyte, thus altering the solvation sheath of lithium ions, and forming a uniform solid electrolyte interphase (SEI), with an abundance of LiF and LiN x O y on a working lithium metal anode with dendrite-free lithium deposition. Ultrahigh Coulombic efficiency (99.96 %) and long lifespans (1000 cycles) were achieved when the FEC/LiNO 3 electrolyte was applied in working batteries. The solvation chemistry of electrolyte was further explored by molecular dynamics simulations and first-principles calculations. This work provides insight into understanding the critical role of the solvation of lithium ions in forming the SEI and delivering an effective route to optimize electrolytes for safe lithium metal batteries. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Preparation, characterization and crystal structures of three salts of the quaterpyridine ligand

NASA Astrophysics Data System (ADS)

Ciesielski, Artur; Stefankiewicz, Artur R.; Patroniak, Violetta; Kubicki, Maciej

2009-07-01

As a result of a reaction between 6,6'''-dimethyl-2,2':6',2'':6'',2'''-quaterpyridine C 22H 18N 4 and lanthanide(III) salts, compounds, [C 22H 20N 4] 2+·2(CF 3SO 3) - ( 1) and [C 22H 20N 4] 2+·2(ClO 4) - ( 2), have been obtained. They were characterized by spectroscopic techniques (ESI-MS, NMR, IR), elemental analysis, and their formulae were confirmed on the basis of X-ray crystallography. It turned out that the perchlorate crystallizes as two solvates: with acetonitrile and disordered water molecules. These are the first structural characterization of a 6,6'″-dimethyl-2,2':6',2″:6″,2'″-quaterpyridinium dication. Due to the intramolecular hydrogen bond it adopts the previously unobserved cis/trans/cis conformation. In all three crystals the dications have C i symmetry, they occupy the special positions in their respective space groups. In the crystal structures the π-π stacking and weak hydrogen bonds add directionality to the dominating electrostatic interactions between cations and anions.

Ammonium Additives to Dissolve Lithium Sulfide through Hydrogen Binding for High-Energy Lithium-Sulfur Batteries.

PubMed

Pan, Huilin; Han, Kee Sung; Vijayakumar, M; Xiao, Jie; Cao, Ruiguo; Chen, Junzheng; Zhang, Jiguang; Mueller, Karl T; Shao, Yuyan; Liu, Jun

2017-02-08

In rechargeable Li-S batteries, the uncontrollable passivation of electrodes by highly insulating Li 2 S limits sulfur utilization, increases polarization, and decreases cycling stability. Dissolving Li 2 S in organic electrolyte is a facile solution to maintain the active reaction interface between electrolyte and sulfur cathode, and thus address the above issues. Herein, ammonium salts are demonstrated as effective additives to promote the dissolution of Li 2 S to 1.25 M in DMSO solvent at room temperature. NMR measurements show that the strong hydrogen binding effect of N-H groups plays a critical role in dissolving Li 2 S by forming complex ligands with S 2- anions coupled with the solvent's solvating surrounding. Ammonium additives in electrolyte can also significantly improve the oxidation kinetics of Li 2 S, and therefore enable the direct use of Li 2 S as cathode material in Li-S battery system in the future. This provides a new approach to manage the solubility of lithium sulfides through cation coordination with sulfide anion.

Detailed solvent, structural, quantum chemical study and antimicrobial activity of isatin Schiff base

NASA Astrophysics Data System (ADS)

Brkić, Dominik R.; Božić, Aleksandra R.; Marinković, Aleksandar D.; Milčić, Miloš K.; Prlainović, Nevena Ž.; Assaleh, Fathi H.; Cvijetić, Ilija N.; Nikolić, Jasmina B.; Drmanić, Saša Ž.

2018-05-01

The ratios of E/Z isomers of sixteen synthesized 1,3-dihydro-3-(substituted phenylimino)-2H-indol-2-one were studied using experimental and theoretical methodology. Linear solvation energy relationships (LSER) rationalized solvent influence of the solvent-solute interactions on the UV-Vis absorption maxima shifts (νmax) of both geometrical isomers using the Kamlet-Taft equation. Linear free energy relationships (LFER) in the form of single substituent parameter equation (SSP) was used to analyze substituent effect on pKa, NMR chemical shifts and νmax values. Electron charge density was obtained by the use of Quantum Theory of Atoms in Molecules, i.e. Bader's analysis. The substituent and solvent effect on intramolecular charge transfer (ICT) were interpreted with the aid of time-dependent density functional (TD-DFT) method. Additionally, the results of TD-DFT calculations quantified the efficiency of ICT from the calculated charge-transfer distance (DCT) and amount of transferred charge (QCT). The antimicrobial activity was evaluated using broth microdilution method. 3D QSAR modeling was used to demonstrate the influence of substituents effect as well as molecule geometry on antimicrobial activity.

Structure and Electronic Spectra of Purine-Methyl Viologen Charge Transfer Complexes

PubMed Central

Jalilov, Almaz S.; Patwardhan, Sameer; Singh, Arunoday; Simeon, Tomekia; Sarjeant, Amy A.; Schatz, George C.; Lewis, Frederick D.

2014-01-01

The structure and properties of the electron donor-acceptor complexes formed between methyl viologen (MV) and purine nucleosides and nucleotides in water and the solid state have been investigated using a combination of experimental and theoretical methods. Solution studies were performed using UV-vis and 1H NMR spectroscopy. Theoretical calculations were performed within the framework of density functional theory (DFT). Energy decomposition analysis indicates that dispersion and induction (charge-transfer) interactions dominate the total binding energy, whereas electrostatic interactions are largely repulsive. The appearance of charge transfer bands in the absorption spectra of the complexes are well described by time-dependent (TD) DFT and are further explained in terms of the redox properties of purine monomers and solvation effects. Crystal structures are reported for complexes of methyl viologen with the purines 2′-deoxyguanosine 3′-monophosphate GMP (DAD′DAD′ type) and 7-deazaguanosine zG (DAD′ADAD′ type). Comparison of the structures determined in the solid state and by theoretical methods in solution provides valuable insights into the nature of charge-transfer interactions involving purine bases as electron donors. PMID:24294996

Synthesis and characterization of d10 metal complexes of 3-Me-5-FcPz: Structural, theoretical and third order nonlinear optical properties

NASA Astrophysics Data System (ADS)

Senthilkumar, Kabali; Thirumoorthy, Krishnan; Vinitha, G.; Soni, Kiran; Bhuvanesh, Nattamai S. P.; Palanisami, Nallasamy

2017-01-01

The d10 metal complexes based on 3-methyl-5-ferrocenyl-1H-pyrazole (L = 3-Me-5-FcPz) ligand [M(L)4(NO3)2] Zn=(1) and Cd=(2), [Hg(L)4(NO3)2].dmf (3) have been synthesized and characterized by FT-IR, NMR, UV-Vis and elemental analysis. The molecular structure of compound 2 and its crystal packing were determined by single crystal X-ray diffraction. The nitrate anions are also involved in intermolecular hydrogen bonding with adjacent ferrocene units and it forms zig-zag one-dimensional polymeric structure. UV-Vis investigations on the positive solvatochromic behavior of 1-3 revealed that the solvation of the push-pull character increases with increasing polarity. The third-order nonlinear optical (NLO) properties of 1-3 have been determined by Z-scan technique and the results indicate that compounds 1-3 exhibits the strong self-defocusing effect. The nonlinear susceptibility χ(3) values are calculated in the order of 10-6 esu.

Preparation and characterization of novel zwitterionic poly(arylene ether sulfone) ultrafiltration membrane with good thermostability and excellent antifouling properties

NASA Astrophysics Data System (ADS)

Rong, Guolong; Zhou, Di; Han, Xiaocui; Pang, Jinhui

2018-01-01

Zwitterionic poly(arylene ether sulfone) (PAES-NS) was synthesized via copolymerization by using a bisphenol monomer with a pyridine group. The chemical structures of the copolymers were confirmed by using Fourier transform infrared (FTIR) and 1H nuclear magnetic resonance (NMR) spectroscopy; the copolymers showed good thermal stability. A series of polyphenysulfone (PPSU)/PAES-NS blend ultrafiltration (UF) membranes was prepared via conventional immersion precipitation phase inversion methods The morphologies of the modified membranes were investigated by scanning electron microscopy (SEM). The surface hydrophilicity of the UF membranes was studied by water contact angle measurement, indicating that the zwitterionic group increased the membrane hydrophilicity. UF of solvated model pollutants using the membranes showed a significant reduction of the irreversible adsorption of the foulants, illustrating the excellent anti-fouling properties of the membrane. The water flux of the PAES-NS membrane was significantly enhanced, being almost three times higher than that of the pristine PPSU membrane, with retention of a high rejection level. After three UF cycles, the water flux recovery of the PAES-NS membrane was as high as 96%.

Protein Conformational Entropy is Independent of Solvent

NASA Astrophysics Data System (ADS)

Nucci, Nathaniel; Moorman, Veronica; Gledhill, John; Valentine, Kathleen; Wand, A. Joshua

Proteins exhibit most of their conformational entropy in individual bond vector motions on the ps-ns timescale. These motions can be examined through determination of the Lipari-Szabo generalized squared order parameter (O2) using NMR spin relaxation measurements. It is often argued that most protein motions are intimately dependent on the nature of the solvating environment. Here the solvent dependence of the fast protein dynamics is directly assessed. Using the model protein ubiquitin, the order parameters of the backbone and methyl groups are shown to be generally unaffected by up to a six-fold increase in bulk viscosity or by encapsulation in the nanoscale interior of a reverse micelle. In addition, the reverse micelle condition permits direct comparison of protein dynamics to the mobility of the hydration layer; no correlation is observed. The dynamics of aromatic side chains are also assessed and provide an estimate of the length- and timescale of protein motions where solvent dependence is seen. These data demonstrate the solvent independence of conformational entropy, clarifying a long-held misconception in the fundamental behavior of biological macromolecules. Supported by the National Science Foundation.

Ammonium Additives to Dissolve Lithium Sulfide through Hydrogen Binding for High-Energy Lithium–Sulfur Batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pan, Huilin; Han, Kee Sung; Vijayakumar, M.

In rechargeable Li-S batteries, the uncontrollable passivation of electrodes by highly insulating Li2S limits sulfur utilization, increases polarization and decreases cycling stability. Dissolving Li2S in organic electrolyte is a facile solution to maintain the active reaction interface between electrolyte and sulfur cathode, and thus address the above issues. Herein, ammonium salts are demonstrated as effective additives to promote the dissolution of Li2S to 1.25 M in DMSO solvent at room temperature. NMR measurements show that the strong hydrogen binding effect of N-H groups plays a critical role in dissolving Li2S by forming complex ligands with S2- anions coupled with themore » solvent’s solvating surrounding. Ammonium additives in electrolyte can also significantly improve the oxidation kinetics of Li2S, therefore enables the direct use of Li2S as cathode material in Li-S battery system in the future. This provides a new approach to manage the solubility of lithium sulfides through cation coordination with sulfide anion.« less

Prediction of solvation enthalpy of gaseous organic compounds in propanol

NASA Astrophysics Data System (ADS)

Golmohammadi, Hassan; Dashtbozorgi, Zahra

2016-09-01

The purpose of this paper is to present a novel way for developing quantitative structure-property relationship (QSPR) models to predict the gas-to-propanol solvation enthalpy (Δ H solv) of 95 organic compounds. Different kinds of descriptors were calculated for each compound using the Dragon software package. The variable selection technique of replacement method (RM) was employed to select the optimal subset of solute descriptors. Our investigation reveals that the dependence of physical chemistry properties of solution on solvation enthalpy is nonlinear and that the RM method is unable to model the solvation enthalpy accurately. The results established that the calculated Δ H solv values by SVM were in good agreement with the experimental ones, and the performances of the SVM models were superior to those obtained by RM model.

Solvation of the fluorine containing anions and their lithium salts in propylene carbonate and dimethoxyethane.

PubMed

Chaban, Vitaly

2015-07-01

Electrolyte solutions based on the propylene carbonate (PC)-dimethoxyethane (DME) mixtures are of significant importance and urgency due to emergence of lithium-ion batteries. Solvation and coordination of the lithium cation in these systems have been recently attended in detail. However, analogous information concerning anions (tetrafluoroborate, hexafluorophosphate) is still missed. This work reports PM7-MD simulations (electronic-structure level of description) to include finite-temperature effects on the anion solvation regularities in the PC-DME mixture. The reported result evidences that the anions appear weakly solvated. This observation is linked to the absence of suitable coordination sites in the solvent molecules. In the concentrated electrolyte solutions, both BF4(-) and PF6(-) prefer to exist as neutral ion pairs (LiBF4, LiPF6).

Negative ion photoelectron spectroscopy of solvated electron cluster anions, (H2O){/n -} and (NH3){/n -}

NASA Astrophysics Data System (ADS)

Lee, G. H.; Arnold, S. T.; Eaton, J. G.; Sarkas, H. W.; Bowen, K. H.; Ludewigt, C.; Haberland, H.

1991-03-01

The photodetachment spectra of (H2O){/n =2-69/-} and (NH3){/n =41-1100/-} have been recorded, and vertical detachment energies (VDEs) were obtained from the spectra. For both systems, the cluster anion VDEs increase smoothly with increasing sizes and most species plot linearly with n -1/3, extrapolating to a VDE ( n=∞) value which is very close to the photoelectric threshold energy for the corresponding condensed phase solvated electron system. The linear extrapolation of this data to the analogous condensed phase property suggests that these cluster anions are gas phase counterparts to solvated electrons, i.e. they are embryonic forms of hydrated and ammoniated electrons which mature with increasing cluster size toward condensed phase solvated electrons.

Solvation of Cr 3+ cation in water-acetonitrile mixture studied by IR spectroscopy: molecular penetration into the solvation shells

NASA Astrophysics Data System (ADS)

Jamróz, Dorota; Wójcik, Marek; Lindgren, Jan

2000-09-01

Infrared spectra of mixtures of water and deuteroacetonitrile containing the Cr 3+ cation have been studied as a function of concentration, time and temperature. The CN stretching vibration of CD 3CN molecules has been used as a probe of the structural environments. The CN band in the spectra of the solutions is a superposition of four subbands, which may be attributed to CD 3CN bound in the first, second, and third solvation shells of the cation and to non-bound CD 3CN. The character of changes of the integral intensities of the subbands with time for various H 2O:Cr 3+ molar ratios are explained by suggesting mechanisms of molecular replacement within the solvation shells of Cr 3+.

Stable adducts of nerve agents sarin, soman and cyclosarin with TRIS, TES and related buffer compounds--characterization by LC-ESI-MS/MS and NMR and implications for analytical chemistry.

PubMed

Gäb, Jürgen; John, Harald; Melzer, Marco; Blum, Marc-Michael

2010-05-15

Buffering compounds like TRIS are frequently used in chemical, biochemical and biomedical applications to control pH in solution. One of the prerequisites of a buffer compound, in addition to sufficient buffering capacity and pH stability over time, is its non-reactivity with other constituents of the solution. This is especially important in the field of analytical chemistry where analytes are to be determined quantitatively. Investigating the enzymatic hydrolysis of G-type nerve agents sarin, soman and cyclosarin in buffered solution we have identified stable buffer adducts of TRIS, TES and other buffer compounds with the nerve agents. We identified the molecular structure of these adducts as phosphonic diesters using 1D (1)H-(31)P HSQC NMR and LC-ESI-MS/MS techniques. Reaction rates with TRIS and TES are fast enough to compete with spontaneous hydrolysis in aqueous solution and to yield substantial amounts (up to 20-40%) of buffer adduct over the course of several hours. A reaction mechanism is proposed in which the amino function of the buffer serves as an intramolecular proton acceptor rendering the buffer hydroxyl groups nucleophilic enough for attack on the phosphorus atom of the agents. Results show that similar buffer adducts are formed with a range of hydroxyl and amino function containing buffers including TES, BES, TRIS, BIS-TRIS, BIS-TRIS propane, Tricine, Bicine, HEPES and triethanol amine. It is recommended to use alternative buffers like MOPS, MES and CHES when working with G-type nerve agents especially at higher concentrations and over prolonged times. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Absorbent Analysis of Anniston Chemical Agent Disposal Facility Munition Demilitarization Building (MDB) Banks 1 and 2 Filter Samples Following Completion of The GB Agent and VX Rocket Campaigns

DTIC Science & Technology

2013-01-01

adsorbed on wet carbon (13 wt% water ). Left to right: initial and t = 6, 13, and 16 days ..............................3 2. 31 P MAS NMR spectra...obtained for 10 wt% VX adsorbed on wet carbon (13 wt% water ) Left to right: initial and t = 24 days ...............................................4...of feed air. Each Class A Type II filter contained approximately 48.2 lb of granular, activated, coconut shell-based carbon. A given filter bank

Reactions of CW Agents HD And GD with the Polymer Fabrics PVAM and CHEMCAT 41

DTIC Science & Technology

2015-09-01

analyses of the rates of G agent decomposition were followed by the methods of solids NMR (high resolution magic angle spinning, HR-MAS). A P-31...molecular weight copolymer of 30-35 kDa. The Erkol copolymer forms a pH 12 solution in water and functions as Lewis base when hydrated .6 GD and DFP...Reactions The hydrated PVAm film, containing 20% glycerol, was found to completely deplete and decompose a two-fold excess of DFP vapor (peaks -8 and

Excess electron localization in solvated DNA bases.

PubMed

Smyth, Maeve; Kohanoff, Jorge

2011-06-10

We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic electron affinities increase systematically upon solvation, as for optimized gas-phase geometries. Dynamical simulations after vertical attachment indicate that the excess electron, which is initially found delocalized, localizes around the nucleobases within a 15 fs time scale. This transition requires small rearrangements in the geometry of the bases.

Excess Electron Localization in Solvated DNA Bases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smyth, Maeve; Kohanoff, Jorge

2011-06-10

We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic electron affinities increase systematically upon solvation, as for optimized gas-phase geometries. Dynamical simulations after vertical attachment indicate that the excess electron, which is initially found delocalized, localizes around the nucleobases within a 15 fs time scale. This transition requires small rearrangements in the geometry of the bases.

Solution NMR Structures of Oxidized and Reduced Ehrlichia chaffeensis thioredoxin: NMR-Invisible Structure Owing to Backbone Dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buchko, Garry W.; Hewitt, Stephen N.; Van Voorhis, Wesley C.

Thioredoxins (Trxs) are small ubiquitous proteins that participate in a diverse variety of redox reactions via the reversible oxidation of two cysteine thiol groups in a structurally conserved active site, CGPC. Here, we describe the NMR solution structures of a Trx from Ehrlichia chaffeensis (Ec-Trx, ECH_0218), the etiological agent responsible for human monocytic ehrlichiosis, in both the oxidized and reduced states. The overall topology of the calculated structures is similar in both redox states and similar to other Trx structures, a five-strand, mixed -sheet (1:3:2:4:5) surrounded by four -helices. Unlike other Trxs studied by NMR in both redox states, themore » 1H-15N HSQC spectra of reduced Ec-Trx was missing eight amide cross peaks relative to the spectra of oxidized Ec-Trx. These missing amides correspond to residues C32-E39 in the active site containing helix (2) and S72-I75 in a loop near the active site and suggest a substantial change in the backbone dynamics associated with the formation of an intramolecular C32-C35 disulfide bond.« less

Unraveling the active hypoglycemic agent trigonelline in Balanites aegyptiaca date fruit using metabolite fingerprinting by NMR.

PubMed

Farag, Mohamed A; Porzel, Andrea; Wessjohann, Ludger A

2015-11-10

Trigonelline (3-carboxy-1-methyl pyridinium) was identified as a relevant bioactivity and taste imparting component in Balanites aegyptiaca fruit, using (1)H NMR of crude extracts without any fractionation or isolation step. The structural integrity of trigonelline was established within the extract matrix via(1)H NMR, (1)H-(1)H COSY, HMQC and HMBC and by comparison with authentic standard. A quantitative (1)H NMR method (qHNMR) was used to determine trigonelline concentrations in the peel and pulp of B. aegyptiaca fruit of 8 and 13mgg(-1), respectively. Trigonelline so far has not been reported from B. aegyptiaca or its genus as it easily escapes LC-MS based detection. Its discovery provides novel insight into the balanite fruits antidiabetic properties as the compound is known for a pronounced hypoglycemic effect. In addition, it is likely to impart the perceptible bitter taste portion to balanites sweet bitter taste. UPLC-MS of the crude extract additionally revealed the fruit flavonoid pattern showing quercetin/isorhamnetin flavonol conjugates in addition to epicatechin, the latter being present at much lower levels. Copyright © 2015 Elsevier B.V. All rights reserved.

The Denaturation Transition of DNA in Mixed Solvents

PubMed Central

Hammouda, Boualem; Worcester, David

2006-01-01

The helix-to-coil denaturation transition in DNA has been investigated in mixed solvents at high concentration using ultraviolet light absorption spectroscopy and small-angle neutron scattering. Two solvents have been used: water and ethylene glycol. The “melting” transition temperature was found to be 94°C for 4% mass fraction DNA/d-water and 38°C for 4% mass fraction DNA/d-ethylene glycol. The DNA melting transition temperature was found to vary linearly with the solvent fraction in the mixed solvents case. Deuterated solvents (d-water and d-ethylene glycol) were used to enhance the small-angle neutron scattering signal and 0.1M NaCl (or 0.0058 g/g mass fraction) salt concentration was added to screen charge interactions in all cases. DNA structural information was obtained by small-angle neutron scattering, including a correlation length characteristic of the inter-distance between the hydrogen-containing (desoxyribose sugar-amine base) groups. This correlation length was found to increase from 8.5 to 12.3 Å across the melting transition. Ethylene glycol and water mixed solvents were found to mix randomly in the solvation region in the helix phase, but nonideal solvent mixing was found in the melted coil phase. In the coil phase, solvent mixtures are more effective solvating agents than either of the individual solvents. Once melted, DNA coils behave like swollen water-soluble synthetic polymer chains. PMID:16815902

NMR diffusion and relaxation studies of 2-nitroimidazole and albumin interactions

NASA Astrophysics Data System (ADS)

Wijesekera, Dj; Willis, Scott A.; Gupta, Abhishek; Torres, Allan M.; Zheng, Gang; Price, William S.

2018-03-01

Nitroimidazole derivatives are of current interest in the development of hypoxia targeting agents and show potential in the establishment of quantitative measures of tumor hypoxia. In this study, the binding of 2-nitroimidazole to albumin was probed using NMR diffusion and relaxation measurements. Binding studies were conducted at three different protein concentrations (0.23, 0.30 and 0.38 mM) with drug concentrations ranging from 0.005-0.16 M at 298 K. Quantitative assessments of the binding model were made by evaluating the number of binding sites, n, and association constant, K. These were determined to be 21 ± 3 and 53 ± 4 M- 1, respectively.

Phase solubility, 1H NMR and molecular modelling studies of bupivacaine hydrochloride complexation with different cyclodextrin derivates

NASA Astrophysics Data System (ADS)

Jug, Mario; Mennini, Natascia; Melani, Fabrizio; Maestrelli, Francesca; Mura, Paola

2010-11-01

A novel method, which simultaneously exploits experimental (NMR) and theoretically calculated data obtained by a molecular modelling technique, was proposed, to obtain deeper insight into inclusion geometry and possible stereoselective binding of bupivacaine hydrochloride with selected cyclodextrin derivatives. Sulphobuthylether-β-cyclodextrin and water soluble polymeric β-cyclodextrin demonstrated to be the best complexing agents for the drug, resulting in formation of the most stable inclusion complexes with the highest increase in aqueous drug solubility. The drug-carrier binding modes with these cyclodextrins and phenomena which may be directly related to the higher stability and better aqueous solubility of complexes formed were discussed in details.

A novel series of N-acyl substituted indole-linked benzimidazoles and naphthoimidazoles as potential anti inflammatory, anti biofilm and anti microbial agents.

PubMed

Abraham, Rajan; Prakash, Periakaruppan; Mahendran, Karthikeyan; Ramanathan, Murugappan

2018-01-01

A novel N-acyl substituted indole-linked benzimidazoles and naphthoimidazoles were synthesized. Their chemical structures were confirmed using spectroscopic tools including 1 H NMR, 13 C NMR and CHN-elemental analyses. Anti inflammatory activity for all target compounds was evaluated in-vitro. The synthesized compounds hinder the biofilm formation and control the growth of the pathogen, Staphylococcus epidermis. Anti microbial activity of the compounds was evaluated against both Gram negative and Gram positive bacteria such as Staphylococcus aureus (MTCC 2940), Pseudomonas aeruginosa (MTCC424), Escherchia coli (MTCC 443) and Enterococcus fecalis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Biopolymer nanocomposite films reinforced with nanocellulose whiskers

Treesearch

Amit Saxena; Marcus Foston; Mohamad Kassaee; Thomas J. Elder; Arthur J. Ragauskas

2011-01-01

A xylan nanocomposite film with improved strength and barrier properties was prepared by a solution casting using nanocellulose whiskers as a reinforcing agent. The 13C cross-polarization magic angle spinning (CP/MAS) nuclear magnetic resonance (NMR) analysis of the spectral data obtained for the NCW/xylan nanocomposite films indicated the signal intensity originating...

