Direct single-molecule dynamic detection of chemical reactions.

PubMed

Guan, Jianxin; Jia, Chuancheng; Li, Yanwei; Liu, Zitong; Wang, Jinying; Yang, Zhongyue; Gu, Chunhui; Su, Dingkai; Houk, Kendall N; Zhang, Deqing; Guo, Xuefeng

2018-02-01

Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry.

Direct single-molecule dynamic detection of chemical reactions

PubMed Central

Guan, Jianxin; Jia, Chuancheng; Li, Yanwei; Liu, Zitong; Wang, Jinying; Yang, Zhongyue; Gu, Chunhui; Su, Dingkai; Houk, Kendall N.; Zhang, Deqing; Guo, Xuefeng

2018-01-01

Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry. PMID:29487914

Dynamic solvophobic effect and its cooperativity in the hydrogen-bonding liquids studied by dielectric and nuclear magnetic resonance relaxation.

PubMed

Yamaguchi, Tsuyoshi; Furuhashi, Hiroki; Matsuoka, Tatsuro; Koda, Shinobu

2008-12-25

The reorientational relaxation of solvent molecules in the mixture of nonpolar solutes and hydrogen-bonding liquids including water, alcohols, and amides are studied by dielectric and 2H-nuclear magnetic resonance (NMR) spin-lattice relaxations. The retardation of the reorientational motion of the solvent by weak solute-solvent interaction is observed in all the solvent systems. On the other hand, no clear correlation between the strength of the solute-solvent interaction and the slowing down of the solvent motion is found in N,N-dimethylacetamide, which suggests the importance of the hydrogen bonding in the dynamic solvophobic effect. The cooperativity of the reorientational relaxation is investigated by the comparison between the collective relaxation measured by the dielectric spectroscopy and the single-molecular reorientation determined by NMR. The modification of the dielectric relaxation time caused by the dissolution of the solute is larger than that of the single-molecular reorientational relaxation time in all the solvents studied here. The effect of the static correlation between the dipole moments of different molecules is calculated from the static dielectric constant, and the effect of the dynamic correlation is estimated. The difference in the effects of the solutes on the collective and single-molecular reorientational relaxation is mainly ascribed to the dynamic cooperativity in the cases of water and alcohols, which is consistent with the picture on the dynamic solvophobicity derived by our previous theoretical analysis (Yamaguchi, T.; Matsuoka, T.; Koda, S. J. Chem. Phys. 2004, 120, 7590). On the other hand, the static correlation plays the principal role in the case of N-methylformamide.

Vibrational energy transfer between carbon nanotubes and nonaqueous solvents: a molecular dynamics study.

PubMed

Nelson, Tammie R; Chaban, Vitaly V; Prezhdo, Victor V; Prezhdo, Oleg V

2011-05-12

We report molecular dynamics (MD) simulation of energy exchange between single-walled carbon nanotubes (CNTs) and two aprotic solvents, acetonitrile and cyclohexane. Following our earlier study of hydrated CNTs, we find that the time scales and molecular mechanisms of the energy transfer are largely independent of the nature of the surrounding medium, and therefore, should hold for other media including polymer matrices and DNA. The vibrational energy exchange between CNT and solvents exhibits two time-scales. Over half of the energy is transferred in less than one picosecond, indicating that the dominant exchange mechanism is inertial relaxation. It occurs by collisions of solvent molecules with CNT walls, facilitated by the short-range Lennard-Jones interaction. Additional several picoseconds are required for the remainder of the vibrational energy exchange, corresponding to the diffusive relaxation mechanism and involving collective molecular motions. The faster stage of the CNT-solvent energy exchange occurs on the same time-scale, and therefore, competes with the vibrational energy relaxation inside CNTs. The energy exchange time-scales are significantly influenced by the arrangement of solvent molecules inside CNTs. Generally, the effects of confinement on the dynamics can be rationalized by analysis of the solvent structure. For the same CNT diameter, the extent of the confinement effect strongly depends on the size of the solvent molecules. Icelike properties in water seen in small CNTs disappear in CNTs with intermediate diameters. In acetonitrile and cyclohexane, medium size CNTs still show strong confinement effects. Rotational motions of acetonitrile molecules are inhibited, and the cyclohexane density is dramatically decreased. The disbalance between the local temperatures of the inside and outside regions of the solvent equilibrates through a tube-mediated interaction, rather than by a direct coupling between the two solvent subsystems. In all cases, the CNT-solvent energy transfer is mediated by slow motions in the frequency range of CNT radial breathing modes.

Solvent empirical scales and their importance for the study of intermolecular interactions

NASA Astrophysics Data System (ADS)

Babusca, Daniela; Benchea, Andreea Celia; Morosanu, Ana Cezarina; Dimitriu, Dan Gheorghe; Dorohoi, Dana Ortansa

2017-01-01

The solvent empirical scales were developed in order to classify the solvents regarding their influence on the absorption or fluorescence spectra of different spectrally active molecules. The intermolecular interactions in binary solutions of three molecule having an intramolecular charge transfer visible absorption band are studied in this paper: 5-[2-(1,2,2,4-tetramethyl-1,2,3,4-tetrahydroquinolin-6-yl)-vinyl]-thiophene-2-carbaldehyde (QTC), 1-cyano-2-{5-[2-(1,2,2,4-tetramethyl-1,2,3,4-tetrahydroquinolin-6-yl)-vinyl]-thiophen-2-yl}-vinyl)-phosphonic acid diethyl ester (QTCP) and p-phenyl pyridazinium-p-nitro-phenacylid (PPNP). The solvent empirical scales with a single parameter (Z scale of Kosower, ET (30) or ETN scale of Reichardt and Dimroth) can be used to describe the strength of intermolecular interactions. The contributions of each type of interactions to the total spectral shift are evaluated using the solvent multiple parameters empirical scales defined by Kamlet and Taft and by Catalan et al.

Local phase separation of co-solvents enhances pretreatment of biomass for bioenergy applications

DOE PAGES

Mostofian, Barmak; Cai, Charles M.; Smith, Micholas Dean; ...

2016-08-02

Pretreatment facilitates more complete deconstruction of plant biomass to enable more economic production of lignocellulosic biofuels and byproducts. Various co-solvent pretreatments have demonstrated advantages relative to aqueous-only methods by enhancing lignin removal to allow unfettered access to cellulose. However, there is a limited mechanistic understanding of the interactions between the co-solvents and cellulose that impedes further improvement of such pretreatment methods. Recently, tetrahydrofuran (THF) has been identified as a highly effective co-solvent for the pretreatment and fractionation of biomass. Here, to elucidate the mechanism of the THF water interactions with cellulose, we pair simulation and experimental data demonstrating that enhancedmore » solubilization of cellulose can be achieved by the THF water co-solvent system at equivolume mixtures and moderate temperatures (≤445 K). The simulations show that THF and water spontaneously phase separate on the local surface of a cellulose fiber, owing to hydrogen bonding of water molecules with the hydrophilic cellulose faces and stacking of THF molecules on the hydrophobic faces. Furthermore, a single fully solvated cellulose chain is shown to be preferentially bound by water molecules in the THF water mixture. In light of these findings, co-solvent reactions were performed on microcrystalline cellulose and maple wood to show that THF significantly enhanced cellulose deconstruction and lignocellulose solubilization at simulation conditions, enabling a highly versatile and efficient biomass pretreatment and fractionation method.« less

Conjugated polymers: Watching polymers dance

NASA Astrophysics Data System (ADS)

Rothberg, Lewis

2011-06-01

Single-molecule spectroscopy allows fluctuations of conjugated polymer conformation to be monitored during solvent vapour annealing. Dramatic changes in fluorescence behaviour are observed and interpreted in terms of transformations between extended and collapsed polymer geometries.

Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics

NASA Astrophysics Data System (ADS)

Mansbach, Rachael A.; Ferguson, Andrew L.

2015-03-01

The conformational states explored by polymers and proteins can be controlled by environmental conditions (e.g., temperature, pressure, and solvent) and molecular chemistry (e.g., molecular weight and side chain identity). We introduce an approach employing the diffusion map nonlinear machine learning technique to recover single molecule free energy landscapes from molecular simulations, quantify changes to the landscape as a function of external conditions and molecular chemistry, and relate these changes to modifications of molecular structure and dynamics. In an application to an n-eicosane chain, we quantify the thermally accessible chain configurations as a function of temperature and solvent conditions. In an application to a family of polyglutamate-derivative homopeptides, we quantify helical stability as a function of side chain length, resolve the critical side chain length for the helix-coil transition, and expose the molecular mechanisms underpinning side chain-mediated helix stability. By quantifying single molecule responses through perturbations to the underlying free energy surface, our approach provides a quantitative bridge between experimentally controllable variables and microscopic molecular behavior, guiding and informing rational engineering of desirable molecular structure and function.

Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics.

PubMed

Mansbach, Rachael A; Ferguson, Andrew L

2015-03-14

The conformational states explored by polymers and proteins can be controlled by environmental conditions (e.g., temperature, pressure, and solvent) and molecular chemistry (e.g., molecular weight and side chain identity). We introduce an approach employing the diffusion map nonlinear machine learning technique to recover single molecule free energy landscapes from molecular simulations, quantify changes to the landscape as a function of external conditions and molecular chemistry, and relate these changes to modifications of molecular structure and dynamics. In an application to an n-eicosane chain, we quantify the thermally accessible chain configurations as a function of temperature and solvent conditions. In an application to a family of polyglutamate-derivative homopeptides, we quantify helical stability as a function of side chain length, resolve the critical side chain length for the helix-coil transition, and expose the molecular mechanisms underpinning side chain-mediated helix stability. By quantifying single molecule responses through perturbations to the underlying free energy surface, our approach provides a quantitative bridge between experimentally controllable variables and microscopic molecular behavior, guiding and informing rational engineering of desirable molecular structure and function.

Long-range single domain array of a 5 nm pattern of supramolecules via solvent annealing in a double-sandwich cell.

PubMed

Kwon, Kiok; Park, Kangho; Jung, Hee-Tae

2018-05-10

In nanotechnology and microelectronics research, the generation of an ultradense, single-grain nanostructure with a long-range lateral order is challenging. In this paper, we report upon a new solvent-annealing method using a double-sandwich confinement to promote the formation of a large-area, single-domain array (>0.3 × 0.3 mm2) of supramolecular cylinders with a small feature size (4.7 nm). The in situ GISAXS experiment result shows the ordering process during solvent evaporation. The diffusion of the solvent molecules led to the disassembly of the supramolecules confined between the top and bottom surfaces and their subsequent mobilization, thereby producing a highly ordered hexagonal array of supramolecular materials under the double-sandwich confinement upon solvent evaporation. In addition, two key factors were found to be crucial in this process for generating highly-ordered supramolecular building blocks: (i) the presence of a top coat during solvent evaporation to provide a geometric confinement template, and (ii) the control of the solvent evaporation rate during the solvent evaporation step to provide the dendrimer sufficient time to self-assemble into the highly ordered state over a large area. Our developed approach, which can be extended to be used for a large family of supramolecules, is of critical importance in providing a new bottom-up lithographic method based on supramolecular self-assembly.

Solvent-modified ultrafast decay dynamics in conjugated polymer/dye labeled single stranded DNA

NASA Astrophysics Data System (ADS)

Kim, Inhong; Kang, Mijeong; Woo, Han Young; Oh, Jin-Woo; Kyhm, Kwangseuk

2015-07-01

We have investigated that organic solvent (DMSO, dimethyl sulfoxide) modifies energy transfer efficiency between conjugated polymers (donors) and fluorescein-labeled single stranded DNAs (acceptors). In a mixture of buffer and organic solvent, fluorescence of the acceptors is significantly enhanced compared to that of pure water solution. This result can be attributed to change of the donor-acceptor environment such as decreased hydrophobicity of polymers, screening effect of organic solvent molecules, resulting in an enhanced energy transfer efficiency. Time-resolved fluorescence decay of the donors and the acceptors was modelled by considering the competition between the energy harvesting Foerster resonance energy transfer and the energy-wasting quenching. This enables to quantity that the Foerster distance (R0 = 43.3 Å) and resonance energy transfer efficiency (EFRET = 58.7 %) of pure buffer solution become R0 = 38.6 Å and EFRET = 48.0 % when 80% DMSO/buffer mixture is added.

Single crystalline growth of a soluble organic semiconductor in a parallel aligned liquid crystal solvent using rubbing-treated polyimide films

NASA Astrophysics Data System (ADS)

Matsuzaki, Tomoya; Shibata, Yosei; Takeda, Risa; Ishinabe, Takahiro; Fujikake, Hideo

2017-01-01

For directional control of organic single crystals, we propose a crystal growth method using liquid crystal as the solvent. In this study, we examined the formation of 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene (C8-BTBT) single crystals using a parallel aligned liquid crystal (LC) cell and rubbing-treated polyimide films in order to clarify the effects of LC alignment on anisotropic C8-BTBT crystal growth. Based on the results, we found that the crystal growth direction of C8-BTBT single crystals was related to the direction of the aligned LC molecules because of rubbing treatment. Moreover, by optical evaluation, we found that the C8-BTBT single crystals have a aligned molecular structure.

Solvent effects on the adsorption and self-organization of Mn12 on Au(111).

PubMed

Pineider, Francesco; Mannini, Matteo; Sessoli, Roberta; Caneschi, Andrea; Barreca, Davide; Armelao, Lidia; Cornia, Andrea; Tondello, Eugenio; Gatteschi, Dante

2007-11-06

A sulfur-containing single molecule magnet, [Mn12O12(O2CC6H4SCH3)16(H2O)4], was assembled from solution on a Au(111) surface affording both submonolayer and monolayer coverages. The adsorbate morphology and the degree of coverage were inspected by scanning tunneling microscopy (STM), while X-ray photoelectron spectroscopy (XPS) allowed the determination of the chemical nature of the adsorbate on a qualitative and quantitative basis. The properties of the adsorbates were found to be strongly dependent on the solvent used to dissolve the magnetic complex. In particular, systems prepared from tetrahydrofuran solutions gave arrays of isolated and partially ordered clusters on the gold substrate, while samples prepared from dichloromethane exhibited a homogeneous monolayer coverage of the whole Au(111) surface. These findings are relevant to the optimization of magnetic addressing of single molecule magnets on surfaces.

Unexpected solvent effects on the UV/Vis absorption spectra of o-cresol in toluene and benzene: in contrast with non-aromatic solvents

PubMed Central

Zheng, Dong; Yuan, Xiang-Ai; Ma, Haibo; Li, Xiaoxiong; Wang, Xizhang; Liu, Ziteng

2018-01-01

Cresol is a prototype molecule in understanding intermolecular interactions in material and biological systems, because it offers different binding sites with various solvents and protonation states under different pH values. It is found that the UV/Vis absorption spectra of o-cresol in aromatic solvents (benzene, toluene) are characterized by a sharp peak, unlike the broad double-peaks in 11 non-aromatic solvents. Both molecular dynamics simulations and electronic structure calculations revealed the formation of intermolecular π-complexation between o-cresol and aromatic solvents. The thermal movements of solvent and solute molecules render the conformations of o-cresol changing between trans and cis isomers. The π-interaction makes the cis configuration a dominant isomer, hence leading to the single keen-edged UV/Vis absorption peak at approximately 283 nm. The free conformation changes between trans and cis in aqueous solution rationalize the broader absorption peaks in the range of 260–280 nm. The pH dependence of the UV/Vis absorption spectra in aqueous solutions is also rationalized by different protonation states of o-cresol. The explicit solvent model with long-ranged interactions is vital to describe the effects of π-complexation and electrostatic interaction on the UV/Vis absorption spectra of o-cresol in toluene and alkaline aqueous (pH > 10.3) solutions, respectively. PMID:29657794

Unexpected solvent effects on the UV/Vis absorption spectra of o-cresol in toluene and benzene: in contrast with non-aromatic solvents.

PubMed

Zheng, Dong; Yuan, Xiang-Ai; Ma, Haibo; Li, Xiaoxiong; Wang, Xizhang; Liu, Ziteng; Ma, Jing

2018-03-01

Cresol is a prototype molecule in understanding intermolecular interactions in material and biological systems, because it offers different binding sites with various solvents and protonation states under different pH values. It is found that the UV/Vis absorption spectra of o -cresol in aromatic solvents (benzene, toluene) are characterized by a sharp peak, unlike the broad double-peaks in 11 non-aromatic solvents. Both molecular dynamics simulations and electronic structure calculations revealed the formation of intermolecular π-complexation between o -cresol and aromatic solvents. The thermal movements of solvent and solute molecules render the conformations of o -cresol changing between trans and cis isomers. The π-interaction makes the cis configuration a dominant isomer, hence leading to the single keen-edged UV/Vis absorption peak at approximately 283 nm. The free conformation changes between trans and cis in aqueous solution rationalize the broader absorption peaks in the range of 260-280 nm. The pH dependence of the UV/Vis absorption spectra in aqueous solutions is also rationalized by different protonation states of o -cresol. The explicit solvent model with long-ranged interactions is vital to describe the effects of π-complexation and electrostatic interaction on the UV/Vis absorption spectra of o -cresol in toluene and alkaline aqueous (pH > 10.3) solutions, respectively.

Solubility Limits in Lennard-Jones Mixtures: Effects of Disparate Molecule Geometries.

PubMed

Dyer, Kippi M; Perkyns, John S; Pettitt, B Montgomery

2015-07-23

In order to better understand general effects of the size and energy disparities between macromolecules and solvent molecules in solution, especially for macromolecular constructs self-assembled from smaller molecules, we use the first- and second-order exact bridge diagram extensions of the HNC integral equation theory to investigate single-component, binary, ternary, and quaternary mixtures of Lennard-Jones fluids. For pure fluids, we find that the HNCH3 bridge function integral equation (i.e., exact to third order in density) is necessary to quantitatively predict the pure gas and pure liquid sides of the coexistence region of the phase diagram of the Lennard-Jones fluid. For the mixtures, we find that the HNCH2 bridge function integral equation is sufficient to qualitatively predict solubility in the binary, ternary, and quaternary mixtures, up to the nominal solubility limit. The results, as limiting cases, should be useful to several problems, including accurate phase diagram predictions for complex mixtures, design of self-assembling nanostructures via solvent controls, and the solvent contributions to the conformational behavior of macromolecules in complex fluids.

Optimizing electrostatic field calculations with the Adaptive Poisson-Boltzmann Solver to predict electric fields at protein-protein interfaces II: explicit near-probe and hydrogen-bonding water molecules.

PubMed

Ritchie, Andrew W; Webb, Lauren J

2014-07-17

We have examined the effects of including explicit, near-probe solvent molecules in a continuum electrostatics strategy using the linear Poisson-Boltzmann equation with the Adaptive Poisson-Boltzmann Solver (APBS) to calculate electric fields at the midpoint of a nitrile bond both at the surface of a monomeric protein and when docked at a protein-protein interface. Results were compared to experimental vibrational absorption energy measurements of the nitrile oscillator. We examined three methods for selecting explicit water molecules: (1) all water molecules within 5 Å of the nitrile nitrogen; (2) the water molecule closest to the nitrile nitrogen; and (3) any single water molecule hydrogen-bonding to the nitrile. The correlation between absolute field strengths with experimental absorption energies were calculated and it was observed that method 1 was only an improvement for the monomer calculations, while methods 2 and 3 were not significantly different from the purely implicit solvent calculations for all protein systems examined. Upon taking the difference in calculated electrostatic fields and comparing to the difference in absorption frequencies, we typically observed an increase in experimental correlation for all methods, with method 1 showing the largest gain, likely due to the improved absolute monomer correlations using that method. These results suggest that, unlike with quantum mechanical methods, when calculating absolute fields using entirely classical models, implicit solvent is typically sufficient and additional work to identify hydrogen-bonding or nearest waters does not significantly impact the results. Although we observed that a sphere of solvent near the field of interest improved results for relative field calculations, it should not be consider a panacea for all situations.

Linear response coupled cluster theory with the polarizable continuum model within the singles approximation for the solvent response.

PubMed

Caricato, Marco

2018-04-07

We report the theory and the implementation of the linear response function of the coupled cluster (CC) with the single and double excitations method combined with the polarizable continuum model of solvation, where the correlation solvent response is approximated with the perturbation theory with energy and singles density (PTES) scheme. The singles name is derived from retaining only the contribution of the CC single excitation amplitudes to the correlation density. We compare the PTES working equations with those of the full-density (PTED) method. We then test the PTES scheme on the evaluation of excitation energies and transition dipoles of solvated molecules, as well as of the isotropic polarizability and specific rotation. Our results show a negligible difference between the PTED and PTES schemes, while the latter affords a significantly reduced computational cost. This scheme is general and can be applied to any solvation model that includes mutual solute-solvent polarization, including explicit models. Therefore, the PTES scheme is a competitive approach to compute response properties of solvated systems using CC methods.

Linear response coupled cluster theory with the polarizable continuum model within the singles approximation for the solvent response

NASA Astrophysics Data System (ADS)

Caricato, Marco

2018-04-01

We report the theory and the implementation of the linear response function of the coupled cluster (CC) with the single and double excitations method combined with the polarizable continuum model of solvation, where the correlation solvent response is approximated with the perturbation theory with energy and singles density (PTES) scheme. The singles name is derived from retaining only the contribution of the CC single excitation amplitudes to the correlation density. We compare the PTES working equations with those of the full-density (PTED) method. We then test the PTES scheme on the evaluation of excitation energies and transition dipoles of solvated molecules, as well as of the isotropic polarizability and specific rotation. Our results show a negligible difference between the PTED and PTES schemes, while the latter affords a significantly reduced computational cost. This scheme is general and can be applied to any solvation model that includes mutual solute-solvent polarization, including explicit models. Therefore, the PTES scheme is a competitive approach to compute response properties of solvated systems using CC methods.

Interfacial free energy governs single polystyrene chain collapse in water and aqueous solutions.

PubMed

Li, Isaac T S; Walker, Gilbert C

2010-05-12

The hydrophobic interaction is significantly responsible for driving protein folding and self-assembly. To understand it, the thermodynamics, the role of water structure, the dewetting process surrounding hydrophobes, and related aspects have undergone extensive investigations. Here, we examine the hypothesis that polymer-solvent interfacial free energy is adequate to describe the energetics of the collapse of a hydrophobic homopolymer chain at fixed temperature, which serves as a much simplified model for studying the hydrophobic collapse of a protein. This implies that changes in polymer-solvent interfacial free energy should be directly proportional to the force to extend a collapsed polymer into a bad solvent. To test this hypothesis, we undertook single-molecule force spectroscopy on a collapsed, single, polystyrene chain in water-ethanol and water-salt mixtures where we measured the monomer solvation free energy from an ensemble average conformations. Different proportions within the binary mixture were used to create solvents with different interfacial free energies with polystyrene. In these mixed solvents, we observed a linear correlation between the interfacial free energy and the force required to extend the chain into solution, which is a direct measure of the solvation free energy per monomer on a single chain at room temperature. A simple analytical model compares favorably with the experimental results. This knowledge supports a common assumption that explicit water solvent may not be necessary for cases whose primary concerns are hydrophobic interactions and hydrophobic hydration.

Solvent Effects on the Conductance of 1,4-benzenediamine

NASA Astrophysics Data System (ADS)

Fatemi, Valla; Kamenetska, Maria; Neaton, Jeffrey; Venkataraman, Latha

2010-03-01

We measured the conductance of 1,4-benzenediamine (BDA) by mechanically forming and breaking Au point contacts with a modified STM in a solution of molecules in ambient conditions, using a variety of solvents. Here, we present reliable experimental results which show that the conductance of BDA can be increased by over 50% when dissolved in aromatic organic solvents solely by varying halogen groups on the solvent molecule. The trends in conductance do not correlate with the solvent dielectric constant, dipole moment, or direct solvent-BDA interactions. First-principles density functional theory calculations of solvent molecule binding to gold surfaces are used to discuss mechanisms behind the conductance shift of the BDA molecule.

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.

Ferutinin as a Ca(2+) complexone: lipid bilayers, conductometry, FT-IR, NMR studies and DFT-B3LYP calculations.

PubMed

Dubis, A; Zamaraeva, M V; Siergiejczyk, L; Charishnikova, O; Shlyonsky, V

2015-10-07

Calcium ionophoretic properties of ferutinin were re-evaluated in solvent-containing bilayer lipid membranes. The slopes of conductance-concentration curves suggest that in the presence of a solvent in the membrane the majority of complexes appear to consist of a single terpenoid molecule bound to one Ca ion. By contrast, the stoichiometry of ferutinin-Ca(2+) complexes in acetone determined using the conductometric method was 2 : 1. While the cation-cation selectivity of ferutinin did not change, the cation-anion selectivity slightly decreased in solvent containing membranes. FT-IR and NMR data together with DFT calculations at the B3LYP/6-31G(d) level of theory indicate that in the absence of Ca ions ferutinin molecules are hydrogen-bonded at the phenol hydroxyl groups. The variations of absorption assigned to -OH and -C-O stretching mode suggest that ferutinin interacts strongly with Ca ions via the hydroxyl group of ferutinol and carboxyl oxygen of the complex ether bond. The coordination through the carbonyl group of ferutinin was demonstrated by theoretical calculations. Taken together, ferutinin molecules form H-bonded dimers, while complexation of Ca(2+) by ferutinin ruptures this hydrogen bond due to spatial re-orientation of the ferutinin molecules from parallel to antiparallel alignment.

A Single-Level Tunnel Model to Account for Electrical Transport through Single Molecule- and Self-Assembled Monolayer-based Junctions

PubMed Central

Garrigues, Alvar R.; Yuan, Li; Wang, Lejia; Mucciolo, Eduardo R.; Thompon, Damien; del Barco, Enrique; Nijhuis, Christian A.

2016-01-01

We present a theoretical analysis aimed at understanding electrical conduction in molecular tunnel junctions. We focus on discussing the validity of coherent versus incoherent theoretical formulations for single-level tunneling to explain experimental results obtained under a wide range of experimental conditions, including measurements in individual molecules connecting the leads of electromigrated single-electron transistors and junctions of self-assembled monolayers (SAM) of molecules sandwiched between two macroscopic contacts. We show that the restriction of transport through a single level in solid state junctions (no solvent) makes coherent and incoherent tunneling formalisms indistinguishable when only one level participates in transport. Similar to Marcus relaxation processes in wet electrochemistry, the thermal broadening of the Fermi distribution describing the electronic occupation energies in the electrodes accounts for the exponential dependence of the tunneling current on temperature. We demonstrate that a single-level tunnel model satisfactorily explains experimental results obtained in three different molecular junctions (both single-molecule and SAM-based) formed by ferrocene-based molecules. Among other things, we use the model to map the electrostatic potential profile in EGaIn-based SAM junctions in which the ferrocene unit is placed at different positions within the molecule, and we find that electrical screening gives rise to a strongly non-linear profile across the junction. PMID:27216489

Solution-Phase Conformation and Dynamics of Conjugated Isoindigo-Based Donor–Acceptor Polymer Single Chains

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

Lee, Franklin L.; Farimani, Amir Barati; Gu, Kevin L.

Conjugated polymers are the key material in thin-film organic optoelectronic devices due to the versatility of these molecules combined with their semiconducting properties. A molecular-scale understanding of conjugated polymers is important to the optimization of the thin-film morphology. We examine the solution-phase behavior of conjugated isoindigo-based donor–acceptor polymer single chains of various chain lengths using atomistic molecular dynamics simulations. Our simulations elucidate the transition from a rod-like to a coil-like conformation from an analysis of normal modes and persistence length. In addition, we find another transition based on the solvent environment, contrasting the coil-like conformation in a good solvent withmore » a globule-like conformation in a poor solvent. Altogether, our results provide valuable insights into the transition between conformational regimes for conjugated polymers as a function of both the chain length and the solvent environment, which will help to accurately parametrize higher level models.« less

Solution-Phase Conformation and Dynamics of Conjugated Isoindigo-Based Donor–Acceptor Polymer Single Chains

DOE PAGES

Lee, Franklin L.; Farimani, Amir Barati; Gu, Kevin L.; ...

2017-10-25

Conjugated polymers are the key material in thin-film organic optoelectronic devices due to the versatility of these molecules combined with their semiconducting properties. A molecular-scale understanding of conjugated polymers is important to the optimization of the thin-film morphology. We examine the solution-phase behavior of conjugated isoindigo-based donor–acceptor polymer single chains of various chain lengths using atomistic molecular dynamics simulations. Our simulations elucidate the transition from a rod-like to a coil-like conformation from an analysis of normal modes and persistence length. In addition, we find another transition based on the solvent environment, contrasting the coil-like conformation in a good solvent withmore » a globule-like conformation in a poor solvent. Altogether, our results provide valuable insights into the transition between conformational regimes for conjugated polymers as a function of both the chain length and the solvent environment, which will help to accurately parametrize higher level models.« less

HF in clusters of molecular hydrogen. I. Size evolution of quantum solvation by parahydrogen molecules.

PubMed

Jiang, Hao; Bacić, Zlatko

2005-06-22

We present a theoretical study of the quantum solvation of the HF molecule by a small number of parahydrogen molecules, having n = 1-13 solvent particles. The minimum-energy cluster structures determined for n = 1-12 have all of the H(2) molecules in the first solvent shell. The first solvent shell closes at n = 12 and its geometry is icosahedral, with the HF molecule at the center. The quantum-mechanical ground-state properties of the clusters are calculated exactly using the diffusion Monte Carlo method. The zero-point energy of (p-H(2))(n)HF clusters is unusually large, amounting to 86% of the potential well depth for n > 7. The radial probability distribution functions (PDFs) confirm that the first solvent shell is complete for n = 12, and that the 13th p-H(2) molecule begins to fill the second solvent shell. The p-H(2) molecules execute large-amplitude motions and are highly mobile, making the solvent cage exceptionally fluxional. The anisotropy of the solvent, very pronounced for small clusters, decreases rapidly with increasing n, so that for n approximately 8-9 the solvent environment is practically isotropic. The analysis of the pair angular PDF reveals that for a given n, the parahydrogen solvent density around the HF is modulated in a pattern which clearly reflects the lowest-energy cluster configuration. The rigidity of the solvent clusters displays an interesting size dependence, increasing from n = 6 to 9, becoming floppier for n = 10, and increasing again up to n = 12, as the solvent shell is filled. The rigidity of the solvent cage appears to reach its maximum for n = 12, the point at which the first solvent shell is closed.

Structural elucidation, molecular representation and solvent interactions of vitrinite-rich and inertinite-rich South African coals

NASA Astrophysics Data System (ADS)

van Niekerk, Daniel

The structural differences and similarities of two Permian-aged South African coals, vitrinite-rich Waterberg and inertinite-rich Highveld coals (similar rank, carbon content and Permian age), were evaluated. With South African coals the opportunity presented itself to study not only Permian-aged Gondwana vitrinite but also inertinite. It was expected that these coals would differ from Northern hemisphere Carboniferous coals. It was concluded from various structural data that both coals, although different in maceral composition and depositional basins, are similar in their base structural composition. The main differences were that the inertinite-rich Highveld coal was more ordered, more aromatic, and had less hydrogen than the vitrinite-rich Waterberg coal. Analytical data were used to construct large-scale advanced molecular representations for vitrinite-rich Waterberg and inertinite-rich Highveld coals. The three-dimensional models were structurally diverse with a molecular weight range of 78 to 1900 amu. The vitrinite-rich coal model consisted of 18,572 atoms and 191 individual molecules and the inertinite-rich coal model consisted of 14,242 atoms and 158 individual molecules. This largescale modeling effort was enabled by the development of various PERL scripts to automate various visualization and analytical aspects. Coal swelling studies were conducted using the traditional pack-bed swelling method and a new novel single-particle stop-motion videography swelling method with NMP and CS2/NMP solvents. The pack-bed swelling showed that vitrinite-rich coal had a greater swelling extent and that swelling extent for both coals was greater in CS2/NMP binary solvent than for NMP. Single-particle swelling experiments showed that both coals, for both solvents, exhibit overshoot-type and climbing-type swelling behaviors. Inertinite-coal had a faster swelling rate, in both solvents, than the vitrinite-rich coal. The single-particle swelling data was used to calculate the kinetic parameters and it was found that the swelling was governed by relaxation of the coal structure (super-Case II swelling). X-ray computed tomography was conducted confirming anisotropic swelling. The petrographic transitions (maceral-group composition and reflectance) with solvent swelling and extraction were quantified. No changes in the maceral compositions were found, but changes in some coal particles were observed. Random reflectance analysis showed that, for both vitrinite and inertinite, there is a decrease in reflectance values with solvent treatment. Vitrinite reflectograms showed a shift from the dominant reflecting V-types to lower V-types. The inertinite reflectograms exhibited an increase in number of I-types (broadening of reflectrograms). Molecular simulation and visualization approaches to solvent swelling and extraction were performed on the proposed molecular models of vitrinite-rich and inertinite-rich coals. A theoretical extraction yield was determined using solubility parameters and showed agreement with experimental extraction yield trends. Statistical Associating Fluid Theory (SAFT) modeling was explored to test whether this method could predict swelling extent. The predicted swelling trends of SAFT were comparable to that of the experimental swelling results. SAFT was found to be a promising tool for solvent-coal interaction predictions. Partially solvent swollen structures were constructed by the addition of solvent molecules to the original coal molecules using a amorphous building approach. This method showed that coal-coal non-bonding interaction changed with the introduction of solvent. A disruption in the van der Waals interaction energies and a change in hydrogen bond distributions were observed in the swollen coal models and quantified. It was concluded that small changes in coal structure translates to significant changes in solvent interaction behavior. These changes were successfully visualized and simulated using atomistic molecular representations.

Biomolecular Doping of Single-Walled Carbon Nanotubes by Thyroid Hormone

NASA Astrophysics Data System (ADS)

Rojas, Enrique; Paulson, Scott; Stern, Mike; Staii, Cristian; Dratman, Mary; Johnson, Alan

2004-03-01

Electron doping of semiconducting single-walled carbon nanotubes (SWNTs) by the thyroid hormone triiodothyronine (T3) is observed. T3 is applied locally, in solution, to SWNT field effect transistors (FETs) and binds along the length of the nanotube. T3 acts as an electron donor, shifting the I-V gate characteristics towards negative values of gate voltage. Shifts in the characteristics are measured as a function of the concentration of the solution. The effect is nearly reversible by rinsing the FETs with the solvent. Several days after application of T3, with no solvent rinsing, the gate characteristics are also nearly reversed. Experiments with a similar molecule for which the phenol ring is brominated as well as experiments with the de-iodinated molecule (T0) are performed to inform the effect of the iodine. The interaction of T3 with SWNTs may suggest a electronic interaction of T3 with other one-dimensional systems such as DNA.

Application of chiral critical clusters to assymetric synthesis

DOEpatents

Ferrieri, Richard A.

2002-01-01

Disclosed is a composition, a method of making and a method of using critical clusters for asymmetric synthesis using substantially optically-pure chiral solvent molecules in a supercritical fluid. The solvent molecules are capable of forming a multipoint hydrogen bonded solvate as they encage at least one solute molecule. The encaged solute molecule is capable of reacting to form an optically active chiral center. In another aspect, there is disclosed a method of directing the position of bonding between a solute molecule and a ligand involving encaging the solute molecule and the ligand with polar solvent molecules in a supercritical fluid under conditions of temperature and pressure sufficient to change electric charge distribution in the solute molecule. In yet another aspect, disclosed is a method of making pharmaceutical compounds involving encaging a solute molecule, which is capable of forming a chiral center, and a ligand with polar solvent molecules in a supercritical fluid under conditions of temperature and pressure sufficient to change electric charge distribution of the solute molecule. The solute molecule and ligand are then reacted whereby the ligand bonds to the solute molecule forming a chiral center. Also disclosed is a method for racemic resolution using critical clusters involving encaging racemic mixtures of solute molecules with substantially optically-pure chiral solvent molecules in a supercritical fluid under conditions of temperature and pressure sufficient to form critical clusters. The solvent molecules are capable of multipoint hydrogen bonding with the solute molecules. The encaged solute molecules are then nonenzymatically reacted to enhance the optical purity of the solute molecules.

Study on four polymorphs of bifendate based on X-ray crystallography.

PubMed

Nie, Jinju; Yang, Dezhi; Hu, Kun; Lu, Yang

2016-05-01

Bifendate, a synthetic anti-hepatitis drug, exhibits polycrystalline mode phenomena with 2 polymorphs reported (forms A and B). Single crystals of the known crystalline form B and 3 new crystallosolvates involving bifendate solvated with tetrahydrofuran (C), dioxane (D), and pyridine (E) in a stoichiometric ratio of 1:1 were obtained and characterized by X-ray crystallography, thermal analysis, and Fourier transform infrared (FT-IR) spectroscopy. The differences in molecular conformation, intermolecular interaction and crystal packing arrangement for the four polymorphs were determined and the basis for the polymorphisms was investigated. The rotation of single bonds resulted in different orientations for the biphenyl, methyl ester and methoxyl groups. All guest solvent molecules interacted with the host molecule via an interesting intercalative mode along the [1 0 0] direction in the channel formed by the host molecules through weak aromatic stacking interactions or non-classical hydrogen bonds, of which the volume and planarity played an important role in the intercalation of the host with the guest. The incorporation of solvent-augmented rotation of the C-C bond of the biphenyl group had a striking effect on the host molecular conformation and contributed to the formation of bifendate polymorphs. Moreover, the simulated powder X-ray diffraction (PXRD) patterns for each form were calculated on the basis of the single-crystal data and proved to be unique. The single-crystal structures of the four crystalline forms are reported in this paper.

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.

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.

Integrated Solvent Design for CO 2 Capture and Viscosity Tuning

DOE PAGES

Cantu, David C.; Malhotra, Deepika; Koech, Phillip K.; ...

2017-08-18

We present novel design strategies for reduced viscosity single-component, water-lean CO 2 capture organic solvent systems. Through molecular simulation, we identify the main molecular-level descriptor that influences bulk solvent viscosity. Upon loading, a zwitterionic structure forms with a small activation energy of ca 16 kJ/mol and a small stabilization of ca 6 kJ/mol. Viscosity increases exponentially with CO 2 loading due to hydrogen-bonding between neighboring Zwitterions. We find that molecular structures that promote internal hydrogen bonding (within the same molecule) and suppress interactions with neighboring molecules have low viscosities. In addition, tuning the acid/base properties leads to a shift ofmore » the equilibrium toward a non-charged (acid) form that further reduces the viscosity. Here, based on the above structural criteria, a reduced order model is also presented that allows for the quick screening of large compound libraries and down selection of promising candidates for synthesis and testing.« less

Formation of blade and slot die coated small molecule multilayers for OLED applications studied theoretically and by XPS depth profiling

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

Peters, Katharina; Raupp, Sebastian, E-mail: sebastian.raupp@kit.edu; Scharfer, Philip

2016-06-15

Slot die coaters especially designed for low material consumption and doctor blades were used to process small molecule solutions for organic light-emitting diodes (OLEDs). Optimum process parameters were developed for the large-scale coating techniques to generate stable single and multiple layers only a few nanometers thick. Achieving a multilayer architecture for solution-processed OLEDs is the most challenging step. X-ray photoelectron spectroscopy sputter depth profiling was performed to determine defined interfaces between coated organic layers. Commercially available small molecules NPB (N,N’-Di(1-naphthyl)-N,N’-diphenyl-(1,1’-biphenyl)-4,4’-diamine) and BAlq (Bis(8-hdroxy-2methylquinoline)-(4-phenylphenoxy)aluminum), originally developed for vacuum deposition, were used as hole, respectively electron transport material. Defined double-layers were processedmore » with both scalable coating methods using the orthogonal solvent approach. The use of non-orthogonal solvents resulted in complete intermixing of the material. The results are explained by calculations of solubilities and simulating drying and diffusion kinetics of the small molecule solutions.« less

Prediction of Water Binding to Protein Hydration Sites with a Discrete, Semiexplicit Solvent Model.

PubMed

Setny, Piotr

2015-12-08

Buried water molecules are ubiquitous in protein structures and are found at the interface of most protein-ligand complexes. Determining their distribution and thermodynamic effect is a challenging yet important task, of great of practical value for the modeling of biomolecular structures and their interactions. In this study, we present a novel method aimed at the prediction of buried water molecules in protein structures and estimation of their binding free energies. It is based on a semiexplicit, discrete solvation model, which we previously introduced in the context of small molecule hydration. The method is applicable to all macromolecular structures described by a standard all-atom force field, and predicts complete solvent distribution within a single run with modest computational cost. We demonstrate that it indicates positions of buried hydration sites, including those filled by more than one water molecule, and accurately differentiates them from sterically accessible to water but void regions. The obtained estimates of water binding free energies are in fair agreement with reference results determined with the double decoupling method.

Formation of blade and slot die coated small molecule multilayers for OLED applications studied theoretically and by XPS depth profiling

NASA Astrophysics Data System (ADS)

Peters, Katharina; Raupp, Sebastian; Hummel, Helga; Bruns, Michael; Scharfer, Philip; Schabel, Wilhelm

2016-06-01

Slot die coaters especially designed for low material consumption and doctor blades were used to process small molecule solutions for organic light-emitting diodes (OLEDs). Optimum process parameters were developed for the large-scale coating techniques to generate stable single and multiple layers only a few nanometers thick. Achieving a multilayer architecture for solution-processed OLEDs is the most challenging step. X-ray photoelectron spectroscopy sputter depth profiling was performed to determine defined interfaces between coated organic layers. Commercially available small molecules NPB (N,N'-Di(1-naphthyl)-N,N'-diphenyl-(1,1'-biphenyl)-4,4'-diamine) and BAlq (Bis(8-hdroxy-2methylquinoline)-(4-phenylphenoxy)aluminum), originally developed for vacuum deposition, were used as hole, respectively electron transport material. Defined double-layers were processed with both scalable coating methods using the orthogonal solvent approach. The use of non-orthogonal solvents resulted in complete intermixing of the material. The results are explained by calculations of solubilities and simulating drying and diffusion kinetics of the small molecule solutions.

A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics

NASA Astrophysics Data System (ADS)

Sun, Hui; Wen, Jiayi; Zhao, Yanxiang; Li, Bo; McCammon, J. Andrew

2015-12-01

Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson-Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum-Chandler-Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods.

A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics.

PubMed

Sun, Hui; Wen, Jiayi; Zhao, Yanxiang; Li, Bo; McCammon, J Andrew

2015-12-28

Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson-Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum-Chandler-Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods.

A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson–Boltzmann electrostatics

PubMed Central

Sun, Hui; Wen, Jiayi; Zhao, Yanxiang; Li, Bo; McCammon, J. Andrew

2015-01-01

Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson–Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum–Chandler–Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods. PMID:26723595

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

Uemura, Kazuhiro, E-mail: k_uemura@gifu-u.ac.j; Onishi, Fumiaki; Yamasaki, Yukari

NO{sub 2} containing dicarboxylate bridging ligands, nitroterephthalate (bdc-NO{sub 2}) and 2,5-dinitroterephthalate (bdc-(NO{sub 2}){sub 2}), afford porous coordination polymers, {l_brace}[Zn{sub 2}(bdc-NO{sub 2}){sub 2}(dabco)].solvents{r_brace}{sub n} (2 contains solvents) and {l_brace}[Zn{sub 2}(bdc-(NO{sub 2}){sub 2}){sub 2}(dabco)].solvents{r_brace}{sub n} (3 contains solvents). Both compounds form jungle-gym-type regularities, where a 2D square grid composed of dinuclear Zn{sub 2} units and dicarboxylate ligands is bridged by dabco molecules to extend the 2D layers into a 3D structure. In 2 contains solvents and 3 contains solvents, a rectangle pore surrounded by eight Zn{sub 2} corners contains two and four NO{sub 2} moieties, respectively. Thermal gravimetry (TG) and X-ray powdermore » diffraction (XRPD) measurements reveal that both compounds maintain the frameworks regularities without guest molecules and with solvents such as MeOH, EtOH, i-PrOH, and Me{sub 2}CO. Adsorption measurements reveal that dried 2 and 3 adsorb H{sub 2}O molecules to be {l_brace}[Zn{sub 2}(bdc-NO{sub 2}){sub 2}(dabco)].4H{sub 2}O{r_brace}{sub n} (2 contains 4H{sub 2}O) and {l_brace}[Zn{sub 2}(bdc-(NO{sub 2}){sub 2}){sub 2}(dabco)].6H{sub 2}O{r_brace}{sub n} (3 contains 6H{sub 2}O), showing the pore hydrophilicity enhancement caused by NO{sub 2} group introduction. - Graphical abstract: Two hydrophilic porous coordination polymers, [Zn{sub 2}(bdc-NO{sub 2}){sub 2}(dabco)]{sub n} (2, bdc-NO{sub 2}=nitroterephthalate, dabco=1,4-diazabicyclo[2.2.2]octane) and [Zn{sub 2}(bdc-(NO{sub 2}){sub 2}){sub 2}(dabco)]{sub n} (3, bdc-(NO{sub 2}){sub 2}=2,5-dinitroterephthalate), have been synthesized and characterized by single X-ray analyses, thermal gravimetry, and adsorption measurements.« less

Watching the Solvation of Atoms in Liquids One Solvent Molecule at a Time

NASA Astrophysics Data System (ADS)

Bragg, Arthur E.; Glover, William J.; Schwartz, Benjamin J.

2010-06-01

We use mixed quantum-classical molecular dynamics simulations and ultrafast transient hole-burning spectroscopy to build a molecular-level picture of the motions of solvent molecules around Na atoms in liquid tetrahydrofuran. We find that even at room temperature, the solvation of Na atoms occurs in discrete steps, with the number of solvent molecules nearest the atom changing one at a time. This explains why the rate of solvent relaxation differs for different initial nonequilibrium states, and reveals how the solvent helps determine the identity of atomic species in liquids.

On a relationship between molecular polarizability and partial molar volume in water.

PubMed

Ratkova, Ekaterina L; Fedorov, Maxim V

2011-12-28

We reveal a universal relationship between molecular polarizability (a single-molecule property) and partial molar volume in water that is an ensemble property characterizing solute-solvent systems. Since both of these quantities are of the key importance to describe solvation behavior of dissolved molecular species in aqueous solutions, the obtained relationship should have a high impact in chemistry, pharmaceutical, and life sciences as well as in environments. We demonstrated that the obtained relationship between the partial molar volume in water and the molecular polarizability has in general a non-homogeneous character. We performed a detailed analysis of this relationship on a set of ~200 organic molecules from various chemical classes and revealed its fine well-organized structure. We found that this structure strongly depends on the chemical nature of the solutes and can be rationalized in terms of specific solute-solvent interactions. Efficiency and universality of the proposed approach was demonstrated on an external test set containing several dozens of polyfunctional and druglike molecules.

WITHDRAWN: Fragmentation of charged aqueous nanodroplets

NASA Astrophysics Data System (ADS)

Ichiki, Kengo

2005-11-01

The whole evaporating process of charged aqueous nanodroplets is studied by systematic molecular dynamics simulations until most of the solvent molecules are evaporated. % The solvent evaporation makes the droplet smaller and smaller, and at a certain point the repulsive force among ions causes an instability, where typically single ion and 10 to 20 water molecules are disintegrated from the main droplet. % This ion fragmentation occurs around 70 to 80% of the charge predicted by the Rayleigh theory [Lord Rayleigh, Phil. Mag. 14, 184 (1882)]. % The numerical results are summarized in the function R(z) which is the fragmentation radius at the charge z. From the fitting by the power law Rz^β, we find that at lower temperature T=350 and 370 K the result is close to the Rayleigh theory β= 2/3, while at higher temperature T=400 and 450 K it is like β= 1/2. % Another fitting on R(z) by the extended ion evaporation mechanism [M. Gamero-Castaño and J. Fern'andez de la Mora, Anal. Chim. Acta 406, 67 (2000)] works well for both cases. % The final state of the evaporation process is typically a single ion with several water molecules. If we put an alanine dipeptide in zwitterionic form at the beginning, two charges remain in some cases.

Thermophoresis of dissolved molecules and polymers: Consideration of the temperature-induced macroscopic pressure gradient

NASA Astrophysics Data System (ADS)

Semenov, Semen; Schimpf, Martin

2004-01-01

The movement of molecules and homopolymer chains dissolved in a nonelectrolyte solvent in response to a temperature gradient is considered a consequence of temperature-induced pressure gradients in the solvent layer surrounding the solute molecules. Local pressure gradients are produced by nonuniform London van der Waals interactions, established by gradients in the concentration (density) of solvent molecules. The density gradient is produced by variations in solvent thermal expansion within the nonuniform temperature field. The resulting expression for the velocity of the solute contains the Hamaker constants for solute-solvent and solute-solute interactions, the radius of the solute molecule, and the viscosity and cubic coefficient of thermal expansion of the solvent. In this paper we consider an additional force that arises from directional asymmetry in the interaction between solvent molecules. In a closed cell, the resulting macroscopic pressure gradient gives rise to a volume force that affects the motion of dissolved solutes. An expression for this macroscopic pressure gradient is derived and the resulting force is incorporated into the expression for the solute velocity. The expression is used to calculate thermodiffusion coefficients for polystyrene in several organic solvents. When these values are compared to those measured in the laboratory, the consistency is better than that found in previous reports, which did not consider the macroscopic pressure gradient that arises in a closed thermodiffusion cell. The model also allows for the movement of solute in either direction, depending on the relative values of the solvent and solute Hamaker constants.

A coordination chemistry study of hydrated and solvated cationic vanadium ions in oxidation states +III, +IV, and +V in solution and solid state

PubMed Central

Krakowiak, Joanna; Lundberg, Daniel

2012-01-01

The coordination chemistry of hydrated and solvated vanadium(III), oxovanadium(IV), and dioxovanadium(V) ions in the oxygen donor solvents water, dimethylsulfoxide (dmso) and N,N′-dimethylpropyleneurea (dmpu) has been studied in solution by EXAFS and large angle X-ray scattering (LAXS) and in solid state by single crystal X-ray diffraction and EXAFS. The hydrated vanadium(III) ion has a regular octahedral configuration with a mean V-O bond distance of 1.99 Å. In the hydrated and dimethylsulfoxide solvated oxovanadium(IV) ions vanadium binds strongly to an oxo group at ca. 1.6 Å. The solvent molecule trans to the oxo group is very weakly bound, at ca. 2.2 Å, while the remaining four solvent molecules, with a mean V-O bond distance of 2.0 Å, form a plane slightly below the vanadium atom; the mean O=V-Operp bond angle is ca. 98°. In the dmpu solvated oxovanadium(IV) ion, the space demanding properties of the dmpu molecule leaving no solvent molecule in the trans position to the oxo group which reduces the coordination number to 5. The O=V-O bond angle is consequently much larger, 106°, and the mean V=O and V-O bond distances decrease to 1.58 and 1.97 Å, respectively. The hydrated and dimethylsulfoxide solvated dioxovanadium(V) ions display a very distorted octahedral configuration with the oxo groups in cis position with mean V=O bond distances of 1.6 Å and a O=V=O bond angle of ca. 105°. The solvent molecules trans to the oxo groups are weakly bound, at ca. 2.2 Å, while the remaining two have bond distances of 2.02 Å. The experimental studies of the coordination chemistry of hydrated and solvated vanadium(III,IV,V) ions are complemented by summarizing previously reported crystal structures to yield a comprehensive description of the coordination chemistry of vanadium with oxygen donor ligands. PMID:22950803

Insights into the effects of solvent properties in graphene based electric double-layer capacitors with organic electrolytes

NASA Astrophysics Data System (ADS)

Zhang, Shuo; Bo, Zheng; Yang, Huachao; Yang, Jinyuan; Duan, Liangping; Yan, Jianhua; Cen, Kefa

2016-12-01

Organic electrolytes are widely used in electric double-layer capacitors (EDLCs). In this work, the microstructure of planar graphene-based EDLCs with different organic solvents are investigated with molecular dynamics simulations. Results show that an increase of solvent polarity could weaken the accumulation of counter-ions nearby the electrode surface, due to the screen of electrode charges and relatively lower ionic desolvation. It thus suggests that solvents with low polarity could be preferable to yield high EDL capacitance. Meanwhile, the significant effects of the size and structure of solvent molecules are reflected by non-electrostatic molecule-electrode interactions, further influencing the adsorption of solvent molecules on electrode surface. Compared with dimethyl carbonate, γ-butyrolactone, and propylene carbonate, acetonitrile with relatively small-size and linear structure owns weak non-electrostatic interactions, which favors the easy re-orientation of solvent molecules. Moreover, the shift of solvent orientation in surface layer, from parallel orientation to perpendicular orientation relative to the electrode surface, deciphers the solvent twin-peak behavior near negative electrode. The as-obtained insights into the roles of solvent properties on the interplays among particles and electrodes elucidate the solvent influences on the microstructure and capacitive behavior of EDLCs using organic electrolytes.

Potential of mean force between two hydrophobic solutes in water.

PubMed

Southall, Noel T; Dill, Ken A

2002-12-10

We study the potential of mean force between two nonpolar solutes in the Mercedes Benz model of water. Using NPT Monte Carlo simulations, we find that the solute size determines the relative preference of two solute molecules to come into contact ('contact minimum') or to be separated by a single layer of water ('solvent-separated minimum'). Larger solutes more strongly prefer the contacting state, while smaller solutes have more tendency to become solvent-separated, particularly in cold water. The thermal driving forces oscillate with solute separation. Contacts are stabilized by entropy, whereas solvent-separated solute pairing is stabilized by enthalpy. The free energy of interaction for small solutes is well-approximated by scaled-particle theory. Copyright 2002 Elsevier Science B.V.

A dual cryogenic ion trap spectrometer for the formation and characterization of solvated ionic clusters

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

Marsh, Brett M.; Voss, Jonathan M.; Garand, Etienne, E-mail: egarand@chem.wisc.edu

2015-11-28

A new experimental approach is presented in which two separate cryogenic ion traps are used to reproducibly form weakly bound solvent clusters around electrosprayed ions and messenger-tag them for single-photon infrared photodissociation spectroscopy. This approach thus enables the vibrational characterization of ionic clusters comprised of a solvent network around large and non-volatile ions. We demonstrate the capabilities of the instrument by clustering water, methanol, and acetone around a protonated glycylglycine peptide. For water, cluster sizes with greater than twenty solvent molecules around a single ion are readily formed. We further demonstrate that similar water clusters can be formed around ionsmore » having a shielded charge center or those that do not readily form hydrogen bonds. Finally, infrared photodissociation spectra of D{sub 2}-tagged GlyGlyH{sup +} ⋅ (H{sub 2}O){sub 1−4} are presented. They display well-resolved spectral features and comparisons with calculations reveal detailed information on the solvation structures of this prototypical peptide.« less

A dual cryogenic ion trap spectrometer for the formation and characterization of solvated ionic clusters

DOE PAGES

Marsh, Brett M.; Voss, Jonathan M.; Garand, Etienne

2015-11-24

A new experimental approach is presented in which two separate cryogenic ion traps are used to reproducibly form weakly bound solvent clusters around electrosprayed ions and messenger-tag them for single-photon infrared photodissociation spectroscopy. This approach thus enables the vibrational characterization of ionic clusters comprised of a solvent network around large and non-volatile ions. We demonstrate the capabilities of the instrument by clustering water, methanol, and acetone around a protonated glycylglycine peptide. For water, cluster sizes with greater than twenty solvent molecules around a single ion are readily formed. We further demonstrate that similar water clusters can be formed around ionsmore » having a shielded charge center or those that do not readily form hydrogen bonds. Finally, infrared photodissociation spectra of D 2-tagged GlyGlyH +·(H 2O) 1–4 are presented. As a result, they display well-resolved spectral features and comparisons with calculations reveal detailed information on the solvation structures of this prototypical peptide.« less

Single crystal X-ray diffraction, spectroscopic and mass spectrometric studies of furanocoumarin peucedanin.

PubMed

Bartnik, Magdalena; Arczewska, Marta; Hoser, Anna A; Mroczek, Tomasz; Kamiński, Daniel M; Głowniak, Kazimierz; Gagoś, Mariusz; Woźniak, Krzysztof

2014-01-01

The structure of peucedanin, isolated from Peucedanum tauricum Bieb. (Apiaceae), has been established using single crystal X-ray diffraction. This furanocoumarin isolated from the light petroleum extract of P. tauricum fruits was characterized by high resolution EI-MS, sATR-FTIR and 2D NMR spectroscopic techniques. The EI-MS showed the typical fragmentation pattern of methoxyfuranocoumarins. Extensive 1D (1H and 13C) as well as 2D NMR data enabled complete assignment of the carbon atoms in the peucedanin molecule. The FTIR data confirms intermolecular hydrogen bonding between peucedanin molecules in polar solvents. Peucedanin crystallises in the R-3 space group from the trigonal system with one molecule in the asymmetric part of the unit cell. The crystal lattice of peucedanin consists of the molecules arranged in separate columns. They are related by two fold screw axes and centres of symmetry. Interestingly, peucedanin columns form two channels per unit cell with a diameter of 7.5angstrom going through the crystal lattice in the Z-direction. These channels are filled with disordered water molecules, which are surrounded by hydrophobic methyl groups and are located exactly at the centres of the channels. The peucedanin molecules are stacked in a single column with the opposite orientation of the neighbouring molecules. These results could be interesting in further application of this molecule, for example in biological tests of its activity.

Theoretical studies of UO(2)(OH)(H(2)O)(n) (+), UO(2)(OH)(2)(H(2)O)(n), NpO(2)(OH)(H(2)O)(n), and PuO(2)(OH)(H(2)O)(n) (+) (n

PubMed

Cao, Zhiji; Balasubramanian, K

2009-10-28

Extensive ab initio calculations have been carried out to study equilibrium structures, vibrational frequencies, and the nature of chemical bonds of hydrated UO(2)(OH)(+), UO(2)(OH)(2), NpO(2)(OH), and PuO(2)(OH)(+) complexes that contain up to 21 water molecules both in first and second hydration spheres in both aqueous solution and the gas phase. The structures have been further optimized by considering long-range solvent effects through a polarizable continuum dielectric model. The hydrolysis reaction Gibbs free energy of UO(2)(H(2)O)(5) (2+) is computed to be 8.11 kcal/mol at the MP2 level in good agreement with experiments. Our results reveal that it is necessary to include water molecules bound to the complex in the first hydration sphere for proper treatment of the hydrated complex and the dielectric cavity although water molecules in the second hydration sphere do not change the coordination complex. Structural reoptimization of the complex in a dielectric cavity seems inevitable to seek subtle structural variations in the solvent and to correlate with the observed spectra and thermodynamic properties in the aqueous environment. Our computations reveal dramatically different equilibrium structures in the gas phase and solution and also confirm the observed facile exchanges between the complex and bulk solvent. Complete active space multiconfiguration self-consistent field followed by multireference singles+doubles CI (MRSDCI) computations on smaller complexes confirm predominantly single-configurational nature of these species and the validity of B3LYP and MP2 techniques for these complexes in their ground states.

Hydrophobic Hydration of Stimulus-Responsive Polyproteins Measured by Single Molecule Force Spectroscopy

NASA Astrophysics Data System (ADS)

Zauscher, Stefan

2007-03-01

We present a new procedure to reduce and analyze force-extension data obtained by single molecule force spectroscopy (SMFS). This approach allows, for the first time, to infer effects of solvent quality and minor changes in molecular architecture on molecular-elasticity of individual (bio)macromolecules. Specifically, we show how changes in the effective Kuhn segment length can be used to interpret the hydrophobic hydration behavior of elastin-like polypeptides (ELPs).Our results are intriguing as they suggest that SMFS in combination with our analysis procedure can be used to study the subtleties of polypeptide-water interactions on the single molecule level. We also report on the force-induced cis-trans isomerization of prolines, which are repeated every fifth residue in the main chain of ELPs. We present evidence for this mechanism by Monte Carlo simulations of the force-extension curves using an elastically coupled two-state system. Our results suggest that SMFS could be used to assay proline cis-trans isomerization in proteins and may thus have significant potential diagnostic utility.

Effect of a magnetic field on molecule-solvent angular momentum transfer

NASA Astrophysics Data System (ADS)

Rzadkowski, Wojciech; Lemeshko, Mikhail

2018-03-01

Recently it was shown that a molecule rotating in a quantum solvent can be described in terms of the "angulon" quasiparticle [M. Lemeshko, Phys. Rev. Lett. 118, 095301 (2017)]. Here we extend the angulon theory to the case of molecules possessing an additional spin-1/2 degree of freedom and study the behavior of the system in the presence of a static magnetic field. We show that exchange of angular momentum between the molecule and the solvent can be altered by the field, even though the solvent itself is non-magnetic. In particular, we demonstrate a possibility to control resonant emission of phonons with a given angular momentum using a magnetic field.

A QSPR study on the solvent-induced frequency shifts of acetone and dimethyl sulfoxide in organic solvents.

PubMed

Ou, Yu Heng; Chang, Chia Ming; Chen, Ying Shao

2016-06-05

In this study, solvent-induced frequency shifts (SIFS) in the infrared spectrum of acetone and dimethyl sulfoxide in organic solvents were investigated by using four types of quantum-chemical reactivity descriptors. The results showed that the SIFS of acetone is mainly affected by the electron-acceptance chemical potential and the maximum nucleophilic condensed local softness of organic solvents, which represent the electron flow and the polarization between acetone and solvent molecules. On the other hand, the SIFS of dimethyl sulfoxide changes with the maximum positive charge of hydrogen atom and the inverse of apolar surface area of solvent molecules, showing that the electrostatic and hydrophilic interactions are main mechanisms between dimethyl sulfoxide and solvent molecules. The introduction of the four-element theory model-based quantitative structure-property relationship approach improved the assessing quality and provided a basis for interpreting the solute-solvent interactions. Copyright © 2016 Elsevier B.V. All rights reserved.

A one-pot, microwave-influenced synthesis of diverse small molecules by multicomponent reaction cascades.

PubMed

Santra, Soumava; Andreana, Peter R

2007-11-22

Small molecule diversity can be achieved in a single synthetic operation from bifunctional substrates in the absence of additives and under the influence of microwaves with complete control of pathway selectivity. The preliminary Ugi four-component coupling products give rise to three structurally distinct scaffolds that are dependent on solvent effects and sterics. 2,5-Diketopiperazines (Type A), 2-azaspiro[4.5]deca-6,9-diene-3,8-diones (Type B), and thiophene-derived Diels-Alder tricyclic lactams (Type C) predominate in this reaction cascade.

Direct measurement for organic solvents diffusion using ultra-sensitive optical resonator

NASA Astrophysics Data System (ADS)

Ali, Amir R.; Elias, Catherine M.

2017-06-01

In this paper, novel techniques using ultra-sensitive chemical optical sensor based on whispering gallery modes (WGM) are proposed through two different configurations. The first one will use a composite micro-sphere, when the solvent interacts with the polymeric optical sensors through diffusion the sphere start to swallow that solvent. In turn, that leads to change the morphology and mechanical properties of the polymeric spheres. Also, these changes could be measured by tracking the WGM shifts. Several experiments were carried out to study the solvent induced WGM shift using microsphere immersed in a solvent atmosphere. It can be potentially used for sensing the trace organic solvents like ethanol and methanol. The second configuration will use a composite beam nitrocellulose composite (NC) structure that acts as a sensing element. In this configuration, a beam is anchored to a substrate in one end, and the other end is compressing the polymeric sphere causing a shift in its WGM. When a chemical molecule is attached to the beam, the resonant frequency of the cantilever will be changed for a certain amount. By sensing this certain resonant frequency change, the existence of a single chemical molecule can be detected. A preliminary experimental model is developed to describe the vibration of the beam structure. The resonant frequency change of the cantilever due to attached mass is examined imperially using acetone as an example. Breath diagnosis can use this configuration in diabetic's diagnosis. Since, solvent like acetone concentration in human breath leads to a quick, convenient, accurate and painless breath diagnosis of diabetics. These micro-optical sensors have been examined using preliminary experiments to fully investigate its response. The proposed chemical sensor can achieve extremely high sensitivity in molecular level.

Brownian motion of a nano-colloidal particle: the role of the solvent.

PubMed

Torres-Carbajal, Alexis; Herrera-Velarde, Salvador; Castañeda-Priego, Ramón

2015-07-15

Brownian motion is a feature of colloidal particles immersed in a liquid-like environment. Usually, it can be described by means of the generalised Langevin equation (GLE) within the framework of the Mori theory. In principle, all quantities that appear in the GLE can be calculated from the molecular information of the whole system, i.e., colloids and solvent molecules. In this work, by means of extensive Molecular Dynamics simulations, we study the effects of the microscopic details and the thermodynamic state of the solvent on the movement of a single nano-colloid. In particular, we consider a two-dimensional model system in which the mass and size of the colloid are two and one orders of magnitude, respectively, larger than the ones associated with the solvent molecules. The latter ones interact via a Lennard-Jones-type potential to tune the nature of the solvent, i.e., it can be either repulsive or attractive. We choose the linear momentum of the Brownian particle as the observable of interest in order to fully describe the Brownian motion within the Mori framework. We particularly focus on the colloid diffusion at different solvent densities and two temperature regimes: high and low (near the critical point) temperatures. To reach our goal, we have rewritten the GLE as a second kind Volterra integral in order to compute the memory kernel in real space. With this kernel, we evaluate the momentum-fluctuating force correlation function, which is of particular relevance since it allows us to establish when the stationarity condition has been reached. Our findings show that even at high temperatures, the details of the attractive interaction potential among solvent molecules induce important changes in the colloid dynamics. Additionally, near the critical point, the dynamical scenario becomes more complex; all the correlation functions decay slowly in an extended time window, however, the memory kernel seems to be only a function of the solvent density. Thus, the explicit inclusion of the solvent in the description of Brownian motion allows us to better understand the behaviour of the memory kernel at those thermodynamic states near the critical region without any further approximation. This information is useful to elaborate more realistic descriptions of Brownian motion that take into account the particular details of the host medium.

Development and Modeling of a Novel Self-Assembly Process for Polymer and Polymeric Composite Nanoparticles

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

Sumpter, Bobby G.; Carrillo, Jan-Michael Y.; Ahn, Suk-Kyun

Extensive computational simulations and experiments have been used to investigate the structure, dynamics and resulting photophysical properties of a number para-phenylenevinylene (PPV) based polymers and oligomers. These studies have shown how the morphology and structure are controlled to a large extent by the nature of the solute-solvent interactions in the initial solution phase preparation. A good solvent such as dichloromethane generates non-compact structures with more of a defect-extended chain like morphology while a bad solvent such as toluene leads to compact organized and folded structures with rod-like morphologies. Secondary structural organization is induced by using the solution phase structures tomore » generate solvent-free single molecule nanoparticles. These nanoparticles are very compact and rod shaped, consisting of near-cofacial ordering of the conjugated PPV chain backbones between folds located at tetrahedral defects (sp3 C-C bonds). The resulting photophysical properties exhibit a significant enhancement in the photoluminescence quantum yield, lifetime, and stability. In addition, the single molecule nanoparticles have Gaussian-like emission spectra with discrete center frequencies that are correlated to a conjugation length, allowing the design of nanoparticles which luminesces at a particular frequency. We followed a similar approach and applied a comparable methodology in our recent work on polythiophenes in order to study the effect of polymer architecture on nanoscale assembly. Unlike linear chains of comparable size, we observed aggregation of the bottlebrush architecture of poly(norbornene)-g-poly(3-hexylthiophene) (PNB-g-P3HT) after the freeze-drying and dissolution processes. The behavior can be attributed to a significant enhancement in the number of π-π interactions between grafted P3HT side chains.« less

Solid-state and solution /sup 13/C NMR in the conformational analysis of methadone-hydrochloride and related narcotic analgesics

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

Sumner, S.C.J.

1986-01-01

Solid state and solution /sup 13/C NMR have been used to study the conformations of the racemic mixtures and single enantiomers of methadone hydrochloride, alpha and beta methadol hydrochloride, and alpha and beta acetylmethadol hydrochloride. The NMR spectra acquired for the compounds as solids, and in polar and nonpolar solvents are compared, in order to determine the conformation of the molecules in solution. To determine the reliability of assigning solution conformations by comparing solution and solid state chemical shift data, three bond coupling constants measured in solution are compared with those calculated from X-ray data. The conformations of the racemicmore » mixture and plus enantiomer of methadone hydrochloride have been shown to be very similar in the solid state, where minor differences in conformation can be seen by comparing NMR spectra obtained for the solids. Also shown is that the molecules of methadone hydrochloride have conformations in polar and in nonpolar solvents which are very similar to the conformation of the molecules in the solid state.« less

The solvent component of macromolecular crystals

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

Weichenberger, Christian X.; Afonine, Pavel V.; Kantardjieff, Katherine

2015-04-30

On average, the mother liquor or solvent and its constituents occupy about 50% of a macromolecular crystal. Ordered as well as disordered solvent components need to be accurately accounted for in modelling and refinement, often with considerable complexity. The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initialmore » phasing and must be included in crystal structure refinement as a bulk-solvent model. Concomitantly, distinct electron density originating from ordered solvent components must be correctly identified and represented as part of the atomic crystal structure model. Herein, are reviewed (i) probabilistic bulk-solvent content estimates, (ii) the use of bulk-solvent density modification in phase improvement, (iii) bulk-solvent models and refinement of bulk-solvent contributions and (iv) modelling and validation of ordered solvent constituents. A brief summary is provided of current tools for bulk-solvent analysis and refinement, as well as of modelling, refinement and analysis of ordered solvent components, including small-molecule ligands.« less

Internal friction in an intrinsically disordered protein—Comparing Rouse-like models with experiments

NASA Astrophysics Data System (ADS)

Soranno, Andrea; Zosel, Franziska; Hofmann, Hagen

2018-03-01

Internal friction is frequently found in protein dynamics. Its molecular origin however is difficult to conceptualize. Even unfolded and intrinsically disordered polypeptide chains exhibit signs of internal friction despite their enormous solvent accessibility. Here, we compare four polymer theories of internal friction with experimental results on the intrinsically disordered protein ACTR (activator of thyroid hormone receptor). Using nanosecond fluorescence correlation spectroscopy combined with single-molecule Förster resonance energy transfer (smFRET), we determine the time scales of the diffusive chain dynamics of ACTR at different solvent viscosities and varying degrees of compaction. Despite pronounced differences between the theories, we find that all models can capture the experimental viscosity-dependence of the chain relaxation time. In contrast, the observed slowdown upon chain collapse of ACTR is not captured by any of the theories and a mechanistic link between chain dimension and internal friction is still missing, implying that the current theories are incomplete. In addition, a discrepancy between early results on homopolymer solutions and recent single-molecule experiments on unfolded and disordered proteins suggests that internal friction is likely to be a composite phenomenon caused by a variety of processes.

Internal friction in an intrinsically disordered protein-Comparing Rouse-like models with experiments.

PubMed

Soranno, Andrea; Zosel, Franziska; Hofmann, Hagen

2018-03-28

Internal friction is frequently found in protein dynamics. Its molecular origin however is difficult to conceptualize. Even unfolded and intrinsically disordered polypeptide chains exhibit signs of internal friction despite their enormous solvent accessibility. Here, we compare four polymer theories of internal friction with experimental results on the intrinsically disordered protein ACTR (activator of thyroid hormone receptor). Using nanosecond fluorescence correlation spectroscopy combined with single-molecule Förster resonance energy transfer (smFRET), we determine the time scales of the diffusive chain dynamics of ACTR at different solvent viscosities and varying degrees of compaction. Despite pronounced differences between the theories, we find that all models can capture the experimental viscosity-dependence of the chain relaxation time. In contrast, the observed slowdown upon chain collapse of ACTR is not captured by any of the theories and a mechanistic link between chain dimension and internal friction is still missing, implying that the current theories are incomplete. In addition, a discrepancy between early results on homopolymer solutions and recent single-molecule experiments on unfolded and disordered proteins suggests that internal friction is likely to be a composite phenomenon caused by a variety of processes.

Organic solvent desorption from two tegafur polymorphs.

PubMed

Bobrovs, Raitis; Actiņš, Andris

2013-11-30

Desorption behavior of 8 different solvents from α and β tegafur (5-fluoro-1-(tetrahydro-2-furyl)uracil) has been studied in this work. Solvent desorption from samples stored at 95% and 50% relative solvent vapor pressure was studied in isothermal conditions at 30 °C. The results of this study demonstrated that: solvent desorption rate did not differ significantly for both phases; solvent desorption in all cases occurred faster from samples with the largest particle size; and solvent desorption in most cases occurred in two steps. Structure differences and their surface properties were not of great importance on the solvent desorption rates because the main factor affecting desorption rate was sample particle size and sample morphology. Inspection of the structure packing showed that solvent desorption rate and amount of solvent adsorbed were mainly affected by surface molecule arrangement and ability to form short contacts between solvent molecule electron donor groups and freely accessible tegafur tetrahydrofuran group hydrogens, as well as between solvents molecule proton donor groups and fluorouracil ring carbonyl and fluoro groups. Solvent desorption rates of acetone, acetonitrile, ethyl acetate and tetrahydrofuran multilayers from α and β tegafur were approximately 30 times higher than those of solvent monolayers. Scanning electron micrographs showed that sample storage in solvent vapor atmosphere promotes small tegafur particles recrystallization to larger particles. Copyright © 2013 Elsevier B.V. All rights reserved.

