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

PubMed

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

2018-04-27

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

Quantum theoretical study of electron solvation dynamics in ice layers on a Cu(111) surface.

PubMed

Andrianov, I; Klamroth, T; Saalfrank, P; Bovensiepen, U; Gahl, C; Wolf, M

2005-06-15

Recent experiments using time- and angle-resolved two-photon photoemission (2PPE) spectroscopy at metal/polar adsorbate interfaces succeeded in time-dependent analysis of the process of electron solvation. A fully quantum mechanical, two-dimensional simulation of this process, which explicitly includes laser excitation, is presented here, confirming the origin of characteristic features, such as the experimental observation of an apparently negative dispersion. The inference of the spatial extent of the localized electron states from the angular dependence of the 2PPE spectra has been found to be non-trivial and system-dependent.

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

NASA Astrophysics Data System (ADS)

Yang, Jianpeng; Kong, Xiangtao; Jiang, Ling

2018-02-01

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

Quantum Simulations of Solvated Biomolecules Using Hybrid Methods

NASA Astrophysics Data System (ADS)

Hodak, Miroslav

2009-03-01

One of the most important challenges in quantum simulations on biomolecules is efficient and accurate inclusion of the solvent, because the solvent atoms usually outnumber those in the biomolecule of interest. We have developed a hybrid method that allows for explicit quantum-mechanical treatment of the solvent at low computational cost. In this method, Kohn-Sham (KS) density functional theory (DFT) is combined with an orbital-free (OF) DFT. Kohn-Sham (KS) DFT is used to describe the biomolecule and its first solvation shells, while the orbital-free (OF) DFT is employed for the rest of the solvent. The OF part is fully O(N) and capable of handling 10^5 solvent molecules on current parallel supercomputers, while taking only ˜ 10 % of the total time. The compatibility between the KS and OF DFT methods enables seamless integration between the two. In particular, the flow of solvent molecules across the KS/OF interface is allowed and the total energy is conserved. As the first large-scale applications, the hybrid method has been used to investigate the binding of copper ions to proteins involved in prion (PrP) and Parkinson's diseases. Our results for the PrP, which causes mad cow disease when misfolded, resolve a contradiction found in experiments, in which a stronger binding mode is replaced by a weaker one when concentration of copper ions is increased, and show how it can act as a copper buffer. Furthermore, incorporation of copper stabilizes the structure of the full-length PrP, suggesting its protective role in prion diseases. For alpha-synuclein, a Parkinson's disease (PD) protein, we show that Cu binding modifies the protein structurally, making it more susceptible to misfolding -- an initial step in the onset of PD. In collaboration with W. Lu, F. Rose and J. Bernholc.

Nonequilibrium quantum solvation with a time-dependent Onsager cavity

NASA Astrophysics Data System (ADS)

Kirchberg, H.; Nalbach, P.; Thorwart, M.

2018-04-01

We formulate a theory of nonequilibrium quantum solvation in which parameters of the solvent are explicitly depending on time. We assume in a simplest approach a spherical molecular Onsager cavity with a time-dependent radius. We analyze the relaxation properties of a test molecular point dipole in a dielectric solvent and consider two cases: (i) a shrinking Onsager sphere and (ii) a breathing Onsager sphere. Due to the time-dependent solvent, the frequency-dependent response function of the dipole becomes time-dependent. For a shrinking Onsager sphere, the dipole relaxation is in general enhanced. This is reflected in a temporally increasing linewidth of the absorptive part of the response. Furthermore, the effective frequency-dependent response function shows two peaks in the absorptive part which are symmetrically shifted around the eigenfrequency. By contrast, a breathing sphere reduces damping as compared to the static sphere. Interestingly, we find a non-monotonous dependence of the relaxation rate on the breathing rate and a resonant suppression of damping when both rates are comparable. Moreover, the linewidth of the absorptive part of the response function is strongly reduced for times when the breathing sphere reaches its maximal extension.

Nonequilibrium quantum solvation with a time-dependent Onsager cavity.

PubMed

Kirchberg, H; Nalbach, P; Thorwart, M

2018-04-28

We formulate a theory of nonequilibrium quantum solvation in which parameters of the solvent are explicitly depending on time. We assume in a simplest approach a spherical molecular Onsager cavity with a time-dependent radius. We analyze the relaxation properties of a test molecular point dipole in a dielectric solvent and consider two cases: (i) a shrinking Onsager sphere and (ii) a breathing Onsager sphere. Due to the time-dependent solvent, the frequency-dependent response function of the dipole becomes time-dependent. For a shrinking Onsager sphere, the dipole relaxation is in general enhanced. This is reflected in a temporally increasing linewidth of the absorptive part of the response. Furthermore, the effective frequency-dependent response function shows two peaks in the absorptive part which are symmetrically shifted around the eigenfrequency. By contrast, a breathing sphere reduces damping as compared to the static sphere. Interestingly, we find a non-monotonous dependence of the relaxation rate on the breathing rate and a resonant suppression of damping when both rates are comparable. Moreover, the linewidth of the absorptive part of the response function is strongly reduced for times when the breathing sphere reaches its maximal extension.

Quantum indistinguishability in chemical reactions.

PubMed

Fisher, Matthew P A; Radzihovsky, Leo

2018-05-15

Quantum indistinguishability plays a crucial role in many low-energy physical phenomena, from quantum fluids to molecular spectroscopy. It is, however, typically ignored in most high-temperature processes, particularly for ionic coordinates, implicitly assumed to be distinguishable, incoherent, and thus well approximated classically. We explore enzymatic chemical reactions involving small symmetric molecules and argue that in many situations a full quantum treatment of collective nuclear degrees of freedom is essential. Supported by several physical arguments, we conjecture a "quantum dynamical selection" (QDS) rule for small symmetric molecules that precludes chemical processes that involve direct transitions from orbitally nonsymmetric molecular states. As we propose and discuss, the implications of the QDS rule include ( i ) a differential chemical reactivity of para- and orthohydrogen, ( ii ) a mechanism for inducing intermolecular quantum entanglement of nuclear spins, ( iii ) a mass-independent isotope fractionation mechanism, ( iv ) an explanation of the enhanced chemical activity of "reactive oxygen species", ( v ) illuminating the importance of ortho-water molecules in modulating the quantum dynamics of liquid water, and ( vi ) providing the critical quantum-to-biochemical linkage in the nuclear spin model of the (putative) quantum brain, among others.

Quantum Entanglement and Chemical Reactivity.

PubMed

Molina-Espíritu, M; Esquivel, R O; López-Rosa, S; Dehesa, J S

2015-11-10

The water molecule and a hydrogenic abstraction reaction are used to explore in detail some quantum entanglement features of chemical interest. We illustrate that the energetic and quantum-information approaches are necessary for a full understanding of both the geometry of the quantum probability density of molecular systems and the evolution of a chemical reaction. The energy and entanglement hypersurfaces and contour maps of these two models show different phenomena. The energy ones reveal the well-known stable geometry of the models, whereas the entanglement ones grasp the chemical capability to transform from one state system to a new one. In the water molecule the chemical reactivity is witnessed through quantum entanglement as a local minimum indicating the bond cleavage in the dissociation process of the molecule. Finally, quantum entanglement is also useful as a chemical reactivity descriptor by detecting the transition state along the intrinsic reaction path in the hypersurface of the hydrogenic abstraction reaction corresponding to a maximally entangled state.

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

PubMed

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

2018-03-22

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

Competitive lithium solvation of linear and cyclic carbonates from quantum chemistry

DOE PAGES

Kent, Paul R. C.; Ganesh, Panchapakesan; Borodin, Oleg; ...

2015-11-17

The composition of the lithium cation (Li+) solvation shell in mixed linear and cyclic carbonate-based electrolytes has been re-examined using Born–Oppenheimer molecular dynamics (BOMD) as a function of salt concentration and cluster calculations with ethylene carbonate:dimethyl carbonate (EC:DMC)–LiPF 6 as a model system. A coordination preference for EC over DMC to a Li+ was found at low salt concentrations, while a slightly higher preference for DMC over EC was found at high salt concentrations. Analysis of the relative binding energies of the (EC) n(DMC) m–Li+ and (EC) n(DMC) m–LiPF 6 solvates in the gas-phase and for an implicit solvent (asmore » a function of the solvent dielectric constant) indicated that the DMC-containing Li+ solvates were stabilized relative to (EC 4)–Li+ and (EC) 3–LiPF 6 by immersing them in the implicit solvent. Such stabilization was more pronounced in the implicit solvents with a high dielectric constant. Results from previous Raman and IR experiments were reanalyzed and reconciled by correcting them for changes of the Raman activities, IR intensities and band shifts for the solvents which occur upon Li+ coordination. After these correction factors were applied to the results of BOMD simulations, the composition of the Li+ solvation shell from the BOMD simulations was found to agree well with the solvation numbers extracted from Raman experiments. Finally, the mechanism of the Li+ diffusion in the dilute (EC:DMC)LiPF 6 mixed solvent electrolyte was studied using the BOMD simulations.« less

Charge-dependent non-bonded interaction methods for use in quantum mechanical modeling of condensed phase reactions

NASA Astrophysics Data System (ADS)

Kuechler, Erich R.

Molecular modeling and computer simulation techniques can provide detailed insight into biochemical phenomena. This dissertation describes the development, implementation and parameterization of two methods for the accurate modeling of chemical reactions in aqueous environments, with a concerted scientific effort towards the inclusion of charge-dependent non-bonded non-electrostatic interactions into currently used computational frameworks. The first of these models, QXD, modifies interactions in a hybrid quantum mechanical/molecular (QM/MM) mechanical framework to overcome the current limitations of 'atom typing' QM atoms; an inaccurate and non-intuitive practice for chemically active species as these static atom types are dictated by the local bonding and electrostatic environment of the atoms they represent, which will change over the course of the simulation. The efficacy QXD model is demonstrated using a specific reaction parameterization (SRP) of the Austin Model 1 (AM1) Hamiltonian by simultaneously capturing the reaction barrier for chloride ion attack on methylchloride in solution and the solvation free energies of a series of compounds including the reagents of the reaction. The second, VRSCOSMO, is an implicit solvation model for use with the DFTB3/3OB Hamiltonian for biochemical reactions; allowing for accurate modeling of ionic compound solvation properties while overcoming the discontinuous nature of conventional PCM models when chemical reaction coordinates. The VRSCOSMO model is shown to accurately model the solvation properties of over 200 chemical compounds while also providing smooth, continuous reaction surfaces for a series of biologically motivated phosphoryl transesterification reactions. Both of these methods incorporate charge-dependent behavior into the non-bonded interactions variationally, allowing the 'size' of atoms to change in meaningful ways with respect to changes in local charge state, as to provide an accurate, predictive and

Natural abundance 17O, 6Li NMR and molecular modeling studies of the solvation structures of lithium bis(fluorosulfonyl)imide/1,2-dimethoxyethane liquid electrolytes

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

Wan, Chuan; Hu, Mary Y.; Borodin, Oleg

2016-03-01

Natural abundance 17O and 6Li NMR experiments, quantum chemistry and molecular dynamics studies were employed to investigate the solvation structures of Li+ at various concentrations of LiFSI in DME electrolytes in an effort to solve this puzzle. It was found that the chemical shifts of both 17O and 6Li changed with the concentration of LiFSI, indicating the changes of solvation structures with concentration. For the quantum chemistry calculations, the coordinated cluster LiFSI(DME)2 forms at first, and its relative ratio increases with increasing LiFSI concentration to 1 M. Then the solvation structure LiFSI(DME) become the dominant component. As a result, themore » coordination of forming contact ion pairs between Li+ and FSI- ion increases, but the association between Li+ and DME molecule decreases. Furthermore, at LiFSI concentration of 4 M the solvation structures associated with Li+(FSI-)2(DME), Li+2(FSI-)(DME)4 and (LiFSI)2(DME)3 become the dominant components. For the molecular dynamics simulation, with increasing concentration, the association between DME and Li+ decreases, and the coordinated number of FSI- increases, which is in perfect accord with the DFT results. These results provide more insight on the fundamental mechanism on the very high CE of Li deposition in these electrolytes, especially at high current density conditions.« less

Semiempirical Quantum Chemical Calculations Accelerated on a Hybrid Multicore CPU-GPU Computing Platform.

PubMed

Wu, Xin; Koslowski, Axel; Thiel, Walter

2012-07-10

In this work, we demonstrate that semiempirical quantum chemical calculations can be accelerated significantly by leveraging the graphics processing unit (GPU) as a coprocessor on a hybrid multicore CPU-GPU computing platform. Semiempirical calculations using the MNDO, AM1, PM3, OM1, OM2, and OM3 model Hamiltonians were systematically profiled for three types of test systems (fullerenes, water clusters, and solvated crambin) to identify the most time-consuming sections of the code. The corresponding routines were ported to the GPU and optimized employing both existing library functions and a GPU kernel that carries out a sequence of noniterative Jacobi transformations during pseudodiagonalization. The overall computation times for single-point energy calculations and geometry optimizations of large molecules were reduced by one order of magnitude for all methods, as compared to runs on a single CPU core.

Chemical and quantum simulation of electron transfer through a polypeptide

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

Ungar, L.W.; Voth, G.A.; Newton, M.D.

1999-08-26

Quantum rate theory, molecular dynamics simulations, and semiempirical electronic structure calculations are used to fully investigate electron transfer mediated by a solvated polypeptide for the first time. Using a stationary-phase approximation, the nonadiabatic electron-transfer rate constant is calculated from the nuclear free energies and the electronic coupling between the initial and final states. The former are obtained from quantum path integral and classical molecular dynamics simulations; the latter are calculated using semiempirical electronic structure calculations and the generalized Mulliken-Hush method. Importantly, no parameters are fit to kinetic data. The simulated system consists of a solvated four-proline polypeptide with a tris(bipyridine)rutheniummore » donor group and an oxypentamminecobalt acceptor group. From the simulation data entropy and energy contributions to the free energies are distinguished. Quantum suppression of the barrier, including important solvent contributions, is demonstrated. Although free energy profiles along the reaction coordinate are nearly parabolic, pronounced departures from harmonic behavior are found for the separate energy and entropy functions. Harmonic models of the system are compared to simulation results in order to quantify anharmonic effects. Electronic structure calculations show that electronic coupling elements vary considerably with system conformation, even when the effective donor-acceptor separation remains roughly constant. The calculations indicate that electron transfer in a significant range of conformations linking the polypeptide to the acceptor may contribute to the overall rate constant. After correction for limitations of the solvent model, the simulations and calculations agree well with the experimental activation energy and Arrhenius prefactor.« less

Hybrid Quantum Mechanics/Molecular Mechanics Solvation Scheme for Computing Free Energies of Reactions at Metal-Water Interfaces.

PubMed

Faheem, Muhammad; Heyden, Andreas

2014-08-12

We report the development of a quantum mechanics/molecular mechanics free energy perturbation (QM/MM-FEP) method for modeling chemical reactions at metal-water interfaces. This novel solvation scheme combines planewave density function theory (DFT), periodic electrostatic embedded cluster method (PEECM) calculations using Gaussian-type orbitals, and classical molecular dynamics (MD) simulations to obtain a free energy description of a complex metal-water system. We derive a potential of mean force (PMF) of the reaction system within the QM/MM framework. A fixed-size, finite ensemble of MM conformations is used to permit precise evaluation of the PMF of QM coordinates and its gradient defined within this ensemble. Local conformations of adsorbed reaction moieties are optimized using sequential MD-sampling and QM-optimization steps. An approximate reaction coordinate is constructed using a number of interpolated states and the free energy difference between adjacent states is calculated using the QM/MM-FEP method. By avoiding on-the-fly QM calculations and by circumventing the challenges associated with statistical averaging during MD sampling, a computational speedup of multiple orders of magnitude is realized. The method is systematically validated against the results of ab initio QM calculations and demonstrated for C-C cleavage in double-dehydrogenated ethylene glycol on a Pt (111) model surface.

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.

Solvation of carbonaceous molecules by para-H2 and ortho-D2 clusters. I. Polycyclic aromatic hydrocarbons.

PubMed

Calvo, F; Yurtsever, E

2016-06-14

This work theoretically examines the progressive coating of planar polycyclic aromatic hydrocarbon (PAH) molecules ranging from benzene to circumcoronene (C54H18) by para-hydrogen and ortho-deuterium. The coarse-grained Silvera-Goldman potential has been extended to model the interactions between hydrogen molecules and individual atoms of the PAH and parametrized against quantum chemical calculations for benzene-H2. Path-integral molecular dynamics simulations at 2 K were performed for increasingly large amounts of hydrogen coating the PAH up to the first solvation shell and beyond. From the simulations, various properties were determined such as the size of the first shell and its thickness as well as the solvation energy. The degree of delocalization was notably quantified from an energy landscape perspective, by monitoring the fluctuations among inherent structures sampled by the trajectories. Our results generally demonstrate a high degree of localization owing to relatively strong interactions between hydrogen and the PAH, and qualitatively minor isotopic effects. In the limit of large hydrogen amounts, the shell size and solvation energy both follow approximate linear relations with the numbers of carbon and hydrogen in the PAH.

Quantum mechanical/molecular mechanical/continuum style solvation model: second order Møller-Plesset perturbation theory.