The Metolachlor Herbicide: An Exercise in Today's Stereochemistry

ERIC Educational Resources Information Center

Mannschreck, Albrecht; von Angerer, Erwin

2009-01-01

Metolachlor is one of the most widely used agents registered for the protection of many cultivated plants against weeds. Because of axial and central chirality, this molecule forms four stereoisomers, the investigation of which by [superscript 1]H NMR and chromatography is described. It is shown that the isomers do not interconvert at room…

H NMR analyses of Citrus macrophylla subjected to Asian citrus psyllid (Diaphorina citri Kuwayama) feeding

USDA-ARS?s Scientific Manuscript database

The Asian citrus psyllid (ACP) is a phloem feeding insect that can host and transmit the bacterium Candidatus Liberibacter asiaticus (CLas), which is the putative causative agent of the economically important citrus disease, Huanglongbing (HLB). ACP are widespread in Florida, and are spreading in Ca...

31P-edited diffusion-ordered 1H NMR spectroscopy for the spectral isolation and identification of organophosphorus compounds related to chemical weapons agents and their degradation products.

PubMed

Mayer, Brian P; Valdez, Carlos A; Hok, Saphon; Chinn, Sarah C; Hart, Bradley R

2012-12-04

Organophosphorus compounds represent a large class of molecules that include pesticides, flame-retardants, biologically relevant molecules, and chemical weapons agents (CWAs). The detection and identification of organophosphorus molecules, particularly in the cases of pesticides and CWAs, are paramount to the verification of international treaties by various organizations. To that end, novel analytical methodologies that can provide additional support to traditional analyses are important for unambiguous identification of these compounds. We have developed an NMR method that selectively edits for organophosphorus compounds via (31)P-(1)H heteronuclear single quantum correlation (HSQC) and provides an additional chromatographic-like separation based on self-diffusivities of the individual species via (1)H diffusion-ordered spectroscopy (DOSY): (1)H-(31)P HSQC-DOSY. The technique is first validated using the CWA VX (O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothioate) by traditional two-dimensional DOSY spectra. We then extend this technique to a complex mixture of VX degradation products and identify all the main phosphorus-containing byproducts generated after exposure to a zinc-cyclen organometallic homogeneous catalyst.

Cytotoxic halogenated monoterpenes from Plocamium cartilagineum.

PubMed

Sabry, Omar M M; Goeger, Douglas E; Valeriote, Frederick A; Gerwick, William H

2017-02-01

As a result of our efforts to identify bioactive agents from marine algae, we have isolated and identified one new halogenated monoterpene 1 [(-)-(5E,7Z)-348-trichloro-7-dichloromethyl-3-methyl-157-octatriene] in addition to three known compounds (2, 3 and 4) from the red alga Plocamium cartilagineum collected by hand from the eastern coast of South Africa. Compound 1 was found to be active as a cytotoxic agent in human lung cancer (NCI-H460) and mouse neuro-2a cell lines (IC 50 4 μg/mL). Two of these compounds (3 and 4) were found to have cytotoxic activity in other cell line assays, especially against human leukaemia and human colon cancers (IC 50 1.3 μg/mL). None of these metabolites were active as sodium channel blockers or activators. All structures were determined by spectroscopic methods (UV, IR, LRMS, HRMS, 1D NMR and 2D NMR). 1D and 2D NOE experiments were carried out on these compounds to confirm the geometry of the double bonds.

Mononuclear Pd(II) complex as a new therapeutic agent: Synthesis, characterization, biological activity, spectral and DNA binding approaches

NASA Astrophysics Data System (ADS)

Saeidifar, Maryam; Mirzaei, Hamidreza; Ahmadi Nasab, Navid; Mansouri-Torshizi, Hassan

2017-11-01

The binding ability between a new water-soluble palladium(II) complex [Pd(bpy)(bez-dtc)]Cl (where bpy is 2,2‧-bipyridine and bez-dtc is benzyl dithiocarbamate), as an antitumor agent, and calf thymus DNA was evaluated using various physicochemical methods, such as UV-Vis absorption, Competitive fluorescence studies, viscosity measurement, zeta potential and circular dichroism (CD) spectroscopy. The Pd(II) complex was synthesized and characterized using elemental analysis, molar conductivity measurements, FT-IR, 1H NMR, 13C NMR and electronic spectra studies. The anticancer activity against HeLa cell lines demonstrated lower cytotoxicity than cisplatin. The binding constants and the thermodynamic parameters were determined at different temperatures (300 K, 310 K and 320 K) and shown that the complex can bind to DNA via electrostatic forces. Furthermore, this result was confirmed by the viscosity and zeta potential measurements. The CD spectral results demonstrated that the binding of Pd(II) complex to DNA induced conformational changes in DNA. We hope that these results will provide a basis for further studies and practical clinical use of anticancer drugs.

Synthesis of new N-substituted 5-arylidene-2,4-thiazolidinediones as anti-inflammatory and antimicrobial agents.

PubMed

Nastasă, Cristina; Tiperciuc, Brînduşa; Pârvu, Alina; Duma, Mihaela; Ionuţ, Ioana; Oniga, Ovidiu

2013-06-01

A novel series of 5-arylidene-2,4-thiazolidinediones (TZDs) 2a-p was synthesized from the condensation of 3-((2-phenylthiazol-4-yl)methyl)thiazolidine-2,4-dione with different benzaldehyde derivatives. All the structures were confirmed by their spectral (IR, ¹H NMR, ¹³C NMR and mass) and elemental analytical data. The new molecules were evaluated in vivo as anti-inflammatory agents in an acute experimental inflammation, evaluating the acute phase bone marrow response and phagocyte activity. All compounds, excepting one, reduced the absolute leukocytes count due to the lower neutrophil percentage. Phagocytary index was decreased by the same molecules, while only half of them reduced the phagocytary activity. The effect was superior to meloxicam, the reference anti-inflammatory drug, for the majority of the TZD derivatives. The new molecules were also investigated for their antimicrobial properties on Gram-positive and Gram-negative bacteria and one fungal strain. Two compounds (2e and 2n) manifested growth inhibition capacity on all the tested strains. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Design, synthesis, evaluation, and molecular docking of ursolic acid derivatives containing a nitrogen heterocycle as anti-inflammatory agents.

PubMed

Wei, Zhi-Yu; Chi, Ke-Qiang; Wang, Ke-Si; Wu, Jie; Liu, Li-Ping; Piao, Hu-Ri

2018-06-01

Ursolic acid derivatives containing oxadiazole, triazolone, and piperazine moieties were synthesized in an attempt to develop potent anti-inflammatory agents. Structures of the synthesized compounds were elucidated by 1 H NMR, 13 C NMR, and HRMS. Most of the synthesized compounds showed pronounced anti-inflammatory effects at 100 mg/kg. In particular, compound 11b, which displayed the most potent anti-inflammatory activity of all of the compounds prepared, with 69.76% inhibition after intraperitoneal administration, was more potent than the reference drugs indomethacin and ibuprofen. The cytotoxicity of the compounds was also assessed by the 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide (MTT) assay, and no compounds showed any appreciable cytotoxic activity (IC 50 >100 μmol/L). Furthermore, molecular docking studies of the synthesized compounds were performed to rationalize the obtained biological results. Overall, the results indicate that compound 11b could be a therapeutic candidate for the treatment of inflammation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.

PubMed

Marenich, Aleksandr V; Cramer, Christopher J; Truhlar, Donald G

2009-05-07

We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the "D" stands for "density" to denote that the full solute electron density is used without defining partial atomic charges. "Continuum" denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute-solvent boundary. SMD is a universal solvation model, where "universal" denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which a few key descriptors are known (in particular, dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the solution of the nonhomogeneous Poisson equation for electrostatics in terms of the integral-equation-formalism polarizable continuum model (IEF-PCM). The cavities for the bulk electrostatic calculation are defined by superpositions of nuclear-centered spheres. The second component is called the cavity-dispersion-solvent-structure term and is the contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell. This contribution is a sum of terms that are proportional (with geometry-dependent proportionality constants called atomic surface tensions) to the solvent-accessible surface areas of the individual atoms of the solute. The SMD model has been parametrized with a training set of 2821 solvation data including 112 aqueous ionic solvation free energies, 220 solvation free energies for 166 ions in acetonitrile, methanol, and dimethyl sulfoxide, 2346 solvation free energies for 318 neutral solutes in 91 solvents (90 nonaqueous organic solvents and water), and 143 transfer free energies for 93 neutral solutes between water and 15 organic solvents. The elements present in the solutes are H, C, N, O, F, Si, P, S, Cl, and Br. The SMD model employs a single set of parameters (intrinsic atomic Coulomb radii and atomic surface tension coefficients) optimized over six electronic structure methods: M05-2X/MIDI!6D, M05-2X/6-31G, M05-2X/6-31+G, M05-2X/cc-pVTZ, B3LYP/6-31G, and HF/6-31G. Although the SMD model has been parametrized using the IEF-PCM protocol for bulk electrostatics, it may also be employed with other algorithms for solving the nonhomogeneous Poisson equation for continuum solvation calculations in which the solute is represented by its electron density in real space. This includes, for example, the conductor-like screening algorithm. With the 6-31G basis set, the SMD model achieves mean unsigned errors of 0.6-1.0 kcal/mol in the solvation free energies of tested neutrals and mean unsigned errors of 4 kcal/mol on average for ions with either Gaussian03 or GAMESS.

Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marenich, Aleksandr; Cramer, Christopher J; Truhlar, Donald G

2009-04-30

We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the “D” stands for “density” to denote that the full solute electron density is used without defining partial atomic charges. “Continuum” denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute-solvent boundary. SMD is a universal solvation model, where “universal” denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which amore » few key descriptors are known (in particular, dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the solution of the nonhomogeneous Poisson equation for electrostatics in terms of the integral-equation-formalism polarizable continuum model (IEF-PCM). The cavities for the bulk electrostatic calculation are defined by superpositions of nuclear-centered spheres. The second component is called the cavity-dispersion-solvent-structure term and is the contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell. This contribution is a sum of terms that are proportional (with geometry-dependent proportionality constants called atomic surface tensions) to the solvent-accessible surface areas of the individual atoms of the solute. The SMD model has been parametrized with a training set of 2821 solvation data including 112 aqueous ionic solvation free energies, 220 solvation free energies for 166 ions in acetonitrile, methanol, and dimethyl sulfoxide, 2346 solvation free energies for 318 neutral solutes in 91 solvents (90 nonaqueous organic solvents and water), and 143 transfer free energies for 93 neutral solutes between water and 15 organic solvents. The elements present in the solutes are H, C, N, O, F, Si, P, S, Cl, and Br. The SMD model employs a single set of parameters (intrinsic atomic Coulomb radii and atomic surface tension coefficients) optimized over six electronic structure methods: M05-2X/MIDI!6D, M05-2X/6-31G*, M05-2X/6-31+G**, M05-2X/cc-pVTZ, B3LYP/6-31G*, and HF/6-31G*. Although the SMD model has been parametrized using the IEF-PCM protocol for bulk electrostatics, it may also be employed with other algorithms for solving the nonhomogeneous Poisson equation for continuum solvation calculations in which the solute is represented by its electron density in real space. This includes, for example, the conductor-like screening algorithm. With the 6-31G* basis set, the SMD model achieves mean unsigned errors of 0.6-1.0 kcal/mol in the solvation free energies of tested neutrals and mean unsigned errors of 4 kcal/mol on average for ions with either Gaussian03 or GAMESS.« less

Development of molecular precursors for deposition of indium sulphide thin film electrodes for photoelectrochemical applications.

PubMed

Ehsan, Muhammad Ali; Peiris, T A Nirmal; Wijayantha, K G Upul; Olmstead, Marilyn M; Arifin, Zainudin; Mazhar, Muhammad; Lo, K M; McKee, Vickie

2013-08-14

Symmetrical and unsymmetrical dithiocarbamato pyridine solvated and non-solvated complexes of indium(III) with the general formula [In(S2CNRR')3]·n(py) [where py = pyridine; R,R' = Cy, n = 2 (1); R,R' = (i)Pr, n = 1.5 (2); NRR' = Pip, n = 0.5 (3) and R = Bz, R' = Me, n = 0 (4)] have been synthesized. The compositions, structures and properties of these complexes have been studied by means of microanalysis, IR and (1)H-NMR spectroscopy, X-ray single crystal and thermogravimetric (TG/DTG) analyses. The applicability of these complexes as single source precursors (SSPs) for the deposition of β-In2S3 thin films on fluorine-doped SnO2 (FTO) coated conducting glass substrates by aerosol-assisted chemical vapour deposition (AACVD) at temperatures of 300, 350 and 400 °C is studied. All films have been characterized by powder X-ray diffraction (PXRD) and energy dispersive X-ray analysis (EDX) for the detection of phase and stoichiometry of the deposit. Scanning electron microscopy (SEM) studies reveal that precursors (1)-(4), irrespective of different metal ligand design, generate comparable morphologies of β-In2S3 thin films at different temperatures. Direct band gap energies of 2.2 eV have been estimated from the UV-vis spectroscopy for the β-In2S3 films fabricated from precursors (1) and (4). The photoelectrochemical (PEC) properties of β-In2S3 were confirmed by recording the current-voltage plots under light and dark conditions. The plots showed anodic photocurrent densities of 1.25 and 0.65 mA cm(-2) at 0.23 V vs. Ag/AgCl for the β-In2S3 films made at 400 and 350 °C from the precursors (1) and (4), respectively. The photoelectrochemical performance indicates that the newly synthesised precursors are highly useful in fabricating β-In2S3 electrodes for solar energy harvesting and optoelectronic application.

Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding.

PubMed

Young, Tom; Abel, Robert; Kim, Byungchan; Berne, Bruce J; Friesner, Richard A

2007-01-16

The thermodynamic properties and phase behavior of water in confined regions can vary significantly from that observed in the bulk. This is particularly true for systems in which the confinement is on the molecular-length scale. In this study, we use molecular dynamics simulations and a powerful solvent analysis technique based on inhomogenous solvation theory to investigate the properties of water molecules that solvate the confined regions of protein active sites. Our simulations and analysis indicate that the solvation of protein active sites that are characterized by hydrophobic enclosure and correlated hydrogen bonds induce atypical entropic and enthalpic penalties of hydration. These penalties apparently stabilize the protein-ligand complex with respect to the independently solvated ligand and protein, which leads to enhanced binding affinities. Our analysis elucidates several challenging cases, including the super affinity of the streptavidin-biotin system.

Mapping the Free Energy of Lithium Solvation in the Protic Ionic Liquid Ethylammonuim Nitrate: A Metadynamics Study.

PubMed

Kachmar, Ali; Carignano, Marcelo; Laino, Teodoro; Iannuzzi, Marcella; Hutter, Jürg

2017-08-10

Understanding lithium solvation and transport in ionic liquids is important due to their possible application in electrochemical devices. Using first-principles simulations aided by a metadynamics approach we study the free-energy landscape for lithium ions at infinite dilution in ethylammonium nitrate, a protic ionic liquid. We analyze the local structure of the liquid around the lithium cation and obtain a quantitative picture in agreement with experimental findings. Our simulations show that the lowest two free energy minima correspond to conformations with the lithium ion being solvated either by three or four nitrate ions with a transition barrier between them of 0.2 eV. Other less probable conformations having different solvation pattern are also investigated. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of the composition of a solution on the enthalpies of solvation of piperidine in methanol-acetonitrile and dimethylsulfoxide-acetonitrile mixed solvents

NASA Astrophysics Data System (ADS)

Kuz'mina, I. A.; Volkova, M. A.; Sitnikova, K. A.; Sharnin, V. A.

2014-01-01

Heat effects of dissolution of piperidine (ppd) are measured by calorimetry at 298.15 K over the range of composition of acetonitrile-methanol (AN-MeOH) mixed solvents. Based on the Δsol H ○(ppd)AN-MeOH values obtained using the literature data on Δsol H ○ (ppd) in acetonitrile-dimethylsulfoxide (AN-DMSO) mixed solvents and the vaporization enthalpy of ppd, the enthalpies of solvation of amine in AN-MeOH and AN-DMSO binary mixtures are calculated. A rise in the exothermicity of solvation of piperidine is observed upon the transition from AN to DMSO and MeOH, due mainly to the enhanced solvation of the amino group of ppd as a result of changes in the acid-base properties of the mixed solvent.

Electrostatic Solvation Free Energy of Amino Acid Side Chain Analogs: Implications for the Validity of Electrostatic Linear Response in Water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Bin; Pettitt, Bernard M.

Electrostatic free energies of solvation for 15 neutral amino acid side chain analogs are computed. We compare three methods of varying computational complexity and accuracy for three force fields: free energy simulations, Poisson-Boltzmann (PB), and linear response approximation (LRA) using AMBER, CHARMM, and OPLSAA force fields. We find that deviations from simulation start at low charges for solutes. The approximate PB and LRA produce an overestimation of electrostatic solvation free energies for most of molecules studied here. These deviations are remarkably systematic. The variations among force fields are almost as large as the variations found among methods. Our study confirmsmore » that success of the approximate methods for electrostatic solvation free energies comes from their ability to evaluate free energy differences accurately.« less

Picosecond solvation dynamics—A potential viewer of DMSO—Water binary mixtures

NASA Astrophysics Data System (ADS)

Banik, Debasis; Kundu, Niloy; Kuchlyan, Jagannath; Roy, Arpita; Banerjee, Chiranjib; Ghosh, Surajit; Sarkar, Nilmoni

2015-02-01

In this work, we have investigated the composition dependent anomalous behavior of dimethyl sulfoxide (DMSO)-water binary mixture by collecting the ultrafast solvent relaxation response around a well known solvation probe Coumarin 480 (C480) by using a femtosecond fluorescence up-conversion spectrometer. Recent molecular dynamics simulations have predicted two anomalous regions of DMSO-water binary mixture. Particularly, these studies encourage us to investigate the anomalies from experimental background. DMSO-water binary mixture has repeatedly given evidences of its dual anomalous nature in front of our systematic investigation through steady-state and time-resolved measurements. We have calculated average solvation times of C480 by two individual well-known methods, among them first one is spectral-reconstruction method and another one is single-wavelength measurement method. The results of both the methods roughly indicate that solvation time of C480 reaches maxima in the mole fraction of DMSO XD = 0.12-0.17 and XD = 0.27-0.35, respectively. Among them, the second region (XD = 0.27-0.35) is very common as most of the thermodynamic properties exhibit deviation in this range. Most probably, the anomalous solvation trend in this region is fully guided by the shear viscosity of the medium. However, the first region is the most interesting one. In this region due to formation of strongly hydrogen bonded 1DMSO:2H2O complexes, hydration around the probe C480 decreases, as a result of which solvation time increases.

Octanol-Water Partition Coefficient from 3D-RISM-KH Molecular Theory of Solvation with Partial Molar Volume Correction.

PubMed

Huang, WenJuan; Blinov, Nikolay; Kovalenko, Andriy

2015-04-30

The octanol-water partition coefficient is an important physical-chemical characteristic widely used to describe hydrophobic/hydrophilic properties of chemical compounds. The partition coefficient is related to the transfer free energy of a compound from water to octanol. Here, we introduce a new protocol for prediction of the partition coefficient based on the statistical-mechanical, 3D-RISM-KH molecular theory of solvation. It was shown recently that with the compound-solvent correlation functions obtained from the 3D-RISM-KH molecular theory of solvation, the free energy functional supplemented with the correction linearly related to the partial molar volume obtained from the Kirkwood-Buff/3D-RISM theory, also called the "universal correction" (UC), provides accurate prediction of the hydration free energy of small compounds, compared to explicit solvent molecular dynamics [ Palmer , D. S. ; J. Phys.: Condens. Matter 2010 , 22 , 492101 ]. Here we report that with the UC reparametrized accordingly this theory also provides an excellent agreement with the experimental data for the solvation free energy in nonpolar solvent (1-octanol) and so accurately predicts the octanol-water partition coefficient. The performance of the Kovalenko-Hirata (KH) and Gaussian fluctuation (GF) functionals of the solvation free energy, with and without UC, is tested on a large library of small compounds with diverse functional groups. The best agreement with the experimental data for octanol-water partition coefficients is obtained with the KH-UC solvation free energy functional.

Investigation of Wyoming Bentonite Hydration in Dry to Water-Saturated Supercritical CH4 and CH4/CO2 Mixtures: Implications for CO2-Enhanced Gas Production

NASA Astrophysics Data System (ADS)

Loring, J.

2015-12-01

Injection of CO2 into low permeability shale formations leads to additional gas recovery and reduces the flux of CO2 into the atmosphere, thus combining a strong economic incentive with a permanent storage option for CO2. Reduced formation transmissivity due to clay swelling is a concern in CO2-enhanced gas production. Clay minerals partly determine the physical (i.e. permeability, brittleness) and certain chemical properties (i.e. wetting ability, gas adsorption) of shales, and montmorillonites are of particular interest because they swell by the uptake of species in their interlayer. In this study, the hydration and expansion of Na-, Cs-, and NH4+-saturated montmorillonite (Na-, Cs-, and NH4-SWy-2) in high-pressure (90 bar) and moderate temperature (50 °C) methane, carbon dioxide, and CO2/CH4 mixtures (3 and 25 mole% CO2) were investigated using in situ IR spectroscopic titrations, in situ XRD, in situ MAS-NMR, and ab initio electronic structure calculations. The overarching goal was to better understand the hydration/expansion behavior of Na-SWy-2 in CO2/CH4 fluid mixtures by comparison to Cs-, and NH4+-saturated clays. Specific aims were to (1) determine if CH4 intercalates the clays, (2) probe the effects of increasing dissolved CO2 and H2O concentrations, and (3) understand the role of cation solvation by H2O and/or CO2. In pure CH4, no evidence of CH4 intercalation was detected by IR for any of the clays. Similarly, no measurable changes to the basal spacing were observed by XRD in the presence of pure CH4. However, when dry Cs- and NH4-SWy-2 were exposed to dry fluids containing CO2, IR showed maximum CO2 penetrated the interlayer, XRD indicated the clays expanded, and NMR showed evidence for cation solvation by CO2, in line with theoretical predictions. IR titration of these clays with water showed sorbed H2O concentrations decreased with increasing dissolved CO2, suggesting competition for interlayer residency by CO2 and H2O. For Na-SWy-2, on the other hand, CO2 intercalated the clay and was at a maximum only after a minimum sorbed H2O was achieved. Further increases in sorbed H2O led to displacement of intercalated CO2. These findings demonstrate that complicated H2O and CO2 intercalation processes could lead to permeability changes that directly impact methane transmissivity in shales.

Layered Lepidocrocite Type Structure Isolated by Revisiting the Sol–Gel Chemistry of Anatase TiO 2 : A New Anode Material for Batteries

DOE PAGES

Ma, Jiwei; Reeves, Kyle G.; Porras Gutierrez, Ana-Gabriela; ...

2017-09-19

Searches for new electrode materials for batteries must comply on financial and environmental costs to be useful in practical devices. The sol-gel chemistry has been widely used to design and implemented new concepts for the emergence of advanced materials such as hydride organic-inorganic composites. Here, we show that the simple reaction system including titanium alkoxide and water can be used to stabilize a new class of electrode materials. By investigating the crystallization path of anatase TiO2, an X-ray amorphous intermediate phase has been identified whose local structure probed by the pair distribution function, 1H solid-state NMR and DFT calculations, consistsmore » of a layered-type structure as found in the lepido-crocite. This phase presents the following general formula Ti 2-x⟂ xO 4-4x(OH) 4x.nH 2O (x ~ 0.5) where the substitution of oxide by hydroxide anions leads to the formation of titanium vacancies (•) and H 2O molecules are located in interlayers. Solid-state 1H NMR has enabled to characterize three main hydroxide environments that are Ti⟂-OH, Ti 2⟂ 2-OH and Ti3⟂-OH and layered H 2O molecules. The electrochemical properties of this phase were further investigated versus lithium and is shown to be very promising with reversible capacities of around 200 mAh.g -1 and an operating voltage of 1.55 V. We further showed that the lithium intercalation proceeds via a solid-solution mechanism. 7Li solid-state NMR and DFT calculations allowed to identify lithium host sites that are located at the titanium vacancies and interlayer space with lithium being solvated by structural water molecules. The easy fabrication, the absence of lithium and easier recycling and the encouraging properties makes this class of materials very attractive for competitive electrodes for batteries. We thus demonstrate that the revisit of an “old” chemistry with advanced characterization tools allows discovering new materials of technological relevance.« less

Layered Lepidocrocite Type Structure Isolated by Revisiting the Sol–Gel Chemistry of Anatase TiO 2 : A New Anode Material for Batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Jiwei; Reeves, Kyle G.; Porras Gutierrez, Ana-Gabriela

Searches for new electrode materials for batteries must comply on financial and environmental costs to be useful in practical devices. The sol-gel chemistry has been widely used to design and implemented new concepts for the emergence of advanced materials such as hydride organic-inorganic composites. Here, we show that the simple reaction system including titanium alkoxide and water can be used to stabilize a new class of electrode materials. By investigating the crystallization path of anatase TiO2, an X-ray amorphous intermediate phase has been identified whose local structure probed by the pair distribution function, 1H solid-state NMR and DFT calculations, consistsmore » of a layered-type structure as found in the lepido-crocite. This phase presents the following general formula Ti 2-x⟂ xO 4-4x(OH) 4x.nH 2O (x ~ 0.5) where the substitution of oxide by hydroxide anions leads to the formation of titanium vacancies (•) and H 2O molecules are located in interlayers. Solid-state 1H NMR has enabled to characterize three main hydroxide environments that are Ti⟂-OH, Ti 2⟂ 2-OH and Ti3⟂-OH and layered H 2O molecules. The electrochemical properties of this phase were further investigated versus lithium and is shown to be very promising with reversible capacities of around 200 mAh.g -1 and an operating voltage of 1.55 V. We further showed that the lithium intercalation proceeds via a solid-solution mechanism. 7Li solid-state NMR and DFT calculations allowed to identify lithium host sites that are located at the titanium vacancies and interlayer space with lithium being solvated by structural water molecules. The easy fabrication, the absence of lithium and easier recycling and the encouraging properties makes this class of materials very attractive for competitive electrodes for batteries. We thus demonstrate that the revisit of an “old” chemistry with advanced characterization tools allows discovering new materials of technological relevance.« less

Interaction Between Cyanine Dye IR-783 and Polystyrene Nanoparticles in Solution.