Modeling of the phase equilibria of polystyrene in methylcyclohexane with semi-empirical quantum mechanical methods I.

PubMed

Wilczura-Wachnik, Hanna; Jónsdóttir, Svava Osk

2003-04-01

A method for calculating interaction parameters traditionally used in phase-equilibrium computations in low-molecular systems has been extended for the prediction of solvent activities of aromatic polymer solutions (polystyrene+methylcyclohexane). Using ethylbenzene as a model compound for the repeating unit of the polymer, the intermolecular interaction energies between the solvent molecule and the polymer were simulated. The semiempirical quantum chemical method AM1, and a method for sampling relevant internal orientations for a pair of molecules developed previously were used. Interaction energies are determined for three molecular pairs, the solvent and the model molecule, two solvent molecules and two model molecules, and used to calculated UNIQUAC interaction parameters, a(ij) and a(ji). Using these parameters, the solvent activities of the polystyrene 90,000 amu+methylcyclohexane system, and the total vapor pressures of the methylcyclohexane+ethylbenzene system were calculated. The latter system was compared to experimental data, giving qualitative agreement. Figure Solvent activities for the methylcylcohexane(1)+polystyrene(2) system at 316 K. Parameters aij (blue line) obtained with the AM1 method; parameters aij (pink line) from VLE data for the ethylbenzene+methylcyclohexane system. The abscissa is the polymer weight fraction defined as y2(x1)=(1mx1)M2/[x1M1+(1mx1)M2], where x1 is the solvent mole fraction and Mi are the molecular weights of the components.

Formation of hydroxyl-functionalized stilbenoid molecular sieves at the liquid/solid interface on top of a 1-decanol monolayer.

PubMed

Bellec, Amandine; Arrigoni, Claire; Douillard, Ludovic; Fiorini-Debuisschert, Céline; Mathevet, Fabrice; Kreher, David; Attias, André-Jean; Charra, Fabrice

2014-10-31

Specific molecular tectons can be designed to form molecular sieves through self-assembly at the solid-liquid interface. After demonstrating a model tecton bearing apolar alkyl chains, we then focus on a modified structure involving asymmetric functionalization of some alkyl chains with polar hydroxyl groups in order to get chemical selectivity in the sieving. As the formation of supramolecular self-assembled networks strongly depends on molecule-molecule, molecule-substrate and molecule-solvent interactions, we compared the tectons' self-assembly on graphite for two types of solvent. We demonstrate the possibility to create hydroxylated stilbenoid molecular sieves by using 1-decanol as a solvent. Interestingly, with this solvent, the porous network is developed on top of a 1-decanol monolayer.

Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins.

PubMed

Nguyen, Bao Linh; Pettitt, B Montgomery

2015-04-14

The proximal distribution of water around proteins is a convenient method of quantifying solvation. We consider the effect of charged and sulfur-containing amino acid side-chain atoms on the proximal radial distribution function (pRDF) of water molecules around proteins using side-chain analogs. The pRDF represents the relative probability of finding any solvent molecule at a distance from the closest or surface perpendicular protein atom. We consider the near-neighbor distribution. Previously, pRDFs were shown to be universal descriptors of the water molecules around C, N, and O atom types across hundreds of globular proteins. Using averaged pRDFs, a solvent density around any globular protein can be reconstructed with controllable relative error. Solvent reconstruction using the additional information from charged amino acid side-chain atom types from both small models and protein averages reveals the effects of surface charge distribution on solvent density and improves the reconstruction errors relative to simulation. Solvent density reconstructions from the small-molecule models are as effective and less computationally demanding than reconstructions from full macromolecular models in reproducing preferred hydration sites and solvent density fluctuations.

Microfluidic production of single micrometer-sized hydrogel beads utilizing droplet dissolution in a polar solvent

PubMed Central

Sugaya, Sari; Yamada, Masumi; Hori, Ayaka; Seki, Minoru

2013-01-01

In this study, a microfluidic process is proposed for preparing monodisperse micrometer-sized hydrogel beads. This process utilizes non-equilibrium aqueous droplets formed in a polar organic solvent. The water-in-oil droplets of the hydrogel precursor rapidly shrunk owing to the dissolution of water molecules into the continuous phase. The shrunken and condensed droplets were then gelled, resulting in the formation of hydrogel microbeads with sizes significantly smaller than the initial droplet size. This study employed methyl acetate as the polar organic solvent, which can dissolve water at 8%. Two types of monodisperse hydrogel beads—Ca-alginate and chitosan—with sizes of 6–10 μm (coefficient of variation < 6%) were successfully produced. In addition, we obtained hydrogel beads with non-spherical morphologies by controlling the degree of droplet shrinkage at the time of gelation and by adjusting the concentration of the gelation agent. Furthermore, the encapsulation and concentration of DNA molecules within the hydrogel beads were demonstrated. The process presented in this study has great potential to produce small and highly concentrated hydrogel beads that are difficult to obtain by using conventional microfluidic processes. PMID:24396529

Microfluidic production of single micrometer-sized hydrogel beads utilizing droplet dissolution in a polar solvent.

PubMed

Sugaya, Sari; Yamada, Masumi; Hori, Ayaka; Seki, Minoru

2013-01-01

In this study, a microfluidic process is proposed for preparing monodisperse micrometer-sized hydrogel beads. This process utilizes non-equilibrium aqueous droplets formed in a polar organic solvent. The water-in-oil droplets of the hydrogel precursor rapidly shrunk owing to the dissolution of water molecules into the continuous phase. The shrunken and condensed droplets were then gelled, resulting in the formation of hydrogel microbeads with sizes significantly smaller than the initial droplet size. This study employed methyl acetate as the polar organic solvent, which can dissolve water at 8%. Two types of monodisperse hydrogel beads-Ca-alginate and chitosan-with sizes of 6-10 μm (coefficient of variation < 6%) were successfully produced. In addition, we obtained hydrogel beads with non-spherical morphologies by controlling the degree of droplet shrinkage at the time of gelation and by adjusting the concentration of the gelation agent. Furthermore, the encapsulation and concentration of DNA molecules within the hydrogel beads were demonstrated. The process presented in this study has great potential to produce small and highly concentrated hydrogel beads that are difficult to obtain by using conventional microfluidic processes.

An ellipsoid-chain model for conjugated polymer solutions

NASA Astrophysics Data System (ADS)

Lee, Cheng K.; Hua, Chi C.; Chen, Show A.

2012-02-01

We propose an ellipsoid-chain model which may be routinely parameterized to capture large-scale properties of semiflexible, amphiphilic conjugated polymers in various solvent media. The model naturally utilizes the defect locations as pivotal centers connecting adjacent ellipsoids (each currently representing ten monomer units), and a variant umbrella-sampling scheme is employed to construct the potentials of mean force (PMF) for specific solvent media using atomistic dynamics data and simplex optimization. The performances, both efficacy and efficiency, of the model are thoroughly evaluated by comparing the simulation results on long, single-chain (i.e., 300-mer) structures with those from two existing, finer-grained models for a standard conjugated polymer (i.e., poly(2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylenevinylene) or MEH-PPV) in two distinct solvents (i.e., chloroform or toluene) as well as a hybrid, binary-solvent medium (i.e., chloroform/toluene = 1:1 in number density). The coarse-grained Monte Carlo (CGMC) simulation of the ellipsoid-chain model is shown to be the most efficient—about 300 times faster than the coarse-grained molecular dynamics (CGMD) simulation of the finest CG model that employs explicit solvents—in capturing elementary single-chain structures for both single-solvent media, and is a few times faster than the coarse-grained Langevin dynamics (CGLD) simulation of another implicit-solvent polymer model with a slightly greater coarse-graining level than in the CGMD simulation. For the binary-solvent system considered, however, both of the two implicit-solvent schemes (i.e., CGMC and CGLD) fail to capture the effects of conspicuous concentration fluctuations near the polymer-solvent interface, arising from a pronounced coupling between the solvent molecules and different parts of the polymer. Essential physical implications are elaborated on the success as well as the failure of the two implicit-solvent CG schemes under varying solvent conditions. Within the ellipsoid-chain model, the impact of synthesized defects on local segmental ordering as well as bulk chain conformation is also scrutinized, and essential consequences in practical applications discussed. In future perspectives, we remark on strategy that takes advantage of the coordination among various CG models and simulation schemes to warrant computational efficiency and accuracy, with the anticipated capability of simulating larger-scale, many-chain aggregate systems.

In situ superexchange electron transfer through a single molecule: a rectifying effect.

PubMed

Kornyshev, Alexei A; Kuznetsov, Alexander M; Ulstrup, Jens

2006-05-02

An increasingly comprehensive body of literature is being devoted to single-molecule bridge-mediated electronic nanojunctions, prompted by their prospective applications in molecular electronics and single-molecule analysis. These junctions may operate in gas phase or electrolyte solution (in situ). For biomolecules, the latter is much closer to their native environment. Convenient target molecules are aromatic molecules, peptides, oligonucleotides, transition metal complexes, and, broadly, molecules with repetitive units, for which the conducting orbitals are energetically well below electronic levels of the solvent. A key feature for these junctions is rectification in the current-voltage relation. A common view is that asymmetric molecules or asymmetric links to the electrodes are needed to acquire rectification. However, as we show here, this requirement could be different in situ, where a structurally symmetric system can provide rectification because of the Debye screening of the electric field in the nanogap if the screening length is smaller than the bridge length. The Galvani potentials of each electrode can be varied independently and lead to a transistor effect. We explore this behavior for the superexchange mechanism of electron transport, appropriate for a wide class of molecules. We also include the effect of conformational fluctuations on the lowest unoccupied molecular orbital (LUMO) energy levels; that gives rise to non-Arrhenius temperature dependence of the conductance, affected by the molecule length. Our study offers an analytical formula for the current-voltage characteristics that demonstrates all these features. A detailed physical interpretation of the results is given with a discussion of reported experimental data.

Dual fluorescence of N-phenylanthranilic acid: Effect of solvents, pH and beta-cyclodextrin.

PubMed

Rajendiran, N; Balasubramanian, T

2007-11-01

Spectral characteristics of N-phenylanthranilic acid (NPAA) have been studied in different solvents, pH and beta-cyclodextrin (beta-CD) and compared with anthranilic acid (2-aminobenzoic acid, 2ABA). In all solvents a dual fluorescence is observed in NPAA, whereas 2ABA gives single emission. Combining the results observed in the absorption, fluorescence emission and fluorescence excitation spectra, it is found that strong intramolecular hydrogen bonding (IHB) interactions present in NPAA molecule. The inclusion complex of NPAA with beta-CD is analysed by UV-vis, fluorimetry, FT-IR, (1)H NMR, scanning electron microscope and AM 1 method. The above spectral studies show that NPAA forms a 1:1 inclusion complex with beta-CD and COOH group present in the beta-CD cavity. A mechanism is proposed to explain the inclusion process.

Dual fluorescence of N-phenylanthranilic acid: Effect of solvents, pH and β-cyclodextrin

NASA Astrophysics Data System (ADS)

Rajendiran, N.; Balasubramanian, T.

2007-11-01

Spectral characteristics of N-phenylanthranilic acid (NPAA) have been studied in different solvents, pH and β-cyclodextrin (β-CD) and compared with anthranilic acid (2-aminobenzoic acid, 2ABA). In all solvents a dual fluorescence is observed in NPAA, whereas 2ABA gives single emission. Combining the results observed in the absorption, fluorescence emission and fluorescence excitation spectra, it is found that strong intramolecular hydrogen bonding (IHB) interactions present in NPAA molecule. The inclusion complex of NPAA with β-CD is analysed by UV-vis, fluorimetry, FT-IR, 1H NMR, scanning electron microscope and AM 1 method. The above spectral studies show that NPAA forms a 1:1 inclusion complex with β-CD and COOH group present in the β-CD cavity. A mechanism is proposed to explain the inclusion process.

Solution-based single molecule imaging of surface-immobilized conjugated polymers.

PubMed

Dalgarno, Paul A; Traina, Christopher A; Penedo, J Carlos; Bazan, Guillermo C; Samuel, Ifor D W

2013-05-15

The photophysical behavior of conjugated polymers used in modern optoelectronic devices is strongly influenced by their structural dynamics and conformational heterogeneity, both of which are dependent on solvent properties. Single molecule studies of these polymer systems embedded in a host matrix have proven to be very powerful to investigate the fundamental fluorescent properties. However, such studies lack the possibility of examining the relationship between conformational dynamics and photophysical response in solution, which is the phase from which films for devices are deposited. By developing a synthetic strategy to incorporate a biotin moiety as a surface attachment point at one end of a polyalkylthiophene, we immobilize it, enabling us to make the first single molecule fluorescence measurements of conjugated polymers for long periods of time in solution. We identify fluctuation patterns in the fluorescence signal that can be rationalized in terms of photobleaching and stochastic transitions to reversible dark states. Moreover, by using the advantages of solution-based imaging, we demonstrate that the addition of oxygen scavengers improves optical stability by significantly decreasing the photobleaching rates.

Droplet-Based Production of Liposomes

NASA Technical Reports Server (NTRS)

Ackley, Donald E.; Forster, Anita

2009-01-01

A process for making monodisperse liposomes having lipid bilayer membranes involves fewer, simpler process steps than do related prior methods. First, a microfluidic, cross junction droplet generator is used to produce vesicles comprising aqueous solution droplets contained in single layer lipid membranes. The vesicles are collected in a lipid-solvent mix that is at most partially soluble in water and is less dense than is water. A layer of water is dispensed on top of the solvent. By virtue of the difference in densities, the water sinks to the bottom and the solvent floats to the top. The vesicles, which have almost the same density as that of water, become exchanged into the water instead of floating to the top. As there are excess lipids in the solvent solution, in order for the vesicles to remain in the water, the addition of a second lipid layer to each vesicle is energetically favored. The resulting lipid bilayers present the hydrophilic ends of the lipid molecules to both the inner and outer membrane surfaces. If lipids of a second kind are dissolved in the solvent in sufficient excess before use, then asymmetric liposomes may be formed.

Scanning tunneling microscopy studies of pulse deposition of dinuclear organometallic molecules on Au(111)

NASA Astrophysics Data System (ADS)

Guo, Song; Alex Kandel, S.

2008-01-01

Ultrahigh-vacuum scanning tunneling microscopy (STM) was used to study trans-[Cl(dppe)2Ru(CC)6Ru(dppe)2Cl] [abbreviated as Ru2, diphenylphosphinoethane (dppe)] on Au(111). This large organometallic molecule was pulse deposited onto the Au(111) surface under ultrahigh-vacuum (UHV) conditions. UHV STM studies on the prepared sample were carried out at room temperature and 77K in order to probe molecular adsorption and to characterize the surface produced by the pulse deposition process. Isolated Ru2 molecules were successfully imaged by STM at room temperature; however, STM images were degraded by mobile toluene solvent molecules that remain on the surface after the deposition. Cooling the sample to 77K allows the solvent molecules to be observed directly using STM, and under these conditions, toluene forms organized striped domains with regular domain boundaries and a lattice characterized by 5.3 and 2.7Å intermolecular distances. When methylene chloride is used as the solvent, it forms analogous domains on the surface at 77K. Mild annealing under vacuum causes most toluene molecules to desorb from the surface; however, this annealing process may lead to thermal degradation of Ru2 molecules. Although pulse deposition is an effective way to deposit molecules on surfaces, the presence of solvent on the surface after pulse deposition is unavoidable without thermal annealing, and this annealing may cause undesired chemical changes in the adsorbates under study. Preparation of samples using pulse deposition must take into account the characteristics of sample molecules, solvent, and surfaces.

Conformation-related exciton localization and charge-pair formation in polythiophenes: ensemble and single-molecule study.

PubMed

Sugimoto, Toshikazu; Habuchi, Satoshi; Ogino, Kenji; Vacha, Martin

2009-09-10

We study conformation-dependent photophysical properties of polythiophene (PT) by molecular dynamics simulations and by ensemble and single-molecule optical experiments. We use a graft copolymer consisting of a polythiophene backbone and long polystyrene branches and compare its properties with those obtained on the same polythiophene derivative without the side chains. Coarse-grain molecular dynamics simulations show that in a poor solvent, the PT without the side chains (PT-R) forms a globulelike conformation in which distances between any two conjugated segments on the chain are within the Forster radius for efficient energy transfer. In the PT with the polystyrene branches (PT-PS), the polymer main PT chain retains an extended coillike conformation, even in a poor solvent, and the calculated distances between conjugated segments favor energy transfer only between a few neighboring chromophores. The theoretical predictions are confirmed by measurements of fluorescence anisotropy and fluorescence blinking of the polymers' single chains. High anisotropy ratios and two-state blinking in PT-R are due to localization of the exciton on a single conjugated segment. These signatures of exciton localization are absent in single chains of PT-PS. Electric-field-induced quenching measured as a function of concentration of PT dispersed in an inert matrix showed that in well-isolated chains of PT-PS, the exciton dissociation is an intrachain process and that aggregation of the PT-R chains causes an increase in quenching due to the onset of interchain interactions. Measurements of the field-induced quenching on single chains indicate that in PT-R, the exciton dissociation is a slower process that takes place only after the exciton is localized on one conjugated segment.

Effect of Solvent and Substrate on the Surface Binding Mode of Carboxylate-Functionalized Aromatic Molecules

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

Domenico, Janna; Foster, Michael E.; Spoerke, Erik D.

Here, the efficiency of dye-sensitized solar cells (DSSCs) is strongly influenced by dye molecule orientation and interactions with the substrate. Understanding the factors controlling the surface orientation of sensitizing organic molecules will aid in the improvement of both traditional DSSCs and other devices that integrate molecular linkers at interfaces. Here, we describe a general approach to understand relative dye–substrate orientation and provide analytical expressions predicting orientation. We consider the effects of substrate, solvent, and protonation state on dye molecule orientation. In the absence of solvent, our model predicts that most carboxylic acid-functionalized molecules prefer to lie flat (parallel) on themore » surface, due to van der Waals interactions, as opposed to a tilted orientation with respect to the surface that is favored by covalent bonding of the carboxylic acid group to the substrate. When solvation effects are considered, however, the molecules are predicted to orient perpendicular to the surface. We extend this approach to help understand and guide the orientation of metal–organic framework (MOF) thin-film growth on various metal–oxide substrates. A two-part analytical model is developed on the basis of the results of DFT calculations and ab initio MD simulations that predicts the binding energy of a molecule by chemical and dispersion forces on rutile and anatase TiO 2 surfaces, and quantifies the dye solvation energy for two solvents. The model is in good agreement with the DFT calculations and enables rapid prediction of dye molecule and MOF linker binding preference on the basis of the size of the adsorbing molecule, identity of the surface, and the solvent environment. We establish the threshold molecular size, governing dye molecule orientation, for each condition.« less

Effect of Solvent and Substrate on the Surface Binding Mode of Carboxylate-Functionalized Aromatic Molecules

DOE PAGES

Domenico, Janna; Foster, Michael E.; Spoerke, Erik D.; ...

2018-04-25

Here, the efficiency of dye-sensitized solar cells (DSSCs) is strongly influenced by dye molecule orientation and interactions with the substrate. Understanding the factors controlling the surface orientation of sensitizing organic molecules will aid in the improvement of both traditional DSSCs and other devices that integrate molecular linkers at interfaces. Here, we describe a general approach to understand relative dye–substrate orientation and provide analytical expressions predicting orientation. We consider the effects of substrate, solvent, and protonation state on dye molecule orientation. In the absence of solvent, our model predicts that most carboxylic acid-functionalized molecules prefer to lie flat (parallel) on themore » surface, due to van der Waals interactions, as opposed to a tilted orientation with respect to the surface that is favored by covalent bonding of the carboxylic acid group to the substrate. When solvation effects are considered, however, the molecules are predicted to orient perpendicular to the surface. We extend this approach to help understand and guide the orientation of metal–organic framework (MOF) thin-film growth on various metal–oxide substrates. A two-part analytical model is developed on the basis of the results of DFT calculations and ab initio MD simulations that predicts the binding energy of a molecule by chemical and dispersion forces on rutile and anatase TiO 2 surfaces, and quantifies the dye solvation energy for two solvents. The model is in good agreement with the DFT calculations and enables rapid prediction of dye molecule and MOF linker binding preference on the basis of the size of the adsorbing molecule, identity of the surface, and the solvent environment. We establish the threshold molecular size, governing dye molecule orientation, for each condition.« less

Would the solvent effect be the main cause of band shift in the theoretical absorption spectrum of large lanthanide complexes?

NASA Astrophysics Data System (ADS)

Freire, Ricardo O.; Rodrigues, Nailton M.; Rocha, Gerd B.; Gimenez, Iara F.; da Costa Junior, Nivan B.

2011-06-01

As most reactions take place in solution, the study of solvent effects on relevant molecular properties - either by experimental or theoretical methods - is crucial for the design of new processes and prediction of technological properties. In spite of this, only few works focusing the influence of the solvent nature specifically on the spectroscopic properties of lanthanide complexes can be found in the literature. The present work describes a theoretical study of the solvent effect on the prediction of the absorption spectra for lanthanide complexes, but other possible relevant factors have been also considered such as the molecular geometry and the excitation window used for interaction configuration (CI) calculations. The [Eu(ETA) 2· nH 2O] +1 complex has been chosen as an ideal candidate for this type of study due to its small number of atoms (only 49) and also because the absorption spectrum exhibits a single band. Two Monte Carlo simulations were performed, the first one considering the [Eu(ETA) 2] +1 complex in 400 water molecules, evidencing that the complex presents four coordinated water molecules. The second simulation considered the [Eu(ETA) 2·4H 2O] +1 complex in 400 ethanol molecules, in order to evaluate the solvent effect on the shift of the maximum absorption in calculated spectra, compared to the experimental one. Quantum chemical studies were also performed in order to evaluate the effect of the accuracy of calculated ground state geometry on the prediction of absorption spectra. The influence of the excitation window used for CI calculations on the spectral shift was also evaluated. No significant solvent effect was found on the prediction of the absorption spectrum for [Eu(ETA) 2·4H 2O] +1 complex. A small but significant effect of the ground state geometry on the transition energy and oscillator strength was also observed. Finally it must be emphasized that the absorption spectra of lanthanide complexes can be predicted with great accuracy by the combined use of semiempirical Sparkle/AM1 and INDO/S-CIS as long as the largest possible excitation window is used in the configuration interaction calculation.

Multiple solvent crystal structures of ribonuclease A: An assessment of the method

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

Dechene, Michelle; Wink, Glenna; Smith, Mychal

2010-11-12

The multiple solvent crystal structures (MSCS) method uses organic solvents to map the surfaces of proteins. It identifies binding sites and allows for a more thorough examination of protein plasticity and hydration than could be achieved by a single structure. The crystal structures of bovine pancreatic ribonuclease A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane, 50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6-hexanediol, 70% isopropanol, 50% R,S,R-bisfuran alcohol, 70% t-butanol, 50% trifluoroethanol, or 1.0M trimethylamine-N-oxide. This set of structures is compared with four sets of crystal structures of RNAse A from the protein data bank (PDB) andmore » with the solution NMR structure to assess the validity of previously untested assumptions associated with MSCS analysis. Plasticity from MSCS is the same as from PDB structures obtained in the same crystal form and deviates only at crystal contacts when compared to structures from a diverse set of crystal environments. Furthermore, there is a good correlation between plasticity as observed by MSCS and the dynamic regions seen by NMR. Conserved water binding sites are identified by MSCS to be those that are conserved in the sets of structures taken from the PDB. Comparison of the MSCS structures with inhibitor-bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot-spots in the active site. The present work firmly establishes the relevance of information obtained by MSCS.« less

Controlled crosslinking of trimethylolpropane trimethacrylate for preparation of organic monolithic columns for capillary liquid chromatography.

PubMed

Gama, Mariana R; Aggarwal, Pankaj; Lee, Milton L; Bottoli, Carla B G

2017-11-01

Organic monolithic columns based on single crosslinking of trimethylolpropane trimethacrylate (TRIM) monomer were prepared in a single step by living/controlled free-radical polymerization. Full optimization of the preparation, such as using different percentages of TRIM and different amounts of radical promoter as well as various porogen solvents were explored. The resulting monolithic columns were characterized by scanning electronic microscopy and nitrogen sorption for structure morphology studies and surface area measurements, respectively. Using capillary liquid chromatography, 150 μm i.d. columns were applied to separate a mixture of small hydrophobic molecules. The results indicated that column performance is highly sensitive to the type and the amount of porogen solvents used in the polymerization mixture composition. Good resolution factors and methylene selectivity were obtained, indicating the promising potential of this material for capillary liquid chromatography separations. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Visible spectrum photofragmentation of O{sub 3}{sup −}(H{sub 2}O){sub n}, n ≤ 16

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

Lehman, Julia H.; Lineberger, W. Carl, E-mail: wcl@jila.colorado.edu

2014-10-21

Photofragmentation of ozonide solvated in water clusters, O{sub 3}{sup −}(H{sub 2}O){sub n}, n ≤ 16, has been studied as a function of photon energy as well as the degree of solvation. Using mass selection, the effect of the presence of the solvent molecule on the O{sub 3}{sup −} photodissociation process is assessed one solvent molecule at a time. The O{sub 3}{sup −} acts as a visible light chromophore within the water cluster, namely the O{sub 3}{sup −}(H{sub 2}O) total photodissociation cross-section exhibits generally the same photon energy dependence as isolated O{sub 3}{sup −} throughout the visible wavelength range studied (430–620more » nm). With the addition of a single solvent molecule, new photodissociation pathways are opened, including the production of recombined O{sub 3}{sup −}. As the degree of solvation of the parent anion increases, recombination to O{sub 3}{sup −}-based products accounts for close to 40% of photoproducts by n = 16. The remainder of the photoproducts exist as O{sup −}-based; no O{sub 2}{sup −}-based products are observed. Upper bounds on the O{sub 3}{sup −} solvation energy (530 meV) and the O{sup −}-OO bond dissociation energy in the cluster (1.06 eV) are derived.« less

A computational study of CH 4 storage in porous framework materials with metalated linkers: connecting the atomistic character of CH 4 binding sites to usable capacity

DOE PAGES

Tsivion, Ehud; Mason, Jarad A.; Gonzalez, Miguel. I.; ...

2016-03-29

In order to store natural gas (NG) inexpensively at adequate densities for use as a fuel in the transportation sector, new porous materials are being developed. Our work uses computational methods to explore strategies for improving the usable methane storage capacity of adsorbents, including metal-organic frameworks (MOFs), that feature open-metal sites incorporated into their structure by postsynthetic modification. The adsorption of CH 4 on several open-metal sites is studied by calculating geometries and adsorption energies and analyzing the relevant interaction factors. Approximate site-specific adsorption isotherms are obtained, and the open-metal site contribution to the overall CH 4 usable capacity ismore » evaluated. It is found that sufficient ionic character is required, as exemplified by the strong CH 4 affinities of 2,2'-bipyridine-CaCl 2 and Mg, Ca-catecholate. In addition, it is found that the capacity of a single metal site depends not only on its affinity but also on its geometry, where trigonal or "bent" low-coordinate exposed sites can accommodate three or four methane molecules, as exemplified by Ca-decorated nitrilotriacetic acid. The effect of residual solvent molecules at the open-metal site is also explored, with some positive conclusions. Not only can residual solvent stabilize the open-metal site, surprisingly, solvent molecules do not necessarily reduce CH 4 affinity, but can contribute to increased usable capacity by modifying adsorption interactions.« less

Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins

PubMed Central

Nguyen, Bao Linh; Pettitt, B. Montgomery

2015-01-01

The proximal distribution of water around proteins is a convenient method of quantifying solvation. We consider the effect of charged and sulfur-containing amino acid side-chain atoms on the proximal radial distribution function (pRDF) of water molecules around proteins using side-chain analogs. The pRDF represents the relative probability of finding any solvent molecule at a distance from the closest or surface perpendicular protein atom. We consider the near-neighbor distribution. Previously, pRDFs were shown to be universal descriptors of the water molecules around C, N, and O atom types across hundreds of globular proteins. Using averaged pRDFs, a solvent density around any globular protein can be reconstructed with controllable relative error. Solvent reconstruction using the additional information from charged amino acid side-chain atom types from both small models and protein averages reveals the effects of surface charge distribution on solvent density and improves the reconstruction errors relative to simulation. Solvent density reconstructions from the small-molecule models are as effective and less computationally demanding than reconstructions from full macromolecular models in reproducing preferred hydration sites and solvent density fluctuations. PMID:26388706

Intensity enhancement and selective detection of proximate solvent molecules by molecular near-field effect in resonance hyper-Raman scattering

NASA Astrophysics Data System (ADS)

Shimada, Rintaro; Kano, Hideaki; Hamaguchi, Hiro-o.

2008-07-01

A new molecular phenomenon associated with resonance hyper-Raman (HR) scattering in solution has been discovered. Resonance HR spectra of all-trans-β-carotene and all-trans-lycopene in various solvents exhibited several extra bands that were not assignable to the solute but were unequivocally assigned to the solvents. Neat solvents did not show detectable HR signals under the same experimental conditions. Similar experiments with all-trans-retinal did not exhibit such enhancement either. All-trans-β-carotene and all-trans-lycopene have thus been shown to induce enhanced HR scattering of solvent molecules through a novel molecular effect that is not associated with all-trans-retinal. We call this new effect the "molecular near-field effect." In order to explain this newly found effect, an extended vibronic theory of resonance HR scattering is developed where the vibronic interaction including the proximate solvent molecule (intermolecular vibronic coupling) is explicitly introduced in the solute hyperpolarizability tensor. The potential of "molecular near-field HR spectroscopy," which selectively detects molecules existing in the close vicinity of a HR probe in complex chemical or biological systems, is discussed.

STABILITY OF A CYLINDRICAL SOLUTE-SOLVENT INTERFACE: EFFECT OF GEOMETRY, ELECTROSTATICS, AND HYDRODYNAMICS.

PubMed

Li, B O; Sun, Hui; Zhou, Shenggao

The solute-solvent interface that separates biological molecules from their surrounding aqueous solvent characterizes the conformation and dynamics of such molecules. In this work, we construct a solvent fluid dielectric boundary model for the solvation of charged molecules and apply it to study the stability of a model cylindrical solute-solvent interface. The motion of the solute-solvent interface is defined to be the same as that of solvent fluid at the interface. The solvent fluid is assumed to be incompressible and is described by the Stokes equation. The solute is modeled simply by the ideal-gas law. All the viscous force, hydrostatic pressure, solute-solvent van der Waals interaction, surface tension, and electrostatic force are balanced at the solute-solvent interface. We model the electrostatics by Poisson's equation in which the solute-solvent interface is treated as a dielectric boundary that separates the low-dielectric solute from the high-dielectric solvent. For a cylindrical geometry, we find multiple cylindrically shaped equilibrium interfaces that describe polymodal (e.g., dry and wet) states of hydration of an underlying molecular system. These steady-state solutions exhibit bifurcation behavior with respect to the charge density. For their linearized systems, we use the projection method to solve the fluid equation and find the dispersion relation. Our asymptotic analysis shows that, for large wavenumbers, the decay rate is proportional to wavenumber with the proportionality half of the ratio of surface tension to solvent viscosity, indicating that the solvent viscosity does affect the stability of a solute-solvent interface. Consequences of our analysis in the context of biomolecular interactions are discussed.

In Situ Oxidation Synthesis of p-Type Composite with Narrow-Bandgap Small Organic Molecule Coating on Single-Walled Carbon Nanotube: Flexible Film and Thermoelectric Performance.

PubMed

Gao, Caiyan; Chen, Guangming

2018-03-01

Although composites of organic polymers or n-type small molecule/carbon nanotube (CNT) have achieved significant advances in thermoelectric (TE) applications, p-type TE composites of small organic molecules as thick surface coating layers on the surfaces of inorganic nanoparticles still remain a great challenge. Taking advantage of in situ oxidation reaction of thieno[3,4-b]pyrazine (TP) into TP di-N-oxide (TPNO) on single-walled CNT (SWCNT) surface, a novel synthesis strategy is proposed to achieve flexible films of TE composites with narrow-bandgap (1.19 eV) small molecule coating on SWCNT surface. The TE performance can be effectively enhanced and conveniently tuned by poly(sodium-p-styrenesulfonate) content, TPNO/SWCNT mass ratio, and posttreatment by various polar solvents. The maximum of the composite power factor at room temperature is 29.4 ± 1.0 µW m -1 K -2 . The work presents a way to achieve flexible films of p-type small organic molecule/inorganic composites with clear surface coating morphology for TE application. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Computational solvation dynamics of oxyquinolinium betaine linked to trehalose.

PubMed

Heid, Esther; Schröder, Christian

2016-10-28

Studying the changed water dynamics in the hydration layers of biomolecules is an important step towards fuller understanding of their function and mechanisms, but has shown to be quite difficult. The measurement of the time-dependent Stokes shift of a chromophore attached to the biomolecule is a promising method to achieve this goal, as published in Sajadi et al. [J. Phys. Chem. Lett., 5, 1845 (2014).] where trehalose was used as biomolecule, 1-methyl-6-oxyquinolinium betaine as chromophore, and water as solvent. An overall retardation of solvent molecules is then obtained by comparison of the linked system to the same system without trehalose, but contributions from different subgroups of solvent molecules, for example, molecules close to or far from trehalose, are unknown. The difficulty arising from these unknown contributions of retarded and possibly unretarded solvent molecules is overcome in this work by conducting computer simulations on this system and decomposing the overall signal into the contributions from various molecules at different locations. We performed non-equilibrium molecular dynamics simulation using a polarizable water model and a non-polarizable solute model and could reproduce the experimental time-dependent Stokes shift accurately for the linked trehalose-oxyquinolinium and the pure oxyquinolinium over a wide temperature range, indicating the correctness of our employed models. Decomposition of the shift into contributions from different solvent subgroups showed that the amplitude of the measured shift is made up only half by the desired retarded solvent molecules in the hydration layer, but to another half by unretarded bulk water, so that measured relaxation times of the overall Stokes shift are only a lower boundary for the true relaxation times in the hydration layer of trehalose. As a side effect, the results on the effect of trehalose on solvation dynamics contribute to the long standing debate on the range of influence of trehalose on water dynamics, the number of retarded solvent molecules, and the observed retardation factor when compared to bulk water.

Computational solvation dynamics of oxyquinolinium betaine linked to trehalose

NASA Astrophysics Data System (ADS)

Heid, Esther; Schröder, Christian

2016-10-01

Studying the changed water dynamics in the hydration layers of biomolecules is an important step towards fuller understanding of their function and mechanisms, but has shown to be quite difficult. The measurement of the time-dependent Stokes shift of a chromophore attached to the biomolecule is a promising method to achieve this goal, as published in Sajadi et al. [J. Phys. Chem. Lett., 5, 1845 (2014).] where trehalose was used as biomolecule, 1-methyl-6-oxyquinolinium betaine as chromophore, and water as solvent. An overall retardation of solvent molecules is then obtained by comparison of the linked system to the same system without trehalose, but contributions from different subgroups of solvent molecules, for example, molecules close to or far from trehalose, are unknown. The difficulty arising from these unknown contributions of retarded and possibly unretarded solvent molecules is overcome in this work by conducting computer simulations on this system and decomposing the overall signal into the contributions from various molecules at different locations. We performed non-equilibrium molecular dynamics simulation using a polarizable water model and a non-polarizable solute model and could reproduce the experimental time-dependent Stokes shift accurately for the linked trehalose-oxyquinolinium and the pure oxyquinolinium over a wide temperature range, indicating the correctness of our employed models. Decomposition of the shift into contributions from different solvent subgroups showed that the amplitude of the measured shift is made up only half by the desired retarded solvent molecules in the hydration layer, but to another half by unretarded bulk water, so that measured relaxation times of the overall Stokes shift are only a lower boundary for the true relaxation times in the hydration layer of trehalose. As a side effect, the results on the effect of trehalose on solvation dynamics contribute to the long standing debate on the range of influence of trehalose on water dynamics, the number of retarded solvent molecules, and the observed retardation factor when compared to bulk water.

Crystal growth, differential gas adsorption, high thermal stability, and reversible coordination of two new barium-organic frameworks, Ba(SBA)(DMF){sub 4} and Ba{sub 2}(BTEC)(H{sub 2}O)

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

Halake, Shobha; Ok, Kang Min, E-mail: kmok@cau.ac.kr

2015-11-15

Single crystals of two barium-organic framework materials, Ba(SBA)(DMF){sub 4} (CAUMOF-15) and Ba{sub 2}(BTEC)(H{sub 2}O) (CAUMOF-16), have been grown through solvothermal reactions (H{sub 2}SBA=4,4′-sulfonyldibenzoic acid and H{sub 4}BTEC=1,2,4,5-benzenetetracarboxylic acid). The crystal structures of the reported frameworks have been determined by single-crystal X-ray diffraction. The materials have been fully characterized by powder X-ray diffraction (PXRD), elemental analyses, Infrared (IR) spectroscopy, and thermogravimetric analyses (TGA). CAUMOF-15 reveals a three-dimensional open-framework that comprises of an inorganic motif with one-dimensional chains and the SBA linkers. CAUMOF-16 shows another three-dimensional backbone consisting of layers of edge-shared BaO{sub 9} and BaO{sub 10} polyhedra, and BTEC pillars. Bothmore » of the 3D frameworks exhibit relatively high thermal stabilities. The PXRD and IR spectral data confirm that CAUMOF-15 and CAUMOF-16 reveal reversible coordinations of the respective solvent molecules, DMF and H{sub 2}O. Gas adsorption properties towards nitrogen, hydrogen, and carbon dioxide have been also investigated. - Graphical abstract: Crystals of two new barium-organic frameworks, Ba(SBA)(DMF){sub 4} and Ba{sub 2}(BTEC)(H{sub 2}O), exhibiting a differential gas adsorption, a high thermal stability, and a reversible coordination of solvent molecules have been grown. - Highlights: • Crystals of two new 3D Ba-MOFs are grown. • The two Ba-MOFs reveal very high thermal stabilities up to ca. 400 °C. • Ba(SBA)(DMF){sub 4} exhibits differential gas adsorption properties. • The two Ba-MOFs show reversible coordination of the solvent molecules.« less

Molecular microenvironments: Solvent interactions with nucleic acid bases and ions

NASA Technical Reports Server (NTRS)

Macelroy, R. D.; Pohorille, A.

1986-01-01

The possibility of reconstructing plausible sequences of events in prebiotic molecular evolution is limited by the lack of fossil remains. However, with hindsight, one goal of molecular evolution was obvious: the development of molecular systems that became constituents of living systems. By understanding the interactions among molecules that are likely to have been present in the prebiotic environment, and that could have served as components in protobiotic molecular systems, plausible evolutionary sequences can be suggested. When stable aggregations of molecules form, a net decrease in free energy is observed in the system. Such changes occur when solvent molecules interact among themselves, as well as when they interact with organic species. A significant decrease in free energy, in systems of solvent and organic molecules, is due to entropy changes in the solvent. Entropy-driven interactioins played a major role in the organization of prebiotic systems, and understanding the energetics of them is essential to understanding molecular evolution.

Translational, rotational and vibrational relaxation dynamics of a solute molecule in a non-interacting solvent.

PubMed

Grubb, Michael P; Coulter, Philip M; Marroux, Hugo J B; Hornung, Balazs; McMullen, Ryan S; Orr-Ewing, Andrew J; Ashfold, Michael N R

2016-11-01

Spectroscopically observing the translational and rotational motion of solute molecules in liquid solutions is typically impeded by their interactions with the solvent, which conceal spectral detail through linewidth broadening. Here we show that unique insights into solute dynamics can be made with perfluorinated solvents, which interact weakly with solutes and provide a simplified liquid environment that helps to bridge the gap in our understanding of gas- and liquid-phase dynamics. Specifically, we show that in such solvents, the translational and rotational cooling of an energetic CN radical can be observed directly using ultrafast transient absorption spectroscopy. We observe that translational-energy dissipation within these liquids can be modelled through a series of classic collisions, whereas classically simulated rotational-energy dissipation is shown to be distinctly faster than experimentally measured. We also observe the onset of rotational hindering from nearby solvent molecules, which arises as the average rotational energy of the solute falls below the effective barrier to rotation induced by the solvent.

Detecting Single-Nucleotides by Tunneling Current Measurements at Sub-MHz Temporal Resolution.

PubMed

Morikawa, Takanori; Yokota, Kazumichi; Tanimoto, Sachie; Tsutsui, Makusu; Taniguchi, Masateru

2017-04-18

Label-free detection of single-nucleotides was performed by fast tunneling current measurements in a polar solvent at 1 MHz sampling rate using SiO₂-protected Au nanoprobes. Short current spikes were observed, suggestive of trapping/detrapping of individual nucleotides between the nanoelectrodes. The fall and rise features of the electrical signatures indicated signal retardation by capacitance effects with a time constant of about 10 microseconds. The high temporal resolution revealed current fluctuations, reflecting the molecular conformation degrees of freedom in the electrode gap. The method presented in this work may enable direct characterizations of dynamic changes in single-molecule conformations in an electrode gap in liquid.

Brooker's merocyanine: Comparison of single crystal structures

NASA Astrophysics Data System (ADS)

Hayes, Kathleen L.; Lasher, Emily M.; Choczynski, Jack M.; Crisci, Ralph R.; Wong, Calvin Y.; Dragonette, Joseph; Deschner, Joshua; Cardenas, Allan Jay P.

2018-06-01

Brooker's merocyanine and its derivatives are well-studied molecules due to their very interesting optical properties. Merocyanine dyes exhibit different colors in solution depending on the solvent's polarity, pH, aggregation and intermolecular interactions. The synthesis of 1-methyl-4-[(oxocyclohexadienylidene)ethylidene]-1,4-dihydropyridine (MOED) dye yielded a particularly interesting solid state structure where in one crystal lattice, MOED and its protonated form are bound by hydrogen bonding interactions.

Single-molecule spectroscopy of the unexpected collapse of an unfolded protein at low pH

NASA Astrophysics Data System (ADS)

Hofmann, Hagen; Nettels, Daniel; Schuler, Benjamin

2013-09-01

The dimensions of intrinsically disordered and unfolded proteins critically depend on the solution conditions, such as temperature, pH, ionic strength, and osmolyte or denarurant concentration. However, a quantitative understanding of how the complex combination of chain-chain and chain-solvent interactions is affected by the solvent is still missing. Here, we take a step towards this goal by investigating the combined effect of pH and denaturants on the dimensions of an unfolded protein. We use single-molecule fluorescence spectroscopy to extract the dimensions of unfolded cold shock protein (CspTm) in mixtures of the denaturants urea and guanidinium chloride (GdmCl) at neutral and acidic pH. Surprisingly, even though a change in pH from 7 to 2.9 increases the net charge of CspTm from -3.8 to +10.2, the radius of gyration of the chain is very similar under both conditions, indicating that protonation of acidic side chains at low pH results in additional hydrophobic interactions. We use a simple shared binding site model that describes the joint effect of urea and GdmCl, together with polyampholyte theory and an ion cloud model that includes the chemical free energy of counterion interactions and side chain protonation, to quantify this effect.

Melt-processing of small molecule organic photovoltaics via bulk heterojunction compatibilization.

PubMed

Rahmanudin, Aiman; Yao, Liang; Jeanbourquin, Xavier A; Liu, Yongpeng; Sekar, Arvindh; Ripaud, Emilie; Sivula, Kevin

2018-05-21

Melt-processing of organic semiconductors (OSCs) is a promising environmentally-friendly technique that can alleviate dependence on toxic chlorinated solvents. While melt-processed single-component OSC devices ( e.g. field-effect-transistors) have been demonstrated, multi-component bulk heterojunctions (BHJs) for organic photovoltaics (OPVs) remain a challenge. Herein, we demonstrate a strategy that affords tunable BHJ phase segregation and domain sizes from a single-phase homogeneous melt by employing strongly-crystalline small-molecule OSCs together with a customized molecular compatibilizing (MCP) additive. An optimized photoactive BHJ with 50 wt% MCP achieved a device power conversion efficiency of ca. 1% after melting the active layer at 240 °C (15 min, followed by slow cooling) before deposition of the top electrode. BHJ morphology characterization using atomic force and Kelvin probe microscopy, X-ray diffraction, and photo-luminescence measurements further demonstrate the trade-off between free charge generation and transport with respect to MCP loading in the BHJ. In addition, a functional OPV was also obtained from the melt-processing of dispersed micron-sized solid BHJ particles into a smooth and homogeneous thin-film by using the MCP approach. These results demonstrate that molecular compatibilization is a key prerequisite for further developments towards true solvent-free melt-processed BHJ OPV systems.

Solvent Flux Method (SFM): A Case Study of Water Access to Candida antarctica Lipase B.

PubMed

Benson, Sven P; Pleiss, Jürgen

2014-11-11

The solvent flux method (SFM) was developed to comprehensively characterize the influx of solvent molecules from the solvent environment into the active site of a protein in the framework of molecular dynamics simulations. This was achieved by introducing a solvent concentration gradient as well as partially reorienting and rescaling the velocity vector of all solvent molecules contained within a spherical volume enclosing the protein, thus inducing an accelerated solvent influx toward the active site. In addition to the detection of solvent access pathway within the protein structure, it is hereby possible to identify potential amino acid positions relevant to solvent-related enzyme engineering with high statistical significance. The method is particularly aimed at improving the reverse hydrolysis reaction rates in nonaqueous media. Candida antarctica lipase B (CALB) binds to a triglyceride-water interface with its substrate entrance channel oriented toward the hydrophobic substrate interface. The lipase-triglyceride-water system served as a model system for SFM to evaluate the influx of water molecules to the active site. As a proof of principle for SFM, a previously known water access pathway in CALB was identified as the primary water channel. In addition, a secondary water channel and two pathways for water access which contribute to water leakage between the protein and the triglyceride-water interface were identified.

Understanding disordered and unfolded proteins using single-molecule FRET and polymer theory.

PubMed

Hofmann, Hagen

2016-11-17

Understanding protein folding and the functional properties of intrinsically disordered proteins (IDPs) requires detailed knowledge of the forces that act in polypeptide chains. These forces determine the dimensions and dynamics of unfolded and disordered proteins and have been suggested to impact processes such as the coupled binding and folding of IDPs, or the rate of protein folding reactions. Much of the progress in understanding the physical and chemical properties of unfolded and intrinsically disordered polypeptide chains has been made possible by the recent developments in single-molecule fluorescence techniques. However, the interpretation of the experimental results requires concepts from polymer physics in order to be understood. Here, I review some of the theories used to describe the dimensions of unfolded polypeptide chains under varying solvent conditions together with their more recent application to experimental data.

Polymorphs and solvatomorphs of azilsartan medoxomil: Elucidation of solvent-induced construction and conformational diversity

NASA Astrophysics Data System (ADS)

Zhang, Xian-Rui; He, Sai-Fei; Zhang, Shuo; Li, Jing; Li, Shan; Liu, Jin-Song; Zhang, Lei

2017-02-01

Two polymorphs (AM-A and AM-B) of azilsartan medoxomil (AM) and four AM solvatomorphs with toluene (AM-TOL), 1,4-dioxane (AM-DIO), chloroform (AM-TCM) and N,N-dimethylacetamide (AM-DMA) have been prepared by the hydrolysis of azilsartan medoxomil potassium in aqueous-organic solutions. In the crystal structures of two polymorphs and three solvatomorphs (AM-TOL, AM-DIO and AM-TCM), two asymmetric AM molecules form the dimeric cycle-like structures via intermolecular Nsbnd H⋯N hydrogen bonds in R22 (26) ring, while AM-DMA shows intramolecular Nsbnd H⋯O hydrogen bond between AM and DMA molecules. The hydrogen bonds (Csbnd H⋯O or Csbnd H⋯N) and π···π (or Csbnd H···π) interactions are helpful to stabilize the conformational diversity of AM. The solvent-induced experiment shows that solvent molecules have great influence on the solvatomorph formation and DIO can form the most steady solvatomorph than other solvents. The thermal study demonstrates that toluene molecules in three solvatomorphs (AM-TOL, AM-DIO and AM-TCM) are the most difficult to remove from the cage. Our results illustrate that the solvent plays significant role in tuning the size of the cage and producing the conformational diversity of AM molecules.

The effect of specific solvent-solute interactions on complexation of alkali-metal cations by a lower-rim calix[4]arene amide derivative.

PubMed

Horvat, Gordan; Stilinović, Vladimir; Kaitner, Branko; Frkanec, Leo; Tomišić, Vladislav

2013-11-04

Complexation of alkali-metal cations with calix[4]arene secondary-amide derivative, 5,11,17,23-tetra(tert-butyl)-25,26,27,28-tetra(N-hexylcarbamoylmethoxy)calix[4]arene (L), in benzonitrile (PhCN) and methanol (MeOH) was studied by means of microcalorimetry, UV and NMR spectroscopies, and in the solid state by X-ray crystallography. The inclusion of solvent molecules (including acetonitrile, MeCN) in the calixarene hydrophobic cavity was also investigated. The classical molecular dynamics (MD) simulations of the systems studied were carried out. By combining the results obtained using the mentioned experimental and computational techniques, an attempt was made to get an as detailed insight into the complexation reactions as possible. The thermodynamic parameters, that is, equilibrium constants, reaction Gibbs energies, enthalpies, and entropies, of the investigated processes were determined and discussed. The stability constants of the 1:1 (metal:ligand) complexes measured by different methods were in very good agreement. Solution Gibbs energies of the ligand and its complexes with Na(+) and K(+) in methanol and acetonitrile were determined. It was established that from the thermodynamic point of view, apart from cation solvation, the most important reason for the huge difference in the stability of these complexes in the two solvents lay in the fact that the transfer of complex species from MeOH to MeCN was quite favorable. That could be at least partly explained by a more exergonic inclusion of the solvent molecule in the complexed calixarene cone in MeCN as compared to MeOH, which was supported by MD simulations. Molecular and crystal structures of the lithium cation complex of L with the benzonitrile molecule bound in the hydrophobic calixarene cavity were determined by single-crystal X-ray diffraction. As far as we are aware, for the first time the alkali-metal cation was found to be coordinated by the solvent nitrile group in a calixarene adduct. According to the results of MD simulations, the probability of such orientation of the benzonitrile molecule included in the ligand cone was by far the largest in the case of LiL(+) complex. Because of the favorable PhCN-Li(+) interaction, L was proven to have the highest affinity toward the lithium ion in benzonitrile, which was not the case in the other solvents examined (in acetonitrile, sodium complex was the most stable, whereas in methanol, complexation of lithium was not even observed). That could serve as a remarkable example showing the importance of specific solvent-solute interactions in determining the equilibrium in solution.

Reaction mechanisms: Stripping down SN2

NASA Astrophysics Data System (ADS)

Orr-Ewing, Andrew J.

2012-07-01

The mechanism of the SN2 reaction is fundamental to understanding and controlling the stereochemistry of organic reactions, but surrounding solvent molecules may complicate the textbook picture. Micro-solvation studies have now explored the stereochemical consequences of the presence of one or two solvent molecules.

Theoretical study on substituent and solvent effects for nanocubes formed with gear-shaped amphiphile molecules.

PubMed

Mashiko, T; Hiraoka, S; Nagashima, U; Tachikawa, M

2017-01-04

Gear-shaped amphiphile molecules (1) recently synthesized by Hiraoka et al. self-assemble into a hexameric structure, nanocubes (1 6 ), in 25% aqueous methanol due to a solvophobic effect. Here we have carried out molecular dynamic simulations to elucidate the stability of these hexameric capsules (1 6 and 2 6 ) in water, 25% aqueous methanol, and methanol. In all solvents, the 1 6 nanocubes are maintained for all trajectories. On the other hand, 2 6 was found to collapse for one trajectory in water and seven trajectories in 25% aqueous methanol. In a pure methanol solvent, 2 6 was found to collapse for all trajectories. The number of collapsed trajectories of 2 6 increased with the amount of methanol in the solvent. We therefore focused on the structure of the π-π stacking between pyridyl groups and the CH-π interactions between the methyl and pyridyl groups within the nanocube. Our study clearly shows the role played by the methanol solvent molecules in the assembly of the nanocube in terms of the substituent and solvent effects at the molecular level, and that these substituent and solvent effects are important for the self-assembly of the nanocubes.

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.

Specific interactions of alcohols and non-alcohols with a biologically active boronic acid derivative: a spectroscopic study.

PubMed

Geethanjali, H S; Melavanki, R M; Nagaraja, D; Patil, N R; Thipperudrappa, J; Kusanur, R A

2016-08-01

The photophysical properties of 4-fluoro-2-methoxyphenyl boronic acid (4FMPBA) are characterized using absorption and fluorescence techniques in series of non-alcohols and alcohols. The results are analyzed using different solvent polarity functions and Kamlet and Catalan's multiple regression approaches. The excited state dipole moment and change in dipole moment are calculated using both the solvatochromic shift method and Reichardt's microscopic solvent polarity parameter ETN. The ground state dipole moment is evaluated using quantum chemical calculations. It is found that general solute-solvent and hydrogen bond interactions are operative in this system. A red shift of ~ 9 nm in the emission spectra is observed with an increase in the solvent polarity, which depicts π→π(*) transitions, as well as the possibility of an intramolecular charge transfer (ICT) character in the emitting singlet state of 4FMPBA. The relative quantum yield, radiative and non-radiative decay constants are calculated in alkanes and alcohols using the single point method. It is found that the quantum yield of the molecule varies from 16.81% to 50.79% with the change in solvent polarity, indicating the dependence of fluorescence on the solvent environment. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Fast electron transfer through a single molecule natively structured redox protein

NASA Astrophysics Data System (ADS)

Della Pia, Eduardo Antonio; Chi, Qijin; MacDonald, J. Emyr; Ulstrup, Jens; Jones, D. Dafydd; Elliott, Martin

2012-10-01

The electron transfer properties of proteins are normally measured as molecularly averaged ensembles. Through these and related measurements, proteins are widely regarded as macroscopically insulating materials. Using scanning tunnelling microscopy (STM), we present new measurements of the conductance through single-molecules of the electron transfer protein cytochrome b562 in its native conformation, under pseudo-physiological conditions. This is achieved by thiol (SH) linker pairs at opposite ends of the molecule through protein engineering, resulting in defined covalent contact between a gold surface and a platinum-iridium STM tip. Two different orientations of the linkers were examined: a long-axis configuration (SH-LA) and a short-axis configuration (SH-SA). In each case, the molecular conductance could be `gated' through electrochemical control of the heme redox state. Reproducible and remarkably high conductance was observed in this relatively complex electron transfer system, with single-molecule conductance values peaking around 18 nS and 12 nS for the SH-SA and SH-LA cytochrome b562 molecules near zero electrochemical overpotential. This strongly points to the important role of the heme co-factor bound to the natively structured protein. We suggest that the two-step model of protein electron transfer in the STM geometry requires a multi-electron transfer to explain such a high conductance. The model also yields a low value for the reorganisation energy, implying that solvent reorganisation is largely absent.The electron transfer properties of proteins are normally measured as molecularly averaged ensembles. Through these and related measurements, proteins are widely regarded as macroscopically insulating materials. Using scanning tunnelling microscopy (STM), we present new measurements of the conductance through single-molecules of the electron transfer protein cytochrome b562 in its native conformation, under pseudo-physiological conditions. This is achieved by thiol (SH) linker pairs at opposite ends of the molecule through protein engineering, resulting in defined covalent contact between a gold surface and a platinum-iridium STM tip. Two different orientations of the linkers were examined: a long-axis configuration (SH-LA) and a short-axis configuration (SH-SA). In each case, the molecular conductance could be `gated' through electrochemical control of the heme redox state. Reproducible and remarkably high conductance was observed in this relatively complex electron transfer system, with single-molecule conductance values peaking around 18 nS and 12 nS for the SH-SA and SH-LA cytochrome b562 molecules near zero electrochemical overpotential. This strongly points to the important role of the heme co-factor bound to the natively structured protein. We suggest that the two-step model of protein electron transfer in the STM geometry requires a multi-electron transfer to explain such a high conductance. The model also yields a low value for the reorganisation energy, implying that solvent reorganisation is largely absent. Electronic supplementary information (ESI) available: Experimental methods, DNA and protein sequences, additional STM statistical analysis and images, electrochemical data and It-z data analysis. See DOI: 10.1039/c2nr32131a

Counteracting chemical chaperone effects on the single-molecule α-synuclein structural landscape.

PubMed

Ferreon, Allan Chris M; Moosa, Mahdi Muhammad; Gambin, Yann; Deniz, Ashok A

2012-10-30

Protein structure and function depend on a close interplay between intrinsic folding energy landscapes and the chemistry of the protein environment. Osmolytes are small-molecule compounds that can act as chemical chaperones by altering the environment in a cellular context. Despite their importance, detailed studies on the role of these chemical chaperones in modulating structure and dimensions of intrinsically disordered proteins have been limited. Here, we used single-molecule Förster resonance energy transfer to test the counteraction hypothesis of counterbalancing effects between the protecting osmolyte trimethylamine-N-oxide (TMAO) and denaturing osmolyte urea for the case of α-synuclein, a Parkinson's disease-linked protein whose monomer exhibits significant disorder. The single-molecule experiments, which avoid complications from protein aggregation, do not exhibit clear solvent-induced cooperative protein transitions for these osmolytes, unlike results from previous studies on globular proteins. Our data demonstrate the ability of TMAO and urea to shift α-synuclein structures towards either more compact or expanded average dimensions. Strikingly, the experiments directly reveal that a 21 [urea][TMAO] ratio has a net neutral effect on the protein's dimensions, a result that holds regardless of the absolute osmolyte concentrations. Our findings shed light on a surprisingly simple aspect of the interplay between urea and TMAO on α-synuclein in the context of intrinsically disordered proteins, with potential implications for the biological roles of such chemical chaperones. The results also highlight the strengths of single-molecule experiments in directly probing the chemical physics of protein structure and disorder in more chemically complex environments.

Counteracting chemical chaperone effects on the single-molecule α-synuclein structural landscape

PubMed Central

Ferreon, Allan Chris M.; Moosa, Mahdi Muhammad; Deniz, Ashok A.

2012-01-01

Protein structure and function depend on a close interplay between intrinsic folding energy landscapes and the chemistry of the protein environment. Osmolytes are small-molecule compounds that can act as chemical chaperones by altering the environment in a cellular context. Despite their importance, detailed studies on the role of these chemical chaperones in modulating structure and dimensions of intrinsically disordered proteins have been limited. Here, we used single-molecule Förster resonance energy transfer to test the counteraction hypothesis of counterbalancing effects between the protecting osmolyte trimethylamine-N-oxide (TMAO) and denaturing osmolyte urea for the case of α-synuclein, a Parkinson’s disease-linked protein whose monomer exhibits significant disorder. The single-molecule experiments, which avoid complications from protein aggregation, do not exhibit clear solvent-induced cooperative protein transitions for these osmolytes, unlike results from previous studies on globular proteins. Our data demonstrate the ability of TMAO and urea to shift α-synuclein structures towards either more compact or expanded average dimensions. Strikingly, the experiments directly reveal that a 2∶1 [urea]∶[TMAO] ratio has a net neutral effect on the protein’s dimensions, a result that holds regardless of the absolute osmolyte concentrations. Our findings shed light on a surprisingly simple aspect of the interplay between urea and TMAO on α-synuclein in the context of intrinsically disordered proteins, with potential implications for the biological roles of such chemical chaperones. The results also highlight the strengths of single-molecule experiments in directly probing the chemical physics of protein structure and disorder in more chemically complex environments. PMID:22826265

On the relation between Marcus theory and ultrafast spectroscopy of solvation kinetics

NASA Astrophysics Data System (ADS)

Roy, Santanu; Galib, Mirza; Schenter, Gregory K.; Mundy, Christopher J.

2018-01-01

The phenomena of solvent exchange control the process of solvating ions, protons, and charged molecules. Building upon our extension of Marcus' philosophy of electron transfer, we provide a new perspective of ultrafast solvent exchange mechanism around ions measurable by two-dimensional infrared (2DIR) spectroscopy. In this theory, solvent rearrangement drives an ion-bound water to an activated state of higher coordination number, triggering ion-water separation that leads to the solvent-bound state of the water molecule. This ion-bound to solvent-bound transition rate for a BF4--water system is computed using ab initio molecular dynamics and Marcus theory, and is found to be in excellent agreement with the 2DIR measurement.

Solvent effects on the properties of hyperbranched polythiophenes.

PubMed

Torras, Juan; Zanuy, David; Aradilla, David; Alemán, Carlos

2016-09-21

The structural and electronic properties of all-thiophene dendrimers and dendrons in solution have been evaluated using very different theoretical approaches based on quantum mechanical (QM) and hybrid QM/molecular mechanics (MM) methodologies: (i) calculations on minimum energy conformations using an implicit solvation model in combination with density functional theory (DFT) or time-dependent DFT (TD-DFT) methods; (ii) hybrid QM/MM calculations, in which the solute and solvent molecules are represented at the DFT level as point charges, respectively, on snapshots extracted from classical molecular dynamics (MD) simulations using explicit solvent molecules, and (iii) QM/MM-MD trajectories in which the solute is described at the DFT or TD-DFT level and the explicit solvent molecules are represented using classical force-fields. Calculations have been performed in dichloromethane, tetrahydrofuran and dimethylformamide. A comparison of the results obtained using the different approaches with the available experimental data indicates that the incorporation of effects associated with both the conformational dynamics of the dendrimer and the explicit solvent molecules is strictly necessary to satisfactorily reproduce the properties of the investigated systems. Accordingly, QM/MM-MD simulations are able to capture such effects providing a reliable description of electronic properties-conformational flexibility relationships in all-Th dendrimers.

Diffusional correlations among multiple active sites in a single enzyme.

PubMed

Echeverria, Carlos; Kapral, Raymond

2014-04-07

Simulations of the enzymatic dynamics of a model enzyme containing multiple substrate binding sites indicate the existence of diffusional correlations in the chemical reactivity of the active sites. A coarse-grain, particle-based, mesoscopic description of the system, comprising the enzyme, the substrate, the product and solvent, is constructed to study these effects. The reactive and non-reactive dynamics is followed using a hybrid scheme that combines molecular dynamics for the enzyme, substrate and product molecules with multiparticle collision dynamics for the solvent. It is found that the reactivity of an individual active site in the multiple-active-site enzyme is reduced substantially, and this effect is analyzed and attributed to diffusive competition for the substrate among the different active sites in the enzyme.

The different conformations and crystal structures of dihydroergocristine

NASA Astrophysics Data System (ADS)

Mönch, B.; Kraus, W.; Köppen, R.; Emmerling, F.

2016-02-01

The identification of different forms of dihydroergocristine (DHEC) was carried out by crystallization from different organic solvents. DHEC was identified as potential template for molecularly imprinted polymers (MIPs) for the epimeric specific analysis of ergot alkaloids (EAs) in food. DHEC was crystallized from different solvents in order to mimic the typical MIP synthesis conditions. Four new solvatomorphs of DHEC were obtained. All solvatomorphs contain a water molecule in the crystal structure, whereas three compounds contain an additional solvent molecule. Based on the conformation of DHEC a comparison with typical EA molecules was possible. The analysis showed that DHEC is a suitable template for MIPs for EAs.

Interaction between morin and AOT reversed micelles--studies with UV-vis at 25 °C.

PubMed

Bhattarai, Ajaya; Wilczura-Wachnik, H

2014-01-30

The precise measurements of morin absorbance in presence of surfactant/solvent/water systems at 25 °C by UV-vis technique are reported. The surfactant used in presented study was sodium bis(2-ethylhexyl) sulfosuccinate called Aerosol-OT or AOT. The solvents selected were: ethanol, ethylene glycol, and n-decanol. The concentrations of AOT were varied between 0.001 and 0.4 mol/kg. Morin concentration in quvette during UV-vis registration was not equals in all solvent because of its different solubility and absorption intensity depending on the solvent. Water concentration in the studied systems was defined by R parameter according to relation: R=[H2O]/[AOT] and was equal 0, 30 and 40 in ethanol; 0, 10, 20 and 30 in ethylene glycol and 0, 10, 20, 30, and 40 in n-decanol. In presented work a Nernstian distribution of morin between the organic and micellar phases was assumed. The intensity of morin absorbance as a function of AOT concentration was analyzed. Using Non-linear Regression Procedure (NLREG) morin binding constant (K' [mol/kg]), and morin distribution constant (K) between organic phase and AOT micellar phase have been calculated. The experimental results have shown a significant influence of solvent, surfactant and water presence on morin UV-vis spectrum. Calculated data pointed out on different transfer of morin molecules from the organic to micellar phase depending on the solvent. Moreover, results of calculations indicate on competition between morin and water molecules interacting with AOT polar heads. Morin molecules privileged location in AOT reversed micelles strongly depends on the solvent. In case of systems with ethylene glycol as solvent is possible morin molecules location in polar cores of AOT reversed micelles as results of strong interaction between AOT polar heads and morin hydroxyl groups, whereas in case of ethanol and n-decanol morin molecules are located in palisade layer. Copyright © 2013 Elsevier B.V. All rights reserved.

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

Rodriguez, Mark A.; Sava Gallis, Dorina F.; Chavez, James S.

We report here the synthesis of a neutral viologen derivative, C 24H 16N 2O 4·2H 2O. The non-solvent portion of the structure (Z-Lig) is a zwitterion, consisting of two positively charged pyridinium cations and two negatively charged carboxylate anions. The carboxylate group is almost coplanar [dihedral angle = 2.04 (11)°] with the benzene ring, whereas the dihedral angle between pyridine and benzene rings is 46.28 (5)°. TheZ-Lig molecule is positioned on a center of inversion (Fig. 1). The presence of the twofold axis perpendicular to thec-glide plane in space groupC2/c generates a screw-axis parallel to thebaxis that is shifted from themore » origin by 1/4 in theaandcdirections. This screw-axis replicates the molecule (and solvent water molecules) through space. TheZ-Lig molecule links to adjacent moleculesviaO—H...O hydrogen bonds involving solvent water molecules as well as intermolecular C—H...O interactions. There are also π–π interactions between benzene rings on adjacent molecules.« less

Small-Molecule Organic Photovoltaic Modules Fabricated via Halogen-Free Solvent System with Roll-to-Roll Compatible Scalable Printing Method.

PubMed

Heo, Youn-Jung; Jung, Yen-Sook; Hwang, Kyeongil; Kim, Jueng-Eun; Yeo, Jun-Seok; Lee, Sehyun; Jeon, Ye-Jin; Lee, Donmin; Kim, Dong-Yu

2017-11-15

For the first time, the photovoltaic modules composed of small molecule were successfully fabricated by using roll-to-roll compatible printing techniques. In this study, blend films of small molecules, BTR and PC 71 BM were slot-die coated using a halogen-free solvent system. As a result, high efficiencies of 7.46% and 6.56% were achieved from time-consuming solvent vapor annealing (SVA) treatment and roll-to-roll compatible solvent additive approaches, respectively. After successful verification of our roll-to-roll compatible method on small-area devices, we further fabricated large-area photovoltaic modules with a total active area of 10 cm 2 , achieving a power conversion efficiency (PCE) of 4.83%. This demonstration of large-area photovoltaic modules through roll-to-roll compatible printing methods, even based on a halogen-free solvent, suggests the great potential for the industrial-scale production of organic solar cells (OSCs).

Preparation and guest-uptake protocol for a porous complex useful for 'crystal-free' crystallography.

PubMed

Inokuma, Yasuhide; Yoshioka, Shota; Ariyoshi, Junko; Arai, Tatsuhiko; Fujita, Makoto

2014-02-01

We recently reported a new method for single-crystal X-ray diffraction (SCD) analysis that does not require the crystallization of the target compound. In this 'crystal-free' crystallography, a tiny crystal of a porous complex is soaked in the solution of the target guest. The guest molecules are absorbed and oriented in the crystal pores and can be analyzed by X-ray diffraction. We describe here a detailed synthetic protocol for the preparation of uniform single crystals of the porous host complex and for the subsequent guest uptake. The protocol describes our most versatile porous complex, which is prepared from commercially available ZnI2 and 2,4,6-tri(4-pyridyl)-1,3,5-triazine. The host complex has large pores with a cross-section of 8 × 5 Å(2). Single crystals of the complex are grown from layered solutions of the two components. The pores of the as-synthesized complex are filled with nitrobenzene, which is replaced with the inert solvent cyclohexane. This solvent exchange is essential for the rapid and effective inclusion of target compounds. The most crucial and delicate step is the selection of high-quality single crystals from the mixture of crystals of various shapes and sizes. We suggest using the facial indices of the single crystals as a criterion for crystal selection. Single-crystal samples for X-ray analysis can be prepared by immersing the selected crystals in a cyclohexane/dichloromethane solution of target compound. After a very slow evaporation of the solvent, typically over 2 d, the final crystal can be picked and directly subjected to SCD analysis. The protocol can be completed within ∼16 d.

Microfluidic Extraction of Biomarkers using Water as Solvent

NASA Technical Reports Server (NTRS)

Amashukeli, Xenia; Manohara, Harish; Chattopadhyay, Goutam; Mehdi, Imran

2009-01-01

A proposed device, denoted a miniature microfluidic biomarker extractor (mu-EX), would extract trace amounts of chemicals of interest from samples, such as soils and rocks. Traditionally, such extractions are performed on a large scale with hazardous organic solvents; each solvent capable of dissolving only those molecules lying within narrow ranges of specific chemical and physical characteristics that notably include volatility, electric charge, and polarity. In contrast, in the mu-EX, extractions could be performed by use of small amounts (typically between 0.1 and 100 L) of water as a universal solvent. As a rule of thumb, in order to enable solvation and extraction of molecules, it is necessary to use solvents that have polarity sufficiently close to the polarity of the target molecules. The mu-EX would make selection of specific organic solvents unnecessary, because mu-EX would exploit a unique property of liquid water: the possibility of tuning its polarity to match the polarity of organic solvents appropriate for extraction of molecules of interest. The change of the permittivity of water would be achieved by exploiting interactions between the translational states of water molecules and an imposed electromagnetic field in the frequency range of 300 to 600 GHz. On a molecular level, these interactions would result in disruption of the three-dimensional hydrogen-bonding network among liquid-water molecules and subsequent solvation and hydrolysis of target molecules. The mu-EX is expected to be an efficient means of hydrolyzing chemical bonds in complex macromolecules as well and, thus, enabling analysis of the building blocks of these complex chemical systems. The mu-EX device would include a microfluidic channel, part of which would lie within a waveguide coupled to an electronically tuned source of broad-band electromagnetic radiation in the frequency range from 300 to 600 GHz (see figure). The part of the microfluidic channel lying in the waveguide would constitute an interaction volume. The dimensions of the interaction volume would be chosen in accordance with the anticipated amount of solid sample material needed to ensure extraction of sufficient amount of target molecules for detection and analysis. By means that were not specified at the time of reporting the information for this article, the solid sample material would be placed in the interaction volume. Then the electromagnetic field would be imposed within the waveguide and water would be pumped through the interaction volume to effect the extraction.

Size-dependent error of the density functional theory ionization potential in vacuum and solution

DOE PAGES

Sosa Vazquez, Xochitl A.; Isborn, Christine M.