PubMed

Thellamurege, Nandun M; Si, Dejun; Cui, Fengchao; Li, Hui

2014-05-07

A combined quantum mechanical/molecular mechanical/continuum (QM/MM/C) style second order Møller-Plesset perturbation theory (MP2) method that incorporates induced dipole polarizable force field and induced surface charge continuum solvation model is established. The Z-vector method is modified to include induced dipoles and induced surface charges to determine the MP2 response density matrix, which can be used to evaluate MP2 properties. In particular, analytic nuclear gradient is derived and implemented for this method. Using the Assisted Model Building with Energy Refinement induced dipole polarizable protein force field, the QM/MM/C style MP2 method is used to study the hydrogen bonding distances and strengths of the photoactive yellow protein chromopore in the wild type and the Glu46Gln mutant.

Quantum mechanical/molecular mechanical/continuum style solvation model: Second order Møller-Plesset perturbation theory

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

Thellamurege, Nandun M.; Si, Dejun; Cui, Fengchao

A combined quantum mechanical/molecular mechanical/continuum (QM/MM/C) style second order Møller-Plesset perturbation theory (MP2) method that incorporates induced dipole polarizable force field and induced surface charge continuum solvation model is established. The Z-vector method is modified to include induced dipoles and induced surface charges to determine the MP2 response density matrix, which can be used to evaluate MP2 properties. In particular, analytic nuclear gradient is derived and implemented for this method. Using the Assisted Model Building with Energy Refinement induced dipole polarizable protein force field, the QM/MM/C style MP2 method is used to study the hydrogen bonding distances and strengths ofmore » the photoactive yellow protein chromopore in the wild type and the Glu46Gln mutant.« less

Deciphering the photochemical mechanisms describing the UV-induced processes occurring in solvated guanine monophosphate

PubMed Central

Altavilla, Salvatore F.; Segarra-Martí, Javier; Nenov, Artur; Conti, Irene; Rivalta, Ivan; Garavelli, Marco

2015-01-01

The photophysics and photochemistry of water-solvated guanine monophosphate (GMP) are here characterized by means of a multireference quantum-chemical/molecular mechanics theoretical approach (CASPT2//CASSCF/AMBER) in order to elucidate the main photo-processes occurring upon UV-light irradiation. The effect of the solvent and of the phosphate group on the energetics and structural features of this system are evaluated for the first time employing high-level ab initio methods and thoroughly compared to those in vacuo previously reported in the literature and to the experimental evidence to assess to which extent they influence the photoinduced mechanisms. Solvated electronic excitation energies of solvated GMP at the Franck-Condon (FC) region show a red shift for the ππ* La and Lb states, whereas the energy of the oxygen lone-pair nπ* state is blue-shifted. The main photoinduced decay route is promoted through a ring-puckering motion along the bright lowest-lying La state toward a conical intersection (CI) with the ground state, involving a very shallow stationary point along the minimum energy pathway in contrast to the barrierless profile found in gas-phase, the point being placed at the end of the minimum energy path (MEP) thus endorsing its ultrafast deactivation in accordance with time-resolved transient and photoelectron spectroscopy experiments. The role of the nπ* state in the solvated system is severely diminished as the crossings with the initially populated La state and also with the Lb state are placed too high energetically to partake prominently in the deactivation photo-process. The proposed mechanism present in solvated and in vacuo DNA/RNA chromophores validates the intrinsic photostability mechanism through CI-mediated non-radiative processes accompanying the bright excited-state population toward the ground state and subsequent relaxation back to the FC region. PMID:25941671

Open-ended formulation of self-consistent field response theory with the polarizable continuum model for solvation.

PubMed

Di Remigio, Roberto; Beerepoot, Maarten T P; Cornaton, Yann; Ringholm, Magnus; Steindal, Arnfinn Hykkerud; Ruud, Kenneth; Frediani, Luca

2016-12-21

The study of high-order absorption properties of molecules is a field of growing importance. Quantum-chemical studies can help design chromophores with desirable characteristics. Given that most experiments are performed in solution, it is important to devise a cost-effective strategy to include solvation effects in quantum-chemical studies of these properties. We here present an open-ended formulation of self-consistent field (SCF) response theory for a molecular solute coupled to a polarizable continuum model (PCM) description of the solvent. Our formulation relies on the open-ended, density matrix-based quasienergy formulation of SCF response theory of Thorvaldsen, et al., [J. Chem. Phys., 2008, 129, 214108] and the variational formulation of the PCM, as presented by Lipparini et al., [J. Chem. Phys., 2010, 133, 014106]. Within the PCM approach to solvation, the mutual solute-solvent polarization is represented by means of an apparent surface charge (ASC) spread over the molecular cavity defining the solute-solvent boundary. In the variational formulation, the ASC is an independent, variational degree of freedom. This allows us to formulate response theory for molecular solutes in the fixed-cavity approximation up to arbitrary order and with arbitrary perturbation operators. For electric dipole perturbations, pole and residue analyses of the response functions naturally lead to the identification of excitation energies and transition moments. We document the implementation of this approach in the Dalton program package using a recently developed open-ended response code and the PCMSolver libraries and present results for one-, two-, three-, four- and five-photon absorption processes of three small molecules in solution.

Teaching Ionic Solvation Structure with a Monte Carlo Liquid Simulation Program

NASA Astrophysics Data System (ADS)

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

2004-09-01

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

Solvation of carbonaceous molecules by para-H{sub 2} and ortho-D{sub 2} clusters. I. Polycyclic aromatic hydrocarbons

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

Calvo, F., E-mail: florent.calvo@univ-grenoble-alpes.fr; Yurtsever, E.

This work theoretically examines the progressive coating of planar polycyclic aromatic hydrocarbon (PAH) molecules ranging from benzene to circumcoronene (C{sub 54}H{sub 18}) by para-hydrogen and ortho-deuterium. The coarse-grained Silvera-Goldman potential has been extended to model the interactions between hydrogen molecules and individual atoms of the PAH and parametrized against quantum chemical calculations for benzene-H{sub 2}. Path-integral molecular dynamics simulations at 2 K were performed for increasingly large amounts of hydrogen coating the PAH up to the first solvation shell and beyond. From the simulations, various properties were determined such as the size of the first shell and its thickness asmore » well as the solvation energy. The degree of delocalization was notably quantified from an energy landscape perspective, by monitoring the fluctuations among inherent structures sampled by the trajectories. Our results generally demonstrate a high degree of localization owing to relatively strong interactions between hydrogen and the PAH, and qualitatively minor isotopic effects. In the limit of large hydrogen amounts, the shell size and solvation energy both follow approximate linear relations with the numbers of carbon and hydrogen in the PAH.« less

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

PubMed

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

2018-02-05

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

Molecular Studies of Complex Soil Organic Matter Interactions with Metal Ions and Mineral Surfaces using Classical Molecular Dynamics and Quantum Chemistry Methods

NASA Astrophysics Data System (ADS)

Andersen, A.; Govind, N.; Laskin, A.

2017-12-01

Mineral surfaces have been implicated as potential protectors of soil organic matter (SOM) against decomposition and ultimate mineralization to small molecules which can provide nutrients for plants and soil microbes and can also contribute to the Earth's elemental cycles. SOM is a complex mixture of organic molecules of biological origin at varying degrees of decomposition and can, itself, self-assemble in such a way as to expose some biomolecule types to biotic and abiotic attack while protecting other biomolecule types. The organization of SOM and SOM with mineral surfaces and solvated metal ions is driven by an interplay of van der Waals and electrostatic interactions leading to partitioning of hydrophilic (e.g. sugars) and hydrophobic (e.g., lipids) SOM components that can be bridged with amphiphilic molecules (e.g., proteins). Classical molecular dynamics simulations can shed light on assemblies of organic molecules alone or complexation with mineral surfaces. The role of chemical reactions is also an important consideration in potential chemical changes of the organic species such as oxidation/reduction, degradation, chemisorption to mineral surfaces, and complexation with solvated metal ions to form organometallic systems. For the study of chemical reactivity, quantum chemistry methods can be employed and combined with structural insight provided by classical MD simulations. Moreover, quantum chemistry can also simulate spectroscopic signatures based on chemical structure and is a valuable tool in interpreting spectra from, notably, x-ray absorption spectroscopy (XAS). In this presentation, we will discuss our classical MD and quantum chemistry findings on a model SOM system interacting with mineral surfaces and solvated metal ions.

Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.

PubMed

Rappoport, Dmitrij; Galvin, Cooper J; Zubarev, Dmitry Yu; Aspuru-Guzik, Alán

2014-03-11

While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles.

Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: a review

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

Wei, Guowei; Baker, Nathan A.

2016-11-11

This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade. A key component of these methods is the differential geometry of surfaces theory, as applied to the solvent-solute boundary. In these approaches, the solvent-solute boundary is determined by a variational principle that determines the major physical observables of interest, for example, biomolecular surface area, enclosed volume, electrostatic potential, ion density, electron density, etc. Recently, differential geometry theory has been used to define the surfaces that separate the microscopic (solute) domains for biomolecules from the macroscopic (solvent) domains. In thesemore » approaches, the microscopic domains are modeled with atomistic or quantum mechanical descriptions, while continuum mechanics models (including fluid mechanics, elastic mechanics, and continuum electrostatics) are applied to the macroscopic domains. This multiphysics description is integrated through an energy functional formalism and the resulting Euler-Lagrange equation is employed to derive a variety of governing partial differential equations for different solvation and transport processes; e.g., the Laplace-Beltrami equation for the solvent-solute interface, Poisson or Poisson-Boltzmann equations for electrostatic potentials, the Nernst-Planck equation for ion densities, and the Kohn-Sham equation for solute electron density. Extensive validation of these models has been carried out over hundreds of molecules, including proteins and ion channels, and the experimental data have been compared in terms of solvation energies, voltage-current curves, and density distributions. We also propose a new quantum model for electrolyte transport.« less

On the nature of the solvated electron in ice Ih.

PubMed

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

2016-02-14

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

Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation models.

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

Kamerlin, Shina C. L.; Haranczyk, Maciej; Warshel, Arieh

2009-05-01

Phosphate hydrolysis is ubiquitous in biology. However, despite intensive research on this class of reactions, the precise nature of the reaction mechanism remains controversial. In this work, we have examined the hydrolysis of three homologous phosphate diesters. The solvation free energy was simulated by means of either an implicit solvation model (COSMO), hybrid quantum mechanical / molecular mechanical free energy perturbation (QM/MM-FEP) or a mixed solvation model in which N water molecules were explicitly included in the ab initio description of the reacting system (where N=1-3), with the remainder of the solvent being implicitly modelled as a continuum. Here, bothmore » COSMO and QM/MM-FEP reproduce Delta Gobs within an error of about 2kcal/mol. However, we demonstrate that in order to obtain any form of reliable results from a mixed model, it is essential to carefully select the explicit water molecules from short QM/MM runs that act as a model for the true infinite system. Additionally, the mixed models tend to be increasingly inaccurate the more explicit water molecules are placed into the system. Thus, our analysis indicates that this approach provides an unreliable way for modelling phosphate hydrolysis in solution.« less

Distinctive Solvation Patterns Make Renal Osmolytes Diverse

PubMed Central

Jackson-Atogi, Ruby; Sinha, Prem Kumar; Rösgen, Jörg

2013-01-01

The kidney uses mixtures of five osmolytes to counter the stress induced by high urea and NaCl concentrations. The individual roles of most of the osmolytes are unclear, and three of the five have not yet been thermodynamically characterized. Here, we report partial molar volumes and activity coefficients of glycerophosphocholine (GPC), taurine, and myo-inositol. We derive their solvation behavior from the experimental data using Kirkwood-Buff theory. We also provide their solubility data, including solubility data for scyllo-inositol. It turns out that renal osmolytes fall into three distinct classes with respect to their solvation. Trimethyl-amines (GPC and glycine-betaine) are characterized by strong hard-sphere-like self-exclusion; urea, taurine, and myo-inositol have a tendency toward self-association; sorbitol and most other nonrenal osmolytes have a relatively constant, intermediate solvation that has components of both exclusion and association. The data presented here show that renal osmolytes are quite diverse with respect to their solvation patterns, and they can be further differentiated based on observations from experiments examining their effect on macromolecules. It is expected, based on the available surface groups, that each renal osmolyte has distinct effects on various classes of biomolecules. This likely allows the kidney to use specific combinations of osmolytes independently to fine-tune the chemical activities of several types of molecules. PMID:24209862

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

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

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

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for coarse grained models of electrolyte solution. Here, we provide rigorous definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation (DFT-MD) and isolate the effects of charge and cavitation,more » comparing to the Born (linear response) model. We show that using uncorrected Ewald summation leads to highly unphysical values for the solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry (CHA) for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. This suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation. We would like to thank Thomas Beck, Shawn Kathmann, Richard Remsing and John Weeks for helpful discussions. Computing resources were generously allocated by PNNL's Institutional Computing program. This research also used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. TTD, GKS, and CJM were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by MS3 (Materials Synthesis and Simulation Across

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

Differential geometry based solvation model II: Lagrangian formulation.

PubMed

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

2011-12-01

Solvation is an elementary process in nature and is of paramount importance to more sophisticated chemical, biological and biomolecular processes. The understanding of solvation is an essential prerequisite for the quantitative description and analysis of biomolecular systems. This work presents a Lagrangian formulation of our differential geometry based solvation models. The Lagrangian representation of biomolecular surfaces has a few utilities/advantages. First, it provides an essential basis for biomolecular visualization, surface electrostatic potential map and visual perception of biomolecules. Additionally, it is consistent with the conventional setting of implicit solvent theories and thus, many existing theoretical algorithms and computational software packages can be directly employed. Finally, the Lagrangian representation does not need to resort to artificially enlarged van der Waals radii as often required by the Eulerian representation in solvation analysis. The main goal of the present work is to analyze the connection, similarity and difference between the Eulerian and Lagrangian formalisms of the solvation model. Such analysis is important to the understanding of the differential geometry based solvation model. The present model extends the scaled particle theory of nonpolar solvation model with a solvent-solute interaction potential. The nonpolar solvation model is completed with a Poisson-Boltzmann (PB) theory based polar solvation model. The differential geometry theory of surfaces is employed to provide a natural description of solvent-solute interfaces. The optimization of the total free energy functional, which encompasses the polar and nonpolar contributions, leads to coupled potential driven geometric flow and PB equations. Due to the development of singularities and nonsmooth manifolds in the Lagrangian representation, the resulting potential-driven geometric flow equation is embedded into the Eulerian representation for the purpose of

Differential geometry based solvation model II: Lagrangian formulation

PubMed Central

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

2010-01-01

Solvation is an elementary process in nature and is of paramount importance to more sophisticated chemical, biological and biomolecular processes. The understanding of solvation is an essential prerequisite for the quantitative description and analysis of biomolecular systems. This work presents a Lagrangian formulation of our differential geometry based solvation model. The Lagrangian representation of biomolecular surfaces has a few utilities/advantages. First, it provides an essential basis for biomolecular visualization, surface electrostatic potential map and visual perception of biomolecules. Additionally, it is consistent with the conventional setting of implicit solvent theories and thus, many existing theoretical algorithms and computational software packages can be directly employed. Finally, the Lagrangian representation does not need to resort to artificially enlarged van der Waals radii as often required by the Eulerian representation in solvation analysis. The main goal of the present work is to analyze the connection, similarity and difference between the Eulerian and Lagrangian formalisms of the solvation model. Such analysis is important to the understanding of the differential geometry based solvation model. The present model extends the scaled particle theory (SPT) of nonpolar solvation model with a solvent-solute interaction potential. The nonpolar solvation model is completed with a Poisson-Boltzmann (PB) theory based polar solvation model. The differential geometry theory of surfaces is employed to provide a natural description of solvent-solute interfaces. The minimization of the total free energy functional, which encompasses the polar and nonpolar contributions, leads to coupled potential driven geometric flow and Poisson-Boltzmann equations. Due to the development of singularities and nonsmooth manifolds in the Lagrangian representation, the resulting potential-driven geometric flow equation is embedded into the Eulerian representation for

From First Principles: The Application of Quantum Mechanics to Complex Molecules and Solvated Systems

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

Freitag, Mark A.

2001-12-31

The major title of this dissertation, 'From first principles,' is a phase often heard in the study of thermodynamics and quantum mechanics. These words embody a powerful idea in the physical sciences; namely, that it is possible to distill the complexities of nature into a set of simple, well defined mathematical laws from which specific relations can then be derived . In thermodynamics, these fundamental laws are immediately familiar to the physical scientist by their numerical order: the First, Second and Third Laws. However, the subject of the present volume is quantum mechanics-specifically, non-relativistic quantum mechanics, which is appropriate formore » most systems of chemical interest.« less

Quantum-chemical insights from deep tensor neural networks

PubMed Central

Schütt, Kristof T.; Arbabzadah, Farhad; Chmiela, Stefan; Müller, Klaus R.; Tkatchenko, Alexandre

2017-01-01

Learning from data has led to paradigm shifts in a multitude of disciplines, including web, text and image search, speech recognition, as well as bioinformatics. Can machine learning enable similar breakthroughs in understanding quantum many-body systems? Here we develop an efficient deep learning approach that enables spatially and chemically resolved insights into quantum-mechanical observables of molecular systems. We unify concepts from many-body Hamiltonians with purpose-designed deep tensor neural networks, which leads to size-extensive and uniformly accurate (1 kcal mol−1) predictions in compositional and configurational chemical space for molecules of intermediate size. As an example of chemical relevance, the model reveals a classification of aromatic rings with respect to their stability. Further applications of our model for predicting atomic energies and local chemical potentials in molecules, reliable isomer energies, and molecules with peculiar electronic structure demonstrate the potential of machine learning for revealing insights into complex quantum-chemical systems. PMID:28067221

Quantum-chemical insights from deep tensor neural networks.