PubMed

Zhang, Yunzhi; Xu, Hui; Casabianca, Leah B

2018-05-17

The interactions between small molecule drugs or dyes and nanoparticles are important to the use of nanoparticles in medicine. Noncovalent adsorption of dyes on nanoparticle surfaces is also important to the development of nanoparticle dual-use imaging contrast agents. In the present work, solution-state NMR is used to examine the noncovalent interaction between a near-infrared cyanine dye and the surface of polystyrene nanoparticles in solution. Using 1D proton NMR, we can approximate the number of dye molecules that associate with each nanoparticle for different sized nanoparticles. Saturation-Transfer Difference (STD)-NMR was also used to show that protons near the positively-charged nitrogen in the dye are more strongly associated with the negatively-charged nanoparticle surface than protons near the negatively-charged sulfate groups of the dye. The methods described here can be used to study similar drug or dye molecules interacting with the surface of organic nanoparticles. This article is protected by copyright. All rights reserved.

Fluorescent probe studies of polarity and solvation within room temperature ionic liquids: a review.

PubMed

Pandey, Shubha; Baker, Sheila N; Pandey, Siddharth; Baker, Gary A

2012-09-01

Ionic liquids display an array of useful and sometimes unconventional, solvent features and have attracted considerable interest in the field of green chemistry for the potential they hold to significantly reduce environmental emissions. Some of these points have a bearing on the chemical reactivity of these systems and have also generated interest in the physical and theoretical aspects of solvation in ionic liquids. This review presents an introduction to the field of ionic liquids, followed by discussion of investigations into the solvation properties of neat ionic liquids or mixed systems including ionic liquids as a major or minor component. The ionic liquid based multicomponent systems discussed are composed of other solvents, other ionic liquids, carbon dioxide, surfactants or surfactant solutions. Although we clearly focus on fluorescence spectroscopy as a tool to illuminate ionic liquid systems, the issues discussed herein are of general relevance to discussions of polarity and solvent effects in ionic liquids. Transient solvation measurements carried out by means of time-resolved fluorescence measurements are particularly powerful for their ability to parameterize the kinetics of the solvation process in ionic liquids and are discussed as well.

Evaluation of DNA Force Fields in Implicit Solvation

PubMed Central

Gaillard, Thomas; Case, David A.

2011-01-01

DNA structural deformations and dynamics are crucial to its interactions in the cell. Theoretical simulations are essential tools to explore the structure, dynamics, and thermodynamics of biomolecules in a systematic way. Molecular mechanics force fields for DNA have benefited from constant improvements during the last decades. Several studies have evaluated and compared available force fields when the solvent is modeled by explicit molecules. On the other hand, few systematic studies have assessed the quality of duplex DNA models when implicit solvation is employed. The interest of an implicit modeling of the solvent consists in the important gain in the simulation performance and conformational sampling speed. In this study, respective influences of the force field and the implicit solvation model choice on DNA simulation quality are evaluated. To this end, extensive implicit solvent duplex DNA simulations are performed, attempting to reach both conformational and sequence diversity convergence. Structural parameters are extracted from simulations and statistically compared to available experimental and explicit solvation simulation data. Our results quantitatively expose the respective strengths and weaknesses of the different DNA force fields and implicit solvation models studied. This work can lead to the suggestion of improvements to current DNA theoretical models. PMID:22043178

Crystal structure and physicochemical characterization of ambazone monohydrate, anhydrous, and acetate salt solvate.

PubMed

Muresan-Pop, Marieta; Braga, Dario; Pop, Mihaela M; Borodi, Gheorghe; Kacso, Irina; Maini, Lucia

2014-11-01

The crystal structures of the monohydrate and anhydrous forms of ambazone were determined by single-crystal X-ray diffraction (SC-XRD). Ambazone monohydrate is characterized by an infinite three-dimensional network involving the water molecules, whereas anhydrous ambazone forms a two-dimensional network via hydrogen bonds. The reversible transformation between the monohydrate and anhydrous forms of ambazone was evidenced by thermal analysis, temperature-dependent X-ray powder diffraction and accelerated stability at elevated temperature, and relative humidity (RH). Additionally, a novel ambazone acetate salt solvate form was obtained and its nature was elucidated by SC-XRD. Powder dissolution measurements revealed a substantial solubility and dissolution rate improvement of acetate salt solvated form in water and physiological media compared with ambazone forms. Also, the acetate salt solvate displayed good thermal and solution stability but it transformed to the monohydrate on storage at elevated temperature and RH. Our study shows that despite the requirement for controlled storage conditions, the acetate salt solvated form could be an alternative to ambazone when solubility and bioavailability improvement is critical for the clinical efficacy of the drug product. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Ion solvation in polymer blends and block copolymer melts: effects of chain length and connectivity on the reorganization of dipoles.

PubMed

Nakamura, Issei

2014-05-29

We studied the thermodynamic properties of ion solvation in polymer blends and block copolymer melts and developed a dipolar self-consistent field theory for polymer mixtures. Our theory accounts for the chain connectivity of polymerized monomers, the compressibility of the liquid mixtures under electrostriction, the permanent and induced dipole moments of monomers, and the resultant dielectric contrast among species. In our coarse-grained model, dipoles are attached to the monomers and allowed to rotate freely in response to electrostatic fields. We demonstrate that a strong electrostatic field near an ion reorganizes dipolar monomers, resulting in nonmonotonic changes in the volume fraction profile and the dielectric function of the polymers with respect to those of simple liquid mixtures. For the parameter sets used, the spatial variations near an ion can be in the range of 1 nm or larger, producing significant differences in the solvation energy among simple liquid mixtures, polymer blends, and block copolymers. The solvation energy of an ion depends substantially on the chain length in block copolymers; thus, our theory predicts the preferential solvation of ions arising from differences in chain length.

Synthesis and characterization of dihexyldithiocarbamate as a chelating agent in extraction of gold(III)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fatimah, Soja Siti, E-mail: soja-sf@upi.edu; Department of Chemistry, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Jl. Raya Bandung-Sumedang, Km. 21, Jatinangor; Bahti, Husein H.

2016-02-08

The use of dialkyldithiocarbamates as chelating agents of transition metals have been developing for decades. Many chelating agents have been synthesized and used in the extraction of the metals. Studies on particular aspects of extraction of the metals, such as the effect of increasing hydrophobicity of chelating agents on the effectiveness of the extraction, have been done. However, despite the many studies on the synthesis and applications of this type of chelating agents, interests in the aspect of molecular structure of the synthesized ligands and of their complexes, have been limited. This study aimed at synthesizing and characterizing dihexylthiocarbamate, andmore » using the ligand for the extraction of gold III). Characterization of the ligand and of its metal complex were done by using elemental analysis, DTG, and spectroscopic methods to include NMR, ({sup 1}H, and {sup 13}C), FTIR, and MS-ESI. Data on the synthesis, characterization, and the application of the ligand as a chelating agent are presented.« less

Synthesis and characterization of dihexyldithiocarbamate as a chelating agent in extraction of gold(III)

NASA Astrophysics Data System (ADS)

Fatimah, Soja Siti; Bahti, Husein H.; Hastiawan, Iwan; Permanasari, Anna

2016-02-01

The use of dialkyldithiocarbamates as chelating agents of transition metals have been developing for decades. Many chelating agents have been synthesized and used in the extraction of the metals. Studies on particular aspects of extraction of the metals, such as the effect of increasing hydrophobicity of chelating agents on the effectiveness of the extraction, have been done. However, despite the many studies on the synthesis and applications of this type of chelating agents, interests in the aspect of molecular structure of the synthesized ligands and of their complexes, have been limited. This study aimed at synthesizing and characterizing dihexylthiocarbamate, and using the ligand for the extraction of gold III). Characterization of the ligand and of its metal complex were done by using elemental analysis, DTG, and spectroscopic methods to include NMR, (1H, and 13C), FTIR, and MS-ESI. Data on the synthesis, characterization, and the application of the ligand as a chelating agent are presented.

NMR Microscopy - Micron-Level Resolution.

NASA Astrophysics Data System (ADS)

Kwok, Wing-Chi Edmund

1990-01-01

Nuclear Magnetic Resonance Imaging (MRI) has been developed into a powerful and widely used diagnostic tool since the invention of techniques using linear magnetic field gradients in 1973. The variety of imaging contrasts obtainable in MRI, such as spin density, relaxation times and flow rate, gives MRI a significant advantage over other imaging techniques. For common diagnostic applications, image resolutions have been in the order of millimeters with slice thicknesses in centimeters. For many research applications, however, resolutions in the order of tens of microns or smaller are needed. NMR Imaging in these high resolution disciplines is known as NMR microscopy. Compared with conventional microscopy, NMR microscopy has the advantage of being non-invasive and non-destructive. The major obstacles of NMR microscopy are low signal-to-noise ratio and effects due to spin diffusion. To overcome these difficulties, more sensitive RF probes and very high magnetic field gradients have to be used. The most effective way to increase sensitivity is to build smaller probes. Microscope probes of different designs have been built and evaluated. Magnetic field gradient coils that can produce linear field gradients up to 450 Gauss/cm were also assembled. In addition, since microscope probes often employ remote capacitors for RF tuning, the associated signal loss in the transmission line was studied. Imaging experiments have been carried out in a 2.1 Tesla small bore superconducting magnet using the typical two-dimensional spin warp imaging technique. Images have been acquired for both biological and non-biological samples. The highest resolution was obtained in an image of a nerve bundle from the spinal cord of a racoon and has an in-plane resolution of 4 microns. These experiments have demonstrated the potential application of NMR microscopy to pathological research, nervous system study and non -destructive testings of materials. One way to further improve NMR microscopy is to implement a higher static magnetic field which will increase signal strength. In the future, NMR microscopy should prove to be useful in the studies of cell linings, T1 & T2 relaxation mechanisms and NMR contrast agents.

Added value of lignin as lignin-based hybrid polyurethane for a compatibilizing agent

NASA Astrophysics Data System (ADS)

Ilmiati, S.; Haris Mustafa, J.; Yaumal, A.; Hanum, F.; Chalid, M.

2017-07-01

As biomass-based material, lignin contains abundant hydroxyl groups promising to be used as chain extender in building hybrid polyurethanes. Consisting of polyehtylene glycol (PEG) content as hydrophobic part and lignin as hydrophilic part, the hybrid PU is expected to be as a novel compatibilizing agent in new materials production such as polyblends and composites. The hybrid PU was synthesized via two reaction stages, viz. pre-polyurethanization through reacting 4,4'-Methylenebis (Cyclohexyl Isocyanate) (HMDI) and PEG as polyol, and chain extention through adding lignin in the pre-polyurethanization system. The composition effect of lignin in hybrid PU syntehsis, to chemical structure corelated to hydrophobic to hydrophilic ratio, thermal and morphological properties, was evaluated by measuring NMR, FTIR, DSC, TGA and FE-SEM. The experiments showed that addition of lignin was able to extend the pre-polyurethane into hybrid polyurethane and to increase the lignin/polyol ratio in the hybrid polyurethanes, which were indicated by NMR and FTIR Analysis. And change of the ratio lead to increase the glass transition from 60.9 until 62.1°C and degradation temperature from 413.9 until 416.0°C. Observation of the morphology implied that addition of lignin gave more agglomerations. A Further investigation for this characterization study should be focused on a feasibility for this modified lignin as a novel compatibilizing agent.

Systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cooks, Robert Graham; Li, Anyin; Luo, Qingjie

The invention generally relates to systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions. In certain aspects, the invention provides methods that involve providing a metal and a solvent. The methods additionally involve applying voltage to the solvated metal to thereby produce solvent droplets including ions of the metal containing compound, and directing the solvent droplets including the metal ions to a target. In certain embodiments, once at the target, the metal ions can react directly or catalyze reactions.

Preferential solvatation of human serum albumin in dimethylsulfoxide-H2O binary solution

NASA Astrophysics Data System (ADS)

Grigoryan, K. R.

2009-12-01

The preferential solvatation of human serum albumin (HSA) in dimethylsulfoxide (DMSO) aqueous solutions were studied using the densitometry method. It has been shown that at DMSO low concentrations HSA undergoes to preferential hydration, but at DMSO higher concentrations preferential binding of DMSO molecules to protein occurs. It has been estimated that DMSO exhibits stabilizing/destabilizing effect on HSA structure which is explained in terms of hydration/solvatation of protein, on the one hand, and the medium structure enhancement/disruption around the protein molecule, on the other hand.

Systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions

DOEpatents

Cooks, Robert Graham; Li, Anyin; Luo, Qingjie

2017-01-24

The invention generally relates to systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions. In certain aspects, the invention provides methods that involve providing a metal and a solvent. The methods additionally involve applying voltage to the solvated metal to thereby produce solvent droplets including ions of the metal containing compound, and directing the solvent droplets including the metal ions to a target. In certain embodiments, once at the target, the metal ions can react directly or catalyze reactions.

Electron Solvation in Two Dimensions

NASA Astrophysics Data System (ADS)

Miller, A. D.; Bezel, I.; Gaffney, K. J.; Garrett-Roe, S.; Liu, S. H.; Szymanski, P.; Harris, C. B.

2002-08-01

Ultrafast two-photon photoemission has been used to study electron solvation at two-dimensional metal/polar-adsorbate interfaces. The molecular motion that causes the excess electron solvation is manifested as a dynamic shift in the electronic energy. Although the initially excited electron is delocalized in the plane of the interface, interactions with the adsorbate can lead to its localization. A method for determining the spatial extent of the localized electron in the plane of the interface has been developed. This spatial extent was measured to be on the order of a single adsorbate molecule.

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

PubMed Central

Marinelli, Fabrizio; Pietrucci, Fabio; Laio, Alessandro; Piana, Stefano

2009-01-01

Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins. Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For the Trp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap. Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at of 4.4 Å from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the and chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data. PMID:19662155

Guest-host interactions in sodium zeolite Y: Structural and dynamical [sup 23]Na double-rotation NMR study of H[sub 2]O, PMe[sub 3], Mo(CO)[sub 6], and Mo(CO)[sub 4](PMe[sub 3])[sub 2] adsorption in Na[sub 56]Y

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jelinek, R.; Oezkar, S.; Malek, A.

1993-01-27

[sup 23]Na double-rotation NMR (DOR) provides site-specific structural and dynamical information on guest-host interactions within sodium zeolite Y pores. Quantitative adsorption of H[sub 2]O, PMe[sub 3], and Mo(CO)[sub 6] guests affects both the positions and line shapes of the [sup 23]Na resonances from specific extraframework Na[sup +] sites. The evolution of the [sup 23]Na DOR spectra with the progressive introduction of guest molecules allows one to probe direct solvation' effects involving the Na[sup +] cations in the larger supercages, as well as indirect effects on the Na[sup +] cations in adjacent smaller sodalite cavities. [sup 23]Na DOR experiments conducted atmore » two magnetic field strengths confirm that PMe[sub 3] coadsorption in 8[l brace]Mo(CO)[sub 6][r brace],16[l brace]PMe[sub 3][r brace]-Na[sub 56]Y, and PMe[sub 3] ligand-substitution in 8[l brace]cis-Mo(CO)[sub 4](PMe[sub 3])[sub 2][r brace]-Na[sub 56]Y give rise to progressive deshielding and enhanced quadrupolar interactions of the anchoring Na[sup +] cations in the [alpha]-cages, relative to those of the starting material, 8[l brace]Mo(CO)[sub 6][r brace]-Na[sub 56]Y. Spin-lattice relaxation measurements indicate that adsorption of PMe[sub 3] facilitates an increased motion of the Na[sup +] cations and/or guest species inside the [alpha]-cages. 22 refs., 6 figs., 1 tab.« less

A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations.

PubMed

Marinelli, Fabrizio; Pietrucci, Fabio; Laio, Alessandro; Piana, Stefano

2009-08-01

Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins.Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For theTrp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap.Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at Calpha-RMSD of 4.4 A from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the Pro12-delta3 and Gly11-alpha3 chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data.

Recent advances in the use of ionic liquids for electrochemical sensing.

PubMed

Silvester, Debbie S

2011-12-07

Ionic Liquids are salts that are liquid at (or just above) room temperature. They possess several advantageous properties (e.g. high intrinsic conductivity, wide electrochemical windows, low volatility, high thermal stability and good solvating ability), which make them ideal as non-volatile electrolytes in electrochemical sensors. This mini-review article describes the recent uses of ionic liquids in electrochemical sensing applications (covering the last 3 years) in the context of voltammetric sensing at solid/liquid, liquid/liquid interfaces and carbon paste electrodes, as well as their use in gas sensing, ion-selective electrodes, and for detecting biological molecules, explosives and chemical warfare agents. A comment on the future direction and challenges in this field is also presented.

Molecular mobility, morphology, and ion conduction in ionomers for electroactive devices

NASA Astrophysics Data System (ADS)

Tudryn, Gregory J.

A sequential study of ion-containing polymers capable of ion solvation with varied ion content, dielectric constant, and counterions is presented in this dissertation in order to compare ion transport properties in ionomers with various ionic interactions. Structure-property relationships in these ion containing polymers are defined using x-ray scattering, rheology and dielectric spectroscopy, enabling the quantification of ion transport dynamics. Poly(ethylene oxide), (PEO) based ionomers are investigated in order to probe the relation between ion conduction and segmental relaxation, and copolymers of PEO and Poly(tetramethylene oxide), (PTMO) further develop an understanding of the trade-off between ion solvation and segmental dynamics. Ionomers with ionic liquid counterions probe diffuse charge interactions and steric effects on ion transport, and incorporation of ionic liquids into ionomer membranes such as Nafion provides desirable thermal and ion conducting properties which extend the use of such membranes for electroactive devices. PEO ionomers exhibit a strong relation between ionic conductivity and segmental dynamics, providing insight that the glass transition temperature, Tg, dominates the ion conduction mechanism. Increasing temperature induces aggregation of ionic groups as evidenced by the static dielectric constant and X-ray scattering as a function of temperature, revealing the contribution of ionic dipoles in the measured dielectric constant. The trade-off between ion solvation and fast polymer segmental dynamics are quantified in copolymer ionomers of PEO and lower Tg PTMO. While conducting ion content remains nearly unchanged, conductivity is lowered upon incorporation of PTMO, because the vast majority of the PTMO microphase separates from the PEO-rich microdomain that remains continuous and contributes most of the ion conduction. Dielectric constants and X-ray scattering show consistent changes with temperature that suggest a cascading aggregation process in Na ionomers as ionic dipoles thermally randomize and lower the measured dielectric constant of the medium, leading to further aggregation. We observe amplified microphase-separation through ionic groups preferentially solvated by PEO chains, as seen in block copolymers with added salt. Even at 25%PEO / 75%PTMO the ionomers have VFT temperature dependence of conducting ion mobility, meaning that the 25% PEO/ion microphase is still continuous A model is developed to describe the frequency dependent storage and loss modulus and the delay in Rouse motion due to ion association lifetime, as functions of ion content and molecular weight for our low molecular weight ionomers. The ion rearrangement relaxation in dielectric spectroscopy is clearly the ion association lifetime that controls terminal dynamics in linear viscoelasticity, allowing a simple sticky Rouse model, using the most-probable distribution based on NMR Mn, to fully describe master curves of the frequency dependent storage and loss modulus. Using insight from ionic interaction strength, ionic liquids are used as counterions, effectively plasticizing the ionomers without added solvent. Ionic interactions were weakened with increasing counterion size, and with modification of cations using ether-oxygen, promoting self-solvation, which increases conducting ion density by an order of magnitude. Room temperature ionic liquids were subsequently used in combination with NafionRTM membranes as electroactive substrates to correlate ion transport to morphology as a function of volume fraction of ionic liquid. This study illuminated the critical volume uptake of ionic liquid in Nafion, identifying percolation of ionic pathways and a significant increase in dielectric constant at low frequencies, indicating an increase in the number density of ions capable of polarizing at the electrode surface. Consequently, the fundamental information obtained about the structure-property relations of ionomers can be used to predict and design advanced ion-containing polymers to be used in battery membranes and a variety of electroactive devices, including actuators and electromechanical sensors.

Evaluating the Free Energies of Solvation and Electronic Structures of Lithium-Ion Battery Electrolytes.

PubMed

Shakourian-Fard, Mehdi; Kamath, Ganesh; Sankaranarayanan, Subramanian K R S

2016-09-19

Adaptive biasing force molecular dynamics simulations and density functional theory calculations were performed to understand the interaction of Li(+) with pure carbonates and ethylene carbonate (EC)-based binary mixtures. The most favorable Li carbonate cluster configurations obtained from molecular dynamics simulations were subjected to detailed structural and thermochemistry calculations on the basis of the M06-2X/6-311++G(d,p) level of theory. We report the ranking of these electrolytes on the basis of the free energies of Li-ion solvation in carbonates and EC-based mixtures. A strong local tetrahedral order involving four carbonates around the Li(+) was seen in the first solvation shell. Thermochemistry calculations revealed that the enthalpy of solvation and the Gibbs free energy of solvation of the Li(+) ion with carbonates are negative and suggested the ion-carbonate complexation process to be exothermic and spontaneous. Natural bond orbital analysis indicated that Li(+) interacts with the lone pairs of electrons on the carbonyl oxygen atom in the primary solvation sphere. These interactions lead to an increase in the carbonyl (C=O) bond lengths, as evidenced by a redshift in the vibrational frequencies [ν(C=O)] and a decrease in the electron density values at the C=O bond critical points in the primary solvation sphere. Quantum theory of atoms in molecules, localized molecular orbital energy decomposition analysis (LMO-EDA), and noncovalent interaction plots revealed the electrostatic nature of the Li(+) ion interactions with the carbonyl oxygen atoms in these complexes. On the basis of LMO-EDA, the strongest attractive interaction in these complexes was found to be the electrostatic interaction followed by polarization, dispersion, and exchange interactions. Overall, our calculations predicted EC and a binary mixture of EC/dimethyl carbonate to be appropriate electrolytes for Li-ion batteries, which complies with experiments and other theoretical results. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure and Dynamics of Solvated Polymers near a Silica Surface: On the Different Roles Played by Solvent.

PubMed

Perrin, Elsa; Schoen, Martin; Coudert, François-Xavier; Boutin, Anne

2018-04-26

Whereas it is experimentally known that the inclusion of nanoparticles in hydrogels can lead to a mechanical reinforcement, a detailed molecular understanding of the adhesion mechanism is still lacking. Here we use coarse-grained molecular dynamics simulations to investigate the nature of the interface between silica surfaces and solvated polymers. We show how differences in the nature of the polymer and the polymer-solvent interactions can lead to drastically different behavior of the polymer-surface adhesion. Comparing explicit and implicit solvent models, we conclude that this effect cannot be fully described in an implicit solvent. We highlight the crucial role of polymer solvation for the adsorption of the polymer chain on the silica surface, the significant dynamics of polymer chains on the surface, and details of the modifications in the structure solvated polymer close to the interface.

Incorporation of the TIP4P water model into a continuum solvent for computing solvation free energy

NASA Astrophysics Data System (ADS)

Yang, Pei-Kun

2014-10-01

The continuum solvent model is one of the commonly used strategies to compute solvation free energy especially for large-scale conformational transitions such as protein folding or to calculate the binding affinity of protein-protein/ligand interactions. However, the dielectric polarization for computing solvation free energy from the continuum solvent is different than that obtained from molecular dynamic simulations. To mimic the dielectric polarization surrounding a solute in molecular dynamic simulations, the first-shell water molecules was modeled using a charge distribution of TIP4P in a hard sphere; the time-averaged charge distribution from the first-shell water molecules were estimated based on the coordination number of the solute, and the orientation distribution of the first-shell waters and the intermediate water molecules were treated as that of a bulk solvent. Based on this strategy, an equation describing the solvation free energy of ions was derived.