2015-12-22

Density functional theory is often the method of choice for modeling the energetics of large molecules and including explicit solvation effects. It is preferable to use a method that treats systems of different sizes and with different amounts of explicit solvent on equal footing. However, recent work suggests that approximate density functional theory has a size-dependent error in the computation of the ionization potential. We here investigate the lack of size-intensivity of the ionization potential computed with approximate density functionals in vacuum and solution. We show that local and semi-local approximations to exchange do not yield a constant ionization potentialmore » for an increasing number of identical isolated molecules in vacuum. Instead, as the number of molecules increases, the total energy required to ionize the system decreases. Rather surprisingly, we find that this is still the case in solution, whether using a polarizable continuum model or with explicit solvent that breaks the degeneracy of each solute, and we find that explicit solvent in the calculation can exacerbate the size-dependent delocalization error. We demonstrate that increasing the amount of exact exchange changes the character of the polarization of the solvent molecules; for small amounts of exact exchange the solvent molecules contribute a fraction of their electron density to the ionized electron, but for larger amounts of exact exchange they properly polarize in response to the cationic solute. As a result, in vacuum and explicit solvent, the ionization potential can be made size-intensive by optimally tuning a long-range corrected hybrid functional.« less

Size-dependent error of the density functional theory ionization potential in vacuum and solution

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

Sosa Vazquez, Xochitl A.; Isborn, Christine M., E-mail: cisborn@ucmerced.edu

2015-12-28

Density functional theory is often the method of choice for modeling the energetics of large molecules and including explicit solvation effects. It is preferable to use a method that treats systems of different sizes and with different amounts of explicit solvent on equal footing. However, recent work suggests that approximate density functional theory has a size-dependent error in the computation of the ionization potential. We here investigate the lack of size-intensivity of the ionization potential computed with approximate density functionals in vacuum and solution. We show that local and semi-local approximations to exchange do not yield a constant ionization potentialmore » for an increasing number of identical isolated molecules in vacuum. Instead, as the number of molecules increases, the total energy required to ionize the system decreases. Rather surprisingly, we find that this is still the case in solution, whether using a polarizable continuum model or with explicit solvent that breaks the degeneracy of each solute, and we find that explicit solvent in the calculation can exacerbate the size-dependent delocalization error. We demonstrate that increasing the amount of exact exchange changes the character of the polarization of the solvent molecules; for small amounts of exact exchange the solvent molecules contribute a fraction of their electron density to the ionized electron, but for larger amounts of exact exchange they properly polarize in response to the cationic solute. In vacuum and explicit solvent, the ionization potential can be made size-intensive by optimally tuning a long-range corrected hybrid functional.« less

Gas-phase geometry optimization of biological molecules as a reasonable alternative to a continuum environment description: fact, myth, or fiction?

PubMed

Sousa, Sérgio Filipe; Fernandes, Pedro Alexandrino; Ramos, Maria João

2009-12-31

Gas-phase optimization of single biological molecules and of small active-site biological models has become a standard approach in first principles computational enzymology. The important role played by the surrounding environment (solvent, enzyme, both) is normally only accounted for through higher-level single point energy calculations performed using a polarizable continuum model (PCM) and an appropriate dielectric constant with the gas-phase-optimized geometries. In this study we analyze this widely used approximation, by comparing gas-phase-optimized geometries with geometries optimized with different PCM approaches (and considering different dielectric constants) for a representative data set of 20 very important biological molecules--the 20 natural amino acids. A total of 323 chemical bonds and 469 angles present in standard amino acid residues were evaluated. The results show that the use of gas-phase-optimized geometries can in fact be quite a reasonable alternative to the use of the more computationally intensive continuum optimizations, providing a good description of bond lengths and angles for typical biological molecules, even for charged amino acids, such as Asp, Glu, Lys, and Arg. This approximation is particularly successful if the protonation state of the biological molecule could be reasonably described in vacuum, a requirement that was already necessary in first principles computational enzymology.

Influence of polarity of solvents on IR absorption and Raman spectra of ascorbic acid

NASA Astrophysics Data System (ADS)

Kutsenko, S. A.; Danyaeva, Y. S.; Maximova, S. V.

2018-04-01

The results of numerical calculations of IR absorption and Raman spectra of ascorbic acid in polar and nonpolar solutions are presented. The dependence of the change in the total energy and the dipole moment of the molecule on the characteristics of the solvents was investigated using the two solvation models. Spectral bands and the corresponding structural groups of the molecule are found, the characteristics of which are most vulnerable to solvents.

Solvent effects on the Raman spectra of the isolated carbon-hydrogen stretches of cyclohexane-d11: A molecular dynamics simulation study of liquid and supercritical solvation

NASA Astrophysics Data System (ADS)

Frankland, Sarah-Jane Victoria

Molecular dynamics simulations of solvent effects on the Raman spectra of isotopically isolated C-H stretches of cyclohexane-d11 were performed in liquids and supercritical CO2. The red spectral shifts from the gas phase origin were derived three different ways: (1) from the Lennard-Jones force on the normal coordinate of the vibration; (2) from this force with an additional term to account for the polarizabilily change on excitation, and (3) as an empirical difference potential between the v = 0 and v = 1 state of the hydrogen atom involved in the vibration. Model 3 was successfully parametrized to reproduce the experimental spectral shifts and linewidths. The simulated lineshapes from these models were homogeneously broadened from gas to liquid densities primarily by collisions of nearby solvent molecules with the solute. Both the simulations and isolated binary collision theory showed the density dependence of the linewidth to be related to that of the collision rate. Two additional projects were done which use Monte-Carlo algorithms involving two molecules. In the first project 1:1 complexes of solute and solvent were formed at the potential surface minima such that the geometries of conformers, energies of formation, and electronic spectral shifts could be studied. Complexes between 7- azaindole, indole, carbazole, and 1-azacarbazole and hydrogen-bonding solvents were most stable when the solvent was hydrogen-bonded at the solute N-H site. The energies of formation compared well with values obtained from ab initio calculations. Complexes of coumarins 102 and 153 and fluorinated alcohols showed the more stable conformers to have the alcohols bound at the coumarin carbonyl group. In the second project, one solvent molecule was randomly placed around the solute molecule in order to simplify bulk liquid simulation to only two molecules. This approximation was rised to show that the dynamic Stokes shift of coumarin 153 in over 30 solvents correlates with the permanent charge distribution of the solvent.

Self-assembly mechanism of 1,3:2,4-di(3,4-dichlorobenzylidene)-D-sorbitol and control of the supramolecular chirality.

PubMed

Li, Jingjing; Fan, Kaiqi; Guan, Xidong; Yu, Yingzhe; Song, Jian

2014-11-11

Dibenzylidene-D-sorbitol (DBS) and its derivatives are known to form gels in organic solvents; however, the mechanism of the gel formation has been a subject of much debate. The present work is undertaken to elucidate the organization mechanism of a DBS derivative, 1,3:2,4-di(3,4-dichlorobenzylidene)-D-sorbitol (DCDBS), by taking into account the solvent effects and comparing the experiment data with theoretical calculation. These molecules form smooth nonhelical fibers with a rest circular dichroism (CD) signal in polar solvents, in contrast to rope-liked left-helical fibers with a strong negative CD signal observed in nonpolar solvents. The molecular complexes thus formed were characterized by means of Fourier transform infrared spectra, ultraviolet-visible spectra, X-ray diffraction patterns, static contact angles, and theoretical calculations. It was proposed that the interactions between the gelator and the solvents could subtly change the stacking of the molecules and hence their self-assembled nanostructures. In nonpolar solvents, the gelator molecules appear as a distorted T-shaped structure with the 6-OH forming intermolecular hydrogen bonds with the acetal oxygens of adjacent gelator molecule. In addition, because of differential stacking interactions on both sides of the 10-member ring skeleton of the gelator, the oligomers may assemble in a helix fashion to minimize the energy, leading to helical fibers. In polar solvents, however, the gelator molecules show a rigid planelike structure and thus stack on top of each other because of strong parallel-displaced π interactions. The balanced driving force on both sides of the 10-member ring skeleton made it difficult for the dimers to bend, thus resulting in nonhelical nanostructure. As expected from the mechanisms proposed here, twisted ribbon fibers with a medium strength CD signal were obtained when solvents of different polarities were mixed. Thus, solvent effects revealed in this work represent an effective means of realizing in situ tuning of nanostructures and control of the expression of chirality at supramolecular levels.

Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel

NASA Astrophysics Data System (ADS)

Zhang, Ce; Zhang, Fang; van Kan, Jeroen A.; van der Maarel, Johan R. C.

2008-06-01

Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range of 150-300 nm casted in a poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules were measured with fluorescence microscopy as a function of the ionic strength and composition of the buffer as well as the DNA intercalation level by the YOYO-1 dye. The data were interpreted with the scaling theory for a wormlike polymer in good solvent, including the effects of confinement, charge, and self-avoidance. It was found that the elongation of the DNA molecules with decreasing ionic strength can be interpreted in terms of an increase of the persistence length. Self-avoidance effects on the extension are moderate, due to the small correlation length imposed by the channel cross-sectional diameter. Intercalation of the dye results in an increase of the DNA contour length and a partial neutralization of the DNA charge, but besides effects of electrostatic origin it has no significant effect on the bare bending rigidity. In the presence of divalent cations, the DNA molecules were observed to contract, but they do not collapse into a condensed structure. It is proposed that this contraction results from a divalent counterion mediated attractive force between the segments of the DNA molecule.

Dynamic acid/base equilibrium in single component switchable ionic liquids and consequences on viscosity

DOE PAGES

Cantu, David C.; Lee, Juntaek; Lee, Mal -Soon; ...

2016-03-28

The deployment of transformational non-aqueous CO 2-capture solvent systems is encumbered by high viscosity even at intermediate uptakes. Using single-molecule CO 2 binding organic liquids as a prototypical example, we identify the key molecular features controlling bulk liquid viscosity and CO 2 uptake kinetics. Fast uptake kinetics arise from close proximity of the alcohol and amine sites that are involved in CO 2 binding. This process results in the concerted formation of a Zwitterion containing both an alkylcarbonate and a protonated amine. The hydrogen bonding between the two functional groups ultimately determines the solution viscosity. Based on molecular simulation, thismore » work reveals options to significantly reduce viscosity with molecular modifications that shift the proton transfer equilibrium towards a neutral acid/amine species as opposed to the ubiquitously accepted Zwitterionic state. Lastly, the molecular design concepts proposed here, for the alkyl-carbonate systems, are readily extensible to other CO 2 capture technologies, such as the carbamate- or imidazole-based solvent chemistries.« less

Dynamics of liquids, molecules, and proteins measured with ultrafast 2D IR vibrational echo chemical exchange spectroscopy.

PubMed

Fayer, M D

2009-01-01

A wide variety of molecular systems undergo fast structural changes under thermal equilibrium conditions. Such transformations are involved in a vast array of chemical problems. Experimentally measuring equilibrium dynamics is a challenging problem that is at the forefront of chemical research. This review describes ultrafast 2D IR vibrational echo chemical exchange experiments and applies them to several types of molecular systems. The formation and dissociation of organic solute-solvent complexes are directly observed. The dissociation times of 13 complexes, ranging from 4 ps to 140 ps, are shown to obey a relationship that depends on the complex's formation enthalpy. The rate of rotational gauche-trans isomerization around a carbon-carbon single bond is determined for a substituted ethane at room temperature in a low viscosity solvent. The results are used to obtain an approximate isomerization rate for ethane. Finally, the time dependence of a well-defined single structural transformation of a protein is measured.

On the relation between Marcus theory and ultrafast spectroscopy of solvation kinetics

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

Roy, Santanu; Galib, Mirza; Schenter, Gregory K.

The phenomena of solvent exchange control the process of solvating ions, protons, and charged molecules. Building upon our extension of Marcus’ philosophy of electron transfer, here we provide a new perspective of ultrafast solvent exchange mechanism around ions measurable by two-dimensional infrared (2DIR) spectroscopy. In this theory, solvent rearrangement drives an ion-bound water to an activated state of higher coordination number, triggering ion-water separation that leads to the solvent-bound state of the water molecule. This ion-bound to solvent-bound transition rate for a BF 4 --water system is then computed using ab initio molecular dynamics and Marcus theory, and is foundmore » to be in excellent agreement with the 2DIR measurement.« less

On the relation between Marcus theory and ultrafast spectroscopy of solvation kinetics

DOE PAGES

Roy, Santanu; Galib, Mirza; Schenter, Gregory K.; ...

2017-12-24

The phenomena of solvent exchange control the process of solvating ions, protons, and charged molecules. Building upon our extension of Marcus’ philosophy of electron transfer, here we provide a new perspective of ultrafast solvent exchange mechanism around ions measurable by two-dimensional infrared (2DIR) spectroscopy. In this theory, solvent rearrangement drives an ion-bound water to an activated state of higher coordination number, triggering ion-water separation that leads to the solvent-bound state of the water molecule. This ion-bound to solvent-bound transition rate for a BF 4 --water system is then computed using ab initio molecular dynamics and Marcus theory, and is foundmore » to be in excellent agreement with the 2DIR measurement.« less

On the relation between Marcus theory and ultrafast spectroscopy of solvation kinetics

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

Roy, Santanu; Galib, Mirza; Schenter, Gregory K.

The phenomena of solvent exchange control the process of solvating ions, protons, and charged molecules. Building upon our extension of Marcus’ philosophy of electron transfer, we provide a new perspective of ultrafast solvent exchange mechanism around ions measurable by two-dimensional infrared (2DIR) spectroscopy. In this theory, solvent rearrangement drives an ion-bound water to an activated state of higher coordination number, triggering ion-water separation that leads to the solvent-bound state of the water molecule. This ion-bound to solvent-bound transition rate for a BF4- water system is computed using ab initio molecular dynamics and Marcus theory, and is found to be inmore » excellent agreement with the 2DIR measurement.« less

Numerical Treatment of Stokes Solvent Flow and Solute-Solvent Interfacial Dynamics for Nonpolar Molecules.

PubMed

Sun, Hui; Zhou, Shenggao; Moore, David K; Cheng, Li-Tien; Li, Bo

2016-05-01

We design and implement numerical methods for the incompressible Stokes solvent flow and solute-solvent interface motion for nonpolar molecules in aqueous solvent. The balance of viscous force, surface tension, and van der Waals type dispersive force leads to a traction boundary condition on the solute-solvent interface. To allow the change of solute volume, we design special numerical boundary conditions on the boundary of a computational domain through a consistency condition. We use a finite difference ghost fluid scheme to discretize the Stokes equation with such boundary conditions. The method is tested to have a second-order accuracy. We combine this ghost fluid method with the level-set method to simulate the motion of the solute-solvent interface that is governed by the solvent fluid velocity. Numerical examples show that our method can predict accurately the blow up time for a test example of curvature flow and reproduce the polymodal (e.g., dry and wet) states of hydration of some simple model molecular systems.

Numerical Treatment of Stokes Solvent Flow and Solute-Solvent Interfacial Dynamics for Nonpolar Molecules

PubMed Central

Sun, Hui; Zhou, Shenggao; Moore, David K.; Cheng, Li-Tien; Li, Bo

2015-01-01

We design and implement numerical methods for the incompressible Stokes solvent flow and solute-solvent interface motion for nonpolar molecules in aqueous solvent. The balance of viscous force, surface tension, and van der Waals type dispersive force leads to a traction boundary condition on the solute-solvent interface. To allow the change of solute volume, we design special numerical boundary conditions on the boundary of a computational domain through a consistency condition. We use a finite difference ghost fluid scheme to discretize the Stokes equation with such boundary conditions. The method is tested to have a second-order accuracy. We combine this ghost fluid method with the level-set method to simulate the motion of the solute-solvent interface that is governed by the solvent fluid velocity. Numerical examples show that our method can predict accurately the blow up time for a test example of curvature flow and reproduce the polymodal (e.g., dry and wet) states of hydration of some simple model molecular systems. PMID:27365866

Thermodynamic Parameters of the Dissolution of 4-Hydroxy-L-Proline and L-Phenylalanine in Mixed Aqueous Solvents at 298 K

NASA Astrophysics Data System (ADS)

Smirnov, V. I.; Badelin, V. G.

2018-01-01

The enthalpies of solution of 4-hydroxy-L-proline and L-phenylalanine in binary mixed aqueous solvents containing acetonitrile (AN), 1,4-dioxane (1,4-DO), or acetone (AC) at mole fractions of 0 to 0.25 are determined at T = 298.15 K via isothermal calorimetry. The standard enthalpies of solution (Δsol H°) and transfer (Δtr H°) of 4-hydroxy-L-proline and L-phenylalanine from water to mixed aqueous solvents are calculated using the experimental calorimetric data, as are the enthalpy coefficients of paired interactions ( h xy ) between the molecules of the investigated amino acids and the organic solvents. The effects the mixed aqueous solvent composition and the structure of the organic solvent molecules have on the enthalpies of solution and transfer for the investigated amino acids are considered. The correlation between the enthalpy of solution of the amino acids and the electron-donating properties of the organic solvents in the mixed aqueous solvent systems is established.

Novel Photovoltaic Nanocomposites Based on Single-Molecule Optoelectronics on Functionalized Carbon Nanotubes Percolated Networks and the Polymer Chain Conformation Effect

DTIC Science & Technology

2009-12-07

intensity increase that may go as high as 20 fold. Almost identical behavior was observed in the dewetting processes induced by solvent vapor...conjugated polymer coating thickness and material systems were explored. 87 Experimental Section MWCNT acid treatment The MWCNT which was...deionized (DI) water by filtration until the solution become neutral, and then dried in the oven with 80. MWCNT grafting 2-(3-thienylethanol

Solvent effect on the synthesis of clarithromycin: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Duran, Dilek; Aviyente, Viktorya; Baysal, Canan

2004-02-01

Clarithromycin (6- O-methylerythromycin A) is a 14-membered macrolide antibiotic which is active in vitro against clinically important gram-positive and gram-negative bacteria. The selectivity of the methylation of the C-6 OH group is studied on erythromycin A derivatives. To understand the effect of the solvent on the methylation process, detailed molecular dynamics (MD) simulations are performed in pure DMSO, pure THF and DMSO:THF (1:1) mixture by using the anions at the C-6, C-11 and C-12 positions of 2',4''-[ O-bis(TMS)]erythromycin A 9-[ O-(dimethylthexylsilyl)oxime] under the assumption that the anions are stable on the sub-nanosecond time scale. The conformations of the anions are not affected by the presence of the solvent mixture. The radial distribution functions are computed for the distribution of different solvent molecules around the `O-' of the anions. At distances shorter than 5 Å, DMSO molecules are found to cluster around the C-11 anion, whereas the anion at the C-12 position is surrounded by the THF molecules. The anion at the C-6 position is not blocked by the solvent molecules. The results are consistent with the experimental finding that the methylation yield at the latter position is increased in the presence of a DMSO:THF (1:1) solvent mixture. Thus, the effect of the solvent in enhancing the yield during the synthesis is not by changing the conformational properties of the anions, but rather by creating a suitable environment for methylation at the C-6 position.

Solvent/co-solvent effects on the electronic properties and adsorption mechanism of anticancer drug Thioguanine on Graphene oxide surface as a nanocarrier: Density functional theory investigation and a molecular dynamics

NASA Astrophysics Data System (ADS)

Hasanzade, Zohre; Raissi, Heidar

2017-11-01

In this work, the adsorption of Thioguanine (TG) anticancer drug on the surface of Graphene oxide (GO) nanosheet has investigated using density functional theory (DFT) and molecular dynamics simulation (MDs). Quantum mechanics calculations by two methods including M06-2X/6-31G**and ωB97X-D/6-31G** have been employed to calculate the details of energetic, geometric, and electronic properties of the TG molecule interacting with Graphene oxide nanosheet (GONS). DFT calculations confirmed that the strongest adsorption is observed when hydrogen bond interactions between TG molecule and the functional groups of Graphene oxide nanosheet are predominate. In all calculations, solvent effects have been considered in water using the PCM method. It is found that TG molecule can be adsorbed on Graphene oxide with negative solvation energy, indicating the TG adsorption on Graphene oxide surfaces is thermodynamically favored. Moreover, MD simulations are examined to understand the solvent/co-solvent effect (water, ethanol, nicotine) on the Thioguanine drug delivery through Graphene oxide. The results of RDF patterns and the van der Waals energy calculations show that interaction between TG drugs and the Graphene oxide surface is stronger in water solvent compared to the other co-solvent. The obtained MD results illustrate that when nicotine and ethanol exist in the system, the drug takes longer time to bind with GO nanosheet and the system becomes unstable. It can be concluded that Graphene oxide can be a promising candidate in water media for delivery the TG molecule.

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

An implicit boundary integral method for computing electric potential of macromolecules in solvent

NASA Astrophysics Data System (ADS)

Zhong, Yimin; Ren, Kui; Tsai, Richard

2018-04-01

A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equation that arises in mathematical models for the electrostatics of molecules in solvent. The proposed method uses an implicit boundary integral formulation to derive a linear system defined on Cartesian nodes in a narrowband surrounding the closed surface that separates the molecule and the solvent. The needed implicit surface is constructed from the given atomic description of the molecules, by a sequence of standard level set algorithms. A fast multipole method is applied to accelerate the solution of the linear system. A few numerical studies involving some standard test cases are presented and compared to other existing results.

Excited state electronic polarization and reappraisal of the n ← π∗ emission of acetone in water

NASA Astrophysics Data System (ADS)

Orozco-González, Yoelvis; Coutinho, Kaline; Canuto, Sylvio

2010-10-01

Electronic polarization of the acetone molecule in the excited n → π∗ state is considered and its influence on the solvent shift in the emission spectrum is analyzed. Using an iterative procedure the electronic polarizations of both the ground and the excited states are included and compared with previous results obtained with Car-Parrinello dynamics. Analysis of the emission transition obtained using CIS(D)/aug-cc-pVDZ on statistically uncorrelated solute-solvent structures, composed of acetone and twelve explicit water molecules embedded in the electrostatic field of remaining 263 water molecules, corroborates that the solvent effect is mild, calculated here between 80 and 380 cm -1.

On the dynamics of water molecules at the protein solute interfaces.

PubMed

Bernini, A; Spiga, O; Ciutti, A; Chiellini, S; Menciassi, N; Venditti, V; Niccolai, N

2004-10-01

Proteins, with the large variety of chemical groups they present at their molecular surface, are a class of molecules which can be very informative on most of the possible solute-solvent interactions. Hen egg white lysozyme has been used as a probe to investigate the complex solvent dynamics occurring at the protein surface, by analysing the results obtained from Nuclear Magnetic Resonance, X-ray diffractometry and Molecular Dynamics simulations. A consistent overall picture for the dynamics of water molecules close to the protein is obtained, suggesting that a rapid exchange occurs, in a picosecond timescale, among all the possible hydration surface sites both in solution and the solid state, excluding the possibility that solvent molecules can form liquid-crystal-like supramolecular adducts, which have been proposed as a molecular basis of 'memory of water'.

Polyelectrolyte properties of single stranded DNA measured using SAXS and single molecule FRET: beyond the wormlike chain model

PubMed Central

Meisburger, Steve P.; Sutton, Julie L.; Chen, Huimin; Pabit, Suzette A.; Kirmizialtin, Serdal; Elber, Ron; Pollack, Lois

2013-01-01

Nucleic acids are highly charged polyelectrolytes that interact strongly with salt ions. Rigid, base-paired regions are successfully described with worm like chain models, but non base-paired single stranded regions have fundamentally different polymer properties because of their greater flexibility. Recently, attention has turned to single stranded nucleic acids due to the growing recognition of their biological importance, as well as the availability of sophisticated experimental techniques sensitive to the conformation of individual molecules. We investigate polyelectrolyte properties of poly(dT), an important and widely studied model system for flexible single stranded nucleic acids, in physiologically important mixed mono- and di-valent salt. We report measurements of the form factor and interparticle interactions using SAXS, end to end distances using smFRET, and number of excess ions using ASAXS. We present a coarse-grained model that accounts for flexibility, excluded volume, and electrostatic interactions in these systems. Predictions of the model are validated against experiment. We also discuss the state of all-atom, explicit solvent Molecular Dynamics simulations of poly(dT), the next step in understanding the complexities of ion interactions with these highly charged and flexible polymers. PMID:23606337

The importance of excluded solvent volume effects in computing hydration free energies.

PubMed

Yang, Pei-Kun; Lim, Carmay

2008-11-27

Continuum dielectric methods such as the Born equation have been widely used to compute the electrostatic component of the solvation free energy, DeltaG(solv)(elec), because they do not need to include solvent molecules explicitly and are thus far less costly compared to molecular simulations. All of these methods can be derived from Gauss Law of Maxwell's equations, which yields an analytical solution for the solvation free energy, DeltaG(Born), when the solute is spherical. However, in Maxwell's equations, the solvent is assumed to be a structureless continuum, whereas in reality, the near-solute solvent molecules are highly structured unlike far-solute bulk solvent. Since we have recently reformulated Gauss Law of Maxwell's equations to incorporate the near-solute solvent structure by considering excluded solvent volume effects, we have used it in this work to derive an analytical solution for the hydration free energy of an ion. In contrast to continuum solvent models, which assume that the normalized induced solvent electric dipole density P(n) is constant, P(n) mimics that observed from simulations. The analytical formula for the ionic hydration free energy shows that the Born radius, which has been used as an adjustable parameter to fit experimental hydration free energies, is no longer ill defined but is related to the radius and polarizability of the water molecule, the hydration number, and the first peak position of the solute-solvent radial distribution function. The resulting DeltaG(solv)(elec) values are shown to be close to the respective experimental numbers.

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.

Structure and dynamics of phosphate ion in aqueous solution: an ab initio QMCF MD study.

PubMed

Pribil, Andreas B; Hofer, Thomas S; Randolf, Bernhard R; Rode, Bernd M

2008-11-15

A simulation of phosphate in aqueous solution was carried out employing the new QMCF MD approach which offers the possibility to investigate composite systems with the accuracy of a QMMM method but without the time consuming creation of solute-solvent potential functions. The data of the simulations give a clear picture of the hydration shells of the phosphate anion. The first shell consists of 13 water molecules and each oxygen of the phosphate forms in average three hydrogens bonds to different solvent molecules. Several structural parameters such as radial distribution functions and coordination number distributions allow to fully characterize the embedding of the highly charged phosphate ion in the solvent water. The dynamics of the hydration structure of phosphate are described by mean residence times of the solvent molecules in the first hydration shell and the water exchange rate. 2008 Wiley Periodicals, Inc.

Super-hydrophobic fluorine containing aerogels

DOEpatents

Coronado, Paul R [Livermore, CA; Poco, John F [Livermore, CA; Hrubesh, Lawrence W [Pleasanton, CA

2007-05-01

An aerogel material with surfaces containing fluorine atoms which exhibits exceptional hydrophobicity, or the ability to repel liquid water. Hydrophobic aerogels are efficient absorbers of solvents from water. Solvents miscible with water are separated from it because the solvents are more volatile than water and they enter the porous aerogel as a vapor across the liquid water/solid interface. Solvents that are immisicble with water are separated from it by selectively wetting the aerogel. The hydrophobic property is achieved by formulating the aerogel using fluorine containing molecules either directly by addition in the sol-gel process, or by treating a standard dried aerogel using the vapor of fluorine containing molecules.

Theoretical investigation on the dimerization of the deprotonated aquo ion of Al(III) in water.

PubMed

Qian, Zhaosheng; Feng, Hui; Zhang, Zhenjiang; Yang, Wenjing; Jin, Jing; Miao, Qiang; He, Lina; Bi, Shuping

2009-01-21

Reaction pathways, solvent effects and energy barriers have been investigated for the dimerization of the deprotonated aquo ion of Al(III) in aqueous solution by performing supramolecule density functional theory calculations. Two competing reaction pathways were investigated, sharing a common first step and third step, i.e. the formation of the aggregate II of two aluminium monomers and the doubly bridged dimer. One pathway involves a nucleophilic attack to undercoordinated metal center in the first step and then the loss of a coordinated water molecule. Another pathway involves a water exchange reaction in the first step and then the formation of the hydroxo bridge. The calculated results indicate that both pathways I and II are possible in aqueous solution. The direct participation of the solvent water molecule facilitates the dimerization, but the extremely large solvent shifts of the energy barriers for each reaction are attributed mainly to the bulk effect. The computed activation energies for the water exchange reactions are in good agreement with the available experimental values, namely, the calculated value 37.5 kJ mol(-1) compared to the experimental value 36.4 (+/-5) kJ mol(-1). In agreement with experimental observations in aqueous solution, the calculated results favor the transformation of singly-bridged to doubly-bridged aluminium ion, which is helpful to understand the complicated hydrolytic polymerizaiton of Al(III).

Threshold-like complexation of conjugated polymers with small molecule acceptors in solution within the neighbor-effect model.

PubMed

Sosorev, Andrey Yu; Parashchuk, Olga D; Zapunidi, Sergey A; Kashtanov, Grigoriy S; Golovnin, Ilya V; Kommanaboyina, Srikanth; Perepichka, Igor F; Paraschuk, Dmitry Yu

2016-02-14

In some donor-acceptor blends based on conjugated polymers, a pronounced charge-transfer complex (CTC) forms in the electronic ground state. In contrast to small-molecule donor-acceptor blends, the CTC concentration in polymer:acceptor solution can increase with the acceptor content in a threshold-like way. This threshold-like behavior was earlier attributed to the neighbor effect (NE) in the polymer complexation, i.e., next CTCs are preferentially formed near the existing ones; however, the NE origin is unknown. To address the factors affecting the NE, we record the optical absorption data for blends of the most studied conjugated polymers, poly(2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene) (MEH-PPV) and poly(3-hexylthiophene) (P3HT), with electron acceptors of fluorene series, 1,8-dinitro-9,10-antraquinone (), and 7,7,8,8-tetracyanoquinodimethane () in different solvents, and then analyze the data within the NE model. We have found that the NE depends on the polymer and acceptor molecular skeletons and solvent, while it does not depend on the acceptor electron affinity and polymer concentration. We conclude that the NE operates within a single macromolecule and stems from planarization of the polymer chain involved in the CTC with an acceptor molecule; as a result, the probability of further complexation with the next acceptor molecules at the adjacent repeat units increases. The steric and electronic microscopic mechanisms of NE are discussed.

Solvent dielectric effect and side chain mutation on the structural stability of Burkholderia cepacia lipase active site: a quantum mechanical/molecular mechanics study.

PubMed

Tahan, A; Monajjemi, M

2011-12-01

Quantum mechanical and molecular dynamics methods were used to analyze the structure and stability of neutral and zwitterionic configurations of the extracted active site sequence from a Burkholderia cepacia lipase, histidyl-seryl-glutamin (His86-Ser87-Gln88) and its mutated form, histidyl-cysteyl-glutamin (His86-Cys87-Gln88) in vacuum and different solvents. The effects of solvent dielectric constant, explicit and implicit water molecules and side chain mutation on the structure and stability of this sequence in both neutral and zwitterionic forms are represented. The quantum mechanics computations represent that the relative stability of zwitterionic and neutral configurations depends on the solvent structure and its dielectric constant. Therefore, in vacuum and the considered non-polar solvents, the neutral form of the interested sequences is more stable than the zwitterionic form, while their zwitterionic form is more stable than the neutral form in the aqueous solution and the investigated polar solvents in most cases. However, on the potential energy surfaces calculated, there is a barrier to proton transfer from the positively charged ammonium group to the negatively charged carboxylat group or from the ammonium group to the adjacent carbonyl oxygen and or from side chain oxygen and sulfur to negatively charged carboxylat group. Molecular dynamics simulations (MD) were also performed by using periodic boundary conditions for the zwitterionic configuration of the hydrated molecules in a box of water molecules. The obtained results demonstrated that the presence of explicit water molecules provides the more compact structures of the studied molecules. These simulations also indicated that side chain mutation and replacement of sulfur with oxygen leads to reduction of molecular flexibility and packing.

Membraneless organelles can melt nucleic acid duplexes and act as biomolecular filters

NASA Astrophysics Data System (ADS)

Nott, Timothy J.; Craggs, Timothy D.; Baldwin, Andrew J.

2016-06-01

Membraneless organelles are cellular compartments made from drops of liquid protein inside a cell. These compartments assemble via the phase separation of disordered regions of proteins in response to changes in the cellular environment and the cell cycle. Here we demonstrate that the solvent environment within the interior of these cellular bodies behaves more like an organic solvent than like water. One of the most-stable biological structures known, the DNA double helix, can be melted once inside the liquid droplet, and simultaneously structures formed from regulatory single-stranded nucleic acids are stabilized. Moreover, proteins are shown to have a wide range of absorption or exclusion from these bodies, and can act as importers for otherwise-excluded nucleic acids, which suggests the existence of a protein-mediated trafficking system. A common strategy in organic chemistry is to utilize different solvents to influence the behaviour of molecules and reactions. These results reveal that cells have also evolved this capability by exploiting the interiors of membraneless organelles.

Molecular near-field antenna effect in resonance hyper-Raman scattering: Intermolecular vibronic intensity borrowing of solvent from solute through dipole-dipole and dipole-quadrupole interactions

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

Shimada, Rintaro; Hamaguchi, Hiro-o, E-mail: hhama@nctu.edu.tw

2014-05-28

We quantitatively interpret the recently discovered intriguing phenomenon related to resonance Hyper-Raman (HR) scattering. In resonance HR spectra of all-trans-β-carotene (β-carotene) in solution, vibrations of proximate solvent molecules are observed concomitantly with the solute β-carotene HR bands. It has been shown that these solvent bands are subject to marked intensity enhancements by more than 5 orders of magnitude under the presence of β-carotene. We have called this phenomenon the molecular-near field effect. Resonance HR spectra of β-carotene in benzene, deuterated benzene, cyclohexane, and deuterated cyclohexane have been measured precisely for a quantitative analysis of this effect. The assignments of themore » observed peaks are made by referring to the infrared, Raman, and HR spectra of neat solvents. It has been revealed that infrared active and some Raman active vibrations are active in the HR molecular near-field effect. The observed spectra in the form of difference spectra (between benzene/deuterated benzene and cyclohexane/deuterated cyclohexane) are quantitatively analyzed on the basis of the extended vibronic theory of resonance HR scattering. The theory incorporates the coupling of excited electronic states of β-carotene with the vibrations of a proximate solvent molecule through solute–solvent dipole–dipole and dipole–quadrupole interactions. It is shown that the infrared active modes arise from the dipole–dipole interaction, whereas Raman active modes from the dipole–quadrupole interaction. It is also shown that vibrations that give strongly polarized Raman bands are weak in the HR molecular near-field effect. The observed solvent HR spectra are simulated with the help of quantum chemical calculations for various orientations and distances of a solvent molecule with respect to the solute. The observed spectra are best simulated with random orientations of the solvent molecule at an intermolecular distance of 10 Å.« less

Communication: Cosolvency and cononsolvency explained in terms of a Flory-Huggins type theory

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

Dudowicz, Jacek, E-mail: dudowicz@jfi.uchicago.edu; Freed, Karl F.; Douglas, Jack F.

2015-10-07

Standard Flory-Huggins (FH) theory is utilized to describe the enigmatic cosolvency and cononsolvency phenomena for systems of polymers dissolved in mixed solvents. In particular, phase boundaries (specifically upper critical solution temperature spinodals) are calculated for solutions of homopolymers B in pure solvents and in binary mixtures of small molecule liquids A and C. The miscibility (or immiscibility) patterns for the ternary systems are classified in terms of the FH binary interaction parameters (χ{sub αβ}) and the ratio r = ϕ{sub A}/ϕ{sub C} of the concentrations ϕ{sub A} and ϕ{sub C} of the two solvents. The trends in miscibility are comparedmore » to those observed for blends of random copolymers (A{sub x}C{sub 1−x}) with homopolymers (B) and to those deduced for A/B/C solutions of polymers B in liquid mixtures of small molecules A and C that associate into polymeric clusters (A{sub p}C{sub q}){sub i}, (i = 1, 2, …, ∞). Although the classic FH theory is able to explain cosolvency and cononsolvency phenomena, the theory does not include a consideration of the mutual association of the solvent molecules and the competitive association between the solvent molecules and the polymer. These interactions can be incorporated in refinements of the FH theory, and the present paper provides a foundation for such extensions for modeling the rich thermodynamics of polymers in mixed solvents.« less

What is the minimum number of water molecules required to dissolve a potassium chloride molecule?

PubMed

Sen, Anik; Ganguly, Bishwajit

2010-12-01

This work answers an unsolved question that consists of determining the least number of water molecules necessary to separate a potassium chloride molecule. The answer based on accurate quantum chemical calculations suggests that tetramers are the smallest clusters necessary to dissociate KCl molecules. The study was made with Møller-Plesset second-order perturbation theory modified with the cluster theory having single, double, and perturbative triple excitations. With this extensive study, the dissociation of KCl molecule in different water clusters was evaluated. The calculated results show that four water molecules stabilize a solvent separated K(+)/Cl(-) ion-pair in prismatic structure and with six water molecules further dissociation was observed. Attenuated total reflection infrared spectroscopy of KCl dissolved in water establishes that clusters are made of closely bound ions with a mean of five water molecules per ion-pair [K(+)(H(2)O)(5)Cl(-)]. (Max and Chapados, Appl Spectrosc 1999, 53, 1601; Max and Chapados, J Chem Phys 2001, 115, 2664.) The calculated results tend to support that five water molecules leads toward the formation of contact ion-pair. The structures, energies, and infrared spectra of KCl molecules in different water clusters are also discussed. © 2010 Wiley Periodicals, Inc.

4,4'-([4,4'-Bipyridine]-1,1'-diium-1,1'-diyl)dibenzoate dihydrate

DOE PAGES

Rodriguez, Mark A.; Sava Gallis, Dorina F.; Chavez, James S.; ...

2016-06-01

We report here the synthesis of a neutral viologen derivative, C 24H 16N 2O 4·2H 2O. The non-solvent portion of the structure (Z-Lig) is a zwitterion, consisting of two positively charged pyridinium cations and two negatively charged carboxylate anions. The carboxylate group is almost coplanar [dihedral angle = 2.04 (11)°] with the benzene ring, whereas the dihedral angle between pyridine and benzene rings is 46.28 (5)°. TheZ-Lig molecule is positioned on a center of inversion (Fig. 1). The presence of the twofold axis perpendicular to thec-glide plane in space groupC2/c generates a screw-axis parallel to thebaxis that is shifted from themore » origin by 1/4 in theaandcdirections. This screw-axis replicates the molecule (and solvent water molecules) through space. TheZ-Lig molecule links to adjacent moleculesviaO—H...O hydrogen bonds involving solvent water molecules as well as intermolecular C—H...O interactions. There are also π–π interactions between benzene rings on adjacent molecules.« less

Structure and Dynamics of Solvent Landscapes in Charge-Transfer Reactions

NASA Astrophysics Data System (ADS)

Leite, Vitor B. Pereira

The dynamics of solvent polarization plays a major role in the control of charge transfer reactions. The success of Marcus theory describing the solvent influence via a single collective quadratic polarization coordinate has been remarkable. Onuchic and Wolynes have recently proposed (J. Chem Phys 98 (3) 2218, 1993) a simple model demonstrating how a many-dimensional-complex model composed by several dipole moments (representing solvent molecules or polar groups in proteins) can be reduced under the appropriate limits into the Marcus Model. This work presents a dynamical study of the same model, which is characterized by two parameters, an average dipole-dipole interaction as a term associated with the potential energy landscape roughness. It is shown why the effective potential, obtained using a thermodynamic approach, is appropriate for the dynamics of the system. At high temperatures, the system exhibits effective diffusive one-dimensional dynamics, where the Born-Marcus limit is recovered. At low temperatures, a glassy phase appears with a slow non-self-averaging dynamics. At intermediate temperatures, the concept of equivalent diffusion paths and polarization dependence effects are discussed. This approach is extended to treat more realistic solvent models. Real solvents are discussed in terms of simple parameters described above, and an analysis of how different regimes affect the rate of charge transfer is presented. Finally, these ideas are correlated to analogous problems in other areas.

Elucidating the Key Role of a Lewis Base Solvent in the Formation of Perovskite Films Fabricated from the Lewis Adduct Approach.

PubMed

Cao, Xiaobing; Zhi, Lili; Li, Yahui; Fang, Fei; Cui, Xian; Yao, Youwei; Ci, Lijie; Ding, Kongxian; Wei, Jinquan

2017-09-27

High-quality perovskite films can be fabricated from Lewis acid-base adducts through molecule exchange. Substantial work is needed to fully understand the formation mechanism of the perovskite films, which helps to further improve their quality. Here, we study the formation of CH 3 NH 3 PbI 3 perovskite films by introducing some dimethylacetamide into the PbI 2 /N,N-dimethylformamide solution. We reveal that there are three key processes during the formation of perovskite films through the Lewis acid-base adduct approach: molecule intercalation of solvent into the PbI 2 lattice, molecule exchange between the solvent and CH 3 NH 3 I, and dissolution-recrystallization of the perovskite grains during annealing. The Lewis base solvents play multiple functions in the above processes. The properties of the solvent, including Lewis basicity and boiling point, play key roles in forming smooth perovskite films with large grains. We also provide some rules for choosing Lewis base additives to prepare high-quality perovskite films through the Lewis adduct approach.

Organic-inorganic nano-composite films for photonic applications made by multi-beam multi-target pulsed laser deposition with remote control of the plume directions

NASA Astrophysics Data System (ADS)

Darwish, Abdalla M.; Moore, Shaelynn; Mohammed, Aziz; Alexander, Deonte'; Bastian, Tyler; Dorlus, Wydglif; Sarkisov, Sergey S.; Patel, Darayas N.; Mele, Paolo; Koplitz, Brent

2016-09-01

There has been an explosive interest in the technique of laser assisted deposition of polymer nano-composite films exploiting the matrix assisted pulsed laser evaporation (MAPLE) with regard to the polymer host as can be judged form recent publications.1-4 In MAPLE, a frozen solution of a polymer in a relatively volatile solvent is used as a laser target. The solvent and concentration are selected so that first, the polymer of interest can dissolve to form a dilute, particulate free solution, second, the majority of the laser energy is initially absorbed by the solvent molecules and not by the solute molecules, and third, there is no photochemical reaction between the solvent and the solute. The light-material interaction in MAPLE can be described as a photothermal process. The photon energy absorbed by the solvent is converted to thermal energy that causes the polymer to be heated but the solvent to vaporize. As the surface solvent molecules are evaporated into the gas phase, polymer molecules are exposed at the gas-target matrix interface. The polymer molecules attain sufficient kinetic energy through collective collisions with the evaporating solvent molecules, to be transferred into the gas phase. By careful optimization of the MAPLE deposition conditions (laser wavelength, repetition rate, solvent type, concentration, temperature, and background gas and gas pressure), this process can occur without any significant polymer decomposition. The MAPLE process proceeds layer-by-layer, depleting the target of solvent and polymer in the same concentration as the starting matrix. When a substrate is positioned directly in the path of the plume, a coating starts to form from the evaporated polymer molecules, while the volatile solvent molecules are evacuated by the pump from the deposition chamber. In case of fabrication of polymer nanocomposites, MAPLE targets are usually prepared as nano-colloids of the additives of interest in the initial polymer solutions. Mixing the components of different nature, organic polymers and inorganic dopants, in the same target at a certain proportion and exposing them to the same laser beam not necessarily brings good quality nano-composite films. The laser pulse energy and wavelength cannot be optimized for each component individually. Also, the mixing proportion in the composite film is dictated by the initial proportion of the target and thus cannot be changed in the process. These limitations were removed in the recently proposed method of multi-beam and multi-target deposition (in its doublebeam/ dual-target variation) using a MAPLE polymer target and one inorganic target, each being concurrently exposed to laser beams of different wavelengths.5-14 Using the method, nano-composite films of polymer poly(methyl methacrylate) known as PMMA doped with a rare earth (RE) inorganic upconversion phosphor compounds were prepared. Also, a nano-composite film of thermoelectric film of inorganic aluminum-doped ZnO known as AZO was impregnated with PMMA nano-fillers with the purpose of improving electrical conductivity and thermoelectric performance.10, 14 The polymer target was a frozen (to a temperature of liquid nitrogen) PMMA solution in chlorobenzene exposed to a 1064- nm laser beam from a Q-switched Nd:YAG pulsed laser. The inorganic targets were the pellets made of the compressed micro-powders of highly efficient RE-doped NaYF4 or the sintered powder of AZO concurrently ablated with the

Unveiling the mechanism of the promising two-dimensional photoswitch - Hemithioindigo

NASA Astrophysics Data System (ADS)

Li, Donglin; Yang, Yonggang; Li, Chaozheng; Liu, Yufang

2018-07-01

The control of internal molecular motions by outside stimuli is a decisive task in the construction of functional molecules and molecular machines. Light-induced intramolecular rotations of photoswitches have attracted increasing research interests because of the high stability and high reversibility of photoswitches. Recently, Henry et al. reported an unprecedented two-dimensional controlled photoswitch, the hemithioindigo (HTI) derivative Z1, whose single bond rotation in dimethyl sulphoxide (DMSO) solvent and double bond rotation in cyclohexane solvent can be induced by visible light (J. Am. Chem. Soc. 2016, 138, 12,219). Here we investigate the intramolecular rotations of the HTI and Z1 in different polar solvents by time-dependent density functional theory (TDDFT) and Nonadiabatic dynamic simulations. Due to the steric hindrance between methyl and thioindigo fragment, the rotations of Z1 in the excited state are obstructed. Interestingly, the HTI exhibits two distinct rotation paths in DMSO and cyclohexane solvents at about 50 fs. The intermolecular hydrogen bonds between HTI and DMSO play an important role in the rotation of HTI in DMSO solvent. Therefore, the HTI is a more promising two-dimensional photoswitch compared with the Z1. Our finding is thus of fundamental importance to understand the mechanisms of this class of photoswitches and design complex molecular behavior.

Synchronous fluorescence spectroscopic study of solvatochromic curcumin dye

NASA Astrophysics Data System (ADS)

Patra, Digambara; Barakat, Christelle

2011-09-01

Curcumin, the main yellow bioactive component of turmeric, has recently acquired attention by chemists due its wide range of potential biological applications as an antioxidant, an anti-inflammatory, and an anti-carcinogenic agent. This molecule fluoresces weakly and poorly soluble in water. In this detailed study of curcumin in thirteen different solvents, both the absorption and fluorescence spectra of curcumin was found to be broad, however, a narrower and simple synchronous fluorescence spectrum of curcumin was obtained at Δ λ = 10-20 nm. Lippert-Mataga plot of curcumin in different solvents illustrated two sets of linearity which is consistent with the plot of Stokes' shift vs. the ET30. When Stokes's shift in wavenumber scale was replaced by synchronous fluorescence maximum in nanometer scale, the solvent polarity dependency measured by λSFSmax vs. Lippert-Mataga plot or ET30 values offered similar trends as measured via Stokes' shift for protic and aprotic solvents for curcumin. Better linear correlation of λSFSmax vs. π* scale of solvent polarity was found compared to λabsmax or λemmax or Stokes' shift measurements. In Stokes' shift measurement both absorption/excitation as well as emission (fluorescence) spectra are required to compute the Stokes' shift in wavenumber scale, but measurement could be done in a very fast and simple way by taking a single scan of SFS avoiding calculation and obtain information about polarity of the solvent. Curcumin decay properties in all the solvents could be fitted well to a double-exponential decay function.

Quantum-Chemical Simulation of the Solvent Effect on Spontaneous Emission of Singlet Oxygen

NASA Astrophysics Data System (ADS)

Ivashin, N. V.; Shchupak, E. E.

2018-01-01

A molecular simulation of the solvent effect on radiative rate constant k r of singlet oxygen is carried out. This study included a search for the most probable conformations of the complexes of molecules of singlet oxygen and ten solvents and calculation of dipole moments M of transitions a 1Δ g -b1Σ g + ( M a-b ) and a 1Δ g - X 3Σ g - ( M a-X ) of the oxygen molecule for them. Averaging of M a-b by conformations, taking into account the probability of their formation for complexes without atoms with a large atomic number (Cl, S), yields values that, as a rule, correlate well with the behavior of k r in the experiment. Taking into account the possibility of decreasing the distance (compared to equilibrium) between molecules in a collision complex at room temperature made it possible to achieve satisfactory agreement of the calculated and experimental data also for complexes with CCl4, C2Cl4, and CS2. The obtained data indicate that a number of factors affect k r . The correlation of k r with molecular polarizability in a number of cases is due, on the one hand, to its effect on the strength of dispersion interactions in the complex and, on the other hand, to the fact that it to some extent reflects the position of the upper filled orbitals of the solvent molecule. Both factors affect the degree of mixing of the π orbitals of the singlet oxygen molecule with the orbitals of the solvent molecule, which, as was found earlier, facilitates the activation of the a 1Δ g -b1Σ g + transition and the borrowing of its intensity by the a 1Δ g - X 3Σ g - transition.

Communication: Strong laser alignment of solvent-solute aggregates in the gas-phase

NASA Astrophysics Data System (ADS)

Trippel, Sebastian; Wiese, Joss; Mullins, Terry; Küpper, Jochen

2018-03-01

Strong quasi-adiabatic laser alignment of the indole-water-dimer clusters, an amino-acid chromophore bound to a single water molecule through a hydrogen bond, was experimentally realized. The alignment was visualized through ion and electron imaging following strong-field ionization. Molecular-frame photoelectron angular distributions showed a clear suppression of the electron yield in the plane of the ionizing laser's polarization, which was analyzed as strong alignment of the molecular cluster with ⟨cos2 θ2D⟩ ≥ 0.9.

Unravelling the mechanisms of vibrational relaxation in solution.

PubMed

Grubb, Michael P; Coulter, Philip M; Marroux, Hugo J B; Orr-Ewing, Andrew J; Ashfold, Michael N R

2017-04-01

We present a systematic study of the mode-specific vibrational relaxation of NO 2 in six weakly-interacting solvents (perfluorohexane, perfluoromethylcyclohexane, perfluorodecalin, carbon tetrachloride, chloroform, and d-chloroform), chosen to elucidate the dominant energy transfer mechanisms in the solution phase. Broadband transient vibrational absorption spectroscopy has allowed us to extract quantum state-resolved relaxation dynamics of the two distinct NO 2 fragments produced from the 340 nm photolysis of N 2 O 4 → NO 2 (X) + NO 2 (A) and their separate paths to thermal equilibrium. Distinct relaxation pathways are observed for the NO 2 bending and stretching modes, even at energies as high as 7000 cm -1 above the potential minimum. Vibrational energy transfer is governed by different interaction mechanisms in the various solvent environments, and proceeds with timescales ranging from 20-1100 ps. NO 2 relaxation rates in the perfluorocarbon solvents are identical despite differences in acceptor mode state densities, infrared absorption cross sections, and local solvent structure. Vibrational energy is shown to be transferred to non-vibrational solvent degrees of freedom (V-T) through impulsive collisions with the perfluorocarbon molecules. Conversely, NO 2 relaxation in chlorinated solvents is reliant on vibrational resonances (V-V) while V-T energy transfer is inefficient and thermal excitation of the surrounding solvent molecules inhibits faster vibrational relaxation through direct complexation. Intramolecular vibrational redistribution allows the symmetric stretch of NO 2 to act as a gateway for antisymmetric stretch energy to exit the molecule. This study establishes an unprecedented level of detail for the cooling dynamics of a solvated small molecule, and provides a benchmark system for future theoretical studies of vibrational relaxation processes in solution.

Effect of dynamic surface polarization on the oxidative stability of solvents in nonaqueous Li-O 2 batteries

NASA Astrophysics Data System (ADS)

Khetan, Abhishek; Pitsch, Heinz; Viswanathan, Venkatasubramanian

2017-09-01

Polarization-induced renormalization of the frontier energy levels of interacting molecules and surfaces can cause significant shifts in the excitation and transport behavior of electrons. This phenomenon is crucial in determining the oxidative stability of nonaqueous electrolytes in high-energy density electrochemical systems such as the Li-O2 battery. On the basis of partially self-consistent first-principles Sc G W0 calculations, we systematically study how the electronic energy levels of four commonly used solvent molecules, namely, dimethylsulfoxide (DMSO), dimethoxyethane (DME), tetrahydrofuran (THF), and acetonitrile (ACN), renormalize when physisorbed on the different stable surfaces of Li2O2 , the main discharge product. Using band level alignment arguments, we propose that the difference between the solvent's highest occupied molecular orbital (HOMO) level and the surface's valence-band maximum (VBM) is a refined metric of oxidative stability. This metric and a previously used descriptor, solvent's gas phase HOMO level, agree quite well for physisorbed cases on pristine surfaces where ACN is oxidatively most stable followed by DME, THF, and DMSO. However, this effect is intrinsically linked to the surface chemistry of the solvent's interaction with the surface states and defects, and depends strongly on their nature. We conclusively show that the propensity of solvent molecules to oxidize will be significantly higher on Li2O2 surfaces with defects as compared to pristine surfaces. This suggests that the oxidative stability of a solvent is dynamic and is a strong function of surface electronic properties. Thus, while gas phase HOMO levels could be used for preliminary solvent candidate screening, a more refined picture of solvent stability requires mapping out the solvent stability as a function of the state of the surface under operating conditions.

Syntheses, crystal structures, and water adsorption behaviors of jungle-gym-type porous coordination polymers containing nitro moieties

NASA Astrophysics Data System (ADS)

Uemura, Kazuhiro; Onishi, Fumiaki; Yamasaki, Yukari; Kita, Hidetoshi

2009-10-01

NO 2 containing dicarboxylate bridging ligands, nitroterephthalate (bdc-NO 2) and 2,5-dinitroterephthalate (bdc-(NO 2) 2), afford porous coordination polymers, {[Zn 2(bdc-NO 2) 2(dabco)]· solvents} n ( 2⊃ solvents) and {[Zn 2(bdc-(NO 2) 2) 2(dabco)]· solvents} n ( 3⊃ solvents). Both compounds form jungle-gym-type regularities, where a 2D square grid composed of dinuclear Zn 2 units and dicarboxylate ligands is bridged by dabco molecules to extend the 2D layers into a 3D structure. In 2⊃ solvents and 3⊃ solvents, a rectangle pore surrounded by eight Zn 2 corners contains two and four NO 2 moieties, respectively. Thermal gravimetry (TG) and X-ray powder diffraction (XRPD) measurements reveal that both compounds maintain the frameworks regularities without guest molecules and with solvents such as MeOH, EtOH, i-PrOH, and Me 2CO. Adsorption measurements reveal that dried 2 and 3 adsorb H 2O molecules to be {[Zn 2(bdc-NO 2) 2(dabco)]·4H 2O} n ( 2⊃4H 2O) and {[Zn 2(bdc-(NO 2) 2) 2(dabco)]·6H 2O} n ( 3⊃6H 2O), showing the pore hydrophilicity enhancement caused by NO 2 group introduction.

Effect of Viscosity and Polar Properties of Solvent on Dynamics of Photoinduced Charge Transfer in BTA-1 Cation — Derivative of Thioflavin T

NASA Astrophysics Data System (ADS)

Gogoleva, S. D.; Stsiapura, V. I.

2018-05-01

It was found that the spectral and fluorescent properties of BTA-1C cation in protic and aprotic solvents differ. It was shown that for solutions in long-chain alcohols viscosity is the main factor that determines the dynamics of intramolecular charge transfer in the excited state of the BTA-1C molecule. In the case of aprotic solvents a correlation was found between the rate constant of twisted intramolecular charge transfer (TICT) during rotation of fragments of the molecule in relation to each other in the excited state and the solvent relaxation rate: k TICT 1/τ S .

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.

Ultra-large supramolecular coordination cages composed of endohedral Archimedean and Platonic bodies

NASA Astrophysics Data System (ADS)

Byrne, Kevin; Zubair, Muhammad; Zhu, Nianyong; Zhou, Xiao-Ping; Fox, Daniel S.; Zhang, Hongzhou; Twamley, Brendan; Lennox, Matthew J.; Düren, Tina; Schmitt, Wolfgang

2017-05-01

Pioneered by Lehn, Cram, Peterson and Breslow, supramolecular chemistry concepts have evolved providing fundamental knowledge of the relationships between the structures and reactivities of organized molecules. A particular fascinating class of metallo-supramolecular molecules are hollow coordination cages that provide cavities of molecular dimensions promoting applications in diverse areas including catalysis, enzyme mimetics and material science. Here we report the synthesis of coordination cages with exceptional cross-sectional diameters that are composed of multiple sub-cages providing numerous distinctive binding sites through labile coordination solvent molecules. The building principles, involving Archimedean and Platonic bodies, renders these supramolecular keplerates as a class of cages whose composition and topological aspects compare to characteristics of edge-transitive {Cu2} MOFs with A3X4 stoichiometry. The nature of the cavities in these double-shell metal-organic polyhedra and their inner/outer binding sites provide perspectives for post-synthetic functionalizations, separations and catalysis. Transmission electron microscopy studies demonstrate that single molecules are experimentally accessible.

Ultra-large supramolecular coordination cages composed of endohedral Archimedean and Platonic bodies

PubMed Central

Byrne, Kevin; Zubair, Muhammad; Zhu, Nianyong; Zhou, Xiao-Ping; Fox, Daniel S.; Zhang, Hongzhou; Twamley, Brendan; Lennox, Matthew J.; Düren, Tina; Schmitt, Wolfgang

2017-01-01

Pioneered by Lehn, Cram, Peterson and Breslow, supramolecular chemistry concepts have evolved providing fundamental knowledge of the relationships between the structures and reactivities of organized molecules. A particular fascinating class of metallo-supramolecular molecules are hollow coordination cages that provide cavities of molecular dimensions promoting applications in diverse areas including catalysis, enzyme mimetics and material science. Here we report the synthesis of coordination cages with exceptional cross-sectional diameters that are composed of multiple sub-cages providing numerous distinctive binding sites through labile coordination solvent molecules. The building principles, involving Archimedean and Platonic bodies, renders these supramolecular keplerates as a class of cages whose composition and topological aspects compare to characteristics of edge-transitive {Cu2} MOFs with A3X4 stoichiometry. The nature of the cavities in these double-shell metal-organic polyhedra and their inner/outer binding sites provide perspectives for post-synthetic functionalizations, separations and catalysis. Transmission electron microscopy studies demonstrate that single molecules are experimentally accessible. PMID:28485392

Formation of vesicles through solvent assisted self-assembly of hydrophobic pentapeptides: encapsulation and pH responsive release of dyes by the vesicles.

PubMed

Kar, Sudeshna; Drew, Michael G B; Pramanik, Animesh

2011-09-01

In the biomimetic design two hydrophobic pentapetides Boc-Ile-Aib-Leu-Phe-Ala-OMe (I) and Boc-Gly-Ile-Aib-Leu-Phe-OMe (II) (Aib: α-aminoisobutyric acid) containing one Aib each are found to undergo solvent assisted self-assembly in methanol/water to form vesicular structures, which can be disrupted by simple addition of acid. The nanovesicles are found to encapsulate dye molecules that can be released by the addition of acid as confirmed by fluorescence microscopy and UV studies. The influence of solvent polarity on the morphology of the materials generated from the peptides has been examined systematically, and shows that fibrillar structures are formed in less polar chloroform/petroleum ether mixture and vesicular structures are formed in more polar methanol/water. Single crystal X-ray diffraction studies reveal that while β-sheet mediated self-assembly leads to the formation of fibrillar structures, the solvated β-sheet structure leads to the formation of vesicular structures. The results demonstrate that even hydrophobic peptides can generate vesicular structures from polar solvent which may be employed in model studies of complex biological phenomena.

Extended solvent-contact model approach to blind SAMPL5 prediction challenge for the distribution coefficients of drug-like molecules

NASA Astrophysics Data System (ADS)

Chung, Kee-Choo; Park, Hwangseo

2016-11-01

The performance of the extended solvent-contact model has been addressed in the SAMPL5 blind prediction challenge for distribution coefficient (LogD) of drug-like molecules with respect to the cyclohexane/water partitioning system. All the atomic parameters defined for 41 atom types in the solvation free energy function were optimized by operating a standard genetic algorithm with respect to water and cyclohexane solvents. In the parameterizations for cyclohexane, the experimental solvation free energy (Δ G sol ) data of 15 molecules for 1-octanol were combined with those of 77 molecules for cyclohexane to construct a training set because Δ G sol values of the former were unavailable for cyclohexane in publicly accessible databases. Using this hybrid training set, we established the LogD prediction model with the correlation coefficient ( R), average error (AE), and root mean square error (RMSE) of 0.55, 1.53, and 3.03, respectively, for the comparison of experimental and computational results for 53 SAMPL5 molecules. The modest accuracy in LogD prediction could be attributed to the incomplete optimization of atomic solvation parameters for cyclohexane. With respect to 31 SAMPL5 molecules containing the atom types for which experimental reference data for Δ G sol were available for both water and cyclohexane, the accuracy in LogD prediction increased remarkably with the R, AE, and RMSE values of 0.82, 0.89, and 1.60, respectively. This significant enhancement in performance stemmed from the better optimization of atomic solvation parameters by limiting the element of training set to the molecules with experimental Δ G sol data for cyclohexane. Due to the simplicity in model building and to low computational cost for parameterizations, the extended solvent-contact model is anticipated to serve as a valuable computational tool for LogD prediction upon the enrichment of experimental Δ G sol data for organic solvents.

Supercritical-Multiple-Solvent Extraction From Coal

NASA Technical Reports Server (NTRS)

Corcoran, W.; Fong, W.; Pichaichanarong, P.; Chan, P.; Lawson, D.

1983-01-01

Large and small molecules dissolve different constituents. Experimental apparatus used to test supercritical extraction of hydrogen rich compounds from coal in various organic solvents. In decreasing order of importance, relevant process parameters were found to be temperature, solvent type, pressure, and residence time.

Concentration-dependent multiple chirality transition in halogen-bond-driven 2D self-assembly process

NASA Astrophysics Data System (ADS)

Miao, Xinrui; Li, Jinxing; Zha, Bao; Miao, Kai; Dong, Meiqiu; Wu, Juntian; Deng, Wenli

2018-03-01

The concentration-dependent self-assembly of iodine substituted thienophenanthrene derivative (5,10-DITD) is investigated at the 1-octanic acid/graphite interface using scanning tunneling microscopy. Three kinds of chiral arrangement and transition of 2D molecular assembly mainly driven by halogen bonding is clearly revealed. At high concentration the molecules self-assembled into a honeycomb-like chiral network. Except for the interchain van der Waals forces, this pattern is stabilized by intermolecular continuous Cdbnd O⋯I⋯S halogen bonds in each zigzag line. At moderate concentration, a chiral kite-like nanoarchitecture are observed, in which the Cdbnd O⋯I⋯S and I⋯Odbnd C halogen bonds, along with the molecule-solvent Cdbnd O⋯I⋯H halogen bonds are the dominated forces to determine the structural formation. At low concentration, the molecules form a chiral cyclic network resulting from the solvent coadsorption mainly by molecule-molecule Cdbnd O⋯I⋯S halogen bonds and molecule-solvent Cdbnd O⋯I⋯H halogen bonds. The density of molecular packing becomes lower with the decreasing of the solution concentration. The solution-concentration dependent self-assembly of thienophenanthrene derivative with iodine and ester chain moieties reveals that the type of intermolecular halogen bond and the number of the co-adsorbing 1-octanic acids by molecule-solvent Cdbnd O⋯I⋯H halogen bonds determine the formation and transformation of chirality. This research emphasizes the role of different types of halogen (I) bonds in the controllable supramolecular structures and provides an approach for the fabrication of chirality.

Solvent dependent frequency shift and Raman noncoincidence effect of S=O stretching mode of Dimethyl sulfoxide in liquid binary mixtures.

PubMed

Upadhyay, Ganesh; Devi, Th Gomti; Singh, Ranjan K; Singh, A; Alapati, P R

2013-05-15

The isotropic and anisotropic Raman peak frequencies of S=O stretching mode of Dimethyl sulfoxide (DMSO) have been discussed in different chemical and isotopic solvent molecules using different mechanisms. The shifting of peak frequency in further dilution of DMSO with solvent molecule is observed for all solvents. Transition dipole - transition dipole interaction and hydrogen bonding may play a major role in shifting of peak frequencies. The non-coincidence effect (NCE) of DMSO was determined for all the solvents and compared with four theoretical models such as McHale's model, Mirone's modification of McHale's model, Logan's model and Onsager-Fröhlich dielectric continuum model respectively. Most of the theoretical models are largely consistent with our experimental data. Copyright © 2013. Published by Elsevier B.V.

Vibrational relaxation in liquid chloroform following ultrafast excitation of the CH stretch fundamental

NASA Astrophysics Data System (ADS)

Sibert, Edwin L.; Rey, Rossend

2002-01-01

Vibrational energy flow in liquid chloroform that follows the ultrafast excitation of the CH stretch fundamental is modeled using semiclassical methods. Relaxation rates are calculated using Landau-Teller theory and a time-dependent method both of which consider a quantum mechanical CHCl3 solute molecule coupled to a classical bath of CHCl3 solvent molecules. Probability flow is examined for several potentials to determine the sensitivity of calculated relaxation rates to the parameters that describe the model potentials. Three stages of relaxation are obtained. Probability is calculated to decay initially to a single acceptor state, a combination state of the solute molecule with two quanta of excitation in the CH bend and one in the CCl stretch, in 13-23 ps depending on the potential model employed. This is followed by rapid and complex intramolecular energy flow into the remaining vibrational degrees of freedom. During this second stage the lowest frequency Cl-C-Cl bend is found to serve as a conduit for energy loss to the solvent. The bottleneck for relaxation back to the ground state is predicted to be the slow 100-200 ps relaxation of the CH bend and CCl stretch fundamentals. Several aspects of the incoherent anti-Stokes scattering that follows strong infrared excitation of the CH fundamental as observed by Graener, Zürl, and Hoffman [J. Phys. Chem. B 101, 1745 (1997)] are elucidated in the present study.

Ultrafast photoinduced dynamics of the 3,6-diaminoacridinium derivative ATTO 465 in solution.

PubMed

Arden-Jacob, Jutta; Drexhage, Karl-Heinz; Druzhinin, Sergey I; Ekimova, Maria; Flender, Oliver; Lenzer, Thomas; Oum, Kawon; Scholz, Mirko

2013-02-14

The excited state dynamics of the dye ATTO 465, a well-known fluorescence marker for biological applications, have been characterized in various solvents including THF, ethanol, methanol, water and the highly polar protic ionic liquid 2-hydroxyethylammonium formate (2-OH-EAF) by combining results from time-correlated single-photon counting (TCSPC) and ultrafast pump-supercontinuum probe (PSCP) spectroscopy as well as steady-state absorption and fluorescence. In water, 2-OH-EAF and two fluorinated alcohols, there is a pronounced blue-shift and broadening of the S(0) → S(1) absorption band and also a larger Stokes shift than in the other solvents, indicating a particular influence of hydrogen-bonding interactions. S(1) lifetimes from TCSPC at 25 °C range from 3.3 ns to 5.6 ns. An unusual increase in the S(1) lifetime with temperature is observed for ethanol and methanol, however water behaves in the opposite way. The behavior can be tentatively explained by a solvent- and temperature-dependent "proximity effect", where coupling of the close-lying S(1) and S(2) states influences the intramolecular relaxation rate of the dye. In addition, temperature-dependent complex equilibria of ATTO 465 with solvent molecules may influence the measured lifetimes. Several excited-state absorption (ESA) transitions are identified in the PSCP spectra, which are in good agreement with the position of the UV bands in the steady-state absorption spectra. Small shifts of the stimulated emission and ESA bands are consistent with solvation dynamics in the excited electronic state. An additional ~16 ps component in water, visible over the entire spectral range, is tentatively ascribed to a fast IC channel which is accessed by a fraction of ATTO 465 molecules.

Effects of Shapes of Solute Molecules on Diffusion: A Study of Dependences on Solute Size, Solvent, and Temperature.

PubMed

Chan, T C; Li, H T; Li, K Y

2015-12-24

Diffusivities of basically linear, planar, and spherical solutes at infinite dilution in various solvents are studied to unravel the effects of solute shapes on diffusion. On the basis of the relationship between the reciprocal of diffusivity and the molecular volume of solute molecules with similar shape in a given solvent at constant temperature, the diffusivities of solutes of equal molecular volume but different shapes are evaluated and the effects due to different shapes of two equal-sized solute molecules on diffusion are determined. It is found that the effects are dependent on the size of the solute pairs studied. Evidence of the dependence of the solute-shape effects on solvent properties is also demonstrated and discussed. Here, some new diffusion data of aromatic compounds in methanol at different temperatures are reported. The result for methanol in this study indicates that the effects of solute shape on diffusivity are only weakly dependent on temperature.

Molecular dynamics of acetamide based ionic deep eutectic solvents

NASA Astrophysics Data System (ADS)

Srinivasan, H.; Dubey, P. S.; Sharma, V. K.; Biswas, R.; Mitra, S.; Mukhopadhyay, R.

2018-04-01

Deep eutectic solvents are multi-component mixtures that have freezing point lower than their individual components. Mixture of acetamide+ lithium nitrate in the molar ratio 78:22 and acetamide+ lithium perchlorate in the molar ratio 81:19 are found to form deep eutectic solvents with melting point lower than the room temperature. It is known that the depression in freezing point is due to the hydrogen bond breaking ability of anions in the system. Quasielastic neutron scattering experiments on these systems were carried out to study the dynamics of acetamide molecules which may be influenced by this hydrogen bond breaking phenomena. The motion of acetamide molecules is modeled using jump diffusion mechanism to demonstrate continuous breaking and reforming hydrogen bonds in the solvent. Using the jump diffusion model, it is inferred that the jump lengths of acetamide molecules are better approximated by a Gaussian distribution. The shorter residence time of acetamide in presence of perchlorate ions suggest that the perchlorate ions have a higher hydrogen bond breaking ability compared to nitrate ions.

First Evidence of Vibrationally Driven Bimolecular Reactions in Solution: Reactions of Br Atoms with Dimethylsulfoxide and Methanol.

PubMed

Shin, Jae Yoon; Shaloski, Michael A; Crim, F Fleming; Case, Amanda S

2017-03-23

We present evidence for vibrational enhancement of the rate of bimolecular reactions of Br atoms with dimethylsulfoxide (DMSO) and methanol (CH 3 OH) in the condensed phase. The abstraction of a hydrogen atom from either of these solvents by a Br atom is highly endoergic: 3269 cm -1 for DMSO and 1416 or 4414 cm -1 for CH 3 OH, depending on the hydrogen atom abstracted. Thus, there is no thermal abstraction reaction at room temperature. Broadband electronic transient absorption shows that following photolysis of bromine precursors Br atoms form van der Waals complexes with the solvent molecules in about 5 ps and this Br • -solvent complex undergoes recombination. To explore the influence of vibrational energy on the abstraction reactions, we introduce a near-infrared (NIR) pump pulse following the photolysis pulse to excite the first overtone of the C-H (or O-H) stretch of the solvent molecules. Using single-wavelength detection, we observe a loss of the Br • -solvent complex that requires the presence of both photolysis and NIR pump pulses. Moreover, the magnitude of this loss depends on the NIR wavelength. Although this loss of reactive Br supports the notion of vibrationally driven chemistry, it is not concrete evidence of the hydrogen-abstraction reaction. To verify that the loss of reactive Br results from the vibrationally driven bimolecular reaction, we examine the pH dependence of the solution (as a measure of the formation of the HBr product) following long-time irradiation of the sample with both photolysis and NIR pump beams. We observe that when the NIR beam is on-resonance, the hydronium ion concentration increases fourfold as compared to that when it is off-resonance, suggesting the formation of HBr via a vibrationally driven hydrogen-abstraction reaction in solution.

"Non-equilibrium" block copolymer micelles with glassy cores: a predictive approach based on theory of equilibrium micelles.

PubMed

Nagarajan, Ramanathan

2015-07-01

Micelles generated in water from most amphiphilic block copolymers are widely recognized to be non-equilibrium structures. Typically, the micelles are prepared by a kinetic process, first allowing molecular scale dissolution of the block copolymer in a common solvent that likes both the blocks and then gradually replacing the common solvent by water to promote the hydrophobic blocks to aggregate and create the micelles. The non-equilibrium nature of the micelle originates from the fact that dynamic exchange between the block copolymer molecules in the micelle and the singly dispersed block copolymer molecules in water is suppressed, because of the glassy nature of the core forming polymer block and/or its very large hydrophobicity. Although most amphiphilic block copolymers generate such non-equilibrium micelles, no theoretical approach to a priori predict the micelle characteristics currently exists. In this work, we propose a predictive approach for non-equilibrium micelles with glassy cores by applying the equilibrium theory of micelles in two steps. In the first, we calculate the properties of micelles formed in the mixed solvent while true equilibrium prevails, until the micelle core becomes glassy. In the second step, we freeze the micelle aggregation number at this glassy state and calculate the corona dimension from the equilibrium theory of micelles. The condition when the micelle core becomes glassy is independently determined from a statistical thermodynamic treatment of diluent effect on polymer glass transition temperature. The predictions based on this "non-equilibrium" model compare reasonably well with experimental data for polystyrene-polyethylene oxide diblock copolymer, which is the most extensively studied system in the literature. In contrast, the application of the equilibrium model to describe such a system significantly overpredicts the micelle core and corona dimensions and the aggregation number. The non-equilibrium model suggests ways to obtain different micelle sizes for the same block copolymer, by the choices we can make of the common solvent and the mode of solvent substitution. Published by Elsevier Inc.