PubMed

Schütt, Kristof T; Arbabzadah, Farhad; Chmiela, Stefan; Müller, Klaus R; Tkatchenko, Alexandre

2017-01-09

Learning from data has led to paradigm shifts in a multitude of disciplines, including web, text and image search, speech recognition, as well as bioinformatics. Can machine learning enable similar breakthroughs in understanding quantum many-body systems? Here we develop an efficient deep learning approach that enables spatially and chemically resolved insights into quantum-mechanical observables of molecular systems. We unify concepts from many-body Hamiltonians with purpose-designed deep tensor neural networks, which leads to size-extensive and uniformly accurate (1 kcal mol -1 ) predictions in compositional and configurational chemical space for molecules of intermediate size. As an example of chemical relevance, the model reveals a classification of aromatic rings with respect to their stability. Further applications of our model for predicting atomic energies and local chemical potentials in molecules, reliable isomer energies, and molecules with peculiar electronic structure demonstrate the potential of machine learning for revealing insights into complex quantum-chemical systems.

Quantum-chemical insights from deep tensor neural networks

NASA Astrophysics Data System (ADS)

Schütt, Kristof T.; Arbabzadah, Farhad; Chmiela, Stefan; Müller, Klaus R.; Tkatchenko, Alexandre

2017-01-01

Learning from data has led to paradigm shifts in a multitude of disciplines, including web, text and image search, speech recognition, as well as bioinformatics. Can machine learning enable similar breakthroughs in understanding quantum many-body systems? Here we develop an efficient deep learning approach that enables spatially and chemically resolved insights into quantum-mechanical observables of molecular systems. We unify concepts from many-body Hamiltonians with purpose-designed deep tensor neural networks, which leads to size-extensive and uniformly accurate (1 kcal mol-1) predictions in compositional and configurational chemical space for molecules of intermediate size. As an example of chemical relevance, the model reveals a classification of aromatic rings with respect to their stability. Further applications of our model for predicting atomic energies and local chemical potentials in molecules, reliable isomer energies, and molecules with peculiar electronic structure demonstrate the potential of machine learning for revealing insights into complex quantum-chemical systems.

Quantum chemical studies of estrogenic compounds

USDA-ARS?s Scientific Manuscript database

Quantum chemical methods are potent tools to provide information on the chemical structure and electronic properties of organic molecules. Modern computational chemistry methods have provided a great deal of insight into the binding of estrogenic compounds to estrogenic receptors (ER), an important ...

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

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

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

DOE PAGES

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

2017-07-26

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

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

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

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

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

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

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

Development of a quantum mechanics-based free-energy perturbation method: use in the calculation of relative solvation free energies.

PubMed

Reddy, M Rami; Singh, U C; Erion, Mark D

2004-05-26

Free-energy perturbation (FEP) is considered the most accurate computational method for calculating relative solvation and binding free-energy differences. Despite some success in applying FEP methods to both drug design and lead optimization, FEP calculations are rarely used in the pharmaceutical industry. One factor limiting the use of FEP is its low throughput, which is attributed in part to the dependence of conventional methods on the user's ability to develop accurate molecular mechanics (MM) force field parameters for individual drug candidates and the time required to complete the process. In an attempt to find an FEP method that could eventually be automated, we developed a method that uses quantum mechanics (QM) for treating the solute, MM for treating the solute surroundings, and the FEP method for computing free-energy differences. The thread technique was used in all transformations and proved to be essential for the successful completion of the calculations. Relative solvation free energies for 10 structurally diverse molecular pairs were calculated, and the results were in close agreement with both the calculated results generated by conventional FEP methods and the experimentally derived values. While considerably more CPU demanding than conventional FEP methods, this method (QM/MM-based FEP) alleviates the need for development of molecule-specific MM force field parameters and therefore may enable future automation of FEP-based calculations. Moreover, calculation accuracy should be improved over conventional methods, especially for calculations reliant on MM parameters derived in the absence of experimental data.

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

NASA Astrophysics Data System (ADS)

Shimizu, Seishi; Matubayasi, Nobuyuki

2018-02-01

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

Accurate quantum chemical calculations

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

1989-01-01

An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

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.

Improvements to the APBS biomolecular solvation software suite.

PubMed

Jurrus, Elizabeth; Engel, Dave; Star, Keith; Monson, Kyle; Brandi, Juan; Felberg, Lisa E; Brookes, David H; Wilson, Leighton; Chen, Jiahui; Liles, Karina; Chun, Minju; Li, Peter; Gohara, David W; Dolinsky, Todd; Konecny, Robert; Koes, David R; Nielsen, Jens Erik; Head-Gordon, Teresa; Geng, Weihua; Krasny, Robert; Wei, Guo-Wei; Holst, Michael J; McCammon, J Andrew; Baker, Nathan A

2018-01-01

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pK a values, and an improved web-based visualization tool for viewing electrostatics. © 2017 The Protein Society.

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

PubMed

Oliveira, Ivan P; Martínez, Leandro

2016-08-21

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

The role of broken symmetry in solvation of a spherical cavity in classical and quantum water models

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

Remsing, Richard C.; Baer, Marcel D.; Schenter, Gregory K.

2014-08-21

Insertion of a hard sphere cavity in liquid water breaks translational symmetry and generates an electrostatic potential difference between the region near the cavity and the bulk. Here, we clarify the physical interpretation of this potential and its calculation. We also show that the electrostatic potential in the center of small, medium, and large cavities depends very sensitively on the form of the assumed molecular interactions for dfferent classical simple point-charge models and quantum mechanical DFT-based interaction potentials, as reected in their description of donor and acceptor hydrogen bonds near the cavity. These dfferences can signifcantly affect the magnitude ofmore » the scalar electrostatic potential. We argue that the result of these studies will have direct consequences toward our understanding of the thermodynamics of ion solvation through the cavity charging process. JDW and RCR are supported by the National Science Foundation (Grants CHE0848574 and CHE1300993). CJM and GKS are supported by the U.S. Department of Energy`s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory (PNNL) is operated for the Department of Energy by Battelle. MDB is grateful for the support of the Linus Pauling Distinguished Postdoctoral Fellowship Program at PNNL. We acknowledge illuminating discussions and sharing of ideas and preprints with Dr. Shawn M. Kathmann and Prof. Tom Beck. The DFT simulations used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Additional computing resources were generously allocated by PNNL's Institutional Computing program.« less

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

PubMed

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

2012-03-01

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

Potentials of Mean Force With Ab Initio Mixed Hamiltonian Models of Solvation

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

Dupuis, Michel; Schenter, Gregory K.; Garrett, Bruce C.

2003-08-01

We give an account of a computationally tractable and efficient procedure for the calculation of potentials of mean force using mixed Hamiltonian models of electronic structure where quantum subsystems are described with computationally intensive ab initio wavefunctions. The mixed Hamiltonian is mapped into an all-classical Hamiltonian that is amenable to a thermodynamic perturbation treatment for the calculation of free energies. A small number of statistically uncorrelated (solute-solvent) configurations are selected from the Monte Carlo random walk generated with the all-classical Hamiltonian approximation. Those are used in the averaging of the free energy using the mixed quantum/classical Hamiltonian. The methodology ismore » illustrated for the micro-solvated SN2 substitution reaction of methyl chloride by hydroxide. We also compare the potential of mean force calculated with the above protocol with an approximate formalism, one in which the potential of mean force calculated with the all-classical Hamiltonian is simply added to the energy of the isolated (non-solvated) solute along the reaction path. Interestingly the latter approach is found to be in semi-quantitative agreement with the full mixed Hamiltonian approximation.« less

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

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

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

2014-10-07

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

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

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

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

2014-10-07

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

Corrosion Thermodynamics of Magnesium and Alloys from First Principles as a Function of Solvation

NASA Astrophysics Data System (ADS)

Limmer, Krista; Williams, Kristen; Andzelm, Jan

Thermodynamics of corrosion processes occurring on magnesium surfaces, such as hydrogen evolution and water dissociation, have been examined with density functional theory (DFT) to evaluate the effect of impurities and dilute alloying additions. The modeling of corrosion thermodynamics requires examination of species in a variety of chemical and electronic states in order to accurately represent the complex electrochemical corrosion process. In this study, DFT calculations for magnesium corrosion thermodynamics were performed with two DFT codes (VASP and DMol3), with multiple exchange-correlation functionals for chemical accuracy, as well as with various levels of implicit and explicit solvation for surfaces and solvated ions. The accuracy of the first principles calculations has been validated against Pourbaix diagrams constructed from solid, gas and solvated charged ion calculations. For aqueous corrosion, it is shown that a well parameterized implicit solvent is capable of accurately representing all but the first coordinating layer of explicit water for charged ions.

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

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

Complexation reactions in pyridine and 2,6-dimethylpyridine-water system: The quantum-chemical description and the path to liquid phase separation.

PubMed

Chernia, Zelig; Tsori, Yoav

2018-03-14

Phase separation in substituted pyridines in water is usually described as an interplay between temperature-driven breakage of hydrogen bonds and the associating interaction of the van der Waals force. In previous quantum-chemical studies, the strength of hydrogen bonding between one water and one pyridine molecules (the 1:1 complex) was assigned a pivotal role. It was accepted that the disassembly of the 1:1 complex at a critical temperature leads to phase separation and formation of the miscibility gap. Yet, for over two decades, notable empirical data and theoretical arguments were presented against that view, thus revealing the need in a revised quantum-mechanical description. In the present study, pyridine-water and 2,6-dimethylpyridine-water systems at different complexation stages are calculated using high level Kohn-Sham theory. The hydrophobic-hydrophilic properties are accounted for by the polarizable continuum solvation model. Inclusion of solvation in free energy of formation calculations reveals that 1:1 complexes are abundant in the organically rich solvents but higher level oligomers (i.e., 2:1 dimers with two pyridines and one water molecule) are the only feasible stable products in the more polar media. At the critical temperature, the dissolution of the external hydrogen bonds between the 2:1 dimer and the surrounding water molecules induces the demixing process. The 1:1 complex acts as a precursor in the formation of the dimers but is not directly involved in the demixing mechanism. The existence of the miscibility gap in one pyridine-water system and the lack of it in another is explained by the ability of the former to maintain stable dimerization. Free energy of formation of several reaction paths producing the 2:1 dimers is calculated and critically analyzed.

Complexation reactions in pyridine and 2,6-dimethylpyridine-water system: The quantum-chemical description and the path to liquid phase separation

NASA Astrophysics Data System (ADS)

Chernia, Zelig; Tsori, Yoav

2018-03-01

Phase separation in substituted pyridines in water is usually described as an interplay between temperature-driven breakage of hydrogen bonds and the associating interaction of the van der Waals force. In previous quantum-chemical studies, the strength of hydrogen bonding between one water and one pyridine molecules (the 1:1 complex) was assigned a pivotal role. It was accepted that the disassembly of the 1:1 complex at a critical temperature leads to phase separation and formation of the miscibility gap. Yet, for over two decades, notable empirical data and theoretical arguments were presented against that view, thus revealing the need in a revised quantum-mechanical description. In the present study, pyridine-water and 2,6-dimethylpyridine-water systems at different complexation stages are calculated using high level Kohn-Sham theory. The hydrophobic-hydrophilic properties are accounted for by the polarizable continuum solvation model. Inclusion of solvation in free energy of formation calculations reveals that 1:1 complexes are abundant in the organically rich solvents but higher level oligomers (i.e., 2:1 dimers with two pyridines and one water molecule) are the only feasible stable products in the more polar media. At the critical temperature, the dissolution of the external hydrogen bonds between the 2:1 dimer and the surrounding water molecules induces the demixing process. The 1:1 complex acts as a precursor in the formation of the dimers but is not directly involved in the demixing mechanism. The existence of the miscibility gap in one pyridine-water system and the lack of it in another is explained by the ability of the former to maintain stable dimerization. Free energy of formation of several reaction paths producing the 2:1 dimers is calculated and critically analyzed.

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

NASA Astrophysics Data System (ADS)

Farajtabar, Ali; Jaberi, Fatemeh; Gharib, Farrokh

2011-12-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

Quantum-chemical Calculations in the Study of Antitumour Compounds

NASA Astrophysics Data System (ADS)

Luzhkov, V. B.; Bogdanov, G. N.

1986-01-01

The results of quantum-chemical calculations on antitumour preparations concerning the mechanism of their action at the electronic and molecular levels and structure-activity correlations are discussed in this review. Preparations whose action involves alkylating and free-radial mechanisms, complex-forming agents, and antimetabolites are considered. Modern quantum-chemical methods for calculations on biologically active substances are described. The bibliography includes 106 references.

Heterogeneous nucleation of polymorphs on polymer surfaces: polymer-molecule interactions using a heterogeneous dielectric solvation model.

PubMed

Wahlberg, Nanna; Madsen, Anders Ø; Mikkelsen, Kurt V

2018-06-09

We have investigated the mechanism of the nucleation of acetaminophen on poly(methyl-methacrylate) and poly(vinyl-acetate) utilizing a combination of quantum mechanical computations and electrostatic models. We have used a heterogeneous dielectric solvation model to determine the stability of different orientations of acetaminophen on polymer surfaces. We find that for the nucleation of acetaminophen on the polymer surfaces in vacuum, the most stable orientation is a flat orientation. For the nucleation process in solution where acetaminophen and the polymer surface are surrounded by a solvent, we find that the heterogeneous dielectric solvation model predicts that a sideways orientation is the most stable orientation.

Solvation of Esters and Ketones in Supercritical CO2.

PubMed

Kajiya, Daisuke; Imanishi, Masayoshi; Saitow, Ken-ichi

2016-02-04

Vibrational Raman spectra for the C═O stretching modes of three esters with different functional groups (methyl, a single phenyl, and two phenyl groups) were measured in supercritical carbon dioxide (scCO2). The results were compared with Raman spectra for three ketones involving the same functional groups, measured at the same thermodynamic states in scCO2. The peak frequencies of the Raman spectra of these six solute molecules were analyzed by decomposition into the attractive and repulsive energy components, based on the perturbed hard-sphere theory. For all solute molecules, the attractive energy is greater than the repulsive energy. In particular, a significant difference in the attractive energies of the ester-CO2 and ketone-CO2 systems was observed when the methyl group is attached to the ester or ketone. This difference was significantly reduced in the solute systems with a single phenyl group and was completely absent in those with two phenyl groups. The optimized structures among the solutes and CO2 molecules based on quantum chemical calculations indicate that greater attractive energy is obtained for a system where the oxygen atom of the ester is solvated by CO2 molecules.

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.

Quantitative measurement of solvation shells using frequency modulated atomic force microscopy

NASA Astrophysics Data System (ADS)

Uchihashi, T.; Higgins, M.; Nakayama, Y.; Sader, J. E.; Jarvis, S. P.

2005-03-01

The nanoscale specificity of interaction measurements and additional imaging capability of the atomic force microscope make it an ideal technique for measuring solvation shells in a variety of liquids next to a range of materials. Unfortunately, the widespread use of atomic force microscopy for the measurement of solvation shells has been limited by uncertainties over the dimensions, composition and durability of the tip during the measurements, and problems associated with quantitative force calibration of the most sensitive dynamic measurement techniques. We address both these issues by the combined use of carbon nanotube high aspect ratio probes and quantifying the highly sensitive frequency modulation (FM) detection technique using a recently developed analytical method. Due to the excellent reproducibility of the measurement technique, additional information regarding solvation shell size as a function of proximity to the surface has been obtained for two very different liquids. Further, it has been possible to identify differences between chemical and geometrical effects in the chosen systems.

Readily Made Solvated Electrons

ERIC Educational Resources Information Center

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

2011-01-01

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

Nonpolar Solvation Free Energy from Proximal Distribution Functions

PubMed Central

Ou, Shu-Ching; Drake, Justin A.; Pettitt, B. Montgomery

2017-01-01

Using precomputed near neighbor or proximal distribution functions (pDFs) that approximate solvent density about atoms in a chemically bonded context one can estimate the solvation structures around complex solutes and the corresponding solute–solvent energetics. In this contribution, we extend this technique to calculate the solvation free energies (ΔG) of a variety of solutes. In particular we use pDFs computed for small peptide molecules to estimate ΔG for larger peptide systems. We separately compute the non polar (ΔGvdW) and electrostatic (ΔGelec) components of the underlying potential model. Here we show how the former can be estimated by thermodynamic integration using pDF-reconstructed solute–solvent interaction energy. The electrostatic component can be approximated with Linear Response theory as half of the electrostatic solute–solvent interaction energy. We test the method by calculating the solvation free energies of butane, propanol, polyalanine, and polyglycine and by comparing with traditional free energy simulations. Results indicate that the pDF-reconstruction algorithm approximately reproduces ΔGvdW calculated by benchmark free energy simulations to within ~ kcal/mol accuracy. The use of transferable pDFs for each solute atom allows for a rapid estimation of ΔG for arbitrary molecular systems. PMID:27992228

Local Aqueous Solvation Structure Around Ca2+ During Ca2+---Cl– Pair Formation

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

Baer, Marcel D.; Mundy, Christopher J.