Solvation of o-hydroxybenzoic acid in pure and modified supercritical carbon dioxide, according to numerical modeling data

NASA Astrophysics Data System (ADS)

Antipova, M. L.; Gurina, D. L.; Odintsova, E. G.; Petrenko, V. E.

2015-08-01

The dissolution of an elementary fragment of crystal structure (an o-hydroxybenzoic acid ( o-HBA) dimer) in both pure and modified supercritical (SC) carbon dioxide by adding methanol (molar fraction, 0.035) at T = 318 K, ρ = 0.7 g/cm3 is simulated. Features of the solvation mechanism in each solvent are revealed. The solvation of o-HBA in pure SC CO2 is shown to occur via electron donor-acceptor interactions. o-HBA forms a solvate complex in modified SC CO2 through hydrogen bonds between the carboxyl group and methanol. The hydroxyl group of o-HBA participates in the formation of an intramolecular hydrogen bond, and not in interactions with the solvent. It is concluded that the o-HBA-methanol complex is a stable molecular structure, and its lifetime is one order of magnitude higher than those of other hydrogen bonds in fluids.

A shell-resolved analysis of preferential solvation of coffee ingredients in aqueous mixtures of the ionic liquid 1-ethyl-3-methylimidazolium acetate

NASA Astrophysics Data System (ADS)

Zeindlhofer, Veronika; Berger, Magdalena; Steinhauser, Othmar; Schröder, Christian

2018-05-01

Ionic liquids increase the solubility of various coffee ingredients in aqueous solution but little is known about the underlying mechanism. Kirkwood-Buff integrals as well as the potential of mean force indicate that the imidazolium cations are accumulated at the surface of the solutes, removing water molecules from the solute surface. Although hydrogen bonding of the anions to hydroxy groups of the solutes can be detected, their concentration at the surface is less enhanced compared to the cations. The decomposition into solvation shells by Voronoi tessellation reveals that structural features are only observed in the first solvation shell. Nevertheless, the depletion of water and the excess concentration of the ions and, in particular, of the cations are visible in the next solvation shells as well. Therefore, classical arguments of hydrotropic theory fail to explain this behavior.

Water-enhanced solvation of organic solutes in ketone and ester solvents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, J.H.; Brunt, V. van; King, C.J.

1994-05-01

Previous research has shown that the solubilities of dicarboxylic acids in certain electron-donor solvents are substantially increased in the presence of water. Information on solubilities, liquid-liquid equilibria and maximum-boiling ternary azeotropes was screened so as to identify other systems where codissolved water appears to enhance solvation of organic solutes in solvents. Several carboxylic acids, an alcohol, diols, and phenols were selected for examination as solutes in ketone and ester solvents. Effects of water upon solute solubilities and volatilities were measured. Results showed that water-enhanced solvation is greatest for carboxylic acids. Solute activity coefficients decreased by factors of 2--3, 6--8, andmore » 7--10 due to the presence of water for mono-, di and tricarboxylic acids, respectively. Activity coefficients decreased by a factor of about 1.5 for ethanol and 1,2-propanediol as solutes. Water-enhanced solvation of phenols is small, when existent.« less

Photo-illuminated diamond as a solid-state source of solvated electrons in water for nitrogen reduction.

PubMed

Zhu, Di; Zhang, Linghong; Ruther, Rose E; Hamers, Robert J

2013-09-01

The photocatalytic reduction of N₂ to NH₃ is typically hampered by poor binding of N₂ to catalytic materials and by the very high energy of the intermediates involved in this reaction. Solvated electrons directly introduced into the reactant solution can provide an alternative pathway to overcome such limitations. Here we demonstrate that illuminated hydrogen-terminated diamond yields facile electron emission into water, thus inducing reduction of N₂ to NH₃ at ambient temperature and pressure. Transient absorption measurements at 632 nm reveal the presence of solvated electrons adjacent to the diamond after photoexcitation. Experiments using inexpensive synthetic diamond samples and diamond powder show that photocatalytic activity is strongly dependent on the surface termination and correlates with the production of solvated electrons. The use of diamond to eject electrons into a reactant liquid represents a new paradigm for photocatalytic reduction, bringing electrons directly to reactants without requiring molecular adsorption to the surface.

Solvation of decane and benzene in mixtures of 1-octanol and N, N-dimethylformamide

NASA Astrophysics Data System (ADS)

Kustov, A. V.; Smirnova, N. L.

2016-09-01

The heats of dissolution of decane and benzene in a model system of octanol-1 (OctOH) and N, N-dimethylformamide (DMF) at 308 K are measured using a variable temperature calorimeter equipped with an isothermal shell. Standard enthalpies are determined and standard heat capacities of dissolution in the temperature range of 298-318 K are calculated using data obtained in [1, 2]. The state of hydrocarbon molecules in a binary mixture is studied in terms of the enhanced coordination model (ECM). Benzene is shown to be preferentially solvated by DMF over the range of physiological temperatures. The solvation shell of decane is found to be strongly enriched with 1-octanol. It is obvious that although both hydrocarbons are nonpolar, the presence of the aromatic π-system in benzene leads to drastic differences in their solvation in a lipid-protein medium.

Solvent effect on the self-assembly of salt solvates of an antihypertensive drug azilsartan and 2-methylimidazole

NASA Astrophysics Data System (ADS)

Zhang, Xian-Rui; Zhang, Lei

2017-06-01

Three salt solvates of azilsartan (AZ) with 2-methylimidazole (2MI) (namely AZ-2MI-H2O, AZ-2MI-ACE and AZ-2MI-THF) and one azilsartan solvate (AZ-DIO, ACE = acetone, THF = tetrahydrofuran, and DIO = 1,4-dioxane) were manufactured by solvent-controlled self-assembly in aqueous-organic solutions. The experimental result of AZ-DIO shows that AZ is high affinity to DIO molecule, which has a unique ability to prevent salt formation between AZ and 2MI. Thermal studies of three salt solvates exhibit poor thermodynamic stability in environmental conditions. Solubility experiments show that AZ-2MI-ACE and AZ-2MI-THF are unstable and convert to AZ-2MI-H2O in aqueous solution, and that AZ-2MI-H2O exhibits increased solubility and retention stability in an aqueous medium compared with the commercial AZ-A crystalline form.

Phase Transition of Poly(acrylic acid-co-N-isopropylacrylamide) Core-shell Nanogels

NASA Astrophysics Data System (ADS)

Liu, Xiao-bing; Zhou, Jian-feng; Ye, Xiao-dong

2012-08-01

A series of poly(acrylic acid) macromolecular chain transfer agents with different molecular weights were synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization and characterized by 1H NMR and gel permeation chromatography. Multiresponsive core-shell nanogels were prepared by dispersion polymerization of N-isopropylacrylamide in water using these poly(potassium acrylate) macro-RAFT agents as the electrosteric stabilizer. The size of the nanogels decreases with the amount of the macro-RAFT agent, indicating that the surface area occupied by per polyelectrolyte group is a critical parameter for stabilizing the nanogels. The volume phase transition and the zeta potentials of the nanogels in aqueous solutions were studied by dynamic light scattering and zetasizer analyzer, respectively.

Competitive lithium solvation of linear and cyclic carbonates from quantum chemistry

DOE PAGES

Kent, Paul R. C.; Ganesh, Panchapakesan; Borodin, Oleg; ...

2015-11-17

The composition of the lithium cation (Li+) solvation shell in mixed linear and cyclic carbonate-based electrolytes has been re-examined using Born–Oppenheimer molecular dynamics (BOMD) as a function of salt concentration and cluster calculations with ethylene carbonate:dimethyl carbonate (EC:DMC)–LiPF 6 as a model system. A coordination preference for EC over DMC to a Li+ was found at low salt concentrations, while a slightly higher preference for DMC over EC was found at high salt concentrations. Analysis of the relative binding energies of the (EC) n(DMC) m–Li+ and (EC) n(DMC) m–LiPF 6 solvates in the gas-phase and for an implicit solvent (asmore » a function of the solvent dielectric constant) indicated that the DMC-containing Li+ solvates were stabilized relative to (EC 4)–Li+ and (EC) 3–LiPF 6 by immersing them in the implicit solvent. Such stabilization was more pronounced in the implicit solvents with a high dielectric constant. Results from previous Raman and IR experiments were reanalyzed and reconciled by correcting them for changes of the Raman activities, IR intensities and band shifts for the solvents which occur upon Li+ coordination. After these correction factors were applied to the results of BOMD simulations, the composition of the Li+ solvation shell from the BOMD simulations was found to agree well with the solvation numbers extracted from Raman experiments. Finally, the mechanism of the Li+ diffusion in the dilute (EC:DMC)LiPF 6 mixed solvent electrolyte was studied using the BOMD simulations.« less

Ions in water: Free energies, surface effects, and geometrical constraints

NASA Astrophysics Data System (ADS)

Herce, Henry David

In this work, we present our results for ion solvation in finite and infinite water clusters. Molecular Dynamic simulations are used to connect the fundamental macroscopic quantities such as free energy, internal energy and entropy with the underlying microscopic description. Molecular dynamics studies complement experimental results and lead to a deeper insight into the solvation and diffusion of ionic species. Beyond its intrinsic interest, the ion solvation problem has practical relevance because of its role as ideal model system with which to construct and test ion-water interaction potentials. The ionic charging free energy is a very sensitive probe for the treatment of electrostatics in any given simulation setting. In this work, we present methods to compute the ionic charging free energy in systems characterized by atomic charges, and higher-order multipoles, mainly dipoles and quadrupoles. The results of these methods under periodic boundary conditions and spherical boundary conditions are then compared. For the treatment of spherical boundary conditions, we introduce a generalization of Gauss' law that links the microscopic variables to the relevant thermodynamic quantities. Ionic solvation in finite clusters is a problem relevant for many areas of chemistry and biology, such as the gas-liquid interface of tropospheric aerosol particles, or the interphase between water and proteins, membranes, etc. Careful evaluations of the free energy, internal energy and entropy are used to address controversial or unresolved issues, related to the underlying physical cause of surface solvation, and the basic assumptions that go with it. Our main conclusions are the following: (i) The main cause of surface solvation of a single ion in a water cluster is both water and ion polarization, coupled to the charge and size of the ion. Interestingly, the total energy of the ion increases near the cluster surface, while the total energy of water decreases. Also, our analysis clearly shows that the cause of surface solvation is not the size of the total water dipole (unless this is too small). (ii) The entropic contribution is the same order of magnitude as the energetic contribution, and therefore cannot be neglected for quantitative results. (iii) A pure energetic analysis can give a qualitative description of the ion position at room temperature. (iv) We have observed surface solvation of a large positive iodine-like ion in a polarizable water cluster, but not in a non-polarizable water cluster.

Theoretical DFT, vibrational and NMR studies of benzimidazole and alkyl derivatives

NASA Astrophysics Data System (ADS)

Infante-Castillo, Ricardo; Rivera-Montalvo, Luis A.; Hernández-Rivera, Samuel P.

2008-04-01

Benzimidazoles are heterocyclic compounds that have awaked great interest during the last few years because of their proven biological activity as antiviral, antimicrobial, and antitumoral agents. For this reason, the development of a systematic FT-IR, FT-Raman and NMR study of 1-substituted compounds in 2-methylbenzimidazole constitutes a significant tool in understanding the molecular dynamics and the structural parameters that govern their behavior. Two new 1-alkyl-2-methylbenzimidazoles compounds were synthesized from reaction of 2-methylbenzimidazole with primary and secondary alkyl halides using a strong base as a catalyst. These compounds were purified and characterized by elemental analysis and different spectroscopic methods. The comparative analysis of vibrational modes of benzimidazole and its alkyl derivatives show that regions of absorption are very similar in all of them. However, changes are produced at low frequencies specifically in the C-H out of plane deformations, ring breathing and ring skeletal vibrations. The ring out-of plane bending modes shift by 10-15 cm -1 in some cases as results of alkyl substitution. The theoretical calculated spectra, using Density Functional Theory (DFT) approximation, and experimental results were consistent with each other. The GIAO method was used to calculate absolute shieldings, which agree consistently with those measured by 1H and 13C NMR. The consistency and efficiency of the GIAO 13C and 1H NMR calculations were thoroughly checked by the analysis of statistical parameters concerning computed and experimental 13C and 1H NMR chemical shift values of the studied compounds.

Cryptophane Nanoscale Assemblies Expand 129Xe NMR Biosensing.

PubMed

Zemerov, Serge D; Roose, Benjamin W; Greenberg, Mara L; Wang, Yanfei; Dmochowski, Ivan J

2018-06-19

Cryptophane-based biosensors are promising agents for the ultrasensitive detection of biomedically relevant targets via 129 Xe NMR. Dynamic light scattering revealed that cryptophanes form water-soluble aggregates tens to hundreds of nanometers in size. Acridine orange fluorescence quenching assays allowed quantitation of the aggregation state, with critical concentrations ranging from 200 nM to 600 nM, depending on the cryptophane species in solution. The addition of excess carbonic anhydrase (CA) protein target to a benzenesulfonamide-functionalized cryptophane biosensor (C8B) led to C8B disaggregation and produced the expected 1:1 C8B-CA complex. C8B showed higher affinity at 298 K for the cytoplasmic isozyme CAII than the extracellular CAXII isozyme, which is a biomarker of cancer. Using hyper-CEST NMR, we explored the role of stoichiometry in detecting these two isozymes. Under CA-saturating conditions, we observed that isozyme CAII produces a larger 129 Xe NMR chemical shift change (δ = 5.9 ppm, relative to free biosensor) than CAXII (δ = 2.7 ppm), which indicates the strong potential for isozyme-specific detection. However, stoichiometry-dependent chemical shift data indicated that biosensor disaggregation contributes to the observed 129 Xe NMR chemical shift change that is normally assigned to biosensor-target binding. Finally, we determined that monomeric cryptophane solutions improve hyper-CEST saturation contrast, which enables ultrasensitive detection of biosensor-protein complexes. These insights into cryptophane-solution behavior support further development of xenon biosensors, but will require reinterpretation of the data previously obtained for many water-soluble cryptophanes.

Interaction of collagen with chlorosulphonated paraffin tanning agents: Fourier transform infrared spectroscopic analysis and molecular dynamics simulations.

PubMed

Monti, Susanna; Bramanti, Emilia; Della Porta, Valentina; Onor, Massimo; D'Ulivo, Alessandro; Barone, Vincenzo

2013-09-21

The binding of chlorosulphonated paraffins to collagen triple helices is studied by means of classical molecular dynamics simulations and experimental spectroscopic techniques in order to disclose the principal characteristics of their interaction during the leather fattening process. Indeed, collagen is the main target to develop new leather modifying agents with specific characteristics, and an accurate design of the collagen binders, supported by predictive computational strategies, could be a successful tool to obtain new effective eco-compatible compounds able to impart to the leather the required functionalities and distinctive mechanical properties. Possible effects caused by the tanning agents on the collagen matrix have been identified from both experimental and theoretical points of view. Computational data in agreement with experiment have revealed that chlorosulphonated paraffins can interact favorably with the collagen residues having amine groups in their side chains (Arg, Lys, Asn and Gln) and reduce the tendency of the solvated collagen matrix to swell. However, the interference of chlorosulphonated paraffins with the unfolding process, which is operated mainly by the action of water, can be due both to covalent cross-linking of the collagen chains and intermolecular hydrogen bonding interactions involving also the hydroxyl groups of Hyp, Ser and Thr residues.

Nuclear magnetic resonance (NMR) study of the effect of cisplatin on the metabolic profile of MG-63 osteosarcoma cells.

PubMed

Duarte, Iola F; Lamego, Ines; Marques, Joana; Marques, M Paula M; Blaise, Benjamin J; Gil, Ana M

2010-11-05

In the present study, (1)H HRMAS NMR spectroscopy was used to assess the changes in the intracellular metabolic profile of MG-63 human osteosarcoma (OS) cells induced by the chemotherapy agent cisplatin (CDDP) at different times of exposure. Multivariate analysis was applied to the cells spectra, enabling consistent variation patterns to be detected and drug-specific metabolic effects to be identified. Statistical recoupling of variables (SRV) analysis and spectral integration enabled the most relevant spectral changes to be evaluated, revealing significant time-dependent alterations in lipids, choline-containing compounds, some amino acids, polyalcohols, and nitrogenated bases. The metabolic relevance of these compounds in the response of MG-63 cells to CDDP treatment is discussed.

Androgen Receptor Antagonists and Anti-Prostate Cancer Activities of Some Newly Synthesized Substituted Fused Pyrazolo-, Triazolo- and Thiazolo-Pyrimidine Derivatives

PubMed Central

Bahashwan, Saleh A.; Fayed, Ahmed A.; Ramadan, Mohamed A.; Amr, Abd El-Galil E.; Al-Harbi, Naif O.

2014-01-01

A series of substituted pyrazole, triazole and thiazole derivatives (2–13) were synthesized from 1-(naphtho[1,2-d]thiazol-2-yl)hydrazine as starting material and evaluated as androgen receptor antagonists and anti-prostate cancer agents. The newly synthesized compounds showed potent androgen receptor antagonists and anti-prostate cancer activities with low toxicity (lethal dose 50 (LD50)) comparable to Bicalutamide as reference drug. The structures of newly synthesized compounds were confirmed by IR, 1H-NMR, 13C-NMR, and MS spectral data and elemental analysis. The detailed synthesis, spectroscopic data, LD50 values and pharmacological activities of the synthesized compounds are reported. PMID:25421248

Acceleration of natural-abundance solid-state MAS NMR measurements on bone by paramagnetic relaxation from gadolinium-DTPA

NASA Astrophysics Data System (ADS)

Mroue, Kamal H.; Zhang, Rongchun; Zhu, Peizhi; McNerny, Erin; Kohn, David H.; Morris, Michael D.; Ramamoorthy, Ayyalusamy

2014-07-01

Reducing the data collection time without affecting the signal intensity and spectral resolution is one of the major challenges for the widespread application of multidimensional nuclear magnetic resonance (NMR) spectroscopy, especially in experiments conducted on complex heterogeneous biological systems such as bone. In most of these experiments, the NMR data collection time is ultimately governed by the proton spin-lattice relaxation times (T1). For over two decades, gadolinium(III)-DTPA (Gd-DTPA, DTPA = Diethylene triamine pentaacetic acid) has been one of the most widely used contrast-enhancement agents in magnetic resonance imaging (MRI). In this study, we demonstrate that Gd-DTPA can also be effectively used to enhance the longitudinal relaxation rates of protons in solid-state NMR experiments conducted on bone without significant line-broadening and chemical-shift-perturbation side effects. Using bovine cortical bone samples incubated in different concentrations of Gd-DTPA complex, the 1H T1 values were calculated from data collected by 1H spin-inversion recovery method detected in natural-abundance 13C cross-polarization magic angle spinning (CPMAS) NMR experiments. Our results reveal that the 1H T1 values can be successfully reduced by a factor of 3.5 using as low as 10 mM Gd-DTPA without reducing the spectral resolution and thus enabling faster data acquisition of the 13C CPMAS spectra. These results obtained from 13C-detected CPMAS experiments were further confirmed using 1H-detected ultrafast MAS experiments on Gd-DTPA doped bone samples. This approach considerably improves the signal-to-noise ratio per unit time of NMR experiments applied to bone samples by reducing the experimental time required to acquire the same number of scans.

Acceleration of natural-abundance solid-state MAS NMR measurements on bone by paramagnetic relaxation from gadolinium-DTPA.

PubMed

Mroue, Kamal H; Zhang, Rongchun; Zhu, Peizhi; McNerny, Erin; Kohn, David H; Morris, Michael D; Ramamoorthy, Ayyalusamy

2014-07-01

Reducing the data collection time without affecting the signal intensity and spectral resolution is one of the major challenges for the widespread application of multidimensional nuclear magnetic resonance (NMR) spectroscopy, especially in experiments conducted on complex heterogeneous biological systems such as bone. In most of these experiments, the NMR data collection time is ultimately governed by the proton spin-lattice relaxation times (T1). For over two decades, gadolinium(III)-DTPA (Gd-DTPA, DTPA=Diethylene triamine pentaacetic acid) has been one of the most widely used contrast-enhancement agents in magnetic resonance imaging (MRI). In this study, we demonstrate that Gd-DTPA can also be effectively used to enhance the longitudinal relaxation rates of protons in solid-state NMR experiments conducted on bone without significant line-broadening and chemical-shift-perturbation side effects. Using bovine cortical bone samples incubated in different concentrations of Gd-DTPA complex, the (1)H T1 values were calculated from data collected by (1)H spin-inversion recovery method detected in natural-abundance (13)C cross-polarization magic angle spinning (CPMAS) NMR experiments. Our results reveal that the (1)H T1 values can be successfully reduced by a factor of 3.5 using as low as 10mM Gd-DTPA without reducing the spectral resolution and thus enabling faster data acquisition of the (13)C CPMAS spectra. These results obtained from (13)C-detected CPMAS experiments were further confirmed using (1)H-detected ultrafast MAS experiments on Gd-DTPA doped bone samples. This approach considerably improves the signal-to-noise ratio per unit time of NMR experiments applied to bone samples by reducing the experimental time required to acquire the same number of scans. Copyright © 2014 Elsevier Inc. All rights reserved.

Modelling the acid/base 1H NMR chemical shift limits of metabolites in human urine.

PubMed

Tredwell, Gregory D; Bundy, Jacob G; De Iorio, Maria; Ebbels, Timothy M D

2016-01-01

Despite the use of buffering agents the 1 H NMR spectra of biofluid samples in metabolic profiling investigations typically suffer from extensive peak frequency shifting between spectra. These chemical shift changes are mainly due to differences in pH and divalent metal ion concentrations between the samples. This frequency shifting results in a correspondence problem: it can be hard to register the same peak as belonging to the same molecule across multiple samples. The problem is especially acute for urine, which can have a wide range of ionic concentrations between different samples. To investigate the acid, base and metal ion dependent 1 H NMR chemical shift variations and limits of the main metabolites in a complex biological mixture. Urine samples from five different individuals were collected and pooled, and pre-treated with Chelex-100 ion exchange resin. Urine samples were either treated with either HCl or NaOH, or were supplemented with various concentrations of CaCl 2 , MgCl 2 , NaCl or KCl, and their 1 H NMR spectra were acquired. Nonlinear fitting was used to derive acid dissociation constants and acid and base chemical shift limits for peaks from 33 identified metabolites. Peak pH titration curves for a further 65 unidentified peaks were also obtained for future reference. Furthermore, the peak variations induced by the main metal ions present in urine, Na + , K + , Ca 2+ and Mg 2+ , were also measured. These data will be a valuable resource for 1 H NMR metabolite profiling experiments and for the development of automated metabolite alignment and identification algorithms for 1 H NMR spectra.

Preparation, spectroscopic and high field NMR relaxometry studies of gadolinium(III) complexes with the asymmetric tetraamine 1,4,7,11-tetraazaundecane

NASA Astrophysics Data System (ADS)

Hatzipanayioti, Despina; Veneris, Antonis

2009-10-01

The reaction of Gd(III) with asymmetric tetramine 1,4,7,11-tetraazaundecane (2,2,3-tet, L1) ligand has been studied via NMR spectroscopy. The ligand proton longitudinal relaxation rates ( R1) have been used to estimate the distances of these protons from the Gd(III) center, in Gd(III)- L1 reaction solutions, in H 2O/D 2O 5/1 mixtures. Two Gd(III) complexes [Gd(III)( L1)(NH 3)(H 2O) 4](CH 3COO) 3·2H 2O ( 1) and [Gd(III)( L1)(NH 3)(H 2O) 2]Cl 3·EtOH ( 2) have been isolated and characterized by elemental analyses, TGA, IR, NMR and relaxometry measurements. The NMR relaxation measurements of 2 in aqueous solutions have been performed, under various temperature or concentration conditions, and compared with those of the commercial contrast agents Gd(III)-DTPA and Gd(III)-DTPA-BMA. It has also been studied the influence of (i) the Gd(III) inner-sphere water molecule number ( q) alteration and (ii) the steric constraint enhancement on the metal site, over the relaxation rate values of the parent aqueous solution of Gd(III)-2,2,3-tet, and of the aqueous solutions of 2.

Synthesis, biological evaluation and molecular modeling of novel series of pyridine derivatives as anticancer, anti-inflammatory and analgesic agents

NASA Astrophysics Data System (ADS)

Helal, M. H.; El-Awdan, S. A.; Salem, M. A.; Abd-elaziz, T. A.; Moahamed, Y. A.; El-Sherif, A. A.; Mohamed, G. A. M.