Persistence length of collagen molecules based on nonlocal viscoelastic model.

PubMed

Ghavanloo, Esmaeal

2017-12-01

Persistence length is one of the most interesting properties of a molecular chain, which is used to describe the stiffness of a molecule. The experimentally measured values of the persistence length of the collagen molecule are widely scattered from 14 to 180 nm. Therefore, an alternative approach is highly desirable to predict the persistence length of a molecule and also to explain the experimental results. In this paper, a nonlocal viscoelastic model is developed to obtain the persistence length of the collagen molecules in solvent. A new explicit formula is proposed for the persistence length of the molecule with the consideration of the small-scale effect, viscoelastic properties of the molecule, loading frequency, and viscosity of the solvent. The presented model indicates that there exists a range of molecule lengths in which the persistence length strongly depends on the frequency and spatial mode of applied loads, small-scale effect, and viscoelastic properties of the collagen.

Theoretical aspects of pressure and solute denaturation of proteins: A Kirkwood-buff-theory approach.

PubMed

Ben-Naim, Arieh

2012-12-21

A new approach to the problem of pressure-denaturation (PD) and solute-denaturation (SD) of proteins is presented. The problem is formulated in terms of Le Chatelier principle, and a solution is sought in terms of the Kirkwood-Buff theory of solutions. It is found that both problems have one factor in common; the excluded volumes of the folded and the unfolded forms with respect to the solvent molecules. It is shown that solvent-induced effects operating on hydrophilic groups along the protein are probably the main reason for PD. On the other hand, the SD depends on the preferential solvation of the folded and the unfolded forms with respect to solvent and co-solvent molecules.

Theoretical aspects of pressure and solute denaturation of proteins: A Kirkwood-buff-theory approach

NASA Astrophysics Data System (ADS)

Ben-Naim, Arieh

2012-12-01

A new approach to the problem of pressure-denaturation (PD) and solute-denaturation (SD) of proteins is presented. The problem is formulated in terms of Le Chatelier principle, and a solution is sought in terms of the Kirkwood-Buff theory of solutions. It is found that both problems have one factor in common; the excluded volumes of the folded and the unfolded forms with respect to the solvent molecules. It is shown that solvent-induced effects operating on hydrophilic groups along the protein are probably the main reason for PD. On the other hand, the SD depends on the preferential solvation of the folded and the unfolded forms with respect to solvent and co-solvent molecules.

Molecular insights into early stage aggregation of di-Fmoc-L-lysine in binary mixture of organic solvent and water

NASA Astrophysics Data System (ADS)

Huda, Md Masrul; Rai, Neeraj

Molecular gels are relatively new class of soft materials, which are formed by the supramolecular aggregation of low molecular weight gelators (LMWGs) in organic solvents and/or water. Hierarchical self-assembly of small gelator molecules lead to three-dimensional complex fibrillar networks, which restricts the flow of solvents and results in viscous solid like materials or gels. These gels have drawn significant attentions for their potential applications for drug delivery, tissue engineering, materials for sensors etc. As of now, self-assembly of gelator molecules into one-dimensional fibers is not well understood, although that is very important to design new gelators for desired applications. Here, we present molecular dynamics study that provides molecular level insight into early stage aggregation of selected gelator, di-Fmoc-L-lysine in binary mixture of organic solvent and water. We will present the role of different functional groups of gelator molecule such as aromatic ring, amide, and carboxylic group on aggregation. We will also present the effect of concentrations of gelator and solvent on self-assembly of gelators. This study has captured helical fiber growth and branching of fiber, which is in good agreement with experimental observations.

Characteristic effects onto C13H12N2O3 molecule dissolved in solvents of argon plasma at atmospheric pressure

NASA Astrophysics Data System (ADS)

Tanışlı, Murat; Taşal, Erol

2017-07-01

We could easily argue that the decomposition of the chemical chain molecules is a compelling application when it comes to the atmospheric pressure plasma. In this paper, we have investigated the effect of the atmospheric pressure argon plasma on 4-((2-methoxyphenyl)diazenyl)benzene-1,3,-diol molecule (abbreviated as 4MBD) at room temperature. 4MBD molecule is one of the industrial dye molecules used widely. When considering the ecological life, this molecule is very harmful and dangerous. As such, we suggest a new decomposing method for such molecules. Atmospheric pressure plasma jet is principally treated for the breakdown of the molecule in question. Fourier transform infrared spectrometry and UV-Vis spectrophotometry tools are used to characterization of the molecules subsequent to the plasma applications to 4MBD molecule in ethanol and methanol solvents. The atmospheric-pressure plasma jet of argon (Ar) as non-equilibrium has been formed by ac-power generator with frequency—24 kHz and voltage—12 kV. Characterizations for solutions prepared with ethanol and methanol solvents of 4MBD molecule have been examined after applying ( duration 3 min) the atmospheric pressure plasma jet. The molecule is broken at 6C-7N-8N=9C stretching peak in consequence of the plasma treatment. The new plasma photo-products for ethanol and methanol solutions are produced as 6C-7N-8N=9C (strong, varying) and 12C=17O (strong, wide) stretching peaks. Also, the bathochromic drifts are discerned.

A New Method to Grow SiC: Solvent-Laser Heated Floating Zone

NASA Technical Reports Server (NTRS)

Woodworth, Andrew A.; Neudeck, Philip G.; Sayir, Ali

2012-01-01

The solvent-laser heated floating zone (solvent-LHFZ) growth method is being developed to grow long single crystal SiC fibers. The technique combines the single crystal fiber growth ability of laser heated floating zone with solvent based growth techniques (e.g. traveling solvent method) ability to grow SiC from the liquid phase. Initial investigations reported in this paper show that the solvent-LHFZ method readily grows single crystal SiC (retains polytype and orientation), but has a significant amount of inhomogeneous strain and solvent rich inclusions.

Self-thermophoresis and thermal self-diffusion in liquids and gases.

PubMed

Brenner, Howard

2010-09-01

This paper demonstrates the existence of self-thermophoresis, a phenomenon whereby a virtual thermophoretic force arising from a temperature gradient in a quiescent single-component liquid or gas acts upon an individual molecule of that fluid in much the same manner as a "real" thermophoretic force acts upon a macroscopic, non-Brownian body immersed in that same fluid. In turn, self-thermophoresis acting in concert with Brownian self-diffusion gives rise to the phenomenon of thermal self-diffusion in single-component fluids. The latter furnishes quantitative explanations of both thermophoresis in pure fluids and thermal diffusion in binary mixtures (the latter composed of a dilute solution of a physicochemically inert solute whose molecules are large compared with those of the solvent continuum). Explicitly, the self-thermophoretic theory furnishes a simple expression for both the thermophoretic velocity U of a macroscopic body in a single-component fluid subjected to a temperature gradient ∇T , and the intimately related binary thermal diffusion coefficient D{T} for a two-component colloidal or macromolecular mixture. The predicted expressions U=-D{T}∇T≡-βD{S}∇T and D{T}=βD{S} (with β and D{S} the pure solvent's respective thermal expansion and isothermal self-diffusion coefficients) are each noted to accord reasonably well with experimental data for both liquids and gases. The likely source of systematic deviations of the predicted values of D{T} from these data is discussed. This appears to be the first successful thermodiffusion theory applicable to both liquids and gases, a not insignificant achievement considering that the respective thermal diffusivities and thermophoretic velocities of these two classes of fluids differ by as much as six orders of magnitude.

Quantifying Dimer and Trimer Formation by Tri- n -butyl Phosphates in n -Dodecane: Molecular Dynamics Simulations

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

Vo, Quynh N.; Dang, Liem X.; Nilsson, Mikael

2016-07-21

Tri-n-butyl phosphate (TBP), a representative of neutral organophosphorous ligands, is an important extractant used in solvent extraction process for the recovery of uranium and plutonium from spent nuclear fuel. Microscopic pictures of TBP isomerism and its behavior in n-dodecane diluent were investigated utilizing MD simulations with previously optimized force field parameters for TBP and n-dodecane. Potential Mean Force (PMF) calculations on a single TBP molecule show seven probable TBP isomers. Radial Distribution Functions (RDF) of TBP suggests the existence of TBP trimers at high TBP concentrations in addition to dimers. 2D PMF calculations were performed to determine the angle andmore » distance criteria for TBP trimers. The dimerization and trimerization constants of TBP in n-dodecane were obtained and match our own experimental values using FTIR technique. The new insights into the conformational behaviors of TBP molecule as a monomer and as part of an aggregate could greatly aid the understanding of the complexation between TBP and metal ions in solvent extraction system. The U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences funded the work performed by LXD.« less

Orientational ordering of a banana-shaped solute molecule in a nematic calamitic solvent by {sup 2}H-NMR spectroscopy: An indication of glasslike behavior

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

Cinacchi, Giorgio; Domenici, Valentina

The Saupe ordering matrix of a banana-shaped mesogenic molecule as a solute in a common nematic calamitic solvent has been determined by {sup 2}H-NMR spectroscopy as a function of temperature. The temperature dependence of the Saupe ordering matrix element associated with the principal molecular axis is consistent with a glassy behavior in the reorientational motion of this particular solute molecule. The Haller expression, appropriately modified, provides a good fit to the experimental data.

Theoretical investigation of the weak interaction between graphene and alcohol solvents

NASA Astrophysics Data System (ADS)

Wang, Haining; Chen, Sian; Lu, Shanfu; Xiang, Yan

2017-05-01

The dispersion of graphene in five different alcohol solvents was investigated by evaluating the binding energy between graphene and alcohol molecules using DFT-D method. The calculation showed the most stable binding energy appeared at the distance of ∼3.5 Å between graphene and alcohol molecules and increased linearly as changing the alcohol from methanol to 1-pentanol. The weak interaction was further graphically illustrated using the reduced density gradient method. The theoretical study revealed alcohols with more carbon atoms could be a good starting point for screening suitable solvents for graphene dispersion.

Interfacial solvation thermodynamics

NASA Astrophysics Data System (ADS)

Ben-Amotz, Dor

2016-10-01

Previous studies have reached conflicting conclusions regarding the interplay of cavity formation, polarizability, desolvation, and surface capillary waves in driving the interfacial adsorptions of ions and molecules at air-water interfaces. Here we revisit these questions by combining exact potential distribution results with linear response theory and other physically motivated approximations. The results highlight both exact and approximate compensation relations pertaining to direct (solute-solvent) and indirect (solvent-solvent) contributions to adsorption thermodynamics, of relevance to solvation at air-water interfaces, as well as a broader class of processes linked to the mean force potential between ions, molecules, nanoparticles, proteins, and biological assemblies.

RECOVERY OF METAL VALUES FROM AQUEOUS SOLUTIONS BY SOLVENT EXTRACTION

DOEpatents

Moore, R.L.

1959-09-01

An organic solvent mixure is described for extracting actinides from aqueous solutions; the solvent mixture consists of from 10 to 25% by volume of tributyl phosphate and the remainder a chlorine-fluorine-substituted saturated hydrocarbon having two carbon atoms in the molecule.

Fluorescence anisotropy of indole molecules under two-photon excitation in the spectral range of 485-510 nm

NASA Astrophysics Data System (ADS)

Sasin, M. E.; Tushkanov, V. I.; Smolin, A. G.; Vasyutinskii, O. S.

2017-10-01

Decay of polarized fluorescence in indole dissolved in propylene glycol under two-photon excitation by femtosecond laser pulses in the wavelength range of 485-510 nm has been studied. It is shown that under the experimental conditions used the fluorescence decay signal can be well described by a single excited state lifetime τf and a single rotation diffusion time τrot. By processing the data obtained, the times τf and τrot as well as anisotropy parameter r 0 characterizing the symmetry of two-photon excitation of indole molecules have been determined. Decreasing of the anisotropy parameter r0 down to zero under two-photon excitation energy higher than 5.1 eV has been observed. Interpretation of the obtained results have been done on the basis of ab initio quantum-mechanical computations. A model of energy relaxation under the condition of twophoton excitation of indole in a polar solvent has been discussed.

Theory for polymer analysis using nanopore-based single-molecule mass spectrometry

PubMed Central

Reiner, Joseph E.; Kasianowicz, John J.; Nablo, Brian J.; Robertson, Joseph W. F.

2010-01-01

Nanometer-scale pores have demonstrated potential for the electrical detection, quantification, and characterization of molecules for biomedical applications and the chemical analysis of polymers. Despite extensive research in the nanopore sensing field, there is a paucity of theoretical models that incorporate the interactions between chemicals (i.e., solute, solvent, analyte, and nanopore). Here, we develop a model that simultaneously describes both the current blockade depth and residence times caused by individual poly(ethylene glycol) (PEG) molecules in a single α-hemolysin ion channel. Modeling polymer-cation binding leads to a description of two significant effects: a reduction in the mobile cation concentration inside the pore and an increase in the affinity between the polymer and the pore. The model was used to estimate the free energy of formation for K+-PEG inside the nanopore (≈-49.7 meV) and the free energy of PEG partitioning into the nanopore (≈0.76 meV per ethylene glycol monomer). The results suggest that rational, physical models for the analysis of analyte-nanopore interactions will develop the full potential of nanopore-based sensing for chemical and biological applications. PMID:20566890

Synchronous fluorescence spectroscopic study of solvatochromic curcumin dye.

PubMed

Patra, Digambara; Barakat, Christelle

2011-09-01

Curcumin, the main yellow bioactive component of turmeric, has recently acquired attention by chemists due its wide range of potential biological applications as an antioxidant, an anti-inflammatory, and an anti-carcinogenic agent. This molecule fluoresces weakly and poorly soluble in water. In this detailed study of curcumin in thirteen different solvents, both the absorption and fluorescence spectra of curcumin was found to be broad, however, a narrower and simple synchronous fluorescence spectrum of curcumin was obtained at Δλ=10-20 nm. Lippert-Mataga plot of curcumin in different solvents illustrated two sets of linearity which is consistent with the plot of Stokes' shift vs. the ET30. When Stokes's shift in wavenumber scale was replaced by synchronous fluorescence maximum in nanometer scale, the solvent polarity dependency measured by λSFSmax vs. Lippert-Mataga plot or ET30 values offered similar trends as measured via Stokes' shift for protic and aprotic solvents for curcumin. Better linear correlation of λSFSmax vs. π* scale of solvent polarity was found compared to λabsmax or λemmax or Stokes' shift measurements. In Stokes' shift measurement both absorption/excitation as well as emission (fluorescence) spectra are required to compute the Stokes' shift in wavenumber scale, but measurement could be done in a very fast and simple way by taking a single scan of SFS avoiding calculation and obtain information about polarity of the solvent. Curcumin decay properties in all the solvents could be fitted well to a double-exponential decay function. Copyright © 2011 Elsevier B.V. All rights reserved.

Predicting hydration free energies with a hybrid QM/MM approach

PubMed Central

König, Gerhard; Pickard, Frank C.; Mei, Ye; Brooks, Bernard R.

2014-01-01

The correct representation of solute-water interactions is essential for the accurate simulation of most biological phenomena. Several highly accurate quantum methods are available to deal with solvation by using both implicit and explicit solvents. So far, however, most evaluations of those methods were based on a single conformation, which neglects solute entropy. Here, we present the first test of a novel approach to determine hydration free energies that uses molecular mechanics (MM) to sample phase space and quantum mechanics (QM) to evaluate the potential energies. Free energies are determined by using re-weighting with the Non-Boltzmann Bennett (NBB) method. In this context, the method is referred to as QM-NBB. Based on snapshots from MM sampling and accounting for their correct Boltzmann weight, it is possible to obtain hydration free energies that incorporate the effect of solute entropy. We evaluate the performance of several QM implicit solvent models, as well as explicit solvent QM/MM for the blind subset of the SAMPL4 hydration free energy challenge. While classical free energy simulations with molecular dynamics give root mean square deviations (RMSD) of 2.8 and 2.3 kcal/mol, the hybrid approach yields an improved RMSD of 1.6 kcal/mol. By selecting an appropriate functional and basis set, the RMSD can be reduced to 1 kcal/mol for calculations based on a single conformation. Results for a selected set of challenging molecules imply that this RMSD can be further reduced by using NBB to reweight MM trajectories with the SMD implicit solvent model. PMID:24504703

Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4

NASA Astrophysics Data System (ADS)

König, Gerhard; Pickard, Frank C.; Mei, Ye; Brooks, Bernard R.

2014-03-01

The correct representation of solute-water interactions is essential for the accurate simulation of most biological phenomena. Several highly accurate quantum methods are available to deal with solvation by using both implicit and explicit solvents. So far, however, most evaluations of those methods were based on a single conformation, which neglects solute entropy. Here, we present the first test of a novel approach to determine hydration free energies that uses molecular mechanics (MM) to sample phase space and quantum mechanics (QM) to evaluate the potential energies. Free energies are determined by using re-weighting with the Non-Boltzmann Bennett (NBB) method. In this context, the method is referred to as QM-NBB. Based on snapshots from MM sampling and accounting for their correct Boltzmann weight, it is possible to obtain hydration free energies that incorporate the effect of solute entropy. We evaluate the performance of several QM implicit solvent models, as well as explicit solvent QM/MM for the blind subset of the SAMPL4 hydration free energy challenge. While classical free energy simulations with molecular dynamics give root mean square deviations (RMSD) of 2.8 and 2.3 kcal/mol, the hybrid approach yields an improved RMSD of 1.6 kcal/mol. By selecting an appropriate functional and basis set, the RMSD can be reduced to 1 kcal/mol for calculations based on a single conformation. Results for a selected set of challenging molecules imply that this RMSD can be further reduced by using NBB to reweight MM trajectories with the SMD implicit solvent model.

Steric Effects of Solvent Molecules on SN2 Substitution Dynamics.

PubMed

Liu, Xu; Xie, Jing; Zhang, Jiaxu; Yang, Li; Hase, William L

2017-04-20

Influences of solvent molecules on S N 2 reaction dynamics of microsolvated F - (H 2 O) n with CH 3 I, for n = 0-3, are uncovered by direct chemical dynamics simulations. The direct substitution mechanism, which is important without microsolvation, is quenched dramatically upon increasing hydration. The water molecules tend to force reactive encounters to proceed through the prereaction collision complex leading to indirect reaction. In contrast to F - (H 2 O), reaction with higher hydrated ions shows a strong propensity for ion desolvation in the entrance channel, diminishing steric hindrance for nucleophilic attack. Thus, nucleophilic substitution avoids the potential energy barrier with all of the solvent molecules intact and instead occurs through the less solvated barrier, which is energetically unexpected because the former barrier has a lower energy. The work presented here reveals a trade-off between reaction energetics and steric effects, with the latter found to be crucial in understanding how hydration influences microsolvated S N 2 dynamics.

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.

A simple and effective solution to the constrained QM/MM simulations

NASA Astrophysics Data System (ADS)

Takahashi, Hideaki; Kambe, Hiroyuki; Morita, Akihiro

2018-04-01

It is a promising extension of the quantum mechanical/molecular mechanical (QM/MM) approach to incorporate the solvent molecules surrounding the QM solute into the QM region to ensure the adequate description of the electronic polarization of the solute. However, the solvent molecules in the QM region inevitably diffuse into the MM bulk during the QM/MM simulation. In this article, we developed a simple and efficient method, referred to as the "boundary constraint with correction (BCC)," to prevent the diffusion of the solvent water molecules by means of a constraint potential. The point of the BCC method is to compensate the error in a statistical property due to the bias potential by adding a correction term obtained through a set of QM/MM simulations. The BCC method is designed so that the effect of the bias potential completely vanishes when the QM solvent is identical with the MM solvent. Furthermore, the desirable conditions, that is, the continuities of energy and force and the conservations of energy and momentum, are fulfilled in principle. We applied the QM/MM-BCC method to a hydronium ion(H3O+) in aqueous solution to construct the radial distribution function (RDF) of the solvent around the solute. It was demonstrated that the correction term fairly compensated the error and led the RDF in good agreement with the result given by an ab initio molecular dynamics simulation.

Formation of solvate structures by the ortho-, meta-, and para-isomers of hydroxybenzoic acid in supercritical fluid

NASA Astrophysics Data System (ADS)

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

2017-04-01

The solvate structures formed by the ortho-, meta-, and para-isomers of hydroxybenzoic acid ( o-HBA, m-HBA, and p-HBA) with a polar co-solvent (methanol at a concentration of 0.030 and 0.035 mole fractions) in supercritical carbon dioxide at a constant density of 0.7 g/cm3 and temperatures of 318 and 328 K have been studied by the classic molecular dynamics. It has been determined that a stable hydrogen-bonded complex with the co-solvent forms via the hydrogen of the carboxyl group for all isomers. The probability of this complex existence is high at all temperatures and concentrations. In the o-HBA molecule, the other functional groups are engaged in the intramolecular hydrogen bond, but not involved in interactions with methanol. It has been found that m-HBA and p-HBA can be involved in hydrogen bonds with methanol via hydroxyl hydrogen and oxygen atoms; they are characterized by the presence of one more co-solvent molecule (rarely, two molecules) in their solvation shell and intermittent formations/breakages of hydrogen bonds via other functional groups. These bonds are far less stable, and their formation is sensitive to change of temperature and co-solvent concentration. It has been concluded that the degree of selective solvation of m-HBA and p-HBA by co-solvent molecules is approximately the same, but the rate of structural rearrangements in the nearest environment of m-HBA is higher than that of p-HBA.

Large-Scale Validation of Mixed-Solvent Simulations to Assess Hotspots at Protein-Protein Interaction Interfaces.

PubMed

Ghanakota, Phani; van Vlijmen, Herman; Sherman, Woody; Beuming, Thijs

2018-04-23

The ability to target protein-protein interactions (PPIs) with small molecule inhibitors offers great promise in expanding the druggable target space and addressing a broad range of untreated diseases. However, due to their nature and function of interacting with protein partners, PPI interfaces tend to extend over large surfaces without the typical pockets of enzymes and receptors. These features present unique challenges for small molecule inhibitor design. As such, determining whether a particular PPI of interest could be pursued with a small molecule discovery strategy requires an understanding of the characteristics of the PPI interface and whether it has hotspots that can be leveraged by small molecules to achieve desired potency. Here, we assess the ability of mixed-solvent molecular dynamic (MSMD) simulations to detect hotspots at PPI interfaces. MSMD simulations using three cosolvents (acetonitrile, isopropanol, and pyrimidine) were performed on a large test set of 21 PPI targets that have been experimentally validated by small molecule inhibitors. We compare MSMD, which includes explicit solvent and full protein flexibility, to a simpler approach that does not include dynamics or explicit solvent (SiteMap) and find that MSMD simulations reveal additional information about the characteristics of these targets and the ability for small molecules to inhibit the PPI interface. In the few cases were MSMD simulations did not detect hotspots, we explore the shortcomings of this technique and propose future improvements. Finally, using Interleukin-2 as an example, we highlight the advantage of the MSMD approach for detecting transient cryptic druggable pockets that exists at PPI interfaces.

1D helical cadmium coordination polymers containing hydrazide ligand: The role of solvent and molar ratio

NASA Astrophysics Data System (ADS)

Notash, Behrouz

2018-03-01

Three new cadmium coordination polymers, [Cd(L)(NO3)2CH3OH]n, 1, {[Cd(L)2(NO3)]NO3}n, 2 and {[Cd(L)2(NO3)]NO3.H2O}n3, which L is nicotinohydrazide have been synthesized and characterized by spectroscopic methods as well as single crystal X-ray diffraction. Compounds 1-3 have been synthesized by changing solvent and metal-to-ligand ratio. X-ray crystallography showed that compounds 1-3 have different 1D helical structural motif. Semi-flexible nature of L ligand causes to syn-syn conformation which leading to form 1D helical chains coordination polymers. Compounds 2 and 3 were synthesized under the same reaction conditions with similar molar ratio, but using different solvent system. These compounds are pseudopolymorph which differs in the presence or absence of water molecule in their crystal packing. Hirshfeld surface analysis of the structures 1-3 have been performed and find the percent of participation of intermolecular interactions in the crystal packing of compounds.

On the theory of electric double layer with explicit account of a polarizable co-solvent.

PubMed

Budkov, Yu A; Kolesnikov, A L; Kiselev, M G

2016-05-14

We present a continuation of our theoretical research into the influence of co-solvent polarizability on a differential capacitance of the electric double layer. We formulate a modified Poisson-Boltzmann theory, using the formalism of density functional approach on the level of local density approximation taking into account the electrostatic interactions of ions and co-solvent molecules as well as their excluded volume. We derive the modified Poisson-Boltzmann equation, considering the three-component symmetric lattice gas model as a reference system and minimizing the grand thermodynamic potential with respect to the electrostatic potential. We apply present modified Poisson-Boltzmann equation to the electric double layer theory, showing that accounting for the excluded volume of co-solvent molecules and ions slightly changes the main result of our previous simplified theory. Namely, in the case of small co-solvent polarizability with its increase under the enough small surface potentials of electrode, the differential capacitance undergoes the significant growth. Oppositely, when the surface potential exceeds some threshold value (which is slightly smaller than the saturation potential), the increase in the co-solvent polarizability results in a differential capacitance decrease. However, when the co-solvent polarizability exceeds some threshold value, its increase generates a considerable enhancement of the differential capacitance in a wide range of surface potentials. We demonstrate that two qualitatively different behaviors of the differential capacitance are related to the depletion and adsorption of co-solvent molecules at the charged electrode. We show that an additive of the strongly polarizable co-solvent to an electrolyte solution can shift significantly the saturation potential in two qualitatively different manners. Namely, a small additive of strongly polarizable co-solvent results in a shift of saturation potential to higher surface potentials. On the contrary, a sufficiently large additive of co-solvent shifts the saturation potential to lower surface potentials. We obtain that an increase in the co-solvent polarizability makes the electrostatic potential profile longer-ranged. However, increase in the co-solvent concentration in the bulk leads to non-monotonic behavior of the electrostatic potential profile. An increase in the co-solvent concentration in the bulk at its sufficiently small values makes the electrostatic potential profile longer-ranged. Oppositely, when the co-solvent concentration in the bulk exceeds some threshold value, its further increase leads to decrease in electrostatic potential at all distances from the electrode.

Nonlocal and nonlinear electrostatics of a dipolar Coulomb fluid.

PubMed

Sahin, Buyukdagli; Ralf, Blossey

2014-07-16

We study a model Coulomb fluid consisting of dipolar solvent molecules of finite extent which generalizes the point-like dipolar Poisson-Boltzmann model (DPB) previously introduced by Coalson and Duncan (1996 J. Phys. Chem. 100 2612) and Abrashkin et al (2007 Phys. Rev. Lett. 99 077801). We formulate a nonlocal Poisson-Boltzmann equation (NLPB) and study both linear and nonlinear dielectric response in this model for the case of a single plane geometry. Our results shed light on the relevance of nonlocal versus nonlinear effects in continuum models of material electrostatics.

Method of Continuous Variations: Applications of Job Plots to the Study of Molecular Associations in Organometallic Chemistry[**

PubMed Central

Renny, Joseph S.; Tomasevich, Laura L.; Tallmadge, Evan H.; Collum, David B.

2014-01-01

Applications of the method of continuous variations—MCV or the Method of Job—to problems of interest to organometallic chemists are described. MCV provides qualitative and quantitative insights into the stoichiometries underlying association of m molecules of A and n molecules of B to form AmBn. Applications to complex ensembles probe associations that form metal clusters and aggregates. Job plots in which reaction rates are monitored provide relative stoichiometries in rate-limiting transition structures. In a specialized variant, ligand- or solvent-dependent reaction rates are dissected into contributions in both the ground states and transition states, which affords insights into the full reaction coordinate from a single Job plot. Gaps in the literature are identified and critiqued. PMID:24166797

Conformation and Aggregation of LKα14 Peptide in Bulk Water and at the Air/Water Interface.

PubMed

Dalgicdir, Cahit; Sayar, Mehmet

2015-12-10

Historically, the protein folding problem has mainly been associated with understanding the relationship between amino acid sequence and structure. However, it is known that both the conformation of individual molecules and their aggregation strongly depend on the environmental conditions. Here, we study the aggregation behavior of the model peptide LKα14 (with amino acid sequence LKKLLKLLKKLLKL) in bulk water and at the air/water interface. We start by a quantitative analysis of the conformational space of a single LKα14 in bulk water. Next, in order to analyze the aggregation tendency of LKα14, by using the umbrella sampling technique we calculate the potential of mean force for pulling a single peptide from an n-molecule aggregate. In agreement with the experimental results, our calculations yield the optimal aggregate size as four. This equilibrium state is achieved by two opposing forces: Coulomb repulsion between the lysine side chains and the reduction of solvent accessible hydrophobic surface area upon aggregation. At the vacuum/water interface, however, even dimers of LKα14 become marginally stable, and any larger aggregate falls apart instantaneously. Our results indicate that even though the interface is highly influential in stabilizing the α-helix conformation for a single molecule, it significantly reduces the attraction between two LKα14 peptides, along with their aggregation tendency.

Crystal growth, characterization and theoretical studies of 4-aminopyridinium picrate

NASA Astrophysics Data System (ADS)

Aditya Prasad, A.; Muthu, K.; Rajasekar, M.; Meenatchi, V.; Meenakshisundaram, S. P.

2015-01-01

Single crystals of 4-aminopyridinium picrate (APP) were grown by slow evaporation of a mixed solvent system methanol-acetone (1:1, v/v) containing equimolar quantities of 4-aminopyridine and picric acid. Structure is elucidated by single crystal XRD analysis and the crystal belongs to monoclinic system with four molecules in the unit cell (space group P21/c) and the cell parameter values are, a = 8.513 Å (±0.015), b = 11.33 Å (±0.02), c = 14.33 Å (±0.03) and β = 104.15° (±0.019), V = 1340 A3 (±6) with refined R factors R1 = 0.0053 and wR2 = 0.0126. The electron density mapping is interpreted to find coordinates for each atom in the crystallized molecules. The various functional groups present in the molecule are confirmed by FT-IR analysis. UV-visible spectral analysis was used to determine the band gap energy of 4-aminopyridinium picrate. Powder X-ray diffraction pattern reveals the crystallinity of the as-grown crystal and it closely resembles the simulated XRD from the single crystal XRD analysis. Scanning electron microscopy reveals the surface morphology of the grown crystal. Optimized geometry is derived by Hartree-Fock theory calculations and the first-order molecular hyperpolarizability (β), theoretically calculated bond length, bond angles and excited state energy from theoretical UV-vis spectrum were estimated.

First-principles calculation of electronic energy level alignment at electrochemical interfaces

NASA Astrophysics Data System (ADS)

Azar, Yavar T.; Payami, Mahmoud

2017-08-01

Energy level alignment at solid-solvent interfaces is an important step in determining the properties of electrochemical systems. The positions of conduction and valence band edges of a semiconductor are affected by its environment. In this study, using first-principles DFT calculation, we have determined the level shifts of the semiconductors TiO2 and ZnO at the interfaces with MeCN and DMF solvent molecules. The level shifts of semiconductor are obtained using the potential difference between the clean and exposed surfaces of asymmetric slabs. In this work, neglecting the effects of present ions in the electrolyte solution, we have shown that the solvent molecules give rise to an up-shift for the levels, and the amount of this shift varies with coverage. It is also shown that the shapes of density of states do not change sensibly near the gap. Molecular dynamics simulations of the interface have shown that at room temperatures the semiconductor surface is not fully covered by the solvent molecules, and one must use intermediate values in an static calculations.

Composite Materials

NASA Technical Reports Server (NTRS)

1988-01-01

Langley Research Center researchers invented an advanced polymer, a chemical compound formed by uniting many small molecules to create a complex molecule with different chemical properties. The material is a thermoplastic polyimide that resists solvents. Other polymers of this generic type are soluble in solvents, thus cannot be used where solvents are present. High Technology Services (HTS), Inc. licensed technology and is engaged in development and manufacture of high performance plastics, resins and composite materials. Techimer Materials Division is using technology for composite matrix resins that offer heat resistance and protection from radiation, electrical and chemical degradation. Applications of new polymer include molding resins, adhesives and matrix resins for fiber reinforced composites.

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.

Phase-field approach to implicit solvation of biomolecules with Coulomb-field approximation

NASA Astrophysics Data System (ADS)

Zhao, Yanxiang; Kwan, Yuen-Yick; Che, Jianwei; Li, Bo; McCammon, J. Andrew

2013-07-01

A phase-field variational implicit-solvent approach is developed for the solvation of charged molecules. The starting point of such an approach is the representation of a solute-solvent interface by a phase field that takes one value in the solute region and another in the solvent region, with a smooth transition from one to the other on a small transition layer. The minimization of an effective free-energy functional of all possible phase fields determines the equilibrium conformations and free energies of an underlying molecular system. All the surface energy, the solute-solvent van der Waals interaction, and the electrostatic interaction are coupled together self-consistently through a phase field. The surface energy results from the minimization of a double-well potential and the gradient of a field. The electrostatic interaction is described by the Coulomb-field approximation. Accurate and efficient methods are designed and implemented to numerically relax an underlying charged molecular system. Applications to single ions, a two-plate system, and a two-domain protein reveal that the new theory and methods can capture capillary evaporation in hydrophobic confinement and corresponding multiple equilibrium states as found in molecular dynamics simulations. Comparisons of the phase-field and the original sharp-interface variational approaches are discussed.

Origin of translocation barriers for polyelectrolyte chains.

PubMed

Kumar, Rajeev; Muthukumar, M

2009-11-21

For single-file translocations of a charged macromolecule through a narrow pore, the crucial step of arrival of an end at the pore suffers from free energy barriers, arising from changes in intrachain electrostatic interaction, distribution of ionic clouds and solvent molecules, and conformational entropy of the chain. All contributing factors to the barrier in the initial stage of translocation are evaluated by using the self-consistent field theory for the polyelectrolyte and the coupled Poisson-Boltzmann description for ions without radial symmetry. The barrier is found to be essentially entropic due to conformational changes. For moderate and high salt concentrations, the barriers for the polyelectrolyte chain are quantitatively equivalent to that of uncharged self-avoiding walks. Electrostatic effects are shown to increase the free energy barriers, but only slightly. The degree of ionization, electrostatic interaction strength, decreasing salt concentration, and the solvent quality all result in increases in the barrier.

The Metal Effect on Self-Assembling of Oxalamide Gelators Explored by Mass Spectrometry and DFT Calculations.

PubMed

Dabić, Dario; Brkljačić, Lidija; Tandarić, Tana; Žinić, Mladen; Vianello, Robert; Frkanec, Leo; Kobetić, Renata

2018-01-01

Gels formed by self-assembly of small organic molecules are of wide interest as dynamic soft materials with numerous possible applications, especially in terms of nanotechnology for functional and responsive biomaterials, biosensors, and nanowires. Four bis-oxalamides were chosen to show if electrospray ionization mass spectrometry (ESI-MS) could be used as a prediction of a good gelator and also to shed light on the gelation processes. By inspecting the gelation of several solvent, we showed that bis(amino acid)oxalamide 1 proved to be the most efficient, also being able of forming the largest observable assemblies in the gas phase. The formation of singly charged assemblies holding from one up to six monomer units is the outcome of the strong intermolecular H-bonds, particularly among terminal carboxyl groups. The variation of solvents from polar aprotic towards polar protic did not have any significant effects on the size of the assemblies. The addition of a salt such as NaOAc or Mg(OAc) 2 , depending on the concentration, altered the assembling. Computational analysis at the DFT level aided in the interpretation of the observed trends and revealed that individual gelator molecules spontaneously assemble to higher aggregates, but the presence of the Na + cation disrupts any gelator organization since it becomes significantly more favorable for gelator molecules to bind Na + cations up to the 3:1 ratio than to self-assemble, being fully in line with experimental observations reported here. Graphical Abstract ᅟ.

The Metal Effect on Self-Assembling of Oxalamide Gelators Explored by Mass Spectrometry and DFT Calculations

NASA Astrophysics Data System (ADS)

Dabić, Dario; Brkljačić, Lidija; Tandarić, Tana; Žinić, Mladen; Vianello, Robert; Frkanec, Leo; Kobetić, Renata

2018-01-01

Gels formed by self-assembly of small organic molecules are of wide interest as dynamic soft materials with numerous possible applications, especially in terms of nanotechnology for functional and responsive biomaterials, biosensors, and nanowires. Four bis-oxalamides were chosen to show if electrospray ionization mass spectrometry (ESI-MS) could be used as a prediction of a good gelator and also to shed light on the gelation processes. By inspecting the gelation of several solvent, we showed that bis(amino acid)oxalamide 1 proved to be the most efficient, also being able of forming the largest observable assemblies in the gas phase. The formation of singly charged assemblies holding from one up to six monomer units is the outcome of the strong intermolecular H-bonds, particularly among terminal carboxyl groups. The variation of solvents from polar aprotic towards polar protic did not have any significant effects on the size of the assemblies. The addition of a salt such as NaOAc or Mg(OAc)2, depending on the concentration, altered the assembling. Computational analysis at the DFT level aided in the interpretation of the observed trends and revealed that individual gelator molecules spontaneously assemble to higher aggregates, but the presence of the Na+ cation disrupts any gelator organization since it becomes significantly more favorable for gelator molecules to bind Na+ cations up to the 3:1 ratio than to self-assemble, being fully in line with experimental observations reported here. [Figure not available: see fulltext.

Effects of Conjugation in Length and Dimension on Spectroscopic Properties of Fluorene-Based Chromophores from Experiment and Theory (Preprint)

DTIC Science & Technology

2006-07-01

catalyzed iodo-bromo exchange reaction and (b) condensation of the resulting iodo-aldehyde precursor with 2-aminothiophenol in dimethylsulfoxide ( DMSO ). The...when compared to results from measurements carried out in a nonpolar solvent , which were available for some molecules. The computed oscillator... solvent , which were available for some molecules. The computed oscillator strengths may resolve discordant experimental values in some cases, for example

Local viscosity and solvent relaxation experienced by rod-like fluorophores in AOT/4-chlorophenol/m-xylene organogels

NASA Astrophysics Data System (ADS)

Dandapat, Manika; Mandal, Debabrata

2017-01-01

Organogels prepared from AOT/4-chlorophenol/m-xylene are immobile in the macroscopic sense, with a well-characterized internal structure. However, the molecular level dynamics inside the gels is not too clear, although a very slow structural relaxation has been reported previously. Using a set of rod-like fluorophores, we find that the rotational mobility of a small guest molecule inside the gel can be extremely fast, indicating presence of sufficiently low-microviscosity domains. These domains consist of m-xylene solvent molecules trapped in the interstices of fiber bundles comprising columnar stacks of 4-chlorophenol surrounded by AOT molecules. However, interstitial trapping of m-xylene does retard its own dynamics, which explains the slow solvent relaxation inside the gels. Hence, the state of m-xylene in the organogel may be characterized as "bound", in contrast to the "free" state in neat m-xylene.

Unique Crystallization of Fullerenes: Fullerene Flowers

PubMed Central

Kim, Jungah; Park, Chibeom; Song, Intek; Lee, Minkyung; Kim, Hyungki; Choi, Hee Cheul

2016-01-01

Solution-phase crystallization of fullerene molecules strongly depends on the types of solvent and their ratios because solvent molecules are easily included in the crystal lattice and distort its structure. The C70 (solute)–mesitylene (solvent) system yields crystals with various morphologies and structures, such as cubes, tubes, and imperfect rods. Herein, using C60 and C70 dissolved in mesitylene, we present a novel way to grow unique flower-shaped crystals with six symmetric petals. The different solubility of C60 and C70 in mesitylene promotes nucleation of C70 with sixfold symmetry in the early stage, which is followed by co-crystallization of both C60 and C70 molecules, leading to lateral petal growth. Based on the growth mechanism, we obtained more complex fullerene crystals, such as multi-deck flowers and tube-flower complexes, by changing the sequence and parameters of crystallization. PMID:27561446

Deactivation of 6-Aminocoumarin Intramolecular Charge Transfer Excited State through Hydrogen Bonding

PubMed Central

Krystkowiak, Ewa; Dobek, Krzysztof; Maciejewski, Andrzej

2014-01-01

This paper presents results of the spectral (absorption and emission) and photophysical study of 6-aminocoumarin (6AC) in various aprotic hydrogen-bond forming solvents. It was established that solvent polarity as well as hydrogen-bonding ability influence solute properties. The hydrogen-bonding interactions between S1-electronic excited solute and solvent molecules were found to facilitate the nonradiative deactivation processes. The energy-gap dependence on radiationless deactivation in aprotic solvents was found to be similar to that in protic solvents. PMID:25244014

Performance of thermally-chargeable supercapacitors in different solvents.

PubMed

Lim, Hyuck; Zhao, Cang; Qiao, Yu

2014-07-07

The influence of solvent on the temperature sensitivity of the electrode potential of thermally-chargeable supercapacitors (TCSs) is investigated. For large electrodes, the output voltage is positively correlated with the dielectric constant of solvent. When nanoporous carbon electrodes are used, different characteristics of system performance are observed, suggesting that possible size effects must be taken into consideration when the solvent molecules and solvated ions are confined in a nanoenvironment.

Surveying implicit solvent models for estimating small molecule absolute hydration free energies

PubMed Central

Knight, Jennifer L.

2011-01-01

Implicit solvent models are powerful tools in accounting for the aqueous environment at a fraction of the computational expense of explicit solvent representations. Here, we compare the ability of common implicit solvent models (TC, OBC, OBC2, GBMV, GBMV2, GBSW, GBSW/MS, GBSW/MS2 and FACTS) to reproduce experimental absolute hydration free energies for a series of 499 small neutral molecules that are modeled using AMBER/GAFF parameters and AM1-BCC charges. Given optimized surface tension coefficients for scaling the surface area term in the nonpolar contribution, most implicit solvent models demonstrate reasonable agreement with extensive explicit solvent simulations (average difference 1.0-1.7 kcal/mol and R2=0.81-0.91) and with experimental hydration free energies (average unsigned errors=1.1-1.4 kcal/mol and R2=0.66-0.81). Chemical classes of compounds are identified that need further optimization of their ligand force field parameters and others that require improvement in the physical parameters of the implicit solvent models themselves. More sophisticated nonpolar models are also likely necessary to more effectively represent the underlying physics of solvation and take the quality of hydration free energies estimated from implicit solvent models to the next level. PMID:21735452

The Effects of Anchor Groups on (1) TiO2-Catalyzed Photooxidation and (2) Linker-Assisted Assembly on TiO2

NASA Astrophysics Data System (ADS)

Anderson, Ian Mark

Quantum dot-sensitized solar cells (QDSSCs) are a popular target for research due to their potential for highly efficient, easily tuned absorption. Typically, light is absorbed by quantum dots attached to a semiconductor substrate, such as TiO2, via bifunctional linker molecules. This research aims to create a patterned monolayer of linker molecules on a TiO2 film, which would in turn allow the attachment of a patterned layer of quantum dots. One method for the creation of a patterned monolayer is the functionalization of a TiO2 film with a linker molecule, followed by illumination with a laser at 355 nm. This initiates a TiO 2-catalyzed oxidation reaction, causing loss of surface coverage. A second linker molecule can then be adsorbed onto the TiO2 surface in the illuminated area. Towards that end, the behaviors of carboxylic and phosphonic acids adsorbed on TiO2 have been studied. TiO2 films were functionalized by immersion in solutions a single adsorbate and surface coverage was determined by IR spectroscopy. It is shown that phosphonic acids attain higher surface coverage than carboxylic acids, and will displace them from TiO2 when in a polar solvent. Alkyl chain lengths, which can influence stabilities of monolayers, are shown not to have an effect on this relationship. Equilibrium binding data for the adsorption of n-hexadecanoic acid to TiO2 from a THF solution are presented. It is shown that solvent polarity can affect monolayer stability; carboxylates and phosphonates undergo more desorption into polar solvents than nonpolar. Through illumination, it was possible to remove nearly all adsorbed linkers from TiO2. However, the illuminated areas were found not to be receptive to attachment by a second adsorbate. A possible reason for this behavior is presented. I also report on the synthesis and characterization of a straight-chain, thiol-terminated phosphonic acid. Initial experiments involving monolayer formation and quantum dot attachment are presented. Finally, it was found that quantum dots attach in high amounts to linker-functionalized TiO2 when suspended in pyridine. This increased surface attachment was present even when the linker molecule used lacked a functional group which would bind to the CdSe surface.

Developments toward more accurate molecular modeling of liquids

NASA Astrophysics Data System (ADS)

Evans, Tom J.

2000-12-01

The general goal of this research has been to improve upon existing combined quantum mechanics/molecular mechanics (QM/MM) methodologies. Error weighting functions have been introduced into the perturbative Monte Carlo (PMC) method for use with QM/MM. The PMC approach, introduced earlier, provides a means to reduce the number of full self-consistent field (SCF) calculations in simulations using the QM/MM potential by evoking perturbation theory to calculate energy changes due to displacements of a MM molecule. This will allow the ab initio QM/MM approach to be applied to systems that require more advanced, computationally demanding treatments of the QM and/or MM regions. Efforts have also been made to improve the accuracy of the representation of the solvent molecules usually represented by MM force fields. Results from an investigation of the applicability of the embedded density functional theory (EDFT) for studying physical properties of solutions will be presented. In this approach, the solute wavefunction is solved self- consistently in the field of individually frozen electron-density solvent molecules. To test its accuracy, the potential curves for interactions between Li+, Cl- and H2O with a single frozen-density H 2O molecule in different orientations have been calculated. With the development of the more sophisticated effective fragment potential (EFP) representation of solvent molecules, a QM/EFP technique was created. This hybrid QM/EFP approach was used to investigate the solvation of Li + by small clusters of water, as a test case for larger ionic dusters. The EFP appears to provide an accurate representation of the strong interactions that exist between Li+ and H2O. With the QM/EFP methodology comes an increased computational expense, resulting in an even greater need to rely on the PMC approach. However, while including the PMC into the hybrid QM/EFP technique, it was discovered that the previous implementation of the PMC was done incorrectly, invalidating earlier test results. The PMC implementation was therefore reworked, and tests were performed to investigate the methods usefulness in reducing the computational load of these types of simulations. The results that were obtained while studying F-(H2O) and F-(H 2O)2 show that PMC can be used cautiously to increase computational efficiency.

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

Cotlet, M.; Mudalige, K.; Habuchi, S.

HcRed is a dimeric intrinsically fluorescent protein with origins in the sea anemone Heteractis crispa. This protein exhibits deep red absorption and emission properties. Using a combination of ensemble and single molecule methods and by varying environmental parameters such as temperature and pH, we found spectroscopic evidence for the presence of two ground state conformers, trans and cis chromophores that are in thermal equilibrium and that follow different excited-state pathways upon exposure to light. The photocycle of HcRed appears to be a combination of both kindling proteins and bright emitting GFP/GFP-like proteins: the trans chromophore undergoes light driven isomerization followedmore » by radiative relaxation with a fluorescence lifetime of 0.5 ns. The cis chromophore exhibits a photocycle similar to bright GFPs and GFP-like proteins such as enhanced GFP, enhanced YFP or DsRed, with radiative relaxation with a fluorescence lifetime of 1.5 ns, singlet-triplet deactivation on a microsecond time scale and solvent controlled protonation/deprotonation in tens of microseconds. Using single molecule spectroscopy, we identify trans and cis conformers at the level of individual moieties and show that it is possible that the two conformers can coexist in a single protein due to the dimeric nature of HcRed.« less

Amyloid oligomer structure characterization from simulations: A general method

NASA Astrophysics Data System (ADS)

Nguyen, Phuong H.; Li, Mai Suan; Derreumaux, Philippe

2014-03-01

Amyloid oligomers and plaques are composed of multiple chemically identical proteins. Therefore, one of the first fundamental problems in the characterization of structures from simulations is the treatment of the degeneracy, i.e., the permutation of the molecules. Second, the intramolecular and intermolecular degrees of freedom of the various molecules must be taken into account. Currently, the well-known dihedral principal component analysis method only considers the intramolecular degrees of freedom, and other methods employing collective variables can only describe intermolecular degrees of freedom at the global level. With this in mind, we propose a general method that identifies all the structures accurately. The basis idea is that the intramolecular and intermolecular states are described in terms of combinations of single-molecule and double-molecule states, respectively, and the overall structures of oligomers are the product basis of the intramolecular and intermolecular states. This way, the degeneracy is automatically avoided. The method is illustrated on the conformational ensemble of the tetramer of the Alzheimer's peptide Aβ9-40, resulting from two atomistic molecular dynamics simulations in explicit solvent, each of 200 ns, starting from two distinct structures.

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.

Computer simulations of the solvatochromism of betaine-30

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

Mente, S.R.; Maroncelli, M.

1999-09-09

Monte Carlo simulations of the pyridinium N-phenolate dye betaine-30 in 12 solvents (20 solvent representations) were performed in order to explore the molecular basis of the E{sub T}(30) scale of solvent polarity. Ab initio (HF/6-31G{sup *}) and semiempirical (AM1 and INDO/S) electronic structure calculations were used to determine the geometry and charge distribution of betaine-30 in its S{sub 0} and S{sub 1} states. The solvent effect on the betaine absorption spectrum was assumed to derive from electrostatic interactions between the effective charge distributions of solvent molecules and the charge shift brought about by the S{sub 0} {r_arrow} S{sub 1} transition.more » Two models for this charge shift, one obtained from INDO/S calculations and the other an idealized two-site model, were used for the spectral calculations. Good agreement between simulated and observed {Delta}E{sub T} shifts (E{sub T}(30) values measured relative to the nonpolar standard tetramethylsilane) was found for both charge-shift models. In water and other hydroxylic solvents, the O atom of the betaine solute was observed to form moderately strong hydrogen bonds to between one and two solvent molecules. The contribution of these specifically coordinated molecules to the {Delta}E{sub T} shift was found to be large, (30--60%) and comparable to experimental estimates. Additional simulations of acetonitrile and methanol in equilibrium with the S{sub 1} state of betaine-30 were used to determine reorganization energies in these solvents and to decide the extent to which the solvent response to the S{sub 0} {leftrightarrow} S{sub 1} transition conforms to linear response predictions. In both solvents, the spectral distributions observed in the S{sub 0} state simulations were {approximately} 15% narrower than those in the S{sub 1} simulations, indicating only a relatively small departure from linear behavior. Reorganization energies were also estimated for a number of other solvents and compared to values reported in previous experimental and theoretical studies.« less

Role of translational entropy in spatially inhomogeneous, coarse-grained models

NASA Astrophysics Data System (ADS)

Langenberg, Marcel; Jackson, Nicholas E.; de Pablo, Juan J.; Müller, Marcus

2018-03-01

Coarse-grained models of polymer and biomolecular systems have enabled the computational study of cooperative phenomena, e.g., self-assembly, by lumping multiple atomistic degrees of freedom along the backbone of a polymer, lipid, or DNA molecule into one effective coarse-grained interaction center. Such a coarse-graining strategy leaves the number of molecules unaltered. In order to treat the surrounding solvent or counterions on the same coarse-grained level of description, one can also stochastically group several of those small molecules into an effective, coarse-grained solvent bead or "fluid element." Such a procedure reduces the number of molecules, and we discuss how to compensate the concomitant loss of translational entropy by density-dependent interactions in spatially inhomogeneous systems.

Enthalpy characteristics of L-proline dissolution in certain water-organic mixtures at 298.15 K

NASA Astrophysics Data System (ADS)

Badelin, V. G.; Smirnov, V. I.

2017-01-01

A thermochemical study of the processes of L-proline dissolution in aqueous solutions of acetonitrile, 1,4-dioxane, acetone, dimethyl sulfoxide, nitromethane and tetrahydrofuran at T = 298.15 K in the range of organic solvent concentrations x2 = 0-0.25 mole fractions is performed. Standard values of the enthalpies of solution and transfer of L-proline from water to mixed solvent, and the enthalpy coefficients of pairwise interactions between L-proline and molecules of organic solvents, are calculated. The effect the composition of a water-organic mixture and the structure of organic solvents have on the enthalpy characteristics of L-proline dissolution and transfer is examined. The effect the energy properties of intermolecular interactions between components of a mixed solvent has on the intermolecular interactions between L-proline and molecules of cosolvent is estimated. The correlation between the enthalpy characteristics of L-proline dissolution and electron-donor properties of organic cosolvent in aqueous solutions is determined.

Positionally isomeric organic gelators: structure-gelation study, racemic versus enantiomeric gelators, and solvation effects.

PubMed

Caplar, Vesna; Frkanec, Leo; Sijaković Vujicić, Natasa; Zinić, Mladen

2010-03-08

Low molecular weight gelator molecules consisting of aliphatic acid, amino acid (phenylglycine), and omega-aminoaliphatic acid units have been designed. By varying the number of methylene units in the aliphatic and omega-aminoaliphatic acid chains, as defined by descriptors m and n, respectively, a series of positionally isomeric gelators having different positions of the peptidic hydrogen-bonding unit within the gelator molecule has been obtained. The gelation properties of the positional isomers have been determined in relation to a defined set of twenty solvents of different structure and polarity and analyzed in terms of gelator versatility (G(ver)) and effectiveness (G(eff)). The results of gelation tests have shown that simple synthetic optimizations of a "lead gelator molecule" by variation of m and n, end-group polarity (carboxylic acid versus sodium carboxylate), and stereochemistry (racemate versus optically pure form) allowed the identification of gelators with tremendously improved versatility (G(ver)) and effectiveness (G(eff)). Dramatic differences in G(eff) values of up to 70 times could be observed between pure racemate/enantiomer pairs of some gelators, which were manifested even in the gelation of very similar solvents such as isomeric xylenes. The combined results of spectroscopic ((1)H NMR, FTIR), electron microscopy (TEM), and X-ray diffraction studies suggest similar organization of the positionally isomeric gelators at the molecular level, comprising parallel beta-sheet hydrogen-bonded primary assemblies that form inversed bilayers at a higher organizational level. Differential scanning calorimetry (DSC) studies of selected enantiomer/racemate gelator pairs and their o- and p-xylene gels revealed the simultaneous presence of different polymorphs in the racemate gels. The increased gelation effectiveness of the racemate compared to that of the single enantiomer is most likely a consequence of its spontaneous resolution into enantiomeric bilayers and their subsequent organization into polymorphic aggregates of different energy. The latter determine the gel fiber thickness and solvent immobilization capacity of the formed gel network.

Microscopic solvent structure of subcritical and supercritical methanol from ultraviolet/visible absorption and fluorescence spectroscopies

NASA Astrophysics Data System (ADS)

Bulgarevich, Dmitry S.; Sako, Takeshi; Sugeta, Tsutomu; Otake, Katsuto; Takebayashi, Yoshihiro; Kamizawa, Chiyoshi; Uesugi, Masayuki; Kato, Masahiro

1999-09-01

Ultraviolet/visible absorption and fluorescence spectroscopies at different temperatures and pressures were applied to investigate the microscopic solvent structures of subcritical and supercritical methanol using 4-nitroanisole, ethyl-(4-dimethylamino)benzoate, Reichardt's dye, and anthracene as the probe molecules. It was found that at temperatures higher than 150 °C the long winding chains of sequentially hydrogen-bonded methanol molecules were probably broken, but the small hydrogen-bonded aggregates possibly existed in methanol even at higher temperature. It was also found that the solvation process of the anthracene molecule in the S0-ground state obeyed the Langmuir adsorption model. However, in the case of fluorescence measurements in supercritical methanol, we detected deviations from the simple Langmuir adsorption model. These deviations were explained in terms of preferential solvation of the solvent molecules around photoexcited anthracene. Judging from the experimental results, it was concluded that the local density augmentation of the supercritical methanol around the nonpolar solute was a short-ranged effect, which did not correspond directly to the large isothermal compressibility of fluid near the critical point.

Direct numerical solution of the Ornstein-Zernike integral equation and spatial distribution of water around hydrophobic molecules

NASA Astrophysics Data System (ADS)

Ikeguchi, Mitsunori; Doi, Junta

1995-09-01

The Ornstein-Zernike integral equation (OZ equation) has been used to evaluate the distribution function of solvents around solutes, but its numerical solution is difficult for molecules with a complicated shape. This paper proposes a numerical method to directly solve the OZ equation by introducing the 3D lattice. The method employs no approximation the reference interaction site model (RISM) equation employed. The method enables one to obtain the spatial distribution of spherical solvents around solutes with an arbitrary shape. Numerical accuracy is sufficient when the grid-spacing is less than 0.5 Å for solvent water. The spatial water distribution around a propane molecule is demonstrated as an example of a nonspherical hydrophobic molecule using iso-value surfaces. The water model proposed by Pratt and Chandler is used. The distribution agrees with the molecular dynamics simulation. The distribution increases offshore molecular concavities. The spatial distribution of water around 5α-cholest-2-ene (C27H46) is visualized using computer graphics techniques and a similar trend is observed.

Nanobubbles do not sit alone at the solid-liquid interface.

PubMed

Peng, Hong; Hampton, Marc A; Nguyen, Anh V

2013-05-21

The unexpected stability and anomalous contact angle of gaseous nanobubbles at the hydrophobic solid-liquid interface has been an issue of debate for almost two decades. In this work silicon-nitride tipped AFM cantilevers are used to probe the highly ordered pyrolytic graphite (HOPG)-water interface with and without solvent-exchange (a common nanobubble production method). Without solvent-exchange the force obtained by the single force and force mapping techniques is consistent over the HOPG atomic layers and described by DLVO theory (strong EDL repulsion). With solvent-exchange the force is non-DLVO (no EDL repulsion) and the range of the attractive jump-in (>10 nm) over the surface is grouped into circular areas of longer range, consistent with nanobubbles, and the area of shorter range. The non-DLVO nature of the area between nanobubbles suggests that the interaction is no longer between a silicon-nitride tip and HOPG. Interfacial gas enrichment (IGE) covering the entire area between nanobubbles is suggested to be responsible for the non-DLVO forces. The absence of EDL repulsion suggests that both IGE and nanobubbles are not charged. The coexistence of nanobubbles and IGE provides further evidence of nanobubble stability by dynamic equilibrium. The IGE cannot be removed by contact mode scanning of a cantilever tip in pure water, but in a surfactant (SDS) solution the mechanical action of the tip and the chemical action of the surfactant molecules can successfully remove the enrichment. Strong EDL repulsion between the tip and nanobubbles/IGE in surfactant solutions is due to the polar heads of the adsorbed surfactant molecules.

Colored spectrum characteristics of thermal noise on the molecular scale.

PubMed

Zhu, Zhi; Sheng, Nan; Fang, Haiping; Wan, Rongzheng

2016-11-02

Thermal noise is of fundamental importance to many processes. Traditionally, thermal noise has been treated as white noise on the macroscopic scale. Using molecular dynamics simulations and power spectrum analysis, we show that the thermal noise of solute molecules in water is non-white on the molecular scale, which is in contrast to the conventional theory. In the frequency domain from 2 × 10 11 Hz to 10 13 Hz, the power spectrum of thermal noise for polar solute molecules resembles the spectrum of 1/f noise. The power spectrum of thermal noise for non-polar solute molecules deviates only slightly from the spectrum of white noise. The key to this phenomenon is the existence of hydrogen bonds between polar solute molecules and solvent water molecules. Furthermore, for polar solute molecules, the degree of power spectrum deviation from that of white noise is associated with the average lifetime of the hydrogen bonds between the solute and the solvent molecules.

N-[2-(2,2-Di-methyl-propanamido)-pyrimidin-4-yl]-2,2-di-methyl-propanamide n-hexane 0.25-solvate hemihydrate.

PubMed

Ośmiałowski, Borys; Valkonen, Arto; Chęcińska, Lilianna

2013-10-05

The asymmetric unit of the title compound, C14H22N4O2·0.25C6H14·0.5H2O, contains two independent mol-ecules of 2,4-bis-(pivaloyl-amino)-pyrimidine (M) with similar conformations, one water mol-ecule and one-half n-hexane solvent mol-ecule situated on an inversion center. In one independent M mol-ecule, one of the two tert-butyl groups is rotationally disordered between two orientations in a 3:2 ratio. The n-hexane solvent mol-ecule is disordered between two conformations in the same ratio. The water mol-ecule bridges two independent M mol-ecules via O-H⋯O, N-H⋯O and O-H⋯N hydrogen bonds into a 2M·H2O unit, and these units are further linked by N-H⋯N hydrogen bonds into chains running in the [010] direction. Weak C-H⋯O inter-actions are observed between the adjacent chains.

Conformation transitions of a single polyelectrolyte chain in a poor solvent: a replica-exchange lattice Monte-Carlo study.

PubMed

Wang, Lang; Wang, Zheng; Jiang, Run; Yin, Yuhua; Li, Baohui

2017-03-15

The thermodynamic behaviors of a strongly charged polyelectrolyte chain in a poor solvent are studied using replica-exchange Monte-Carlo simulations on a lattice model, focusing on the effects of finite chain length and the solvent quality on the chain conformation and conformation transitions. The neutralizing counterions and solvent molecules are considered explicitly. The thermodynamic quantities that vary continuously with temperature over a wide range are computed using the multiple histogram reweighting method. Our results suggest that the strength of the short-range hydrophobic interaction, the chain length, and the temperature of the system, characterized by ε, N, and T, respectively, are important parameters that control the conformations of a charged chain. When ε is moderate, the competition between the electrostatic energy and the short-range hydrophobic interaction leads to rich conformations and conformation transitions for a longer chain with a fixed length. Our results have unambiguously demonstrated the stability of the n-pearl-necklace structures, where n has a maximum value and decreases with decreasing temperature. The maximum n value increases with increasing chain length. Our results have also demonstrated the first-order nature of the conformation transitions between the m-pearl and the (m-1)-pearl necklaces. With the increase of ε, the transition temperature increases and the first-order feature becomes more pronounced. It is deduced that at the thermodynamic limit of infinitely long chain length, the conformational transitions between the m-pearl and the (m-1)-pearl necklaces may remain first order when ε > 0 and m = 2 or 3. Pearl-necklace conformations cannot be observed when either ε is too large or N is too small. To observe a pearl-necklace conformation, the T value needs to be carefully chosen for simulations performed at only a single temperature.

Solvent effect on FRET spectroscopic ruler

NASA Astrophysics Data System (ADS)

Qu, Songyuan; Liu, Chuanbo; Liu, Qiong; Wu, Wei; Du, Baoji; Wang, Jin

2018-03-01

A discrepancy has emerged in recent years between single-molecule Förster resonance energy transfer (smFRET) measurements and small angle X-ray scattering (SAXS) or small angle neutron scattering experiments in the study of unfolded or intrinsically disordered proteins in denaturing solutions. Despite significant advances that have been made in identifying various factors which may have contributed to the manifestation of the so-called smFRET-SAXS discrepancy, no consensus has been reached so far on its original source or eventual resolution. In this study, we investigate this problem from the perspective of the solvent effect on FRET spectroscopic ruler (SEFSR), a generic term we use to describe various solvent-dependent factors affecting the accuracy of the FRET experimental method that is known as a "spectroscopic ruler." Some factors belonging to SEFSR, such as direct dye-solvent interaction and labeling configuration, seem to have not received due attention regarding their significance in contributing to the discrepancy. We identify SEFSR by measuring a rigid segment of a double-stranded DNA in various solutions using the smFRET method and evaluate its relative importance in smFRET experiments by measuring segments of a single-stranded DNA and polyethylene glycol (PEG) in solutions. We find that SEFSR can produce non-negligible FRET-inferred interdye distance changes in various solutions, with an intensity following the Hofmeister series in ionic solutions and dependent on labeling configurations. SEFSR is found to be significant in GuHCl and urea solutions, which can fully cover the apparent expansion signal of dye-labeled PEG. Our findings suggest that SEFSR may have played an important role in contributing to the smFRET-SAXS discrepancy.

On-Surface Synthesis and Characterization of Honeycombene Oligophenylene Macrocycles.

PubMed

Chen, Min; Shang, Jian; Wang, Yongfeng; Wu, Kai; Kuttner, Julian; Hilt, Gerhard; Hieringer, Wolfgang; Gottfried, J Michael

2017-01-24

We report the on-surface formation and characterization of [30]-honeycombene, a cyclotriacontaphenylene, which consists of 30 phenyl rings (C 180 H 120 ) and has a diameter of 4.0 nm. This shape-persistent, conjugated, and unsubstituted hexagonal hydrocarbon macrocycle was obtained by solvent-free synthesis on a silver (111) single-crystal surface, making solubility-enhancing alkyl side groups unnecessary. Side products include strained macrocycles with square, pentagonal, and heptagonal shape. The molecules were characterized by scanning tunneling microscopy and density functional theory (DFT) calculations. On the Ag(111) surface, the macrocycles act as molecular quantum corrals and lead to the confinement of surface-state electrons inside the central cavity. The energy of the confined surface state correlates with the size of the macrocycle and is well described by a particle-in-the-box model. Tunneling spectroscopy suggests conjugation within the planar rings and reveals influences of self-assembly on the electronic structure. While the adsorbed molecules appear to be approximately planar, the free molecules have nonplanar conformation, according to DFT.

Tracking solvents in the skin through atomically resolved measurements of molecular mobility in intact stratum corneum

PubMed Central

Topgaard, Daniel; Sparr, Emma

2017-01-01

Solvents are commonly used in pharmaceutical and cosmetic formulations and sanitary products and cleansers. The uptake of solvent into the skin may change the molecular organization of skin lipids and proteins, which may in turn alter the protective skin barrier function. We herein examine the molecular effects of 10 different solvents on the outermost layer of skin, the stratum corneum (SC), using polarization transfer solid-state NMR on natural abundance 13C in intact SC. With this approach it is possible to characterize the molecular dynamics of solvent molecules when present inside intact SC and to simultaneously monitor the effects caused by the added solvent on SC lipids and protein components. All solvents investigated cause an increased fluidity of SC lipids, with the most prominent effects shown for the apolar hydrocarbon solvents and 2-propanol. However, no solvent other than water shows the ability to fluidize amino acids in the keratin filaments. The solvent molecules themselves show reduced molecular mobility when incorporated in the SC matrix. Changes in the molecular properties of the SC, and in particular alternation in the balance between solid and fluid SC components, may have significant influences on the macroscopic SC barrier properties as well as mechanical properties of the skin. Deepened understanding of molecular effects of foreign compounds in SC fluidity can therefore have strong impact on the development of skin products in pharmaceutical, cosmetic, and sanitary applications. PMID:28028209

Crystal engineering of ibuprofen compounds: From molecule to crystal structure to morphology prediction by computational simulation and experimental study

NASA Astrophysics Data System (ADS)

Zhang, Min; Liang, Zuozhong; Wu, Fei; Chen, Jian-Feng; Xue, Chunyu; Zhao, Hong

2017-06-01

We selected the crystal structures of ibuprofen with seven common space groups (Cc, P21/c, P212121, P21, Pbca, Pna21, and Pbcn), which was generated from ibuprofen molecule by molecular simulation. The predicted crystal structures of ibuprofen with space group P21/c has the lowest total energy and the largest density, which is nearly indistinguishable with experimental result. In addition, the XRD patterns for predicted crystal structure are highly consistent with recrystallization from solvent of ibuprofen. That indicates that the simulation can accurately predict the crystal structure of ibuprofen from the molecule. Furthermore, based on this crystal structure, we predicted the crystal habit in vacuum using the attachment energy (AE) method and considered solvent effects in a systematic way using the modified attachment energy (MAE) model. The simulation can accurately construct a complete process from molecule to crystal structure to morphology prediction. Experimentally, we observed crystal morphologies in four different polarity solvents compounds (ethanol, acetonitrile, ethyl acetate, and toluene). We found that the aspect ratio decreases of crystal habits in this ibuprofen system were found to vary with increasing solvent relative polarity. Besides, the modified crystal morphologies are in good agreement with the observed experimental morphologies. Finally, this work may guide computer-aided design of the desirable crystal morphology.

Laser Raman spectroscopy of the effect of solvent on the low-frequency oscillations of organic molecules

NASA Astrophysics Data System (ADS)

Brandt, N. N.; Chikishev, A. Yu.; Dolgovskii, V. I.; Lebedenko, S. I.

2007-09-01

The effect of solvent on low-frequency oscillations is studied using an example of the 1,1,2,2-tetrachloroethane (TCE) and 1,1,2,2-tetrabromoethane (TBE) molecules, which exhibit torsional oscillations in the terahertz range. Dimethylsulfoxide (DMSO) and carbon tetrachloride (CTC) are used as solvents. It is demonstrated that a decrease in the concentration of the substance under study in the TBE/CTC, TCE/DMSO, and TCE/CTC mixtures leads to a frequency shift of the low-frequency oscillation. The shift is not observed in the TBE/DMSO mixture but a decrease in the TBE concentration causes significant broadening of the low-frequency line.

Opportunities for Bio-Based Solvents Created as Petrochemical and Fuel Products Transition towards Renewable Resources

PubMed Central

Clark, James H.; Farmer, Thomas J.; Hunt, Andrew J.; Sherwood, James

2015-01-01

The global bio-based chemical market is growing in size and importance. Bio-based solvents such as glycerol and 2-methyltetrahydrofuran are often discussed as important introductions to the conventional repertoire of solvents. However adoption of new innovations by industry is typically slow. Therefore it might be anticipated that neoteric solvent systems (e.g., ionic liquids) will remain niche, while renewable routes to historically established solvents will continue to grow in importance. This review discusses bio-based solvents from the perspective of their production, identifying suitable feedstocks, platform molecules, and relevant product streams for the sustainable manufacturing of conventional solvents. PMID:26225963

Opportunities for Bio-Based Solvents Created as Petrochemical and Fuel Products Transition towards Renewable Resources.

PubMed

Clark, James H; Farmer, Thomas J; Hunt, Andrew J; Sherwood, James

2015-07-28

The global bio-based chemical market is growing in size and importance. Bio-based solvents such as glycerol and 2-methyltetrahydrofuran are often discussed as important introductions to the conventional repertoire of solvents. However adoption of new innovations by industry is typically slow. Therefore it might be anticipated that neoteric solvent systems (e.g., ionic liquids) will remain niche, while renewable routes to historically established solvents will continue to grow in importance. This review discusses bio-based solvents from the perspective of their production, identifying suitable feedstocks, platform molecules, and relevant product streams for the sustainable manufacturing of conventional solvents.

SOLVENT EXTRACTION OF URANIUM VALUES

DOEpatents

Feder, H.M.; Ader, M.; Ross, L.E.

1959-02-01

A process is presented for extracting uranium salt from aqueous acidic solutions by organic solvent extraction. It consists in contacting the uranium bearing solution with a water immiscible dialkylacetamide having at least 8 carbon atoms in the molecule. Mentioned as a preferred extractant is dibutylacetamide. The organic solvent is usually used with a diluent such as kerosene or CCl/sub 4/.

An RF-Powered Micro-Reactor for Efficient Extraction and Hydrolysis

NASA Astrophysics Data System (ADS)

Scott, V.

2014-12-01

An RF sample-processing micro-reactor that was developed as part of potential in situ Exploration Missions to inner- and outer-planetary bodies was designed to utilize aqueous solutions subjected to 60 GHz radiation at 730 mW of input power to extract target organic compounds and molecular and inorganic ions as well as to hydrolyze complex polymeric materials. Successful identification and characterization of these molecules relies on the sample-processing techniques utilized alongside state-of-the-art detection and analysis. For mass and power restrictions put on space exploration missions, smaller and more efficient instruments are highly desirable. The RF micro-reactor potentially offers a simplified alternative to the typical gold-standard extractions that often use solvents, chemicals, and conditions that can vary wildly and depend on the targeted molecules. Instead, this instrument uses a single solvent ­— water — that can be "tuned" under the different experimental conditions, leveraging the operating principles of the Sub-Critical Water Extractor. Proof-of-concept experiments examining the hydrolysis of glycosidic and peptide bonds were successful in demonstrating the RF micro-reactor's capabilities. Progress toward coupling the reactor with a micro-scale sample-handling system enabling slurry delivery has been made and preliminary results on heterogeneous reactions and extractions will be presented.