2016-03-03

The molecular details of single ion solvation around Ca2+ and ion-pairing of Ca2--Cl- are investigated using ab initio molecular dynamics. The use of empirical dispersion corrections to the BLYP functional are investigated by comparison to experimentally available extended X-ray absorption fine structure (EXAFS) measurements, which probes the first solvation shell in great detail. Besides finding differences in the free-energy for both ion-pairing and the coordination number of ion solvation between the quantum and classical descriptions of interaction, there were important differences found between dispersion corrected and uncorrected density functional theory (DFT). Specifically, we show significantly different free-energy landscapes for bothmore » coordination number of Ca2+ and its ion-pairing with Cl- depending on the DFT simulation protocol. Our findings produce a self-consistent treatment of short-range solvent response to the ion and the intermediate to long-range collective response of the electrostatics of the ion-ion interaction to produce a detailed picture of ion-pairing that is consistent with experiment. MDB is supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative at Pacific Northwest National Laboratory. It was conducted under the Laboratory Directed Research and Development Program at PNNL, a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy. CJM acknowledges support from US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. This research used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Additional computing resources were generously allocated by PNNL's Institutional Computing program. The authors thank Prof. Tom Beck for discussions

Preparation of cerium halide solvate complexes

DOEpatents

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

2013-08-06

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

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

NASA Astrophysics Data System (ADS)

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

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

Thermodynamic-ensemble independence of solvation free energy.

PubMed

Chong, Song-Ho; Ham, Sihyun

2015-02-10

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

Significance of solvated electrons (e(aq)-) as promoters of life on earth.

PubMed

Getoff, Nikola

2014-01-01

Based on the present state of knowledge a new hypothesis concerning the origin of life on Earth is presented, and emphasizes the particular significance of solvated electrons (e(aq)(-)). Solvated electrons are produced in seawater, mainly by (40)K radiation and in atmospheric moisture by VUV light, electrical discharges and cosmic ray. Solvated electrons are involved in primary chemical processes and in biological processes. The conversion of aqueous CO2 and CO into simple organic substances, the generation of ammonia from N2 and water, the formation of amines, amino acids and simple proteins under the action of e(aq)(-) has been experimentally proven. Furthermore, it is supposed that the generation of the primitive cell and equilibria of primitive enzymes are also realized due to the strong reducing property of e(aq)(-). The presented hypothesis is mainly founded on recently obtained experimental results. The involvement of e(aq)(-) in such mechanisms, as well as their action as an initiator of life is also briefly discussed.

Hydrophobic Solvation: Aqueous Methane Solutions

ERIC Educational Resources Information Center

Konrod, Oliver; Lankau, Timm

2007-01-01

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

The chemical interpretation and practice of linear solvation energy relationships in chromatography.

PubMed

Vitha, Mark; Carr, Peter W

2006-09-08

This review focuses on the use of linear solvation energy relationships (LSERs) to understand the types and relative strength of the chemical interactions that control retention and selectivity in the various modes of chromatography ranging from gas chromatography to reversed phase and micellar electrokinetic capillary chromatography. The most recent, widely accepted symbolic representation of the LSER model, as proposed by Abraham, is given by the equation: SP=c + eE + sS + aA + bB + vV, in which, SP can be any free energy related property. In chromatography, SP is most often taken as logk' where k' is the retention factor. The letters E, S, A, B, and V denote solute dependent input parameters that come from scales related to a solute's polarizability, dipolarity (with some contribution from polarizability), hydrogen bond donating ability, hydrogen bond accepting ability, and molecular size, respectively. The e-, s-, a-, b-, and v-coefficients and the constant, c, are determined via multiparameter linear least squares regression analysis of a data set comprised of solutes with known E, S, A, B, and V values and which span a reasonably wide range in interaction abilities. Thus, LSERs are designed to probe the type and relative importance of the interactions that govern solute retention. In this review, we include a synopsis of the various solvent and solute scales in common use in chromatography. More importantly, we emphasize the development and physico-chemical basis of - and thus meaning of - the solute parameters. After establishing the meaning of the parameters, we discuss their use in LSERs as applied to understanding the intermolecular interactions governing various gas-liquid and liquid-liquid phase equilibria. The gas-liquid partition process is modeled as the sum of an endoergic cavity formation/solvent reorganization process and exoergic solute-solvent attractive forces, whereas the partitioning of a solute between two solvents is thermodynamically

A solvated electron lithium electrode for secondary batteries

NASA Astrophysics Data System (ADS)

Sammells, A. F.; Semkow, K. W.

1986-09-01

Attention is given to a novel method for the achievement of high electro-chemical reversibility in Li-based nonaqueous cells, using a liquid negative electrode that consists of Li dissolved in liquid ammonia as a solvated electron Li electrode. The containment of this liquid negative active material from direct contact to a liquid nonaqueous electrolyte in the positive electrode compartment was realized through the use of a Li-intercalated, electronically conducting ceramic membrane.

Polynomial-time quantum algorithm for the simulation of chemical dynamics

PubMed Central

Kassal, Ivan; Jordan, Stephen P.; Love, Peter J.; Mohseni, Masoud; Aspuru-Guzik, Alán

2008-01-01

The computational cost of exact methods for quantum simulation using classical computers grows exponentially with system size. As a consequence, these techniques can be applied only to small systems. By contrast, we demonstrate that quantum computers could exactly simulate chemical reactions in polynomial time. Our algorithm uses the split-operator approach and explicitly simulates all electron-nuclear and interelectronic interactions in quadratic time. Surprisingly, this treatment is not only more accurate than the Born–Oppenheimer approximation but faster and more efficient as well, for all reactions with more than about four atoms. This is the case even though the entire electronic wave function is propagated on a grid with appropriately short time steps. Although the preparation and measurement of arbitrary states on a quantum computer is inefficient, here we demonstrate how to prepare states of chemical interest efficiently. We also show how to efficiently obtain chemically relevant observables, such as state-to-state transition probabilities and thermal reaction rates. Quantum computers using these techniques could outperform current classical computers with 100 qubits. PMID:19033207

Theoretical calculations of physico-chemical and spectroscopic properties of bioinorganic systems: current limits and perspectives.

PubMed

Rokob, Tibor András; Srnec, Martin; Rulíšek, Lubomír

2012-05-21

In the last decade, we have witnessed substantial progress in the development of quantum chemical methodologies. Simultaneously, robust solvation models and various combined quantum and molecular mechanical (QM/MM) approaches have become an integral part of quantum chemical programs. Along with the steady growth of computer power and, more importantly, the dramatic increase of the computer performance to price ratio, this has led to a situation where computational chemistry, when exercised with the proper amount of diligence and expertise, reproduces, predicts, and complements the experimental data. In this perspective, we review some of the latest achievements in the field of theoretical (quantum) bioinorganic chemistry, concentrating mostly on accurate calculations of the spectroscopic and physico-chemical properties of open-shell bioinorganic systems by wave-function (ab initio) and DFT methods. In our opinion, the one-to-one mapping between the calculated properties and individual molecular structures represents a major advantage of quantum chemical modelling since this type of information is very difficult to obtain experimentally. Once (and only once) the physico-chemical, thermodynamic and spectroscopic properties of complex bioinorganic systems are quantitatively reproduced by theoretical calculations may we consider the outcome of theoretical modelling, such as reaction profiles and the various decompositions of the calculated parameters into individual spatial or physical contributions, to be reliable. In an ideal situation, agreement between theory and experiment may imply that the practical problem at hand, such as the reaction mechanism of the studied metalloprotein, can be considered as essentially solved.

Applications of the solvation parameter model in reversed-phase liquid chromatography.

PubMed

Poole, Colin F; Lenca, Nicole

2017-02-24

The solvation parameter model is widely used to provide insight into the retention mechanism in reversed-phase liquid chromatography, for column characterization, and in the development of surrogate chromatographic models for biopartitioning processes. The properties of the separation system are described by five system constants representing all possible intermolecular interactions for neutral molecules. The general model can be extended to include ions and enantiomers by adding new descriptors to encode the specific properties of these compounds. System maps provide a comprehensive overview of the separation system as a function of mobile phase composition and/or temperature for method development. The solvation parameter model has been applied to gradient elution separations but here theory and practice suggest a cautious approach since the interpretation of system and compound properties derived from its use are approximate. A growing application of the solvation parameter model in reversed-phase liquid chromatography is the screening of surrogate chromatographic systems for estimating biopartitioning properties. Throughout the discussion of the above topics success as well as known and likely deficiencies of the solvation parameter model are described with an emphasis on the role of the heterogeneous properties of the interphase region on the interpretation and understanding of the general retention mechanism in reversed-phase liquid chromatography for porous chemically bonded sorbents. Copyright © 2016 Elsevier B.V. All rights reserved.

Evaluating the Free Energies of Solvation and Electronic Structures of Lithium-Ion Battery Electrolytes.

PubMed

Shakourian-Fard, Mehdi; Kamath, Ganesh; Sankaranarayanan, Subramanian K R S

2016-09-19

Adaptive biasing force molecular dynamics simulations and density functional theory calculations were performed to understand the interaction of Li(+) with pure carbonates and ethylene carbonate (EC)-based binary mixtures. The most favorable Li carbonate cluster configurations obtained from molecular dynamics simulations were subjected to detailed structural and thermochemistry calculations on the basis of the M06-2X/6-311++G(d,p) level of theory. We report the ranking of these electrolytes on the basis of the free energies of Li-ion solvation in carbonates and EC-based mixtures. A strong local tetrahedral order involving four carbonates around the Li(+) was seen in the first solvation shell. Thermochemistry calculations revealed that the enthalpy of solvation and the Gibbs free energy of solvation of the Li(+) ion with carbonates are negative and suggested the ion-carbonate complexation process to be exothermic and spontaneous. Natural bond orbital analysis indicated that Li(+) interacts with the lone pairs of electrons on the carbonyl oxygen atom in the primary solvation sphere. These interactions lead to an increase in the carbonyl (C=O) bond lengths, as evidenced by a redshift in the vibrational frequencies [ν(C=O)] and a decrease in the electron density values at the C=O bond critical points in the primary solvation sphere. Quantum theory of atoms in molecules, localized molecular orbital energy decomposition analysis (LMO-EDA), and noncovalent interaction plots revealed the electrostatic nature of the Li(+) ion interactions with the carbonyl oxygen atoms in these complexes. On the basis of LMO-EDA, the strongest attractive interaction in these complexes was found to be the electrostatic interaction followed by polarization, dispersion, and exchange interactions. Overall, our calculations predicted EC and a binary mixture of EC/dimethyl carbonate to be appropriate electrolytes for Li-ion batteries, which complies with experiments and other theoretical results

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

PubMed

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

2004-02-23

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

Octanol-Water Partition Coefficient from 3D-RISM-KH Molecular Theory of Solvation with Partial Molar Volume Correction.

PubMed

Huang, WenJuan; Blinov, Nikolay; Kovalenko, Andriy

2015-04-30

The octanol-water partition coefficient is an important physical-chemical characteristic widely used to describe hydrophobic/hydrophilic properties of chemical compounds. The partition coefficient is related to the transfer free energy of a compound from water to octanol. Here, we introduce a new protocol for prediction of the partition coefficient based on the statistical-mechanical, 3D-RISM-KH molecular theory of solvation. It was shown recently that with the compound-solvent correlation functions obtained from the 3D-RISM-KH molecular theory of solvation, the free energy functional supplemented with the correction linearly related to the partial molar volume obtained from the Kirkwood-Buff/3D-RISM theory, also called the "universal correction" (UC), provides accurate prediction of the hydration free energy of small compounds, compared to explicit solvent molecular dynamics [ Palmer , D. S. ; J. Phys.: Condens. Matter 2010 , 22 , 492101 ]. Here we report that with the UC reparametrized accordingly this theory also provides an excellent agreement with the experimental data for the solvation free energy in nonpolar solvent (1-octanol) and so accurately predicts the octanol-water partition coefficient. The performance of the Kovalenko-Hirata (KH) and Gaussian fluctuation (GF) functionals of the solvation free energy, with and without UC, is tested on a large library of small compounds with diverse functional groups. The best agreement with the experimental data for octanol-water partition coefficients is obtained with the KH-UC solvation free energy functional.

Development and application of QM/MM methods to study the solvation effects and surfaces

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

Dibya, Pooja Arora

2010-01-01

Quantum mechanical (QM) calculations have the advantage of attaining high-level accuracy, however QM calculations become computationally inefficient as the size of the system grows. Solving complex molecular problems on large systems and ensembles by using quantum mechanics still poses a challenge in terms of the computational cost. Methods that are based on classical mechanics are an inexpensive alternative, but they lack accuracy. A good trade off between accuracy and efficiency is achieved by combining QM methods with molecular mechanics (MM) methods to use the robustness of the QM methods in terms of accuracy and the MM methods to minimize themore » computational cost. Two types of QM combined with MM (QM/MM) methods are the main focus of the present dissertation: the application and development of QM/MM methods for solvation studies and reactions on the Si(100) surface. The solvation studies were performed using a discreet solvation model that is largely based on first principles called the effective fragment potential method (EFP). The main idea of combining the EFP method with quantum mechanics is to accurately treat the solute-solvent and solvent-solvent interactions, such as electrostatic, polarization, dispersion and charge transfer, that are important in correctly calculating solvent effects on systems of interest. A second QM/MM method called SIMOMM (surface integrated molecular orbital molecular mechanics) is a hybrid QM/MM embedded cluster model that mimics the real surface.3 This method was employed to calculate the potential energy surfaces for reactions of atomic O on the Si(100) surface. The hybrid QM/MM method is a computationally inexpensive approach for studying reactions on larger surfaces in a reasonably accurate and efficient manner. This thesis is comprised of four chapters: Chapter 1 describes the general overview and motivation of the dissertation and gives a broad background of the computational methods that have been employed in this

Electron-beam generated porous dextran gels: experimental and quantum chemical studies.

PubMed

Naumov, Sergej; Knolle, Wolfgang; Becher, Jana; Schnabelrauch, Matthias; Reichelt, Senta

2014-06-01

The aim of this work was to investigate the reaction mechanism of electron-beam generated macroporous dextran cryogels by quantum chemical calculation and electron paramagnetic resonance measurements. Electron-beam radiation was used to initiate the cross-linking reaction of methacrylated dextran in semifrozen aqueous solutions. The pore morphology of the resulting cryogels was visualized by scanning electron microscopy. Quantum chemical calculations and electron paramagnetic resonance studies provided information on the most probable reaction pathway and the chain growth radicals. The most probable reaction pathway was a ring opening reaction and the addition of a C-atom to the double-bond of the methacrylated dextran molecule. First detailed quantum chemical calculation on the reaction mechanism of electron-beam initiated cross-linking reaction of methacrylated dextran are presented.

Quantum chemical investigation of levofloxacin-boron complexes: A computational approach

NASA Astrophysics Data System (ADS)

Sayin, Koray; Karakaş, Duran

2018-04-01

Quantum chemical calculations are performed over some boron complexes with levofloxacin. Boron complex with fluorine atoms are optimized at three different methods (HF, B3LYP and M062X) with 6-31 + G(d) basis set. The best level is determined as M062X/6-31 + G(d) by comparison of experimental and calculated results of complex (1). The other complexes are optimized by using the best level. Structural properties, IR and NMR spectrum are examined in detail. Biological activities of mentioned complexes are investigated by some quantum chemical descriptors and molecular docking analyses. As a result, biological activities of complex (2) and (4) are close to each other and higher than those of other complexes. Additionally, NLO properties of mentioned complexes are investigated by some quantum chemical parameters. It is found that complex (3) is the best candidate for NLO applications.

Ab initio Quantum Chemical and Experimental Reaction Kinetics Studies in the Combustion of Bipropellants

DTIC Science & Technology

2017-03-24

NUMBER (Include area code) 24 March 2017 Briefing Charts 01 March 2017 - 31 March 2017 Ab initio Quantum Chemical and Experimental Reaction Kinetics...Laboratory AFRL/RQRS 1 Ara Road Edwards AFB, CA 93524 *Email: ghanshyam.vaghjiani@us.af.mil Ab initio Quantum Chemical and Experimental Reaction ...Clearance 17161 Zador et al., Prog. Energ. Combust. Sci., 37 371 (2011) Why Quantum Chemical Reaction Kinetics Studies? DISTRIBUTION A: Approved for

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

DOE PAGES

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

2016-10-21

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

Quantum chemical approach to estimating the thermodynamics of metabolic reactions.

PubMed

Jinich, Adrian; Rappoport, Dmitrij; Dunn, Ian; Sanchez-Lengeling, Benjamin; Olivares-Amaya, Roberto; Noor, Elad; Even, Arren Bar; Aspuru-Guzik, Alán

2014-11-12

Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism.

Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions

PubMed Central

Jinich, Adrian; Rappoport, Dmitrij; Dunn, Ian; Sanchez-Lengeling, Benjamin; Olivares-Amaya, Roberto; Noor, Elad; Even, Arren Bar; Aspuru-Guzik, Alán

2014-01-01

Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions. The errors in standard Gibbs reaction energy estimates are correlated with the charges of the participating molecules. The quantum chemical approach is amenable to systematic improvements and holds potential for providing thermodynamic data for all of metabolism. PMID:25387603

Anion Solvation in Carbonate-Based Electrolytes

DOE PAGES

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

2015-11-16

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

Fluorescent probe studies of polarity and solvation within room temperature ionic liquids: a review.

PubMed

Pandey, Shubha; Baker, Sheila N; Pandey, Siddharth; Baker, Gary A

2012-09-01

Ionic liquids display an array of useful and sometimes unconventional, solvent features and have attracted considerable interest in the field of green chemistry for the potential they hold to significantly reduce environmental emissions. Some of these points have a bearing on the chemical reactivity of these systems and have also generated interest in the physical and theoretical aspects of solvation in ionic liquids. This review presents an introduction to the field of ionic liquids, followed by discussion of investigations into the solvation properties of neat ionic liquids or mixed systems including ionic liquids as a major or minor component. The ionic liquid based multicomponent systems discussed are composed of other solvents, other ionic liquids, carbon dioxide, surfactants or surfactant solutions. Although we clearly focus on fluorescence spectroscopy as a tool to illuminate ionic liquid systems, the issues discussed herein are of general relevance to discussions of polarity and solvent effects in ionic liquids. Transient solvation measurements carried out by means of time-resolved fluorescence measurements are particularly powerful for their ability to parameterize the kinetics of the solvation process in ionic liquids and are discussed as well.