2015-01-01

This paper presents a combined synthesis; characterization, computational and biological activity studies of novel series of pyridines heterocyclic compounds. The compounds have been characterized by elemental analyses and spectral like IR, 1H NMR, 13C NMR and MS studies. Michael addition of substituted-2-methoxycarbonylacetanilide 2a,b on the α-substituted cinnamonitriles 3a-d gave the corresponding 2-pyridone derivatives 5-10. Structures of the titled compounds cited in this article were elucidated by spectrometric data (IR, 1H NMR, 13C NMR and MS). The molecular modeling of the synthesized compounds has been drawn and their molecular parameters were calculated. Also, valuable information is obtained from the calculation of molecular parameters including electronegativity, net dipole moment of the compounds, total energy, electronic energy, binding energy, HOMO and LUMO energy. Various in vitro antitumor as well as in vivo anti-inflammatory and analgesic activities of the synthesized compounds were investigated. Evaluation of anti-inflammatory activity of test compounds was performed using carrageenan induced paw edema in rats. All the tested compounds showed moderate to good activity. The SAR results indicate that all compounds showed moderate to good activity, among these 7 and 10 compounds having -N(CH3)2 group are most effective.

In vivo quantitative NMR imaging of fruit tissues during growth using Spoiled Gradient Echo sequence.

PubMed

Kenouche, S; Perrier, M; Bertin, N; Larionova, J; Ayadi, A; Zanca, M; Long, J; Bezzi, N; Stein, P C; Guari, Y; Cieslak, M; Godin, C; Goze-Bac, C

2014-12-01

Nondestructive studies of physiological processes in agronomic products require increasingly higher spatial and temporal resolutions. Nuclear Magnetic Resonance (NMR) imaging is a non-invasive technique providing physiological and morphological information on biological tissues. The aim of this study was to design a robust and accurate quantitative measurement method based on NMR imaging combined with contrast agent (CA) for mapping and quantifying water transport in growing cherry tomato fruits. A multiple flip-angle Spoiled Gradient Echo (SGE) imaging sequence was used to evaluate the intrinsic parameters maps M0 and T1 of the fruit tissues. Water transport and paths flow were monitored using Gd(3+)/[Fe(CN)6](3-)/D-mannitol nanoparticles as a tracer. This dynamic study was carried out using a compartmental modeling. The CA was preferentially accumulated in the surrounding tissues of columella and in the seed envelopes. The total quantities and the average volume flow of water estimated are: 198 mg, 1.76 mm(3)/h for the columella and 326 mg, 2.91 mm(3)/h for the seed envelopes. We demonstrate in this paper that the NMR imaging technique coupled with efficient and biocompatible CA in physiological medium has the potential to become a major tool in plant physiology research. Copyright © 2014 Elsevier Inc. All rights reserved.

Recombinant expression of Ixolaris, a Kunitz-type inhibitor from the tick salivary gland, for NMR studies.

PubMed

De Paula, V S; Silva, F H S; Francischetti, I M B; Monteiro, R Q; Valente, A P

2017-11-01

Ixolaris is an anticoagulant protein identified in the tick saliva of Ixodes scapularis. Ixolaris contains 2 Kunitz like domains and binds to Factor Xa or Factor X as a scaffold for inhibition of the Tissue Factor (TF)/Factor VIIa (FVIIa). In contrast to tissue factor pathway inhibitor (TFPI), however, Ixolaris does not bind to the active site cleft of FXa. Instead, complex formation is mediated by the FXa heparin-binding exosite. Due to its potent and long-lasting antithrombotic activity, Ixolaris is a promising agent for anticoagulant therapy. Although numerous functional studies of Ixolaris exist, three-dimensional structure of Ixolaris has not been obtained at atomic resolution. Using the pET32 vector, we successfully expressed a TRX-His 6 -Ixolaris fusion protein. By combining Ni-NTA chromatography, enterokinase protease cleavage, and reverse phase HPLC (RP-HPLC), we purified isotopically labeled Ixolaris for NMR studies. 1D 1 H and 2D 15 N- 1 H NMR analysis yielded high quality 2D 15 N- 1 H HSQC spectra revealing that the recombinant protein is folded. These studies represent the first steps in obtaining high-resolution structural information by NMR for Ixolaris enabling the investigation of the molecular basis for Ixolaris-coagulation factors interactions. Copyright © 2017 Elsevier Inc. All rights reserved.

Solid-state NMR on bacterial cells: selective cell wall signal enhancement and resolution improvement using dynamic nuclear polarization.

PubMed

Takahashi, Hiroki; Ayala, Isabel; Bardet, Michel; De Paëpe, Gaël; Simorre, Jean-Pierre; Hediger, Sabine

2013-04-03

Dynamic nuclear polarization (DNP) enhanced solid-state nuclear magnetic resonance (NMR) has recently emerged as a powerful technique for the study of material surfaces. In this study, we demonstrate its potential to investigate cell surface in intact cells. Using Bacillus subtilis bacterial cells as an example, it is shown that the polarizing agent 1-(TEMPO-4-oxy)-3-(TEMPO-4-amino)propan-2-ol (TOTAPOL) has a strong binding affinity to cell wall polymers (peptidoglycan). This particular interaction is thoroughly investigated with a systematic study on extracted cell wall materials, disrupted cells, and entire cells, which proved that TOTAPOL is mainly accumulating in the cell wall. This property is used on one hand to selectively enhance or suppress cell wall signals by controlling radical concentrations and on the other hand to improve spectral resolution by means of a difference spectrum. Comparing DNP-enhanced and conventional solid-state NMR, an absolute sensitivity ratio of 24 was obtained on the entire cell sample. This important increase in sensitivity together with the possibility of enhancing specifically cell wall signals and improving resolution really opens new avenues for the use of DNP-enhanced solid-state NMR as an on-cell investigation tool.

Solvation thermodynamics of L-cystine, L-tyrosine, and L-leucine in aqueous-electrolyte media

NASA Astrophysics Data System (ADS)

Roy, Sanjay; Guin, Partha Sarathi; Mahali, Kalachand; Dolui, Bijoy Krishna

2017-12-01

Solubilities of L-cystine, L-tyrosine, and L-leucine in aqueous NaCl media at 298.15 K have been studied. Indispensable and related solvent parameters such as molar mass, molar volume, etc., were also determined. The results are used to evaluate the standard transfer Gibbs free energy, cavity forming enthalpy of transfer, cavity forming transfer Gibbs free energy and dipole-dipole interaction effects during the course of solvation. Various weak interactions involving solute-solvent or solvent-solvent molecules were characterized in order to find their role on the solvation of these amino acids.

Phase Equilibria and Ionic Solvation in the Lithium Tetrafluoroborate-Dimethylsulfoxide System

NASA Astrophysics Data System (ADS)

Gafurov, M. M.; Kirillov, S. A.; Gorobets, M. I.; Rabadanov, K. Sh.; Ataev, M. B.; Tretyakov, D. O.; Aydemirov, K. M.

2015-01-01

The phase diagram and electrical conductivity isotherms for the lithium tetrafluoroborate (LiBF4)-dimethylsulfoxide (DMSO) system and Raman spectra of DMSO and the LiBF4-DMSO solution were studied. Spectroscopic signatures of a H-bond between DMSO and BF4 - ions were found. The bonds of Li+ ions to the solvent were stronger than the bonds in DMSO dimers because formation of the solvate destroyed dimeric DMSO molecules. The τω values for DMSO molecules in the Li+-ion solvate shell of the LiBF4-DMSO system were similar to those for associated solvent molecules.

Angle-Resolved Photoemission of Solvated Electrons in Sodium-Doped Clusters.

PubMed

West, Adam H C; Yoder, Bruce L; Luckhaus, David; Saak, Clara-Magdalena; Doppelbauer, Maximilian; Signorell, Ruth

2015-04-16

Angle-resolved photoelectron spectroscopy of the unpaired electron in sodium-doped water, methanol, ammonia, and dimethyl ether clusters is presented. The experimental observations and the complementary calculations are consistent with surface electrons for the cluster size range studied. Evidence against internally solvated electrons is provided by the photoelectron angular distribution. The trends in the ionization energies seem to be mainly determined by the degree of hydrogen bonding in the solvent and the solvation of the ion core. The onset ionization energies of water and methanol clusters do not level off at small cluster sizes but decrease slightly with increasing cluster size.

Predictions of the physicochemical properties of amino acid side chain analogs using molecular simulation.

PubMed

Ahmed, Alauddin; Sandler, Stanley I

2016-03-07

A candidate drug compound is released for clinical trails (in vivo activity) only if its physicochemical properties meet desirable bioavailability and partitioning criteria. Amino acid side chain analogs play vital role in the functionalities of protein and peptides and as such are important in drug discovery. We demonstrate here that the predictions of solvation free energies in water, in 1-octanol, and self-solvation free energies computed using force field-based expanded ensemble molecular dynamics simulation provide good accuracy compared to existing empirical and semi-empirical methods. These solvation free energies are then, as shown here, used for the prediction of a wide range of physicochemical properties important in the assessment of bioavailability and partitioning of compounds. In particular, we consider here the vapor pressure, the solubility in both water and 1-octanol, and the air-water, air-octanol, and octanol-water partition coefficients of amino acid side chain analogs computed from the solvation free energies. The calculated solvation free energies using different force fields are compared against each other and with available experimental data. The protocol here can also be used for a newly designed drug and other molecules where force field parameters and charges are obtained from density functional theory.

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models.

PubMed

Genheden, Samuel

2017-10-01

We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.

Computing pKa Values in Different Solvents by Electrostatic Transformation.

PubMed

Rossini, Emanuele; Netz, Roland R; Knapp, Ernst-Walter

2016-07-12

We introduce a method that requires only moderate computational effort to compute pKa values of small molecules in different solvents with an average accuracy of better than 0.7 pH units. With a known pKa value in one solvent, the electrostatic transform method computes the pKa value in any other solvent if the proton solvation energy is known in both considered solvents. To apply the electrostatic transform method to a molecule, the electrostatic solvation energies of the protonated and deprotonated molecular species are computed in the two considered solvents using a dielectric continuum to describe the solvent. This is demonstrated for 30 molecules belonging to 10 different molecular families by considering 77 measured pKa values in 4 different solvents: water, acetonitrile, dimethyl sulfoxide, and methanol. The electrostatic transform method can be applied to any other solvent if the proton solvation energy is known. It is exclusively based on physicochemical principles, not using any empirical fetch factors or explicit solvent molecules, to obtain agreement with measured pKa values and is therefore ready to be generalized to other solute molecules and solvents. From the computed pKa values, we obtained relative proton solvation energies, which agree very well with the proton solvation energies computed recently by ab initio methods, and used these energies in the present study.

Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

PubMed Central

2012-01-01

Implicit solvation is a mean force approach to model solvent forces acting on a solute molecule. It is frequently used in molecular simulations to reduce the computational cost of solvent treatment. In the first instance, the free energy of solvation and the associated solvent–solute forces can be approximated by a function of the solvent-accessible surface area (SASA) of the solute and differentiated by an atom–specific solvation parameter σiSASA. A procedure for the determination of values for the σiSASA parameters through matching of explicit and implicit solvation forces is proposed. Using the results of Molecular Dynamics simulations of 188 topologically diverse protein structures in water and in implicit solvent, values for the σiSASA parameters for atom types i of the standard amino acids in the GROMOS force field have been determined. A simplified representation based on groups of atom types σgSASA was obtained via partitioning of the atom–type σiSASA distributions by dynamic programming. Three groups of atom types with well separated parameter ranges were obtained, and their performance in implicit versus explicit simulations was assessed. The solvent forces are available at http://mathbio.nimr.mrc.ac.uk/wiki/Solvent_Forces. PMID:23180979

Water Lone Pair Delocalization in Classical and Quantum Descriptions of the Hydration of Model Ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Remsing, Richard C.; Duignan, Timothy T.; Baer, Marcel D.

Understanding the nature of ionic hydration at a fundamental level has eluded scientists despite intense interest for nearly a century. In particular, the microscopic origins of the asymmetry of ion solvation thermodynamics with respect to the sign of the ionic charge remains a mystery. Here, we determine the response of accurate quantum mechanical water models to strong nanoscale solvation forces arising from excluded volumes and ionic electrostatic fields. This is compared to the predictions of two important limiting classes of classical models of water with fixed point changes, differing in their treatment of "lone-pair" electrons. Using the quantum water modelmore » as our standard of accuracy, we find that a single fixed classical treatment of lone pair electrons cannot accurately describe solvation of both apolar and cationic solutes, underlining the need for a more flexible description of local electronic effects in solvation processes. However, we explicitly show that all water models studied respond to weak long-ranged electrostatic perturbations in a manner that follows macroscopic dielectric continuum models, as would be expected. We emphasize the importance of these findings in the context of realistic ion models, using density functional theory and empirical models, and discuss the implications of our results for quantitatively accurate reduced descriptions of solvation in dielectric media.« less

Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation models.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kamerlin, Shina C. L.; Haranczyk, Maciej; Warshel, Arieh

2009-05-01

Phosphate hydrolysis is ubiquitous in biology. However, despite intensive research on this class of reactions, the precise nature of the reaction mechanism remains controversial. In this work, we have examined the hydrolysis of three homologous phosphate diesters. The solvation free energy was simulated by means of either an implicit solvation model (COSMO), hybrid quantum mechanical / molecular mechanical free energy perturbation (QM/MM-FEP) or a mixed solvation model in which N water molecules were explicitly included in the ab initio description of the reacting system (where N=1-3), with the remainder of the solvent being implicitly modelled as a continuum. Here, bothmore » COSMO and QM/MM-FEP reproduce Delta Gobs within an error of about 2kcal/mol. However, we demonstrate that in order to obtain any form of reliable results from a mixed model, it is essential to carefully select the explicit water molecules from short QM/MM runs that act as a model for the true infinite system. Additionally, the mixed models tend to be increasingly inaccurate the more explicit water molecules are placed into the system. Thus, our analysis indicates that this approach provides an unreliable way for modelling phosphate hydrolysis in solution.« less

Aqueous TMAO solutions as seen by theoretical THz spectroscopy: hydrophilic versus hydrophobic water.

PubMed

Imoto, Sho; Forbert, Harald; Marx, Dominik

2018-02-28

Solvation of trimethylamine-N-oxide (TMAO) by water is of great fundamental interest because this small molecule has both strongly hydrophilic and large hydrophobic groups at its opposite ends and, furthermore, stabilizes proteins against temperature and pressure denaturation. Since hydrophilic and hydrophobic groups affect the structural dynamics of the respective solvation water molecules in vastly different ways, we dissect their distinct influences on the THz spectrum of TMAO(aq) by using ab initio molecular dynamics simulations. In particular, we demonstrate that exclusively electronic polarization and charge transfer effects, being absent in the usual fixed-charge biomolecular force fields, are responsible for the significant enhancement of the effective molecular dipole moment of hydrophilic solvation water. This, in turn, leads to pronounced solute-solvent couplings and thus to specific THz modes that involve well-defined H-bond bending and stretching motion being characteristic to hydrophilic solvation. The THz response of individual H-bonded pairs of water molecules involving hydrophobic solvation water, in stark contrast, is nearly indistinguishable from such pairs in bulk water. Transcending the specific case, THz spectroscopy is suggested to be an ideal experimental approach to unravel the controversial piezolytic properties of TMAO including its counteracting effect on pressure-induced denaturation of proteins.

Microcalorimetric study of thermal unfolding of lysozyme in water/glycerol mixtures: An analysis by solvent exchange model

NASA Astrophysics Data System (ADS)

Spinozzi, Francesco; Ortore, Maria Grazia; Sinibaldi, Raffaele; Mariani, Paolo; Esposito, Alessandro; Cinelli, Stefania; Onori, Giuseppe

2008-07-01

Folded protein stabilization or destabilization induced by cosolvent in mixed aqueous solutions has been studied by differential scanning microcalorimetry and related to difference in preferential solvation of native and denatured states. In particular, the thermal denaturation of a model system formed by lysozyme dissolved in water in the presence of the stabilizing cosolvent glycerol has been considered. Transition temperatures and enthalpies, heat capacity, and standard free energy changes have been determined when applying a two-state denaturation model to microcalorimetric data. Thermodynamic parameters show an unexpected, not linear, trend as a function of solvent composition; in particular, the lysozyme thermodynamic stability shows a maximum centered at water molar fraction of about 0.6. Using a thermodynamic hydration model based on the exchange equilibrium between glycerol and water molecules from the protein solvation layer to the bulk, the contribution of protein-solvent interactions to the unfolding free energy and the changes of this contribution with solvent composition have been derived. The preferential solvation data indicate that lysozyme unfolding involves an increase in the solvation surface, with a small reduction of the protein-preferential hydration. Moreover, the derived changes in the excess solvation numbers at denaturation show that only few solvent molecules are responsible for the variation of lysozyme stability in relation to the solvent composition.

Distinctive Solvation Patterns Make Renal Osmolytes Diverse

PubMed Central

Jackson-Atogi, Ruby; Sinha, Prem Kumar; Rösgen, Jörg

2013-01-01

The kidney uses mixtures of five osmolytes to counter the stress induced by high urea and NaCl concentrations. The individual roles of most of the osmolytes are unclear, and three of the five have not yet been thermodynamically characterized. Here, we report partial molar volumes and activity coefficients of glycerophosphocholine (GPC), taurine, and myo-inositol. We derive their solvation behavior from the experimental data using Kirkwood-Buff theory. We also provide their solubility data, including solubility data for scyllo-inositol. It turns out that renal osmolytes fall into three distinct classes with respect to their solvation. Trimethyl-amines (GPC and glycine-betaine) are characterized by strong hard-sphere-like self-exclusion; urea, taurine, and myo-inositol have a tendency toward self-association; sorbitol and most other nonrenal osmolytes have a relatively constant, intermediate solvation that has components of both exclusion and association. The data presented here show that renal osmolytes are quite diverse with respect to their solvation patterns, and they can be further differentiated based on observations from experiments examining their effect on macromolecules. It is expected, based on the available surface groups, that each renal osmolyte has distinct effects on various classes of biomolecules. This likely allows the kidney to use specific combinations of osmolytes independently to fine-tune the chemical activities of several types of molecules. PMID:24209862

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models

NASA Astrophysics Data System (ADS)

Genheden, Samuel

2017-10-01

We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.

A combined variable temperature 600 MHz NMR/MD study of the calcium release agent cyclic adenosine diphosphate ribose (cADPR): Structure, conformational analysis, and thermodynamics of the conformational equilibria.

PubMed

Javornik, Uroš; Plavec, Janez; Wang, Baifan; Graham, Steven M

2018-01-02

A combined variable temperature 600 MHz NMR/molecular dynamics study of the Ca 2+ -release agent cyclic adenosine 5'-diphosphate ribose (cADPR) was conducted. In addition to elucidating the major and minor orientations of the conformationally flexible furanose rings, γ- (C4'-C5'), and β- (C5'-O5') bonds, the thermodynamics (ΔH o , ΔS o ) associated with each of these conformational equilibria were determined. Both furanose rings were biased towards a south conformation (64-74%) and both β-bonds heavily favored trans conformations. The R-ring γ-bond was found to exist almost exclusively as the γ + conformer, whereas the A-ring γ-bond was a mixture of the γ + and γ t conformers, with the trans conformer being slightly favored. Enthalpic factors accounted for most of the observed conformational preferences, although the R-ring furanose exists as its major conformation based solely on entropic factors. There was excellent agreement between the NMR and MD results, particularly with regard to the conformer identities, but the MD showed a bias towards γ + conformers. The MD results showed that both N-glycosidic χ-bonds are exclusively syn. Collectively the data allowed for the construction of a model for cADPR in which many of the conformationally flexible units in fact effectively adopt single orientations and where most of the conformational diversity resides in its A-ring furanose and γ-bond. Copyright © 2017 Elsevier Ltd. All rights reserved.

Grewia gum as a potential aqueous film coating agent. I: Some physicochemical characteristics of fractions of grewia gum

PubMed Central

Ogaji, Ikoni J.; Okafor, Ignatius S.; Hoag, Stephen W.

2013-01-01

Background: Grewia gum has received attention as a polymeric pharmaceutical excipient in the recent times, being employed as a suspending, film coating, mucoadhesive, and binding agent. The low aqueous solubility, however, has limited its characterization and application. Objective: The purpose of this study was to fractionate and evaluate some physicochemical properties of the gum. Materials and Methods: Aqueous dispersion of the gum was treated at 80°C for 30 min in the presence of sodium chloride and was subsequently fractionated by successively centrifuging it at 3445 rpm for 30 min. Skeletal density, solubility, particle size, and rheological as well as thermal characteristics of the fractions were evaluated. The 1H nuclear magnetic resonance (NMR) and near infrared (NIR) profiles of the fractions were also investigated. The solubility of the gum increased up to fourfold while the viscosity decreased from 244 to as low as70 cP at 40 rpm with some fractions. Results: Grewia gum and the fractions showed good thermal stability exhibiting no thermal events, but charred irreversibly at 297°C irrespective of the fraction. The molecular weight averages by weight and by number of the fractions were between 233,100 and 235,000. The 1H nuclear magnetic resonance (NMR) spectra showed broad peaks. The NMR and NIR spectra suggested the presence of –OH and –OCH3 functional groups in this gum. Conclusion: The fractionation improved solubility and facilitated further investigations on its characteristics that may have implication on its processing, application, and optimization as a potential pharmaceutical excipient. PMID:23559825

Semisynthesis and bioactive evaluation of oxidized products from 20(S)-ginsenoside Rg3, Rh2, protopanaxadiol (PPD) and their 20(R)-epimers as cytotoxic agents.

PubMed

Yang, Jie; Li, Xuwen; Sun, Ting; Gao, Yan; Chen, Yanxin; Jin, Yongri; Li, Yang

2016-02-01

A series of oxidized products have been systematically semisynthesized from 20(S)-ginsenoside Rg3, Rh2, 20(S)-protopanaxadiol (PPD) and their 20(R)-epimers and the majority of these products were evaluated for their cytotoxic activity against HeLa cells and HepG2 cells by MTT assay for the first time. Twenty-two products were obtained and elucidated based on comprehensive (1)H NMR, (13)C NMR, two-dimensional (2D) NMR, and mass spectral data and the results reported in previous literature. All the four ocotillol type saponins (20S,24R(δ86, δ85); 20S,24S(δ87, δ88); 20R,24R(δ86, δ86); 20R,24S(δ86, δ87) were obtained. In addition, eight compounds (3, 8, 9, 10, 15, 16, 19 and 22) with the cyclized side chain were firstly identified. Most of the tested compounds possessed cytotoxicity to a certain degree against the two types of cells which implied these oxidized products could play a certain role on anti-cancer functions of the raw materials in vivo. Meanwhile, the results proved that the configurations at C-20 or C-24 and the number of glycosyl at C-3 have important influence on the cytotoxicity. The products 1, 2, 11-17, 20 and 22 should possess great activities and deserved further investigation as potential cytotoxic agents. Copyright © 2015 Elsevier Inc. All rights reserved.

Theoretical Prediction of Am(III)/Eu(III) Selectivity to Aid the Design of Actinide-Lanthanide Separation Agents

DOE PAGES

Bryantsev, Vyacheslav S.; Hay, Benjamin P.

2015-03-20

Selective extraction of minor actinides from lanthanides is a critical step in the reduction of radiotoxicity of spent nuclear fuels. However, the design of suitable ligands for separating chemically similar 4f- and 5f-block trivalent metal ions poses a significant challenge. Furthermore, first-principles calculations should play an important role in the design of new separation agents, but their ability to predict metal ion selectivity has not been systematically evaluated. We examine the ability of several density functional theory methods to predict selectivity of Am(III) and Eu(III) with oxygen, mixed oxygen–nitrogen, and sulfur donor ligands. The results establish a computational method capablemore » of predicting the correct order of selectivities obtained from liquid–liquid extraction and aqueous phase complexation studies. To allow reasonably accurate predictions, it was critical to employ sufficiently flexible basis sets and provide proper account of solvation effects. The approach is utilized to estimate the selectivity of novel amide-functionalized diazine and 1,2,3-triazole ligands.« less

Diethylenetriaminepentaacetic acid-gadolinium (DTPA-Gd)-conjugated polysuccinimide derivatives as magnetic resonance imaging contrast agents.

PubMed

Lee, Ha Young; Jee, Hye Won; Seo, Sung Mi; Kwak, Byung Kook; Khang, Gilson; Cho, Sun Hang

2006-01-01

Biocompatible polysuccinimide (PSI) derivatives conjugated with diethylenetriaminepentaacetic acid gadolinium (DTPA-Gd) were prepared as magnetic resonance imaging (MRI) contrast agents. In this study, we synthesized PSI derivatives incorporating methoxy-poly(ethylene glycol) (mPEG) as hydrophilic ligand, hexadecylamine as hydrophobic ligand, and DTPA-Gd as contrast agent. PSI was synthesized by the polycondensation polymerization of aspartic acid. All the synthesized materials were characterized by proton nuclear magnetic resonance (1H NMR). Critical micellization concentrations were determined using fluorescent probes (pyrene). Micelle size and shape were measured by electro-photometer light scattering (ELS) and atomic force microscopy (AFM). The formed micelle size ranged from 100 to 300 nm. The T1-weighted MR images of the phantom prepared with PSI-mPEG-C16-(DTPA-Gd) were obtained in a 3.0 T clinical MR imager, and the conjugates showed a great potential as MRI contrast agents.