Lipase in aqueous-polar organic solvents: Activity, structure, and stability

PubMed Central

Kamal, Md Zahid; Yedavalli, Poornima; Deshmukh, Mandar V; Rao, Nalam Madhusudhana

2013-01-01

Studying alterations in biophysical and biochemical behavior of enzymes in the presence of organic solvents and the underlying cause(s) has important implications in biotechnology. We investigated the effects of aqueous solutions of polar organic solvents on ester hydrolytic activity, structure and stability of a lipase. Relative activity of the lipase monotonically decreased with increasing concentration of acetone, acetonitrile, and DMF but increased at lower concentrations (upto ∼20% v/v) of dimethylsulfoxide, isopropanol, and methanol. None of the organic solvents caused any appreciable structural change as evident from circular dichorism and NMR studies, thus do not support any significant role of enzyme denaturation in activity change. Change in 2D [15N, 1H]-HSQC chemical shifts suggested that all the organic solvents preferentially localize to a hydrophobic patch in the active-site vicinity and no chemical shift perturbation was observed for residues present in protein's core. This suggests that activity alteration might be directly linked to change in active site environment only. All organic solvents decreased the apparent binding of substrate to the enzyme (increased Km); however significantly enhanced the kcat. Melting temperature (Tm) of lipase, measured by circular dichroism and differential scanning calorimetry, altered in all solvents, albeit to a variable extent. Interestingly, although the effect of all organic solvents on various properties on lipase is qualitatively similar, our study suggest that magnitudes of effects do not appear to follow bulk solvent properties like polarity and the solvent effects are apparently dictated by specific and local interactions of solvent molecule(s) with the protein. PMID:23625694

Modified two-step emulsion solvent evaporation technique for fabricating biodegradable rod-shaped particles in the submicron size range.

PubMed

Safari, Hanieh; Adili, Reheman; Holinstat, Michael; Eniola-Adefeso, Omolola

2018-05-15

Though the emulsion solvent evaporation (ESE) technique has been previously modified to produce rod-shaped particles, it cannot generate small-sized rods for drug delivery applications due to the inherent coupling and contradicting requirements for the formation versus stretching of droplets. The separation of the droplet formation from the stretching step should enable the creation of submicron droplets that are then stretched in the second stage by manipulation of the system viscosity along with the surface-active molecule and oil-phase solvent. A two-step ESE protocol is evaluated where oil droplets are formed at low viscosity followed by a step increase in the aqueous phase viscosity to stretch droplets. Different surface-active molecules and oil phase solvents were evaluated to optimize the yield of biodegradable PLGA rods. Rods were assessed for drug loading via an imaging agent and vascular-targeted delivery application via blood flow adhesion assays. The two-step ESE method generated PLGA rods with major and minor axis down to 3.2 µm and 700 nm, respectively. Chloroform and sodium metaphosphate was the optimal solvent and surface-active molecule, respectively, for submicron rod fabrication. Rods demonstrated faster release of Nile Red compared to spheres and successfully targeted an inflamed endothelium under shear flow in vitro and in vivo. Copyright © 2018 Elsevier Inc. All rights reserved.

Theoretical evidence of charge transfer interaction between SO₂ and deep eutectic solvents formed by choline chloride and glycerol.

PubMed

Li, Hongping; Chang, Yonghui; Zhu, Wenshuai; Wang, Changwei; Wang, Chao; Yin, Sheng; Zhang, Ming; Li, Huaming

2015-11-21

The nature of the interaction between deep eutectic solvents (DESs), formed by ChCl and glycerol, and SO2 has been systematically investigated using the M06-2X density functional combined with cluster models. Block-localized wave function energy decomposition (BLW-ED) analysis shows that the interaction between SO2 and DESs is dominated by a charge transfer interaction. After this interaction, the SO2 molecule becomes negatively charged, whereas the ChCl-glycerol molecule is positively charged, which is the result of Lewis acid-base interaction. The current result affords a theoretical proof that it is highly useful and efficient to manipulate the Lewis acidity of absorbents for SO2 capture. Moreover, hydrogen bonding as well as electrostatic interactions may also contribute to the stability of the complex. Structure analysis shows that solvent molecules will adjust their geometries to interact with SO2. In addition, the structure of SO2 is barely changed after interaction. The interaction energy between different cluster models and SO2 ranges from -6.8 to -14.4 kcal mol(-1). It is found that the interaction energy is very sensitive to the solvent structure. The moderate interaction between ChCl-glycerol and SO2 is consistent with the concept that highly efficient solvents for SO2 absorption should not only be solvable but also regenerable.

Electronic excitation of molecules in solution calculated using the symmetry-adapted cluster–configuration interaction method in the polarizable continuum model

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

Fukuda, Ryoichi, E-mail: fukuda@ims.ac.jp; Ehara, Masahiro; Elements Strategy Initiative for Catalysts and Batteries

2015-12-31

The effects from solvent environment are specific to the electronic states; therefore, a computational scheme for solvent effects consistent with the electronic states is necessary to discuss electronic excitation of molecules in solution. The PCM (polarizable continuum model) SAC (symmetry-adapted cluster) and SAC-CI (configuration interaction) methods are developed for such purposes. The PCM SAC-CI adopts the state-specific (SS) solvation scheme where solvent effects are self-consistently considered for every ground and excited states. For efficient computations of many excited states, we develop a perturbative approximation for the PCM SAC-CI method, which is called corrected linear response (cLR) scheme. Our test calculationsmore » show that the cLR PCM SAC-CI is a very good approximation of the SS PCM SAC-CI method for polar and nonpolar solvents.« less

An adaptive quantum mechanics/molecular mechanics method for the infrared spectrum of water: incorporation of the quantum effect between solute and solvent.

PubMed

Watanabe, Hiroshi C; Banno, Misa; Sakurai, Minoru

2016-03-14

Quantum effects in solute-solvent interactions, such as the many-body effect and the dipole-induced dipole, are known to be critical factors influencing the infrared spectra of species in the liquid phase. For accurate spectrum evaluation, the surrounding solvent molecules, in addition to the solute of interest, should be treated using a quantum mechanical method. However, conventional quantum mechanics/molecular mechanics (QM/MM) methods cannot handle free QM solvent molecules during molecular dynamics (MD) simulation because of the diffusion problem. To deal with this problem, we have previously proposed an adaptive QM/MM "size-consistent multipartitioning (SCMP) method". In the present study, as the first application of the SCMP method, we demonstrate the reproduction of the infrared spectrum of liquid-phase water, and evaluate the quantum effect in comparison with conventional QM/MM simulations.

Columnar to nematic mesophase transition in mixtures of rhodium or copper soaps with hydrocarbon solvents

NASA Astrophysics Data System (ADS)

Ibn-Elhaj, M.; Guillon, D.; Skoulios, A.; Giroud-Godquin, A. M.; Marchon, J.-C.

1992-12-01

This paper describes observations of the mesomorphic behaviour of mixtures of rhodium eicosanoate or copper dodecanoate with solvents such as toluene, decahydronaphthalene, and (+) camphene. The mesophase found with these compounds at high temperatures turns from columnar to nematic when the weight fraction of the solvent (toluene, decahydronaphthalene is increased beyond a value of about 50%. The binary phase diagram of the copper compound with toluene was experimentally determined using polarizing optical microscopy, differential scanning calorimetry and X-ray diffraction. The novel feature of the nematic phase is that the basic physical object which align parallel to the nematic director are not individual molecules, but columns of molecules (one-dimensional supramolecular assemblies) which have lost the long-range lateral positional order characteristic of the columnar mesophase. These observations are discussed on the grounds of recent theoretical calculations. Cholesteric-like textures are observed for mixtures of rhodium eicosanoate with the chiral solvent (+) camphene.

Boost the electron mobility of solution-grown organic single crystals via reducing the amount of polar solvent residues

DOE PAGES

Xue, Guobiao; Xin, Huolin L.; Wu, Jiake; ...

2015-10-29

Enhancing electron transport to match with the development in hole transport is critical for organic electronics in the future. As electron motion is susceptible to extrinsic factors, seeking these factors and avoiding their negative effects have become the central challenge. Here, the existence of polar solvent residues in solution-grown single-crystals of 6,13-bis(triisopropylsilylethynyl)-5,7,12,14-tetraazapentacene is identified as a factor detrimental to electron motion. Field-effect transistors of the crystals exhibit electron mobility boosted by about 60% after the residues are removed. The average electron mobility reaches up to 8.0 ± 2.2 cm 2 V –1 s –1 with a highest value of 13.3more » cm 2 V –1 s –1; these results are significantly higher than those obtained previously for the same molecule (1.0–5.0 cm 2 V –1 s –1). Furthermore, the achieved mobility is also higher than the maximum reported electron mobility for organic materials (11 cm 2 V –1 s –1). As a result, this work should greatly accelerate the advancement of organic electron-transporting materials.« less

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.

How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?

PubMed

Šponer, Jiří; Krepl, Miroslav; Banáš, Pavel; Kührová, Petra; Zgarbová, Marie; Jurečka, Petr; Havrila, Marek; Otyepka, Michal

2017-05-01

We provide a critical assessment of explicit-solvent atomistic molecular dynamics (MD) simulations of RNA and protein/RNA complexes, written primarily for non-specialists with an emphasis to explain the limitations of MD. MD simulations can be likened to hypothetical single-molecule experiments starting from single atomistic conformations and investigating genuine thermal sampling of the biomolecules. The main advantage of MD is the unlimited temporal and spatial resolution of positions of all atoms in the simulated systems. Fundamental limitations are the short physical time-scale of simulations, which can be partially alleviated by enhanced-sampling techniques, and the highly approximate atomistic force fields describing the simulated molecules. The applicability and present limitations of MD are demonstrated on studies of tetranucleotides, tetraloops, ribozymes, riboswitches and protein/RNA complexes. Wisely applied simulations respecting the approximations of the model can successfully complement structural and biochemical experiments. WIREs RNA 2017, 8:e1405. doi: 10.1002/wrna.1405 For further resources related to this article, please visit the WIREs website. © 2016 Wiley Periodicals, Inc.

Metal Cationization Extractive Electrospray Ionization Mass Spectrometry of Compounds Containing Multiple Oxygens

NASA Astrophysics Data System (ADS)

Swanson, Kenneth D.; Spencer, Sandra E.; Glish, Gary L.

2017-06-01

Extractive electrospray ionization is an ambient ionization technique that allows real-time sampling of liquid samples, including organic aerosols. Similar to electrospray ionization, the composition of the electrospray solvent used in extractive electrospray ionization can easily be altered to form metal cationized molecules during ionization simply by adding a metal salt to the electrospray solvent. An increase in sensitivity is observed for some molecules that are lithium, sodium, or silver cationized compared with the protonated molecule formed in extractive electrospray ionization with an acid additive. Tandem mass spectrometry of metal cationized molecules can also significantly improve the ability to identify a compound. Tandem mass spectrometry of lithium and silver cationized molecules can result in an increase in the number and uniqueness of dissociation pathways relative to [M + H]+. These results highlight the potential for extractive electrospray ionization with metal cationization in analyzing complex aerosol mixtures. [Figure not available: see fulltext.

Unravelling the mechanisms of vibrational relaxation in solution† †All experimental data are archived in the University of Bristol's Research Data Storage Facility (DOI: 10.5523/bris.2vk036f35m5aq2dnlb79c0wcsh). ‡ ‡Electronic supplementary information (ESI) available: Further discussion of spectral lineshapes, concentration dependence of transient absorption data, theoretical calculations, IR-pump IR-probe spectra, transient absorption spectra including animation of spectra. See DOI: 10.1039/c6sc05234g Click here for additional data file. Click here for additional data file.

PubMed Central

Grubb, Michael P.; Coulter, Philip M.; Marroux, Hugo J. B.

2017-01-01

We present a systematic study of the mode-specific vibrational relaxation of NO2 in six weakly-interacting solvents (perfluorohexane, perfluoromethylcyclohexane, perfluorodecalin, carbon tetrachloride, chloroform, and d-chloroform), chosen to elucidate the dominant energy transfer mechanisms in the solution phase. Broadband transient vibrational absorption spectroscopy has allowed us to extract quantum state-resolved relaxation dynamics of the two distinct NO2 fragments produced from the 340 nm photolysis of N2O4 → NO2(X) + NO2(A) and their separate paths to thermal equilibrium. Distinct relaxation pathways are observed for the NO2 bending and stretching modes, even at energies as high as 7000 cm–1 above the potential minimum. Vibrational energy transfer is governed by different interaction mechanisms in the various solvent environments, and proceeds with timescales ranging from 20–1100 ps. NO2 relaxation rates in the perfluorocarbon solvents are identical despite differences in acceptor mode state densities, infrared absorption cross sections, and local solvent structure. Vibrational energy is shown to be transferred to non-vibrational solvent degrees of freedom (V-T) through impulsive collisions with the perfluorocarbon molecules. Conversely, NO2 relaxation in chlorinated solvents is reliant on vibrational resonances (V-V) while V-T energy transfer is inefficient and thermal excitation of the surrounding solvent molecules inhibits faster vibrational relaxation through direct complexation. Intramolecular vibrational redistribution allows the symmetric stretch of NO2 to act as a gateway for antisymmetric stretch energy to exit the molecule. This study establishes an unprecedented level of detail for the cooling dynamics of a solvated small molecule, and provides a benchmark system for future theoretical studies of vibrational relaxation processes in solution. PMID:28451375

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.

Solvent jet desorption capillary photoionization-mass spectrometry.

PubMed

Haapala, Markus; Teppo, Jaakko; Ollikainen, Elisa; Kiiski, Iiro; Vaikkinen, Anu; Kauppila, Tiina J; Kostiainen, Risto

2015-03-17

A new ambient mass spectrometry method, solvent jet desorption capillary photoionization (DCPI), is described. The method uses a solvent jet generated by a coaxial nebulizer operated at ambient conditions with nitrogen as nebulizer gas. The solvent jet is directed onto a sample surface, from which analytes are extracted into the solvent and ejected from the surface in secondary droplets formed in collisions between the jet and the sample surface. The secondary droplets are directed into the heated capillary photoionization (CPI) device, where the droplets are vaporized and the gaseous analytes are ionized by 10 eV photons generated by a vacuum ultraviolet (VUV) krypton discharge lamp. As the CPI device is directly connected to the extended capillary inlet of the MS, high ion transfer efficiency to the vacuum of MS is achieved. The solvent jet DCPI provides several advantages: high sensitivity for nonpolar and polar compounds with limit of detection down to low fmol levels, capability of analyzing small and large molecules, and good spatial resolution (250 μm). Two ionization mechanisms are involved in DCPI: atmospheric pressure photoionization, capable of ionizing polar and nonpolar compounds, and solvent assisted inlet ionization capable of ionizing larger molecules like peptides. The feasibility of DCPI was successfully tested in the analysis of polar and nonpolar compounds in sage leaves and chili pepper.

The solvent dependent shift of the amide I band of a fully solvated peptide in methanol/water mixtures as a local probe for the solvent composition in the peptide/solvent interface

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

Gnanakaran, S

2008-01-01

We determine the shift and line-shape of the amide I band of a model AK-peptide from molecular dynamics (MD) simulations of the peptide dissolved in methanol/water mixtures with varying composition. The IR-spectra are determined from a transition dipole coupling exciton model. A simplified empirical model Hamiltonian is employed, taking both the effect of hydrogen bonding, as well as intramolecular vibrational coupling into account. We consider a single isolated AK-peptide in a mostly helical conformation, while the solvent is represented by 2600 methanol or water molecules, simulated for a pressure of 1 bar and a temperature of 300 K. Over themore » course of the simulations minor reversible conformational changes at the termini are observed, which are found to only slightly affect the calculated spectral properties. Over the entire composition range, varying from pure water to the pure methanol solvent, a monotonous blue-shift of the IR amide I band of about 8 wavenumbers is observed. The shift is found to be caused by two counter-compensating effects: An intramolecular red-shift of about 1.2 wavenumbers, due to stronger intramolecular hydrogen-bonding in a methanol-rich environment. Dominating, however, is the intermolecular solvent-dependent blue-shift of about 10 wavenumbers, being attributed to the less effective hydrogen bond donor capabilities of methanol compared to water. The importance of solvent-contribution to the IR-shift, as well as the significantly different hydrogen formation capabilities of water and methanol make the amide I band sensitive to composition changes in the local environment close the peptide/solvent interface. This allows, in principle, an experimental determination of the composition of the solvent in close proximity to the peptide surface. For the AK-peptide case they observe at low methanol concentrations a significantly enhanced methanol concentration at the peptide/solvent-interface, supposedly promoted by the partially hydrophobic character of the AK-peptide's solvent accessible surface.« less

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

Two-step adsorption on jungle-gym-type porous coordination polymers: dependence on hydrogen-bonding capability of adsorbates, ligand-substituent effect, and temperature.

PubMed

Uemura, Kazuhiro; Yamasaki, Yukari; Onishi, Fumiaki; Kita, Hidetoshi; Ebihara, Masahiro

2010-11-01

A preliminary study of isopropanol (IPA) adsorption/desorption isotherms on a jungle-gym-type porous coordination polymer, [Zn(2)(bdc)(2)(dabco)](n) (1, H(2)bdc = 1,4-benzenedicarboxylic acid, dabco =1,4-diazabicyclo[2.2.2]octane), showed unambiguous two-step profiles via a highly shrunk intermediate framework. The results of adsorption measurements on 1, using probing gas molecules of alcohol (MeOH and EtOH) for the size effect and Me(2)CO for the influence of hydrogen bonding, show that alcohol adsorption isotherms are gradual two-step profiles, whereas the Me(2)CO isotherm is a typical type-I isotherm, indicating that a two-step adsorption/desorption is involved with hydrogen bonds. To further clarify these characteristic adsorption/desorption behaviors, selecting nitroterephthalate (bdc-NO(2)), bromoterephthalate (bdc-Br), and 2,5-dichloroterephthalate (bdc-Cl(2)) as substituted dicarboxylate ligands, isomorphous jungle-gym-type porous coordination polymers, {[Zn(2)(bdc-NO(2))(2)(dabco)]·solvents}(n) (2 ⊃ solvents), {[Zn(2)(bdc-Br)(2)(dabco)]·solvents}(n) (3 ⊃ solvents), and {[Zn(2)(bdc-Cl(2))(2)(dabco)]·solvents}(n) (4 ⊃ solvents), were synthesized and characterized by single-crystal X-ray analyses. Thermal gravimetry, X-ray powder diffraction, and N(2) adsorption at 77 K measurements reveal that [Zn(2)(bdc-NO(2))(2)(dabco)](n) (2), [Zn(2)(bdc-Br)(2)(dabco)](n) (3), and [Zn(2)(bdc-Cl(2))(2)(dabco)](n) (4) maintain their frameworks without guest molecules with Brunauer-Emmett-Teller (BET) surface areas of 1568 (2), 1292 (3), and 1216 (4) m(2) g(-1). As found in results of MeOH, EtOH, IPA, and Me(2)CO adsorption/desorption on 2-4, only MeOH adsorption on 2 shows an obvious two-step profile. Considering the substituent effects and adsorbate sizes, the hydrogen bonds, which are triggers for two-step adsorption, are formed between adsorbates and carboxylate groups at the corners in the pores, inducing wide pores to become narrow pores. Interestingly, such a two-step MeOH adsorption on 2 depends on the temperature, attributed to the small free-energy difference (ΔF(host)) between the two guest-free forms, wide and narrow pores.

Single Molecule Spectroelectrochemistry of Interfacial Charge Transfer Dynamics In Hybrid Organic Solar Cell

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

Pan, Shanlin

2014-11-16

Our research under support of this DOE grant is focused on applied and fundamental aspects of model organic solar cell systems. Major accomplishments are: 1) we developed a spectroelectorchemistry technique of single molecule single nanoparticle method to study charge transfer between conjugated polymers and semiconductor at the single molecule level. The fluorescence of individual fluorescent polymers at semiconductor surfaces was shown to exhibit blinking behavior compared to molecules on glass substrates. Single molecule fluorescence excitation anisotropy measurements showed the conformation of the polymer molecules did not differ appreciably between glass and semiconductor substrates. The similarities in molecular conformation suggest thatmore » the observed differences in blinking activity are due to charge transfer between fluorescent polymer and semiconductor, which provides additional pathways between states of high and low fluorescence quantum efficiency. Similar spectroelectrochemistry work has been done for small organic dyes for understand their charge transfer dynamics on various substrates and electrochemical environments; 2) We developed a method of transferring semiconductor nanoparticles (NPs) and graphene oxide (GO) nanosheets into organic solvent for a potential electron acceptor in bulk heterojunction organic solar cells which employed polymer semiconductor as the electron donor. Electron transfer from the polymer semiconductor to semiconductor and GO in solutions and thin films was established through fluorescence spectroscopy and electroluminescence measurements. Solar cells containing these materials were constructed and evaluated using transient absorption spectroscopy and dynamic fluorescence techniques to understand the charge carrier generation and recombination events; 3) We invented a spectroelectorchemistry technique using light scattering and electroluminescence for rapid size determination and studying electrochemistry of single NPs in an electrochemical cell. For example, we are able to use this technique to track electroluminescence of single Au NPs, and the electrodeposition of individual Ag NPs in-situ. These metallic NPs are useful to enhance light harvesting in organic photovoltaic systems. The scattering at the surface of an indium tin oxide (ITO) working electrode was measured during a potential sweep. Utilizing Mie scattering theory and high resolution scanning electron microscopy (SEM), the scattering data were used to calculate current-potential curves depicting the electrodeposition of individual Ag NPs. The oxidation of individual presynthesized and electrodeposited Ag NPs was also investigated using fluorescence and DFS microscopies. Our work has produced 1 US provisional patent, 15 published manuscripts, 1 submitted and two additional in-writing manuscripts. 5 graduate students, 1 postdoctoral student, 1 visiting professor, and two undergraduate students have received research training in the area of electrochemistry and optical spectroscopy under support of this award.« less

Effect of molecular side groups and local nanoenvironment on photodegradation and its reversibility

NASA Astrophysics Data System (ADS)

Quist, Nicole; Li, Mark; Tollefsen, Ryan; Haley, Michael; Anthony, John; Ostroverkhova, Oksana

2018-02-01

Degradation of organic semiconductors in the presence of oxygen is one of the bottlenecks preventing their wide-spread use in optoelectronic devices. The first step towards such degradation in functionalized pentacene (Pn) derivatives is formation of endoperoxide (EPO), which can either revert back to the parent molecule or proceed to molecule decomposition. We present the study of reversibility of EPO formation through probing the photophysical properties of functionalized fluorinated pentacene (Pn-R-F8) derivatives. Experiments are done in solutions and in films both at the single molecule level and in the bulk. In solutions, degradation of optical absorption and its partial recovery after thermolysis were quantified for various derivatives depending on the solvent. At the single molecule level, low concentrations of each type of molecules were imaged in a variety of polymer matrices at 633 nm excitation at room temperature in air using wide-field fluorescence microscopy. Fluorescence time trajectories were collected and statistically analyzed to quantify blinking due to reversible EPO formation depending on the host matrix. To understand the physical changes of the molecular system, a Monte Carlo method was used to create a multi-level simulation, which enabled us to relate the change in the molecular transition rates to the experimentally measured parameters. At the bulk level, photoluminescence decay due to photobleaching and recovery due to EPO reconversion were measured for the same derivatives incorporated into various matrices. These studies provide insight into the synergistic effect of the local nanoenvironment and molecular side groups on the oxygen-related degradation and subsequent recovery which is important for development of organic electronic devices.

Efficient molecular density functional theory using generalized spherical harmonics expansions.

PubMed

Ding, Lu; Levesque, Maximilien; Borgis, Daniel; Belloni, Luc

2017-09-07

We show that generalized spherical harmonics are well suited for representing the space and orientation molecular density in the resolution of the molecular density functional theory. We consider the common system made of a rigid solute of arbitrary complexity immersed in a molecular solvent, both represented by molecules with interacting atomic sites and classical force fields. The molecular solvent density ρ(r,Ω) around the solute is a function of the position r≡(x,y,z) and of the three Euler angles Ω≡(θ,ϕ,ψ) describing the solvent orientation. The standard density functional, equivalent to the hypernetted-chain closure for the solute-solvent correlations in the liquid theory, is minimized with respect to ρ(r,Ω). The up-to-now very expensive angular convolution products are advantageously replaced by simple products between projections onto generalized spherical harmonics. The dramatic gain in speed of resolution enables to explore in a systematic way molecular solutes of up to nanometric sizes in arbitrary solvents and to calculate their solvation free energy and associated microscopic solvent structure in at most a few minutes. We finally illustrate the formalism by tackling the solvation of molecules of various complexities in water.

Molecular Level Structure and Dynamics of Electrolytes Using 17O Nuclear Magnetic Resonance Spectroscopy

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

Murugesan, Vijayakumar; Han, Kee Sung; Hu, Jianzhi

2017-03-19

Electrolytes help harness the energy from electrochemical processes by serving as solvents and transport media for redox-active ions. Molecular-level interactions between ionic solutes and solvent molecules – commonly referred to as solvation phenomena – give rise to many functional properties of electrolytes such as ionic conductivity, viscosity, and stability. It is critical to understand the evolution of solvation phenomena as a function of competing counterions and solvent mixtures to predict and design the optimal electrolyte for a target application. Probing oxygen environments is of great interest as oxygens are located at strategic molecular sites in battery solvents and are directlymore » involved in inter- and intramolecular solvation interactions. NMR signals from 17O nuclei in battery electrolytes offer nondestructive bulk measurements of isotropic shielding, electric field gradient tensors, and transverse and longitudinal relaxation rates, which are excellent means for probing structure, bonding, and dynamics of both solute and solvent molecules. This article describes the use of 17O NMR spectroscopy in probing the solvation structures of various electrolyte systems ranging from transition metal ions in aqueous solution to lithium cations in organic solvent mixtures.« less

Superior Thermostability, Good Detonation Properties, Insensitivity, and the Effect on the Thermal Decomposition of Ammonium Perchlorate for a New Solvent-Free 3D Energetic PbII -MOF.

PubMed

Yang, Qi; Yang, Guoli; Zhang, Wendou; Zhang, Sheng; Yang, Zhaohui; Xie, Gang; Wei, Qing; Chen, Sanping; Gao, Shengli

2017-07-06

A new solvent-free energetic MOF, [Pb(HBTI)] n (1) (H 3 BTI=4,5-bis(1H-tetrazole)-1H-imidazole), has been synthesized under hydrothermal and acidic conditions. It was characterized by elemental analysis, IR, thermogravimetric, differential scanning calorimetry (DSC) and SEM. Single crystal X-ray diffraction analysis revealed that 1 features a rigid 3D framework architecture free of solvent molecules. Thermal analysis demonstrated that the thermostability of 1 was up to 325 °C. Non-isothermal kinetic and apparent thermodynamic parameters of exothermic decomposition process of 1 were determined by Kissinger's and Ozawa's methods. Through oxygen-bomb combustion calorimetry, the standard molar enthalpy of formation of 1 was determined. The calculated detonation properties (heat of detonation, detonation velocity and detonation pressure) and sensitivity tests of 1 were carried out. In addition, 1 was explored as combustion promoter to accelerate the thermal decompositions of ammonium perchlorate (AP) by differential scanning calorimetry. Experimental results indicated that 1 possesses potential application prospects in the field of explosives and propellants. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure–property reduced order model for viscosity prediction in single-component CO 2 -binding organic liquids

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

Cantu, David C.; Malhotra, Deepika; Koech, Phillip K.

2016-01-01

CO2 capture from power generation with aqueous solvents remains energy intensive due to the high water content of the current technology, or the high viscosity of non-aqueous alternatives. Quantitative reduced models, connecting molecular structure to bulk properties, are key for developing structure-property relationships that enable molecular design. In this work, we describe such a model that quantitatively predicts viscosities of CO2 binding organic liquids (CO2BOLs) based solely on molecular structure and the amount of bound CO2. The functional form of the model correlates the viscosity with the CO2 loading and an electrostatic term describing the charge distribution between the CO2-bearingmore » functional group and the proton-receiving amine. Molecular simulations identify the proton shuttle between these groups within the same molecule to be the critical indicator of low viscosity. The model, developed to allow for quick screening of solvent libraries, paves the way towards the rational design of low viscosity non-aqueous solvent systems for post-combustion CO2 capture. Following these theoretical recommendations, synthetic efforts of promising candidates and viscosity measurement provide experimental validation and verification.« less

Aromatic sulfonation with sulfur trioxide: mechanism and kinetic model.

PubMed

Moors, Samuel L C; Deraet, Xavier; Van Assche, Guy; Geerlings, Paul; De Proft, Frank

2017-01-01

Electrophilic aromatic sulfonation of benzene with sulfur trioxide is studied with ab initio molecular dynamics simulations in gas phase, and in explicit noncomplexing (CCl 3 F) and complexing (CH 3 NO 2 ) solvent models. We investigate different possible reaction pathways, the number of SO 3 molecules participating in the reaction, and the influence of the solvent. Our simulations confirm the existence of a low-energy concerted pathway with formation of a cyclic transition state with two SO 3 molecules. Based on the simulation results, we propose a sequence of elementary reaction steps and a kinetic model compatible with experimental data. Furthermore, a new alternative reaction pathway is proposed in complexing solvent, involving two SO 3 and one CH 3 NO 2 .

Solvent effects on the ultrafast nonradiative deactivation mechanisms of thymine in aqueous solution: Excited-state QM/MM molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Nakayama, Akira; Arai, Gaku; Yamazaki, Shohei; Taketsugu, Tetsuya

2013-12-01

On-the-fly excited-state quantum mechanics/molecular mechanics molecular dynamics (QM/MM-MD) simulations of thymine in aqueous solution are performed to investigate the role of solvent water molecules on the nonradiative deactivation process. The complete active space second-order perturbation theory (CASPT2) method is employed for a thymine molecule as the QM part in order to provide a reliable description of the excited-state potential energies. It is found that, in addition to the previously reported deactivation pathway involving the twisting of the C-C double bond in the pyrimidine ring, another efficient deactivation pathway leading to conical intersections that accompanies the out-of-plane displacement of the carbonyl group is observed in aqueous solution. Decay through this pathway is not observed in the gas phase simulations, and our analysis indicates that the hydrogen bonds with solvent water molecules play a key role in stabilizing the potential energies of thymine in this additional decay pathway.

Extractables analysis of single-use flexible plastic biocontainers.

PubMed

Marghitoiu, Liliana; Liu, Jian; Lee, Hans; Perez, Lourdes; Fujimori, Kiyoshi; Ronk, Michael; Hammond, Matthew R; Nunn, Heather; Lower, Asher; Rogers, Gary; Nashed-Samuel, Yasser

2015-01-01

Studies of the extractable profiles of bioprocessing components have become an integral part of drug development efforts to minimize possible compromise in process performance, decrease in drug product quality, and potential safety risk to patients due to the possibility of small molecules leaching out from the components. In this study, an effective extraction solvent system was developed to evaluate the organic extractable profiles of single-use bioprocess equipment, which has been gaining increasing popularity in the biopharmaceutical industry because of the many advantages over the traditional stainless steel-based bioreactors and other fluid mixing and storage vessels. The chosen extraction conditions were intended to represent aggressive conditions relative to the application of single-use bags in biopharmaceutical manufacture, in which aqueous based systems are largely utilized. Those extraction conditions, along with a non-targeted analytical strategy, allowed for the generation and identification of an array of extractable compounds; a total of 53 organic compounds were identified from four types of commercially available single-use bags, the majority of which are degradation products of polymer additives. The success of this overall extractables analysis strategy was reflected partially by the effectiveness in the extraction and identification of a compound that was later found to be highly detrimental to mammalian cell growth. The usage of single-use bioreactors has been increasing in biopharmaceutical industry because of the appealing advantages that it promises regarding to the cleaning, sterilization, operational flexibility, and so on, during manufacturing of biologics. However, compared to its conventional counterparts based mainly on stainless steel, single-use bioreactors are more susceptible to potential problems associated with compound leaching into the bioprocessing fluid. As a result, extractable profiling of the single-use system has become essential in the qualification of such systems for its use in drug manufacturing. The aim of this study is to evaluate the effectiveness of an extraction solvent system developed to study the extraction profile of single-use bioreactors in which aqueous-based systems are largely used. The results showed that with a non-targeted analytical approach, the extraction solvent allowed the generation and identification of an array of extractable compounds from four commercially available single-use bioreactors. Most of extractables are degradation products of polymer additives, among which was a compound that was later found to be highly detrimental to mammalian cell growth. © PDA, Inc. 2015.

Microhydration and the Enhanced Acidity of Free Radicals.

PubMed

Walton, John C

2018-02-14

Recent theoretical research employing a continuum solvent model predicted that radical centers would enhance the acidity (RED-shift) of certain proton-donor molecules. Microhydration studies employing a DFT method are reported here with the aim of establishing the effect of the solvent micro-structure on the acidity of radicals with and without RED-shifts. Microhydration cluster structures were obtained for carboxyl, carboxy-ethynyl, carboxy-methyl, and hydroperoxyl radicals. The numbers of water molecules needed to induce spontaneous ionization were determined. The hydration clusters formed primarily round the CO₂ units of the carboxylate-containing radicals. Only 4 or 5 water molecules were needed to induce ionization of carboxyl and carboxy-ethynyl radicals, thus corroborating their large RED-shifts.

Effects analysis of substituent characteristics and solvents on the photodegradation of polybrominated diphenyl ethers.

PubMed

Jiang, Long; Qiu, Youli; Li, Yu

2017-10-01

The ultraviolet spectra and electron transition information of 209 polybrominated diphenyl ethers (PBDEs) in gas were first calculated via time-dependent density functional theory using Gaussian 09 software. The main and second-order interactional effects of substituent characteristics on the photodegradation of PBDEs were then analysed using a full factorial experimental design. Solvent effects were considered to research the effect and promotion mechanism of solvent molecules on the photodegradation of PBDEs compared with that in gas. The results showed that the introduction of substituents at each position promoted excitation of PBDEs from their ground states to excited states to induce photodegradation. The different positions affected the photodegradation of PBDEs with magnitudes of para > meta > ortho. The congeners with a concentrated distribution of substituents can always be photodegraded more easily than those with separated substituents. From the viewpoint of light-induced reactions, the electron transfer reactions between molecules of PBDE* T1 and Solvent* T1 are the main driving force for the enhanced photodegradation of PBDEs in solvents compared with that in gas. Copyright © 2017 Elsevier Ltd. All rights reserved.

Taking the plunge: chemical reaction dynamics in liquids.

PubMed

Orr-Ewing, Andrew J

2017-12-11

The dynamics of chemical reactions in liquid solutions are now amenable to direct study using ultrafast laser spectroscopy techniques and advances in computer simulation methods. The surrounding solvent affects the chemical reaction dynamics in numerous ways, which include: (i) formation of complexes between reactants and solvent molecules; (ii) modifications to transition state energies and structures relative to the reactants and products; (iii) coupling between the motions of the reacting molecules and the solvent modes, and exchange of energy; (iv) solvent caging of reactants and products; and (v) structural changes to the solvation shells in response to the changing chemical identity of the solutes, on timescales which may be slower than the reactive events. This article reviews progress in the study of bimolecular chemical reaction dynamics in solution, concentrating on reactions which occur on ground electronic states. It illustrates this progress with reference to recent experimental and computational studies, and considers how the various ways in which a solvent affects the chemical reaction dynamics can be unravelled. Implications are considered for research in fields such as mechanistic synthetic chemistry.

Peptide-based ambidextrous bifunctional gelator: applications in oil spill recovery and removal of toxic organic dyes for waste water management.

PubMed

Basu, Kingshuk; Nandi, Nibedita; Mondal, Biplab; Dehsorkhi, Ashkan; Hamley, Ian W; Banerjee, Arindam

2017-12-06

A low molecular weight peptide-based ambidextrous gelator molecule has been discovered for efficient control of water pollution. The gelator molecules can gel various organic solvents with diverse polarity, e.g. n -hexane, n -octane, petroleum ether, petrol, diesel, aromatic solvents like chlorobenzene, toluene, benzene, o -xylene and even aqueous phosphate buffer of pH 7.5. These gels have been thoroughly characterized using various techniques including field emission scanning electron microscopy, Fourier transform infrared spectroscopy, X-ray powder diffraction analysis, small angle X-ray scattering and rheological experiments. Interestingly, hydrogel obtained from the gelator molecule has been found to absorb toxic organic dyes (both cationic and anionic dyes) from dye-contaminated water. The gelator molecule can be reused for several cycles, indicating its possible future use in waste water management. Moreover, this gelator can selectively gel petrol, diesel, pump oil from an oil-water mixture in the presence of a carrier solvent, ethyl acetate, suggesting its efficient application for oil spill recovery. These results indicate that the peptide-based ambidextrous gelator produces soft materials (gels) with dual function: (i) removal of toxic organic dyes in waste water treatment and (ii) oil spill recovery.

A supramolecular strategy to leverage the liquid-phase exfoliation of graphene in the presence of surfactants: unraveling the role of the length of fatty acids.

PubMed

Haar, Sébastien; Ciesielski, Artur; Clough, Joseph; Yang, Huafeng; Mazzaro, Raffaello; Richard, Fanny; Conti, Simone; Merstorf, Nicolas; Cecchini, Marco; Morandi, Vittorio; Casiraghi, Cinzia; Samorì, Paolo

2015-04-08

Achieving the full control over the production as well as processability of high-quality graphene represents a major challenge with potential interest in the field of fabrication of multifunctional devices. The outstanding effort dedicated to tackle this challenge in the last decade revealed that certain organic molecules are capable of leveraging the exfoliation of graphite with different efficiencies. Here, a fundamental understanding on a straightforward supramolecular approach for producing homogenous dispersions of unfunctionalized and non-oxidized graphene nanosheets in four different solvents is attained, namely N-methyl-2-pyrrolidinone, N,N-dimethylformamide, ortho-dichlorobenzene, and 1,2,4-trichlorobenzene. In particular, a comparative study on the liquid-phase exfoliation of graphene in the presence of linear alkanes of different lengths terminated by a carboxylic-acid head group is performed. These molecules act as graphene dispersion-stabilizing agents during the exfoliation process. The efficiency of the exfoliation in terms of concentration of exfoliated graphene is found to be proportional to the length of the employed fatty acid. Importantly, a high percentage of single-layer graphene flakes is revealed by high-resolution transmission electron microscopy and Raman spectroscopy analyses. A simple yet effective thermodynamic model is developed to interpret the chain-length dependence of the exfoliation yield. This approach relying on the synergistic effect of a ad-hoc solvent and molecules to promote the exfoliation of graphene in liquid media represents a promising and modular strategy towards the rational design of improved dispersion-stabilizing agents. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An Inexpensive, Single Use Carbon-Based Sensor for the Rapid and Early Detection of Hydrocarbon Leaks.

PubMed

Sebastian, H Bri; Mayall, Robert M; Pilonieta, Roberto J; Bryant, Steven L

2017-06-23

A novel fabrication process for a single use, low-cost organic solvent sensor has been developed. The process is simple, and the materials are readily available. Carbon nanomaterials are self-assembled at a water/hexane interface, where the hexane phase contains dissolved paraffin wax. Upon the controlled evaporation of hexane, the paraffin wax precipitates, trapping the carbon nanoparticles at the surface in a paraffin wax backbone, realizing a carbon-nanoparticle-decorated film. The film is hydrophobic and highly electrically conductive. When exposed to hydrocarbons or a mixture of hydrocarbons, the conductive carbon network deteriorates and an increase in film resistivity is monitored. The rate of change in resistivity is proportional to the concentration and composition of organic molecules in contact with the film.

Motion of Molecular Probes and Viscosity Scaling in Polyelectrolyte Solutions at Physiological Ionic Strength

PubMed Central

Sozanski, Krzysztof; Wisniewska, Agnieszka; Kalwarczyk, Tomasz; Sznajder, Anna; Holyst, Robert

2016-01-01

We investigate transport properties of model polyelectrolyte systems at physiological ionic strength (0.154 M). Covering a broad range of flow length scales—from diffusion of molecular probes to macroscopic viscous flow—we establish a single, continuous function describing the scale dependent viscosity of high-salt polyelectrolyte solutions. The data are consistent with the model developed previously for electrically neutral polymers in a good solvent. The presented approach merges the power-law scaling concepts of de Gennes with the idea of exponential length scale dependence of effective viscosity in complex liquids. The result is a simple and applicable description of transport properties of high-salt polyelectrolyte solutions at all length scales, valid for motion of single molecules as well as macroscopic flow of the complex liquid. PMID:27536866

Photoresponsive Release from Azobenzene-Modified Single Cubic Crystal NaCl/Silica Particles

DOE PAGES

Jiang, Xingmao; Liu, Nanguo; Assink, Roger A.; ...

2011-01-01

Azobenzene ligands were uniformly anchored to the pore surfaces of nanoporous silica particles with single crystal NaCl using 4-(3-triethoxysilylpropylureido)azobenzene (TSUA). The functionalization delayed the release of NaCl significantly. The modified particles demonstrated a photocontrolled release by trans/cis isomerization of azobenzene moieties. The addition of amphiphilic solvents, propylene glycol (PG), propylene glycol propyl ether (PGPE), and dipropylene glycol propyl ether (DPGPE) delayed the release in water, although the wetting behavior was improved and the delay is the most for the block molecules with the longest carbon chain. The speedup by UV irradiation suggests a strong dependence of diffusion on the switchablemore » pore size. TGA, XRD, FTIR, and NMR techniques were used to characterize the structures.« less

Nonadiabatic dynamics of electron transfer in solution: Explicit and implicit solvent treatments that include multiple relaxation time scales

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

Schwerdtfeger, Christine A.; Soudackov, Alexander V.; Hammes-Schiffer, Sharon, E-mail: shs3@illinois.edu

2014-01-21

The development of efficient theoretical methods for describing electron transfer (ET) reactions in condensed phases is important for a variety of chemical and biological applications. Previously, dynamical dielectric continuum theory was used to derive Langevin equations for a single collective solvent coordinate describing ET in a polar solvent. In this theory, the parameters are directly related to the physical properties of the system and can be determined from experimental data or explicit molecular dynamics simulations. Herein, we combine these Langevin equations with surface hopping nonadiabatic dynamics methods to calculate the rate constants for thermal ET reactions in polar solvents formore » a wide range of electronic couplings and reaction free energies. Comparison of explicit and implicit solvent calculations illustrates that the mapping from explicit to implicit solvent models is valid even for solvents exhibiting complex relaxation behavior with multiple relaxation time scales and a short-time inertial response. The rate constants calculated for implicit solvent models with a single solvent relaxation time scale corresponding to water, acetonitrile, and methanol agree well with analytical theories in the Golden rule and solvent-controlled regimes, as well as in the intermediate regime. The implicit solvent models with two relaxation time scales are in qualitative agreement with the analytical theories but quantitatively overestimate the rate constants compared to these theories. Analysis of these simulations elucidates the importance of multiple relaxation time scales and the inertial component of the solvent response, as well as potential shortcomings of the analytical theories based on single time scale solvent relaxation models. This implicit solvent approach will enable the simulation of a wide range of ET reactions via the stochastic dynamics of a single collective solvent coordinate with parameters that are relevant to experimentally accessible systems.« less

Homopolymer Micelles in Heterogeneous Solvent Mixtures

PubMed Central

Basu, Subhadeep; Vutukuri, Dharma Rao

2008-01-01

Amphiphilic homopolymers containing a hydrophilic and a hydrophobic functionality in each monomer unit have been shown to form polar or apolar containers depending on the solvent environment. When presented with a mixture of solvents, these polymeric containers are capable of releasing certain guest molecules. The fundamental mechanism behind these properties is investigated and the utility of these assemblies in separations has been demonstrated with an example. PMID:16316219

Solvent dependent triphenylamine based D-(pi-A)n type dye molecules and optical properties.

PubMed

Li, Xiaochuan; Son, Young-A; Kim, Young-Sung; Kim, Sung-Hoon; Kun, Jun; Shin, Jong-Il

2012-02-01

D-(pi-A)n type dyes of triphenylamine derivatives were synthesized and their absorption and luminescence in different solvents were examined to investigate solvent dependent properties observed for their emissions in solvents with different dielectric constants. The emission wavelengths showed a dramatic blue shift with increasing solvent polarity. The results of molecular orbital calculations by computer simulation, based on Material Studio suite of programs, were found to reasonably account for the spectral properties. Relative levels of HOMO and LUMO were measured and calculated and all derivatives exhibited strong solid fluorescence with distinctively different FWHMs.

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

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

Nakayasu, Ernesto S.; Nicora, Carrie D.; Sims, Amy C.

2016-05-03

ABSTRACT Integrative multi-omics analyses can empower more effective investigation and complete understanding of complex biological systems. Despite recent advances in a range of omics analyses, multi-omic measurements of the same sample are still challenging and current methods have not been well evaluated in terms of reproducibility and broad applicability. Here we adapted a solvent-based method, widely applied for extracting lipids and metabolites, to add proteomics to mass spectrometry-based multi-omics measurements. Themetabolite,protein, andlipidextraction (MPLEx) protocol proved to be robust and applicable to a diverse set of sample types, including cell cultures, microbial communities, and tissues. To illustrate the utility of thismore » protocol, an integrative multi-omics analysis was performed using a lung epithelial cell line infected with Middle East respiratory syndrome coronavirus, which showed the impact of this virus on the host glycolytic pathway and also suggested a role for lipids during infection. The MPLEx method is a simple, fast, and robust protocol that can be applied for integrative multi-omic measurements from diverse sample types (e.g., environmental,in vitro, and clinical). IMPORTANCEIn systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such studies are challenging due to the fact that the extraction conditions differ according to the molecule type. Here, we adapted an organic solvent-based extraction method that demonstrated broad applicability and robustness, which enabled comprehensive proteomics, metabolomics, and lipidomics analyses from the same sample.« less

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.

Solvent-induced controllable synthesis, single-crystal to single-crystal transformation and encapsulation of Alq3 for modulated luminescence in (4,8)-connected metal-organic frameworks.

PubMed

Lan, Ya-Qian; Jiang, Hai-Long; Li, Shun-Li; Xu, Qiang

2012-07-16

In this work, for the first time, we have systematically demonstrated that solvent plays crucial roles in both controllable synthesis of metal-organic frameworks (MOFs) and their structural transformation process. With solvent as the only variable, five new MOFs with different structures have been constructed, in which one MOF undergoes solvent-induced single-crystal to single-crystal (SCSC) transformation that involves not only solvent exchange but also the cleavage and formation of coordination bonds. Particularly, a significant crystallographic change has been realized through an unprecedented three-step SCSC transformation process. Furthermore, we have demonstrated that the obtained MOF could be an excellent host for chromophores such as Alq3 for modulated luminescent properties.

Monitoring and quantifying the passive transport of molecules through patch-clamp suspended real and model cell membranes.

PubMed

Messina, Pierluca; Lemaître, Frédéric; Huet, François; Ngo, Kieu An; Vivier, Vincent; Labbé, Eric; Buriez, Olivier; Amatore, Christian

2014-03-17

Transport of active molecules across biological membranes is a central issue for the success of many pharmaceutical strategies. Herein, we combine the patch-clamp principle with amperometric detection for monitoring fluxes of redox-tagged molecular species across a suspended membrane patched from a macrophage. Solvent- and protein-free lipid bilayers (DPhPC, DOPC, DOPG) patched from single-wall GUV have been thoroughly investigated and the corresponding fluxes measurements quantified. The quality of the patches and their proper sealing were successfully characterized by electrochemical impedance spectroscopy. This procedure appears versatile and perfectly adequate to allow the investigation of transport and quantification of the transport properties through direct measurement of the coefficients of partition and diffusion of the compound in the membrane, thus offering insight on such important biological and pharmacological issues. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Investigation of the graphene-electrolyte interface in Li-air batteries: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Pavlov, S. V.; Kislenko, S. A.

2018-01-01

In this work the behavior of the main reactants (Li+, O2) of the oxygen reduction reaction (ORR) in acetonitrile solvent near the multi-layer graphene edge has been studied. It was observed by molecular dynamics simulations that the concentration distributions of the Li+ and O2 represent a “chessboard” structure. It was ascertained that the concentrations of the lithium ions and oxygen molecules reach their maximum values near the graphene edges pushed out from the surface, which may act as nucleation centers for the formation of crystalline products of the ORR. The maps of the free energy were estimated for the Li+ and O2. Energy optimal trajectories for the adsorption of oxygen molecules and lithium ions were found. Moreover, the distributions of the electric potential were obtained near the following carbon surfaces: single- and multi-layer graphene edge, graphene plane, which shows the qualitative differences in the double-layer structure.

Real-space analysis of diffusion behavior and activation energy of individual monatomic ions in a liquid.

PubMed

Miyata, Tomohiro; Uesugi, Fumihiko; Mizoguchi, Teruyasu

2017-12-01

Investigation of the local dynamic behavior of atoms and molecules in liquids is crucial for revealing the origin of macroscopic liquid properties. Therefore, direct imaging of single atoms to understand their motions in liquids is desirable. Ionic liquids have been studied for various applications, in which they are used as electrolytes or solvents. However, atomic-scale diffusion and relaxation processes in ionic liquids have never been observed experimentally. We directly observe the motion of individual monatomic ions in an ionic liquid using scanning transmission electron microscopy (STEM) and reveal that the ions diffuse by a cage-jump mechanism. Moreover, we estimate the diffusion coefficient and activation energy for the diffusive jumps from the STEM images, which connect the atomic-scale dynamics to macroscopic liquid properties. Our method is the only available means to observe the motion, reactions, and energy barriers of atoms/molecules in liquids.

Photoinduced fluorescence intensity oscillation in a reaction-diffusion cell containing a colloidal quantum dot dispersion

NASA Astrophysics Data System (ADS)

Komoto, Atsushi; Maenosono, Shinya

2006-09-01

The nonlinear spontaneous oscillation of photoluminescence (PL) intensity in an ensemble of semiconductor quantum dots (QDs), which differs from the fluorescence intermittency of a single QD, is investigated. The PL intensity in a QD dispersion slowly oscillates with time under continuous illumination. The oscillatory behavior is found to vary with changing QD concentration, solvent viscosity, volume fraction of irradiated region, and irradiation intensity. On the basis of the Gray-Scott model [Chemical Oscillation and Instabilities: Non-linear Chemical Kinetics (Clarendon, Oxford, 1994); J. Phys. Chem. 89, 22 (1985); Chem. Eng. Sci. 42, 307 (1987)], and its comparison with the experimental results, it is revealed that the following processes are important for PL oscillation: (1) mass transfer of QDs between the illuminated and dark regions, (2) autocatalytic formation of vacant sites on QD surfaces via photodesorption of ligand molecules, and (3) passivation of vacant sites via photoadsorption of water molecules.

Photoinduced fluorescence intensity oscillation in a reaction-diffusion cell containing a colloidal quantum dot dispersion.

PubMed

Komoto, Atsushi; Maenosono, Shinya

2006-09-21

The nonlinear spontaneous oscillation of photoluminescence (PL) intensity in an ensemble of semiconductor quantum dots (QDs), which differs from the fluorescence intermittency of a single QD, is investigated. The PL intensity in a QD dispersion slowly oscillates with time under continuous illumination. The oscillatory behavior is found to vary with changing QD concentration, solvent viscosity, volume fraction of irradiated region, and irradiation intensity. On the basis of the Gray-Scott model [Chemical Oscillation and Instabilities: Non-linear Chemical Kinetics (Clarendon, Oxford, 1994); J. Phys. Chem. 89, 22 (1985); Chem. Eng. Sci. 42, 307 (1987)], and its comparison with the experimental results, it is revealed that the following processes are important for PL oscillation: (1) mass transfer of QDs between the illuminated and dark regions, (2) autocatalytic formation of vacant sites on QD surfaces via photodesorption of ligand molecules, and (3) passivation of vacant sites via photoadsorption of water molecules.

Quantification of the hydrophobic interaction by simulations of the aggregation of small hydrophobic solutes in water

PubMed Central

Raschke, Tanya M.; Tsai, Jerry; Levitt, Michael

2001-01-01

The hydrophobic interaction, the tendency for nonpolar molecules to aggregate in solution, is a major driving force in biology. In a direct approach to the physical basis of the hydrophobic effect, nanosecond molecular dynamics simulations were performed on increasing numbers of hydrocarbon solute molecules in water-filled boxes of different sizes. The intermittent formation of solute clusters gives a free energy that is proportional to the loss in exposed molecular surface area with a constant of proportionality of 45 ± 6 cal/mol⋅Å2. The molecular surface area is the envelope of the solute cluster that is impenetrable by solvent and is somewhat smaller than the more traditional solvent-accessible surface area, which is the area transcribed by the radius of a solvent molecule rolled over the surface of the cluster. When we apply a factor relating molecular surface area to solvent-accessible surface area, we obtain 24 cal/mol⋅Å2. Ours is the first direct calculation, to our knowledge, of the hydrophobic interaction from molecular dynamics simulations; the excellent qualitative and quantitative agreement with experiment proves that simple van der Waals interactions and atomic point-charge electrostatics account for the most important driving force in biology. PMID:11353861

Solvent friction effects propagate over the entire protein molecule through low-frequency collective modes.

PubMed

Moritsugu, Kei; Kidera, Akinori; Smith, Jeremy C

2014-07-24

Protein solvation dynamics has been investigated using atom-dependent Langevin friction coefficients derived directly from molecular dynamics (MD) simulations. To determine the effect of solvation on the atomic friction coefficients, solution and vacuum MD simulations were performed for lysozyme and staphylococcal nuclease and analyzed by Langevin mode analysis. The coefficients thus derived are roughly correlated with the atomic solvent-accessible surface area (ASA), as expected from the fact that friction occurs as the result of collisions with solvent molecules. However, a considerable number of atoms with higher friction coefficients are found inside the core region. Hence, the influence of solvent friction propagates into the protein core. The internal coefficients have large contributions from the low-frequency modes, yielding a simple picture of the surface-to-core long-range damping via solvation governed by collective low-frequency modes. To make use of these findings in implicit-solvent modeling, we compare the all-atom friction results with those obtained using Langevin dynamics (LD) with two empirical representations: the constant-friction and the ASA-dependent (Pastor-Karplus) friction models. The constant-friction model overestimates the core and underestimates the surface damping whereas the ASA-dependent friction model, which damps protein atoms only on the solvent-accessible surface, reproduces well the friction coefficients for both the surface and core regions observed in the explicit-solvent MD simulations. Therefore, in LD simulation, the solvent friction coefficients should be imposed only on the protein surface.

Solvent friction effects propagate over the entire protein molecule through low-frequency collective modes

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

Moritsugu, Kei; Kidera, Akinori; Smith, Jeremy C.

2014-06-25

Protein solvation dynamics has been investigated using atom-dependent Langevin friction coefficients derived directly from molecular dynamics (MD) simulations. To determine the effect of solvation on the atomic friction coefficients, solution and vacuum MD simulations were performed for lysozyme and staphylococcal nuclease and analyzed by Langevin mode analysis. The coefficients thus derived are roughly correlated with the atomic solvent-accessible surface area (ASA), as expected from the fact that friction occurs as the result of collisions with solvent molecules. However, a considerable number of atoms with higher friction coefficients are found inside the core region. Hence, the influence of solvent friction propagatesmore » into the protein core. The internal coefficients have large contributions from the low-frequency modes, yielding a simple picture of the surface-to-core long-range damping via solvation governed by collective low-frequency modes. To make use of these findings in implicit-solvent modeling, we compare the all-atom friction results with those obtained using Langevin dynamics (LD) with two empirical representations: the constant-friction and the ASA-dependent (Pastor Karplus) friction models. The constant-friction model overestimates the core and underestimates the surface damping whereas the ASA-dependent friction model, which damps protein atoms only on the solvent-accessible surface, reproduces well the friction coefficients for both the surface and core regions observed in the explicit-solvent MD simulations. Furthermore, in LD simulation, the solvent friction coefficients should be imposed only on the protein surface.« less

Molecular dynamics simulation of solute diffusion in Lennard-Jones fluids

NASA Astrophysics Data System (ADS)

Yamaguchi, T.; Kimura, Y.; Hirota, N.

We performed a molecular dynamics (MD) simulation for a system of 5 solute molecules in 495 solvent molecules interacting through the Lennard-Jones (LJ) 12-6 potential, in order to study solvent density effects on the diffusion coefficients in supercritical fluids. The effects of the size of the solute and the strength of the solute-solvent attractive interaction on the diffusion coefficient of the solute were examined. The diffusion coefficients of the solute molecules were calculated at T = 1.5 (in the LJ reduced unit), slightly above the critical temperature, from rho = 0.1 to rho = 0.95, where rho is the number density in the LJ reduced unit. The memory function in the generalized Langevin equation was calculated, in order to know the molecular origin of the friction on a solute. The memory function is separated into fast and slow components. The former arises from the solute-solvent repulsive interaction, and is interpreted as collisional Enskog-like friction. The interaction strength dependence of the collisional friction is larger in the low- and medium-density regions, which is consistent with the 'clustering' picture, i.e., the local density enhancement due to the solute-solvent attractive interaction. However, the slow component of the memory function suppresses the effect of the local density on the diffusion coefficients, and as a result the effect of the attractive interaction is smaller on the diffusion coefficients than on the local density. Nonetheless, the solvent density dependence of the effect of the attraction on the diffusion coefficient varies with the local density, and it is concluded that the local density is the principal factor that determines the interaction strength dependence of the diffusion coefficient in the low- and medium-density regions (p < 0.6).

Electronic excitation spectra of molecules in solution calculated using the symmetry-adapted cluster-configuration interaction method in the polarizable continuum model with perturbative approach

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

Fukuda, Ryoichi, E-mail: fukuda@ims.ac.jp; Ehara, Masahiro; Elements Strategy Initiative for Catalysts and Batteries

A perturbative approximation of the state specific polarizable continuum model (PCM) symmetry-adapted cluster-configuration interaction (SAC-CI) method is proposed for efficient calculations of the electronic excitations and absorption spectra of molecules in solutions. This first-order PCM SAC-CI method considers the solvent effects on the energies of excited states up to the first-order with using the zeroth-order wavefunctions. This method can avoid the costly iterative procedure of the self-consistent reaction field calculations. The first-order PCM SAC-CI calculations well reproduce the results obtained by the iterative method for various types of excitations of molecules in polar and nonpolar solvents. The first-order contribution ismore » significant for the excitation energies. The results obtained by the zeroth-order PCM SAC-CI, which considers the fixed ground-state reaction field for the excited-state calculations, are deviated from the results by the iterative method about 0.1 eV, and the zeroth-order PCM SAC-CI cannot predict even the direction of solvent shifts in n-hexane for many cases. The first-order PCM SAC-CI is applied to studying the solvatochromisms of (2,2{sup ′}-bipyridine)tetracarbonyltungsten [W(CO){sub 4}(bpy), bpy = 2,2{sup ′}-bipyridine] and bis(pentacarbonyltungsten)pyrazine [(OC){sub 5}W(pyz)W(CO){sub 5}, pyz = pyrazine]. The SAC-CI calculations reveal the detailed character of the excited states and the mechanisms of solvent shifts. The energies of metal to ligand charge transfer states are significantly sensitive to solvents. The first-order PCM SAC-CI well reproduces the observed absorption spectra of the tungsten carbonyl complexes in several solvents.« less

Probing water dynamics with OH -

NASA Astrophysics Data System (ADS)

Corridoni, T.; Sodo, A.; Bruni, F.; Ricci, M. A.; Nardone, M.

2007-07-01

Isotropic Raman spectra of aqueous solutions of LiOH, NaOH and KOH at concentrations ranging from high dilution to saturation have been measured and the frequency and width of the OH - stretching band have been analyzed. The dependence of the bandwidth on solute concentration suggests that the OH - vibration undergoes a transition from fast to slow modulation regimes as the solvent concentration decreases below the value of ˜20 water molecules per solute molecule. A correlation between this finding and structural modifications of the H-bond network of the solvent at similar concentrations is envisaged.

Solvent additive effects on small molecule crystallization in bulk heterojunction solar cells probed during spin casting.

PubMed

Perez, Louis A; Chou, Kang Wei; Love, John A; van der Poll, Thomas S; Smilgies, Detlef-M; Nguyen, Thuc-Quyen; Kramer, Edward J; Amassian, Aram; Bazan, Guillermo C

2013-11-26

Solvent additive processing can lead to drastic improvements in the power conversion efficiency (PCE) in solution processable small molecule (SPSM) bulk heterojunction solar cells. In situ grazing incidence wide-angle X-ray scattering is used to investigate the kinetics of crystallite formation during and shortly after spin casting. The additive is shown to have a complex effect on structural evolution invoking polymorphism and enhanced crystalline quality of the donor SPSM. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rectification of nanopores in aprotic solvents - transport properties of nanopores with surface dipoles

NASA Astrophysics Data System (ADS)

Plett, Timothy; Shi, Wenqing; Zeng, Yuhan; Mann, William; Vlassiouk, Ivan; Baker, Lane A.; Siwy, Zuzanna S.

2015-11-01

Nanopores have become a model system to understand transport properties at the nanoscale. We report experiments and modeling of ionic current in aprotic solvents with different dipole moments through conically shaped nanopores in a polycarbonate film and through glass nanopipettes. We focus on solutions of the salt LiClO4, which is of great importance in modeling lithium based batteries. Results presented suggest ion current rectification observed results from two effects: (i) adsorption of Li+ ions to the pore walls, and (ii) a finite dipole moment rendered by adsorbed solvent molecules. Properties of surfaces in various solvents were probed by means of scanning ion conductance microscopy, which confirmed existence of an effectively positive surface potential in aprotic solvents with high dipole moments.Nanopores have become a model system to understand transport properties at the nanoscale. We report experiments and modeling of ionic current in aprotic solvents with different dipole moments through conically shaped nanopores in a polycarbonate film and through glass nanopipettes. We focus on solutions of the salt LiClO4, which is of great importance in modeling lithium based batteries. Results presented suggest ion current rectification observed results from two effects: (i) adsorption of Li+ ions to the pore walls, and (ii) a finite dipole moment rendered by adsorbed solvent molecules. Properties of surfaces in various solvents were probed by means of scanning ion conductance microscopy, which confirmed existence of an effectively positive surface potential in aprotic solvents with high dipole moments. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr06340j

Estimation of boiling points using density functional theory with polarized continuum model solvent corrections.

PubMed

Chan, Poh Yin; Tong, Chi Ming; Durrant, Marcus C

2011-09-01

An empirical method for estimation of the boiling points of organic molecules based on density functional theory (DFT) calculations with polarized continuum model (PCM) solvent corrections has been developed. The boiling points are calculated as the sum of three contributions. The first term is calculated directly from the structural formula of the molecule, and is related to its effective surface area. The second is a measure of the electronic interactions between molecules, based on the DFT-PCM solvation energy, and the third is employed only for planar aromatic molecules. The method is applicable to a very diverse range of organic molecules, with normal boiling points in the range of -50 to 500 °C, and includes ten different elements (C, H, Br, Cl, F, N, O, P, S and Si). Plots of observed versus calculated boiling points gave R²=0.980 for a training set of 317 molecules, and R²=0.979 for a test set of 74 molecules. The role of intramolecular hydrogen bonding in lowering the boiling points of certain molecules is quantitatively discussed. Crown Copyright © 2011. Published by Elsevier Inc. All rights reserved.

Spectroscopy of nitrophenolates in vacuo: effect of spacer, configuration, and microsolvation on the charge-transfer excitation energy.

PubMed

Brøndsted Nielsen, Steen; Brøndsted Nielsen, Mogens; Rubio, Angel

2014-04-15

In a charge-transfer (CT) transition, electron density moves from one end of the molecule (donor) to the other end (acceptor). This type of transition is of paramount importance in nature, for example, in photosynthesis, and it governs the excitation of several protein biochromophores and luminophores such as the oxyluciferin anion that accounts for light emission from fireflies. Both transition energy and oscillator strength are linked to the coupling between the donor and acceptor groups: The weaker the coupling, the smaller the excitation energy. But a weak coupling necessarily also causes a low oscillator strength possibly preventing direct excitation (basically zero probability in the noncoupling case). The coupling is determined by the actual spacer between the two groups, and whether the spacer acts as an insulator or a conductor. However, it can be difficult or even impossible to distinguish the effect of the spacer from that of local solvent molecules that often cause large solvent shifts due to different ground-state and excited-state stabilization. This calls for gas-phase spectroscopy experiments where absorption by the isolated molecule is identified to unequivocally establish the intrinsic molecular properties with no perturbations from a microenvironment. From such insight, the effect of a protein microenvironment on the CT excited state can be deduced. In this Account, we review our results over the last 5 years from mass spectroscopy experiments using specially designed apparatus on several charged donor-acceptor ions that are based on the nitrophenolate moiety and π-extended derivatives, which are textbook examples of donor-acceptor chromophores. The phenolate oxygen is the donor, and the nitro group is the acceptor. The choice of this system is also based on the fact that phenolate is a common structural motif of biochromophores and luminophores, for example, it is a constituent of the oxyluciferin anion. A presentation of the setups used for gas-phase ion spectroscopy in Aarhus is given, and we address issues of whether double bonds or triple bonds best convey electronic coupling between the phenolate oxygen and the nitro group, the significance of separating the donor and acceptor spatially, the influence of cross-conjugation versus linear conjugation, and along this line ortho versus meta versus para configuration, and not least the effect of a single solvent molecule (water, methanol, or acetonitrile). From systematic studies, a clear picture has emerged that has been supported by high-level calculations of electronically excited states. Our work shows that CC2 coupled-cluster calculations of vertical excitation energies are within 0.2 eV of experimental band maxima, and importantly, that the theoretical method is excellent in predicting the relative order of excitation energies of a series of nitrophenolates. Finally, we discuss future challenges such as following the change in absorption as a function of the number of solvent molecules and when gradually approaching the bulk limit.

Synthesis of size controllable cu-phthalocyanine nanofibers by simple solvent diffusion method and their electrochemical properties.

PubMed

Gao, Junshan; Cheng, Chuanwei; Zhou, Xuechao; Li, Yingying; Xu, Xiaoqi; Du, Xiguang; Zhang, Haiqian

2010-02-15

Tetra (2-isopropyl-5-methylphenoxy) substituted Cu-phthalocyanine nanofibers were obtained in large scale by a simple solvent diffusion method. The sizes of the fibers can be finely tuned under different solvent temperature. FE-SEM micrographs indicate that the length of the fibers changed from several hundreds micrometers to several hundreds nanometers and the width changed from several micrometers to several decade nanometers. XRD measurement showed a highly long-range ordered lamellar arrangement of the substituted Cu-phthalocyanine molecules in the microfiber and the UV-vis absorption spectrum of the fibers indicated an H-aggregate of the phthalocyanine molecules. The CV curves elucidate the CuPc fibers can be fabricated Faraday pseudocapacitor. Crown Copyright 2009. Published by Elsevier Inc. 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

Thermoplastic composite matrices with improved solvent resistance

NASA Technical Reports Server (NTRS)

Hergenrother, P. M.; Jensen, B. J.; Havens, S. J.

1984-01-01

In order to improve solvent resistance of aromatic thermoplastic polymers, ethynyl-terminated aromatic sulfone polymers (ETS), sulfone/ester polymers (SEPE) containing pendent ethynyl groups, and phenoxy resin containing pendent ethynyl groups are synthesized. Cured polysulfones and phenoxy resins containing ethynyl groups on the ends or pendent on the molecules exhibited systematic behavior in solvent resistance, film flexibility, and toughness as a function of crosslink density. The film and composite properties of a cured solvent-resistant ETS were better than those of a commercially available solvent sensitive polysulfone. The study was part of a NASA program to better understand the trade-offs between solvent resistance, processability and mechanical properties which may be useful in designing composite structures for aerospace vehicles.

A recipe for free-energy functionals of polarizable molecular fluids

NASA Astrophysics Data System (ADS)

Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Arias, T. A.

2014-04-01

Classical density-functional theory is the most direct approach to equilibrium structures and free energies of inhomogeneous liquids, but requires the construction of an approximate free-energy functional for each liquid of interest. We present a general recipe for constructing functionals for small-molecular liquids based only on bulk experimental properties and ab initio calculations of a single solvent molecule. This recipe combines the exact free energy of the non-interacting system with fundamental measure theory for the repulsive contribution and a weighted density functional for the short-ranged attractive interactions. We add to these ingredients a weighted polarization functional for the long-range correlations in both the rotational and molecular-polarizability contributions to the dielectric response. We also perform molecular dynamics calculations for the free energy of cavity formation and the high-field dielectric response, and show that our free-energy functional adequately describes these properties (which are key for accurate solvation calculations) for all three solvents in our study: water, chloroform, and carbon tetrachloride.

Environment effect on spectral and charge distribution characteristics of some drugs of folate derivatives

NASA Astrophysics Data System (ADS)

Khadem Sadigh, M.; Zakerhamidi, M. S.; Seyed Ahmadian, S. M.; Johari-Ahar, M.; Zare Haghighi, L.

2017-01-01

Molecular surrounding media as an important factor can effect on the operation of wide variety of drugs. For more study in this paper, spectral properties of Methotrexate and Folinic acid have been studied in various solvents. Our results show that the photo-physical of solute molecules depend strongly on solute-solvent interactions and active groups in their chemical structures. In order to investigate the contribution of specific and nonspecific interactions on the various properties of drug molecules, the linear solvation energy relationships concept is used. Moreover, charge distribution characteristics of used samples with various resonance structures in solvent environments were calculated by means of solvatochromic method. The high value of dipole moments in excited state show that local intramolecular charge transfer can occur by excitation. These results about molecular interactions can be extended to biological systems and can indicate completely the behaviors of Methotrexate and Folinic acid in polar solvents such as water in body system.

Dissolution of covalent adaptable network polymers in organic solvent

NASA Astrophysics Data System (ADS)

Yu, Kai; Yang, Hua; Dao, Binh H.; Shi, Qian; Yakacki, Christopher M.

2017-12-01

It was recently reported that thermosetting polymers can be fully dissolved in a proper organic solvent utilizing a bond-exchange reaction (BER), where small molecules diffuse into the polymer, break the long polymer chains into short segments, and eventually dissolve the network when sufficient solvent is provided. The solvent-assisted dissolution approach was applied to fully recycle thermosets and their fiber composites. This paper presents the first multi-scale modeling framework to predict the dissolution kinetics and mechanics of thermosets in organic solvent. The model connects the micro-scale network dynamics with macro-scale material properties: in the micro-scale, a model is developed based on the kinetics of BERs to describe the cleavage rate of polymer chains and evolution of chain segment length during the dissolution. The micro-scale model is then fed into a continuum-level model with considerations of the transportation of solvent molecules and chain segments in the system. The model shows good prediction on conversion rate of functional groups, degradation of network mechanical properties, and dissolution rate of thermosets during the dissolution. It identifies the underlying kinetic factors governing the dissolution process, and reveals the influence of different material and processing variables on the dissolution process, such as time, temperature, catalyst concentration, and chain length between cross-links.

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.

Solubility of structurally complicated materials: 3. Hair.

PubMed

Horvath, Ari L

2009-04-27

Hair is composed of proteins, lipids, water, and small amounts of trace elements. All proteins in animal and human bodies are built from permutations of amino acid molecules in a polypeptide string. The polypeptide chains of protein keratin are organized into filaments in hair cells. Hair is one of the most difficult proteins to digest or solubilize. Among the most common dissolving procedures for hair are acidic, alkaline, and enzymatic hydrolysis. For the analysis of hair, the solid samples are transferred by solubilization via digestion into a liquid phase. Small molecular solvents and molecules with hydrophobic groups appear to have higher affinity for hair. A good solvent attacks the disulfide bonds between cystine molecules and hydrates the hair shaft. Consequently, the hair becomes a jelly-like mass.