Biomolecular electrostatics and solvation: a computational perspective

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

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

2012-11-01

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

Biomolecular electrostatics and solvation: a computational perspective

PubMed Central

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

2012-01-01

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

Biomolecular electrostatics and solvation: a computational perspective.

PubMed

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

2012-11-01

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

Simple and exact approach to the electronic polarization effect on the solvation free energy: formulation for quantum-mechanical/molecular-mechanical system and its applications to aqueous solutions.

PubMed

Takahashi, Hideaki; Omi, Atsushi; Morita, Akihiro; Matubayasi, Nobuyuki

2012-06-07

We present a simple and exact numerical approach to compute the free energy contribution δμ in solvation due to the electron density polarization and fluctuation of a quantum-mechanical solute in the quantum-mechanical/molecular-mechanical (QM/MM) simulation combined with the theory of the energy representation (QM/MM-ER). Since the electron density fluctuation is responsible for the many-body QM-MM interactions, the standard version of the energy representation method cannot be applied directly. Instead of decomposing the QM-MM polarization energy into the pairwise additive and non-additive contributions, we take sum of the polarization energies in the QM-MM interaction and adopt it as a new energy coordinate for the method of energy representation. Then, it is demonstrated that the free energy δμ can be exactly formulated in terms of the energy distribution functions for the solution and reference systems with respect to this energy coordinate. The benchmark tests were performed to examine the numerical efficiency of the method with respect to the changes in the individual properties of the solvent and the solute. Explicitly, we computed the solvation free energy of a QM water molecule in ambient and supercritical water, and also the free-energy change associated with the isomerization reaction of glycine from neutral to zwitterionic structure in aqueous solution. In all the systems examined, it was demonstrated that the computed free energy δμ agrees with the experimental value, irrespective of the choice of the reference electron density of the QM solute. The present method was also applied to a prototype reaction of adenosine 5'-triphosphate hydrolysis where the effect of the electron density fluctuation is substantial due to the excess charge. It was demonstrated that the experimental free energy of the reaction has been accurately reproduced with the present approach.

Kamlet-Taft solvent parameters, NMR spectroscopic analysis and thermoelectrochemistry of lithium-glyme solvate ionic liquids and their dilute solutions.

PubMed

Black, Jeffrey J; Dolan, Andrew; Harper, Jason B; Aldous, Leigh

2018-06-06

Solvate ionic liquids are a relatively new class of liquids produced by combining a coordinating solvent with a salt. They have a variety of uses and their suitability for such depends upon the ratio of salt to coordinating solvent. This work investigates the Kamlet-Taft solvent parameters of, NMR chemical shifts of nuclei in, and thermoelectrochemistry of a selected set of solvate ionic liquids produced from glymes (methyl terminated oligomers of ethylene glycol) and lithium bis(trifluoromethylsulfonyl)imide at two different compositions. The aim is to improve the understanding of the interactions occurring in these ionic liquids to help select suitable solvate ionic liquids for future applications.

Effects of nonadditive interactions on ion solvation at the water/vapor interface: a molecular dynamics study.

PubMed

Yagasaki, Takuma; Saito, Shinji; Ohmine, Iwao

2010-12-09

The solvation of halide ions at the water/vapor interface is investigated by using molecular dynamics simulations with nonpolarizable molecular mechanical (MM), polarizable MM, and quantum mechanical (QM)/MM methods. The free energy profile of the ion solvation is decomposed into the energy and the entropic contributions along the ion displacement from inside to the surface of water. It is found that the surface affinity of the ion, relative to the bulk value, is determined by a subtle balance between the energetic destabilization and the entropic stabilization with the ion displacement. The amount of energetic destabilization is found to be reduced when nonadditive interactions are included, as in the polarizable MM and QM/MM models. The structure of water around the ion at the interface is also largely modified when the higher order effects are considered. For example, the induced dipole effect enhances the solvation structure around the ion at the interface significantly and thus reduces the amount of entropic stabilization at the interface, relative to in the bulk. It is found that this induced dipole effect causes the slowing in the ion-water hydrogen bond dynamics at the interface. On the other hand, the higher order induced multipole effects in the QM/MM method suppress both the excessive enhancement of the solvation structure and the slowing of the ion-water hydrogen bond dynamics at the interface. The present study demonstrates that not only the induced dipole moment but also the higher order induced multipole moments, which are neglected in standard empirical models, are essential for the correct description of the ion solvation at the water/vapor interface.

Solvation structure of the halides from x-ray absorption spectroscopy

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

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

2016-07-28

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

Intrinsic Optical Activity and Environmental Perturbations: Solvation Effects in Chiral Building Blocks

NASA Astrophysics Data System (ADS)

Lemler, Paul M.; Vaccaro, Patrick

2016-06-01

The non-resonant interaction of electromagnetic radiation with an isotropic ensemble of chiral molecules, which causes the incident state of linear polarization to undergo a signed rotation, long has served as a metric for gauging the enantiomeric purity of asymmetric syntheses. While the underlying phenomenon of circular birefringence (CB) typically is probed in the condensed phase, recent advances in ultrasensitive circular-differential detection schemes, as exemplified by the techniques of Cavity Ring-Down Polarimetry (CRDP), have permitted the first quantitative analyses of such processes to be performed in rarefied media. Efforts to extend vapor-phase investigations of CB to new families of chiral substrates will be discussed, with particular emphasis directed towards the elucidation of intrinsic (e.g., solvent-free) properties and their mediation by environmental perturbations (e.g., solvation). Specific species targeted by this work will include the stereoselective building blocks phenylpropylene oxide and α-methylbenzyl amine, both of which exhibit pronounced solvent-dependent changes in measured optical activity. The nature of chiroptical response in different environments will be highlighted, with quantum-chemical calculations serving to unravel the structural and electronic provenance of observed behavior.

Role of Solvation Effects in Protein Denaturation: From Thermodynamics to Single Molecules and Back

PubMed Central

England, Jeremy L.; Haran, Gilad

2011-01-01

Protein stability often is studied in vitro through the use of urea and guanidinium chloride, chemical cosolvents that disrupt protein native structure. Much controversy still surrounds the underlying mechanism by which these molecules denature proteins. Here we review current thinking on various aspects of chemical denaturation. We begin by discussing classic models of protein folding and how the effects of denaturants may fit into this picture through their modulation of the collapse, or coil-globule transition, which typically precedes folding. Subsequently, we examine recent molecular dynamics simulations that have shed new light on the possible microscopic origins of the solvation effects brought on by denaturants. It seems likely that both denaturants operate by facilitating solvation of hydrophobic regions of proteins. Finally, we present recent single-molecule fluorescence studies of denatured proteins, the analysis of which corroborates the role of denaturants in shifting the equilibrium of the coil-globule transition. PMID:21219136

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

PubMed

Omelyan, Igor; Kovalenko, Andriy

2015-04-14

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

Chemical application of diffusion quantum Monte Carlo

NASA Technical Reports Server (NTRS)

Reynolds, P. J.; Lester, W. A., Jr.

1984-01-01

The diffusion quantum Monte Carlo (QMC) method gives a stochastic solution to the Schroedinger equation. This approach is receiving increasing attention in chemical applications as a result of its high accuracy. However, reducing statistical uncertainty remains a priority because chemical effects are often obtained as small differences of large numbers. As an example, the single-triplet splitting of the energy of the methylene molecule CH sub 2 is given. The QMC algorithm was implemented on the CYBER 205, first as a direct transcription of the algorithm running on the VAX 11/780, and second by explicitly writing vector code for all loops longer than a crossover length C. The speed of the codes relative to one another as a function of C, and relative to the VAX, are discussed. The computational time dependence obtained versus the number of basis functions is discussed and this is compared with that obtained from traditional quantum chemistry codes and that obtained from traditional computer architectures.

Water Lone Pair Delocalization in Classical and Quantum Descriptions of the Hydration of Model Ions

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

Remsing, Richard C.; Duignan, Timothy T.; Baer, Marcel D.

Understanding the nature of ionic hydration at a fundamental level has eluded scientists despite intense interest for nearly a century. In particular, the microscopic origins of the asymmetry of ion solvation thermodynamics with respect to the sign of the ionic charge remains a mystery. Here, we determine the response of accurate quantum mechanical water models to strong nanoscale solvation forces arising from excluded volumes and ionic electrostatic fields. This is compared to the predictions of two important limiting classes of classical models of water with fixed point changes, differing in their treatment of "lone-pair" electrons. Using the quantum water modelmore » as our standard of accuracy, we find that a single fixed classical treatment of lone pair electrons cannot accurately describe solvation of both apolar and cationic solutes, underlining the need for a more flexible description of local electronic effects in solvation processes. However, we explicitly show that all water models studied respond to weak long-ranged electrostatic perturbations in a manner that follows macroscopic dielectric continuum models, as would be expected. We emphasize the importance of these findings in the context of realistic ion models, using density functional theory and empirical models, and discuss the implications of our results for quantitatively accurate reduced descriptions of solvation in dielectric media.« less

Solvated Electrons in Organic Chemistry Laboratory

ERIC Educational Resources Information Center

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

2010-01-01

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

Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models.

PubMed

Martínez-Fernández, L; Pepino, A J; Segarra-Martí, J; Banyasz, A; Garavelli, M; Improta, R

2016-09-13

The optical spectra of 5-methylcytidine in three different solvents (tetrahydrofuran, acetonitrile, and water) is measured, showing that both the absorption and the emission maximum in water are significantly blue-shifted (0.08 eV). The absorption spectra are simulated based on CAM-B3LYP/TD-DFT calculations but including solvent effects with three different approaches: (i) a hybrid implicit/explicit full quantum mechanical approach, (ii) a mixed QM/MM static approach, and (iii) a QM/MM method exploiting the structures issuing from molecular dynamics classical simulations. Ab-initio Molecular dynamics simulations based on CAM-B3LYP functionals have also been performed. The adopted approaches all reproduce the main features of the experimental spectra, giving insights on the chemical-physical effects responsible for the solvent shifts in the spectra of 5-methylcytidine and providing the basis for discussing advantages and limitations of the adopted solvation models.

Electron solvation and localization at interfaces

NASA Astrophysics Data System (ADS)

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

2003-12-01

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

Chemical accuracy from quantum Monte Carlo for the benzene dimer.

PubMed

Azadi, Sam; Cohen, R E

2015-09-14

We report an accurate study of interactions between benzene molecules using variational quantum Monte Carlo (VMC) and diffusion quantum Monte Carlo (DMC) methods. We compare these results with density functional theory using different van der Waals functionals. In our quantum Monte Carlo (QMC) calculations, we use accurate correlated trial wave functions including three-body Jastrow factors and backflow transformations. We consider two benzene molecules in the parallel displaced geometry, and find that by highly optimizing the wave function and introducing more dynamical correlation into the wave function, we compute the weak chemical binding energy between aromatic rings accurately. We find optimal VMC and DMC binding energies of -2.3(4) and -2.7(3) kcal/mol, respectively. The best estimate of the coupled-cluster theory through perturbative triplets/complete basis set limit is -2.65(2) kcal/mol [Miliordos et al., J. Phys. Chem. A 118, 7568 (2014)]. Our results indicate that QMC methods give chemical accuracy for weakly bound van der Waals molecular interactions, comparable to results from the best quantum chemistry methods.

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.

Quantum mechanical/molecular mechanical/continuum style solvation model: linear response theory, variational treatment, and nuclear gradients.

PubMed

Li, Hui

2009-11-14

Linear response and variational treatment are formulated for Hartree-Fock (HF) and Kohn-Sham density functional theory (DFT) methods and combined discrete-continuum solvation models that incorporate self-consistently induced dipoles and charges. Due to the variational treatment, analytic nuclear gradients can be evaluated efficiently for these discrete and continuum solvation models. The forces and torques on the induced point dipoles and point charges can be evaluated using simple electrostatic formulas as for permanent point dipoles and point charges, in accordance with the electrostatic nature of these methods. Implementation and tests using the effective fragment potential (EFP, a polarizable force field) method and the conductorlike polarizable continuum model (CPCM) show that the nuclear gradients are as accurate as those in the gas phase HF and DFT methods. Using B3LYP/EFP/CPCM and time-dependent-B3LYP/EFP/CPCM methods, acetone S(0)-->S(1) excitation in aqueous solution is studied. The results are close to those from full B3LYP/CPCM calculations.

Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model.

PubMed

Muddana, Hari S; Gilson, Michael K

2012-06-12

The prediction of protein-ligand binding affinities is of central interest in computer-aided drug discovery, but it is still difficult to achieve a high degree of accuracy. Recent studies suggesting that available force fields may be a key source of error motivate the present study, which reports the first mining minima (M2) binding affinity calculations based on a quantum mechanical energy model, rather than an empirical force field. We apply a semi-empirical quantum-mechanical energy function, PM6-DH+, coupled with the COSMO solvation model, to 29 host-guest systems with a wide range of measured binding affinities. After correction for a systematic error, which appears to derive from the treatment of polar solvation, the computed absolute binding affinities agree well with experimental measurements, with a mean error 1.6 kcal/mol and a correlation coefficient of 0.91. These calculations also delineate the contributions of various energy components, including solute energy, configurational entropy, and solvation free energy, to the binding free energies of these host-guest complexes. Comparison with our previous calculations, which used empirical force fields, point to significant differences in both the energetic and entropic components of the binding free energy. The present study demonstrates successful combination of a quantum mechanical Hamiltonian with the M2 affinity method.

Sparingly Solvating Electrolytes for High Energy Density Lithium-Sulfur Batteries

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

Cheng, Lei; Curtiss, Larry A.; Zavadil, Kevin R.

2016-07-11

Moving to lighter and less expensive battery chemistries compared to lithium-ion requires the control of energy storage mechanisms based on chemical transformations rather than intercalation. Lithium sulfur (Li/S) has tremendous theoretical specific energy, but contemporary approaches to control this solution-mediated, precipitation-dissolution chemistry requires using large excesses of electrolyte to fully solubilize the polysulfide intermediate. Achieving reversible electrochemistry under lean electrolyte operation is the only path for Li/S to move beyond niche applications to potentially transformational performance. An emerging topic for Li/S research is the use of sparingly solvating electrolytes and the creation of design rules for discovering new electrolyte systemsmore » that fundamentally decouple electrolyte volume from reaction mechanism. This perspective presents an outlook for sparingly solvating electrolytes as the key path forward for longer-lived, high-energy density Li/S batteries including an overview of this promising new concept and some strategies for accomplishing it.« less

Sparingly solvating electrolytes for high energy density Lithium–sulfur batteries

DOE PAGES

Cheng, Lei; Curtiss, Larry A.; Zavadil, Kevin R.; ...

2016-07-11

Moving to lighter and less expensive battery chemistries compared to lithium-ion requires the control of energy storage mechanisms based on chemical transformations rather than intercalation. Lithium sulfur (Li/S) has tremendous theoretical specific energy, but contemporary approaches to control this solution-mediated, precipitation-dissolution chemistry requires using large excesses of electrolyte to fully solubilize the polysulfide intermediate. Achieving reversible electrochemistry under lean electrolyte operation is the only path for Li/S to move beyond niche applications to potentially transformational performance. An emerging topic for Li/S research is the use of sparingly solvating electrolytes and the creation of design rules for discovering new electrolyte systemsmore » that fundamentally decouple electrolyte volume from reaction mechanism. Furthermore, this perspective presents an outlook for sparingly solvating electrolytes as the key path forward for longer-lived, high-energy density Li/S batteries including an overview of this promising new concept and some strategies for accomplishing it.« less

Relationship between Solvation Thermodynamics from IST and DFT Perspectives.

PubMed

Levy, Ronald M; Cui, Di; Zhang, Bin W; Matubayasi, Nobuyuki

2017-04-20

Inhomogeneous solvation theory (IST) and classical density functional theory (DFT) each provide a framework for relating distribution functions of solutions to their thermodynamic properties. As reviewed in this work, both IST and DFT can be formulated in a way that use two "end point" simulations, one of the pure solvent and the other of the solution, to determine the solute chemical potential and other thermodynamic properties of the solution and of subvolumes in regions local to the solute containing hydrating waters. In contrast to IST, where expressions for the excess energy and entropy of solution are the object of analysis, in the DFT end point formulation of the problem, the solute-solvent potential of mean force (PMF) plays a central role. The indirect part of the PMF corresponds to the lowest order (1-body) truncation of the IST expression. Because the PMF is a free energy function, powerful numerical methods can be used to estimate it. We show that the DFT expressions for the solute excess chemical potential can be written in a form which is local, involving integrals only over regions proximate to the solute. The DFT end point route to estimating solvation free energies provides an alternative path to that of IST for analyzing solvation effects on molecular recognition and conformational changes in solution, which can lead to new insights. In order to illustrate the kind of information that is contained in the solute-solvent PMF, we have carried out simulations of β-cyclodextrin in water. This solute is a well studied "host" molecule to which "guest" molecules bind; host-guest systems serve as models for molecular recognition. We illustrate the range of values the direct and indirect parts of the solute-solvent PMF can have as a water molecule is brought to the interface of β-cyclodextrin from the bulk; we discuss the "competition" between these two terms, and the role it plays in molecular recognition.