Rapid Catalyst Capture Enables Metal-Free para-Hydrogen-Based Hyperpolarized Contrast Agents.

PubMed

Barskiy, Danila A; Ke, Lucia A; Li, Xingyang; Stevenson, Vincent; Widarman, Nevin; Zhang, Hao; Truxal, Ashley; Pines, Alexander

2018-05-10

Hyperpolarization techniques based on the use of para-hydrogen provide orders of magnitude signal enhancement for magnetic resonance spectroscopy and imaging. The main drawback limiting widespread applicability of para-hydrogen-based techniques in biomedicine is the presence of organometallic compounds (the polarization transfer catalysts) in solution with hyperpolarized contrast agents. These catalysts are typically complexes of platinum-group metals, and their administration in vivo should be avoided. Herein, we show how extraction of a hyperpolarized compound from an organic phase to an aqueous phase combined with a rapid (less than 10 s) Ir-based catalyst capture by metal scavenging agents can produce pure para-hydrogen-based hyperpolarized contrast agents, as demonstrated by high-resolution nuclear magnetic resonance (NMR) spectroscopy and inductively coupled plasma atomic emission spectroscopy (ICP-AES). The presented methodology enables fast and efficient means of producing pure hyperpolarized aqueous solutions for biomedical and other uses.

Effects of nonadditive interactions on ion solvation at the water/vapor interface: a molecular dynamics study.

PubMed

Yagasaki, Takuma; Saito, Shinji; Ohmine, Iwao

2010-12-09

The solvation of halide ions at the water/vapor interface is investigated by using molecular dynamics simulations with nonpolarizable molecular mechanical (MM), polarizable MM, and quantum mechanical (QM)/MM methods. The free energy profile of the ion solvation is decomposed into the energy and the entropic contributions along the ion displacement from inside to the surface of water. It is found that the surface affinity of the ion, relative to the bulk value, is determined by a subtle balance between the energetic destabilization and the entropic stabilization with the ion displacement. The amount of energetic destabilization is found to be reduced when nonadditive interactions are included, as in the polarizable MM and QM/MM models. The structure of water around the ion at the interface is also largely modified when the higher order effects are considered. For example, the induced dipole effect enhances the solvation structure around the ion at the interface significantly and thus reduces the amount of entropic stabilization at the interface, relative to in the bulk. It is found that this induced dipole effect causes the slowing in the ion-water hydrogen bond dynamics at the interface. On the other hand, the higher order induced multipole effects in the QM/MM method suppress both the excessive enhancement of the solvation structure and the slowing of the ion-water hydrogen bond dynamics at the interface. The present study demonstrates that not only the induced dipole moment but also the higher order induced multipole moments, which are neglected in standard empirical models, are essential for the correct description of the ion solvation at the water/vapor interface.

Advanced dielectric continuum model of preferential solvation

NASA Astrophysics Data System (ADS)

Basilevsky, Mikhail; Odinokov, Alexey; Nikitina, Ekaterina; Grigoriev, Fedor; Petrov, Nikolai; Alfimov, Mikhail

2009-01-01

A continuum model for solvation effects in binary solvent mixtures is formulated in terms of the density functional theory. The presence of two variables, namely, the dimensionless solvent composition y and the dimensionless total solvent density z, is an essential feature of binary systems. Their coupling, hidden in the structure of the local dielectric permittivity function, is postulated at the phenomenological level. Local equilibrium conditions are derived by a variation in the free energy functional expressed in terms of the composition and density variables. They appear as a pair of coupled equations defining y and z as spatial distributions. We consider the simplest spherically symmetric case of the Born-type ion immersed in the benzene/dimethylsulfoxide (DMSO) solvent mixture. The profiles of y(R ) and z(R ) along the radius R, which measures the distance from the ion center, are found in molecular dynamics (MD) simulations. It is shown that for a given solute ion z(R ) does not depend significantly on the composition variable y. A simplified solution is then obtained by inserting z(R ), found in the MD simulation for the pure DMSO, in the single equation which defines y(R ). In this way composition dependences of the main solvation effects are investigated. The local density augmentation appears as a peak of z(R ) at the ion boundary. It is responsible for the fine solvation effects missing when the ordinary solvation theories, in which z =1, are applied. These phenomena, studied for negative ions, reproduce consistently the simulation results. For positive ions the simulation shows that z ≫1 (z =5-6 at the maximum of the z peak), which means that an extremely dense solvation shell is formed. In such a situation the continuum description fails to be valid within a consistent parametrization.

The solvation structure of Mg ions in dichloro complex solutions from first-principles molecular dynamics and simulated X-ray absorption spectra.

PubMed

Wan, Liwen F; Prendergast, David

2014-10-15

The knowledge of Mg solvation structure in the electrolyte is requisite to understand the transport behavior of Mg ions and their dissolution/deposition mechanism at electrolyte/electrode interfaces. In the first established rechargeable Mg-ion battery system [D. Aurbach et al. Nature 2000, 407, 724], the electrolyte is of the dichloro complex (DCC) solution family, Mg(AlCl2BuEt)2/THF, resulting from the reaction of Bu2Mg and EtAlCl2 with a molar ratio of 1:2. There is disagreement in the literature regarding the exact solvation structure of Mg ions in such solutions, i.e., whether Mg(2+) is tetra- or hexacoordinated by a combination of Cl(-) and THF. In this work, theoretical insight into the solvation complexes present is provided based on first-principles molecular dynamics simulations (FPMD). Both Mg monomer and dimer structures are considered in both neutral and positively charged states. We found that, at room temperature, the Mg(2+) ion tends to be tetracoordinated in the THF solution phase instead of hexacoordinated, which is the predominant solid-phase coordination. Simulating the X-ray absorption spectra (XAS) at the Mg K-edge by sampling our FPMD trajectories, our predicted solvation structure can be readily compared with experimental measurements. It is found that when changing from tetra- to hexacoordination, the onset of X-ray absorption should exhibit at least a 1 eV blue shift. We propose that this energy shift can be used to monitor changes in the Mg solvation sphere as it migrates through the electrolyte to electrolyte/electrode interfaces and to elucidate the mechanism of Mg dissolution/deposition.

Solvation Thermodynamic Properties of Hydrogen Sulfide in [C4mim][PF6], [C4mim][BF4], and [C4mim][Cl] Ionic Liquids, Determined by Molecular Simulations.

PubMed

Sánchez-Badillo, Joel; Gallo, Marco; Alvarado, Sandra; Glossman-Mitnik, Daniel

2015-08-20

Removal of hydrogen sulfide (H2S) and acid gases from natural gas is accomplished by absorption processes using a solvent. The gas solubility in a liquid can be used to measure the degree of removal of the gas and is quantified by the Henry's constant, the free energy of solvation at infinite dilution, or the excess chemical potential. In this work, Henry's constants and thermodynamic properties of solvation of H2S were calculated in three ionic liquids: [C4mim][PF6], [C4mim][BF4], and [C4mim][Cl] ([C4mim], 1-butyl-3-methyl imidazolium). The first step in this work was the evaluation of the force fields for the gas and condensed phases in order to obtain accurate values for the excess chemical potential for H2S on each ionic liquid using free energy perturbation techniques. In the H2S-[C4mim][PF6] and H2S-[C4mim][BF4] systems, the results obtained by molecular simulation agree with the experimental values reported in the literature. However, the solvation free energy calculated for the H2S-[C4mim][Cl] system can be considered predictive because of the lack of experimental data at the simulated conditions. Based on these results, the best solvent for removing H2S is [C4mim][Cl] because it has the highest affinity for this species (lowest value of the Henry's constant). Also, solvation thermodynamic properties such as enthalpy and entropy were calculated in order to evaluate their contribution to the free energy of solvation.

Complexation of buffer constituents with neutral complexation agents: part I. Impact on common buffer properties.

PubMed

Riesová, Martina; Svobodová, Jana; Tošner, Zdeněk; Beneš, Martin; Tesařová, Eva; Gaš, Bohuslav

2013-09-17

The complexation of buffer constituents with the complexation agent present in the solution can very significantly influence the buffer properties, such as pH, ionic strength, or conductivity. These parameters are often crucial for selection of the separation conditions in capillary electrophoresis or high-pressure liquid chromatography (HPLC) and can significantly affect results of separation, particularly for capillary electrophoresis as shown in Part II of this paper series (Beneš, M.; Riesová, M.; Svobodová, J.; Tesařová, E.; Dubský, P.; Gaš, B. Anal. Chem. 2013, DOI: 10.1021/ac401381d). In this paper, the impact of complexation of buffer constituents with a neutral complexation agent is demonstrated theoretically as well as experimentally for the model buffer system composed of benzoic acid/LiOH or common buffers (e.g., CHES/LiOH, TAPS/LiOH, Tricine/LiOH, MOPS/LiOH, MES/LiOH, and acetic acid/LiOH). Cyclodextrins as common chiral selectors were used as model complexation agents. We were not only able to demonstrate substantial changes of pH but also to predict the general complexation characteristics of selected compounds. Because of the zwitterion character of the common buffer constituents, their charged forms complex stronger with cyclodextrins than the neutral ones do. This was fully proven by NMR measurements. Additionally complexation constants of both forms of selected compounds were determined by NMR and affinity capillary electrophoresis with a very good agreement of obtained values. These data were advantageously used for the theoretical descriptions of variations in pH, depending on the composition and concentration of the buffer. Theoretical predictions were shown to be a useful tool for deriving some general rules and laws for complexing systems.

NMR and computational methods applied to the 3- dimensional structure determination of DNA and ligand-DNA complexes in solution

NASA Astrophysics Data System (ADS)

Smith, Jarrod Anson

2D homonuclear 1H NMR methods and restrained molecular dynamics (rMD) calculations have been applied to determining the three-dimensional structures of DNA and minor groove-binding ligand-DNA complexes in solution. The structure of the DNA decamer sequence d(GCGTTAACGC)2 has been solved both with a distance-based rMD protocol and an NOE relaxation matrix backcalculation-based protocol in order to probe the relative merits of the different refinement methods. In addition, three minor groove binding ligand-DNA complexes have been examined. The solution structure of the oligosaccharide moiety of the antitumor DNA scission agent calicheamicin γ1I has been determined in complex with a decamer duplex containing its high affinity 5'-TCCT- 3' binding sequence. The structure of the complex reinforces the belief that the oligosaccharide moiety is responsible for the sequence selective minor-groove binding activity of the agent, and critical intermolecular contacts are revealed. The solution structures of both the (+) and (-) enantiomers of the minor groove binding DNA alkylating agent duocarmycin SA have been determined in covalent complex with the undecamer DNA duplex d(GACTAATTGTC).d(GAC AATTAGTC). The results support the proposal that the alkylation activity of the duocarmycin antitumor antibiotics is catalyzed by a binding-induced conformational change in the ligand which activates the cyclopropyl group for reaction with the DNA. Comparisons between the structures of the two enantiomers covalently bound to the same DNA sequence at the same 5'-AATTA-3 ' site have provided insight into the binding orientation and site selectivity, as well as the relative rates of reactivity of these two agents.

Interfacial Effects and Organization of Inorganic-Organic Composite Solids.

DTIC Science & Technology

1998-05-20

SITU NMR STUDY OF THE HYDROTHERMAL SYNTHESIS OF TEMPLATE-MEDIATED MICROPOROUS ALUMINOPHOSPHATE MATERIALS, Conne M Gersrdin, Pnnccton Univ, Dept...quantitatively characterize the hydrothermal medium while the synthesis proceeds can yield to a better description of the different steps of the...Inorganic-Organic Composite Solids," focused on recent applications in materials synthesis that use structure-directing agents and self-assembly

Use of Magnetic Nanoparticles to Monitor Alginate-Encapsulated βTC-tet Cells

PubMed Central

Constantinidis, Ioannis; Grant, Samuel C.; Simpson, Nicholas E.; Oca-Cossio, Jose A.; Sweeney, Carol A.; Mao, Hui; Blackband, Stephen J.; Sambanis, Athanassios

2008-01-01

Non-invasive monitoring of tissue-engineered constructs is an important component in optimizing construct design and assessing therapeutic efficacy. In recent years, cellular and molecular imaging initiatives have spurred the use of iron oxide based contrast agents in the field of NMR imaging. Although their use in medical research has been widespread, their application in tissue engineering has been limited. In this study, the utility of Monocrystalline Iron Oxide Nanoparticles (MION) as an NMR contrast agent was evaluated for βTC-tet cells encapsulated within alginate/poly-L-lysine/alginate (APA) microbeads. The constructs were labeled with MION in two different ways: (a) MION-labeled βTC-tet cells were encapsulated in APA beads (i.e., intracellular compartment); and (b) MION particles were suspended in the alginate solution prior to encapsulation so that the alginate matrix was labeled with MION instead of the cells (i.e., extracellular compartment). The data show that although the location of cells can be identified within APA beads, cell growth or rearrangement within these constructs cannot be effectively monitored, regardless of the location of MION compartmentalization. The advantages and disadvantages of these techniques and their potential use in tissue engineering are discussed. PMID:19165877

Plaster mortars with polymer fibers and additives investigated by 1H NMR relaxometry

NASA Astrophysics Data System (ADS)

Mustea, Andrei; Manea, Daniela L.; Jumate, Elena; Orbán, Yvette A.; Fechete, Radu

2017-12-01

Plaster mortars with polypropylene (pp) fibers and/or additives were investigated by 1H NMR relaxometry. Two recipes are proposed and are based on a commercially available mortar or are self-prepared and have different content of polypropylene fibers, which play the role of reinforcement agent, and/or Sika additive which is a waterproofing agent. The distributions of transverse relaxation times, T2 were obtained at 1, 3, 7 and 28 days after preparation. For the majority of T2-distributions four peaks are observed and, are associated with the hydration water (to the mineralogical components) and water in small, medium and large pores. The evolution in time, from 1 to 28 days, of the T2-distributions indicates the effects of pp fibers and Sika additive in the formation of pore microstructure. The degree of homogeneity of prepared receipts was evaluated from the relative peak-width and compared with mechanical measurements. Finally, we shown that the inverse of the transverse relaxation time values, T2-1, characteristic to the hydration water depends linearly on the resistance at compression measured for the 1÷28 days period, proving the important role of hydrations to the mechanical properties of the final product.

Synthesis, in vitro anticancer and antimycobacterial evaluation of new 5-(2,5-dimethoxyphenyl)-1,3,4-thiadiazole-2-amino derivatives.

PubMed

Polkam, Naveen; Rayam, Parsharamulu; Anireddy, Jaya Shree; Yennam, Satyanarayana; Anantaraju, Hasitha Shilpa; Dharmarajan, Sriram; Perumal, Yogeeswari; Kotapalli, Sudha Sravanti; Ummanni, Ramesh; Balasubramanian, Sridhar

2015-04-01

A series of 2,5-disubstituted-1,3,4-thiadiazole derivatives 5a-5l, 7a-7e and 9 have been synthesised and screened for in vitro antimycobacterial activity against Mycobacterium smegmatis MC-155. In addition these compounds have also been screened for cytotoxic activity against cancer cell lines HT-29, MDA-MB-231 by MTT colorimetric assay. The compounds are well characterized by spectral analysis viz. (1)H NMR, (13)C NMR, FT-IR, mass and HRMS. Screening results indicate that compounds 5g, 7a possess good antitubercular activity with MIC value 65.74 and 40.86, respectively, compounds 5g, 7a, 7b, 7d, 7e and 9 displayed promising cytotoxic activity against the cell lines tested. 5g and 7a stand out to be potent antimycobacterial and anticancer agents among the tested series. Further the title compounds were also tested on human normal cells HEK293T and are found to be safer with lesser cytotoxicity. It is interesting to observe that compound 5g has come out to be safer, potent anticancer and antimycobacterial agent. Copyright © 2015 Elsevier Ltd. All rights reserved.

DESTRUCTION OF HALOGENATED HYDROCARBONS WITH SOLVATED ELECTRONS IN THE PRESENCE OF WATER. (R826180)

EPA Science Inventory

Model halogenated aromatic and aliphatic hydrocarbons and halogenated phenols were dehalogenated in seconds by solvated electrons generated from sodium in both anhydrous liquid ammonia and ammonia/water solutions. The minimum sodium required to completely dehalogenate these mo...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vijayakumar, M.; Nie, Zimin; Walter, Eric D.

Redox flow battery (RFB) is a promising candidate for energy storage component in designing resilient grid scale power supply due to the advantage of the separation of power and energy. However, poorly understood chemical and thermal stability issues of electrolytes currently limit the performance of RFB. Designing of high performance stable electrolytes requires comprehensive knowledge about the molecular level solvation structure and dynamics of their redox active species. The molecular level understanding of detrimental V2O5 precipitation process led to successful designing of mixed acid based electrolytes for vanadium redox flow batteries (VRFB). The higher stability of mixed acid based electrolytesmore » is attributed to the choice of hydrochloric acid as optimal co-solvent, which provides chloride anions for ligand exchange process in vanadium solvation structure. The role of chloride counter anion on solvation structure and dynamics of vanadium species were studied using combined magnetic resonance spectroscopy and DFT based theoretical methods. Finally, the solvation phenomenon of multiple vanadium species and their impact on VRFB electrolyte chemical stability were discussed.« less

Corrosion Thermodynamics of Magnesium and Alloys from First Principles as a Function of Solvation

NASA Astrophysics Data System (ADS)

Limmer, Krista; Williams, Kristen; Andzelm, Jan

Thermodynamics of corrosion processes occurring on magnesium surfaces, such as hydrogen evolution and water dissociation, have been examined with density functional theory (DFT) to evaluate the effect of impurities and dilute alloying additions. The modeling of corrosion thermodynamics requires examination of species in a variety of chemical and electronic states in order to accurately represent the complex electrochemical corrosion process. In this study, DFT calculations for magnesium corrosion thermodynamics were performed with two DFT codes (VASP and DMol3), with multiple exchange-correlation functionals for chemical accuracy, as well as with various levels of implicit and explicit solvation for surfaces and solvated ions. The accuracy of the first principles calculations has been validated against Pourbaix diagrams constructed from solid, gas and solvated charged ion calculations. For aqueous corrosion, it is shown that a well parameterized implicit solvent is capable of accurately representing all but the first coordinating layer of explicit water for charged ions.

Solvent-driven reductive activation of carbon dioxide by gold anions.

PubMed

Knurr, Benjamin J; Weber, J Mathias

2012-11-14

Catalytic activation and electrochemical reduction of CO(2) for the formation of chemically usable feedstock and fuel are central goals for establishing a carbon neutral fuel cycle. The role of solvent molecules in catalytic processes is little understood, although solvent-solute interactions can strongly influence activated intermediate species. We use vibrational spectroscopy of mass-selected Au(CO(2))(n)(-) cluster ions to probe the solvation of AuCO(2)(-) as a model for a reactive intermediate in the reductive activation of a CO(2) ligand by a single-atom catalyst. For the first few solvent molecules, solvation of the complex preferentially occurs at the CO(2) moiety, enhancing reductive activation through polarization of the excess charge onto the partially reduced ligand. At higher levels of solvation, direct interaction of additional solvent molecules with the Au atom diminishes reduction. The results show how the solvation environment can enhance or diminish the effects of a catalyst, offering design criteria for single-atom catalyst engineering.

Free Energy Wells and Barriers to Ion Transport Across Membranes

NASA Astrophysics Data System (ADS)

Rempe, Susan

2014-03-01

The flow of ions across cellular membranes is essential to many biological processes. Ion transport is also important in synthetic materials used as battery electrolytes. Transport often involves specific ions and fast conduction. To achieve those properties, ion conduction pathways must solvate specific ions by just the ``right amount.'' The right amount of solvation avoids ion traps due to deep free energy wells, and avoids ion block due to high free energy barriers. Ion channel proteins in cellular membranes demonstrate this subtle balance in solvation of specific ions. Using ab initio molecular simulations, we have interrogated the link between binding site structure and ion solvation free energies in biological ion binding sites. Our results emphasize the surprisingly important role of the environment that surrounds ion-binding sites for fast transport of specific ions. We acknowledge support from Sandia's LDRD program. Sandia National Labs is a multi-program laboratory operated by Sandia Corp., a wholly owned subsidiary of Lockheed Martin Corp., for the US DOE's NNSA under contract DE-AC04-94AL85000.

Ultrafast fluxional exchange dynamics in electrolyte solvation sheath of lithium ion battery

PubMed Central

Lee, Kyung-Koo; Park, Kwanghee; Lee, Hochan; Noh, Yohan; Kossowska, Dorota; Kwak, Kyungwon; Cho, Minhaeng

2017-01-01

Lithium cation is the charge carrier in lithium-ion battery. Electrolyte solution in lithium-ion battery is usually based on mixed solvents consisting of polar carbonates with different aliphatic chains. Despite various experimental evidences indicating that lithium ion forms a rigid and stable solvation sheath through electrostatic interactions with polar carbonates, both the lithium solvation structure and more importantly fluctuation dynamics and functional role of carbonate solvent molecules have not been fully elucidated yet with femtosecond vibrational spectroscopic methods. Here we investigate the ultrafast carbonate solvent exchange dynamics around lithium ions in electrolyte solutions with coherent two-dimensional infrared spectroscopy and find that the time constants of the formation and dissociation of lithium-ion···carbonate complex in solvation sheaths are on a picosecond timescale. We anticipate that such ultrafast microscopic fluxional processes in lithium-solvent complexes could provide an important clue to understanding macroscopic mobility of lithium cation in lithium-ion battery on a molecular level. PMID:28272396

Quantitative measurement of solvation shells using frequency modulated atomic force microscopy

NASA Astrophysics Data System (ADS)

Uchihashi, T.; Higgins, M.; Nakayama, Y.; Sader, J. E.; Jarvis, S. P.

2005-03-01

The nanoscale specificity of interaction measurements and additional imaging capability of the atomic force microscope make it an ideal technique for measuring solvation shells in a variety of liquids next to a range of materials. Unfortunately, the widespread use of atomic force microscopy for the measurement of solvation shells has been limited by uncertainties over the dimensions, composition and durability of the tip during the measurements, and problems associated with quantitative force calibration of the most sensitive dynamic measurement techniques. We address both these issues by the combined use of carbon nanotube high aspect ratio probes and quantifying the highly sensitive frequency modulation (FM) detection technique using a recently developed analytical method. Due to the excellent reproducibility of the measurement technique, additional information regarding solvation shell size as a function of proximity to the surface has been obtained for two very different liquids. Further, it has been possible to identify differences between chemical and geometrical effects in the chosen systems.

Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms

PubMed Central

Wagoner, Jason A.; Baker, Nathan A.

2006-01-01

Continuum solvation models provide appealing alternatives to explicit solvent methods because of their ability to reproduce solvation effects while alleviating the need for expensive sampling. Our previous work has demonstrated that Poisson-Boltzmann methods are capable of faithfully reproducing polar explicit solvent forces for dilute protein systems; however, the popular solvent-accessible surface area model was shown to be incapable of accurately describing nonpolar solvation forces at atomic-length scales. Therefore, alternate continuum methods are needed to reproduce nonpolar interactions at the atomic scale. In the present work, we address this issue by supplementing the solvent-accessible surface area model with additional volume and dispersion integral terms suggested by scaled particle models and Weeks–Chandler–Andersen theory, respectively. This more complete nonpolar implicit solvent model shows very good agreement with explicit solvent results and suggests that, although often overlooked, the inclusion of appropriate dispersion and volume terms are essential for an accurate implicit solvent description of atomic-scale nonpolar forces. PMID:16709675

Ultrafast fluxional exchange dynamics in electrolyte solvation sheath of lithium ion battery

NASA Astrophysics Data System (ADS)

Lee, Kyung-Koo; Park, Kwanghee; Lee, Hochan; Noh, Yohan; Kossowska, Dorota; Kwak, Kyungwon; Cho, Minhaeng

2017-03-01

Lithium cation is the charge carrier in lithium-ion battery. Electrolyte solution in lithium-ion battery is usually based on mixed solvents consisting of polar carbonates with different aliphatic chains. Despite various experimental evidences indicating that lithium ion forms a rigid and stable solvation sheath through electrostatic interactions with polar carbonates, both the lithium solvation structure and more importantly fluctuation dynamics and functional role of carbonate solvent molecules have not been fully elucidated yet with femtosecond vibrational spectroscopic methods. Here we investigate the ultrafast carbonate solvent exchange dynamics around lithium ions in electrolyte solutions with coherent two-dimensional infrared spectroscopy and find that the time constants of the formation and dissociation of lithium-ion...carbonate complex in solvation sheaths are on a picosecond timescale. We anticipate that such ultrafast microscopic fluxional processes in lithium-solvent complexes could provide an important clue to understanding macroscopic mobility of lithium cation in lithium-ion battery on a molecular level.