Effects of monohydric alcohols and polyols on the thermal stability of a protein

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

Murakami, Shota; Kinoshita, Masahiro, E-mail: kinoshit@iae.kyoto-u.ac.jp

2016-03-28

The thermal stability of a protein is lowered by the addition of a monohydric alcohol, and this effect becomes larger as the size of hydrophobic group in an alcohol molecule increases. By contrast, it is enhanced by the addition of a polyol possessing two or more hydroxyl groups per molecule, and this effect becomes larger as the number of hydroxyl groups increases. Here, we show that all of these experimental observations can be reproduced even in a quantitative sense by rigid-body models focused on the entropic effect originating from the translational displacement of solvent molecules. The solvent is either puremore » water or water-cosolvent solution. Three monohydric alcohols and five polyols are considered as cosolvents. In the rigid-body models, a protein is a fused hard spheres accounting for the polyatomic structure in the atomic detail, and the solvent is formed by hard spheres or a binary mixture of hard spheres with different diameters. The effective diameter of cosolvent molecules and the packing fractions of water and cosolvent, which are crucially important parameters, are carefully estimated using the experimental data of properties such as the density of solid crystal of cosolvent, parameters in the pertinent cosolvent-cosolvent interaction potential, and density of water-cosolvent solution. We employ the morphometric approach combined with the integral equation theory, which is best suited to the physical interpretation of the calculation result. It is argued that the degree of solvent crowding in the bulk is the key factor. When it is made more serious by the cosolvent addition, the solvent-entropy gain upon protein folding is magnified, leading to the enhanced thermal stability. When it is made less serious, the opposite is true. The mechanism of the effects of monohydric alcohols and polyols is physically the same as that of sugars. However, when the rigid-body models are employed for the effect of urea, its addition is predicted to enhance the thermal stability, which conflicts with the experimental fact. We then propose, as two essential factors, not only the solvent-entropy gain but also the loss of protein-solvent interaction energy upon protein folding. The competition of changes in these two factors induced by the cosolvent addition determines the thermal-stability change.« less

Effects of monohydric alcohols and polyols on the thermal stability of a protein

NASA Astrophysics Data System (ADS)

Murakami, Shota; Kinoshita, Masahiro

2016-03-01

The thermal stability of a protein is lowered by the addition of a monohydric alcohol, and this effect becomes larger as the size of hydrophobic group in an alcohol molecule increases. By contrast, it is enhanced by the addition of a polyol possessing two or more hydroxyl groups per molecule, and this effect becomes larger as the number of hydroxyl groups increases. Here, we show that all of these experimental observations can be reproduced even in a quantitative sense by rigid-body models focused on the entropic effect originating from the translational displacement of solvent molecules. The solvent is either pure water or water-cosolvent solution. Three monohydric alcohols and five polyols are considered as cosolvents. In the rigid-body models, a protein is a fused hard spheres accounting for the polyatomic structure in the atomic detail, and the solvent is formed by hard spheres or a binary mixture of hard spheres with different diameters. The effective diameter of cosolvent molecules and the packing fractions of water and cosolvent, which are crucially important parameters, are carefully estimated using the experimental data of properties such as the density of solid crystal of cosolvent, parameters in the pertinent cosolvent-cosolvent interaction potential, and density of water-cosolvent solution. We employ the morphometric approach combined with the integral equation theory, which is best suited to the physical interpretation of the calculation result. It is argued that the degree of solvent crowding in the bulk is the key factor. When it is made more serious by the cosolvent addition, the solvent-entropy gain upon protein folding is magnified, leading to the enhanced thermal stability. When it is made less serious, the opposite is true. The mechanism of the effects of monohydric alcohols and polyols is physically the same as that of sugars. However, when the rigid-body models are employed for the effect of urea, its addition is predicted to enhance the thermal stability, which conflicts with the experimental fact. We then propose, as two essential factors, not only the solvent-entropy gain but also the loss of protein-solvent interaction energy upon protein folding. The competition of changes in these two factors induced by the cosolvent addition determines the thermal-stability change.

Ab Initio Modeling of the Electronic Absorption Spectrum of Previtamin D in Solution

NASA Astrophysics Data System (ADS)

Zhu, Tianyang

To study the solvent effects of water on the previtamin D absorption spectrum, we use the quantum mechanics (QM)/molecular mechanics (MM) method combined with replica-exchange molecular dynamics (REMD). The QM method is applied for the previtamin D molecule and the MM method is used for the water molecules. To enhance conformational sampling of the flexible previtamin D molecule we apply REMD. Based on the REMD structures, we calculate the macroscopic ensemble of the absorption spectrum in solution by time-dependent density functional theory (TDDFT). Comparison between the calculated spectrum in the gas phase and in the solution reveals minor influences of the solvent on the absorption spectrum. In the conventional molecule dynamics simulation, the previtamin D molecule can be trapped by local minimum and cannot overcome energetics barriers when it is calculated at the room temperature. In addition, the higher temperature calculation for the molecule in REMD allows to overcome energetics barriers and to change the structure to other rotational isomers, then switch to the lower temperature and gives a more complete result in the configuration space for the lower temperature.

Coordination-chemistry control of proton conductivity in the iconic metal-organic framework material HKUST-1.

PubMed

Jeong, Nak Cheon; Samanta, Bappaditya; Lee, Chang Yeon; Farha, Omar K; Hupp, Joseph T

2012-01-11

HKUST-1, a metal-organic framework (MOF) material containing Cu(II)-paddlewheel-type nodes and 1,3,5-benzenetricarboxylate struts, features accessible Cu(II) sites to which solvent or other desired molecules can be intentionally coordinated. As part of a broader investigation of ionic conductivity in MOFs, we unexpectedly observed substantial proton conductivity with the "as synthesized" version of this material following sorption of methanol. Although HKUST-1 is neutral, coordinated water molecules are rendered sufficiently acidic by Cu(II) to contribute protons to pore-filling methanol molecules and thereby enhance the alternating-current conductivity. At ambient temperature, the chemical identities of the node-coordinated and pore-filling molecules can be independently varied, thus enabling the proton conductivity to be reversibly modulated. The proton conductivity of HKUST-1 was observed to increase by ~75-fold, for example, when node-coordinated acetonitrile molecules were replaced by water molecules. In contrast, the conductivity became almost immeasurably small when methanol was replaced by hexane as the pore-filling solvent. © 2011 American Chemical Society

'Single molecule': theory and experiments, an introduction

PubMed Central

2013-01-01

At scales below micrometers, Brownian motion dictates most of the behaviors. The simple observation of a colloid is striking: a permanent and random motion is seen, whereas inertial forces play a negligible role. This Physics, where velocity is proportional to force, has opened new horizons in biology. The random feature is challenged in living systems where some proteins - molecular motors - have a directed motion whereas their passive behaviors of colloid should lead to a Brownian motion. Individual proteins, polymers of living matter such as DNA, RNA, actin or microtubules, molecular motors, all these objects can be viewed as chains of colloids. They are submitted to shocks from molecules of the solvent. Shapes taken by these biopolymers or dynamics imposed by motors can be measured and modeled from single molecules to their collective effects. Thanks to the development of experimental methods such as optical tweezers, Atomic Force Microscope (AFM), micropipettes, and quantitative fluorescence (such as Förster Resonance Energy Transfer, FRET), it is possible to manipulate these individual biomolecules in an unprecedented manner: experiments allow to probe the validity of models; and a new Physics has thereby emerged with original biological insights. Theories based on statistical mechanics are needed to explain behaviors of these systems. When force-extension curves of these molecules are extracted, the curves need to be fitted with models that predict the deformation of free objects or submitted to a force. When velocity of motors is altered, a quantitative analysis is required to explain the motions of individual molecules under external forces. This lecture will give some elements of introduction to the lectures of the session 'Nanophysics for Molecular Biology'. PMID:24565227

Humoral and cell-mediated immune responses elicited by poly (DL-lactide) adjuvanted filarial antigen molecules.

PubMed

Saini, Vinay; Verma, Atul Kumar; Kushwaha, Vikas; Joseph, Sujith Kurian; Murthy, P Kalpna; Kohli, Dharmveer

2014-05-01

In our recent studies, Brugia malayi molecules have shown interesting immune-stimulating and immune-suppressive properties. Among these, F6 a pro-inflammatory (54-68 kDa) SDS-PAGE resolved fraction of the parasite when administered with Freund's complete/incomplete adjuvant in animals, elicited both Th1 and Th2 type immune responses and protects the host from filarial parasite. The present study was aimed at developing biodegradable microspheres for filarial antigenic protein molecules and to investigate the immunoadjuvanticity of microspheres (Ms)-loaded F6 molecules. Poly-lactide microspheres (DL-PLA-Ms) were prepared using double emulsification and solvent evaporation method; and studied their size, shape, antigen adsorption efficiency, in-process stability, and antigen release profiles. F6 and B. malayi adult worm (BmA: ∼ 17 to 180 kDa) protein molecules adsorbed on the Ms were administered in a single shot into Swiss mice, subcutaneously, and investigated their immunoadjuvant effect and compared with one/two doses-schedule of plain F6/BmA. Immunization with F6/BmA-loaded DL-PLA-Ms resulted in upregulation of cellular proliferation, IFN- γ, TNF-α and NO release from host's cells stimulated with F6/BmA or LPS/Con A, IgG, IgG1 and IgG2a levels. These responses were well comparable with the responses produced by two doses of plain BmA/F6. In conclusion, a single dose of DL-PLA-Ms-F6 induced predominantly Th1 immune responses and well comparable with two doses of plain F6. This is the first ever report on potential of DL-PLA-Ms as adjuvant for filarial immunogen.

TMAO and urea in the hydration shell of the protein SNase.

PubMed

Smolin, Nikolai; Voloshin, Vladimir P; Anikeenko, Alexey V; Geiger, Alfons; Winter, Roland; Medvedev, Nikolai N

2017-03-01

We performed all-atom MD simulations of the protein SNase in aqueous solution and in the presence of two major osmolytes, trimethylamine-N-oxide (TMAO) and urea, as cosolvents at various concentrations and compositions and at different pressures and temperatures. The distributions of the cosolvent molecules and their orientation in the surroundings of the protein were analyzed in great detail. The distribution of urea is largely conserved near the protein. It varies little with pressure and temperature, and does practically not depend on the addition of TMAO. The slight decrease with temperature of the number of urea molecules that are in contact with the SNase molecule is consistent with the view that the interaction of the protein with urea is mainly of enthalpic nature. Most of the TMAO molecules tend to be oriented to the protein by its methyl groups, a small amount of these molecules contact the protein by its oxygen, forming hydrogen bonds with the protein, only. Unlike urea, the fraction of TMAO in the hydration shell of SNase slightly increases with temperature (a signature of a prevailing hydrophobic interaction between TMAO and SNase), and decreases significantly upon the addition of urea. This behavior reflects the diverse nature of the interaction of the two osmolytes with the protein. Using the Voronoi volume of the atoms of the solvent molecules (water, urea, TMAO), we compared the fraction of the volume occupied by a given type of solvent molecule in the hydration shell and in the bulk solvent. The volume fraction of urea in the hydration shell is more than two times larger than in the bulk, whereas the volume fraction of TMAO in the hydration shell is only slightly larger in the binary solvent (TMAO + water) and becomes even less than in the bulk in the ternary solvent (TMAO + water + urea). Thus, TMAO tends to be excluded from the hydration shell of the protein. The behavior of the two cosolvents in the vicinity of the protein does not change much with pressure (from 1 to 5000 bar) and temperature (from 280 to 330 K). This is also in line with the conception of the "osmophobic effect" of TMAO to protect proteins from denaturation also at harsh environmental conditions. We also calculated the volumetric parameters of SNase and found that the cosolvents have a small but significant effect on the apparent volume and its contributions, i.e. the intrinsic, molecular and thermal volumes.

Microsolvation of the potassium ion with aromatic rings: comparison between hexafluorobenzene and benzene.

PubMed

Marques, J M C; Llanio-Trujillo, J L; Albertí, M; Aguilar, A; Pirani, F

2013-08-22

We employ a recently developed methodology to study structural and energetic properties of the first solvation shells of the potassium ion in nonpolar environments due to aromatic rings, which is important to understand the selectivity of several biochemical phenomena. Our evolutionary algorithm is used in the global optimization study of clusters formed of K(+) solvated with hexafluorobenzene (HFBz) molecules. The global intermolecular interaction for these clusters has been decomposed in HFBz-HFBz and in K(+)-HFBz contributions, using a potential model based on different decompositions of the molecular polarizability of hexafluorobenzene. Putative global minimum structures of microsolvation clusters up to 21 hexafluorobenzene molecules were obtained and compared with the analogous K(+)-benzene clusters reported in our previous work (J. Phys. Chem. A 2012, 116, 4947-4956). We have found that both K(+)-(Bz)n and K(+)-(HFBz)n clusters show a strong magic number around the closure of the first solvation shell. Nonetheless, all K(+)-benzene clusters have essentially the same first solvation shell geometry with four solvent molecules around the ion, whereas the corresponding one for K(+)-(HFBz)n is completed with nine HFBz species, and its structural motif varies as n increases. This is attributed to the ion-solvent interaction that has a larger magnitude for K(+)-Bz than in the case of K(+)-HFBz. In addition, the ability of having more HFBz than Bz molecules around K(+) in the first solvation shell is intimately related to the inversion in the sign of the quadrupole moment of the two solvent species, which leads to a distinct ion-solvent geometry of approach.

Molecular Dynamics Study of the Solution Structure, Clustering, and Diffusion of Four Aqueous Alkanolamines.

PubMed

Melnikov, Sergey M; Stein, Matthias

2018-03-15

CO 2 sequestration from anthropogenic resources is a challenge to the design of environmental processes at a large scale. Reversible chemical absorption by amine-based solvents is one of the most efficient methods of CO 2 removal. Molecular simulation techniques are very useful tools to investigate CO 2 binding by aqueous alkanolamine molecules for further technological application. In the present work, we have performed detailed atomistic molecular dynamics simulations of aqueous solutions of three prototype amines: monoethanolamine (MEA) as a standard, 3-aminopropanol (MPA), 2-methylaminoethanol (MMEA), and 4-diethylamino-2-butanol (DEAB) as potential novel CO 2 absorptive solvents. Solvent densities, radial distribution functions, cluster size distributions, hydrogen-bonding statistics, and diffusion coefficients for a full range of mixture compositions have been obtained. The solvent densities and diffusion coefficients from simulations are in good agreement with those in the experiment. In aqueous solution, MEA, MPA, and MMEA molecules prefer to be fully solvated by water molecules, whereas DEAB molecules tend to self-aggregate. In a range from 30/70-50/50 (w/w) alkanolamine/water mixtures, they form a bicontinuous phase (both alkanolamine and water are organized in two mutually percolating clusters). Among the studied aqueous alkanolamine solutions, the diffusion coefficients decrease in the following order MEA > MPA = MMEA > DEAB. With an increase of water content, the diffusion coefficients increase for all studied alkanolamines. The presented results are a first step for process-scale simulation and provide important qualitative and quantitative information for the design and engineering of efficient new CO 2 removal processes.

Effect of Organic Solvents on Microalgae Growth, Metabolism and Industrial Bioproduct Extraction: A Review.

PubMed

Miazek, Krystian; Kratky, Lukas; Sulc, Radek; Jirout, Tomas; Aguedo, Mario; Richel, Aurore; Goffin, Dorothee

2017-07-04

In this review, the effect of organic solvents on microalgae cultures from molecular to industrial scale is presented. Traditional organic solvents and solvents of new generation-ionic liquids (ILs), are considered. Alterations in microalgal cell metabolism and synthesis of target products (pigments, proteins, lipids), as a result of exposure to organic solvents, are summarized. Applications of organic solvents as a carbon source for microalgal growth and production of target molecules are discussed. Possible implementation of various industrial effluents containing organic solvents into microalgal cultivation media, is evaluated. The effect of organic solvents on extraction of target compounds from microalgae is also considered. Techniques for lipid and carotenoid extraction from viable microalgal biomass (milking methods) and dead microalgal biomass (classical methods) are depicted. Moreover, the economic survey of lipid and carotenoid extraction from microalgae biomass, by means of different techniques and solvents, is conducted.

Effect of Organic Solvents on Microalgae Growth, Metabolism and Industrial Bioproduct Extraction: A Review

PubMed Central

Miazek, Krystian; Sulc, Radek; Jirout, Tomas; Aguedo, Mario; Goffin, Dorothee

2017-01-01

In this review, the effect of organic solvents on microalgae cultures from molecular to industrial scale is presented. Traditional organic solvents and solvents of new generation-ionic liquids (ILs), are considered. Alterations in microalgal cell metabolism and synthesis of target products (pigments, proteins, lipids), as a result of exposure to organic solvents, are summarized. Applications of organic solvents as a carbon source for microalgal growth and production of target molecules are discussed. Possible implementation of various industrial effluents containing organic solvents into microalgal cultivation media, is evaluated. The effect of organic solvents on extraction of target compounds from microalgae is also considered. Techniques for lipid and carotenoid extraction from viable microalgal biomass (milking methods) and dead microalgal biomass (classical methods) are depicted. Moreover, the economic survey of lipid and carotenoid extraction from microalgae biomass, by means of different techniques and solvents, is conducted. PMID:28677659

Face-Dependent Solvent Adsorption: A Comparative Study on the Interfaces of HMX Crystal with Three Solvents.

PubMed

Liu, Yingzhe; Lai, Weipeng; Ma, Yiding; Yu, Tao; Kang, Ying; Ge, Zhongxue

2017-07-27

To understand the crystal-solvent interfacial interactions on the molecular scale, the interfaces between three solvents, that is, acetone, γ-butyrolactone, and cyclohexanone, and three growth faces of 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX) crystal have been investigated with the aid of theoretical chemistry. The results show that the structural features of crystal faces play a critical role in the energetic, structural, and dynamic properties at the interfaces. For each solvent, the same change trend of some properties among the three faces of HMX crystal is observed, including adsorption affinity, local mass density, and solvent diffusion. For example, the rate of solvent diffusion at the three faces ranks as (011) > (110) > (020) regardless of solvent species. This can be attributed to the similar adsorption sites for solvent incorporation at the same face, which are concentrated at the cavities formed by surficial HMX molecules.

Solvent effects in time-dependent self-consistent field methods. I. Optical response calculations

DOE PAGES

Bjorgaard, J. A.; Kuzmenko, V.; Velizhanin, K. A.; ...

2015-01-22

In this study, we implement and examine three excited state solvent models in time-dependent self-consistent field methods using a consistent formalism which unambiguously shows their relationship. These are the linear response, state specific, and vertical excitation solvent models. Their effects on energies calculated with the equivalent of COSMO/CIS/AM1 are given for a set of test molecules with varying excited state charge transfer character. The resulting solvent effects are explained qualitatively using a dipole approximation. It is shown that the fundamental differences between these solvent models are reflected by the character of the calculated excitations.

Spectroscopic, DFT, and XRD Studies of Hydrogen Bonds in N-Unsubstituted 2-Aminobenzamides.

PubMed

Mphahlele, Malose Jack; Maluleka, Marole Maria; Rhyman, Lydia; Ramasami, Ponnadurai; Mampa, Richard Mokome

2017-01-04

The structures of the mono- and the dihalogenated N -unsubstituted 2-aminobenzamides were characterized by means of the spectroscopic (¹H-NMR, UV-Vis, FT-IR, and FT-Raman) and X-ray crystallographic techniques complemented with a density functional theory (DFT) method. The hindered rotation of the C(O)-NH₂ single bond resulted in non-equivalence of the amide protons and therefore two distinct resonances of different chemical shift values in the ¹H-NMR spectra of these compounds were observed. 2-Amino-5-bromobenzamide ( ABB ) as a model confirmed the presence of strong intramolecular hydrogen bonds between oxygen and the amine hydrogen. However, intramolecular hydrogen bonding between the carbonyl oxygen and the amine protons was not observed in the solution phase due to a rapid exchange of these two protons with the solvent and fast rotation of the Ar-NH₂ single bond. XRD also revealed the ability of the amide unit of these compounds to function as a hydrogen bond donor and acceptor simultaneously to form strong intermolecular hydrogen bonding between oxygen of one molecule and the NH moiety of the amine or amide group of the other molecule and between the amine nitrogen and the amide hydrogen of different molecules. DFT calculations using the B3LYP/6-311++G(d,p) basis set revealed that the conformer ( A ) with oxygen and 2-amine on the same side predominates possibly due to the formation of a six-membered intramolecular ring, which is assisted by hydrogen bonding as observed in the single crystal XRD structure.

Computational screening of biomolecular adsorption and self-assembly on nanoscale surfaces.

PubMed

Heinz, Hendrik

2010-05-01

The quantification of binding properties of ions, surfactants, biopolymers, and other macromolecules to nanometer-scale surfaces is often difficult experimentally and a recurring challenge in molecular simulation. A simple and computationally efficient method is introduced to compute quantitatively the energy of adsorption of solute molecules on a given surface. Highly accurate summation of Coulomb energies as well as precise control of temperature and pressure is required to extract the small energy differences in complex environments characterized by a large total energy. The method involves the simulation of four systems, the surface-solute-solvent system, the solute-solvent system, the solvent system, and the surface-solvent system under consideration of equal molecular volumes of each component under NVT conditions using standard molecular dynamics or Monte Carlo algorithms. Particularly in chemically detailed systems including thousands of explicit solvent molecules and specific concentrations of ions and organic solutes, the method takes into account the effect of complex nonbond interactions and rotational isomeric states on the adsorption behavior on surfaces. As a numerical example, the adsorption of a dodecapeptide on the Au {111} and mica {001} surfaces is described in aqueous solution. Copyright 2009 Wiley Periodicals, Inc.

Dynamical discrete/continuum linear response shells theory of solvation: convergence test for NH4+ and OH- ions in water solution using DFT and DFTB methods.

PubMed

de Lima, Guilherme Ferreira; Duarte, Hélio Anderson; Pliego, Josefredo R

2010-12-09

A new dynamical discrete/continuum solvation model was tested for NH(4)(+) and OH(-) ions in water solvent. The method is similar to continuum solvation models in a sense that the linear response approximation is used. However, different from pure continuum models, explicit solvent molecules are included in the inner shell, which allows adequate treatment of specific solute-solvent interactions present in the first solvation shell, the main drawback of continuum models. Molecular dynamics calculations coupled with SCC-DFTB method are used to generate the configurations of the solute in a box with 64 water molecules, while the interaction energies are calculated at the DFT level. We have tested the convergence of the method using a variable number of explicit water molecules and it was found that even a small number of waters (as low as 14) are able to produce converged values. Our results also point out that the Born model, often used for long-range correction, is not reliable and our method should be applied for more accurate calculations.

(η(6)-Benzene)(carbonato-κ(2) O,O')[di-cyclohex-yl(naphthalen-1-ylmeth-yl)phosphane-κP]ruthenium(II) chloro-form tris-olvate.

PubMed

Gowrisankar, Saravanan; Neumann, Helfried; Spannenberg, Anke; Beller, Matthias

2014-07-01

The title compound, [Ru(CO3)(η(6)-C6H6){(C6H11)2P(CH2C10H7)}]·3CHCl3, was synthesized by carbonation of [RuCl2(η(6)-C6H6){(C6H11)2P(CH2C10H7)}] with NaHCO3 in methanol at room temperature. The Ru(II) atom is surrounded by a benzene ligand, a chelating carbonate group and a phosphane ligand in a piano-stool configuration. The crystal packing is consolidated by C-H⋯O and C-H⋯Cl hydrogen-bonding inter-actions between adjacent metal complexes and between the complexes and the solvent mol-ecules. The asymmetric unit contains one metal complex and three chloro-form solvent mol-ecules of which only one was modelled. The estimated diffraction contributions of the other two strongly disordered chloro-form solvent mol-ecules were substracted from the observed diffraction data using the SQUEEZE procedure in PLATON [Spek (2009 ▶). Acta Cryst. D65, 148-155].

Co(II)-doped MOF-5 nano/microcrystals: Solvatochromic behaviour, sensing solvent molecules and gas sorption property

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

Yang, Ji-Min; School of Chemistry and Chemical Engineering, Linyi University, Linyi 276005; Liu, Qing

2014-10-15

Co(II)-doped MOF-5 nano/microcrystals with controllable morphology and size were successfully obtained by solvothermal method. The products were characterized by powder X-ray diffraction (PXRD), energy dispersive spectrometry (EDS), field emission scanning electron microscopy (FESEM), thermogravimetric analysis (TGA), inductively coupled plasma optical emission spectrometer (ICP-OES), elemental analysis, UV–vis and infrared (IR) spectroscopy. The factors influencing the crystal morphology and size were investigated. The gas sorption measurements reveal that highly crystalline particles have large Langmuir surface area. It was found that the Co(II)-doped MOF-5 shows enhanced hydrostability and the sorption profiles of the Co(II)-doped MOF-5 nano/microcrystals are dependent on the morphology and sizemore » of the particles. Porous Co(II)-doped MOF-5 is stable upon the removal of guest molecules and exhibits different colour with accommodating different solvent molecule, which means that it can act as solvatochromic sensing materials for recognition of solvent molecules. - Graphical abstract: Co(II)-doped MOF-5 nano/microcrystals with different shapes and sizes were synthesized by a facile hydrothermal method, which not only enhance gas sorption properties and structural stability of MOFs towards moisture, but also act as new sensing materials for sensing small molecules. - Highlights: • Co(II)-doped MOF-5 nano/microcrystals with controllable morphology and size were obtained. • Co(II)-doped MOF-5 nano/microcrystals enhance the structural stability towards moisture. • Co(II)-doped MOF-5 can act as new sensing material for sensing small molecules.« less

Hydrogen/deuterium (H/D) exchange of gelatinized starch studied by two-dimensional (2D) near-infrared (NIR) correlation spectroscopy

NASA Astrophysics Data System (ADS)

Shinzawa, Hideyuki; Mizukado, Junji

2018-05-01

Hydrogen/deuterium (H/D) exchange of gelatinized starch was probed by in-situ near-infrared (NIR) monitoring coupled with two-dimensional (2D) correlation spectroscopy. Gelatinized starch undergoes spontaneous H/D exchange in D2O. During the substitution, the exchange rate essentially becomes different depending on solvent accessibility of various parts of the molecule. Thus, by analyzing the change in the NIR feature observed during the substitution, it becomes possible to sort out local structure and dynamics of the system. 2D correlation analysis of the time-dependent NIR spectra reveals the presence of different local structure of the starch, each having different solvent accessibility. For example, during the H/D exchange, the D2O is first absorbed by starch molecules especially around the surface area between the starch and water, where the water molecules are weakly interacted with the starch molecules. This absorption is quickly followed by the development of HDO species. Further absorption of the D2O results in the penetration of the molecules inside the starch and eventually develops the relatively strong interaction between the HDO and starch molecules because of the presence of dominant starch molecules.

Heterometallic molecular precursors for a lithium-iron oxide material: synthesis, solid state structure, solution and gas-phase behaviour, and thermal decomposition.

PubMed

Han, Haixiang; Wei, Zheng; Barry, Matthew C; Filatov, Alexander S; Dikarev, Evgeny V

2017-05-02

Three heterometallic single-source precursors with a Li : Fe = 1 : 1 ratio for a LiFeO 2 oxide material are reported. Heterometallic compounds LiFeL 3 (L = tbaoac (1), ptac (2), and acac(3)) have been obtained on a large scale, in nearly quantitative yields by one-step reactions that employ readily available reagents. The heterometallic precursor LiFe(acac) 3 (3) with small, symmetric substituents on the ligand (acac = pentane-2,4-dionate), maintains a 1D polymeric structure in the solid state that limits its volatility and prevents solubility in non-coordinating solvents. The application of the unsymmetrical ligands, tbaoac (tert-butyl acetoacetate) and ptac (1,1,1-trifluoro-5,5-dimethyl-2,4-hexanedionate), that exhibit different bridging properties at the two ends of the ligand, allowed us to change the connectivity pattern within the heterometallic assembly. The latter was demonstrated by structural characterization of heterometallic complexes LiFe(tbaoac) 3 (1) and LiFe(ptac) 3 (2) that consist of discrete heterocyclic tetranuclear molecules Li 2 Fe 2 L 6 . The compounds are highly volatile and exhibit a congruent sublimation character. DART mass spectrometric investigation revealed the presence of heterometallic molecules in the gas phase. The positive mode spectra are dominated by the presence of [M - L] + peaks (M = Li 2 Fe 2 L 6 ). In accord with their discrete molecular structure, complexes 1 and 2 are highly soluble in nearly all common solvents. In order to test the retention of the heterometallic structure in solution, the diamagnetic analog of 1, LiMg(tbaoac) 3 (4), has been isolated. Its tetranuclear molecular structure was found to be isomorphous to that of the iron counterpart. 1 H and 7 Li NMR spectroscopy unambiguously confirmed the presence of heterometallic molecules in solutions of non-coordinating solvents. The heterometallic precursor 1 was shown to exhibit clean thermal decomposition in air that results in phase-pure α-modification of layered oxide LiFeO 2 , the prospective cathode material for lithium ion batteries.

Influence of solvent composition on the performance of carbodiimide cross-linked gelatin carriers for retinal sheet delivery.

PubMed

Lai, Jui-Yang

2013-09-01

Gelatin is a protein molecule that displays bioaffinity and provides a template to guide retinal pigment epithelial (RPE) cell organization and growth. We have recently demonstrated that the carbodiimide cross-linked gelatin membranes can be used as retinal sheet carriers. The purpose of this work was to further determine the role of solvent composition in the tissue delivery performance of chemically modified biopolymer matrices. The gelatin molecules were treated with 1-ethyl-3-(3-dimethyl aminopropyl) carbodiimide (EDC) in the presence of binary ethanol/water mixtures with varying ethanol concentrations (70-95 vol%) to obtain the carriers with different cross-linking efficiencies and mechanical properties. Results of melting point measurements and in vitro degradation tests showed that when the cross-linking index reached a high level of around 45 %, the EDC cross-linked gelatin materials have sufficient thermal stability and resistance to enzymatic degradation, indicating their suitability for the development of carriers for retinal sheet delivery. Irrespective of the solvent composition, the chemically modified gelatin samples are compatible toward human RPE cells without causing toxicity and inflammation. In particular, the membrane carriers prepared by the cross-linking in the presence of solvent mixtures containing 80-90 vol% of ethanol have no impact on the proliferative capacity of ARPE-19 cultures and possess good efficiency in transferring and encapsulating the retinal tissues. It is concluded that, except for cell viability and pro-inflammatory cytokine expression, the retinal sheet delivery performance strongly depends on the solvent composition for EDC cross-linking of gelatin molecules.

Crystal Nucleation of Tolbutamide in Solution: Relationship to Solvent, Solute Conformation, and Solution Structure.

PubMed

Zeglinski, Jacek; Kuhs, Manuel; Khamar, Dikshitkumar; Hegarty, Avril C; Devi, Renuka K; Rasmuson, Åke C

2018-04-03

The influence of the solvent in nucleation of tolbutamide, a medium-sized, flexible and polymorphic organic molecule, has been explored by measuring nucleation induction times, estimating solvent-solute interaction enthalpies using molecular modelling and calorimetric data, probing interactions and clustering with spectroscopy, and modelling solvent-dependence of molecular conformation in solution. The nucleation driving force required to reach the same induction time is strongly solvent-dependent, increasing in the order: acetonitrile

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

Riedel, Clement; Gabizon, Ronen; Wilson, Christian A. M.

Recent studies have shown that the diffusivity of enzymes increases in a substrate-dependent manner during catalysis. Although this observation has been reported and characterized for several different systems, the precise origin of this phenomenon is unknown. Calorimetric methods are often used to determine enthalpies from enzyme-catalysed reactions and can therefore provide important insight into their reaction mechanisms. The ensemble averages involved in traditional bulk calorimetry cannot probe the transient effects that the energy exchanged in a reaction may have on the catalyst. Here we obtain single-molecule fluorescence correlation spectroscopy data and analyse them within the framework of a stochastic theorymore » to demonstrate a mechanistic link between the enhanced diffusion of a single enzyme molecule and the heat released in the reaction. We propose that the heat released during catalysis generates an asymmetric pressure wave that results in a differential stress at the protein-solvent interface that transiently displaces the centre-of-mass of the enzyme (chemoacoustic effect). We find this novel perspective on how enzymes respond to the energy released during catalysis suggests a possible effect of the heat of reaction on the structural integrity and internal degrees of freedom of the enzyme.« less

The heat released during catalytic turnover enhances the diffusion of an enzyme

PubMed Central

Riedel, Clement; Gabizon, Ronen; Wilson, Christian A. M.; Hamadani, Kambiz; Tsekouras, Konstantinos; Marqusee, Susan; Pressé, Steve; Bustamante, Carlos

2015-01-01

Recent studies have shown that the diffusivity of enzymes increases in a substrate-dependent manner during catalysis1,2. Although this observation has been reported and characterized for several different systems3–10, the precise origin of this phenomenon is unknown. Calorimetric methods are often used to determine enthalpies from enzyme-catalysed reactions and can therefore provide important insight into their reaction mechanisms11,12. The ensemble averages involved in traditional bulk calorimetry cannot probe the transient effects that the energy exchanged in a reaction may have on the catalyst. Here we obtain single-molecule fluorescence correlation spectroscopy data and analyse them within the framework of a stochastic theory to demonstrate a mechanistic link between the enhanced diffusion of a single enzyme molecule and the heat released in the reaction. We propose that the heat released during catalysis generates an asymmetric pressure wave that results in a differential stress at the protein–solvent interface that transiently displaces the centre-of-mass of the enzyme (chemoacoustic effect). This novel perspective on how enzymes respond to the energy released during catalysis suggests a possible effect of the heat of reaction on the structural integrity and internal degrees of freedom of the enzyme. PMID:25487146

The heat released during catalytic turnover enhances the diffusion of an enzyme

DOE PAGES

Riedel, Clement; Gabizon, Ronen; Wilson, Christian A. M.; ...

2014-12-10

Recent studies have shown that the diffusivity of enzymes increases in a substrate-dependent manner during catalysis. Although this observation has been reported and characterized for several different systems, the precise origin of this phenomenon is unknown. Calorimetric methods are often used to determine enthalpies from enzyme-catalysed reactions and can therefore provide important insight into their reaction mechanisms. The ensemble averages involved in traditional bulk calorimetry cannot probe the transient effects that the energy exchanged in a reaction may have on the catalyst. Here we obtain single-molecule fluorescence correlation spectroscopy data and analyse them within the framework of a stochastic theorymore » to demonstrate a mechanistic link between the enhanced diffusion of a single enzyme molecule and the heat released in the reaction. We propose that the heat released during catalysis generates an asymmetric pressure wave that results in a differential stress at the protein-solvent interface that transiently displaces the centre-of-mass of the enzyme (chemoacoustic effect). We find this novel perspective on how enzymes respond to the energy released during catalysis suggests a possible effect of the heat of reaction on the structural integrity and internal degrees of freedom of the enzyme.« less

Programmable colloidal molecules from sequential capillarity-assisted particle assembly

PubMed Central

Ni, Songbo; Leemann, Jessica; Buttinoni, Ivo; Isa, Lucio; Wolf, Heiko

2016-01-01

The assembly of artificial nanostructured and microstructured materials which display structures and functionalities that mimic nature’s complexity requires building blocks with specific and directional interactions, analogous to those displayed at the molecular level. Despite remarkable progress in synthesizing “patchy” particles encoding anisotropic interactions, most current methods are restricted to integrating up to two compositional patches on a single “molecule” and to objects with simple shapes. Currently, decoupling functionality and shape to achieve full compositional and geometrical programmability remains an elusive task. We use sequential capillarity-assisted particle assembly which uniquely fulfills the demands described above. This is a new method based on simple, yet essential, adaptations to the well-known capillary assembly of particles over topographical templates. Tuning the depth of the assembly sites (traps) and the surface tension of moving droplets of colloidal suspensions enables controlled stepwise filling of traps to “synthesize” colloidal molecules. After deposition and mechanical linkage, the colloidal molecules can be dispersed in a solvent. The template’s shape solely controls the molecule’s geometry, whereas the filling sequence independently determines its composition. No specific surface chemistry is required, and multifunctional molecules with organic and inorganic moieties can be fabricated. We demonstrate the “synthesis” of a library of structures, ranging from dumbbells and triangles to units resembling bar codes, block copolymers, surfactants, and three-dimensional chiral objects. The full programmability of our approach opens up new directions not only for assembling and studying complex materials with single-particle-level control but also for fabricating new microscale devices for sensing, patterning, and delivery applications. PMID:27051882

Water solvent effects using continuum and discrete models: The nitromethane molecule, CH3NO2.

PubMed

Modesto-Costa, Lucas; Uhl, Elmar; Borges, Itamar

2015-11-15

The first three valence transitions of the two nitromethane conformers (CH3NO2) are two dark n → π* transitions and a very intense π → π* transition. In this work, these transitions in gas-phase and solvated in water of both conformers were investigated theoretically. The polarizable continuum model (PCM), two conductor-like screening (COSMO) models, and the discrete sequential quantum mechanics/molecular mechanics (S-QM/MM) method were used to describe the solvation effect on the electronic spectra. Time dependent density functional theory (TDDFT), configuration interaction including all single substitutions and perturbed double excitations (CIS(D)), the symmetry-adapted-cluster CI (SAC-CI), the multistate complete active space second order perturbation theory (CASPT2), and the algebraic-diagrammatic construction (ADC(2)) electronic structure methods were used. Gas-phase CASPT2, SAC-CI, and ADC(2) results are in very good agreement with published experimental and theoretical spectra. Among the continuum models, PCM combined either with CASPT2, SAC-CI, or B3LYP provided good agreement with available experimental data. COSMO combined with ADC(2) described the overall trends of the transition energy shifts. The effect of increasing the number of explicit water molecules in the S-QM/MM approach was discussed and the formation of hydrogen bonds was clearly established. By including explicitly 24 water molecules corresponding to the complete first solvation shell in the S-QM/MM approach, the ADC(2) method gives more accurate results as compared to the TDDFT approach and with similar computational demands. The ADC(2) with S-QM/MM model is, therefore, the best compromise for accurate solvent calculations in a polar environment. © 2015 Wiley Periodicals, Inc.

Optoelectronic functional materials based on alkylated-π molecules: self-assembled architectures and nonassembled liquids.

PubMed

Li, Hongguang; Choi, Jiyoung; Nakanishi, Takashi

2013-05-07

The engineering of single molecules into higher-order hierarchical assemblies is a current research focus in molecular materials chemistry. Molecules containing π-conjugated units are an important class of building blocks because their self-assembly is not only of fundamental interest, but also the key to fabricating functional systems for organic electronic and photovoltaic applications. Functionalizing the π-cores with "alkyl chains" is a common strategy in the molecular design that can give the system desirable properties, such as good solubility in organic solvents for solution processing. Moreover, the alkylated-π system can regulate the self-assembly behavior by fine-tuning the intermolecular forces. The optimally assembled structures can then exhibit advanced functions. However, while some general rules have been revealed, a comprehensive understanding of the function played by the attached alkyl chains is still lacking, and current methodology is system-specific in many cases. Better clarification of this issue requires contributions from carefully designed libraries of alkylated-π molecular systems in both self-assembly and nonassembly materialization strategies. Here, based on recent efforts toward this goal, we show the power of the alkyl chains in controlling the self-assembly of soft molecular materials and their resulting optoelectronic properties. The design of alkylated-C60 is selected from our recent research achievements, as the most attractive example of such alkylated-π systems. Some other closely related systems composed of alkyl chains and π-units are also reviewed to indicate the universality of the methodology. Finally, as a contrast to the self-assembled molecular materials, nonassembled, solvent-free, novel functional liquid materials are discussed. In doing so, a new journey toward the ultimate organic "soft" materials is introduced, based on alkylated-π molecular design.

Extended Hansen solubility approach: naphthalene in individual solvents.

PubMed

Martin, A; Wu, P L; Adjei, A; Beerbower, A; Prausnitz, J M

1981-11-01

A multiple regression method using Hansen partial solubility parameters, delta D, delta p, and delta H, was used to reproduce the solubilities of naphthalene in pure polar and nonpolar solvents and to predict its solubility in untested solvents. The method, called the extended Hansen approach, was compared with the extended Hildebrand solubility approach and the universal-functional-group-activity-coefficient (UNIFAC) method. The Hildebrand regular solution theory was also used to calculate naphthalene solubility. Naphthalene, an aromatic molecule having no side chains or functional groups, is "well-behaved', i.e., its solubility in active solvents known to interact with drug molecules is fairly regular. Because of its simplicity, naphthalene is a suitable solute with which to initiate the difficult study of solubility phenomena. The three methods tested (Hildebrand regular solution theory was introduced only for comparison of solubilities in regular solution) yielded similar results, reproducing naphthalene solubilities within approximately 30% of literature values. In some cases, however, the error was considerably greater. The UNIFAC calculation is superior in that it requires only the solute's heat of fusion, the melting point, and a knowledge of chemical structures of solute and solvent. The extended Hansen and extended Hildebrand methods need experimental solubility data on which to carry out regression analysis. The extended Hansen approach was the method of second choice because of its adaptability to solutes and solvents from various classes. Sample calculations are included to illustrate methods of predicting solubilities in untested solvents at various temperatures. The UNIFAC method was successful in this regard.

FINAL REPORT: Room Temperature Hydrogen Storage in Nano-Confined Liquids

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

VAJO, JOHN

2014-06-12

DOE continues to seek solid-state hydrogen storage materials with hydrogen densities of ≥6 wt% and ≥50 g/L that can deliver hydrogen and be recharged at room temperature and moderate pressures enabling widespread use in transportation applications. Meanwhile, development including vehicle engineering and delivery infrastructure continues for compressed-gas hydrogen storage systems. Although compressed gas storage avoids the materials-based issues associated with solid-state storage, achieving acceptable volumetric densities has been a persistent challenge. This project examined the possibility of developing storage materials that would be compatible with compressed gas storage technology based on enhanced hydrogen solubility in nano-confined liquid solvents. These materialsmore » would store hydrogen in molecular form eliminating many limitations of current solid-state materials while increasing the volumetric capacity of compressed hydrogen storage vessels. Experimental methods were developed to study hydrogen solubility in nano-confined liquids. These methods included 1) fabrication of composites comprised of volatile liquid solvents for hydrogen confined within the nano-sized pore volume of nanoporous scaffolds and 2) measuring the hydrogen uptake capacity of these composites without altering the composite composition. The hydrogen storage capacities of these nano-confined solvent/scaffold composites were compared with bulk solvents and with empty scaffolds. The solvents and scaffolds were varied to optimize the enhancement in hydrogen solubility that accompanies confinement of the solvent. In addition, computational simulations were performed to study the molecular-scale structure of liquid solvent when confined within an atomically realistic nano-sized pore of a model scaffold. Confined solvent was compared with similar simulations of bulk solvent. The results from the simulations were used to formulate a mechanism for the enhanced solubility and to guide the experiments. Overall, the combined experimental measurements and simulations indicate that hydrogen storage based on enhanced solubility in nano-confined liquids is unlikely to meet the storage densities required for practical use. Only low gravimetric capacities of < 0.5 wt% were achieved. More importantly, solvent filled scaffolds had lower volumetric capacities than corresponding empty scaffolds. Nevertheless, several of the composites measured did show significant (>~ 5x) enhanced hydrogen solubility relative to bulk solvent solubility, when the hydrogen capacity was attributed only to dissolution in the confined solvent. However, when the hydrogen capacity was compared to an empty scaffold that is known to store hydrogen by surface adsorption on the scaffold walls, including the solvent always reduced the hydrogen capacity. For the best composites, this reduction relative to an empty scaffold was ~30%; for the worst it was ~90%. The highest capacities were obtained with the largest solvent molecules and with scaffolds containing 3- dimensionally confined pore geometries. The simulations suggested that the capacity of the composites originated from hydrogen adsorption on the scaffold pore walls at sites not occupied by solvent molecules. Although liquid solvent filled the pores, not all of the adsorption sites on the pore walls were occupied due to restricted motion of the solvent molecules within the confined pore space.« less

Single crystal growth in spin-coated films of polymorphic phthalocyanine derivative under solvent vapor

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

Higashi, T.; Ohmori, M.; Ramananarivo, M. F.

2015-12-01

The effects of solvent vapor on spin-coated films of a polymorphic phthalocyanine derivative were investigated. Growth of single crystal films via redissolving organic films under solvent vapor was revealed by in situ microscopic observations of the films. X-ray diffraction measurement of the films after exposing to solvent vapor revealed the phase transition of polymorphs under solvent vapor. The direction of crystal growth was clarified by measuring the crystal orientation in a grown monodomain film. The mechanism of crystal growth based on redissolving organic films under solvent vapor was discussed in terms of the different solubilities of the polymorphs.

Dynamical studies of confined fluids and polymers

NASA Astrophysics Data System (ADS)

Grabowski, Christopher A.

Soft matter, a class of materials including polymers, colloids, and surfactant molecules, are ubiquitous in our everyday lives. Plastics, soaps, foods and living organisms are mostly comprised of soft materials. Research conducted to understand soft matter behavior at the molecular level is essential to create new materials with unique properties. Self-healing plastics, targeted drug delivery, and nanowire assemblies have all been further advanced by soft matter research. The author of this dissertation investigates fundamental soft matter systems, including polymer solutions and melts, colloid dispersions in polymer melts, and interfacial fluids. The dynamics of polymers and confined fluids were studied using the single-molecule sensitive technique of fluorescence correlation spectroscopy (FCS). Here, fluorescent dyes are attached to polymer coils or by introducing free dyes directly into the solution/film. Complementary experiments were also performed, utilizing atomic force microscopy (AFM) and ellipsometry. FCS and AFM experiments demonstrated the significant difference in properties of thin fluid films of the nearly spherical, nonpolar molecule TEHOS (tetrakis(2-ethylhexoxy)silane) when compared to its bulk counterpart. AFM experiments confirmed TEHOS orders in layers near a solid substrate. FCS experiments show that free dyes introduced in these thin films do not have a single diffusion coefficient, indicating that these films have heterogeneity at the molecular level. FCS experiments have been applied to study the diffusion of gold colloids. The diffusion of gold colloids in polymer melts was found to dramatically depart from the Stokes-Einstein prediction when colloid size was smaller than the surrounding polymer mesh size. This effect is explained by noting the viscosity experienced by the colloid is not equivalent to the overall bulk viscosity of the polymer melt. The conformational change of polymers immersed in a binary solvent was measured via FCS. This experiment was conducted to test a theory proposed by Brochard and de Gennes, who postulated a polymer chain undergoes a collapse and a dramatic re-swelling as the critical point of the binary mixture is approached. Measuring polymer chain diffusion as a function of temperature, this theory was confirmed. To my knowledge, this was the first experimental evidence of contraction/re-swelling for polymers in critical binary solvents.

Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies.

PubMed

Bardhan, Jaydeep P; Jungwirth, Pavel; Makowski, Lee

2012-09-28

Two mechanisms have been proposed to drive asymmetric solvent response to a solute charge: a static potential contribution similar to the liquid-vapor potential, and a steric contribution associated with a water molecule's structure and charge distribution. In this work, we use free-energy perturbation molecular-dynamics calculations in explicit water to show that these mechanisms act in complementary regimes; the large static potential (∼44 kJ/mol/e) dominates asymmetric response for deeply buried charges, and the steric contribution dominates for charges near the solute-solvent interface. Therefore, both mechanisms must be included in order to fully account for asymmetric solvation in general. Our calculations suggest that the steric contribution leads to a remarkable deviation from the popular "linear response" model in which the reaction potential changes linearly as a function of charge. In fact, the potential varies in a piecewise-linear fashion, i.e., with different proportionality constants depending on the sign of the charge. This discrepancy is significant even when the charge is completely buried, and holds for solutes larger than single atoms. Together, these mechanisms suggest that implicit-solvent models can be improved using a combination of affine response (an offset due to the static potential) and piecewise-linear response (due to the steric contribution).

Intramolecular charge transfer and trans-cis isomerization of the DCM styrene dye in polar solvents. A CS INDO MRCI study

NASA Astrophysics Data System (ADS)

Marguet, S.; Mialocq, J. C.; Millie, P.; Berthier, G.; Momicchioli, F.

1992-03-01

The solvent-induced changes of trans-cis isomerization efficiency and electronic structure of the excited state of the DCM dye have been considered by means of CS INDO MRCI calculations. The potential energy curves, dipole moments and atomic charge densities as a function of two internal coordinates, namely the rotation angle about the central "double" bond and the twisting of the dimethylamino group, have been obtained for the ground state and the lowest excited states. The structural requirements for the existence of ICT (intramolecular charge transfer) excited states have been investigated by considering internal rotations about three single bonds. The reliability of the potential surfaces and of the solvation models has been discussed with reference to test-calculations on the DMABN molecule. In the first excited singlet state of DCM, the low-energy barrier for the trans-cis isomerization has been found unaffected by the solvent polarity. The only singlet excited state presenting a large ICT character has been found to be the S 2 state for a perpendicularly twisted conformation of the dimethylamino group (TICT state). The assumption of a deactivation of the trans-isomer in the locally excited state through the TICT funnel has been largely discussed with reference to the simplifications of the present theoretical approach.

Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies

PubMed Central

Bardhan, Jaydeep P.; Jungwirth, Pavel; Makowski, Lee

2012-01-01

Two mechanisms have been proposed to drive asymmetric solvent response to a solute charge: a static potential contribution similar to the liquid-vapor potential, and a steric contribution associated with a water molecule's structure and charge distribution. In this work, we use free-energy perturbation molecular-dynamics calculations in explicit water to show that these mechanisms act in complementary regimes; the large static potential (∼44 kJ/mol/e) dominates asymmetric response for deeply buried charges, and the steric contribution dominates for charges near the solute-solvent interface. Therefore, both mechanisms must be included in order to fully account for asymmetric solvation in general. Our calculations suggest that the steric contribution leads to a remarkable deviation from the popular “linear response” model in which the reaction potential changes linearly as a function of charge. In fact, the potential varies in a piecewise-linear fashion, i.e., with different proportionality constants depending on the sign of the charge. This discrepancy is significant even when the charge is completely buried, and holds for solutes larger than single atoms. Together, these mechanisms suggest that implicit-solvent models can be improved using a combination of affine response (an offset due to the static potential) and piecewise-linear response (due to the steric contribution). PMID:23020318

Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations

PubMed Central

Henriksen, Niel M.; Roe, Daniel R.; Cheatham, Thomas E.

2013-01-01

Molecular dynamics force field development and assessment requires a reliable means for obtaining a well-converged conformational ensemble of a molecule in both a time-efficient and cost-effective manner. This remains a challenge for RNA because its rugged energy landscape results in slow conformational sampling and accurate results typically require explicit solvent which increases computational cost. To address this, we performed both traditional and modified replica exchange molecular dynamics simulations on a test system (alanine dipeptide) and an RNA tetramer known to populate A-form-like conformations in solution (single-stranded rGACC). A key focus is on providing the means to demonstrate that convergence is obtained, for example by investigating replica RMSD profiles and/or detailed ensemble analysis through clustering. We found that traditional replica exchange simulations still require prohibitive time and resource expenditures, even when using GPU accelerated hardware, and our results are not well converged even at 2 microseconds of simulation time per replica. In contrast, a modified version of replica exchange, reservoir replica exchange in explicit solvent, showed much better convergence and proved to be both a cost-effective and reliable alternative to the traditional approach. We expect this method will be attractive for future research that requires quantitative conformational analysis from explicitly solvated simulations. PMID:23477537

Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations.

PubMed

Henriksen, Niel M; Roe, Daniel R; Cheatham, Thomas E

2013-04-18

Molecular dynamics force field development and assessment requires a reliable means for obtaining a well-converged conformational ensemble of a molecule in both a time-efficient and cost-effective manner. This remains a challenge for RNA because its rugged energy landscape results in slow conformational sampling and accurate results typically require explicit solvent which increases computational cost. To address this, we performed both traditional and modified replica exchange molecular dynamics simulations on a test system (alanine dipeptide) and an RNA tetramer known to populate A-form-like conformations in solution (single-stranded rGACC). A key focus is on providing the means to demonstrate that convergence is obtained, for example, by investigating replica RMSD profiles and/or detailed ensemble analysis through clustering. We found that traditional replica exchange simulations still require prohibitive time and resource expenditures, even when using GPU accelerated hardware, and our results are not well converged even at 2 μs of simulation time per replica. In contrast, a modified version of replica exchange, reservoir replica exchange in explicit solvent, showed much better convergence and proved to be both a cost-effective and reliable alternative to the traditional approach. We expect this method will be attractive for future research that requires quantitative conformational analysis from explicitly solvated simulations.

Liquid Catholyte Molecules for Nonaqueous Redox Flow Batteries

DOE PAGES

Huang, Jinhua; Cheng, Lei; Assary, Rajeev S.; ...

2014-11-25

In this study, a series of dimethoxybenzene-based catholyte molecules, which are electrochemically reversible at high potential (4.0 V vs Li/Li +) and in the form of liquid, is developed. The liquid nature offers the molecules the possibility of being a solo or co-solvent for nonaqueous redox flow batteries. This could dramatically improve the energy density.

Expansion of access tunnels and active-site cavities influence activity of haloalkane dehalogenases in organic cosolvents.

PubMed

Stepankova, Veronika; Khabiri, Morteza; Brezovsky, Jan; Pavelka, Antonin; Sykora, Jan; Amaro, Mariana; Minofar, Babak; Prokop, Zbynek; Hof, Martin; Ettrich, Rudiger; Chaloupkova, Radka; Damborsky, Jiri

2013-05-10

The use of enzymes for biocatalysis can be significantly enhanced by using organic cosolvents in the reaction mixtures. Selection of the cosolvent type and concentration range for an enzymatic reaction is challenging and requires extensive empirical testing. An understanding of protein-solvent interaction could provide a theoretical framework for rationalising the selection process. Here, the behaviour of three model enzymes (haloalkane dehalogenases) was investigated in the presence of three representative organic cosolvents (acetone, formamide, and isopropanol). Steady-state kinetics assays, molecular dynamics simulations, and time-resolved fluorescence spectroscopy were used to elucidate the molecular mechanisms of enzyme-solvent interactions. Cosolvent molecules entered the enzymes' access tunnels and active sites, enlarged their volumes with no change in overall protein structure, but surprisingly did not act as competitive inhibitors. At low concentrations, the cosolvents either enhanced catalysis by lowering K(0.5) and increasing k(cat), or caused enzyme inactivation by promoting substrate inhibition and decreasing k(cat). The induced activation and inhibition of the enzymes correlated with expansion of the active-site pockets and their occupancy by cosolvent molecules. The study demonstrates that quantitative analysis of the proportions of the access tunnels and active-sites occupied by organic solvent molecules provides the valuable information for rational selection of appropriate protein-solvent pair and effective cosolvent concentration. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular receptors in metal oxide sol-gel materials prepared via molecular imprinting

DOEpatents

Sasaki, Darryl Y.; Brinker, C. Jeffrey; Ashley, Carol S.; Daitch, Charles E.; Shea, Kenneth J.; Rush, Daniel J.

2000-01-01

A method is provided for molecularly imprinting the surface of a sol-gel material, by forming a solution comprised of a sol-gel material, a solvent, an imprinting molecule, and a functionalizing siloxane monomer of the form Si(OR).sub.3-n X.sub.n, wherein n is an integer between zero and three and X is a functional group capable of reacting with the imprinting molecule, evaporating the solvent, and removing the imprinting molecule to form the molecularly imprinted metal oxide sol-gel material. The use of metal oxide sol-gels allows the material porosity, pore size, density, surface area, hardness, electrostatic charge, polarity, optical density, and surface hydrophobicity to be tailored and be employed as sensors and in catalytic and separations operations.

Solubility of Structurally Complicated Materials: 3. Hair

PubMed Central

Horvath, Ari L.

2009-01-01

Hair is composed of proteins, lipids, water, and small amounts of trace elements. All proteins in animal and human bodies are built from permutations of amino acid molecules in a polypeptide string. The polypeptide chains of protein keratin are organized into filaments in hair cells. Hair is one of the most difficult proteins to digest or solubilize. Among the most common dissolving procedures for hair are acidic, alkaline, and enzymatic hydrolysis. For the analysis of hair, the solid samples are transferred by solubilization via digestion into a liquid phase. Small molecular solvents and molecules with hydrophobic groups appear to have higher affinity for hair. A good solvent attacks the disulfide bonds between cystine molecules and hydrates the hair shaft. Consequently, the hair becomes a jelly-like mass. PMID:19412554

SOLVENT-FREE ALTERNATIVES TO ORGANIC SYNTHESES USING MICROWAVES

EPA Science Inventory

Microwave irradiation has been used for a variety of synthetic transformations wherein chemical reactions are accelerated because of selective adsorption of microwave (MW) energy by polar molecules, non-polar molecules being inert to the MW dielectric loss. The application of mic...

Solvent and temperature effects on the decay dynamics of [p-N,N-(dialkylamino)benzylidene]malononitriles

NASA Astrophysics Data System (ADS)

Safarzadeh-Amiri, A.

1986-08-01

The effects of solvent and temperature on the decay kinetics of p-(dialkylamino)benzylidenemalononitrile (1) and julodinemalononitrile (3) has been studied in glycerol and triacetin. The fluorescence decay curves of these compounds were non-exponential and varied slightly with wavelength. This is attributed to the existence of two ground state conformers and to reorientation of the solvent cage around solute molecules. The results were explained in terms of trans → cisphotoisomerization.

Density functional theory and conductivity studies of boron-based anion receptors

DOE PAGES

Leung, Kevin; Chaudhari, Mangesh I.; Rempe, Susan B.; ...

2015-07-10

Anion receptors that bind strongly to fluoride anions in organic solvents can help dissolve the lithium fluoride discharge products of primary carbon monofluoride (CFx) batteries, thereby preventing the clogging of cathode surfaces and improving ion conductivity. The receptors are also potentially beneficial to rechargeable lithium ion and lithium air batteries. We apply Density Functional Theory (DFT) to show that an oxalate-based pentafluorophenyl-boron anion receptor binds as strongly, or more strongly, to fluoride anions than many phenyl-boron anion receptors proposed in the literature. Experimental data shows marked improvement in electrolyte conductivity when this oxalate anion receptor is present. The receptor ismore » sufficiently electrophilic that organic solvent molecules compete with F – for boron-site binding, and specific solvent effects must be considered when predicting its F – affinity. To further illustrate the last point, we also perform computational studies on a geometrically constrained boron ester that exhibits much stronger gas-phase affinity for both F – and organic solvent molecules. After accounting for specific solvent effects, however, its net F – affinity is about the same as the simple oxalate-based anion receptor. Lastly, we propose that LiF dissolution in cyclic carbonate organic solvents, in the absence of anion receptors, is due mostly to the formation of ionic aggregates, not isolated F – ions.« less

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.

Capping the calix: How toluene completes cesium(i) coordination with calix[4]pyrrole

DOE PAGES

Ellis, Ross J.; Reinhart, Benjamin; Williams, Neil J.; ...

2017-05-04

The role of solvent in molecular recognition systems is under-researched and often ignored, especially when the solvent is considered “non-interacting”. This study concerns the role of toluene solvent in cesium(I) recognition by calix[4]pyrrole. We show that π-donor interactions bind toluene molecules onto the open face of the cation-receptor complex, thus “capping the calix.” As a result, by characterizing this unusual aromatically-saturated complex, we show how “non-interacting” aromatic solvents can directly coordinate receptor-bound cations and thus influence recognition.

Capping the calix: How toluene completes cesium(i) coordination with calix[4]pyrrole

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

Ellis, Ross J.; Reinhart, Benjamin; Williams, Neil J.

The role of solvent in molecular recognition systems is under-researched and often ignored, especially when the solvent is considered “non-interacting”. This study concerns the role of toluene solvent in cesium(I) recognition by calix[4]pyrrole. We show that π-donor interactions bind toluene molecules onto the open face of the cation-receptor complex, thus “capping the calix.” As a result, by characterizing this unusual aromatically-saturated complex, we show how “non-interacting” aromatic solvents can directly coordinate receptor-bound cations and thus influence recognition.

Effects of solvation on partition and dimerization of benzoic acid in mixed solvent systems.

PubMed

Yamada, H; Yajima, K; Wada, H; Nakagawa, G

1995-06-01

The partition of benzoic acid between 0.1M perchloric acid solution and two kinds of mixed solvents has been carried out at 25 degrees C. The partition and dimerization constants of benzoic acid have been determined in the 1-octanol-benzene and 2-octanone-benzene systems. In both the mixed solvent systems, with increasing content of 1-octanol and 2-octanone in each mixed solvent, the partition constant of benzoic acid has been found to increase, and the dimerization constant of benzoic acid in each organic phase to decrease. These phenomena are attributable to solvation of monomeric benzoic acid by 1-octanol and 2-octanone molecules in each mixed solvent.

Investigation of the dipole formation and growth behavior at In2O3|TiO2 heterojunctions using photoemission spectroscopy and atomic force microscopy

NASA Astrophysics Data System (ADS)

Schaefer, Michael; Halpegamage, Sandamali; Batzill, Matthias; Schlaf, Rudy

2016-02-01

This paper discusses the investigation of the dipole formation at In2O3|TiO2 heterojunctions depending on preparation conditions, i.e., cleaning methods. In2O3 films were deposited using atomic layer deposition (ALD) onto solvent and in situ cleaned anatase and rutile film substrates. The interface dipole strength and film thickness were evaluated by photoemission spectroscopy. Our results indicate the formation of a large intrinsic and film thickness dependent interface dipole that reaches its maximum strength at monolayer thick ALD films. In addition, it was observed that UV photoelectron spectroscopy measurements introduced UV induced surface hydroxylation, which resulted in dipole potentials of -0.70 eV and -0.50 eV on solvent cleaned anatase and rutile, respectively. The overlayers also introduced small amounts of band bending (˜0.10 eV) at the interfaces. Taking these effects into account, the total dipole strength at monolayer thick In2O3 films was determined to be -0.96 eV for solvent cleaned anatase and rutile and -0.81 eV for in situ cleaned rutile. The deposition of single ALD cycles on differently cleaned rutile substrates resulted in similar work function values, suggesting little influence of the sample preparation method prior to ALD deposition on the dipole formation. This was assigned to the fact that ALD oxides benefit from ambient water related contamination by integrating the molecules into the growing ALD layer. Highest initial growth was observed on solvent cleaned rutile, followed by in-situ cleaned rutile and solvent cleaned anatase. The In2O3 growth converged at 0.3 Å/c past the nucleation regime.

Synthesis, structure and study of azo-hydrazone tautomeric equilibrium of 1,3-dimethyl-5-(arylazo)-6-amino-uracil derivatives.

PubMed

Debnath, Diptanu; Roy, Subhadip; Li, Bing-Han; Lin, Chia-Her; Misra, Tarun Kumar

2015-04-05

Azo dyes, 1,3-dimethyl-5-(arylazo)-6-aminouracil (aryl=-C6H5 (1), -p-CH3C6H4 (2), -p-ClC6H4 (3), -p-NO2C6H4 (4)) were prepared and characterized by UV-vis, FT-IR, 1H NMR, 13C NMR spectroscopic techniques and single crystal X-ray crystallographic analysis. In the light of spectroscopic analysis it evidences that of the tautomeric forms, the azo-enamine-keto (A) form is the predominant form in the solid state whereas in different solvents it is the hydrazone-imine-keto (B) form. The study also reveals that the hydrazone-imine-keto (B) form exists in an equilibrium mixture with its anionic form in various organic solvents. The solvatochromic and photophysical properties of the dyes in various solvents with different hydrogen bonding parameter were investigated. The dyes exhibit positive solvatochromic property on moving from polar protic to polar aprotic solvents. They are fluorescent active molecules and exhibit high intense fluorescent peak in some solvents like DMSO and DMF. It has been demonstrated that the anionic form of the hydrazone-imine form is responsible for the high intense fluorescent peak. In addition, the acid-base equilibrium in between neutral and anionic form of hydrazone-imine form in buffer solution of varying pH was investigated and evaluated the pKa values of the dyes by making the use of UV-vis spectroscopic methods. The determined acid dissociation constant (pKa) values increase according to the sequence of 2>1>3>4. Copyright © 2014 Elsevier B.V. All rights reserved.

Synthesis of single-molecule nanocars.

PubMed

Vives, Guillaume; Tour, James M

2009-03-17

The drive to miniaturize devices has led to a variety of molecular machines inspired by macroscopic counterparts such as molecular motors, switches, shuttles, turnstiles, barrows, elevators, and nanovehicles. Such nanomachines are designed for controlled mechanical motion and the transport of nanocargo. As researchers miniaturize devices, they can consider two complementary approaches: (1) the "top-down" approach, which reduces the size of macroscopic objects to reach an equivalent microscopic entity using photolithography and related techniques and (2) the "bottom-up" approach, which builds functional microscopic or nanoscopic entities from molecular building blocks. The top-down approach, extensively used by the semiconductor industry, is nearing its scaling limits. On the other hand, the bottom-up approach takes advantage of the self-assembly of smaller molecules into larger networks by exploiting typically weak molecular interactions. But self-assembly alone will not permit complex assembly. Using nanomachines, we hope to eventually consider complex, enzyme-like directed assembly. With that ultimate goal, we are currently exploring the control of nanomachines that would provide a basis for the future bottom-up construction of complex systems. This Account describes the synthesis of a class of molecular machines that resemble macroscopic vehicles. We designed these so-called nanocars for study at the single-molecule level by scanning probe microscopy (SPM). The vehicles have a chassis connected to wheel-terminated axles and convert energy inputs such as heat, electric fields, or light into controlled motion on a surface, ultimately leading to transport of nanocargo. At first, we used C(60) fullerenes as wheels, which allowed the demonstration of a directional rolling mechanism of a nanocar on a gold surface by STM. However, because of the low solubility of the fullerene nanocars and the incompatibility of fullerenes with photochemical processes, we developed new p-carborane- and ruthenium-based wheels with greater solubility in organic solvents. Although fullerene wheels must be attached in the final synthetic step, p-carborane- and ruthenium-based wheels do not inhibit organometallic coupling reactions, which allows a more convergent synthesis of molecular machines. We also prepared functional nanotrucks for the transport of atoms and molecules, as well as self-assembling nanocars and nanotrains. Although engineering challenges such as movement over long distance and non-atomically flat surfaces remain, the greatest current research challenge is imaging. The detailed study of nanocars requires complementary single molecule imaging techniques such as STM, AFM, TEM, or single-molecule fluorescence microscopy. Further developments in engineering and synthesis could lead to enzyme-like manipulation and assembly of atoms and small molecules in nonbiological environments.

Conformational Changes of the Alanine Dipeptide in Water-Ethanol Binary Mixtures.

PubMed

Almeida, Glauco G; Cordeiro, João M M; Martín, M Elena; Aguilar, Manuel A

2016-04-12

Experimental work developed in the last years has evidenced the capacity of alcohols and polyalcohols to modify the energy landscape of peptides and proteins. However, the mechanism underlying this effect is not clear. Taking as a model system the alanine dipeptide (AD) we perform a QM/MM study in water, ethanol, and a 40-60% in volume water-ethanol mixture. The AD molecule was described at the MP2/aug-cc-pVDZ level. In polar solution, only αR and PPII conformers contribute in an appreciable way to the conformational equilibrium. The final in solution αR-PPII free energy difference is determined from the interplay between the internal energy of the dipeptide and the solute-solvent interaction free energy. Internal energy favors the formation of PPII, whereas, on the contrary, solute-solvent interaction is favorable to αR, so any factor that decreases the solute-solvent interaction free energy will increase the PPII population. The addition of ethanol increases the stability of the PPII conformer. Our results point to the presence of preferential solvation in this system, the composition of the first solvation shell in the binary mixture being dominated by water molecules. Remarkably, this fact does not affect the differential conformational stability that is controlled by long-range interactions. From the analysis of solvent density maps it is concluded that, in the water-ethanol mixture, ethanol molecules are more likely found around the alanine side chain and the carbonyl group, but while in PPII ethanol molecules interact mainly with the carbonyl group of the N-terminal end, in C5 the interaction is with the carbonyl group of the C-terminal end. In αR, ethanol interacts with both carbonyl groups.

Comparative theoretical study of the structures and stabilities of four typical gadolinium carboxylates in different scintillator solvents.

PubMed

Huang, Pin-Wen

2016-03-01

The structural properties and stabilities of four typical gadolinium carboxylates (Gd-CBX) in toluene, linear alkyl benzene (LAB), and phenyl xylyl ethane (PXE) solvents were theoretically studied using density functional theory (DFT/B3LYP with the basis sets 6-311G(d) and MWB54) and the polarizable continuum model (PCM). The average Gd-ligand interaction energies (E int, corrected for dispersion) and the values of the energy gap between the highest occupied molecular orbital and lowest unoccupied molecular orbital (ΔHL) for the gadolinium complexes were calculated to compare the relative stabilities of the four Gd-CBX molecules in the three liquid scintillator solvents. According to the calculations, the values of E int and ΔHL for Gd-CBX in LAB are larger than the corresponding values in PXE and toluene. Gd-CBX may therefore be more compatible with LAB than with PXE and toluene. It was also found that, in the three scintillator solvents, the stabilities of the four Gd-CBX molecules increase in the order Gd-2EHA < Gd-2MVA < Gd-pivalate < Gd-TMHA.

Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field

PubMed Central

Mohamed, Noor Asidah; Bradshaw, Richard T.

2016-01-01

The effects of electronic polarization in biomolecular interactions will differ depending on the local dielectric constant of the environment, such as in solvent, DNA, proteins, and membranes. Here the performance of the AMOEBA polarizable force field is evaluated under nonaqueous conditions by calculating the solvation free energies of small molecules in four common organic solvents. Results are compared with experimental data and equivalent simulations performed with the GAFF pairwise‐additive force field. Although AMOEBA results give mean errors close to “chemical accuracy,” GAFF performs surprisingly well, with statistically significantly more accurate results than AMOEBA in some solvents. However, for both models, free energies calculated in chloroform show worst agreement to experiment and individual solutes are consistently poor performers, suggesting non‐potential‐specific errors also contribute to inaccuracy. Scope for the improvement of both potentials remains limited by the lack of high quality experimental data across multiple solvents, particularly those of high dielectric constant. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:27757978

Leucine/Pd-loaded (5,5) single-walled carbon nanotube matrix as a novel nanobiosensors for in silico detection of protein.

PubMed

Yoosefian, Mehdi; Etminan, Nazanin

2018-06-01

We have designed a novel nanobiosensor for in silico detecting proteins based on leucine/Pd-loaded single-walled carbon nanotube matrix. Density functional theory at the B3LYP/6-31G (d) level of theory was realized to analyze the geometrical and electronic structure of the proposed nanobiosensor. The solvent effects were investigated using the Tomasi's polarized continuum model. Atoms-in-molecules theory was used to study the nature of interactions by calculating the electron density ρ(r) and Laplacian at the bond critical points. Natural bond orbital analysis was performed to achieve a deep understanding of the nature of the interactions. The biosensor has potential application for high sensitive and rapid response to protein due to the chemical adsorption of L-leucine amino acid onto Pd-loaded single-walled carbon nanotube and reactive functional groups that can incorporate in hydrogen binding, hydrophobic interactions and van der Waals forces with the protein surface in detection process.

Hydration and conformational mechanics of single, end-tethered elastin-like polypeptides.

PubMed

Valiaev, Alexei; Lim, Dong Woo; Schmidler, Scott; Clark, Robert L; Chilkoti, Ashutosh; Zauscher, Stefan

2008-08-20

We investigated the effect of temperature, ionic strength, solvent polarity, and type of guest residue on the force-extension behavior of single, end-tethered elastin-like polypeptides (ELPs), using single molecule force spectroscopy (SMFS). ELPs are stimulus-responsive polypeptides that contain repeats of the five amino acids Val-Pro-Gly-Xaa-Gly (VPGXG), where Xaa is a guest residue that can be any amino acid with the exception of proline. We fitted the force-extension data with a freely jointed chain (FJC) model which allowed us to resolve small differences in the effective Kuhn segment length distributions that largely arise from differences in the hydrophobic hydration behavior of ELP. Our results agree qualitatively with predictions from recent molecular dynamics simulations and demonstrate that hydrophobic hydration modulates the molecular elasticity for ELPs. Furthermore, our results show that SMFS, when combined with our approach for data analysis, can be used to study the subtleties of polypeptide-water interactions and thus provides a basis for the study of hydrophobic hydration in intrinsically unstructured biomacromolecules.

Crystal structure of the formal 20 electron zirconocene penta-fulvene complex Cp2Zr(η5,η1-adamantyl-idene-penta-fulvene):toluene:n-hexane = 1:0.125:0.125.

PubMed

Fischer, Malte; Schmidtmann, Marc; Beckhaus, Rüdiger

2017-12-01

The crystal structure of a solvated zirconocene penta-fulvene complex with a bulky adamantyl-idene substitution pattern, namely (η 5 ,η 1 -adamantyl-idene-penta-fulvene)bis-(η 5 -cyclo-penta-dien-yl)zirconium(IV)-toluene- n -hexane (8/1/1), [Zr(C 15 H 18 )(C 5 H 5 ) 2 ]·0.125C 7 H 8 ·0.125C 6 H 14 , is reported. Reducing zirconocene dichloride with magnesium results in the formation of a low-valent zirconocene reagent that reacts readily with adamantyl-idene-penta-fulvene to give the aforementioned complex. Single crystal X-ray diffraction proves the dianion-like η 5 :η 1 binding mode of the fulvene ligand to the central Zr IV atom. The asymmetric unit contains four independent mol-ecules of [η 5 :η 1 -adamantyl-idene-penta-fulvene]bis-[(η 5 )-cyclo-penta-dien-yl]zirconium(IV), together with half a mol-ecule of toluene disordered with half a mol-ecule of n -hexane (the solvent mol-ecules have no direct influence on the complex). In each of the four complex mol-ecules, the central Zr IV atom has a distorted tetra-hedral coordination environment. The measured crystal consisted of two domains with a refined ratio of 0.77:0.23.

Influence of solvents on the habit modification of alpha lactose monohydrate single crystals

NASA Astrophysics Data System (ADS)

Parimaladevi, P.; Srinivasan, K.