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.

Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level.

PubMed

Wang, Meiting; Li, Pengfei; Jia, Xiangyu; Liu, Wei; Shao, Yihan; Hu, Wenxin; Zheng, Jun; Brooks, Bernard R; Mei, Ye

2017-10-23

The partitioning of solute molecules between immiscible solvents with significantly different polarities is of great importance. The polarization between the solute and solvent molecules plays an essential role in determining the solubility of the solute, which makes computational studies utilizing molecular mechanics (MM) rather difficult. In contrast, quantum mechanics (QM) can provide more reliable predictions. In this work, the partition coefficients of the side chain analogs of some amino acids between water and chloroform were computed. The QM solvation free energies were calculated indirectly via a series of MM states using the multistate Bennett acceptance ratio (MBAR) and the MM-to-QM corrections were applied at the two endpoints using thermodynamic perturbation (TP). Previously, it has been shown (Jia et al. J. Chem. Theory Comput. 2016, 12, 499-511) that this method provides the minimal variance in the results without running QM simulations. However, if there is insufficient overlap in phase space between the MM and QM Hamiltonians, this method fails. In this work, we propose, for the first time, a quantity termed the reweighting entropy that serves as a metric for the reliability of the TP calculations. If the reweighting entropy is below a certain threshold (0.65 for the solvation free energy calculations in this work), this MM-to-QM correction should be avoided and two alternative methods can be employed by either introducing a semiempirical state or conducting nonequilibrium simulations. However, the results show that the QM methods are not guaranteed to yield better results than the MM methods. Further improvement of the QM methods are imperative, especially the treatment of the van der Waals and the electrostatic interactions between the QM region and the MM region in the first shell. We also propose a scheme for the calculation of the van der Waals parameters for the solute molecules in nonaqueous solvent, which improves the quality of the

Linear solvation energy relationships for toxicity of selected organic chemicals to Daphnia pulex and Daphnia magna

USGS Publications Warehouse

Passino, Dora R.M.; Hickey, James P.; Frank, Anthony M.

1988-01-01

In the Laurentian Great Lakes, more than 300 contaminants have been identified in fish, other biota, water, and sediment. Current hazard assessment of these chemicals by the National Fisheries Research Center-Great Lakes is based on their toxicity, occurrence in the environment, and source. Although scientists at the Center have tested over 70 chemicals with the crustacean Daphnia pulex, the number of experimental data needed to screen the huge array of chemicals in the Great Lakes exceeds the practical capabilities of conducting bioassays. This limitation can be partly circumvented, however, by using mathematical models based on quantitative structure-activity relationships (QSAR) to provide rapid, inexpensive estimates of toxicity. Many properties of chemicals, including toxicity, bioaccumulation and water solubility are well correlated and can be predicted by equations of the generalized linear solvation energy relationships (LSER). The equation we used to model solute toxicity is Toxicity = constant + mVI/100 + s (π* + dδ) + bβm + aαm where VI = intrinsic (Van der Waals) molar volume; π* = molecular dipolarity/polarizability; δ = polarizability 'correction term'; βm = solute hydrogen bond acceptor basicity; and αm = solute hydrogen bond donor acidity. The subscript m designates solute monomer values for α and β. We applied the LSER model to 48-h acute toxicity data (measured as immobilization) for six classes of chemicals detected in Great Lakes fish. The following regression was obtained for Daphnia pulex (concentration = μM): log EC50 = 4.86 - 4.35 VI/100; N = 38, r2 = 0.867, sd = 0.403 We also used the LSER modeling approach to analyze to a large published data set of 24-h acute toxicity for Daphnia magna; the following regression resulted, for eight classes of compounds (concentration = mM): log EC50 = 3.88 - 4.52 VI/100 - 1.62 π* + 1.66 βm - 0.916 αm; N = 62, r2 = 0.859, sd = 0.375 In addition we developed computer software that identifies

Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite

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

Jurrus, Elizabeth; Engel, Dave; Star, Keith

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suitemore » of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.« less

Quantum chemical approach for condensed-phase thermochemistry (IV): Solubility of gaseous molecules

NASA Astrophysics Data System (ADS)

Ishikawa, Atsushi; Kamata, Masahiro; Nakai, Hiromi

2016-07-01

The harmonic solvation model (HSM) was applied to the solvation of gaseous molecules and compared to a procedure based on the ideal gas model (IGM). Examination of 25 molecules showed that (i) the accuracy of ΔGsolv was similar for both methods, but the HSM shows advantages for calculating ΔHsolv and TΔSsolv; (ii) TΔSsolv contributes more than ΔHsolv to ΔGsolv in the HSM, i.e. the solvation of gaseous molecules is entropy-driven, which agrees well with experimental understanding (the IGM does not show this); (iii) the temperature dependence of Henry's law coefficient was correctly reproduced with the HSM.

Effect of the Hydrofluoroether Cosolvent Structure in Acetonitrile-Based Solvate Electrolytes on the Li+ Solvation Structure and Li-S Battery Performance.

PubMed

Shin, Minjeong; Wu, Heng-Liang; Narayanan, Badri; See, Kimberly A; Assary, Rajeev S; Zhu, Lingyang; Haasch, Richard T; Zhang, Shuo; Zhang, Zhengcheng; Curtiss, Larry A; Gewirth, Andrew A

2017-11-15

We evaluate hydrofluoroether (HFE) cosolvents with varying degrees of fluorination in the acetonitrile-based solvate electrolyte to determine the effect of the HFE structure on the electrochemical performance of the Li-S battery. Solvates or sparingly solvating electrolytes are an interesting electrolyte choice for the Li-S battery due to their low polysulfide solubility. The solvate electrolyte with a stoichiometric ratio of LiTFSI salt in acetonitrile, (MeCN) 2 -LiTFSI, exhibits limited polysulfide solubility due to the high concentration of LiTFSI. We demonstrate that the addition of highly fluorinated HFEs to the solvate yields better capacity retention compared to that of less fluorinated HFE cosolvents. Raman and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that HFEs exhibiting a higher degree of fluorination coordinate to Li + at the expense of MeCN coordination, resulting in higher free MeCN content in solution. However, the polysulfide solubility remains low, and no crossover of polysulfides from the S cathode to the Li anode is observed.

Effect of the Hydrofluoroether Cosolvent Structure in Acetonitrile-Based Solvate Electrolytes on the Li+ Solvation Structure and Li-S Battery Performance.

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

Shin, Minjeong; Wu, Heng-Liang; Narayanan, Badri

We evaluate hydrofluoroether (HFE) cosolvents with varying degrees of fluorination in the acetonitrile-based solvate electrolyte to determine the effect of the HFE structure on the electrochemical performance of the Li-S battery. Solvates or sparingly solvating electrolytes are an interesting electrolyte choice for the Li-S battery due to their low polysulfide solubility. The solvate electrolyte with a stoichiometric ratio of LiTFSI salt in acetonitrile, (MeCN)(2)-LiTFSI, exhibits limited polysulfide solubility due to the high concentration of LiTFSI. We demonstrate that the addition of highly fluorinated HFEs to the solvate yields better capacity retention compared to that of less fluorinated HFE cosolvents. Ramanmore » and NMR spectroscopy coupled with ab initio molecular dynamics simulations show that HFEs exhibiting a higher degree of fluorination coordinate to Li+ at the expense of MeCN coordination, resulting in higher free MeCN content in solution. However, the polysulfide solubility remains low, and no crossover of polysulfides from the S cathode to the Li anode is observed.« less

Acidity in DMSO from the embedded cluster integral equation quantum solvation model.

PubMed

Heil, Jochen; Tomazic, Daniel; Egbers, Simon; Kast, Stefan M

2014-04-01

The embedded cluster reference interaction site model (EC-RISM) is applied to the prediction of acidity constants of organic molecules in dimethyl sulfoxide (DMSO) solution. EC-RISM is based on a self-consistent treatment of the solute's electronic structure and the solvent's structure by coupling quantum-chemical calculations with three-dimensional (3D) RISM integral equation theory. We compare available DMSO force fields with reference calculations obtained using the polarizable continuum model (PCM). The results are evaluated statistically using two different approaches to eliminating the proton contribution: a linear regression model and an analysis of pK(a) shifts for compound pairs. Suitable levels of theory for the integral equation methodology are benchmarked. The results are further analyzed and illustrated by visualizing solvent site distribution functions and comparing them with an aqueous environment.

Multiply Reduced Oligofluorenes: Their Nature and Pairing with THF-Solvated Sodium Ions

DOE PAGES

Wu, Qin; Zaikowski, Lori; Kaur, Parmeet; ...

2016-07-01

Conjugated oligofluorenes are chemically reduced up to five charges in tetrahydrofuran solvent and confirmed with clear spectroscopic evidence. Stimulated by these experimental results, we have conducted a comprehensive computational study of the electronic structure and the solvation structure of representative oligofluorene anions with a focus on the pairing between sodium ions and these multianions. In addition, using density functional theory (DFT) methods and a solvation model of both explicit solvent molecules and implicit polarizable continuum, we first elucidate the structure of tightly solvated free sodium ions, and then explore the pairing of sodium ions either in contact with reduced oligofluorenesmore » or as solvent-separated ion pairs. Computed time-dependent-DFT absorption spectra are compared with experiments to assign the dominant ion pairing structure for each multianion. Computed ion pair binding energies further support our assignment. Lastly, the availability of different length and reducing level of oligofluorenes enables us to investigate the effects of total charge and charge density on the binding with sodium ions, and our results suggest both factors play important roles in ion pairing for small molecules. However, as the oligofluorene size grows, its charge density determines the binding strength with the sodium ion.« less

Electron Solvation in Two Dimensions

NASA Astrophysics Data System (ADS)

Miller, A. D.; Bezel, I.; Gaffney, K. J.; Garrett-Roe, S.; Liu, S. H.; Szymanski, P.; Harris, C. B.

2002-08-01

Ultrafast two-photon photoemission has been used to study electron solvation at two-dimensional metal/polar-adsorbate interfaces. The molecular motion that causes the excess electron solvation is manifested as a dynamic shift in the electronic energy. Although the initially excited electron is delocalized in the plane of the interface, interactions with the adsorbate can lead to its localization. A method for determining the spatial extent of the localized electron in the plane of the interface has been developed. This spatial extent was measured to be on the order of a single adsorbate molecule.

The solvated electron battery

NASA Astrophysics Data System (ADS)

Bennett, J.; Harney, D.; Mitchell, T.

A novel ambient temperture secondary battery using sodium and sulfur dissolved in liquid ammonia is being developed at ELTECH Systems corpooration. The key element of the system is the solvated electron electrode, a metallic liquid which is formed by ammonia and a number of alkali and alkaline earth metals. These solutions are excellent ionic and electronic conductors and have been shown to contain 'free' solvated electrons as the anionic species in solution. Sulfur was chosen as the cathodic reactant because of its high solubility in ammonia, and also because of the high solubiity and good conductivity of the polysulfide reaction products. Development efforts have thus far concentrated on basic electrochemical measurements and establishment of system feasibility.

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

PubMed

Frach, Roland; Kast, Stefan M

2014-12-11

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

Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport.

PubMed

Komarov, Pavel V; Khalatur, Pavel G; Khokhlov, Alexei R

2013-01-01

Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic) and minority (hydrophilic) subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25-50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping) mechanism as a significant contributor to the proton conductivity.

Interaction of silicene with amino acid analogues—from physical to chemical adsorption in gas and solvated phases

NASA Astrophysics Data System (ADS)

Jagvaral, Yesukhei; He, Haiying; Pandey, Ravindra

2018-01-01

Silicene is an emerging 2D material, and an understanding of its interaction with amino acids, the basic building blocks of protein, is of fundamental importance. In this paper, we investigate the nature of adsorption of amino-acid analogues on silicene employing density functional theory and an implicit solvation model. Amino acid analogues are defined as CH3-R molecules, where R is the functional group of the amino acid side chain. The calculated results find three distinct groups within the amino-acid analogues considered: (i) group I, which includes MeCH3 and MeSH, interacts with silicene via the van der Waals dispersive terms leading to physisorbed configurations; (ii) group II strongly interacts with silicene forming Si-O/N chemical bonds in the chemisorbed configurations; and (iii) group III, which consists of the phenyl group, interacts with silicene via π-π interactions leading to physisorbed configurations. The results show that the lateral chains of the amino acids intrinsically determine the interactions between protein and silicene at the interface under the given physiological conditions.

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

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

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

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

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

PubMed

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

2016-12-21

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

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

DOE PAGES

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

2016-11-16

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

Anion photoelectron spectroscopy of acid-base systems, solvated molecules and MALDI matrix molecules

NASA Astrophysics Data System (ADS)

Eustis, Soren Newman

Gas phase, mass-selected, anion photoelectron spectroscopic studies were performed on a variety of molecular systems. These studies can be grouped into three main themes: acid-base interactions, solvation, and ions of analytical interest. Acid-base interactions represent some of the most fundamental processes in chemistry. The study of these processes elucidates elementary principles such as inner and outer sphere complexes, hard and soft ions, and salt formation---to name a few. Apart from their appeal from a pedagogical standpoint, the ubiquity of chemical reactions which involve acids, bases or the resulting salts makes the study of their fundamental interactions both necessary and fruitful. With this in mind, the neutral and anionic series (NH3···HX) (X= F, Cl, Br, I) were examined experimentally and theoretically. The relatively small size of these systems, combined with the advances in computational methods, allowed our experimental results to be compared with very high level ab initio theoretical results. The synergy between theory and experiment yielded an understanding of the nature of the complexes that could not be achieved with either method in isolation. The second theme present in this body or work is molecular solvation. Solvation is a phenomenon which is present in biology, chemistry and physics. Many biological molecules do not become 'active' until they are solvated by water. Thus, the study of biologically relevant species solvated by water is one step in a bottom up approach to studying the biochemical interactions in living organisms. Furthermore, the hydration of acidic molecules in the atmosphere is what drives the formation of 'free' protons or hydronium ions which are the key players in acid driven chemistry. Here are presented two unique solvation studies, Adenine(H2O)-n and C6F6(H2O)-n, these systems are very distinct, but show somewhat similar responses to hydration. The last theme presented in this work is the electronic properties

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

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

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

2015-09-16

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

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

PubMed

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

2015-06-07

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

An efficient matrix product operator representation of the quantum chemical Hamiltonian

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

Keller, Sebastian, E-mail: sebastian.keller@phys.chem.ethz.ch; Reiher, Markus, E-mail: markus.reiher@phys.chem.ethz.ch; Dolfi, Michele, E-mail: dolfim@phys.ethz.ch

We describe how to efficiently construct the quantum chemical Hamiltonian operator in matrix product form. We present its implementation as a density matrix renormalization group (DMRG) algorithm for quantum chemical applications. Existing implementations of DMRG for quantum chemistry are based on the traditional formulation of the method, which was developed from the point of view of Hilbert space decimation and attained higher performance compared to straightforward implementations of matrix product based DMRG. The latter variationally optimizes a class of ansatz states known as matrix product states, where operators are correspondingly represented as matrix product operators (MPOs). The MPO construction schememore » presented here eliminates the previous performance disadvantages while retaining the additional flexibility provided by a matrix product approach, for example, the specification of expectation values becomes an input parameter. In this way, MPOs for different symmetries — abelian and non-abelian — and different relativistic and non-relativistic models may be solved by an otherwise unmodified program.« less

Intrinsic Atomic Orbitals: An Unbiased Bridge between Quantum Theory and Chemical Concepts.

PubMed

Knizia, Gerald

2013-11-12

Modern quantum chemistry can make quantitative predictions on an immense array of chemical systems. However, the interpretation of those predictions is often complicated by the complex wave function expansions used. Here we show that an exceptionally simple algebraic construction allows for defining atomic core and valence orbitals, polarized by the molecular environment, which can exactly represent self-consistent field wave functions. This construction provides an unbiased and direct connection between quantum chemistry and empirical chemical concepts, and can be used, for example, to calculate the nature of bonding in molecules, in chemical terms, from first principles. In particular, we find consistency with electronegativities (χ), C 1s core-level shifts, resonance substituent parameters (σR), Lewis structures, and oxidation states of transition-metal complexes.

A quantum informational approach for dissecting chemical reactions

NASA Astrophysics Data System (ADS)

Duperrouzel, Corinne; Tecmer, Paweł; Boguslawski, Katharina; Barcza, Gergely; Legeza, Örs; Ayers, Paul W.

2015-02-01

We present a conceptionally different approach to dissect bond-formation processes in metal-driven catalysis using concepts from quantum information theory. Our method uses the entanglement and correlation among molecular orbitals to analyze changes in electronic structure that accompany chemical processes. As a proof-of-principle example, the evolution of nickel-ethene bond-formation is dissected, which allows us to monitor the interplay of back-bonding and π-donation along the reaction coordinate. Furthermore, the reaction pathway of nickel-ethene complexation is analyzed using quantum chemistry methods, revealing the presence of a transition state. Our study supports the crucial role of metal-to-ligand back-donation in the bond-forming process of nickel-ethene.

Quantum chemical parameters in QSAR: what do I use when?

USGS Publications Warehouse

Hickey, James P.; Ostrander, Gary K.

1996-01-01

This chapter provides a brief overview of the numerous quantum chemical parameters that have been/are currently being used in quantitative structure activity relationships (QSAR), along with a representative bibliography. The parameters will be grouped according to their mechanistic interpretations, and representative biological and physical chemical applications will be mentioned. Parmater computation methods and the appropriate software are highlighted, as are sources for software.