Significance of solvated electrons (e(aq)-) as promoters of life on earth.

PubMed

Getoff, Nikola

2014-01-01

Based on the present state of knowledge a new hypothesis concerning the origin of life on Earth is presented, and emphasizes the particular significance of solvated electrons (e(aq)(-)). Solvated electrons are produced in seawater, mainly by (40)K radiation and in atmospheric moisture by VUV light, electrical discharges and cosmic ray. Solvated electrons are involved in primary chemical processes and in biological processes. The conversion of aqueous CO2 and CO into simple organic substances, the generation of ammonia from N2 and water, the formation of amines, amino acids and simple proteins under the action of e(aq)(-) has been experimentally proven. Furthermore, it is supposed that the generation of the primitive cell and equilibria of primitive enzymes are also realized due to the strong reducing property of e(aq)(-). The presented hypothesis is mainly founded on recently obtained experimental results. The involvement of e(aq)(-) in such mechanisms, as well as their action as an initiator of life is also briefly discussed.

Ultrafast fluxional exchange dynamics in electrolyte solvation sheath of lithium ion battery.

PubMed

Lee, Kyung-Koo; Park, Kwanghee; Lee, Hochan; Noh, Yohan; Kossowska, Dorota; Kwak, Kyungwon; Cho, Minhaeng

2017-03-08

Lithium cation is the charge carrier in lithium-ion battery. Electrolyte solution in lithium-ion battery is usually based on mixed solvents consisting of polar carbonates with different aliphatic chains. Despite various experimental evidences indicating that lithium ion forms a rigid and stable solvation sheath through electrostatic interactions with polar carbonates, both the lithium solvation structure and more importantly fluctuation dynamics and functional role of carbonate solvent molecules have not been fully elucidated yet with femtosecond vibrational spectroscopic methods. Here we investigate the ultrafast carbonate solvent exchange dynamics around lithium ions in electrolyte solutions with coherent two-dimensional infrared spectroscopy and find that the time constants of the formation and dissociation of lithium-ion···carbonate complex in solvation sheaths are on a picosecond timescale. We anticipate that such ultrafast microscopic fluxional processes in lithium-solvent complexes could provide an important clue to understanding macroscopic mobility of lithium cation in lithium-ion battery on a molecular level.

Exit channel dynamics in a micro-hydrated SN2 reaction of the hydroxyl anion.

PubMed

Otto, R; Brox, J; Trippel, S; Stei, M; Best, T; Wester, R

2013-08-29

We report on the reaction dynamics of the monosolvated SN2 reaction of cold OH(-)(H2O) with CH3I that have been studied using crossed beam ion imaging. Two SN2 reaction channels are possible for this reaction: Formation of unsolvated I(-) and of solvated I(-)(H2O) products. We find a strong preference for the formation of unsolvated I(-) reaction products with respect to the energetically favored reaction toward solvated I(-)(H2O). Angle differential cross section measurements reveal similar velocity and angular distributions for all solvated and parts of the unsolvated reaction products. We furthermore find that the contribution of these two products to the total product flux can be described by the same collision energy dependence. We interpret our findings in terms of a joint reaction mechanism in which a CH3OH(H2O)···I(-) complex is formed that decays into either solvated or unsolvated products. Quantum chemical calculation are used to support this assumption.

Atomistic characterization of the active-site solvation dynamics of a model photocatalyst

DOE PAGES

van Driel, Tim B.; Kjær, Kasper S.; Hartsock, Robert W.; ...

2016-11-28

The interactions between the reactive excited state of molecular photocatalysts and surrounding solvent dictate reaction mechanisms and pathways, but are not readily accessible to conventional optical spectroscopic techniques. Here we report an investigation of the structural and solvation dynamics following excitation of a model photocatalytic molecular system [Ir 2(dimen) 4] 2+, where dimen is para-diisocyanomenthane. The time-dependent structural changes in this model photocatalyst, as well as the changes in the solvation shell structure, have been measured with ultrafast diffuse X-ray scattering and simulated with Born-Oppenheimer Molecular Dynamics. Both methods provide direct access to the solute–solvent pair distribution function, enabling themore » solvation dynamics around the catalytically active iridium sites to be robustly characterized. Our results provide evidence for the coordination of the iridium atoms by the acetonitrile solvent and demonstrate the viability of using diffuse X-ray scattering at free-electron laser sources for studying the dynamics of photocatalysis.« less

Molecular dynamics study of thermodynamic stability and dynamics of [Li(glyme)]+ complex in lithium-glyme solvate ionic liquids

NASA Astrophysics Data System (ADS)

Shinoda, Wataru; Hatanaka, Yuta; Hirakawa, Masashi; Okazaki, Susumu; Tsuzuki, Seiji; Ueno, Kazuhide; Watanabe, Masayoshi

2018-05-01

Equimolar mixtures of glymes and organic lithium salts are known to produce solvate ionic liquids, in which the stability of the [Li(glyme)]+ complex plays an important role in determining the ionic dynamics. Since these mixtures have attractive physicochemical properties for application as electrolytes, it is important to understand the dependence of the stability of the [Li(glyme)]+ complex on the ion dynamics. A series of microsecond molecular dynamics simulations has been conducted to investigate the dynamic properties of these solvate ionic liquids. Successful solvate ionic liquids with high stability of the [Li(glyme)]+ complex have been shown to have enhanced ion dynamics. Li-glyme pair exchange rarely occurs: its characteristic time is longer than that of ion diffusion by one or two orders of magnitude. Li-glyme pair exchange most likely occurs through cluster formation involving multiple [Li(glyme)]+ pairs. In this process, multiple exchanges likely take place in a concerted manner without the production of energetically unfavorable free glyme or free Li+ ions.

Anion photoelectron spectroscopy of acid-base systems, solvated molecules and MALDI matrix molecules

NASA Astrophysics Data System (ADS)

Eustis, Soren Newman

Gas phase, mass-selected, anion photoelectron spectroscopic studies were performed on a variety of molecular systems. These studies can be grouped into three main themes: acid-base interactions, solvation, and ions of analytical interest. Acid-base interactions represent some of the most fundamental processes in chemistry. The study of these processes elucidates elementary principles such as inner and outer sphere complexes, hard and soft ions, and salt formation---to name a few. Apart from their appeal from a pedagogical standpoint, the ubiquity of chemical reactions which involve acids, bases or the resulting salts makes the study of their fundamental interactions both necessary and fruitful. With this in mind, the neutral and anionic series (NH3···HX) (X= F, Cl, Br, I) were examined experimentally and theoretically. The relatively small size of these systems, combined with the advances in computational methods, allowed our experimental results to be compared with very high level ab initio theoretical results. The synergy between theory and experiment yielded an understanding of the nature of the complexes that could not be achieved with either method in isolation. The second theme present in this body or work is molecular solvation. Solvation is a phenomenon which is present in biology, chemistry and physics. Many biological molecules do not become 'active' until they are solvated by water. Thus, the study of biologically relevant species solvated by water is one step in a bottom up approach to studying the biochemical interactions in living organisms. Furthermore, the hydration of acidic molecules in the atmosphere is what drives the formation of 'free' protons or hydronium ions which are the key players in acid driven chemistry. Here are presented two unique solvation studies, Adenine(H2O)-n and C6F6(H2O)-n, these systems are very distinct, but show somewhat similar responses to hydration. The last theme presented in this work is the electronic properties of molecules relevant to analytical chemistry, or more specifically, Matrix Assisted Laser Desorption Interaction (MALDI) chemistry. For the first time electron affinities are presented for many of the common MALDI matrix compounds.

Incorporation of Hydrogen Bond Angle Dependency into the Generalized Solvation Free Energy Density Model.

PubMed

Ma, Songling; Hwang, Sungbo; Lee, Sehan; Acree, William E; No, Kyoung Tai

2018-04-23

To describe the physically realistic solvation free energy surface of a molecule in a solvent, a generalized version of the solvation free energy density (G-SFED) calculation method has been developed. In the G-SFED model, the contribution from the hydrogen bond (HB) between a solute and a solvent to the solvation free energy was calculated as the product of the acidity of the donor and the basicity of the acceptor of an HB pair. The acidity and basicity parameters of a solute were derived using the summation of acidities and basicities of the respective acidic and basic functional groups of the solute, and that of the solvent was experimentally determined. Although the contribution of HBs to the solvation free energy could be evenly distributed to grid points on the surface of a molecule, the G-SFED model was still inadequate to describe the angle dependency of the HB of a solute with a polarizable continuum solvent. To overcome this shortcoming of the G-SFED model, the contribution of HBs was formulated using the geometric parameters of the grid points described in the HB coordinate system of the solute. We propose an HB angle dependency incorporated into the G-SFED model, i.e., the G-SFED-HB model, where the angular-dependent acidity and basicity densities are defined and parametrized with experimental data. The G-SFED-HB model was then applied to calculate the solvation free energies of organic molecules in water, various alcohols and ethers, and the log P values of diverse organic molecules, including peptides and a protein. Both the G-SFED model and the G-SFED-HB model reproduced the experimental solvation free energies with similar accuracy, whereas the distributions of the SFED on the molecular surface calculated by the G-SFED and G-SFED-HB models were quite different, especially for molecules having HB donors or acceptors. Since the angle dependency of HBs was included in the G-SFED-HB model, the SFED distribution of the G-SFED-HB model is well described as compared to that of the G-SFED model.

Investigation of efflorescence of inorganic aerosols using fluorescence spectroscopy.

PubMed

Choi, Man Yee; Chan, Chak K

2005-02-17

The phase transition is one of the most fundamental phenomena affecting the physical and chemical properties of atmospheric aerosols. Efflorescence, in particular, is not well understood, partly because the molecular interactions between the solute and water molecules of saturated or supersaturated solution droplets have not been well characterized. Recently, we developed a technique that combines the use of an electrodynamic balance and a fluorescence dye, 8-hydroxyl-1,3,6-pyrenetrisulfonate (pyranine), to study the distributions of solvated and free water in aqueous droplets (Choi, M. Y.; Chan, C. K.; Zhang, Y. H. J. Phys. Chem. A 2004, 108, 1133). We found that the equality of the amounts of solvated and free water is a necessary but not sufficient condition for efflorescence. For efflorescing compounds such as Na2SO4, (NH4)2SO4, and a mixture of NaCl and Na2SO4, the amount of free water decreases, while that of solvated water is roughly constant in bulk measurements and decreases less dramatically than that of free water in single-particle measurements as the relative humidity (RH) decreases. Efflorescence of the supersaturated droplets of these solutions occurs when the amounts of free and solvated water are equal, which is consistent with our previous observation for NaCl. For nonefflorescing compounds in single-particle levitation experiments such as MgSO4 and Mg(NO3)2, the amounts of free and solvated water are equal at a water-to-solute molar ratio of about 6, at which spectral changes due to the formation of contact ion pairs between magnesium and the anions occur as shown by Raman spectroscopy. Fluorescence imaging shows that the droplets of diluted Mg(NO3)2 (at 80% RH) and MgSO4 are homogeneous but those of NaCl, Na2SO4, (NH4)2SO4, and supersaturated Mg(NO3)2 (at 10% RH) are heterogeneous in terms of the solvated-to-free water distribution. The solvated-to-free water ratios in NaCl, Na2SO4, and (NH4)2SO4 droplets are higher in the outer regions by about half a radius deep than at the center of the droplets.

Excited state intramolecular proton transfer reaction of 4'-N,N-diethylamino-3-hydroxyflavone and solvation dynamics in room temperature ionic liquids studied by optical Kerr gate fluorescence measurement.

PubMed

Kimura, Yoshifumi; Fukuda, Masanori; Suda, Kayo; Terazima, Masahide

2010-09-16

Fluorescence dynamics of 4'-N,N-diethylamino-3-hydroxyflavone (DEAHF) and its methoxy derivative (DEAMF) in various room temperature ionic liquids (RTILs) have been studied mainly by an optical Kerr gate method. DEAMF showed a single band fluorescence whose peak shifted with time by the solvation dynamics. The averaged solvation time determined by the fluorescence peak shift was proportional to the viscosity of the solvent except for tetradecyltrihexylphosphonium bis(trifluoromethanesulfonyl)amide. The solvation times were consistent with reported values determined with different probe molecules. DEAHF showed dual fluorescence due to the normal and tautomer forms produced by the excited state intramolecular proton transfer (ESIPT), and the relative intensities were dependent on the time and the solvent cation or anion species. By using the information of the fluorescence spectrum of DEAMF, the fluorescence spectrum of DEAHF at each delay time after the photoexcitation was decomposed into the normal and the tautomer fluorescence components, respectively. The normal component showed a very fast decay simulated by a biexponential function (2-3 and 20-30 ps) with an additional slower decay component. The tautomer component showed a rise with the time constants corresponding to the faster decay of the normal form with an additional instantaneous rise. The faster dynamics of the normal and tautomer population changes were assigned to the ESIPT process, while the slower decay of the fluorescence was attributed to the population decay from the excited state through the radiative and nonradiative processes. The average ESIPT time was much faster than the averaged solvation time of RTILs. Basically, the ESIPT kinetics in RTILs is similar to those in conventional liquid solvents like acetonitrile (Chou et al. J. Phys. Chem. A 2005, 109, 3777). The faster ESIPT is interpreted in terms of the activation barrierless process from the Franck-Condon state before the solvation of the normal state in the electronic excited state. With the advance of the solvation in the excited state, the normal form becomes relatively more stable than the tautomer form, which makes the ESIPT become an activation process.

Biocompatible Polyhydroxyethylaspartamide-based Micelles with Gadolinium for MRI Contrast Agents

NASA Astrophysics Data System (ADS)

Jeong, Sang Young; Kim, Hyo Jeong; Kwak, Byung-Kook; Lee, Ha-Young; Seong, Hasoo; Shin, Byung Cheol; Yuk, Soon Hong; Hwang, Sung-Joo; Cho, Sun Hang

2010-12-01

Biocompatible poly-[ N-(2-hydroxyethyl)- d, l-aspartamide]-methoxypoly(ethyleneglycol)-hexadecylamine (PHEA-mPEG-C16) conjugated with 1,4,7,10-tetraazacyclododecan-1,4,7,10-tetraacetic acid-gadolinium (DOTA-Gd) via ethylenediamine (ED) was synthesized as a magnetic resonance imaging (MRI) contrast agent. Amphiphilic PHEA-mPEG-C16-ED-DOTA-Gd forms micelle in aqueous solution. All the synthesized materials were characterized by proton nuclear magnetic resonance (1H NMR). Micelle size and shape were examined by dynamic light scattering (DLS) and atomic force microscopy (AFM). Micelles with PHEA-mPEG-C16-ED-DOTA-Gd showed higher relaxivities than the commercially available gadolinium contrast agent. Moreover, the signal intensity of a rabbit liver was effectively increased after intravenous injection of PHEA-mPEG-C16-ED-DOTA-Gd.

NMR relaxometric properties and cytotoxicity of Gd2O3 nanoparticle suspensions in an organic liquid

NASA Astrophysics Data System (ADS)

Babić-Stojić, Branka; Jokanović, Vukoman; Milivojević, Dušan; Požek, Miroslav; Jagličić, Zvonko; Makovec, Darko; Arsikin, Katarina; Paunović, Verica

2014-10-01

Gd2O3 nanoparticles and their agglomerates from approximately 10 to 80 nm in size suspended in an organic liquid were synthesized via polyol route. The reaction between diethylene glycol and added acetic acid, which occurred simultaneously with the synthesis of Gd2O3 nanoparticles, was catalyzed by sodium bisulfate to transform as much as possible diethylene glycol in corresponding ester at the end of complete reaction. The produced nanosized material of gadolinium oxide was investigated by TEM, DLS, FTIR spectroscopy, and NMR relaxometry. Biological evaluation of this material was done by MTT and crystal violet assays to determine the cell viability. Longitudinal and transverse relaxivities of water-diluted Gd2O3 nanoparticle suspensions estimated to be r 1 = 13.6 and r 2 = 14.7 s-1 mM-1 are about three times higher compared to the relaxivities obtained for standard contrast agent Gd-DTPA (Magnevist). Good MRI signal intensities of the water-diluted Gd2O3 nanoparticle suspensions were recorded in the Gd concentration range 0.2-0.3 mM for which the suspensions were not toxic exhibiting simultaneously higher signal intensities than those for Magnevist in the Gd concentration range 0.4-1 mM for which this standard contrast agent was not toxic. These properties make the produced Gd2O3 nanoparticle material promising for potential application as MRI contrast agent.

Residue length and solvation model dependency of elastinlike polypeptides

NASA Astrophysics Data System (ADS)

Bilsel, Mustafa; Arkin, Handan

2010-05-01

We have performed exhaustive multicanonical Monte Carlo simulations of elastinlike polypeptides with a chain including amino acids (valine-proline-glycine-valine-glycine)n or in short (VPGVG)n , where n changes from 1 to 4, in order to investigate the thermodynamic and structural properties. To predict the characteristic secondary structure motifs of the molecules, Ramachandran plots were prepared and analyzed as well. In these studies, we utilized a realistic model where the interactions between all types of atoms were taken into account. Effects of solvation were also simulated by using an implicit-solvent model with two commonly used solvation parameter sets and compared with the vacuum case.

Quantum chemical approach for condensed-phase thermochemistry (IV): Solubility of gaseous molecules

NASA Astrophysics Data System (ADS)

Ishikawa, Atsushi; Kamata, Masahiro; Nakai, Hiromi

2016-07-01

The harmonic solvation model (HSM) was applied to the solvation of gaseous molecules and compared to a procedure based on the ideal gas model (IGM). Examination of 25 molecules showed that (i) the accuracy of ΔGsolv was similar for both methods, but the HSM shows advantages for calculating ΔHsolv and TΔSsolv; (ii) TΔSsolv contributes more than ΔHsolv to ΔGsolv in the HSM, i.e. the solvation of gaseous molecules is entropy-driven, which agrees well with experimental understanding (the IGM does not show this); (iii) the temperature dependence of Henry's law coefficient was correctly reproduced with the HSM.

Preferential Solvation of Silver (I) Bromate in Methanol-Dimethylsulfoxide Mixtures

NASA Astrophysics Data System (ADS)

Janardhanan, S.; Kalidas, C.

1984-06-01

The solubiltiy of silver bromate, the Gibbs transfer energy of Ag+ and BrO3- and the solvent transport number in methanol-dimethyl sulfoxide mixtures are reported. The solubility of silver bromate increases with addition of DMSO. The Gibbs energy of transfer of the silver ion (based on the ferrocene reference method) decreases, while that of the bromate ion becomes slightly negative with the addition of DMSO. The solvent transport number A passes through a maximum (⊿ = 1.0 at XDMSO = 0.65. From these results, it is concluded that the silver ion is preferentially solvated by DMSO whereas the bromate ion shows no preferential solvation.

Physical transformation of niclosamide solvates in pharmaceutical suspensions determined by DSC and TG analysis.

PubMed

de Villiers, M M; Mahlatji, M D; Malan, S F; van Tonder, E C; Liebenberg, W

2004-07-01

This study reports the preparation of four niclosamide solvates and the determination of the stability of the crystal forms in different suspension vehicles by DSC and TG analysis. Thermal analysis showed that the niclosamide solvates were extremely unstable in a PVP-vehicle and rapidly changed to monohydrated crystals. A suspension in propylene glycol was more stable and TG analysis showed that crystal transformation was less rapid. In this vehicle, the crystals transformed to the anhydrate, rather than the monohydrate, since the vehicle was non-aqueous. The TEG-hemisolvate was the most stable in suspension and offered the best possibility of commercial exploitation.

WtF‐Nano: One‐Pot Dewatering and Water‐Free Topochemical Modification of Nanocellulose in Ionic Liquids or γ‐Valerolactone

PubMed Central

Laaksonen, Tiina; Helminen, Jussi K. J.; Lemetti, Laura; Långbacka, Jesper; Rico del Cerro, Daniel; Hummel, Michael; Rantamäki, Antti H.; Kakko, Tia; Kemell, Marianna L.; Wiedmer, Susanne K.; Heikkinen, Sami; Kilpeläinen, Ilkka

2017-01-01

Abstract Ionic liquids are used to dewater a suspension of birch Kraft pulp cellulose nanofibrils (CNF) and as a medium for water‐free topochemical modification of the nanocellulose (a process denoted as “WtF‐Nano”). Acetylation was applied as a model reaction to investigate the degree of modification and scope of effective ionic liquid structures. Little difference in reactivity was observed when water was removed, after introduction of an ionic liquid or molecular co‐solvent. However, the viscoelastic properties of the CNF suspended in two ionic liquids show that the more basic, but non‐dissolving ionic liquid, allows for better solvation of the CNF. Vibrio fischeri bacterial tests show that all ionic liquids in this study were harmless. Scanning electron microscopy and wide‐angle X‐ray scattering on regenerated samples show that the acetylated CNF is still in a fibrillar form. 1 D and 2 D NMR analyses, after direct dissolution in a novel ionic liquid electrolyte solution, indicate that both cellulose and residual xylan on the surface of the nanofibrils reacts to give acetate esters. PMID:29112334

Modulators of heterogeneous protein surface water dynamics

NASA Astrophysics Data System (ADS)

Han, Songi

The hydration water that solvates proteins is a major factor in driving or enabling biological events, including protein-protein and protein-ligand interactions. We investigate the role of the protein surface in modulating the hydration water fluctuations on both the picosecond and nanosecond timescale with an emerging experimental NMR technique known as Overhauser Dynamic Nuclear Polarization (ODNP). We carry out site-specific ODNP measurements of the hydration water fluctuations along the surface of Chemotaxis Y (CheY), and correlate the measured fluctuations to hydropathic and topological properties of the CheY surface as derived from molecular dynamics (MD) simulation. Furthermore, we compare hydration water fluctuations measured on the CheY surface to that of other globular proteins, as well as intrinsically disordered proteins, peptides, and liposome surfaces to systematically test characteristic effects of the biomolecular surface on the hydration water dynamics. Our results suggest that the labile (ps) hydration water fluctuations are modulated by the chemical nature of the surface, while the bound (ns) water fluctuations are present on surfaces that feature a rough topology and chemical heterogeneity such as the surface of a folded and structured protein. In collaboration with: Ryan Barnes, Dept of Chemistry and Biochemistry, University of California Santa Barbara

Isatinphenylsemicarbazones as efficient colorimetric sensors for fluoride and acetate anions - anions induce tautomerism.

PubMed

Jakusová, Klaudia; Donovalová, Jana; Cigáň, Marek; Gáplovský, Martin; Garaj, Vladimír; Gáplovský, Anton

2014-04-05

The anion induced tautomerism of isatin-3-4-phenyl(semicarbazone) derivatives is studied herein. The interaction of F(-), AcO(-), H2PO4(-), Br(-) or HSO4(-) anions with E and Z isomers of isatin-3-4-phenyl(semicarbazone) and N-methylisatin-3-4-phenyl(semicarbazone) as sensors influences the tautomeric equilibrium of these sensors in the liquid phase. This tautomeric equilibrium is affected by (1) the inter- and intra-molecular interactions' modulation of isatinphenylsemicarbazone molecules due to the anion induced change in the solvation shell of receptor molecules and (2) the sensor-anion interaction with the urea hydrogens. The acid-base properties of anions and the difference in sensor structure influence the equilibrium ratio of the individual tautomeric forms. Here, the tautomeric equilibrium changes were indicated by "naked-eye" experiment, UV-VIS spectral and (1)H NMR titration, resulting in confirmation that appropriate selection of experimental conditions leads to a high degree of sensor selectivity for some investigated anions. Sensors' E and Z isomers differ in sensitivity, selectivity and sensing mechanism. Detection of F(-) or CH3COO(-) anions at high weakly basic anions' excess is possible. Copyright © 2014 Elsevier B.V. All rights reserved.