2013-02-01

Restricted evaporation of solvent method was adopted for the growth of alpha lactose monohydrate single crystals from different solvents. The crystal habits of grown crystals were analysed. The form of crystallization was confirmed by powder x-ray diffraction analysis. Thermal behaviour of the grown crystals was studied by using differential scanning calorimetry.

Qualitative assessment of ultra-fast non-Grotthuss proton dynamics in S1 excited state of liquid H2O from ab initio time-dependent density functional theory★

NASA Astrophysics Data System (ADS)

Ziaei, Vafa; Bredow, Thomas

2017-11-01

We study qualitatively ultra-fast proton transfer (PT) in the first singlet (S1) state of liquid water (absorption onset) through excited-state dynamics by means of time-dependent density functional theory and ab initio Born-Oppenheimer molecular dynamics. We find that after the initial excitation, a PT occurs in S1 in form of a rapid jump to a neighboring water molecule, on which the proton either may rest for a relatively long period of time (as a consequence of possible defect in the hydrogen bond network) followed by back and forth hops to its neighboring water molecule or from which it further moves to the next water molecule accompanied by back and forth movements. In this way, the proton may become delocalized over a long water wire branch, followed again by back and forth jumps or short localization on a water molecule for some femtoseconds. As a result, the mechanism of PT in S1 is in most cases highly non-Grotthuss-like, delayed and discrete. Furthermore, upon PT an excess charge is ejected to the solvent trap, the so-called solvated electron. The spatial extent of the ejected solvated electron is mainly localized within one solvent shell with overlappings on the nearest neighbor water molecules and delocalizing (diffuse) tails extending beyond the first solvent sphere. During the entire ultra-short excited-state dynamics the remaining OH radical from the initially excited water molecule exhibits an extremely low mobility and is non-reactive. Supplementary material in the form of one pdf file available from the Journal web page at http://https://doi.org/10.1140/epjb/e2017-80329-7.

Investigation of migrant-polymer interaction in pharmaceutical packaging material using the linear interaction energy algorithm.

PubMed

Feenstra, Peter; Brunsteiner, Michael; Khinast, Johannes

2014-10-01

The interaction between drug products and polymeric packaging materials is an important topic in the pharmaceutical industry and often associated with high costs because of the required elaborative interaction studies. Therefore, a theoretical prediction of such interactions would be beneficial. Often, material parameters such as the octanol water partition coefficient are used to predict the partitioning of migrant molecules between a solvent and a polymeric packaging material. Here, we present the investigation of the partitioning of various migrant molecules between polymers and solvents using molecular dynamics simulations for the calculation of interaction energies. Our results show that the use of a model for the interaction between the migrant and the polymer at atomistic detail can yield significantly better results when predicting the polymer solvent partitioning than a model based on the octanol water partition coefficient. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Solvation structures and dynamics of alkaline earth metal halides in supercritical water: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Keshri, Sonanki; Mandal, Ratnamala; Tembe, B. L.

2016-09-01

Constrained molecular dynamics simulations of alkaline earth metal halides have been carried out to investigate their structural and dynamical properties in supercritical water. Potentials of mean force (PMFs) for all the alkaline earth metal halides in supercritical water have been computed. Contact ion pairs (CIPs) are found to be more stable than all other configurations of the ion pairs except for MgI2 where solvent shared ion pair (SShIP) is more stable than the CIP. There is hardly any difference in the PMFs between the M2+ (M = Mg, Ca, Sr, Ba) and the X- (X = F, Cl, Br, I) ions whether the second X- ion is present in the first coordination shell of the M2+ ion or not. The solvent molecules in the solvation shells diffuse at a much slower rate compared to the bulk. Orientational distribution functions of solvent molecules are sharper for smaller ions.

Identification of Thiols in Yellow Onion (Allium cepa L.) Using Solvent Vented Large Volume Injection GC-MS.

PubMed

Wermes, Clint; Cannon, Robert; Haasnoot, Sytze; Colstee, Hans; Niedeveld, Cor; Koopmanschap, Gijs; Da Costa, Neil C

2017-11-01

Thiols are often highly odor active molecules and as such can significantly contribute to aroma while being present at extremely low concentrations. This paper details the identification of thiols in yellow onion juice by solvent extraction followed by thiol enrichment using a mercuric agarose gel column. Due to the inherent thermal instability and low concentrations of thiols in onion, chromatographic analysis utilized larger volume solvent elimination injections. New sulfur compounds in onion included 1,1-propanedithiol, bis-(1-sulfanylpropyl)-sulfide, 1-methylsulfanyl-1-propanethiol, 1-propylsulfanyl-1-propanethiol, and 1-allylsulfanyl-1-propanethiol. A discussion on the potential route of formation for each compound is included along with the orthonasal and retronasal evaluations of the synthesized molecules. This work investigated and identified 5 newly identified compounds present in onions that can impart onion character at low concentrations levels. © 2017 Institute of Food Technologists®.

Dynamics of water in sulfonated poly(phenylene) membranes

NASA Astrophysics Data System (ADS)

Osti, Naresh; Etampawala, Thusitha; Shrestha, Umesh; Perahia, Dvora; Cornelius, Christopher

2011-03-01

The dynamics of water in networks formed by highly rigid ionic polymers, sulfonated poly(phenylene) as observed by quasi elastic neutron scattering (QENS) is presented. These rigid ionic polymers have potential as effective ion exchange membranes with impact on a large number of applications from water purification to clean energy, where its rigidity distinguishes it from other ionic polymers. Its transport characteristics are affected by its rigidness as well as by direct interactions with the solvent. Our QENS studies as a function of sulfonation levels, temperature and solvent content have shown that on the time scale of the measurement, the polymers are rigid. While macroscopically all samples swell, and transport water, the water molecules appear locally rather confined. Water however remind non-frozen to subzero temperatures. The results will be discussed in view of theoretical models including continues diffusion and hopping of solvent molecules.

Solvent Dependent Disorder in M 2(BzOip) 2(H 2O)·Solvate (M = Co or Zn)

DOE PAGES

McCormick, Laura; Morris, Samuel A.; Teat, Simon J.; ...

2017-12-24

Coordination polymers derived from 5-benzyloxy isophthalic acid (H 2BzOip) are rare, with only three reported that do not contain additional bridging ligands, of which two M 2(BzOip) 2(H 2O) (M = Co and Zn) are isomorphous. It was hoped that by varying the solvent system in a reaction between H 2BzOip and M(OAc) 2 (M = Co and Zn), from water to a water/alcohol mixture, coordination polymers of different topology could be formed. Instead, two polymorphs of the existing M 2(BzOip) 2(H 2O) (M = Co and Zn) were isolated from aqueous methanol and aqueous ethanol, in which a smallmore » number of guest solvent molecules are present in the crystals. These guest water molecules disrupt the hexaphenyl embrace motif, leading to varying degrees of disorder of the benzyl groups.« less

Solvent Dependent Disorder in M 2(BzOip) 2(H 2O)·Solvate (M = Co or Zn)

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

McCormick, Laura; Morris, Samuel A.; Teat, Simon J.

Coordination polymers derived from 5-benzyloxy isophthalic acid (H 2BzOip) are rare, with only three reported that do not contain additional bridging ligands, of which two M 2(BzOip) 2(H 2O) (M = Co and Zn) are isomorphous. It was hoped that by varying the solvent system in a reaction between H 2BzOip and M(OAc) 2 (M = Co and Zn), from water to a water/alcohol mixture, coordination polymers of different topology could be formed. Instead, two polymorphs of the existing M 2(BzOip) 2(H 2O) (M = Co and Zn) were isolated from aqueous methanol and aqueous ethanol, in which a smallmore » number of guest solvent molecules are present in the crystals. These guest water molecules disrupt the hexaphenyl embrace motif, leading to varying degrees of disorder of the benzyl groups.« less

The spectral properties of (-)-epigallocatechin 3-O-gallate (EGCG) fluorescence in different solvents: dependence on solvent polarity.

PubMed

Snitsarev, Vladislav; Young, Michael N; Miller, Ross M S; Rotella, David P

2013-01-01

(-)-Epigallocatechin 3-O-gallate (EGCG) a molecule found in green tea and known for a plethora of bioactive properties is an inhibitor of heat shock protein 90 (HSP90), a protein of interest as a target for cancer and neuroprotection. Determination of the spectral properties of EGCG fluorescence in environments similar to those of binding sites found in proteins provides an important tool to directly study protein-EGCG interactions. The goal of this study is to examine the spectral properties of EGCG fluorescence in an aqueous buffer (AB) at pH=7.0, acetonitrile (AN) (a polar aprotic solvent), dimethylsulfoxide (DMSO) (a polar aprotic solvent), and ethanol (EtOH) (a polar protic solvent). We demonstrate that EGCG is a highly fluorescent molecule when excited at approximately 275 nm with emission maxima between 350 and 400 nm depending on solvent. Another smaller excitation peak was found when EGCG is excited at approximately 235 nm with maximum emission between 340 and 400 nm. We found that the fluorescence intensity (FI) of EGCG in AB at pH=7.0 is significantly quenched, and that it is about 85 times higher in an aprotic solvent DMSO. The Stokes shifts of EGCG fluorescence were determined by solvent polarity. In addition, while the emission maxima of EGCG fluorescence in AB, DMSO, and EtOH follow the Lippert-Mataga equation, its fluorescence in AN points to non-specific solvent effects on EGCG fluorescence. We conclude that significant solvent-dependent changes in both fluorescence intensity and fluorescence emission shifts can be effectively used to distinguish EGCG in aqueous solutions from EGCG in environments of different polarity, and, thus, can be used to study specific EGCG binding to protein binding sites where the environment is often different from aqueous in terms of polarity.

Investigating the Effect of Charge Hydration Asymmetry and Incorporating it in Continuum Solvation Framework

NASA Astrophysics Data System (ADS)

Mukhopadhyay, Abhishek

One of the essential requirements of biomolecular modeling is an accurate description of water as a solvent. The challenge is to make this description computationally facile - reasonably fast, simple, robust and easy to incorporate into existing software packages, yet accurate. The most rigorous procedure to model the effect of aqueous solvent is to explicitly model every water molecule in the system. For many practical applications, this approach is computationally too intense, as the number of required water atoms is on an average at least one order of magnitude larger than the number of atoms of the molecule of interest. Implicit solvent models, in which solvent molecules are replaced by a continuous dielectric, have become a popular alternative to explicit solvent methods. However, implicit solvation models often lack various microscopic details which are crucial for accuracy. One such missing effect that is currently missing from popular implicit models is the so called effect of charge hydration asymmetry (CHA). The missing effect of charge hydration asymmetry - the asymmetric response of water upon the sign of solute charge - manifests a characteristic, strong dependence of solvation free energies on the sign of solute charge. Here, we incorporate this missing effect into the continuum solvation framework via the conceptually simplest Born equation and also in the generalized Born model. We identify the key electric multipole moments of model water molecules critical for the various degrees of CHA effect observed in studies based on molecular dynamics simulations using different rigid water models. We then use this gained insight to incorporate this effect first into the Born model and then into the generalized Born model. The proposed framework significantly improves accuracy of the hydration free energy estimates tested on a comprehensive set of varied molecular solutes - monovalent and divalent ions, small drug-like molecules, charged and uncharged amino acid dipeptides, and small proteins. We finally develop a methodology to resolve the issue with unacceptably large uncertainty that stems from a variety of fundamental and technical difficulties in experimental quantification of CHA from charged solutes. Using the proposed corrections in the continuum framework, we untangle the charge-asymmetric response of water from its symmetric response, and further circumvent the difficulties by extracting accurate estimate propensity of water to cause CHA from accurate experimental hydration free energies of neutral polar molecules. We show that the asymmetry in water's response is strong, about 50% of the symmetric response.

Micropolarity and Hydrogen-Bond Donor Ability of Environmentally Friendly Anionic Reverse Micelles Explored by UV/Vis Absorption of a Molecular Probe and FTIR Spectroscopy.

PubMed

Girardi, Valeria R; Silber, Juana J; Falcone, Ruben Darío; Correa, N Mariano

2018-03-19

In the present work we show how two biocompatible solvents, methyl laurate (ML) and isopropyl myristate (IPM), can be used as a less toxic alternative to replace the nonpolar component in a sodium 1,4-bis-2-ethylhexylsulfosuccinate (AOT) reverse micelles (RMs) formulation. In this sense, the micropolarity and the hydrogen-bond ability of the interface were monitored through the use of the solvatochromism of a molecular probe (1-methyl-8-oxyquinolinium betaine, QB) and Fourier transform infrared spectroscopy (FTIR). Our results demonstrate that the micropolarity sensed by QB in ML RMs is lower than in IPM RMs. Additionally, the water molecules form stronger H-bond interactions with the polar head of AOT in ML than in IPM. By FTIR was revealed that more water molecules interact with the interface in ML/AOT RMs. On the other hand, for AOT RMs generated in IPM, the weaker water-surfactant interaction allows the water molecules to establish hydrogen bonds with each other trending to bulk water more easily than in ML RMs, a consequence of the dissimilar penetration of nonpolar solvents into the interfacial region. The penetration process is strongly controlled by the polarity and viscosity of the external solvents. All of these results allow us to characterize these biocompatible systems, providing information about interfacial properties and how they can be altered by changing the external solvent. The ability of the nontoxic solvent to penetrate or not into the AOT interface produces a new interface with attractive properties. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluation of Kirkwood-Buff integrals via finite size scaling: a large scale molecular dynamics study

NASA Astrophysics Data System (ADS)

Dednam, W.; Botha, A. E.

2015-01-01

Solvation of bio-molecules in water is severely affected by the presence of co-solvent within the hydration shell of the solute structure. Furthermore, since solute molecules can range from small molecules, such as methane, to very large protein structures, it is imperative to understand the detailed structure-function relationship on the microscopic level. For example, it is useful know the conformational transitions that occur in protein structures. Although such an understanding can be obtained through large-scale molecular dynamic simulations, it is often the case that such simulations would require excessively large simulation times. In this context, Kirkwood-Buff theory, which connects the microscopic pair-wise molecular distributions to global thermodynamic properties, together with the recently developed technique, called finite size scaling, may provide a better method to reduce system sizes, and hence also the computational times. In this paper, we present molecular dynamics trial simulations of biologically relevant low-concentration solvents, solvated by aqueous co-solvent solutions. In particular we compare two different methods of calculating the relevant Kirkwood-Buff integrals. The first (traditional) method computes running integrals over the radial distribution functions, which must be obtained from large system-size NVT or NpT simulations. The second, newer method, employs finite size scaling to obtain the Kirkwood-Buff integrals directly by counting the particle number fluctuations in small, open sub-volumes embedded within a larger reservoir that can be well approximated by a much smaller simulation cell. In agreement with previous studies, which made a similar comparison for aqueous co-solvent solutions, without the additional solvent, we conclude that the finite size scaling method is also applicable to the present case, since it can produce computationally more efficient results which are equivalent to the more costly radial distribution function method.

Investigation of solvent polarity effect on molecular structure and vibrational spectrum of xanthine with the aid of quantum chemical computations.

PubMed

Polat, Turgay; Yıldırım, Gurcan

2014-04-05

The main scope of this study is to determine the effects of 8 solvents on the geometric structure and vibrational spectra of the title compound, xanthine, by means of the DFT/B3LYP level of theory in the combination with the polarizable conductor continuum model (CPCM) for the first time. After determination of the most-steady state (favored structure) of the xanthine molecule, the role of the solvent polarity on the SCF energy (for the molecule stability), atomic charges (for charge distribution) and dipole moments (for molecular charge transfer) belonging to tautomer is discussed in detail. The results obtained indicate not only the presence of the hydrogen bonding and strong intra-molecular charge transfer (ICT) in the compound but the increment of the molecule stability with the solvent polarity, as well. Moreover, it is noted that the optimized geometric parameters and the theoretical vibrational frequencies are in good agreement with the available experimental results found in the literature. In fact, the correlations between the experimental and theoretical findings for the molecular structures improve with the enhancement of the solvent polarity. At the same time, the dimer forms of the xanthine compound are simulated to describe the effect of intermolecular hydrogen bonding on the molecular geometry and vibrational frequencies. It is found that the CO and NH stretching vibrations shift regularly to lower frequency value with higher IR intensity as the dielectric medium enhances systematically due to the intermolecular NH⋯O hydrogen bonds. Theoretical vibrational spectra are also assigned based on the potential energy distribution (PED) using the VEDA 4 program. Copyright © 2013 Elsevier B.V. All rights reserved.

The Importance of Water for High Fidelity Information Processing and for Life

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.; Pohorille, Andrew

2011-01-01

Is water an absolute prerequisite for life? Life depends on a variety of non-covalent interactions among molecules, the nature of which is determined as much by the solvent in which they occur as by the molecules themselves. Catalysis and information processing, two essential functions of life, require non-covalent molecular recognition with very high specificity. For example, to correctly reproduce a string consisting of 600,000 units of information (e.g ., 600 kilobases, equivalent to the genome of the smallest free living terrestrial organisms) with a 90% success rate requires specificity > 107 : 1 for the target molecule vs. incorrect alternatives. Such specificity requires (i) that the correct molecular association is energetically stabilized by at least 40 kJ/mol relative to alternatives, and (ii) that the system is able to sample among possible states (alternative molecular associations) rapidly enough to allow the system to fall under thermodynamic control and express the energetic stabilization. We argue that electrostatic interactions are required to confer the necessary energetic stabilization vs. a large library of molecular alternatives, and that a solvent with polarity and dielectric properties comparable to water is required for the system to sample among possible states and express thermodynamic control. Electrostatic associations can be made in non-polar solvents, but the resulting complexes are too stable to be "unmade" with sufficient frequency to confer thermodynamic control on the system. An electrostatic molecular complex representing 3 units of information (e.g., 3 base pairs) with specificity > 107 per unit has a stability in non-polar solvent comparable to that of a carbon-carbon bond at room temperature. These considerations suggest that water, or a solvent with properties very like water, is necessary to support high-fidelity information processing, and can therefore be considered a critical prerequisite for life.

π-π Interaction among violanthrone molecules: observation, enhancement, and resulting charge transport properties.

PubMed

Shi, Min-Min; Chen, Yi; Nan, Ya-Xiong; Ling, Jun; Zuo, Li-Jian; Qiu, Wei-Ming; Wang, Mang; Chen, Hong-Zheng

2011-02-03

To investigate the relationship between π-π stacking and charge transport property of organic semiconductors, a highly soluble violanthrone derivative, 16,17-bis(2-ethylhexyloxy)anthra[9,1,2-cde-]benzo[rst]pentaphene-5,10-dione (3), is designed and synthesized. The π-π stacking behavior and the aggregation of compound 3 in both solution and thin film were studied in detail by (1)H nuclear magnetic resonance (NMR) spectroscopy, ultraviolet-visible (UV-vis) absorption, X-ray diffraction (XRD), and atomic force microscopy (AFM). When (1)H NMR spectroscopy and theoretical modeling results were combined, the arrangements of compound 3 molecules in the aggregates are demonstrated, where the dipole moments of the two adjacent molecules are nearly reversed to achieve efficient intermolecular π-π overlapping. Furthermore, it is interesting to find that the π-π stacking of compound 3, in both solution and thin films, can be enhanced by introducing a poor solvent n-hexane into the dilute chloroform solution. The resulting film exhibits more red-shifted absorption and higher crystallinity than the film made from pure chloroform solvent, suggesting that π-π interactions in the solid state are intensified by the poor solvent. Organic field-effect transistors (OFETs) with compound 3 film as the transportation layer were fabricated. It is disclosed that the compound 3 film obtained from the chloroform/n-hexane mixed solvents exhibits 1 order of magnitude higher hole mobility than that from the pure chloroform solvent because of the enhanced π-π interactions and the higher crystallinity in the former film. This work provided us valuable information in the improvement of electronic and optoelectronic performances of organic semiconductors by tuning their aggregate structures.

Structural Transformation of Li-Excess Cathode Materials via Facile Preparation and Assembly of Sonication-Induced Colloidal Nanocrystals for Enhanced Lithium Storage Performance.

PubMed

Zhao, Jianqing; Huang, Ruiming; Ramos, Pablo; Yue, Yiying; Wu, Qinglin; Pavanello, Michele; Zhou, Jieyu; Kuai, Xiaoxiao; Gao, Lijun; He, Huixin; Wang, Ying

2017-09-13

A surfactant-free sonication-induced route is developed to facilely prepare colloidal nanocrystals of Li-excess layered Li 1.2 Mn 0.54 Ni 0.13 Co 0.13 O 2 (marked as LMNCO) material. The sonication process plays a critical role in forming LMNCO nanocrystals in ethanol (ethanol molecules marked as EtOHs) and inducing the interaction between LMNCO and solvent molecules. The formation mechanism of LMNCO-EtOH supramolecules in the colloidal dispersion system is proposed and examined by the theoretical simulation and light scattering technique. It is suggested that the as-formed supramolecule is composed of numerous ethanol molecules capping the surface of the LMNCO nanocrystal core via hydrogen bonding. Such chemisorption gives rise to dielectric polarization of the absorbed ethanol molecules, resulting in a negative surface charge of LMNCO colloids. The self-assembly behaviors of colloidal LMNCO nanocrystals are then tentatively investigated by tuning the solvent evaporation condition, which results in diverse superstructures of LMNCO materials after the evaporation of ethanol. The reassembled LMNCO architectures exhibit remarkably improved capacity and cyclability in comparison with the original LMNCO particles, demonstrating a very promising cathode material for high-energy lithium-ion batteries. This work thus provides new insights into the formation and self-assembly of multiple-element complex inorganic colloids in common and surfactant-free solvents for enhanced performance in device applications.

Crystal structure of triosephosphate isomerase from Trypanosoma cruzi in hexane

PubMed Central

Gao, Xiu-Gong; Maldonado, Ernesto; Pérez-Montfort, Ruy; Garza-Ramos, Georgina; de Gómez-Puyou, Marietta Tuena; Gómez-Puyou, Armando; Rodríguez-Romero, Adela

1999-01-01

To gain insight into the mechanisms of enzyme catalysis in organic solvents, the x-ray structure of some monomeric enzymes in organic solvents was determined. However, it remained to be explored whether the structure of oligomeric proteins is also amenable to such analysis. The field acquired new perspectives when it was proposed that the x-ray structure of enzymes in nonaqueous media could reveal binding sites for organic solvents that in principle could represent the starting point for drug design. Here, a crystal of the dimeric enzyme triosephosphate isomerase from the pathogenic parasite Trypanosoma cruzi was soaked and diffracted in hexane and its structure solved at 2-Å resolution. Its overall structure and the dimer interface were not altered by hexane. However, there were differences in the orientation of the side chains of several amino acids, including that of the catalytic Glu-168 in one of the monomers. No hexane molecules were detected in the active site or in the dimer interface. However, three hexane molecules were identified on the surface of the protein at sites, which in the native crystal did not have water molecules. The number of water molecules in the hexane structure was higher than in the native crystal. Two hexanes localized at <4 Å from residues that form the dimer interface; they were in close proximity to a site that has been considered a potential target for drug design. PMID:10468562

Crystal structure of triosephosphate isomerase from Trypanosoma cruzi in hexane.

PubMed

Gao, X G; Maldonado, E; Pérez-Montfort, R; Garza-Ramos, G; de Gómez-Puyou, M T; Gómez-Puyou, A; Rodríguez-Romero, A

1999-08-31

To gain insight into the mechanisms of enzyme catalysis in organic solvents, the x-ray structure of some monomeric enzymes in organic solvents was determined. However, it remained to be explored whether the structure of oligomeric proteins is also amenable to such analysis. The field acquired new perspectives when it was proposed that the x-ray structure of enzymes in nonaqueous media could reveal binding sites for organic solvents that in principle could represent the starting point for drug design. Here, a crystal of the dimeric enzyme triosephosphate isomerase from the pathogenic parasite Trypanosoma cruzi was soaked and diffracted in hexane and its structure solved at 2-A resolution. Its overall structure and the dimer interface were not altered by hexane. However, there were differences in the orientation of the side chains of several amino acids, including that of the catalytic Glu-168 in one of the monomers. No hexane molecules were detected in the active site or in the dimer interface. However, three hexane molecules were identified on the surface of the protein at sites, which in the native crystal did not have water molecules. The number of water molecules in the hexane structure was higher than in the native crystal. Two hexanes localized at <4 A from residues that form the dimer interface; they were in close proximity to a site that has been considered a potential target for drug design.

Holographic Methods for the Investigation of Photophysical Properties.

DTIC Science & Technology

1983-04-22

terphenyl doped with 10- 3 mol/mol of pentacene . Obtaining k from decay curves as in * A -Fig. 14a and plotting k as a function of 02 (see Fig. 14b...translation diffusion of molecules in liquid solvents can be used to probe solute conformations, solvent-solute interactions and local solvent structure...eiion of 1.7omoAr WauW by TrArWAOn GFarinP So far, local heating by the absorption of the two interfering light pulses has not been taken into

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.

Stabilization of Li Metal Anode in DMSO-Based Electrolytes via Optimization of Salt-Solvent Coordination for Li-O 2 Batteries

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

Liu, Bin; Xu, Wu; Yan, Pengfei

The conventional DMSO-based electrolyte (1 M lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) in DMSO) is unstable against the Li metal anode and therefore cannot be used directly in practical Li-O2 batteries. Here, we demonstrate that a highly concentrated electrolyte based on LiTFSI in DMSO (with a molar ratio of 1:3) can greatly improve the stability of the Li metal anode against DMSO and significantly improve the cycling stability of Li-O2 batteries. This highly concentrated electrolyte contains no free DMSO solvent molecules, but only complexes of (TFSI–)a-Li+-(DMSO)b (where a + b = 4), and thus enhances their stability with Li metal anodes. In addition,more » such salt-solvent complexes have higher Gibbs activation energy barriers than the free DMSO solvent molecules, indicating improved stability of the electrolyte against the attack of superoxide radical anions. Therefore, the stability of this highly concentrated electrolyte at both Li metal anodes and carbon-based air electrodes has been greatly enhanced, resulting in improved cyclic stability of Li-O2 batteries. The fundamental stability of the electrolyte with free-solvent against the chemical and electrochemical reactions can also be used to enhance the stability of other electrochemical systems.« less

SOLVENT-FREE APPROACH TO EXPEDITIOUS ORGANIC SYNTHESES USING MICROWAVE IRRADIATION

EPA Science Inventory

Microwave irradiation has been used for a variety of organic transformations wherein chemical reactions are accelerated because of selective adsorption of microwave (MW) energy by polar molecules, non-polar molecules being inert to the MW dielectric loss. The application of MW ir...

Crystal structure of 5,15-bis-(4-methyl-phen-yl)-10,20-bis-(4-nitro-phen-yl)porphyrin nitro-benzene disolvate.

PubMed

Baptayev, Bakhytzhan; Adilov, Salimgerey

2018-01-01

The whole mol-ecule of the title porphyrin, C 46 H 32 N 6 O 4 ·2C 6 H 5 NO 2 , which crystallized as a nitro-benzene disolvate, is generated by inversion symmetry. The porphyrin macrocycle is almost planar, the maximum deviation from the mean plane of the non-hydrogen atoms is 0.097 (2) Å. The aryl rings at the meso positions are inclined to this mean plane by 74.84 (6)° for the nitro-phenyl rings and 73.37 (7)° for the tolyl rings. In the crystal, the porphyrin mol-ecules are linked by C-H⋯O hydrogen bonds, forming chains along [100]. The solvent mol-ecules are also linked by C-H⋯O hydrogen bonds, forming chains along [100]. Inter-digitation of the p -tolyl groups along the c axis creates rectangular channels in which the solvent mol-ecules are located.

Electrostatic Repulsion-Induced Desorption of Dendritic Viologen-Arranged Molecules Anchored on a Gold Surface through a Gold-Thiolate Bond Leading to a Tunable Molecular Template.

PubMed

Kawauchi, Takehiro; Kojima, Takahiro; Sakaguchi, Hiroshi; Iyoda, Tomokazu

2018-06-05

We investigated the adsorption and desorption behavior of self-assembled monolayers (SAMs) on gold derived from dendritic viologen-arranged molecules with an ω-mercaptodecyl group (A n, n (dendritic generation) = 0-3) at the apex of the dendritic structure in polar solvents. The adsorption of the dendritic molecules occurred quickly and saturated within a few minutes in an acetonitrile/ethanol (1/1, v/v) mixture at a concentration of 2 mM. Atomic force microscopy images of the SAMs showed flat surfaces regardless of the dendritic generation because the peripheral viologen units were closely packed at the surface of the molecular layer. Individual A3 molecules immobilized on the substrate were observed by scanning tunneling microscopy measurements of a mixed SAM with decanethiol. The desorption behaviors of dendritic molecules from the A n-SAMs in several solvents such as water were also investigated. The spontaneous desorption of the A n-SAM occurred more rapidly than that of a conventional n-alkanethiol SAM. However, the desorption was inhibited by adding electrolytes such as NaNO 3 due to the shielding effect on the electrostatic repulsion between the dendritic molecules. These results indicate that the surface density of the dendritic molecules can be controlled through the desorption.

Stabilization of gold nanoparticles by 6-mercaptopurine monolayers. Effects of the solvent properties.

PubMed

Viudez, Alfonso J; Madueño, Rafael; Pineda, Teresa; Blázquez, Manuel

2006-09-14

6-Mercaptopurine-coated gold nanoparticles (6MP-AuNPs) have been prepared by modification of the nanoparticle surface with 6MP upon displacement of the protective layer of citrate anions. The modification has been studied by UV-vis and FTIR spectroscopies. A study of the stability of these 6MP-AuNPs in aqueous solutions as a function of ionic strength and pH has shown the importance of the charges on the stabilization. The protonation of N9 of the 6MP molecules brings about a sudden flocculation phenomenon. However, the flocculation is reversible upon changing the pH to values where the molecules become newly charged. Evidence of the competence between the interaction of capping solvent molecules and the attractive forces between particles is also shown in this paper.

The Structure of Ethylbenzene, Styrene and Phenylacetylene Determined by Total Neutron Scattering

PubMed Central

Szala‐Bilnik, Joanna; Falkowska, Marta; Bowron, Daniel T.

2017-01-01

Abstract Organic solvents such as phenylacetylene, styrene and ethylbenzene are widely used in industrial processes, especially in the production of rubber or thermoplastics. Despite their important applications detailed knowledge about their structure is limited. In this paper the structures of these three aromatic solvents were investigated using neutron diffraction. The results show that many of their structural characteristics are similar, although the structure of phenylacetylene is more ordered and has a smaller solvation sphere than either ethylbenzene or styrene. Two regions within the first coordination sphere, in which the surrounding molecules show different preferable orientations with respect to the central molecule, were found for each liquid. Additionally, the localisation of the aliphatic chains reveals that they tend to favour closer interactions with each other than to the aromatic rings of the adjacent molecules. PMID:28672104

Time-resolved emission spectra of 4-dimethylamino-4‧-cyano-stilbene and resveratrol in high viscosity solvents and silica matrices

NASA Astrophysics Data System (ADS)

Borowiak, Małgorzata; Grobelna, Beata; Synak, Anna; Bojarski, Piotr; Kubicki, Aleksander A.

2013-11-01

Time-resolved emission spectra of 4-dimethylamino-4‧-cyano-stilbene (DMACS) and 3,5,4‧-trihydroxy-stilbene (resveratrol, RSV) in propylene glycol and in rigid silica xerogel matrix at 23 °C were studied. For the polar molecule DMACS in propylene glycol, a 66 nm shift of maximum wavelength of emission spectra was observed within 1 ns after excitation, and most of the shift occurred during the first 200 ps. For resveratrol in propylene glycol no such a shift was observed. The rigid silica environment eliminates some deactivation pathways and stabilizes spectroscopic properties of both molecules. Spectral properties of nonpolar and high dipole moment molecules in viscous liquids and rigid environments are compared. Results are explained on the basis of intramolecular processes and solute-solvent relaxation, as well.

A simple model of solvent-induced symmetry-breaking charge transfer in excited quadrupolar molecules

NASA Astrophysics Data System (ADS)

Ivanov, Anatoly I.; Dereka, Bogdan; Vauthey, Eric

2017-04-01

A simple model has been developed to describe the symmetry-breaking of the electronic distribution of AL-D-AR type molecules in the excited state, where D is an electron donor and AL and AR are identical acceptors. The origin of this process is usually associated with the interaction between the molecule and the solvent polarization that stabilizes an asymmetric and dipolar state, with a larger charge transfer on one side than on the other. An additional symmetry-breaking mechanism involving the direct Coulomb interaction of the charges on the acceptors is proposed. At the same time, the electronic coupling between the two degenerate states, which correspond to the transferred charge being localised either on AL or AR, favours a quadrupolar excited state with equal amount of charge-transfer on both sides. Because of these counteracting effects, symmetry breaking is only feasible when the electronic coupling remains below a threshold value, which depends on the solvation energy and the Coulomb repulsion energy between the charges located on AL and AR. This model allows reproducing the solvent polarity dependence of the symmetry-breaking reported recently using time-resolved infrared spectroscopy.

Molecular gels in the gas phase? Gelator-gelator and gelator-solvent interactions probed by vibrational spectroscopy.

PubMed

Lozada-Garcia, Rolando; Mu, Dan; Plazanet, Marie; Çarçabal, Pierre

2016-08-10

Benzylidene glucose (BzGlc) is a member of the benzylidene glycoside family. These molecules have the ability to form molecular physical gels. These materials are formed when gelator molecules create a non-covalently bound frame where solvent molecules are trapped. Since the gel formation process and its properties are determined by the subtle balance between non-covalent forces, it is difficult to anticipate them. Quantitative and qualitative understanding of the gelator-gelator and gelator-solvent interactions is needed to better control these materials for important potential applications. We have used gas phase vibrational spectroscopy and theoretical chemistry to study the conformational choices of BzGlc, its dimer and the complexes it forms with water or toluene. To interpret the vibrational spectra we have used the dispersion corrected functional B97D which we have calibrated for the calculation of OH stretching frequencies. Even at the most basic molecular level, it is possible to interrogate a large range of non-covalent interactions ranging from OH → OH hydrogen bonding, to OH → π, and CH → π, all being at the center of gel properties at the macroscopic level.

Multi-wavelength spectrophotometric determination of acidity constant of some newly synthesized Schiff bases and their QSPR study

NASA Astrophysics Data System (ADS)

Hemmateenejad, Bahram; Emami, Leila; Sharghi, Hashem

2010-01-01

The acidity constants of some newly synthesized Schiff base derivatives were determined by hard-model based multivariate data analysis of the spectrophotometric data in the course of pH-metric titration in 50% (v/v) methanol-water binary solvent. The employed data analysis method was also able to extract the pure spectra and pH-dependent concentration profiles of the acid-base species. The molecules that possess different substituents (both electron donating and withdrawing) on the ortho-, meta- and para-positions of one of the phenyl ring showed variable acidity constants ranging from 8.77 to 11.07 whereas the parent molecule had an acidity constant of 10.25. To investigate the quantitative effects of changing of substitution pattern on the acidity constant, a quantitative structure-property relation analysis was conducted using substituent constants and molecular descriptor. Some models with high statistical quality (measured by cross-validation Q2) were obtained. It was found that the acidity constant of the studied molecules in the methanol-water mixed solvent not only is affected by electronic features of the solutes but also by the lipophilic interaction between methanol part of solvent and the deprotonated solutes.

Additive effect on reductive decomposition and binding of carbonate-based solvent toward solid electrolyte interphase formation in lithium-ion battery.

PubMed

Ushirogata, Keisuke; Sodeyama, Keitaro; Okuno, Yukihiro; Tateyama, Yoshitaka

2013-08-14

The solid-electrolyte interphase (SEI) formed through the reductive decomposition of solvent molecules plays a crucial role in the stability and capability of a lithium-ion battery (LIB). Here we investigated the effects of adding vinylene carbonate (VC) to ethylene carbonate (EC) solvent, a typical electrolyte in LIBs, on the reductive decomposition. We focused on both thermodynamics and kinetics of the possible processes and used density functional theory-based molecular dynamics with explicit solvent and Blue-moon ensemble technique for the free energy change. We considered Li(+) in only EC solvent (EC system) and in EC solvent with a VC additive (EC/VC system) to elucidate the additive effects. In addition to clarifying the equilibrium properties, we evaluated the free energy changes along several EC or VC decomposition pathways under one-electron (1e) reduction condition. Two-electron (2e) reduction and attacks of anion radicals to intact molecules were also examined. The present results completely reproduce the gaseous products observed in the experiments. We also found a new mechanism involving the VC additive: the VC additive preferentially reacts with the EC anion radical to suppress the 2e reduction of EC and enhance the initial SEI formation, contrary to the conventional scenario in which VC additive is sacrificially reduced and its radical oligomerization becomes the source of SEI. Because our mechanism needs only 1e reduction, the irreversible capacity at the SEI formation will decrease, which is also consistent with the experimental observations. These results reveal the primary role of VC additive in the EC solvent.

Active Solvent Modulation: A Valve-Based Approach To Improve Separation Compatibility in Two-Dimensional Liquid Chromatography.

PubMed

Stoll, Dwight R; Shoykhet, Konstantin; Petersson, Patrik; Buckenmaier, Stephan

2017-09-05

Two-dimensional liquid chromatography (2D-LC) is increasingly being viewed as a viable tool for solving difficult separation problems, ranging from targeted separations of structurally similar molecules to untargeted separations of highly complex mixtures. In spite of this performance potential, though, many users find method development challenging and most frequently cite the "incompatibility" between the solvent systems used in the first and second dimensions as a major obstacle. This solvent strength related incompatibility can lead to severe peak distortion and loss of resolution and sensitivity in the second dimension. In this paper, we describe a novel approach to address the incompatibility problem, which we refer to as Active Solvent Modulation (ASM). This valve-based approach enables dilution of 1 D effluent with weak solvent prior to transfer to the 2 D column but without the need for additional instrument hardware. ASM is related to the concept we refer to as Fixed Solvent Modulation (FSM), with the important difference being that ASM allows toggling of the diluent stream during each 2 D separation cycle. In this work, we show that ASM eliminates the major drawbacks of FSM including complex elution solvent profiles, baseline disturbances, and slow 2 D re-equilibration and demonstrate improvements in 2 D separation quality using both simple small molecule probes and degradants of heat-treated bovine insulin as case studies. We believe that ASM will significantly ease method development for 2D-LC, providing a path to practical methods that involve both highly complementary 1 D and 2 D separations and sensitive detection.

Host-Guest Chemistry in Integrated Porous Space Formed by Molecular Self-Assembly at Liquid-Solid Interfaces.

PubMed

Iritani, Kohei; Tahara, Kazukuni; De Feyter, Steven; Tobe, Yoshito

2017-05-16

Host-guest chemistry in two-dimensional (2D) space, that is, physisorbed monolayers of a single atom or a single molecular thickness on surfaces, has become a subject of intense current interest because of perspectives for various applications in molecular-scale electronics, selective sensors, and tailored catalysis. Scanning tunneling microscopy has been used as a powerful tool for the visualization of molecules in real space on a conducting substrate surface. For more than a decade, we have been investigating the self-assembly of a series of triangle-shaped phenylene-ethynylene macrocycles called dehydrobenzo[12]annulenes (DBAs). These molecules are substituted with six alkyl chains and are capable of forming hexagonal porous 2D molecular networks via van der Waals interactions between interdigitated alkyl chains at the interface of organic solvents and graphite. The dimension of the nanoporous space or nanowell formed by the self-assembly of DBAs can be controlled from 1.6 to 4.7 nm by simply changing the alkyl chain length from C 6 to C 20 . Single molecules as well as homoclusters and heteroclusters are capable of coadsorbing within the host matrix using shape- and size-complementarity principles. Moreover, on the basis of the versatility of the DBA molecules that allows chemical modification of the alkyl chain terminals, we were able to decorate the interior space of the nanoporous networks with functional groups such as azobenzenedicarboxylic acid for photoresponsive guest adsorption/desorption or fluoroalkanes and tetraethylene glycol groups for selective guest binding by electrostatic interactions and zinc-porphyrin units for complexation with a guest by charge-transfer interactions. In this Feature Article, we describe the general aspects of molecular self-assembly at liquid/solid interfaces, followed by the formation of programmed porous molecular networks using rationally designed molecular building blocks. We focus on our own work involving host-guest chemistry in integrated nanoporous space that is modified for specific purposes.

Novel strategy for diameter-selective separation and functionalization of single-wall carbon nanotubes.

PubMed

Tromp, R M; Afzali, A; Freitag, M; Mitzi, D B; Chen, Zh

2008-02-01

The problem of separating single-wall carbon nanotubes (CNTs) by diameter and/or chirality is one of the greatest impediments toward the widespread application of these promising materials in nanoelectronics. In this paper, we describe a novel physical-chemical method for diameter-selective CNT separation that is both simple and effective and that allows up-scaling to large volumes at modest cost. Separation is based on size-selective noncovalent matching of an appropriate anchor molecule to the wall of the CNT, enabling suspension of the CNTs in solvents in which they would otherwise not be soluble. We demonstrate size-selective separation in the 1-2 nm diameter range using easily synthesized oligo-acene adducts as a diameter-selective molecular anchor. CNT field effect transistors fabricated from diameter-selected CNTs show markedly improved electrical properties as compared to nonselected CNTs.

Solvent exchange in a metal–organic framework single crystal monitored by dynamic in situ X-ray diffraction

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

Cox, Jordan M.; Walton, Ian M.; Bateman, Gage

2017-07-25

Understanding the processes by which porous solid-state materials adsorb and release guest molecules would represent a significant step towards developing rational design principles for functional porous materials. To elucidate the process of liquid exchange in these materials, dynamicin situX-ray diffraction techniques have been developed which utilize liquid-phase chemical stimuli. Using these time-resolved diffraction techniques, the ethanol solvation process in a flexible metal–organic framework [Co(AIP)(bpy) 0.5(H 2O)]·2H 2O was examined. The measurements provide important insight into the nature of the chemical transformation in this system including the presence of a previously unreported neat ethanol solvate structure.

The development of a revised version of multi-center molecular Ornstein-Zernike equation

NASA Astrophysics Data System (ADS)

Kido, Kentaro; Yokogawa, Daisuke; Sato, Hirofumi

2012-04-01

Ornstein-Zernike (OZ)-type theory is a powerful tool to obtain 3-dimensional solvent distribution around solute molecule. Recently, we proposed multi-center molecular OZ method, which is suitable for parallel computing of 3D solvation structure. The distribution function in this method consists of two components, namely reference and residue parts. Several types of the function were examined as the reference part to investigate the numerical robustness of the method. As the benchmark, the method is applied to water, benzene in aqueous solution and single-walled carbon nanotube in chloroform solution. The results indicate that fully-parallelization is achieved by utilizing the newly proposed reference functions.

Conformational State Distributions and Catalytically Relevant Dynamics of a Hinge-Bending Enzyme Studied by Single-Molecule FRET and a Coarse-Grained Simulation

PubMed Central

Gabba, Matteo; Poblete, Simón; Rosenkranz, Tobias; Katranidis, Alexandros; Kempe, Daryan; Züchner, Tina; Winkler, Roland G.; Gompper, Gerhard; Fitter, Jörg

2014-01-01

Over the last few decades, a view has emerged showing that multidomain enzymes are biological machines evolved to harness stochastic kicks of solvent particles into highly directional functional motions. These intrinsic motions are structurally encoded, and Nature makes use of them to catalyze chemical reactions by means of ligand-induced conformational changes and states redistribution. Such mechanisms align reactive groups for efficient chemistry and stabilize conformers most proficient for catalysis. By combining single-molecule Förster resonance energy transfer measurements with normal mode analysis and coarse-grained mesoscopic simulations, we obtained results for a hinge-bending enzyme, namely phosphoglycerate kinase (PGK), which support and extend these ideas. From single-molecule Förster resonance energy transfer, we obtained insight into the distribution of conformational states and the dynamical properties of the domains. The simulations allowed for the characterization of interdomain motions of a compact state of PGK. The data show that PGK is intrinsically a highly dynamic system sampling a wealth of conformations on timescales ranging from nanoseconds to milliseconds and above. Functional motions encoded in the fold are performed by the PGK domains already in its ligand-free form, and substrate binding is not required to enable them. Compared to other multidomain proteins, these motions are rather fast and presumably not rate-limiting in the enzymatic reaction. Ligand binding slightly readjusts the orientation of the domains and feasibly locks the protein motions along a preferential direction. In addition, the functionally relevant compact state is stabilized by the substrates, and acts as a prestate to reach active conformations by means of Brownian motions. PMID:25418172

Water-Stable Metal-Organic Framework with Three Hydrogen-Bond Acceptors: Versatile Theoretical and Experimental Insights into Adsorption Ability and Thermo-Hydrolytic Stability.

PubMed

Roztocki, Kornel; Lupa, Magdalena; Sławek, Andrzej; Makowski, Wacław; Senkovska, Irena; Kaskel, Stefan; Matoga, Dariusz

2018-03-19

A new microporous cadmium metal-organic framework was synthesized both mechanochemically and in solution by using a sulfonyl-functionalized dicarboxylate linker and an acylhydrazone colinker. The three-dimensional framework is highly stable upon heating to 300 °C as well as in aqueous solutions at elevated temperatures or acidic conditions. The thermally activated material exhibits steep water vapor uptake at low relative pressures at 298 K and excellent recyclability up to 260 °C as confirmed by both quasi-equilibrated temperature-programmed desorption and adsorption (QE-TPDA) method as well as adsorption isotherm measurements. Reversible isotherms and hysteretic isobars recorded for the desorption-adsorption cycles indicate the maximum uptake of 0.19 g/g (at 298 K, up to p/p 0 = 1) or 0.18 g/g (at 1 bar, within 295-375 K range), respectively. The experimental isosteric heat of adsorption (48.9 kJ/mol) indicates noncoordinative interactions of water molecules with the framework. Exchange of the solvent molecules in the as-made material with water, performed in the single-crystal to single-crystal manner, allows direct comparison of both X-ray crystal structures. The single-crystal X-ray diffraction for the water-loaded framework demonstrates the orientation of water clusters in the framework cavities and reveals their strong hydrogen bonding with sulfonyl, acyl, and carboxylate groups of the two linkers. The grand canonical Monte Carlo (GCMC) simulations of H 2 O adsorption corroborate the experimental findings and reveal preferable locations of guest molecules in the framework voids at various pressures. Additionally, both experimental and GCMC simulation insights into the adsorption of CO 2 (at 195 K) on the activated framework are presented.

Determination of thermodynamics and kinetics of RNA reactions by force

PubMed Central

Tinoco, Ignacio; Li, Pan T. X.; Bustamante, Carlos

2008-01-01

Single-molecule methods have made it possible to apply force to an individual RNA molecule. Two beads are attached to the RNA; one is on a micropipette, the other is in a laser trap. The force on the RNA and the distance between the beads are measured. Force can change the equilibrium and the rate of any reaction in which the product has a different extension from the reactant. This review describes use of laser tweezers to measure thermodynamics and kinetics of unfolding/refolding RNA. For a reversible reaction the work directly provides the free energy; for irreversible reactions the free energy is obtained from the distribution of work values. The rate constants for the folding and unfolding reactions can be measured by several methods. The effect of pulling rate on the distribution of force-unfolding values leads to rate constants for unfolding. Hopping of the RNA between folded and unfolded states at constant force provides both unfolding and folding rates. Force-jumps and force-drops, similar to the temperature jump method, provide direct measurement of reaction rates over a wide range of forces. The advantages of applying force and using single-molecule methods are discussed. These methods, for example, allow reactions to be studied in non-denaturing solvents at physiological temperatures; they also simplify analysis of kinetic mechanisms because only one intermediate at a time is present. Unfolding of RNA in biological cells by helicases, or ribosomes, has similarities to unfolding by force. PMID:17040613

Conditional solvation thermodynamics of isoleucine in model peptides and the limitations of the group-transfer model.

PubMed

Tomar, Dheeraj S; Weber, Valéry; Pettitt, B Montgomery; Asthagiri, D

2014-04-17

The hydration thermodynamics of the amino acid X relative to the reference G (glycine) or the hydration thermodynamics of a small-molecule analog of the side chain of X is often used to model the contribution of X to protein stability and solution thermodynamics. We consider the reasons for successes and limitations of this approach by calculating and comparing the conditional excess free energy, enthalpy, and entropy of hydration of the isoleucine side chain in zwitterionic isoleucine, in extended penta-peptides, and in helical deca-peptides. Butane in gauche conformation serves as a small-molecule analog for the isoleucine side chain. Parsing the hydrophobic and hydrophilic contributions to hydration for the side chain shows that both of these aspects of hydration are context-sensitive. Furthermore, analyzing the solute-solvent interaction contribution to the conditional excess enthalpy of the side chain shows that what is nominally considered a property of the side chain includes entirely nonobvious contributions of the background. The context-sensitivity of hydrophobic and hydrophilic hydration and the conflation of background contributions with energetics attributed to the side chain limit the ability of a single scaling factor, such as the fractional solvent exposure of the group in the protein, to map the component energetic contributions of the model-compound data to their value in the protein. But ignoring the origin of cancellations in the underlying components the group-transfer model may appear to provide a reasonable estimate of the free energy for a given error tolerance.

Ground-State Charge-Density Distribution in a Crystal of the Luminescent ortho-Phenylenediboronic Acid Complex with 8-Hydroxyquinoline.

PubMed

Jarzembska, Katarzyna N; Kamiński, Radosław; Durka, Krzysztof; Woźniak, Krzysztof

2018-05-10

This contribution is devoted to the first electron density studies of a luminescent oxyquinolinato boron complex in the solid state. ortho-Phenylenediboronic acid mixed with 8-hydroxyquinoline in dioxane forms high-quality single crystals via slow solvent evaporation, which allows successful high resolution data collection (sin θ/λ = 1.2 Å -1 ) and charge density distribution modeling. Particular attention has been paid to the boron-oxygen fragment connecting the two parts of the complex, and to the solvent species exhibiting anharmonic thermal motion. The experiment and theory compared rather well in terms of atomic charges and volumes, except for the boron centers. Boron atoms, as expected, constitute the most electron-deficient species in the complex molecule, whereas the neighboring oxygen and carbon atoms are the most significantly negatively charged ones. This part of the molecule appears to be very much involved in the charge transfer occurring between the acid fragment and oxyquinoline moiety leading to the observed fluorescence, as supported by the time-dependent density functional theory (TDDFT) results and the generated transition density maps. TDDFT calculations indicated that p-type atomic orbitals contributing to the HOMO-1, HOMO, and LUMO play the major role in the lowest energy transitions, and enabled further comparison with the charge density features, which is discussed in details. Furthermore, the results confirmed the known fact the Q ligand character is most important for the spectroscopic properties of this class of complexes.

Selective CO2 adsorption by a new metal-organic framework: synergy between open metal sites and a charged imidazolinium backbone.

PubMed

Kochetygov, Ilia; Bulut, Safak; Asgari, Mehrdad; Queen, Wendy L

2018-05-30

Metal-organic frameworks (MOFs) are porous, tunable crystalline materials that are attracting widespread scientific attention for their potential use in post-combustion CO2 capture. In this work, we report the synthesis of a new ligand, 1,3-bis(4-carboxyphenyl)-4,5-dihydro-1H-imidazol-3-ium tetrafluoroborate, H2Sp5-BF4, that is subsequently used for the construction of a novel MOF, Cu-Sp5-EtOH. This highly crystalline material has a charged framework that is expected to give rise to high CO2/N2 selectivity. However, the pores of the parent structure could not be accessed due to the presence of strongly coordinated ethanol molecules. After solvent exchange with methanol and subsequently heating Cu-Sp5-MeOH under vacuum, we are able to liberate the solvent providing other small molecules like CO2 access to the inside of the now porous structure, Cu-Sp5. The combination of open metal sites and framework charge leads to an exceptionally high CO2/N2 selectivity, as determined by Ideal Adsorbed Solution Theory (IAST) calculations performed on single-component adsorption isotherms. The CO2/N2 selectivity of Cu-Sp5 reaches a value of over 200 at pressures typically found in post-combustion flue gas (0.15 bar CO2/0.85 bar N2), a value that is among the highest reported to date.

Influence of dilution with organic solvents on emission spectra of CdSe/ZnS quantum dots

NASA Astrophysics Data System (ADS)

Kumakura, Mitsutaka; Kinan, Asuka; Moriyasu, Takeshi

2017-04-01

The emission spectra of CdSe/ZnS core-shell dots have been monitored after the dilution of their toluene solution with organic solvents (toluene, n-hexane, diethyl ether, acetone, ethanol, and methanol). In addition to the well-known difference of the emission efficiency according to the solvent, we found their time variation depending on the solvent. From the discussion based on the solubility of the capping organic ligand, hexadecylamine (HDA), to each solvent it is suggested that the observed time variation is caused by the liquation of the capping molecules form the dot surface and the resulting change of the number of the trap site for charges in the quantum dot.

Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation

NASA Astrophysics Data System (ADS)

Pandey, R. B.; Jacobs, D. J.; Farmer, B. L.

2017-05-01

The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (Rg) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in Rg occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ˜ 1.3), random-coil (D ˜ 1.75), and globular (D ˜ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale.

Examination of the solventlike nature of zeolites based on a solvatochromic indicator

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

Dutta, P.K.; Turbeville, W.

1991-05-16

Zeolites are crystalline aluminosilicates with cages and channel systems that can host a variety of organic transformations. This intracrystalline space is akin to a solvent, and description of this space in terms of solventlike properties is appropriate. The concept of solvatochromic indicators has been successfully used to define the physicochemical properties of organic solvents. In this study, the authors have investigated the electronic and Raman spectroscopy of the molecule N-(2-hydroxybenzylidene)aniline and established a quantitative correlation between the spectral intensities of the benzenoid and zwitterionic forms of this molecule and the {alpha}-value of various hydroxylic solvents. The {alpha} value is amore » measure of the hydrogen bond donor ability of the solvent. This correlation has been used to establish an {alpha} value scale for a series of faujasitic zeolites with varying Si/Al ratios. It was found that the {alpha} value of the zeolite increased with Si/Al ratio to reach a maximum around 7.8, followed by a decrease at higher Si/Al ratios. Since Na{sup +}-exchanged zeolites were examined in all cases, the interaction of the anil molecule in its zwitterionic form with Lewis acids (Na{sup +}) and bases (oxygen of the framework) was considered to be responsible for its formation. The Si/Al ratio of the framework determines the acid-base character of the zeolite and is reflected in a quantitative manner by the {alpha} value determined in this study.« less

The influence of self-assembling supramolecular structures on the passive membrane transport of ion-paired molecules.

PubMed

Benaouda, F; Brown, M B; Shah, B; Martin, G P; Jones, S A

2012-12-15

Weak ion-ion interactions, such as those associated with ion-pair formation, are difficult to isolate and characterise in the liquid state, but they have the potential to alter significantly the physicochemical behaviour of molecules in solution. The aim of this work was to gain a better understanding of how ion-ion interactions influenced passive membrane transport. The test system was composed of propylene (PG) glycol, water and diclofenac diethylamine (DDEA). Infrared spectroscopy was employed to determine the nature of the DDEA ion-pair interactions and the drug-vehicle association. Passive transport was assessed using homogeneous synthetic membranes. Solution-state analysis demonstrated that the ion-pair was unperturbed by vehicle composition changes, but the solvent-DDEA interactions were modified. DDEA-PG/water hydrogen bonding influenced the ion-pair solubility (X(dev)) and the solvent interactions slowed transport rate in PG-rich vehicles (0.84±0.05 μg cm(-2) h(-1), at ln(X(dev))=0.57). In water-rich co-solvents, the presence of strong water structuring facilitated a significant increase (p<0.05) in transmembrane penetration rate (e.g. 4.33±0.92 μg cm(-2) h(-1), at ln(X(dev))=-0.13). The data demonstrates that weak ion-ion interactions can result in the embedding of polar entities within a stable solvent complex and spontaneous supramolecular assembly should be considered when interpreting transmembrane transport processes of ionic molecules. Copyright © 2012 Elsevier B.V. All rights reserved.

Theoretical study of solvent effects on the electronic coupling matrix elements in rigidly linked donor-acceptor systems

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

Cave, R.J.; Newton, M.D.; Kumar, K.

1995-12-07

The recently developed generalized Mulliken-Hush approach for the calculation of the electronic coupling matrix element for electron-transfer processes is applied to two rigidly linked donor-bridge-acceptor systems having dimethoxyanthracene as the donor and a dicarbomethoxycyclobutene unit as the acceptor. The dependence of the electronic coupling matrix element as a function of bridge type is examined with and without solvent molecules present. For clamp-shaped bridge structures solvent can have a dramatic effect on the electronic coupling matrix element. The behavior with variation of solvent is in good agreement with that observed experimentally for these systems. 23 refs., 2 tabs.

Effect of viscosity on photoinduced electron transfer reaction: An observation of the Marcus inverted region in homogeneous solvents

NASA Astrophysics Data System (ADS)

Saini, Rajesh Kumar; Kuchlyan, Jagannath; Sarkar, Nilmoni

2016-09-01

The viscosity effect of homogeneous solvents on the dynamics of photoinduced electron transfer (PET) reaction among the coumarins and N,N-dimethylaniline (DMA) is investigated using steady-state and time-resolved fluorescence spectroscopy. A bell shape Marcus inversion in the ET rates has been detected in the plot of ET rate constant (kq) with free energy change (ΔG0) in viscous solvents decanol and EG, but it is not observed in DMSO like low viscous solvent. We have also reported that there is no complex formation between the coumarin dye and DMA molecule by using fluorescence correlation spectroscopy.

CO 2 Binding Organic Liquids Gas Capture with Polarity Swing Assisted Regeneration

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

Heldebrant, David

This report outlines the comprehensive bench-scale testing of the CO 2-binding organic liquids (CO 2BOLs) solvent platform and its unique Polarity Swing Assisted Regeneration (PSAR). This study outlines all efforts on a candidate CO 2BOL solvent molecule, including solvent synthesis, material characterization, preliminary toxicology studies, and measurement of all physical, thermodynamic and kinetic data, including bench-scale testing. Equilibrium and kinetic models and analysis were made using Aspen Plus™. Preliminary process configurations, a technoeconomic assessment and solvent performance projections for separating CO 2 from a subcritical coal-fired power plant are compared to the U.S. Department of Energy's Case 10 monoethanolamine baseline.

Energy decomposition analysis for exciplexes using absolutely localized molecular orbitals

NASA Astrophysics Data System (ADS)

Ge, Qinghui; Mao, Yuezhi; Head-Gordon, Martin

2018-02-01

An energy decomposition analysis (EDA) scheme is developed for understanding the intermolecular interaction involving molecules in their excited states. The EDA utilizes absolutely localized molecular orbitals to define intermediate states and is compatible with excited state methods based on linear response theory such as configuration interaction singles and time-dependent density functional theory. The shift in excitation energy when an excited molecule interacts with the environment is decomposed into frozen, polarization, and charge transfer contributions, and the frozen term can be further separated into Pauli repulsion and electrostatics. These terms can be added to their counterparts obtained from the ground state EDA to form a decomposition of the total interaction energy. The EDA scheme is applied to study a variety of systems, including some model systems to demonstrate the correct behavior of all the proposed energy components as well as more realistic systems such as hydrogen-bonding complexes (e.g., formamide-water, pyridine/pyrimidine-water) and halide (F-, Cl-)-water clusters that involve charge-transfer-to-solvent excitations.

Hierarchical self-assembly of a bow-shaped molecule bearing self-complementary hydrogen bonding sites into extended supramolecular assemblies.

PubMed

Ikeda, Masato; Nobori, Tadahito; Schmutz, Marc; Lehn, Jean-Marie

2005-01-07

The bow-shaped molecule 1 bearing a self-complementary DAAD-ADDA (D=donor A=acceptor) hydrogen-bonding array generates, in hydrocarbon solvents, highly ordered supramolecular sheet aggregates that subsequently give rise to gels by formation of an entangled network. The process of hierarchical self-assembly of compound 1 was investigated by the concentration and temperature dependence of UV-visible and (1)H NMR spectra, fluorescence spectra, and electron microscopy data. The temperature dependence of the UV-visible spectra indicates a highly cooperative process for the self-assembly of compound 1 in decaline. The electron micrograph of the decaline solution of compound 1 (1.0 mM) revealed supramolecular sheet aggregates forming an entangled network. The selected area electronic diffraction patterns of the supramolecular sheet aggregates were typical for single crystals, indicative of a highly ordered assembly. The results exemplify the generation, by hierarchical self-assembly, of highly organized supramolecular materials presenting novel collective properties at each level of organization.

Cell-free metabolic engineering: production of chemicals by minimized reaction cascades.

PubMed

Guterl, Jan-Karl; Garbe, Daniel; Carsten, Jörg; Steffler, Fabian; Sommer, Bettina; Reiße, Steven; Philipp, Anja; Haack, Martina; Rühmann, Broder; Koltermann, Andre; Kettling, Ulrich; Brück, Thomas; Sieber, Volker

2012-11-01

The limited supply of fossil resources demands the development of renewable alternatives to petroleum-based products. Here, biobased higher alcohols such as isobutanol are versatile platform molecules for the synthesis of chemical commodities and fuels. Currently, their fermentation-based production is limited by the low tolerance of microbial production systems to the end products and also by the low substrate flux into cell metabolism. We developed an innovative cell-free approach, utilizing an artificial minimized glycolytic reaction cascade that only requires one single coenzyme. Using this toolbox the cell-free production of ethanol and isobutanol from glucose was achieved. We also confirmed that these streamlined cascades functioned under conditions at which microbial production would have ceased. Our system can be extended to an array of industrially-relevant molecules. Application of solvent-tolerant biocatalysts potentially allows for high product yields, which significantly simplifies downstream product recovery. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hybrid Nanomaterials with Single-Site Catalysts by Spatially Controllable Immobilization of Nickel Complexes via Photoclick Chemistry for Alkene Epoxidation.

PubMed

Ghosh, Dwaipayan; Febriansyah, Benny; Gupta, Disha; Ng, Leonard Kia-Sheun; Xi, Shibo; Du, Yonghua; Baikie, Tom; Dong, ZhiLi; Soo, Han Sen

2018-05-22

Catalyst deactivation is a persistent problem not only for the scientific community but also in industry. Isolated single-site heterogeneous catalysts have shown great promise to overcome these problems. Here, a versatile anchoring strategy for molecular complex immobilization on a broad range of semiconducting or insulating metal oxide ( e. g., titanium dioxide, mesoporous silica, cerium oxide, and tungsten oxide) nanoparticles to synthesize isolated single-site catalysts has been studied systematically. An oxidatively stable anchoring group, maleimide, is shown to form covalent linkages with surface hydroxyl functionalities of metal oxide nanoparticles by photoclick chemistry. The nanocomposites have been thoroughly characterized by techniques including UV-visible diffuse reflectance spectroscopy, high-resolution transmission electron microscopy, X-ray photoelectron spectroscopy, infrared spectroscopy, and X-ray absorption spectroscopy (XAS). The IR spectroscopic studies confirm the covalent linkages between the maleimide group and surface hydroxyl functionalities of the oxide nanoparticles. The hybrid nanomaterials function as highly efficient catalysts for essentially quantitative oxidations of terminal and internal alkenes and show molecular catalyst product selectivities even in more eco-friendly solvents. XAS studies verify the robustness of the catalysts after several catalytic cycles. We have applied the photoclick anchoring methodology to precisely control the deposition of a luminescent variant of our catalyst on the metal oxide nanoparticles. Overall, we demonstrate a general approach to use irradiation to anchor molecular complexes on oxide nanoparticles to create recyclable, hybrid, single-site catalysts that function with high selectivity in a broad range of solvents. We have achieved a facile, spatially and temporally controllable photoclick method that can potentially be extended to other ligands, catalysts, functional molecules, and surfaces.

UV-Vis spectroscopic study and DFT calculation on the solvent effect of trimethoprim in neat solvents and aqueous mixtures.

PubMed

Almandoz, M C; Sancho, M I; Duchowicz, P R; Blanco, S E

2014-08-14

The solvatochromic behavior of trimethoprim (TMP) was analyzed using UV-Vis spectroscopy and DFT methods in neat and binary aqueous solvent mixtures. The effects of solvent dipolarity/polarizability and solvent-solute hydrogen bonding interactions on the absorption maxima were evaluated by means of the linear solvation energy relationship concept of Kamlet and Taft. This analysis indicated that both interactions play an important role in the position of the absorption maxima in neat solvents. The simulated absorption spectra of TMP and TMP:(solvent)n complexes in ACN and H2O using TD-DFT methods were in agreement with the experimental ones. Binary aqueous mixtures containing as co-solvents DMSO, ACN and EtOH were studied. Preferential solvation was detected as a nonideal behavior of the wavenumber curve respective to the analytical mole fraction of co-solvent in all binary systems. TMP molecules were preferentially solvated by the organic solvent over the whole composition range. Index of preferential solvation, as well as the influence of solvent parameters were calculated as a function of solvent composition. Copyright © 2014 Elsevier B.V. All rights reserved.

A combined interfacial and in-situ polymerization strategy to construct well-defined core-shell epoxy-containing SiO2-based microcapsules with high encapsulation loading, super thermal stability and nonpolar solvent tolerance

NASA Astrophysics Data System (ADS)

Jia; Wang; Tian; Li; Xu; Jiao; Cao; Wu

2016-10-01

SiO2-based microcapsules containing hydrophobic molecules exhibited potential applications such as extrinsic self-healing, drug delivery, due to outstanding thermal and chemical stability of SiO2. However, to construct SiO2-based microcapsules with both high encapsulation loading and long-term structural stability is still a troublesome issue, limiting their further utilization. We herein design a single-batch route, a combined interfacial and in-situ polymerization strategy, to fabricate epoxy-containing SiO2-based microcapsules with both high encapsulation loading and long-term structural stability. The final SiO2-based microcapsules preserve high encapsulation loading of 85.7 wt% by controlling exclusively hydrolysis and condensed polymerization at oil/water interface in the initial interfacial polymerization step. In the subsequent in-situ polymerization step, the initial SiO2-based microcapsules as seeds could efficiently harvest SiO2 precursors and primary SiO2 particles to finely tune the SiO2 wall thickness, thereby enhancing long-term structural stability of the final SiO2-based microcapsules including high thermal stability with almost no any weight loss until 250°C, and strong tolerance against nonpolar solvents such as CCl4 with almost unchanged core-shell structure and unchanged core weight after immersing into strong solvents for up to 5 days. These SiO2-based microcapsules are extremely suited for processing them into anticorrosive coating in the presence of nonpolar solvents for self-healing application.

Using elaborative interrogation to induce characteristics of polar and nonpolar solvents from animations of their molecular structures

NASA Astrophysics Data System (ADS)

Ems-Wilson, Janice

This study concerned (a) how general chemistry students learn to classify solvent polarity from animated molecules, (b) whether peer interaction increases the number of correct classifications, and (c) whether language, academic ability, logical thinking ability, or prior knowledge interact with rate of learning or posttest performance. Two types of interaction were compared, group discussion and elaborative interrogation. The study rested on three assumptions: (a) animated molecules are appropriate for learning the concept of solvent polarity, (b) question stems and a guided interrogation enhance learning of a visual concept, (c) general chemistry students can induce the concept of solvent polarity from animated molecules when no guiding cues, either visual or verbal, are given. After a review of molecular geometry and bonding theories, students were presented with four trials of ten animated molecular structures. Ten three-to-five minute discussions were distributed among the four trials. Prior to the trials the experimental group received a 45-minute training session on elaborative interrogation; the topic was what happens on the molecular level when a carbonated beverage is opened. The control group received a 45-minute expository lecture on the same carbonated beverage topic. Participants were given a four-part posttest immediately following the trials. Results of the study suggest that most students tend to classify the solvent polarity of animated molecules based on certain structural features using a prototype or feature-frequency categorization strategy. Elaborative interrogation did not show a significant effect on the rate of learning or on the performance of learners on posttest measures of recall and comprehension. The experimental group noted a significantly greater number and range of types of features, and offered higher quality generalizations and explanations of their polarity classification procedure. Finally, the results implied that learning from animations depends more on prior knowledge of relevant concepts than on academic ability, logical thinking ability, or preferred language. Although some benefits may arise from accompanying computer animation with an interactive discussion, additional visual and verbal, cueing may be necessary for optimal outcomes.

Metathesis depolymerizable surfactants

DOEpatents

Jamison, Gregory M [Albuquerque, NM; Wheeler, David R [Albuquerque, NM; Loy, Douglas A [Tucson, AZ; Simmons, Blake A [San Francisco, CA; Long, Timothy M [Evanston, IL; McElhanon, James R [Manteca, CA; Rahimian, Kamyar [Albuquerque, NM; Staiger, Chad L [Albuquerque, NM

2008-04-15

A class of surfactant molecules whose structure includes regularly spaced unsaturation in the tail group and thus, can be readily decomposed by ring-closing metathesis, and particularly by the action of a transition metal catalyst, to form small molecule products. These small molecules are designed to have increased volatility and/or enhanced solubility as compared to the original surfactant molecule and are thus easily removed by solvent extraction or vacuum extraction at low temperature. By producing easily removable decomposition products, the surfactant molecules become particularly desirable as template structures for preparing meso- and microstructural materials with tailored properties.

Ab initio characterization of electron transfer coupling in photoinduced systems: generalized Mulliken-Hush with configuration-interaction singles.

PubMed

Chen, Hung-Cheng; Hsu, Chao-Ping

2005-12-29

To calculate electronic couplings for photoinduced electron transfer (ET) reactions, we propose and test the use of ab initio quantum chemistry calculation for excited states with the generalized Mulliken-Hush (GMH) method. Configuration-interaction singles (CIS) is proposed to model the locally excited (LE) and charge-transfer (CT) states. When the CT state couples with other high lying LE states, affecting coupling values, the image charge approximation (ICA), as a simple solvent model, can lower the energy of the CT state and decouple the undesired high-lying local excitations. We found that coupling strength is weakly dependent on many details of the solvent model, indicating the validity of the Condon approximation. Therefore, a trustworthy value can be obtained via this CIS-GMH scheme, with ICA used as a tool to improve and monitor the quality of the results. Systems we tested included a series of rigid, sigma-linked donor-bridge-acceptor compounds where "through-bond" coupling has been previously investigated, and a pair of molecules where "through-space" coupling was experimentally demonstrated. The calculated results agree well with experimentally inferred values in the coupling magnitudes (for both systems studied) and in the exponential distance dependence (for the through-bond series). Our results indicate that this new scheme can properly account for ET coupling arising from both through-bond and through-space mechanisms.

Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process

PubMed Central

Miao, Yinglong; Baudry, Jerome

2011-01-01

Long-timescale molecular dynamics simulations (300 ns) are performed on both the apo- (i.e., camphor-free) and camphor-bound cytochrome P450cam (CYP101). Water diffusion into and out of the protein active site is observed without biased sampling methods. During the course of the molecular dynamics simulation, an average of 6.4 water molecules is observed in the camphor-binding site of the apo form, compared to zero water molecules in the binding site of the substrate-bound form, in agreement with the number of water molecules observed in crystal structures of the same species. However, as many as 12 water molecules can be present at a given time in the camphor-binding region of the active site in the case of apo-P450cam, revealing a highly dynamic process for hydration of the protein active site, with water molecules exchanging rapidly with the bulk solvent. Water molecules are also found to exchange locations frequently inside the active site, preferentially clustering in regions surrounding the water molecules observed in the crystal structure. Potential-of-mean-force calculations identify thermodynamically favored trans-protein pathways for the diffusion of water molecules between the protein active site and the bulk solvent. Binding of camphor in the active site modifies the free-energy landscape of P450cam channels toward favoring the diffusion of water molecules out of the protein active site. PMID:21943431

High Level ab initio Predictions of the Energetics of mCO2•(H2O)n (n = 1-3, m = 1-12) Clusters

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

Thanthiriwatte, Sahan; Duke, Jessica R.; Jackson, Virgil E.

Electronic structure calculations at the correlated molecular orbital theory and density functional theory levels have been used to generate a reliable set of clustering energies for up to three water molecules in carbon dioxide clusters up to n = 12. The structures and energetics are dominated by Lewis acid-base interactions with hydrogen bonding interactions playing a lesser energetic role. The actual binding energies are somewhat larger than might be expected. The correlated molecular orbital MP2 method and density functional theory with the ωB97X exchange-correlation functional provide good results for the energetics of the clusters but the B3LYP and ωB97X-D functionalsmore » do not. Seven CO2 molecules form the first solvent shell about a single H2O with four CO2 molecules interacting with the H2O via Lewis acid-base interactions, two CO2 interacting with the H2O by hydrogen bonds, and the seventh CO2 completing the shell. The Lewis acid-base and weak hydrogen bond interactions between the water molecules and the CO2 molecules are strong enough to disrupt the trimer ring configuration for as few as seven CO2 molecules. Calculated 13C NMR chemical shifts for mCO2•(H2O)n show little change with respect to the number of H2O or CO2 molecules in the cluster. The O-H stretching frequencies do exhibit shifts that can provide information about the interactions between water and CO2 molecules.« less

Solution-grown small-molecule organic semiconductor with enhanced crystal alignment and areal coverage for organic thin film transistors

DOE PAGES

Bi, Sheng; He, Zhengran; Chen, Jihua; ...