Spectroscopic and computational studies of ionic clusters as models of solvation and atmospheric reactions

NASA Astrophysics Data System (ADS)

Kuwata, Keith T.

Ionic clusters are useful as model systems for the study of fundamental processes in solution and in the atmosphere. Their structure and reactivity can be studied in detail using vibrational predissociation spectroscopy, in conjunction with high level ab initio calculations. This thesis presents the applications of infrared spectroscopy and computation to a variety of gas-phase cluster systems. A crucial component of the process of stratospheric ozone depletion is the action of polar stratospheric clouds (PSCs) to convert the reservoir species HCl and chlorine nitrate (ClONO2) to photochemically labile compounds. Quantum chemistry was used to explore one possible mechanism by which this activation is effected: Cl- + ClONO2 /to Cl2 + NO3- eqno(1)Correlated ab initio calculations predicted that the direct reaction of chloride ion with ClONO2 is facile, which was confirmed in an experimental kinetics study. In the reaction a weakly bound intermediate Cl2-NO3- is formed, with ~70% of the charge localized on the nitrate moiety. This enables the Cl2-NO3- cluster to be well solvated even in bulk solution, allowing (1) to be facile on PSCs. Quantum chemistry was also applied to the hydration of nitrosonium ion (NO+), an important process in the ionosphere. The calculations, in conjunction with an infrared spectroscopy experiment, revealed the structure of the gas-phase clusters NO+(H2O)n. The large degree of covalent interaction between NO+ and the lone pairs of the H2O ligands is contrasted with the weak electrostatic bonding between iodide ion and H2O. Finally, the competition between ion solvation and solvent self-association is explored for the gas-phase clusters Cl/-(H2O)n and Cl-(NH3)n. For the case of water, vibrational predissociation spectroscopy reveals less hydrogen bonding among H2O ligands than predicted by ab initio calculations. Nevertheless, for n /ge 5, cluster structure is dominated by water-water interactions, with Cl- only partially solvated by the

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.

Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport

PubMed Central

Komarov, Pavel V; Khokhlov, Alexei R

2013-01-01

Summary Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic) and minority (hydrophilic) subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25–50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping) mechanism as a significant contributor to the proton conductivity. PMID:24205452

Ab initio joint density-functional theory of solvated electrodes, with model and explicit solvation

NASA Astrophysics Data System (ADS)

Arias, Tomas

2015-03-01

First-principles guided design of improved electrochemical systems has the potential for great societal impact by making non-fossil-fuel systems economically viable. Potential applications include improvements in fuel-cells, solar-fuel systems (``artificial photosynthesis''), supercapacitors and batteries. Economical fuel-cell systems would enable zero-carbon footprint transportation, solar-fuel systems would directly convert sunlight and water into hydrogen fuel for such fuel-cell vehicles, supercapacitors would enable nearly full recovery of energy lost during vehicle braking thus extending electric vehicle range and acceptance, and economical high-capacity batteries would be central to mitigating the indeterminacy of renewable resources such as wind and solar. Central to the operation of all of the above electrochemical systems is the electrode-electrolyte interface, whose underlying physics is quite rich, yet remains remarkably poorly understood. The essential underlying technical challenge to the first principles studies which could explore this physics is the need to properly represent simultaneously both the interaction between electron-transfer events at the electrode, which demand a quantum mechanical description, and multiscale phenomena in the liquid environment such as the electrochemical double layer (ECDL) and its associated shielding, which demand a statistical description. A direct ab initio approach to this challenge would, in principle, require statistical sampling and thousands of repetitions of already computationally demanding quantum mechanical calculations. This talk will begin with a brief review of a recent advance, joint density-functional theory (JDFT), which allows for a fully rigorous and, in principle, exact representation of the thermodynamic equilibrium between a system described at the quantum-mechanical level and a liquid environment, but without the need for costly sampling. We then shall demonstrate how this approach applies in

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.

Multibody correlations in the hydrophobic solvation of glycine peptides

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

Harris, Robert C.; Drake, Justin A.; Pettitt, B. Montgomery, E-mail: mpettitt@utmb.edu

2014-12-14

Protein collapse during folding is often assumed to be driven by a hydrophobic solvation energy (ΔG{sub vdw}) that scales linearly with solvent-accessible surface area (A). In a previous study, we argued that ΔG{sub vdw}, as well as its attractive (ΔG{sub att}) and repulsive (ΔG{sub rep}) components, was not simply a linear function of A. We found that the surface tensions, γ{sub rep}, γ{sub att}, and γ{sub vdw}, gotten from ΔG{sub rep}, ΔG{sub att}, and ΔG{sub vdw} against A for four configurations of deca-alanine differed from those obtained for a set of alkanes. In the present study, we extend our analysismore » to fifty decaglycine structures and atomic decompositions. We find that different configurations of decaglycine generate different estimates of γ{sub rep}. Additionally, we considered the reconstruction of the solvation free energy from scaling the free energy of solvation of each atom type, free in solution. The free energy of the isolated atoms, scaled by the inverse surface area the atom would expose in the molecule does not reproduce the γ{sub rep} for the intact decaglycines. Finally, γ{sub att} for the decaglycine conformations is much larger in magnitude than those for deca-alanine or the alkanes, leading to large negative values of γ{sub vdw} (−74 and −56 cal/mol/Å{sup 2} for CHARMM27 and AMBER ff12sb force fields, respectively). These findings imply that ΔG{sub vdw} favors extended rather than compact structures for decaglycine. We find that ΔG{sub rep} and ΔG{sub vdw} have complicated dependencies on multibody correlations between solute atoms, on the geometry of the molecular surface, and on the chemical identities of the atoms.« less

Thin Metallic Films From Solvated Metal Atoms

NASA Astrophysics Data System (ADS)

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

1988-02-01

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

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

PubMed

Matyushov, Dmitry V

2009-06-21

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

Solvated dissipative electro-elastic network model of hydrated proteins

NASA Astrophysics Data System (ADS)

Martin, Daniel

2013-03-01

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

Solvated dissipative electro-elastic network model of hydrated proteins

NASA Astrophysics Data System (ADS)

Martin, Daniel R.; Matyushov, Dmitry V.

2012-10-01

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

Advanced dielectric continuum model of preferential solvation

NASA Astrophysics Data System (ADS)

Basilevsky, Mikhail; Odinokov, Alexey; Nikitina, Ekaterina; Grigoriev, Fedor; Petrov, Nikolai; Alfimov, Mikhail

2009-01-01

A continuum model for solvation effects in binary solvent mixtures is formulated in terms of the density functional theory. The presence of two variables, namely, the dimensionless solvent composition y and the dimensionless total solvent density z, is an essential feature of binary systems. Their coupling, hidden in the structure of the local dielectric permittivity function, is postulated at the phenomenological level. Local equilibrium conditions are derived by a variation in the free energy functional expressed in terms of the composition and density variables. They appear as a pair of coupled equations defining y and z as spatial distributions. We consider the simplest spherically symmetric case of the Born-type ion immersed in the benzene/dimethylsulfoxide (DMSO) solvent mixture. The profiles of y(R ) and z(R ) along the radius R, which measures the distance from the ion center, are found in molecular dynamics (MD) simulations. It is shown that for a given solute ion z(R ) does not depend significantly on the composition variable y. A simplified solution is then obtained by inserting z(R ), found in the MD simulation for the pure DMSO, in the single equation which defines y(R ). In this way composition dependences of the main solvation effects are investigated. The local density augmentation appears as a peak of z(R ) at the ion boundary. It is responsible for the fine solvation effects missing when the ordinary solvation theories, in which z =1, are applied. These phenomena, studied for negative ions, reproduce consistently the simulation results. For positive ions the simulation shows that z ≫1 (z =5-6 at the maximum of the z peak), which means that an extremely dense solvation shell is formed. In such a situation the continuum description fails to be valid within a consistent parametrization.

The Generalized Born solvation model: What is it?

NASA Astrophysics Data System (ADS)

Onufriev, Alexey

2004-03-01

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

Exploring Strong Interactions in Proteins with Quantum Chemistry and Examples of Their Applications in Drug Design.

PubMed

Xie, Neng-Zhong; Du, Qi-Shi; Li, Jian-Xiu; Huang, Ri-Bo

2015-01-01

Three strong interactions between amino acid side chains (salt bridge, cation-π, and amide bridge) are studied that are stronger than (or comparable to) the common hydrogen bond interactions, and play important roles in protein-protein interactions. Quantum chemical methods MP2 and CCSD(T) are used in calculations of interaction energies and structural optimizations. The energies of three types of amino acid side chain interactions in gaseous phase and in aqueous solutions are calculated using high level quantum chemical methods and basis sets. Typical examples of amino acid salt bridge, cation-π, and amide bridge interactions are analyzed, including the inhibitor design targeting neuraminidase (NA) enzyme of influenza A virus, and the ligand binding interactions in the HCV p7 ion channel. The inhibition mechanism of the M2 proton channel in the influenza A virus is analyzed based on strong amino acid interactions. (1) The salt bridge interactions between acidic amino acids (Glu- and Asp-) and alkaline amino acids (Arg+, Lys+ and His+) are the strongest residue-residue interactions. However, this type of interaction may be weakened by solvation effects and broken by lower pH conditions. (2) The cation- interactions between protonated amino acids (Arg+, Lys+ and His+) and aromatic amino acids (Phe, Tyr, Trp and His) are 2.5 to 5-fold stronger than common hydrogen bond interactions and are less affected by the solvation environment. (3) The amide bridge interactions between the two amide-containing amino acids (Asn and Gln) are three times stronger than hydrogen bond interactions, which are less influenced by the pH of the solution. (4) Ten of the twenty natural amino acids are involved in salt bridge, or cation-, or amide bridge interactions that often play important roles in protein-protein, protein-peptide, protein-ligand, and protein-DNA interactions.

Evaluation of DNA Force Fields in Implicit Solvation

PubMed Central

Gaillard, Thomas; Case, David A.

2011-01-01

DNA structural deformations and dynamics are crucial to its interactions in the cell. Theoretical simulations are essential tools to explore the structure, dynamics, and thermodynamics of biomolecules in a systematic way. Molecular mechanics force fields for DNA have benefited from constant improvements during the last decades. Several studies have evaluated and compared available force fields when the solvent is modeled by explicit molecules. On the other hand, few systematic studies have assessed the quality of duplex DNA models when implicit solvation is employed. The interest of an implicit modeling of the solvent consists in the important gain in the simulation performance and conformational sampling speed. In this study, respective influences of the force field and the implicit solvation model choice on DNA simulation quality are evaluated. To this end, extensive implicit solvent duplex DNA simulations are performed, attempting to reach both conformational and sequence diversity convergence. Structural parameters are extracted from simulations and statistically compared to available experimental and explicit solvation simulation data. Our results quantitatively expose the respective strengths and weaknesses of the different DNA force fields and implicit solvation models studied. This work can lead to the suggestion of improvements to current DNA theoretical models. PMID:22043178

Quantum Degeneracy in Atomic Point Contacts Revealed by Chemical Force and Conductance

NASA Astrophysics Data System (ADS)

Sugimoto, Yoshiaki; Ondráček, Martin; Abe, Masayuki; Pou, Pablo; Morita, Seizo; Perez, Ruben; Flores, Fernando; Jelínek, Pavel

2013-09-01

Quantum degeneracy is an important concept in quantum mechanics with large implications to many processes in condensed matter. Here, we show the consequences of electron energy level degeneracy on the conductance and the chemical force between two bodies at the atomic scale. We propose a novel way in which a scanning probe microscope can detect the presence of degenerate states in atomic-sized contacts even at room temperature. The tunneling conductance G and chemical binding force F between two bodies both tend to decay exponentially with distance in a certain distance range, usually maintaining direct proportionality G∝F. However, we show that a square relation G∝F2 arises as a consequence of quantum degeneracy between the interacting frontier states of the scanning tip and a surface atom. We demonstrate this phenomenon on the Si(111)-(7×7) surface reconstruction where the Si adatom possesses a strongly localized dangling-bond state at the Fermi level.

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

DTIC Science & Technology

2017-04-01

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

Excess Electron Localization in Solvated DNA Bases

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

Smyth, Maeve; Kohanoff, Jorge

2011-06-10

We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic electron affinities increase systematically upon solvation, as for optimized gas-phase geometries. Dynamical simulations after vertical attachment indicate that the excess electron, which is initially found delocalized, localizes around the nucleobases within a 15 fs time scale. This transition requires small rearrangements in the geometry of the bases.

Excess electron localization in solvated DNA bases.

PubMed

Smyth, Maeve; Kohanoff, Jorge

2011-06-10

We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic electron affinities increase systematically upon solvation, as for optimized gas-phase geometries. Dynamical simulations after vertical attachment indicate that the excess electron, which is initially found delocalized, localizes around the nucleobases within a 15 fs time scale. This transition requires small rearrangements in the geometry of the bases.

Molecular Dynamics Simulations of Hydration Effects on Solvation, Diffusivity, and Permeability in Chitosan/Chitin Films.

PubMed

McDonnell, Marshall T; Greeley, Duncan A; Kit, Kevin M; Keffer, David J

2016-09-01

The effects of hydration on the solvation, diffusivity, solubility, and permeability of oxygen molecules in sustainable, biodegradable chitosan/chitin food packaging films were studied via molecular dynamics and confined random walk simulations. With increasing hydration, the membrane has a more homogeneous water distribution with the polymer chains being fully solvated. The diffusivity increased by a factor of 4 for oxygen molecules and by an order of magnitude for water with increasing the humidity. To calculate the Henry's constant and solubility of oxygen in the membranes with changing hydration, the excess chemical potential was calculated via free energy perturbation, thermodynamic integration and direct particle deletion methods. The simulations predicted a higher solubility and permeability for the lower humidity, in contradiction to experimental results. All three methods for calculating the solubility were in good agreement. It was found that the Coulombic interactions in the potential caused the oxygen to bind too strongly to the protonated amine group. Insight from this work will help guide molecular modeling of chitosan/chitin membranes, specifically permeability measurements for small solute molecules. Efforts to chemically tailor chitosan/chitin membranes to favor discrete as opposed to continuous aqueous domains could reduce oxygen permeability.

Comparison of the Marcus and Pekar partitions in the context of non-equilibrium, polarizable-continuum solvation models

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

You, Zhi-Qiang; Herbert, John M., E-mail: herbert@chemistry.ohio-state.edu; Mewes, Jan-Michael

2015-11-28

The Marcus and Pekar partitions are common, alternative models to describe the non-equilibrium dielectric polarization response that accompanies instantaneous perturbation of a solute embedded in a dielectric continuum. Examples of such a perturbation include vertical electronic excitation and vertical ionization of a solution-phase molecule. Here, we provide a general derivation of the accompanying polarization response, for a quantum-mechanical solute described within the framework of a polarizable continuum model (PCM) of electrostatic solvation. Although the non-equilibrium free energy is formally equivalent within the two partitions, albeit partitioned differently into “fast” versus “slow” polarization contributions, discretization of the PCM integral equations failsmore » to preserve certain symmetries contained in these equations (except in the case of the conductor-like models or when the solute cavity is spherical), leading to alternative, non-equivalent matrix equations. Unlike the total equilibrium solvation energy, however, which can differ dramatically between different formulations, we demonstrate that the equivalence of the Marcus and Pekar partitions for the non-equilibrium solvation correction is preserved to high accuracy. Differences in vertical excitation and ionization energies are <0.2 eV (and often <0.01 eV), even for systems specifically selected to afford a large polarization response. Numerical results therefore support the interchangeability of the Marcus and Pekar partitions, but also caution against relying too much on the fast PCM charges for interpretive value, as these charges differ greatly between the two partitions, especially in polar solvents.« less

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

Supramolecular Interactions in Secondary Plant Cell Walls: Effect of Lignin Chemical Composition Revealed with the Molecular Theory of Solvation.

PubMed

Silveira, Rodrigo L; Stoyanov, Stanislav R; Gusarov, Sergey; Skaf, Munir S; Kovalenko, Andriy

2015-01-02

Plant biomass recalcitrance, a major obstacle to achieving sustainable production of second generation biofuels, arises mainly from the amorphous cell-wall matrix containing lignin and hemicellulose assembled into a complex supramolecular network that coats the cellulose fibrils. We employed the statistical-mechanical, 3D reference interaction site model with the Kovalenko-Hirata closure approximation (or 3D-RISM-KH molecular theory of solvation) to reveal the supramolecular interactions in this network and provide molecular-level insight into the effective lignin-lignin and lignin-hemicellulose thermodynamic interactions. We found that such interactions are hydrophobic and entropy-driven, and arise from the expelling of water from the mutual interaction surfaces. The molecular origin of these interactions is carbohydrate-π and π-π stacking forces, whose strengths are dependent on the lignin chemical composition. Methoxy substituents in the phenyl groups of lignin promote substantial entropic stabilization of the ligno-hemicellulosic matrix. Our results provide a detailed molecular view of the fundamental interactions within the secondary plant cell walls that lead to recalcitrance.

Elucidation of Mechanisms and Selectivities of Metal-Catalyzed Reactions using Quantum Chemical Methodology.