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

NASA Astrophysics Data System (ADS)

Shao, Yihan; Gan, Zhengting; Epifanovsky, Evgeny; Gilbert, Andrew T. B.; Wormit, Michael; Kussmann, Joerg; Lange, Adrian W.; Behn, Andrew; Deng, Jia; Feng, Xintian; Ghosh, Debashree; Goldey, Matthew; Horn, Paul R.; Jacobson, Leif D.; Kaliman, Ilya; Khaliullin, Rustam Z.; Kuś, Tomasz; Landau, Arie; Liu, Jie; Proynov, Emil I.; Rhee, Young Min; Richard, Ryan M.; Rohrdanz, Mary A.; Steele, Ryan P.; Sundstrom, Eric J.; Woodcock, H. Lee, III; Zimmerman, Paul M.; Zuev, Dmitry; Albrecht, Ben; Alguire, Ethan; Austin, Brian; Beran, Gregory J. O.; Bernard, Yves A.; Berquist, Eric; Brandhorst, Kai; Bravaya, Ksenia B.; Brown, Shawn T.; Casanova, David; Chang, Chun-Min; Chen, Yunqing; Chien, Siu Hung; Closser, Kristina D.; Crittenden, Deborah L.; Diedenhofen, Michael; DiStasio, Robert A., Jr.; Do, Hainam; Dutoi, Anthony D.; Edgar, Richard G.; Fatehi, Shervin; Fusti-Molnar, Laszlo; Ghysels, An; Golubeva-Zadorozhnaya, Anna; Gomes, Joseph; Hanson-Heine, Magnus W. D.; Harbach, Philipp H. P.; Hauser, Andreas W.; Hohenstein, Edward G.; Holden, Zachary C.; Jagau, Thomas-C.; Ji, Hyunjun; Kaduk, Benjamin; Khistyaev, Kirill; Kim, Jaehoon; Kim, Jihan; King, Rollin A.; Klunzinger, Phil; Kosenkov, Dmytro; Kowalczyk, Tim; Krauter, Caroline M.; Lao, Ka Un; Laurent, Adèle D.; Lawler, Keith V.; Levchenko, Sergey V.; Lin, Ching Yeh; Liu, Fenglai; Livshits, Ester; Lochan, Rohini C.; Luenser, Arne; Manohar, Prashant; Manzer, Samuel F.; Mao, Shan-Ping; Mardirossian, Narbe; Marenich, Aleksandr V.; Maurer, Simon A.; Mayhall, Nicholas J.; Neuscamman, Eric; Oana, C. Melania; Olivares-Amaya, Roberto; O'Neill, Darragh P.; Parkhill, John A.; Perrine, Trilisa M.; Peverati, Roberto; Prociuk, Alexander; Rehn, Dirk R.; Rosta, Edina; Russ, Nicholas J.; Sharada, Shaama M.; Sharma, Sandeep; Small, David W.; Sodt, Alexander; Stein, Tamar; Stück, David; Su, Yu-Chuan; Thom, Alex J. W.; Tsuchimochi, Takashi; Vanovschi, Vitalii; Vogt, Leslie; Vydrov, Oleg; Wang, Tao; Watson, Mark A.; Wenzel, Jan; White, Alec; Williams, Christopher F.; Yang, Jun; Yeganeh, Sina; Yost, Shane R.; You, Zhi-Qiang; Zhang, Igor Ying; Zhang, Xing; Zhao, Yan; Brooks, Bernard R.; Chan, Garnet K. L.; Chipman, Daniel M.; Cramer, Christopher J.; Goddard, William A., III; Gordon, Mark S.; Hehre, Warren J.; Klamt, Andreas; Schaefer, Henry F., III; Schmidt, Michael W.; Sherrill, C. David; Truhlar, Donald G.; Warshel, Arieh; Xu, Xin; Aspuru-Guzik, Alán; Baer, Roi; Bell, Alexis T.; Besley, Nicholas A.; Chai, Jeng-Da; Dreuw, Andreas; Dunietz, Barry D.; Furlani, Thomas R.; Gwaltney, Steven R.; Hsu, Chao-Ping; Jung, Yousung; Kong, Jing; Lambrecht, Daniel S.; Liang, WanZhen; Ochsenfeld, Christian; Rassolov, Vitaly A.; Slipchenko, Lyudmila V.; Subotnik, Joseph E.; Van Voorhis, Troy; Herbert, John M.; Krylov, Anna I.; Gill, Peter M. W.; Head-Gordon, Martin

2015-01-01

A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

X-ray and 1H-NMR spectroscopic studies of the structures and conformations of the new nootropic agents RU-35929, RU-47010 and RU-35965

NASA Astrophysics Data System (ADS)

Amato, Maria E.; Bandoli, Giuliano; Casellato, Umberto; Pappalardo, Giuseppe C.; Toja, Emilio

1990-10-01

The crystal and molecular structures of the nootropics (±)1-benzenesulphonyl-2-oxo-5-ethoxypyrrolidine ( 1), (±)1-(3-pyridinylsulphonyl)-2-oxo-5-ethoxypyrrolidine ( 2) and (±)1-benzenesulphonyl-2-oxo-5-isopropyloxypyrrolidine ( 3) have been determined by X-ray analysis. The solution conformation of 1, 2 and 3 has been investigated by 1H NMR spectroscopy. In the solid state, the main feature consists of the similar structural parameters and conformations, with the exception of the conformation adopted by the 5-ethoxy moiety which changes on passing from 1 to 2. The solid state overall enveloped conformation of the 2-pyrrolidinone ring for the three nootropics is found to be retained in solution on the basis of NMR evidence. Comparison between calculated and experimental coupling constant values shows that one of the two possible puckered opposite conformational isomers (half-chair shapes) occurs in solution. The relative pharmacological potencies of 1, 2 and 3 cannot therefore be interpreted in terms of the different conformation features presently detectable by available experimental methods.

Synthesis of flexirubin-mediated silver nanoparticles using Chryseobacterium artocarpi CECT 8497 and investigation of its anticancer activity.

PubMed

Venil, Chidambaram Kulandaisamy; Sathishkumar, Palanivel; Malathi, Mahalingam; Usha, Rajamanickam; Jayakumar, Rajarajeswaran; Yusoff, Abdull Rahim Mohd; Ahmad, Wan Azlina

2016-02-01

In this work, the synthesis of silver nanoparticles from a pigment produced by a recently-discovered bacterium, Chryseobacterium artocarpi CECT 8497, was achieved, followed by an investigation of its anticancer properties. The bacterial pigment was identified as flexirubin following NMR ((1)H NMR and (13)C NMR), UV-Vis, and LC-MS analysis. An aqueous silver nitrate solution was treated with isolated flexirubin to produce silver nanoparticles. The synthesised silver nanoparticles were subsequently characterised by UV-Vis spectroscopy, Scanning Electron Microscopy (SEM), Energy Dispersive X-ray Spectroscopy (EDX), X-Ray Diffraction (XRD), and Fourier Transform Infrared (FTIR) Spectroscopy methodologies. Furthermore, the anticancer effects of synthesised silver nanoparticles in a human breast cancer cell line (MCF-7) were evaluated. The tests showed significant cytotoxicity activity of the silver nanoparticles in the cultured cells, with an IC50 value of 36μgmL(-1). This study demonstrates that silver nanoparticles, synthesised from flexirubin from C. artocarpi CECT 8497, may have potential as a novel chemotherapeutic agent. Copyright © 2015 Elsevier B.V. All rights reserved.

Predicting solvation free energies and thermodynamics in polar solvents and mixtures using a solvation-layer interface condition

PubMed Central

Goossens, Spencer; Mehdizadeh Rahimi, Ali

2017-01-01

We demonstrate that with two small modifications, the popular dielectric continuum model is capable of predicting, with high accuracy, ion solvation thermodynamics (Gibbs free energies, entropies, and heat capacities) in numerous polar solvents. We are also able to predict ion solvation free energies in water–co-solvent mixtures over available concentration series. The first modification to the classical dielectric Poisson model is a perturbation of the macroscopic dielectric-flux interface condition at the solute–solvent interface: we add a nonlinear function of the local electric field, giving what we have called a solvation-layer interface condition (SLIC). The second modification is including the microscopic interface potential (static potential) in our model. We show that the resulting model exhibits high accuracy without the need for fitting solute atom radii in a state-dependent fashion. Compared to experimental results in nine water–co-solvent mixtures, SLIC predicts transfer free energies to within 2.5 kJ/mol. The co-solvents include both protic and aprotic species, as well as biologically relevant denaturants such as urea and dimethylformamide. Furthermore, our results indicate that the interface potential is essential to reproduce entropies and heat capacities. These and previous tests of the SLIC model indicate that it is a promising dielectric continuum model for accurate predictions in a wide range of conditions.

Nonlinear functional for solvation in Density Functional Theory

NASA Astrophysics Data System (ADS)

Gunceler, Deniz; Sundararaman, Ravishankar; Schwarz, Kathleen; Letchworth-Weaver, Kendra; Arias, T. A.

2013-03-01

Density functional calculations of molecules and surfaces in a liquid can accelerate the development of many technologies ranging from solar energy harvesting to lithium batteries. Such studies require the development of robust functionals describing the liquid. Polarizable continuum models (PCM's) have been applied to some solvated systems; but they do not sufficiently capture solvation effects to describe highly polar systems like surfaces of ionic solids. In this work, we present a nonlinear fluid functional within the framework of Joint Density Functional Theory. The fluid is treated not as a linear dielectric, but as a distribution of dipoles that responds to the solute, which we describe starting from the exact free energy functional for point dipoles. We also show PCM's can be recovered as the linear limit of our functional. Our description is of similar computational cost to PCM's, and captures complex solvation effects like dielectric saturation without requiring new fit parameters. For polar and nonpolar molecules, it achieves millihartree level agreement with experimental solvation energies. Furthermore, our functional now makes it possible to investigate chemistry on the surface of lithium battery materials, which PCM's predict to be unstable. Supported as part of the Energy Materials Center at Cornell, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001086

Applications of the solvation parameter model in reversed-phase liquid chromatography.

PubMed

Poole, Colin F; Lenca, Nicole

2017-02-24

The solvation parameter model is widely used to provide insight into the retention mechanism in reversed-phase liquid chromatography, for column characterization, and in the development of surrogate chromatographic models for biopartitioning processes. The properties of the separation system are described by five system constants representing all possible intermolecular interactions for neutral molecules. The general model can be extended to include ions and enantiomers by adding new descriptors to encode the specific properties of these compounds. System maps provide a comprehensive overview of the separation system as a function of mobile phase composition and/or temperature for method development. The solvation parameter model has been applied to gradient elution separations but here theory and practice suggest a cautious approach since the interpretation of system and compound properties derived from its use are approximate. A growing application of the solvation parameter model in reversed-phase liquid chromatography is the screening of surrogate chromatographic systems for estimating biopartitioning properties. Throughout the discussion of the above topics success as well as known and likely deficiencies of the solvation parameter model are described with an emphasis on the role of the heterogeneous properties of the interphase region on the interpretation and understanding of the general retention mechanism in reversed-phase liquid chromatography for porous chemically bonded sorbents. Copyright © 2016 Elsevier B.V. All rights reserved.

Predicting solvation free energies and thermodynamics in polar solvents and mixtures using a solvation-layer interface condition

NASA Astrophysics Data System (ADS)

Molavi Tabrizi, Amirhossein; Goossens, Spencer; Mehdizadeh Rahimi, Ali; Knepley, Matthew; Bardhan, Jaydeep P.

2017-03-01

We demonstrate that with two small modifications, the popular dielectric continuum model is capable of predicting, with high accuracy, ion solvation thermodynamics (Gibbs free energies, entropies, and heat capacities) in numerous polar solvents. We are also able to predict ion solvation free energies in water-co-solvent mixtures over available concentration series. The first modification to the classical dielectric Poisson model is a perturbation of the macroscopic dielectric-flux interface condition at the solute-solvent interface: we add a nonlinear function of the local electric field, giving what we have called a solvation-layer interface condition (SLIC). The second modification is including the microscopic interface potential (static potential) in our model. We show that the resulting model exhibits high accuracy without the need for fitting solute atom radii in a state-dependent fashion. Compared to experimental results in nine water-co-solvent mixtures, SLIC predicts transfer free energies to within 2.5 kJ/mol. The co-solvents include both protic and aprotic species, as well as biologically relevant denaturants such as urea and dimethylformamide. Furthermore, our results indicate that the interface potential is essential to reproduce entropies and heat capacities. These and previous tests of the SLIC model indicate that it is a promising dielectric continuum model for accurate predictions in a wide range of conditions.

Unraveling Complexity in the Solid Form Screening of a Pharmaceutical Salt: Why so Many Forms? Why so Few?

PubMed Central

2017-01-01

The solid form landscape of 5-HT2a antagonist 3-(4-(benzo[d]isoxazole-3-yl)piperazin-1-yl)-2,2-dimethylpropanoic acid hydrochloride (B5HCl) proved difficult to establish. Many crystalline materials were produced by solid form screening, but few forms readily grew high quality crystals to afford a clear picture or understanding of the solid form landscape. Careful control of crystallization conditions, a range of experimental methods, computational modeling of solvate structures, and crystal structure prediction were required to see potential arrangements of the salt in its crystal forms. Structural diversity in the solid form landscape of B5HCl was apparent in the layer structures for the anhydrate polymorphs (Forms I and II), dihydrate and a family of solvates with alcohols. The alcohol solvates, which provided a distinct packing from the neat forms and the dihydrate, form layers with conserved hydrogen bonding between B5HCl and the solvent, as well as stacking of the aromatic rings. The ability of the alcohol hydrocarbon moieties to efficiently pack between the layers accounted for the difficulty in growing some solvate crystals and the inability of other solvates to crystallize altogether. Through a combination of experiment and computation, the crystallization problems, form stability, and desolvation pathways of B5HCl have been rationalized at a molecular level. PMID:29018305

Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces

DOE PAGES

Herron, Jeffrey A.; Morikawa, Yoshitada; Mavrikakis, Manos

2016-08-08

Using ab initio molecular dynamics (as implemented in periodic, self-consistent (GGA-PBE) density functional theory (DFT) we investigated the mechanism of methanol electro-oxidation on Pt(111). We investigated the role of solvation and electrode potential on the energetics of the first proton transfer step, methanol electro-oxidation to methoxy (CH 3O) or hydroxymethyl (CH 2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), while the binding energy of methanol and hydroxymethyl are not significantly affected. The free energies of activation for breaking the C-H and O-H bonds in methanol were calculated through a Blue Moon Ensemble using constrainedmore » ab initio molecular dynamics. Calculated barriers for these elementary steps on unsolvated, uncharged Pt(111) are similar to results for climbing-image nudged elastic band calculations from the literature. Solvation reduces the barrier for both C-H and O-H bond activation steps with respect to their vapor phase values, though the effect is more pronounced for C-H bond activation due to less disruption of the hydrogen-bond network. The calculated activation energy barriers show that breaking the C-H bond of methanol is more facile than the O-H bond on solvated negatively biased, or uncharged Pt(111). Furthermore, with positive bias, O-H bond activation is enhanced, becoming slightly more facile than C-H bond activation.« less

NMR- and GC/MS-based metabolomics of sulfur mustard exposed individuals: a pilot study.

PubMed

Nobakht, B Fatemeh; Aliannejad, Rasoul; Rezaei-Tavirani, Mostafa; Arefi Oskouie, Afsaneh; Naseri, Mohammad Taghi; Parastar, Hadi; Aliakbarzadeh, Ghazaleh; Fathi, Fariba; Taheri, Salman

2016-09-01

Sulfur mustard (SM) is a potent alkylating agent and its effects on cells and tissues are varied and complex. Due to limitations in the diagnostics of sulfur mustard exposed individuals (SMEIs) by noninvasive approaches, there is a great necessity to develop novel techniques and biomarkers for this condition. We present here the first nuclear magnetic resonance (NMR) and gas chromatography-mass spectrometry (GC/MS) metabolic profiling of serum from and healthy controls to identify novel biomarkers in blood serum for better diagnostics. Of note, SMEIs were exposed to SM 30 years ago and that differences between two groups could still be found. Pathways in which differences between SMEIs and healthy controls are observed are related to lipid metabolism, ketogenesis, tricarboxylic acid (TCA) cycle and amino acid metabolism.

Synthesis, characterization and fluorescent properties of water-soluble glycopolymer bearing curcumin pendant residues.

PubMed

Zhang, Haisong; Yu, Meng; Zhang, Hailei; Bai, Libin; Wu, Yonggang; Wang, Sujuan; Ba, Xinwu

2016-08-01

Curcumin is a potential natural anticancer drug with low oral bioavailability because of poor water solubility. The aqueous solubility of curcumin is enhanced by means of modification with the carbohydrate units. Polymerization of the curcumin-containing monomer with carbohydrate-containing monomer gives the water-soluble glycopolymer bearing curcumin pendant residues. The obtained copolymers (P1 and P2) having desirable water solubility were well-characterized by infrared spectroscopy (IR), nuclear magnetic resonance (NMR), gel permeation chromatography (GPC), UV-Vis absorption spectroscopy, and photoluminescence spectroscopy. The copolymer P2 with a molar ratio of 1:6 (curcumin/carbohydrate) calculated from the proton NMR results exhibits a similar anticancer activity compared to original curcumin, which may serve as a potential chemotherapeutic agent in the field of anticancer medicine.

Microwave assisted synthesis and anti-lipase activity of some new fluorine-containing benzimidazoles.

PubMed

Menteşe, E; Yilmaz, F; Ülker, S; Kahveci, B

2015-01-01

In this study, a new series of fluorine containing benzimidazoles (4a-l) and bisbenzimidazoles (6a-c, 8) were synthesized by the reaction of o-phenylenediamines with iminoester hydrochlorides (3a-l, 7) in methanol under microwave irradiation. The structures of these newly synthesized compounds were identified by IR, (1)H-NMR, (13)C-NMR, mass spectroscopy and elemental analysis data. The synthesized compounds were screened for their pancreatic lipase activities. Our results indicate that the compounds 6a, 6b and 6c can serve as an anti-lipase agent. The compounds 6b and 6c inhibited pancreatic lipase activity by 84.03% and 97.49% at a concentration of 3 µg/mL, respectively. © Georg Thieme Verlag KG Stuttgart · New York.

Crystal structure and theoretical calculations of Julocrotine, a natural product with antileishmanial activity

NASA Astrophysics Data System (ADS)

Moreira, Rafael Y. O.; Brasil, Davi S. B.; Alves, Cláudio N.; Guilhon, Giselle M. S. P.; Santos, Lourivaldo S.; Arruda, Mara S. P.; Müller, Adolfo H.; Barbosa, Patrícia S.; Abreu, Alcicley S.; Silva, Edilene O.; Rumjanek, Victor M.; Souza, Jaime, Jr.; da Silva, Albérico B. F.; Santos, Regina H. De A.

Julocrotine, N-(2,6-dioxo-1-phenethyl-piperidin-3-yl)-2-methyl-butyramide, is a potent antiproliferative agent against the promastigote and amastigote forms of Leishmania amazonensis (L.). In this work, the crystal structure of Julocrotine was solved by X-ray diffraction, and its geometrical parameters were compared with theoretical calculations at the B3LYP and HF level of theory. IR and NMR spectra also have been obtained and compared with theoretical calculations. IR absorptions calculated with the B3LYP level of theory employed together with the 6-311G+(d,p) basis set, are close to those observed experimentally. Theoretical NMR calculations show little deviation from experimental results. The results show that the theory is in accordance with the experimental data.0

Decursin: a cytotoxic agent and protein kinase C activator from the root of Angelica gigas.

PubMed

Ahn, K S; Sim, W S; Kim, I H

1996-02-01

A cytotoxic compound was purified from the root of Angelica gigas Nakai by silica gel chromatography and preparative HPLC. As a result of the structure analysis by mass, IR, 1H-NMR, and 13C-NMR spectrometry, the effective compound was identified as decursin, a pyranocoumarin characterized originally from Angelica decursiva Fr. et Sav. In vitro cytotoxicity testing showed that decursin displayed toxic activity against various human cancer cell lines, for which the ED50 of decursin was about 5-16 micrograms/ml. On the other hand, decursin displayed relatively low cytotoxicity against normal fibroblasts. Decursin also activated protein kinase C (PKC) in vitro, which indicates that the cytotoxic activity of decursin may be related to the protein kinase C activation.

Synthesis, crystal structure, and biological evaluation of a series of phloretin derivatives.

PubMed

Wang, Li; Li, Zheng-Wei; Zhang, Wei; Xu, Rui; Gao, Fei; Liu, Yang-Feng; Li, Ya-Jun

2014-10-13

A one-step synthesis of phloretin derivatives 2-11 from phloretin in good to excellent yields is reported. Their structures were characterized by 1H-NMR, 13C-NMR and MS, and the structures of 8 and 11 were determined by X-ray diffraction analysis. A mechanism for the formation of 9-11 is proposed. Compared with the anticancer drug docetaxel, phloretin, phloretin derivatives and phlorizin exhibited moderate cytotoxicity toward the MDA-MB-231, SPC-A1, A549, MCF-7 and EC109 cell lines. Among all of the tested compounds, 7 exhibited the strongest cytotoxicity toward the five cell lines and was more active than docetaxel in MDA-MB-231 cells. Our findings suggest that these derivatives hold great promise for further development as anticancer agents.

Novel pyrrolopyrimidines and triazolopyrrolopyrimidines carrying a biologically active sulfonamide moieties as anticancer agents.

PubMed

Ghorab, Mostafa M; Alsaisd, Mansour S; Nissan, Yassin M

2015-01-01

A new series of pyrroles 5, 6, pyrrolopyrimidines 8, 11-14, 16-29, triazolo-pyrrolopyrimidines 9, 10 and 15 carrying a biologically active sulfonamide moities were synthesized using 2-amino-3-cyano-4-(4-bromophenyl)pyrrole 5 as a strategic starting material. The structures of the prepared compounds were confirmed by elemental analyses, IR, 1H-NMR and 13C-NMR data. All of the synthesized compounds showed promising anticancer activity against breast cancer cell line (MCF7) compared to doxorubicin as reference drug, especially compounds 5-17, 21-24 and 28 with better IC50 than that of doxorubicin. In order to suggest the mechanism of action of their cytotoxic activities, molecular docking on the active site of c-Src was done and good results were obtained.

129 Xe NMR Relaxation-Based Macromolecular Sensing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gomes, Muller D.; Dao, Phuong; Jeong, Keunhong

2016-07-29

A 129Xe NMR relaxation-based sensing approach is reported on that exploits changes in the bulk xenon relaxation rate induced by slowed tumbling of a cryptophane-based sensor upon target binding. The amplification afforded by detection of the bulk dissolved xenon allows sensitive detection of targets. The sensor comprises a xenon-binding cryptophane cage, a target interaction element, and a metal chelating agent. Xenon associated with the target-bound cryptophane cage is rapidly relaxed and then detected after exchange with the bulk. Here we show that large macromolecular targets increase the rotational correlation time of xenon, increasing its relaxation rate. Upon binding of amore » biotin-containing sensor to avidin at 1.5 μM concentration, the free xenon T 2 is reduced by a factor of 4.« less

New series of aromatic/ five-membered heteroaromatic butanesulfonyl hydrazones as potent biological agents: Synthesis, physicochemical and electronic properties

NASA Astrophysics Data System (ADS)

Hamurcu, Fatma; Mamaş, Serhat; Ozdemir, Ummuhan Ozmen; Gündüzalp, Ayla Balaban; Senturk, Ozan Sanlı

2016-08-01

The aromatic/five-membered heteroaromatic butanesulfonylhydrazone derivatives; 5-bromosalicylaldehydebutanesulfonylhydrazone(1), 2-hydroxy-1-naphthaldehydebutane sulfonylhydrazone(2), indole-3-carboxaldehydebutanesulfonylhydrazone (3), 2-acetylfuran- carboxyaldehydebutanesulfonylhydrazone(4), 2-acetylthiophenecarboxyaldehydebutane- sulfonylhydrazone(5) and 2-acetyl-5-chlorothiophenecarboxyaldehydebutanesulfonyl hydrazone (6) were synthesized by the reaction of butane sulfonic acid hydrazide with aldehydes/ketones and characterized by using elemental analysis, 1H NMR, 13C NMR and FT-IR technique. Their geometric parameters and electronic properties consist of global reactivity descriptors were also determined by theoretical methods. The electrochemical behavior of the butanesulfonylhydrazones were investigated by using cyclic voltammetry (CV), controlled potential electrolysis and chronoamperometry (CA) techniques. The number of electrons transferred (n), diffusion coefficient (D) and standard heterogeneous rate constants (ks) were determined by electrochemical methods.

Diastereoselective Synthesis of a Strawberry Flavoring Agent by Epoxidation of Ethyl trans-b-Methylcinnamate

NASA Astrophysics Data System (ADS)

Pageau, Gayle J.; Mabaera, Rodwell; Kosuda, Kathryn M.; Sebelius, Tamara A.; Ghaffari, Ali H.; Kearns, Kenneth A.; McIntyre, Jean P.; Beachy, Tina M.; Thamattoor, Dasan M.

2002-01-01

The diastereoselective synthesis of ethyl (E)-3-methyl-3-phenylglycidate, a strawberry flavoring agent, is carried out by epoxidizing ethyl trans-b-methylcinnamate with m-chloroperbenzoic acid. This epoxidation is appropriate for the introductory organic laboratory and augments the small number of such experiments currently available for undergraduate education. In the course of performing this exercise, students are exposed to many important facets of organic chemistry such as synthesis, reaction mechanism, stereochemistry, chromatography, quantitative analysis, spectroscopy, and computational chemistry. The 1H NMR spectrum of this compound is especially interesting and presents instructive examples of diastereotopic protons and shielding effects of the aromatic ring current.

Thin Metallic Films from Solvated Metal Atoms.

DTIC Science & Technology

1987-07-14

platinium , and especially indium are discussed. N, ; ,, -- !, : N) By Dist , , . N S f1 -- ~~r, 821-19 C[ Thin metallic films from solvated metal atoms...metallic films. Cold, palladium, platinium , and especially indium are discussed. 1- INTRQDUCTION In the field of chemistry an active and broad area of