2015-07-24

Drop casting of small-molecule organic semiconductors typically forms crystals with random orientation and poor areal coverage, which leads to significant performance variations of organic thin-film transistors (OTFTs). In this study, we utilize the controlled evaporative self-assembly (CESA) method combined with binary solvent system to control the crystal growth. A small-molecule organic semiconductor,2,5-Di-(2-ethylhexyl)-3,6-bis(5"-n-hexyl-2,2',5',2"]terthiophen-5-yl)-pyrrolo[3,4-c]pyrrole-1,4-dione (SMDPPEH), is used as an example to demonstrate the effectiveness of our approach. By optimizing the double solvent ratios, well-aligned SMDPPEH crystals with significantly improved areal coverage were achieved. As a result, the SMDPPEH based OTFTs exhibit a mobility of 1.6 × 10 -2 cm 2/V s, whichmore » is the highest mobility from SMDPPEH ever reported.« less

On the nature of hydrogen bonding between the phosphatidylcholine head group and water and dimethylsulfoxide

NASA Astrophysics Data System (ADS)

Dabkowska, Aleksandra P.; Lawrence, M. Jayne; McLain, Sylvia E.; Lorenz, Christian D.

2013-01-01

Molecular dynamics simulations are used to provide a detailed investigation of the hydrogen bond networks around the phosphatidylcholine (PC) head group in 1,2-dipropionyl-sn-glycero-3-phosphocholine in pure water, 10 mol.% and 30 mol.% dimethylsulfoxide (DMSO)-water solutions. Specifically, it is observed that DMSO replaces those water molecules that are within the first solvation shell of the choline, phosphate and ester groups of the PC head group, but are not hydrogen-bonded to the group. The effect of the presence of DMSO on the hydrogen bond network around the PC head groups of the lipid changes with the concentration of DMSO. In comparison to the hydrogen bond network observed in the pure water system, the number of hydrogen-bonded chains of solvent molecules increases slightly for the 10 mol.% DMSO system, while, in the 30 mol.% DMSO system, the number of hydrogen-bonded chains of solvent molecules decreases.

The Structure of Ethylbenzene, Styrene and Phenylacetylene Determined by Total Neutron Scattering.

PubMed

Szala-Bilnik, Joanna; Falkowska, Marta; Bowron, Daniel T; Hardacre, Christopher; Youngs, Tristan G A

2017-09-20

Organic solvents such as phenylacetylene, styrene and ethylbenzene are widely used in industrial processes, especially in the production of rubber or thermoplastics. Despite their important applications detailed knowledge about their structure is limited. In this paper the structures of these three aromatic solvents were investigated using neutron diffraction. The results show that many of their structural characteristics are similar, although the structure of phenylacetylene is more ordered and has a smaller solvation sphere than either ethylbenzene or styrene. Two regions within the first coordination sphere, in which the surrounding molecules show different preferable orientations with respect to the central molecule, were found for each liquid. Additionally, the localisation of the aliphatic chains reveals that they tend to favour closer interactions with each other than to the aromatic rings of the adjacent molecules. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

PubMed Central

Nakayasu, Ernesto S.; Nicora, Carrie D.; Sims, Amy C.; Burnum-Johnson, Kristin E.; Kim, Young-Mo; Kyle, Jennifer E.; Matzke, Melissa M.; Shukla, Anil K.; Chu, Rosalie K.; Schepmoes, Athena A.; Jacobs, Jon M.; Baric, Ralph S.; Webb-Robertson, Bobbie-Jo; Smith, Richard D.

2016-01-01

ABSTRACT Integrative multi-omics analyses can empower more effective investigation and complete understanding of complex biological systems. Despite recent advances in a range of omics analyses, multi-omic measurements of the same sample are still challenging and current methods have not been well evaluated in terms of reproducibility and broad applicability. Here we adapted a solvent-based method, widely applied for extracting lipids and metabolites, to add proteomics to mass spectrometry-based multi-omics measurements. The metabolite, protein, and lipid extraction (MPLEx) protocol proved to be robust and applicable to a diverse set of sample types, including cell cultures, microbial communities, and tissues. To illustrate the utility of this protocol, an integrative multi-omics analysis was performed using a lung epithelial cell line infected with Middle East respiratory syndrome coronavirus, which showed the impact of this virus on the host glycolytic pathway and also suggested a role for lipids during infection. The MPLEx method is a simple, fast, and robust protocol that can be applied for integrative multi-omic measurements from diverse sample types (e.g., environmental, in vitro, and clinical). IMPORTANCE In systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such studies are challenging due to the fact that the extraction conditions differ according to the molecule type. Here, we adapted an organic solvent-based extraction method that demonstrated broad applicability and robustness, which enabled comprehensive proteomics, metabolomics, and lipidomics analyses from the same sample. Author Video: An author video summary of this article is available. PMID:27822525

Investigation of Solvation Effects on Optical Rotatory Dispersion Using the Polarizable Continuum Model

NASA Astrophysics Data System (ADS)

Aharon, Tal; Lemler, Paul M.; Vaccaro, Patrick; Caricato, Marco

2017-06-01

The Optical Rotatory Dispersion (ORD) of a chiral solute is heavily affected by solvation, but this effect does not follow the usual correlation with the solvent polarity, i.e., larger solvent polarity does not imply a larger change in the solute's property. Therefore, a great deal of experimental and theoretical effort has been directed towards correlating the solvation effect on the ORD and the solvent properties. This discovery followed from the development of cavity ring down polarimetry (CRPD), which allows measurements of gas-phase ORD. In order to investigate this phenomenon, we chose a set of five rigid molecules to limit the effect of molecular vibrations and isolate the role of solvation. The latter was investigated with the Polarizable Continuum Model (PCM), and compared to experimental results. We used Bondi radii to build the PCM cavity, and performed extensive calculations at multiple frequencies using density functional theory (DFT) with two functionals: B3LYP and CAM-B3LYP, together with the aug-cc-pVDZ basis set. We also performed coupled cluster singles and doubles (CCSD/aug-cc-pVDZ) calculations at the wavelengths where gas-phase data are available, all of which are augmented with zero point vibrational corrections. These results are compared to experimental data and seem to indicate that PCM does not entirely account for the environmental effects on the ORD.

Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials.

PubMed

Boereboom, Jelle M; Potestio, Raffaello; Donadio, Davide; Bulo, Rosa E

2016-08-09

Adaptive quantum mechanical (QM)/molecular mechanical (MM) methods enable efficient molecular simulations of chemistry in solution. Reactive subregions are modeled with an accurate QM potential energy expression while the rest of the system is described in a more approximate manner (MM). As solvent molecules diffuse in and out of the reactive region, they are gradually included into (and excluded from) the QM expression. It would be desirable to model such a system with a single adaptive Hamiltonian, but thus far this has resulted in distorted structures at the boundary between the two regions. Solving this long outstanding problem will allow microcanonical adaptive QM/MM simulations that can be used to obtain vibrational spectra and dynamical properties. The difficulty lies in the complex QM potential energy expression, with a many-body expansion that contains higher order terms. Here, we outline a Hamiltonian adaptive multiscale scheme within the framework of many-body potentials. The adaptive expressions are entirely general, and complementary to all standard (nonadaptive) QM/MM embedding schemes available. We demonstrate the merit of our approach on a molecular system defined by two different MM potentials (MM/MM'). For the long-range interactions a numerical scheme is used (particle mesh Ewald), which yields energy expressions that are many-body in nature. Our Hamiltonian approach is the first to provide both energy conservation and the correct solvent structure everywhere in this system.

A challenge for green chemistry: designing molecules that readily dissolve in carbon dioxide.

PubMed

Beckman, E J

2004-09-07

Carbon dioxide is a green yet feeble solvent whose full potential won't be realized until we develop a more thorough understanding of its solvent behavior at the molecular level. Fortunately, advances in molecular modeling coupled with experiments are rapidly improving our understanding of CO(2)'s behavior, permitting design of new, more sustainable "CO(2)-philes".

New methods for the analysis of the protein-solvent interface

NASA Astrophysics Data System (ADS)

Goodfellow, Julia M.; Pitt, William R.; Smart, Oliver S.; Williams, Mark A.

1995-09-01

The protein-solvent interface is complex and may include solvent channels and cavities as well as the normal surface water molecules. We describe several algorithms for investigating the intra- and inter-molecular interactions of proteins in general but with the aim of developing methods to accurately and definitively characterise the interactions of water and other small ligands with proteins. Specifically, we present the methods which underlie three programs (AQUARIUS2, HOLE and PRO_ACT) which can be used to to look at different aspects of these interactions.

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.

Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

PubMed Central

Nagy, Peter I.

2014-01-01

A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed. PMID:25353178

PHEA-PLA biocompatible nanoparticles by technique of solvent evaporation from multiple emulsions.

PubMed

Cavallaro, Gennara; Craparo, Emanuela Fabiola; Sardo, Carla; Lamberti, Gaetano; Barba, Anna Angela; Dalmoro, Annalisa

2015-11-30

Nanocarriers of amphiphilic polymeric materials represent versatile delivery systems for poorly water soluble drugs. In this work the technique of solvent evaporation from multiple emulsions was applied to produce nanovectors based on new amphiphilic copolymer, the α,β-poly(N-2-hydroxyethyl)-DL-aspartamide-polylactic acid (PHEA-PLA), purposely synthesized to be used in the controlled release of active molecules poorly soluble in water. To this aim an amphiphilic derivative of PHEA, a hydrophilic polymer, was synthesized by derivatization of the polymeric backbone with hydrophobic grafts of polylactic acid (PLA). The achieved copolymer was thus used to produce nanoparticles loaded with α tocopherol (vitamin E) adopted as lipophilic model molecule. Applying a protocol based on solvent evaporation from multiple emulsions assisted by ultrasonic energy and optimizing the emulsification process (solvent selection/separation stages), PHEA-PLA nanostructured particles with total α tocopherol entrapment efficiency (100%), were obtained. The drug release is expected to take place in lower times with respect to PLA due to the presence of the hydrophilic PHEA, therefore the produced nanoparticles can be used for semi-long term release drug delivery systems. Copyright © 2015 Elsevier B.V. All rights reserved.

Solvent, Temperature And Concentration Effects on the Optical Activity of Chiral FIVE-And-SIX Membered Ring Ketones Conformers

NASA Astrophysics Data System (ADS)

Al-Basheer, Watheq

2017-06-01

Chiral five-and-six membered ring ketones are important molecules that are found in many biological systems and can exist in many possible conformers. In this talk, experimental and computational investigation of solvent, temperature and concentration effects on the circular dichroism (CD) and optical rotation (OR) of (R)-3 -methylcyclohexanone (R3MCH), (R)-3-methylcyclopentanone (R3MCP) and carvone conformers will be discussed. CD and OR measurements of these ketones gaseous samples and in ten common solvents of wide polarity range for different concentrations and sample temperatures were recorded and related to molecular conformation. Density functional theoretical calculations were performed using Gaussian09 at B3LYP functions with aug-cc-pVDZ level of theory. Also, CD and OR spectra for the optimized geometries of the ketones dominant conformers were computed over the ultraviolet and visible region in the gas phase as well as in ten solvents of varying polarity range, and under the umbrella of the polarizable continuum model (PCM). By comparing theoretical and experimental results, few thermodynamic parameters were deduced for the individual equatorial and axial conformers of each molecule in gas phase and in solvation.

Single-molecule tracking studies of flow-induced microdomain alignment in cylinder-forming polystyrene-poly(ethylene oxide) diblock copolymer films.

PubMed

Tran-Ba, Khanh-Hoa; Higgins, Daniel A; Ito, Takashi

2014-09-25

Flow-based approaches are promising routes to preparation of aligned block copolymer microdomains within confined spaces. An in-depth characterization of such nanoscale morphologies within macroscopically nonuniform materials under ambient conditions is, however, often challenging. In this study, single-molecule tracking (SMT) methods were employed to probe the flow-induced alignment of cylindrical microdomains (ca. 22 nm in diameter) in polystyrene-poly(ethylene oxide) diblock copolymer (PS-b-PEO) films. Films of micrometer-scale thicknesses were prepared by overlaying a benzene solution droplet on a glass coverslip with a rectangular glass plate, followed by solvent evaporation under a nitrogen atmosphere. The microdomain alignment was quantitatively assessed from SMT data exhibiting the diffusional motions of individual sulforhodamine B fluorescent probes that preferentially partitioned into cylindrical PEO microdomains. Better overall microdomain orientation along the flow direction was observed near the substrate interface in films prepared at a higher flow rate, suggesting that the microdomain alignment was primarily induced by shear flow. The SMT data also revealed the presence of micrometer-scale grains consisting of highly ordered microdomains with coherent orientation. The results of this study provide insights into shear-based preparation of aligned cylindrical microdomains in block copolymer films from solutions within confined spaces.

Elementary kinematical model of thermal diffusion in liquids and gases.

PubMed

Brenner, Howard

2006-09-01

An elementary hydrodynamic and Brownian motion model of the thermal diffusivity D(T) of a restricted class of binary liquid mixtures, previously proposed by the author, is given a more transparent derivation than originally, exposing thereby the strictly kinematic-hydrodynamic nature of an important class of thermodiffusion separation phenomena. Moreover, it is argued that the solvent's thermometric diffusivity alpha appearing in that theory as one of the two fundamental parameters governing D(T) should be replaced by the solvent's (isothermal) self-diffusivity D(S). In addition, a corrective multiplier of O(1) is inserted to reflect the general physicochemical noninertness of the solute relative to the solvent, thus enhancing the applicability of the resulting formula D(T)=lambdaD(S)beta to "nonideal" solutions. Here, beta is the solvent's thermal expansivity and lambda is a term of O(1), insensitive to the physicochemical nature of the solute (thus rendering D(T) primarily dependent upon only the properties of the solvent). This formula is, on the basis of its derivation, presumably valid only under certain idealized, albeit well-defined, circumstances. This occurs when the solute molecules are: (i) large compared with those of the solvent; and (ii) present only in small proportions relative to those of the solvent. When the solute is physicochemically inert, it is expected that lambda=1. When these conditions are met, the resulting thermal diffusivity of the mixture is, in theory, independent of any and all properties of the solute. Moreover, because beta is algebraically signed, the thermal diffusivity can either by positive or negative, according as the solvent expands or contracts upon being heated. This formula for D(T) is compared with available experimental data for selected binary liquid mixtures. Reasonable agreement is found in almost all circumstances with lambda near unity, the more so the higher the temperature, especially when the solute-solvent mixture properties closely approximate those where agreement would be expected and conversely. Finally, it is pointed out that for the restricted circumstances described, the formula D(T)=lambdaD(S)beta is equally credible for gases. Here, based on gas-kinetic theory, it is possible to furnish the theoretical value of lambda. Overall, while spanning a range of about five orders of magnitude, the D(T) values given by this elementary formula are shown to apply with reasonable accuracy to: (i) liquids (including circumstances for which D(T) is negative) as well as gases; (ii) all combinations of solvents and solutes tested (the latter including, for example, polymer molecules and metallic colloidal particles); and (iii) all sizes of solute molecules, from angstroms to submicron.

Discrete and continuum modeling of solvent effects in a twisted intramolecular charge transfer system: The 4-N,N-dimethylaminobenzonitrile (DMABN) molecule.

PubMed

Modesto-Costa, Lucas; Borges, Itamar

2018-08-05

The 4-N,N-dimethylaminobenzonitrile (DMABN) molecule is a prototypical system displaying twisted intramolecular (TICT) charge transfer effects. The ground and the first four electronic excited states (S 1 -S 4 ) in gas phase and upon solvation were studied. Charge transfer values as function of the torsion angle between the donor group (dimethylamine) and the acceptor moiety (benzonitrile) were explicitly computed. Potential energy curves were also obtained. The algebraic diagrammatic construction method at the second-order [ADC(2)] ab initio wave function was employed. Three solvents of increased polarities (benzene, DMSO and water) were investigated using discrete (average solvent electrostatic configuration - ASEC) and continuum (conductor-like screening model - COSMO) models. The results for the S 3 and S 4 excited states and the S 1 -S 4 charge transfer curves were not previously available in the literature. Electronic gas phase and solvent vertical spectra are in good agreement with previous theoretical and experimental results. In the twisted (90°) geometry the optical oscillator strengths have negligible values even for the S 2 bright state. Potential energy curves show two distinct pairs of curves intersecting at decreasing angles or not crossing in the more polar solvents. Charge transfer and electric dipole values allowed the rationalization of these results. The former effects are mostly independent of the solvent model and polarity. Although COSMO and ASEC solvent models mostly lead to similar results, there is an important difference: some crossings of the excitation energy curves appear only in the ASEC solvation model, which has important implications to the photochemistry of DMABN. Copyright © 2018 Elsevier B.V. All rights reserved.

Rectification of nanopores in aprotic solvents--transport properties of nanopores with surface dipoles.

PubMed

Plett, Timothy; Shi, Wenqing; Zeng, Yuhan; Mann, William; Vlassiouk, Ivan; Baker, Lane A; Siwy, Zuzanna S

2015-12-07

Nanopores have become a model system to understand transport properties at the nanoscale. We report experiments and modeling of ionic current in aprotic solvents with different dipole moments through conically shaped nanopores in a polycarbonate film and through glass nanopipettes. We focus on solutions of the salt LiClO4, which is of great importance in modeling lithium based batteries. Results presented suggest ion current rectification observed results from two effects: (i) adsorption of Li(+) ions to the pore walls, and (ii) a finite dipole moment rendered by adsorbed solvent molecules. Properties of surfaces in various solvents were probed by means of scanning ion conductance microscopy, which confirmed existence of an effectively positive surface potential in aprotic solvents with high dipole moments.

How many molecular layers of polar solvent molecules control chemistry? The concept of compensating dipoles.

PubMed

Langhals, Heinz; Braun, Patricia; Dietl, Christian; Mayer, Peter

2013-09-27

The extension of the solvent influence of the shell into the volume of a polar medium was examined by means of anti-collinear dipoles on the basis of the E(T)(30) solvent polarity scale (i.e., the molar energy of excitation of a pyridinium-N-phenolatebetaine dye; generally: E(T) =28,591 nm kcal mol(-1)/λmax) where no compensation effects were found. As a consequence, solvent polarity effects are concentrated to a very thin layer of a few thousand picometres around the solute where extensions into the bulk solvent become unimportant. A parallelism to the thin surface layer of water to the gas phase is discussed. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Diffusion coefficients of nitric oxide in water: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Pokharel, Sunil; Pantha, Nurapati; Adhikari, N. P.

2016-09-01

Self-diffusion coefficients along with the mutual diffusion coefficients of nitric oxide (NO) and SPC/E water (H2O) as solute and solvent of the mixture, have been studied within the framework of classical molecular dynamics level of calculations using GROMACS package. The radial distribution function (RDF) of the constituent compounds are calculated to study solute-solute, solute-solvent and solvent-solvent molecular interactions as a function of temperature. A dilute solution of five NO molecules (mole fraction 0.018) and 280 H2O molecules (mole fraction 0.982) has been taken as the sample. The self-diffusion coefficient of the solvent is calculated by using mean square displacement (MSD) where as that for solute (NO) is calculated by using MSD and velocity auto-correlation function (VACF). The results are then compared with the available experimental values. The results from the present work for water come in good agreement, very precise at low temperatures, with the experimental values. The diffusion coefficients of NO, on the other hands, agree well with the available theoretical studies, and also with experiment at low temperatures (up to 310 K). The results at the higher temperatures (up to 333 K), however, deviate significantly with the experimental observations. Also, the mutual diffusion coefficients of NO in water have been calculated by using Darken’s relation. The temperature dependence of the calculated diffusion coefficients follow the Arrhenius behavior.

A molecularly based theory for electron transfer reorganization energy.

PubMed

Zhuang, Bilin; Wang, Zhen-Gang

2015-12-14

Using field-theoretic techniques, we develop a molecularly based dipolar self-consistent-field theory (DSCFT) for charge solvation in pure solvents under equilibrium and nonequilibrium conditions and apply it to the reorganization energy of electron transfer reactions. The DSCFT uses a set of molecular parameters, such as the solvent molecule's permanent dipole moment and polarizability, thus avoiding approximations that are inherent in treating the solvent as a linear dielectric medium. A simple, analytical expression for the free energy is obtained in terms of the equilibrium and nonequilibrium electrostatic potential profiles and electric susceptibilities, which are obtained by solving a set of self-consistent equations. With no adjustable parameters, the DSCFT predicts activation energies and reorganization energies in good agreement with previous experiments and calculations for the electron transfer between metallic ions. Because the DSCFT is able to describe the properties of the solvent in the immediate vicinity of the charges, it is unnecessary to distinguish between the inner-sphere and outer-sphere solvent molecules in the calculation of the reorganization energy as in previous work. Furthermore, examining the nonequilibrium free energy surfaces of electron transfer, we find that the nonequilibrium free energy is well approximated by a double parabola for self-exchange reactions, but the curvature of the nonequilibrium free energy surface depends on the charges of the electron-transferring species, contrary to the prediction by the linear dielectric theory.

The influence of solvent on conformational properties of peptides with Aib residue-a DFT study.

PubMed

Wałęsa, Roksana; Broda, Małgorzata A

2017-11-21

The conformational propensities of the Aib residue on the example of two model peptides Ac-Aib-NHMe (1) and Ac-Aib-NMe 2 (2), were studied by B3LYP and M06-2X functionals, in the gas phase and in the polar solvents. To verify the reliability of selected functionals, we also performed MP2 calculations for the tested molecules in vacuum. Polarizable continuum models (PCM and SMD) were used to estimate the solvent effect. Ramachandran maps were calculated to find all energy minima. Noncovalent intramolecular interactions due to hydrogen-bonds and dipole attractions between carbonyl groups are responsible for the relative stabilities of the conformers. In order to verify the theoretical results, the available conformations of similar X-ray structures from the Cambridge Crystallographic Data Center (CCDC) were analyzed. The results of the calculations show that both derivatives with the Aib residue in the gas phase prefer structures stabilized by intramolecular N-H⋯O hydrogen bonds, i.e., C 5 and C 7 conformations, while polar solvent promotes helical conformation with φ, ψ values equal to +/-60°, +/-40°. In addition, in the case of molecule 2, the helical conformation is the only one available in the polar environment. This result is fully consistent with the X-ray data. Graphical abstract Effect of solvent on the Ramachandran maps of the model peptides with Aib residue.

Simultaneously 'pushing' and 'pulling' graphene oxide into low-polar solvents through a designed interface.

PubMed

Liu, Zhen; Liu, Jingquan; Wang, Yichao; Razal, Joselito M; Francis, Paul S; Biggs, Mark J; Barrow, Colin J; Yang, Wenrong

2018-08-03

Dispersing graphene oxide (GO) in low-polar solvents can realize a perfect self-assembly with functional molecules and application in removal of organic impurities that only dissolve in low-polar solvents. The surface chemistry of GO plays an important role in its dispersity in these solvents. The direct transfer of hydrophilic GO into low-polar solvents, however, has remained an experimental challenge. In this study, we design an interface to transfer GO by simultaneously 'pushing and pulling' the nanosheets into low-polar solvents. Our approach is outstanding due to the ability to obtain monolayers of chemically reduced GO (CRGO) with designed surface properties in the organic phase. Using the transferred GO or CRGO dispersions, we have fabricated GO/fullerene nanocomposites and assessed the ability of CRGOs for dye adsorption. We hope our work can provide a universal approach for the phase transfer of other nanomaterials.

Effects of Solvent and Ion Source Pressure on the Analysis of Anabolic Steroids by Low Pressure Photoionization Mass Spectrometry.

PubMed

Liu, Chengyuan; Zhu, Yanan; Yang, Jiuzhong; Zhao, Wan; Lu, Deen; Pan, Yang

2017-04-01

Solvent and ion source pressure were two important factors relating to the photon induced ion-molecule reactions in low pressure photoionization (LPPI). In this work, four anabolic steroids were analyzed by LPPI mass spectrometry. Both the ion species present and their relative abundances could be controlled by switching the solvent and adjusting the ion source pressure. Whereas M •+ , MH + , [M - H 2 O] + , and solvent adducts were observed in positive LPPI, [M - H] - and various oxidation products were abundant in negative LPPI. Changing the solvent greatly affected formation of the ion species in both positive and negative ion modes. The ion intensities of the solvent adduct and oxygen adduct were selectively enhanced when the ion source pressure was elevated from 68 to 800 Pa. The limit of detection could be decreased by increasing the ion source pressure. Graphical Abstract ᅟ.

Behaviour of a solvent trapped in a physical molecular gel

NASA Astrophysics Data System (ADS)

Morfin, I.; Spagnoli, S.; Rambaud, C.; Longeville, S.; Plazanet, M.

2016-03-01

Physical gels formed by amphiphilic molecules, namely in this study Methyl-4,6-O-benzylidene-? -D-mannopyranoside, can be form either in polar and protic liquid-like water or in organic apolar solvent such as toluene. The solvent, that influences the supramolecular organization of the gelators, plays an important role in the stability and formation of the gel phase. Gelator-solvent interactions govern not only the assembly but also the solvent diffusion in the material. We present here measurements of neutron scattering (Time of Flight and Neutron Spin Echo) characterizing this microscopic behaviour. In addition, we show that transient grating spectroscopy provides valuable information through the characterization of the longitudinal acoustic wave propagating in the system. Opposite effects on the speed of sound in the gels are observed for the two solvents investigated, being relevant of the interactions between the gelators and the surrounding liquid.

Effects of Solvent and Ion Source Pressure on the Analysis of Anabolic Steroids by Low Pressure Photoionization Mass Spectrometry

NASA Astrophysics Data System (ADS)

Liu, Chengyuan; Zhu, Yanan; Yang, Jiuzhong; Zhao, Wan; Lu, Deen; Pan, Yang

2017-04-01

Solvent and ion source pressure were two important factors relating to the photon induced ion-molecule reactions in low pressure photoionization (LPPI). In this work, four anabolic steroids were analyzed by LPPI mass spectrometry. Both the ion species present and their relative abundances could be controlled by switching the solvent and adjusting the ion source pressure. Whereas M•+, MH+, [M - H2O]+, and solvent adducts were observed in positive LPPI, [M - H]- and various oxidation products were abundant in negative LPPI. Changing the solvent greatly affected formation of the ion species in both positive and negative ion modes. The ion intensities of the solvent adduct and oxygen adduct were selectively enhanced when the ion source pressure was elevated from 68 to 800 Pa. The limit of detection could be decreased by increasing the ion source pressure.

Adsorption behavior of acetone solvent at the HMX crystal faces: A molecular dynamics study.

PubMed

Liu, Yingzhe; Yu, Tao; Lai, Weipeng; Ma, Yiding; Kang, Ying; Ge, Zhongxue

2017-06-01

Molecular dynamics simulations have been performed to understand the adsorption behavior of acetone (AC) solvent at the three surfaces of 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctan (HMX) crystal, i.e. (011), (110), and (020) faces. The simulation results show that the structural features and electrostatic potentials of crystal faces are determined by the HMX molecular packing, inducing distinct mass density distribution, dipole orientation, and diffusion of solvent molecules in the interfacial regions. The solvent adsorption is mainly governed by the van der Waals forces, and the crystal-solvent interaction energies among three systems are ranked as (020)≈(110)>(011). The adsorption sites for solvent incorporation at the crystal surface were found and visualized with the aid of occupancy analysis. A uniform arrangement of adsorption sites is observed at the rough (020) surface as a result of ordered adsorption motif. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Solvent organization around the perfluoro group of coumarin 153 governs its photophysical properties: An experimental and simulation study of coumarin dyes in ethanol as well as fluorinated ethanol solvents.

PubMed

Mondal, Saptarsi; Halder, Ritaban; Biswas, Biswajit; Jana, Biman; Singh, Prashant Chandra

2016-05-14

The self-aggregation property of the perfluoro group containing molecules makes it important in the research fields of biology and polymer and organic synthesis. In the quest of understanding the role of the perfluoro group on the photophysical properties of perfluoro-containing molecules in biologically important fluoroethanol solvents, we have applied photophysical as well as molecular dynamics simulation techniques to explore the properties of perfluoro groups containing molecule coumarin-153 (C153) in ethanol (ETH), monofluoroethanol (MFE), difluoroethanol (DFE), and trifluoroethanol (TFE) and compared them with the molecules without perfluoro moiety, namely coumarin-6H (C6H) and coumarin-480 (C480). In contrast to C6H and C480, the excited state lifetime of C153 in fluorinated ETHs is not monotonic. The excited state lifetime of C153 decreases in MFE and DFE as compared to ETH, whereas in TFE, it increases as compared to MFE and DFE. Molecular dynamics simulation reveals that the carbon terminal away from the OH group of fluorinated ETHs has a preferential orientation near the perfluoro (CF3) group of C153. In MFE and DFE, the CF3 group of C153 prefers to have a CF2-F⋯H -(CHF) type of electrostatic interaction over CF2-F⋯F -(CH2) kind of dispersion interaction which increases the rate of nonradiative decay, probably due to the electrostatic nature of the CF2-F⋯H -(CHF) hydrogen bond. On the other hand, in TFE, C-F⋯ F-C type of dispersion interaction, also known as fluorous interaction, takes place between the CF3 groups of C153 and TFE which decreases the rate of nonradiative rate as compared to MFE and DFE, leading to the increased lifetime of C153 in TFE. Photophysical and MD simulation studies clearly depict that the structural organization of solvents and their interaction with the fluorocarbon group are crucial factors for the photophysical behavior of the fluorocarbon containing molecules.

Solvent organization around the perfluoro group of coumarin 153 governs its photophysical properties: An experimental and simulation study of coumarin dyes in ethanol as well as fluorinated ethanol solvents

NASA Astrophysics Data System (ADS)

Mondal, Saptarsi; Halder, Ritaban; Biswas, Biswajit; Jana, Biman; Singh, Prashant Chandra

2016-05-01

The self-aggregation property of the perfluoro group containing molecules makes it important in the research fields of biology and polymer and organic synthesis. In the quest of understanding the role of the perfluoro group on the photophysical properties of perfluoro-containing molecules in biologically important fluoroethanol solvents, we have applied photophysical as well as molecular dynamics simulation techniques to explore the properties of perfluoro groups containing molecule coumarin-153 (C153) in ethanol (ETH), monofluoroethanol (MFE), difluoroethanol (DFE), and trifluoroethanol (TFE) and compared them with the molecules without perfluoro moiety, namely coumarin-6H (C6H) and coumarin-480 (C480). In contrast to C6H and C480, the excited state lifetime of C153 in fluorinated ETHs is not monotonic. The excited state lifetime of C153 decreases in MFE and DFE as compared to ETH, whereas in TFE, it increases as compared to MFE and DFE. Molecular dynamics simulation reveals that the carbon terminal away from the OH group of fluorinated ETHs has a preferential orientation near the perfluoro (CF3) group of C153. In MFE and DFE, the CF3 group of C153 prefers to have a CF2—F⋯H —(CHF) type of electrostatic interaction over CF2—F⋯F —(CH2) kind of dispersion interaction which increases the rate of nonradiative decay, probably due to the electrostatic nature of the CF2—F⋯H —(CHF) hydrogen bond. On the other hand, in TFE, C—F⋯ F—C type of dispersion interaction, also known as fluorous interaction, takes place between the CF3 groups of C153 and TFE which decreases the rate of nonradiative rate as compared to MFE and DFE, leading to the increased lifetime of C153 in TFE. Photophysical and MD simulation studies clearly depict that the structural organization of solvents and their interaction with the fluorocarbon group are crucial factors for the photophysical behavior of the fluorocarbon containing molecules.

Toward a Molecular Understanding of Energetics in Li–S Batteries Using Nonaqueous Electrolytes: A High-Level Quantum Chemical Study

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

Assary, Rajeev S.; Curtiss, Larry A.; Moore, Jeffrey S.

2014-06-05

The Li-S battery (secondary cell or redox flow) technology is a promising future alternative to the present lithium intercalation-based energy storage and, therefore, a molecular level understanding of the chemical processes and properties such as stability of intermediates, reactivity of polysulfides and reactivity towards the non-aqueous electrolytes in the Li-S batteries is of great interest. In this paper, quantum chemical methods (G4MP2, MP2, and B3LYP) were utilized to compute reduction potentials of lithium polysulfides and polysulfide molecular clusters, energetics of disproportionation and association reactions of likely intermediates, and their reactions with ether-based electrolytes. Based on the computed reaction energetics inmore » solution, a probable mechanism during the discharge process for polysulfide anions and lithium polysulfides in solution is proposed and likely intermediates such as S42-,S32-, S22-, and S31- radical were identified. Additionally, the stability and reactivity of propylene carbonate and tetraglyme solvent molecules were assessed against the above-mentioned intermediates and other reactive species by computing the reaction energetics required to initiate the solvent decomposition reactions in solution. Calculations suggest that the propylene carbonate molecule is unstable against the polysulfide anions such as S22-, S32-, and S42- (ΔH† < 0.8 eV) and highly reactive towards Li2S2 and Li2S3. Even though the tetraglyme solvent molecule exhibits increased stability towards polysulfide anions compared to propylene carbonate, this molecule too is vulnerable to nucleophilic attack from Li2S2 and Li2S3 species in solutions. Hence, a long- term stability of the ether molecules is unlikely if high concentration of these reactive intermediates present in the Li-S energy storage systems.« less

Lid opening and conformational stability of T1 Lipase is mediated by increasing chain length polar solvents

PubMed Central

Mohamad Ali, Mohd Shukuri; Salleh, Abu Bakar; Rahman, Raja Noor Zaliha Raja Abd; Normi, Yahaya M.; Mohd Shariff, Fairolniza

2017-01-01

The dynamics and conformational landscape of proteins in organic solvents are events of potential interest in nonaqueous process catalysis. Conformational changes, folding transitions, and stability often correspond to structural rearrangements that alter contacts between solvent molecules and amino acid residues. However, in nonaqueous enzymology, organic solvents limit stability and further application of proteins. In the present study, molecular dynamics (MD) of a thermostable Geobacillus zalihae T1 lipase was performed in different chain length polar organic solvents (methanol, ethanol, propanol, butanol, and pentanol) and water mixture systems to a concentration of 50%. On the basis of the MD results, the structural deviations of the backbone atoms elucidated the dynamic effects of water/organic solvent mixtures on the equilibrium state of the protein simulations in decreasing solvent polarity. The results show that the solvent mixture gives rise to deviations in enzyme structure from the native one simulated in water. The drop in the flexibility in H2O, MtOH, EtOH and PrOH simulation mixtures shows that greater motions of residues were influenced in BtOH and PtOH simulation mixtures. Comparing the root mean square fluctuations value with the accessible solvent area (SASA) for every residue showed an almost correspondingly high SASA value of residues to high flexibility and low SASA value to low flexibility. The study further revealed that the organic solvents influenced the formation of more hydrogen bonds in MtOH, EtOH and PrOH and thus, it is assumed that increased intraprotein hydrogen bonding is ultimately correlated to the stability of the protein. However, the solvent accessibility analysis showed that in all solvent systems, hydrophobic residues were exposed and polar residues tended to be buried away from the solvent. Distance variation of the tetrahedral intermediate packing of the active pocket was not conserved in organic solvent systems, which could lead to weaknesses in the catalytic H-bond network and most likely a drop in catalytic activity. The conformational variation of the lid domain caused by the solvent molecules influenced its gradual opening. Formation of additional hydrogen bonds and hydrophobic interactions indicates that the contribution of the cooperative network of interactions could retain the stability of the protein in some solvent systems. Time-correlated atomic motions were used to characterize the correlations between the motions of the atoms from atomic coordinates. The resulting cross-correlation map revealed that the organic solvent mixtures performed functional, concerted, correlated motions in regions of residues of the lid domain to other residues. These observations suggest that varying lengths of polar organic solvents play a significant role in introducing dynamic conformational diversity in proteins in a decreasing order of polarity. PMID:28533982

Viscoelastic properties of model segments of collagen molecules.

PubMed

Gautieri, Alfonso; Vesentini, Simone; Redaelli, Alberto; Buehler, Markus J

2012-03-01

Collagen is the prime construction material in vertebrate biology, determining the mechanical behavior of connective tissues such as tendon, bone and skin. Despite extensive efforts in the investigation of the origin of collagen unique mechanical properties, a deep understanding of the relationship between molecular structure and mechanical properties remains elusive, hindered by the complex hierarchical structure of collagen-based tissues. In particular, although extensive studies of viscoelastic properties have been pursued at the macroscopic (fiber/tissue) level, fewer investigations have been performed at the smaller scales, including in particular collagen molecules and fibrils. These scales are, however, important for a complete understanding of the role of collagen as an important constituent in the extracellular matrix. Here, using an atomistic modeling approach, we perform in silico creep tests of a collagen-like peptide, monitoring the strain-time response for different values of applied external load. The results show that individual collagen molecules exhibit a nonlinear viscoelastic behavior, with a Young's modulus increasing from 6 to 16GPa (for strains up to 20%), a viscosity of 3.84.±0.38Pa·s, and a relaxation time in the range of 0.24-0.64ns. The single molecule viscosity, for the first time reported here, is several orders of magnitude lower than the viscosity found for larger-scale single collagen fibrils, suggesting that the viscous behavior of collagen fibrils and fibers involves additional mechanisms, such as molecular sliding between collagen molecules within the fibril or the effect of relaxation of larger volumes of solvent. Based on our molecular modeling results we propose a simple structural model that describes collagen tissue as a hierarchical structure, providing a bottom-up description of elastic and viscous properties form the properties of the tissue basic building blocks. Copyright © 2011 International Society of Matrix Biology. Published by Elsevier B.V. All rights reserved.

Cyclic tetraureas with variable flexibility--synthesis, crystal structures and properties.

PubMed

Meshcheryakov, Denys; Arnaud-Neu, Françoise; Böhmer, Volker; Bolte, Michael; Cavaleri, Julien; Hubscher-Bruder, Véronique; Thondorf, Iris; Werner, Sabine

2008-09-21

Macrocyclic molecules containing several amide or urea functions may serve as anion receptors. We describe the synthesis of 32-membered macrocycles, in which four rigid xanthene units (X) and/or diphenyl ether units (D) as flexible analogues are linked via urea groups. All six possible combinations of these units (XXXX, XXXD, XXDD, XDXD, XDDD and DDDD) were synthesized and two examples were characterised by single-crystal X-ray analyses (DDDD and two structures for XXXD). Both macrocycles showed distinct differences in their overall conformation and consequently in their hydrogen-bonding pattern. Hydrogen-bonded solvent molecules are found for both compounds and intramolecular hydrogen bonds for the two structures of XXXD, but surprisingly no direct intermolecular hydrogen bonds between the macrocyclic tetraurea molecules. The interaction with various anions was studied by (1)H NMR spectroscopy. Stability constants for all tetramers were determined by UV spectroscopy for complexes with chloride, bromide, acetate and dihydrogenphosphate in acetonitrile-THF (3:1). The strongest binding was found for XXXD and acetate (log beta = 7.4 +/- 0.2), the weakest for XXXX and acetate (log beta = 5.1 +/- 0.5). MD simulations in chloroform and acetonitrile boxes show that all molecules except DDDD adopt very similar conformations characterized by an up-down-up-down arrangement of the spacer groups. Clustered solvation shells of acetonitrile molecules around XXXX and DDDD suggest their preorganization for spherical/planar and tetrahedral/bidentate anions, respectively, which in turn was corroborated by simulation of the corresponding complexes with chloride and dihydrogenphosphate.

Crystalline order of a water/glycine film coadsorbed on the (104) calcite surface.

PubMed

Magdans, Uta; Torrelles, Xavier; Angermund, Klaus; Gies, Hermann; Rius, Jordi

2007-04-24

For biomineralization processes, the interaction of the surface of calcite crystals with organic molecules is of particular importance. Especially, biologically controlled biomineralization as in exoskeletons of mollusks and echinoderms, e.g., sea urchin with single-crystal-like spines and shells,1-3 requires molecular control of seed formation and growth process. So far, experiments showing the obvious influence of organic molecules on the morphology and habit of calcite crystals have demonstrated the molecular dimension of the interaction.4-7 Details of the kinetics of growth and dissolution of mineral surfaces influenced by additives are available,8,9 but other experimental data about the structure of the organic/inorganic interface on the atomic scale are rare. On the other hand, complicated organic macromolecules which are involved in biomineralization are numerous, with only a small fraction solved in structure and function so far.10-13 Therefore, model systems have to be designed to provide a basic understanding for the interaction process.14 Using grazing incidence X-ray diffraction combined with molecular modeling techniques, we show that glycine molecules order periodically on the calcite (104) face in competition with the solvent water when exposed to an aqueous solution of the most simple amino acid. In contrast to the general concept of the charge-matching fit of organic molecules on mineral surfaces,4,14 glycine is not attached to the calcite surface directly but substitutes for water molecules in the second hydration layer.

Operando Solid-State NMR Observation of Solvent-Mediated Adsorption-Reaction of Carbohydrates in Zeolites

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

Qi, Long; Alamillo, Ricardo; Elliott, William A.

Liquid-phase processing of molecules using heterogeneous catalysts – an important strategy for obtaining renewable chemicals sustainably from biomass – involves reactions that occur at solid-liquid interfaces. In glucose isomerization catalyzed by basic faujasite zeolites, the catalytic activity depends strongly on the solvent composition: initially, it declines precipitously when water is mixed with a small amount of the organic co-solvent γ-valerolactone (GVL), then recovers as the GVL content increases. Using solid-state 13C NMR spectroscopy, we observed glucose isomers located inside the zeolite pores directly, and followed their transformations into fructose and mannose in real time. At low GVL concentrations, glucose ismore » depleted in the zeolite pores relative to the liquid phase, while higher GVL concentrations in solution drive glucose inside the pores, resulting in up to a 32 enhancement in the local glucose concentration. Although their populations exchange rapidly, molecules present at the reactive interface experience a significantly different environment from the bulk solution.« less

Relevance of supramolecular interactions, texture and lattice occupancy in the designer iron(II) spin crossover complexes

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

Naik, Anil D.; Tinant, Bernard; Muffler, Kai

New Fe{sup II} complexes of formula [Fe(3-Br-phen){sub 2}(NCS){sub 2}].Solvent (Solvent=0.5 CH{sub 3}OH (1), 2 CH{sub 2}Cl{sub 2} (2), desolvation of 2 (3), 0.5 CH{sub 3}COCH{sub 3} (4) and 0 (5)) have been synthesized. {sup 57}Fe Moessbauer and magnetic investigation reveal unique features atypical of classic [Fe(phen){sub 2}(NCS){sub 2}] polymorphs. Complex 1, prepared by precipitation in MeOH, undergoes upon cooling below room temperature an incomplete and gradual thermally induced spin conversion, while 4 prepared by an extraction method remains mostly in the low-spin state. The non solvated compounds 3 and 5, display a more abrupt spin crossover on cooling around T{submore » 1/2}=175 K and T{sub 1/2}=198 K, respectively. Defects/soft lattice inclusion due to different methods of material synthesis, extent of aging, reaction medium and associated solvent molecules have enormous influence on the particle size and magnetic properties of these complexes. Scanning electron micrographs helps to establish a logical relationship among methods employed for synthesis, texture of materials and their effect on magnetic properties. The crystal structure of 2 determined in the monoclinic space group P2/c (100 K) reveals a mononuclear complex consisting of a distorted FeN{sub 6} octahedron in the low-spin state, constructed from two 3-bromo-1, 10-phenanthroline and two isothiocyanato anions in cis position. Intermolecular interactions between mononuclear units of the S...Br, S...C(H) and pi-pi type afford a 2D supramolecular network. DFT calculations for the single molecule 2 reveals an energy difference between high-spin and low-spin isomers of 7 kJ/mol suggesting a slight destabilization of the low-spin state compared to [Fe(phen){sub 2}(NCS){sub 2}]. Normal co-ordinate analysis was also carried out for 3 and compared with experimental temperature dependent Raman spectra for 5. - Graphical abstract: New Fe{sup II} complexes of formula [Fe(3-Br-phen){sub 2}(NCS){sub 2}].Solvent have been synthesized by precipitation (1) and extraction (4) methods. {sup 57}Fe Moessbauer and magnetic investigation reveal unique features atypical of classic [Fe(phen){sub 2}(NCS){sub 2}] polymorphs. Complex 1, undergoes upon cooling below room temperature an incomplete and gradual thermally induced spin conversion, while 4 remains mostly in the low-spin state. Role of supramolecular interactions, particles size, lattice solvents have profound influence on magnetic properties.« less

Crystal structures and properties of two new pseudopolymorphic modifications of the glucocorticoide triamcinolone diacetate

NASA Astrophysics Data System (ADS)

Suitchmezian, Viktor; Jeß, Inke; Näther, Christian

2006-11-01

Two new solvates of triamcinolone diacetate were found in addition, to those reported previously. The acetonitrile solvate (form E) crystallizes monoclinic in space group P2 1, whereas the methylene chloride solvate (form F) crystallizes orthorhombic in space group P2 12 12 1. In all forms the triamcinolone diacetate molecules are linked by intermolecular hydrogen bonding. From this arrangement channels are formed in which the solvent molecules are embedded. Both forms were investigated by differential thermoanalysis and thermogravimetry. On heating, for each form a mass loss is observed, which is accompanied with endothermic events in the DTA curve. Mass spectroscopic investigations clearly shows that in this step the solvent molecules are emitted. In these measurements one cannot differ between desolvation and melting. If the residues formed after the first TG steps are investigated by X-ray powder diffraction, only amorphous samples are obtained. If the solvents are removed at room temperature under normal pressure or in vacuum the commercial available form of triamcinolone diacetate is obtained which is also used in therapy. If the acetonitrile solvate is tempered at 80 °C for several days significant changes in the powder pattern are observed, which may indicate the formation of a new polymorphic form.

Electronic spectroscopy and photodissociation dynamics of Co(2+)-methanol clusters: Co2+ (CH3OH)n (n = 4-7).

PubMed

Thompson, Christopher J; Faherty, Kieron P; Stringer, Kay L; Metz, Ricardo B

2005-03-07

Solvated cluster ions Co2+ (CH3OH)n (n = 4-7) have been produced by electrospray and studied using photofragment spectroscopy. There are notable differences between the photodissociation spectra of these complexes and the analogous water complexes. Co2+ (CH3OH)6 absorbs significantly more strongly than Co2+ (H2O)6. The photodissociation spectra of Co2+ (CH3OH)n (n = 4, 5 and 6) are very similar, which suggests that they share the Co2+ (CH3OH)4 chromophore, with additional solvent molecules in the second shell. In contrast, our earlier studies indicate that Co2+ (H2O)6 is six coordinate, and its spectrum is significantly different from that of Co2+ (H2O)4. The larger clusters Co2+ (CH3OH)n (n = 5-7) dissociate by simple loss of one or more solvent molecules. Larger clusters tend to lose more solvent molecules, especially at higher photon energies. As with the corresponding water cluster, Co2+ (CH3OH)4 photodissociates by proton transfer through a salt-bridge intermediate. This is accompanied by a modest kinetic energy release of 170 kJ mol(-1) and occurs with a lifetime of 145 ns.

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

Solvent and solute ingress into hydrogels resolved by a combination of imaging techniques

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

Wagner, D.; Burbach, J.; Egelhaaf, S. U.

2016-05-28

Using simultaneous neutron, fluorescence, and optical brightfield transmission imaging, the diffusion of solvent, fluorescent dyes, and macromolecules into a crosslinked polyacrylamide hydrogel was investigated. This novel combination of different imaging techniques enables us to distinguish the movements of the solvent and fluorescent molecules. Additionally, the swelling or deswelling of the hydrogels can be monitored. From the sequence of images, dye and solvent concentrations were extracted spatially and temporally resolved. Diffusion equations and different boundary conditions, represented by different models, were used to quantitatively analyze the temporal evolution of these concentration profiles and to determine the diffusion coefficients of solvent andmore » solutes. Solute size and network properties were varied and their effect was investigated. Increasing the crosslinking ratio or partially drying the hydrogel was found to hinder solute diffusion due to the reduced pore size. By contrast, solvent diffusion seemed to be slightly faster if the hydrogel was only partially swollen and hence solvent uptake enhanced.« less

Testing the Use of Implicit Solvent in the Molecular Dynamics Modelling of DNA Flexibility

NASA Astrophysics Data System (ADS)

Mitchell, J.; Harris, S.

DNA flexibility controls packaging, looping and in some cases sequence specific protein binding. Molecular dynamics simulations carried out with a computationally efficient implicit solvent model are potentially a powerful tool for studying larger DNA molecules than can be currently simulated when water and counterions are represented explicitly. In this work we compare DNA flexibility at the base pair step level modelled using an implicit solvent model to that previously determined from explicit solvent simulations and database analysis. Although much of the sequence dependent behaviour is preserved in implicit solvent, the DNA is considerably more flexible when the approximate model is used. In addition we test the ability of the implicit solvent to model stress induced DNA disruptions by simulating a series of DNA minicircle topoisomers which vary in size and superhelical density. When compared with previously run explicit solvent simulations, we find that while the levels of DNA denaturation are similar using both computational methodologies, the specific structural form of the disruptions is different.

Advanced solvent based methods for molecular characterization of soil organic matter by high-resolution mass spectrometry

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

Tfaily, Malak M.; Chu, Rosalie K.; Tolic, Nikola

2015-05-19

Soil organic matter (SOM) a complex, heterogeneous mixture of above and belowground plant litter and animal and microbial residues at various degrees of decomposition, is a key reservoir for carbon (C) and nutrient biogeochemical cycling in soil based ecosystems. A limited understanding of the molecular composition of SOM limits the ability to routinely decipher chemical processes within soil and predict accurately how terrestrial carbon fluxes will response to changing climatic conditions and land use. To elucidate the molecular-level structure of SOM, we selectively extracted a broad range of intact SOM compounds by a combination of different organic solvents from soilsmore » with a wide range of C content. Our use of Electrospray ionization (ESI) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and a suite of solvents with varying polarity significantly expands the inventory of the types of organic molecules present in soils. Specifically, we found that hexane is selective for lipid-like compounds with very low O:C ratios; water was selective for carbohydrates with high O:C ratios; acetonitrile preferentially extracts lignin, condensed structures, and tannin poly phenolic compounds with O:C > 0.5; methanol has higher selectivity towards compounds characterized with low O:C < 0.5; and hexane, MeOH, ACN and water solvents increase the number and types of organic molecules extracted from soil for a broader range of chemically diverse soil types. Our study of SOM molecules by ESI-FTICR MS revealed new insight into the molecular-level complexity of organics contained in soils.« less

Structural analysis of benzothienobenzothiophene-based soluble organic semiconducting crystals grown by liquid crystal solvent

NASA Astrophysics Data System (ADS)

Shibata, Yosei; Matsuzaki, Tomoya; Ishinabe, Takahiro; Fujikake, Hideo

2018-06-01

In this study, we analyzed organic semiconducting single crystals composed of benzothienobenzothiophene derivatives (2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene, C8-BTBT) grown by nematic-phase liquid crystal (LC) solvent. As a result, we clarified that the crystal b-axis direction of the C8-BTBT single crystals was consistent with the LC alignment direction. By optical evaluation and simulation based on density functional theory, we found that the C8-BTBT single crystals in LC solvent exhibited a novel molecular conformation having alkyl chains oriented toward the b-axis.

Dendritic brushes under theta and poor solvent conditions

NASA Astrophysics Data System (ADS)

Gergidis, Leonidas N.; Kalogirou, Andreas; Charalambopoulos, Antonios; Vlahos, Costas

2013-07-01

The effects of solvent quality on the internal stratification of polymer brushes formed by dendron polymers up to third generation were studied by means of molecular dynamics simulations with Langevin thermostat. The distributions of polymer units, of the free ends, the radii of gyration, and the back folding probabilities of the dendritic spacers were studied at the macroscopic states of theta and poor solvent. For high grafting densities we observed a small decrease in the height of the brush as the solvent quality decreases. The internal stratification in theta solvent was similar to the one we found in good solvent, with two and in some cases three kinds of populations containing short dendrons with weakly extended spacers, intermediate-height dendrons, and tall dendrons with highly stretched spacers. The differences increase as the grafting density decreases and single dendron populations were evident in theta and poor solvent. In poor solvent at low grafting densities, solvent micelles, polymeric pinned lamellae, spherical and single chain collapsed micelles were observed. The scaling dependence of the height of the dendritic brush at high density brushes for both solvents was found to be in agreement with existing analytical results.

Computational Elucidation of a Role That Brønsted Acidification of the Lewis Acid-Bound Water Might Play in the Hydrogenation of Carbonyl Compounds with H2 in Lewis Basic Solvents.

PubMed

Heshmat, Mojgan; Privalov, Timofei

2017-08-25

Brønsted acidification of water by Lewis acid (LA) complexation is one of the fundamental principles in chemistry. Using transition-state calculations (TS), herein we investigate the role that Brønsted acidification of the LA-bound water might play in the mechanism of the hydrogenation of carbonyl compounds in Lewis basic solvents under non-anhydrous conditions. The potential energy scans and TS calculations were carried out with a series of eight borane LAs as well as the commonly known strong LA AlCl 3 in 1,4-dioxane or THF as Lewis basic solvents. Our molecular model consists of the dative LA-water adduct with hydrogen bonds to acetone and a solvent molecule plus one additional solvent molecule that participates is the TS structure describing the cleavage of H 2 at acetone's carbonyl carbon atom. In all the molecular models applied here, acetone (O=CMe 2 ) is the archetypical carbonyl substrate. We demonstrate that Brønsted acidification of the LA-bound water can indeed lower the barrier height of the solvent-involving H 2 -cleavage at the acetone's carbonyl carbon atom. This is significant because at present it is believed that the mechanism of the herein considered reaction is described by the same mechanism regardless of whether the reaction conditions are strictly anhydrous or non-anhydrous. Our results offer an alternative to this belief that warrants consideration and further study. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Using solvent-free sample preparation to promote protonation of poly(ethylene oxide)s with labile end-groups in matrix-assisted laser desorption/ionisation.

PubMed

Mazarin, Michael; Phan, Trang N T; Charles, Laurence

2008-12-01

Protonation is usually required to observe intact ions during matrix-assisted laser desorption/ionization (MALDI) of polymers containing fragile end-groups while cation adduction induces chain-end degradation. These polymers, generally obtained via living free radical polymerization techniques, are terminated with a functionality in which a bond is prone to homolytic cleavage, as required by the polymerization process. A solvent-free sample preparation method was used here to avoid salt contaminant from the solvent traditionally used in the dried-droplet MALDI procedure. Solvent-based and solvent-free sample preparations were compared for a series of three poly(ethylene oxide) polymers functionalized with a labile end-group in a nitroxide-mediated polymerization reaction, using 2,4,6-trihydroxyacetophenone (THAP) as the matrix without any added salt. Intact oligomer ions could only be produced as protonated molecules in solvent-free MALDI while sodium adducts of degraded polymers were formed from the dried-droplet samples. Although MALDI analysis was performed at the laser threshold, fragmentation of protonated macromolecules was still observed to occur. However, in contrast to sodiated molecules, dissociation of protonated oligomers does not involve the labile C--ON bond of the end-group. As the macromolecule size increased, protonation appeared to be less efficient and sodium adduction became the dominant ionization process, although no sodium salt was added in the preparation. Formation of sodiated degraded macromolecules would be dictated by increasing cation affinity as the size of the oligomers increases and would reveal the presence of salts at trace levels in the MALDI samples.

Volatile anesthetic binding to proteins is influenced by solvent and aliphatic residues.

PubMed

Streiff, John H; Jones, Keith A

2008-10-01

The main objective of this work was to characterize VA binding sites in multiple anesthetic target proteins. A computational algorithm was used to quantify the solvent exclusion and aliphatic character of amphiphilic pockets in the structures of VA binding proteins. VA binding sites in the protein structures were defined as the pockets with solvent exclusion and aliphatic character that exceeded minimum values observed in the VA binding sites of serum albumin, firefly luciferase, and apoferritin. We found that the structures of VA binding proteins are enriched in these pockets and that the predicted binding sites were consistent with experimental determined binding locations in several proteins. Autodock3 was used to dock the simulated molecules of 1,1,1,2,2-pentafluoroethane, difluoromethyl 1,1,1,2-tetrafluoroethyl ether, and sevoflurane and the isomers of halothane and isoflurane into these potential binding sites. We found that the binding of the various VA molecules to the amphiphilic pockets is driven primarily by VDW interactions and to a lesser extent by weak hydrogen bonding and electrostatic interactions. In addition, the trend in Delta G binding values follows the Meyer-Overton rule. These results suggest that VA potencies are related to the VDW interactions between the VA ligand and protein target. It is likely that VA bind to sites with a high degree of solvent exclusion and aliphatic character because aliphatic residues provide favorable VDW contacts and weak hydrogen bond donors. Water molecules occupying these sites maintain pocket integrity, associate with the VA ligand, and diminish the unfavorable solvation enthalpy of the VA. Water molecules displaced into the bulk by the VA ligand may provide an additional favorable enthalpic contribution to VA binding. Anesthesia is a component of many health related procedures, the outcomes of which could be improved with a better understanding of the molecular targets and mechanisms of anesthetic action.

Statics and dynamics of DNA knotting

NASA Astrophysics Data System (ADS)

Orlandini, Enzo

2018-02-01

Knots and entanglement in polymers and biopolymers such as DNA and proteins constitute a timely topic that spans various scientific disciplines ranging from physics to chemistry, biology and mathematics. Although in the past many advancements have been made in understanding the equilibrium knotting probability and knot complexity of long polymer chains in solutions, many questions have been addressed in recent years by both experimental and theoretical means—for instance, how the knotting probability depends on the quality of the solvent, the elastic properties of the molecule and its degree of confinement. How knots form, evolve and eventually disappear in a fluctuating chain. Are the equilibrium and non-equilibrium properties of knotted molecules affected by the knot swelling/shrinking dynamics? Moreover, thanks to the great advance in nanotechnology and micromanipulation techniques, nowadays knots can be ‘manually’ tied in a single DNA molecule, followed during their motion along the chains, forced to pass through nanopores, or stretched by external forces or elongational flows. All these experimental approaches allow access to new information on the interplay of topology and polymer physics, and this has opened new perspectives in the field. Here, we provide an overview of the current knowledge of this topic, stressing the main results obtained, including the recent developments in experimental and computational approaches. Since almost all experiments on knotting involve DNA, the review will be mainly focused on the topological properties of this fascinating and biologically relevant molecule.

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.

Apparatus for reducing solvent luminescence background emissions

DOEpatents

Affleck, Rhett L.; Ambrose, W. Patrick; Demas, James N.; Goodwin, Peter M.; Johnson, Mitchell E.; Keller, Richard A.; Petty, Jeffrey T.; Schecker, Jay A.; Wu, Ming

1998-01-01

The detectability of luminescent molecules in solution is enhanced by reducing the background luminescence due to impurity species also present in the solution. A light source that illuminates the solution acts to photolyze the impurities so that the impurities do not luminesce in the fluorescence band of the molecule of interest. Molecules of interest may be carried through the photolysis region in the solution or may be introduced into the solution after the photolysis region.

Hybrid MC/QC simulations of water-assisted proton transfer in nucleosides. Guanosine and its analog acyclovir.

PubMed

Markova, Nadezhda; Pejov, Ljupco; Stoyanova, Nina; Enchev, Venelin

2017-05-01

To provide an in-depth insight into the molecular basis of spontaneous tautomerism in DNA and RNA base pairs, a hybrid Monte Carlo (MC)-quantum chemical (QC) methodology is implemented to map two-dimensional potential energy surfaces along the reaction coordinates of solvent-assisted proton transfer processes in guanosine and its analog acyclovir in aqueous solution. The solvent effects were simulated by explicit inclusion of water molecules that model the relevant part of the first hydration shell around the solute. The position of these water molecules was estimated by carrying out a classical Metropolis Monte Carlo simulation of dilute water solutions of the guanosine (Gs) and acyclovir (ACV) and subsequently analyzing solute-solvent intermolecular interactions in the statistically-independent MC-generated configurations. The solvent-assisted proton transfer processes were further investigated using two different ab initio MP2 quantum chemical approaches. In the first one, potential energy surfaces of the 'bare' finite solute-solvent clusters containing Gs/ACV and four water molecules (MP2/6-31+G(d,p) level) were explored, while within the second approach, these clusters were embedded in 'bulk' solvent treated as polarizable continuum (C-PCM/MP2/6-31+G(d,p) level of theory). It was found that in the gas phase and in water solution, the most stable tautomer for guanosine and acyclovir is the 1H-2-amino-6-oxo form followed by the 2-amino-6-(sZ)-hydroxy form. The energy barriers of the water-assisted proton transfer reaction in guanosine and in acyclovir are found to be very similar - 11.74 kcal mol -1 for guanosine and 11.16 kcal mol -1 for acyclovir, and the respective rate constants (k = 1.5 × 10 1 s -1 , guanosine and k = 4.09 × 10 1 s -1 , acyclovir), are sufficiently large to generate the 2-amino-6-(sZ)-hydroxy tautomer. The analysis of the reaction profiles in both compounds shows that the proton transfer processes occur through the asynchronous concerted mechanism.

Synthesis and Self-Assembly of the "Tennis Ball" Dimer and Subsequent Encapsulation of Methane. An Advanced Organic Chemistry Laboratory Experiment

NASA Astrophysics Data System (ADS)

Hof, Fraser; Palmer, Liam C.; Rebek, Julius, Jr.

2001-11-01

While important to the biological and materials sciences, noncovalent interactions, self-folding, and self-assembly often receive little discussion in the undergraduate chemistry curriculum. The synthesis and NMR characterization of a molecular "tennis ball" in an advanced undergraduate organic chemistry laboratory is a simple and effective way to introduce the relevance of these concepts. In appropriate solvents, the monomer dimerizes through a seam of eight hydrogen bonds with encapsulation of a guest molecule and symmetry reminiscent of a tennis ball. The entire experiment can be completed in three lab periods, however large-scale synthetic preparation of the starting monomer by a teaching assistant would reduce the laboratory to a single lab period for NMR studies.

Overexpression, crystallization and preliminary X-­ray crystallographic analysis of the RNA polymerase domain of primase from Streptococcus mutans strain UA159

PubMed Central

Im, Dong-Won; Kim, Tae-O; Jung, Ha Yun; Oh, Ji Eun; Lee, Se Jin; Heo, Yong-Seok

2012-01-01

Primase is the enzyme that synthesizes RNA primers on single-stranded DNA during normal DNA replication. In this study, the catalytic core domain of primase from Streptococcus mutans UA159 was overexpressed in Escherichia coli, purified and crystallized. Diffraction data were collected to 1.60 Å resolution using a synchrotron-radiation source. The crystal belonged to space group P41 or P43, with unit-cell parameters a = b = 52.63, c = 110.31 Å. The asymmetric unit is likely to contain one molecule, with a corresponding V M of 1.77 Å3 Da−1 and a solvent content of 30.7%. PMID:22232183

Reaction of iminopropadienones with amines: mechanistic explanations of zwitterionic intermediate, ketene and ketenimine formation.

PubMed

Koch, Rainer; Finnerty, Justin J; Bruhn, Torsten; Borget, Fabien; Wentrup, Curt

2008-09-25

The complex reaction of thermally generated iminopropadienones with amines in the gas phase and upon matrix deposition and its varying product composition is investigated using density functional theory. In the high energy gas phase addition a single amine molecule reacts readily with iminopropadienone with the decisive step being a 1,3-hydrogen shift and activation barriers of at least 100 kJ/mol. In accordance with the experiment, the formation of ketenes is favored. In the condensed phase of an amine matrix, the utilization of amine dimers both as reagents and as explicit solvents lowers the activation energy required to a feasible 20-30 kJ/mol and predicts ketenimines as the main products, as observed experimentally.

An Integrated approach (thermodynamic, structural, and computational) to the study of complexation of alkali-metal cations by a lower-rim calix[4]arene amide derivative in acetonitrile.

PubMed

Horvat, Gordan; Stilinović, Vladimir; Hrenar, Tomica; Kaitner, Branko; Frkanec, Leo; Tomišić, Vladislav

2012-06-04

The calix[4]arene secondary-amide derivative L was synthesized, and its complexation with alkali-metal cations in acetonitrile (MeCN) was studied by means of spectrophotometric, NMR, conductometric, and microcalorimetric titrations at 25 °C. The stability constants of the 1:1 (metal/ligand) complexes determined by different methods were in excellent agreement. For the complexation of M(+) (M = Li, Na, K) with L, both enthalpic and entropic contributions were favorable, with their values and mutual relations being quite strongly dependent on the cation. The enthalpic and overall stability was the largest in the case of the sodium complex. Molecular and crystal structures of free L, its methanol and MeCN solvates, the sodium complex, and its MeCN solvate were determined by single-crystal X-ray diffraction. The inclusion of a MeCN molecule in the calixarene hydrophobic cavity was observed both in solution and in the solid state. This specific interaction was found to be stronger in the case of metal complexes compared to the free ligand because of the better preorganization of the hydrophobic cone to accept the solvent molecule. Density functional theory calculations showed that the flattened cone conformation (C(2) point group) of L was generally more favorable than the square cone conformation (C(4) point group). In the complex with Na(+), L was in square cone conformation, whereas in its adduct with MeCN, the conformation was slightly distorted from the full symmetry. These conformations were in agreement with those observed in the solid state. The classical molecular dynamics simulations indicated that the MeCN molecule enters the L hydrophobic cavity of both the free ligand and its alkali-metal complexes. The inclusion of MeCN in the cone of free L was accompanied by the conformational change from C(2) to C(4) symmetry. As in solution studies, in the case of ML(+) complexes, an allosteric effect was observed: the ligand was already in the appropriate square cone conformation to bind the solvent molecule, allowing it to more easily and faster enter the calixarene cavity.

25 Mg NMR and computational modeling studies of the solvation structures and molecular dynamics in magnesium based liquid electrolytes

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

Hu, Jian Zhi; Rajput, Nav Nidhi; Wan, Chuan

There is increasing evidence that the solvation structure of the active components in a liquid electrolyte solution strongly impacts the performance in electrochemical applications. In this work, the nanoscale solvation structures and dynamics of Mg(BH4)2 and Mg(TFSI)2 dissolved in diglyme (DGM) at various concentrations and ratios of Mg(BH4)2/Mg(TFSI)2 were investigated using a combination of natural abundance 25Mg NMR, quantum chemistry calculations of 25Mg NMR chemical shifts, classical molecular dynamics (MD) calculations, and electrochemical performance tests. By mixing two competing Mg salts, we were able to reduce the strong covalent interactions between Mg2+ and BH4– anions. A small increase is observedmore » in the coordination number of Mg-TFSI and a significant increase in the interaction of Mg2+ ions with glymes. Through a combination of NMR, DFT and MD simulations, various stable species around 1 nm in size were detected in the mixed salt solution, which play key roles in the enhanced electrochemical performance of the mixed electrolyte. It is established that for the neat Mg(TFSI)2 in DGM electrolyte at dilute concentrations the TFSI- is fully dissociated from Mg2+. At higher concentrations, Mg2+ and TFSI- are only partially dissociated as contact ion pairs are formed. In contrast, at 0.01 M Mg(BH4)2 (saturated concentration) in DGM, the first solvation shell of a Mg2+ ion contains two BH4- anions and one DGM molecule, while the second solvation shell consists of five to six DGM molecules. An exchange mechanism between the solvation structures in the combined electrolyte containing both Mg(BH4)2 and Mg(TFSI)2 in DGM was found to result in the observation of a single 25Mg NMR peak. This exchange is responsible for an increase in uncoordinated anions, as well as improved stability and ionic conductivity as compared to single anion solution. Solvent molecule rearrangement and direct Mg-ion exchange between the basic solvation structures are hypothesized as likely reasons for the exchange. We elucidate that the solvent rearrangement is energetically much more favorable than direct Mg-ion hopping and is thus suggested as the dominant exchange mechanism.« less

25Mg NMR and Computational Modeling Studies of the Solvation Structures and Molecular Dynamics in Magnesium Based Liquid Electrolytes

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

Hu, Jian Z.; Rajput, Nav Nidhi; Wan, Chuan

There is increasing evidence that the solvation structure of the active components in a liquid electrolyte solution strongly impacts the performance in electrochemical applications. In this work, the nanoscale solvation structures and dynamics of Mg(BH4)2 and Mg(TFSI)2 dissolved in diglyme (DGM) at various concentrations and ratios of Mg(BH4)2/Mg(TFSI)2 were investigated using a combination of natural abundance 25Mg NMR, quantum chemistry calculations of 25Mg NMR chemical shifts, classical molecular dynamics (MD) calculations, and electrochemical performance tests. By mixing two competing Mg salts, we were able to reduce the strong covalent interactions between Mg2+ and BH4– anions. A small increase is observedmore » in the coordination number of Mg-TFSI and a significant increase in the interaction of Mg2+ ions with glymes. Through a combination of NMR, DFT and MD simulations, various stable species around 1 nm in size were detected in the mixed salt solution, which play key roles in the enhanced electrochemical performance of the mixed electrolyte. It is established that for the neat Mg(TFSI)2 in DGM electrolyte at dilute concentrations the TFSI- is fully dissociated from Mg2+. At higher concentrations, Mg2+ and TFSI- are only partially dissociated as contact ion pairs are formed. In contrast, at 0.01 M Mg(BH4)2 (saturated concentration) in DGM, the first solvation shell of a Mg2+ ion contains two BH4- anions and one DGM molecule, while the second solvation shell consists of five to six DGM molecules. An exchange mechanism between the solvation structures in the combined electrolyte containing both Mg(BH4)2 and Mg(TFSI)2 in DGM was found to result in the observation of a single 25Mg NMR peak. This exchange is responsible for an increase in uncoordinated anions, as well as improved stability and ionic conductivity as compared to single anion solution. Solvent molecule rearrangement and direct Mg-ion exchange between the basic solvation structures are hypothesized as likely reasons for the exchange. We elucidate that the solvent rearrangement is energetically much more favorable than direct Mg-ion hopping and is thus suggested as the dominant exchange mechanism.« less

Solvent effect on the conformation of Benzil

NASA Astrophysics Data System (ADS)

Pawelka, Z.; Koll, A.; Zeegers-Huyskens, Th.

2001-10-01

The conformation of benzil is investigated by PM3 and density functional theory (B3LYP) combined with the 6-31G(d,p) basis set. The variation of the relative energy with the Odbnd C-Cdbnd O torsion angle indicates only one rather flat minimum, reflecting the flexibility of the benzil molecule. The dipole moment is measured in several organic solvents of various polarity and the IR and Raman spectra investigated in the Cdbnd O stretching region in the same solvents. The torsional Odbnd C-Cdbnd O angle is evaluated from the dipolar and vibrational data. The results indicate that, in all the solvents, benzil is in a skewed conformation, the cisoid conformation being slightly favoured when the polarity of the solvent increases. The contribution of electrostatic and specific interactions to the reduction of the torsional angle is discussed.

Purification of semiconducting single-walled carbon nanotubes by spiral counter-current chromatography.

PubMed

Knight, Martha; Lazo-Portugal, Rodrigo; Ahn, Saeyoung Nate; Stefansson, Steingrimur

2017-02-03

Over the last decade man-made carbon nanostructures have shown great promise in electronic applications, but they are produced as very heterogeneous mixtures with different properties so the achievement of a significant commercial application has been elusive. The dimensions of single-wall carbon nanotubes are generally a nanometer wide, up to hundreds of microns long and the carbon nanotubes have anisotropic structures. They are processed to have shorter lengths but they need to be sorted by diameter and chirality. Thus counter-current chromatography methods developed for large molecules are applied to separate these compounds. A modified mixer-settler spiral CCC rotor made with 3 D printed disks was used with a polyethylene glycol-dextran 2-phase solvent system and a surfactant gradient to purify the major species in a commercial preparation. We isolated the semi-conducting single walled carbon nanotube chiral species identified by UV spectral analysis. The further development of spiral counter-current chromatography instrumentation and methods will enable the scalable purification of carbon nanotubes useful for the next generation electronics. Copyright © 2016 Elsevier B.V. All rights reserved.