PubMed

Santoro, Stefano; Kalek, Marcin; Huang, Genping; Himo, Fahmi

2016-05-17

Quantum chemical techniques today are indispensable for the detailed mechanistic understanding of catalytic reactions. The development of modern density functional theory approaches combined with the enormous growth in computer power have made it possible to treat quite large systems at a reasonable level of accuracy. Accordingly, quantum chemistry has been applied extensively to a wide variety of catalytic systems. A huge number of problems have been solved successfully, and vast amounts of chemical insights have been gained. In this Account, we summarize some of our recent work in this field. A number of examples concerned with transition metal-catalyzed reactions are selected, with emphasis on reactions with various kinds of selectivities. The discussed cases are (1) copper-catalyzed C-H bond amidation of indoles, (2) iridium-catalyzed C(sp(3))-H borylation of chlorosilanes, (3) vanadium-catalyzed Meyer-Schuster rearrangement and its combination with aldol- and Mannich-type additions, (4) palladium-catalyzed propargylic substitution with phosphorus nucleophiles, (5) rhodium-catalyzed 1:2 coupling of aldehydes and allenes, and finally (6) copper-catalyzed coupling of nitrones and alkynes to produce β-lactams (Kinugasa reaction). First, the methodology adopted in these studies is presented briefly. The electronic structure method in the great majority of these kinds of mechanistic investigations has for the last two decades been based on density functional theory. In the cases discussed here, mainly the B3LYP functional has been employed in conjunction with Grimme's empirical dispersion correction, which has been shown to improve the calculated energies significantly. The effect of the surrounding solvent is described by implicit solvation techniques, and the thermochemical corrections are included using the rigid-rotor harmonic oscillator approximation. The reviewed examples are chosen to illustrate the usefulness and versatility of the adopted methodology in

SISGR: Linking Ion Solvation and Lithium Battery Electrolyte Properties

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

Trulove, Paul C.; Foley, Matthew P.

2012-09-30

The solvation and phase behavior of the model battery electrolyte salt lithium trifluoromethanesulfonate (LiCF 3SO 3) in commonly used organic solvents; ethylene carbonate (EC), gamma-butyrolactone (GBL), and propylene carbonate (PC) was explored. Data from differential scanning calorimetry (DSC), Raman spectroscopy, and X-ray diffraction were correlated to provide insight into the solvation states present within a sample mixture. Data from DSC analyses allowed the construction of phase diagrams for each solvent system. Raman spectroscopy enabled the determination of specific solvation states present within a solvent-salt mixture, and X-ray diffraction data provided exact information concerning the structure of a solvates that couldmore » be isolated Thermal analysis of the various solvent-salt mixtures revealed the phase behavior of the model electrolytes was strongly dependent on solvent symmetry. The point groups of the solvents were (in order from high to low symmetry): C2V for EC, CS for GBL, and C1 for PC(R). The low symmetry solvents exhibited a crystallinity gap that increased as solvent symmetry decreased; no gap was observed for EC-LiTf, while a crystallinity gap was observed spanning 0.15 to 0.3 mole fraction for GBL-LiTf, and 0.1 to 0.33 mole fraction for PC(R)-LiTf mixtures. Raman analysis demonstrated the dominance of aggregated species in almost all solvent compositions. The AGG and CIP solvates represent the majority of the species in solutions for the more concentrated mixtures, and only in very dilute compositions does the SSIP solvate exist in significant amounts. Thus, the poor charge transport characteristics of CIP and AGG account for the low conductivity and transport properties of LiTf and explain why is a poor choice as a source of Li + ions in a Li-ion battery.« less

Quantum chemical study of methane oxidation species

NASA Technical Reports Server (NTRS)

Jackels, Charles F.

1993-01-01

The research funded by this project has focused on quantum chemical investigations of molecular species thought to be important in the chemistry of the earth's upper and lower atmospheres. The body of this report contains brief discussions of the results of the several phases of this investigation. In many instances these results have been presented at scientific meetings and/or published in refereed journals. Those bibliographic references are given. In addition to the study of specific chemical systems, there were several phases during the course of this investigation where much of the effort went into the development and modification of computer codes necessary to carry out these calculations on the wide range of computer equipment used during this study. This type of code maintenance and development work did not generally result in publications and presentations, but a brief review is given.

Automated chemical kinetic modeling via hybrid reactive molecular dynamics and quantum chemistry simulations.

PubMed

Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai

2018-06-13

An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.

Chemically Triggered Formation of Two-Dimensional Epitaxial Quantum Dot Superlattices.

PubMed

Walravens, Willem; De Roo, Jonathan; Drijvers, Emile; Ten Brinck, Stephanie; Solano, Eduardo; Dendooven, Jolien; Detavernier, Christophe; Infante, Ivan; Hens, Zeger

2016-07-26

Two dimensional superlattices of epitaxially connected quantum dots enable size-quantization effects to be combined with high charge carrier mobilities, an essential prerequisite for highly performing QD devices based on charge transport. Here, we demonstrate that surface active additives known to restore nanocrystal stoichiometry can trigger the formation of epitaxial superlattices of PbSe and PbS quantum dots. More specifically, we show that both chalcogen-adding (sodium sulfide) and lead oleate displacing (amines) additives induce small area epitaxial superlattices of PbSe quantum dots. In the latter case, the amine basicity is a sensitive handle to tune the superlattice symmetry, with strong and weak bases yielding pseudohexagonal or quasi-square lattices, respectively. Through density functional theory calculations and in situ titrations monitored by nuclear magnetic resonance spectroscopy, we link this observation to the concomitantly different coordination enthalpy and ligand displacement potency of the amine. Next to that, an initial ∼10% reduction of the initial ligand density prior to monolayer formation and addition of a mild, lead oleate displacing chemical trigger such as aniline proved key to induce square superlattices with long-range, square micrometer order; an effect that is the more pronounced the larger the quantum dots. Because the approach applies to PbS quantum dots as well, we conclude that it offers a reproducible and rational method for the formation of highly ordered epitaxial quantum dot superlattices.

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

PubMed

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

2016-07-18

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

Quantum Monte Carlo tunneling from quantum chemistry to quantum annealing

NASA Astrophysics Data System (ADS)

Mazzola, Guglielmo; Smelyanskiy, Vadim N.; Troyer, Matthias

2017-10-01

Quantum tunneling is ubiquitous across different fields, from quantum chemical reactions and magnetic materials to quantum simulators and quantum computers. While simulating the real-time quantum dynamics of tunneling is infeasible for high-dimensional systems, quantum tunneling also shows up in quantum Monte Carlo (QMC) simulations, which aim to simulate quantum statistics with resources growing only polynomially with the system size. Here we extend the recent results obtained for quantum spin models [Phys. Rev. Lett. 117, 180402 (2016), 10.1103/PhysRevLett.117.180402], and we study continuous-variable models for proton transfer reactions. We demonstrate that QMC simulations efficiently recover the scaling of ground-state tunneling rates due to the existence of an instanton path, which always connects the reactant state with the product. We discuss the implications of our results in the context of quantum chemical reactions and quantum annealing, where quantum tunneling is expected to be a valuable resource for solving combinatorial optimization problems.

Extrapolating Single Organic Ion Solvation Thermochemistry from Simulated Water Nanodroplets.

PubMed

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

2016-09-08

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

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

PubMed Central

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

2006-01-01

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

On the molecular origins of biomass recalcitrance: the interaction network and solvation structures of cellulose microfibrils.

PubMed

Gross, Adam S; Chu, Jhih-Wei

2010-10-28

Biomass recalcitrance is a fundamental bottleneck to producing fuels from renewable sources. To understand its molecular origin, we characterize the interaction network and solvation structures of cellulose microfibrils via all-atom molecular dynamics simulations. The network is divided into three components: intrachain, interchain, and intersheet interactions. Analysis of their spatial dependence and interaction energetics indicate that intersheet interactions are the most robust and strongest component and do not display a noticeable dependence on solvent exposure. Conversely, the strength of surface-exposed intrachain and interchain hydrogen bonds is significantly reduced. Comparing the interaction networks of I(β) and I(α) cellulose also shows that the number of intersheet interactions is a clear descriptor that distinguishes the two allomorphs and is consistent with the observation that I(β) is the more stable form. These results highlight the dominant role of the often-overlooked intersheet interactions in giving rise to biomass recalcitrance. We also analyze the solvation structures around the surfaces of microfibrils and show that the structural and chemical features at cellulose surfaces constrict water molecules into specific density profiles and pair correlation functions. Calculations of water density and compressibility in the hydration shell show noticeable but not drastic differences. Therefore, specific solvation structures are more prominent signatures of different surfaces.

Nonlinear functional for solvation in Density Functional Theory

NASA Astrophysics Data System (ADS)

Gunceler, Deniz; Sundararaman, Ravishankar; Schwarz, Kathleen; Letchworth-Weaver, Kendra; Arias, T. A.

2013-03-01

Density functional calculations of molecules and surfaces in a liquid can accelerate the development of many technologies ranging from solar energy harvesting to lithium batteries. Such studies require the development of robust functionals describing the liquid. Polarizable continuum models (PCM's) have been applied to some solvated systems; but they do not sufficiently capture solvation effects to describe highly polar systems like surfaces of ionic solids. In this work, we present a nonlinear fluid functional within the framework of Joint Density Functional Theory. The fluid is treated not as a linear dielectric, but as a distribution of dipoles that responds to the solute, which we describe starting from the exact free energy functional for point dipoles. We also show PCM's can be recovered as the linear limit of our functional. Our description is of similar computational cost to PCM's, and captures complex solvation effects like dielectric saturation without requiring new fit parameters. For polar and nonpolar molecules, it achieves millihartree level agreement with experimental solvation energies. Furthermore, our functional now makes it possible to investigate chemistry on the surface of lithium battery materials, which PCM's predict to be unstable. Supported as part of the Energy Materials Center at Cornell, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001086

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

PubMed

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

2018-02-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Existence of a new emitting singlet state of proflavine: femtosecond dynamics of the excited state processes and quantum chemical studies in different solvents.

PubMed

Kumar, Karuppannan Senthil; Selvaraju, Chellappan; Malar, Ezekiel Joy Padma; Natarajan, Paramasivam

2012-01-12

Proflavine (3,6-diaminoacridine) shows fluorescence emission with lifetime, 4.6 ± 0.2 ns, in all the solvents irrespective of the solvent polarity. To understand this unusual photophysical property, investigations were carried out using steady state and time-resolved fluorescence spectroscopy in the pico- and femtosecond time domain. Molecular geometries in the ground and low-lying excited states of proflavine were examined by complete structural optimization using ab initio quantum chemical computations at HF/6-311++G** and CIS/6-311++G** levels. Time dependent density functional theory (TDDFT) calculations were performed to study the excitation energies in the low-lying excited states. The steady state absorption and emission spectral details of proflavine are found to be influenced by solvents. The femtosecond fluorescence decay of the proflavine in all the solvents follows triexponential function with two ultrafast decay components (τ(1) and τ(2)) in addition to the nanosecond component. The ultrafast decay component, τ(1), is attributed to the solvation dynamics of the particular solvent used. The second ultrafast decay component, τ(2), is found to vary from 50 to 215 ps depending upon the solvent. The amplitudes of the ultrafast decay components vary with the wavelength and show time dependent spectral shift in the emission maximum. The observation is interpreted that the time dependent spectral shift is not only due to solvation dynamics but also due to the existence of more than one emitting state of proflavine in the solvent used. Time resolved area normalized emission spectral (TRANES) analysis shows an isoemissive point, indicating the presence of two emitting states in homogeneous solution. Detailed femtosecond fluorescence decay analysis allows us to isolate the two independent emitting components of the close lying singlet states. The CIS and TDDFT calculations also support the existence of the close lying emitting states. The near constant

Establishing linear solvation energy relationships between VOCs and monolayer-protected gold nanoclusters using quartz crystal microbalance.

PubMed

Li, Chi-Lin; Lu, Chia-Jung

2009-08-15

Linear solvation energy relationships (LSERs) have been recognized as a useful model for investigating the chemical forces behind the partition coefficients between vapor molecules and absorbents. This study is the first to determine the solvation properties of monolayer-protected gold nanoclusters (MPCs) with different surface ligands. The ratio of partition coefficients/MPC density (K/rho) of 18 volatile organic compounds (VOCs) for four different MPCs obtained through quartz crystal microbalance (QCM) experiments were used for the LSER model calculations. LSER modeling results indicate that all MPC surfaces showed a statistically significant (p<0.05) preference to hydrogen-bond acidic molecules. Through dipole-dipole attraction, 4-methoxythiophenol-capped MPCs can also interact with polar organics (s=1.04). Showing a unique preference for the hydrogen bond basicity of vapors (b=1.11), 2-benzothiazolethiol-capped MPCs provide evidence of an intra-molecular, proton-shift mechanism on surface of nano-gold.

Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy

NASA Astrophysics Data System (ADS)

Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy

2015-10-01

Proton NMR spectroscopy in the solid state has recently attracted much attention owing to the significant enhancement in spectral resolution afforded by the remarkable advances in ultrafast magic angle spinning (MAS) capabilities. In particular, proton chemical shift anisotropy (CSA) has become an important tool for obtaining specific insights into inter/intra-molecular hydrogen bonding. However, even at the highest currently feasible spinning frequencies (110-120 kHz), 1H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong 1H-1H homonuclear dipolar couplings and narrow 1H chemical shift (CS) ranges, which render it difficult to determine the CSA of specific proton sites in the standard CSA/single-quantum (SQ) chemical shift correlation experiment. Herein, we propose a three-dimensional (3D) 1H double-quantum (DQ) chemical shift/CSA/SQ chemical shift correlation experiment to extract the CS tensors of proton sites whose signals are not well resolved along the single-quantum chemical shift dimension. As extracted from the 3D spectrum, the F1/F3 (DQ/SQ) projection provides valuable information about 1H-1H proximities, which might also reveal the hydrogen-bonding connectivities. In addition, the F2/F3 (CSA/SQ) correlation spectrum, which is similar to the regular 2D CSA/SQ correlation experiment, yields chemical shift anisotropic line shapes at different isotropic chemical shifts. More importantly, since the F2/F1 (CSA/DQ) spectrum correlates the CSA with the DQ signal induced by two neighboring proton sites, the CSA spectrum sliced at a specific DQ chemical shift position contains the CSA information of two neighboring spins indicated by the DQ chemical shift. If these two spins have different CS tensors, both tensors can be extracted by numerical fitting. We believe that this robust and elegant single-channel proton-based 3D experiment provides useful atomistic-level structural and dynamical information for

Double quantum coherence ESR spectroscopy and quantum chemical calculations on a BDPA biradical.

PubMed

Haeri, Haleh Hashemi; Spindler, Philipp; Plackmeyer, Jörn; Prisner, Thomas

2016-10-26

Carbon-centered radicals are interesting alternatives to otherwise commonly used nitroxide spin labels for dipolar spectroscopy techniques because of their narrow ESR linewidth. Herein, we present a novel BDPA biradical, where two BDPA (α,α,γ,γ-bisdiphenylene-β-phenylallyl) radicals are covalently tethered by a saturated biphenyl acetylene linker. The inter-spin distance between the two spin carrier fragments was measured using double quantum coherence (DQC) ESR methodology. The DQC experiment revealed a mean distance of only 1.8 nm between the two unpaired electron spins. This distance is shorter than the predictions based on a simple modelling of the biradical geometry with the electron spins located at the central carbon atoms. Therefore, DFT (density functional theory) calculations were performed to obtain a picture of the spin delocalization, which may give rise to a modified dipolar interaction tensor, and to find those conformations that correspond best to the experimentally observed inter-spin distance. Quantum chemical calculations showed that the attachment of the biphenyl acetylene linker at the second position of the fluorenyl ring of BDPA did not affect the spin population or geometry of the BDPA radical. Therefore, spin delocalization and geometry optimization of each BDPA moiety could be performed on the monomeric unit alone. The allylic dihedral angle θ 1 between the fluorenyl rings in the monomer subunit was determined to be 30° or 150° using quantum chemical calculations. The proton hyperfine coupling constant calculated from both energy minima was in very good agreement with literature values. Based on the optimal monomer geometries and spin density distributions, the dipolar coupling interaction between both BDPA units could be calculated for several dimer geometries. It was shown that the rotation of the BDPA units around the linker axis (θ 2 ) does not significantly influence the dipolar coupling strength when compared to the allylic

Aqueous solvation from the water perspective.

PubMed

Ahmed, Saima; Pasti, Andrea; Fernández-Terán, Ricardo J; Ciardi, Gustavo; Shalit, Andrey; Hamm, Peter

2018-06-21

The response of water re-solvating a charge-transfer dye (deprotonated Coumarin 343) after photoexcitation has been measured by means of transient THz spectroscopy. Two steps of increasing THz absorption are observed, a first ∼10 ps step on the time scale of Debye relaxation of bulk water and a much slower step on a 3.9 ns time scale, the latter of which reflecting heating of the bulk solution upon electronic relaxation of the dye molecules from the S 1 back into the S 0 state. As an additional reference experiment, the hydroxyl vibration of water has been excited directly by a short IR pulse, establishing that the THz signal measures an elevated temperature within ∼1 ps. This result shows that the first step upon dye excitation (10 ps) is not limited by the response time of the THz signal; it rather reflects the reorientation of water molecules in the solvation layer. The apparent discrepancy between the relatively slow reorientation time and the general notion that water is among the fastest solvents with a solvation time in the sub-picosecond regime is discussed. Furthermore, non-equilibrium molecular dynamics simulations have been performed, revealing a close-to-quantitative agreement with experiment, which allows one to disentangle the contribution of heating to the overall THz response from that of water orientation.

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

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

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

1986-04-01

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

A rapidly-reversible absorptive and emissive vapochromic Pt(II) pincer-based chemical sensor

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

Bryant, M. J.; Skelton, J. M.; Hatcher, L. E.

Selective, robust and cost-effective chemical sensors for detecting small volatile-organic compounds (VOCs) have widespread applications in industry, healthcare and environmental monitoring. Here we design a Pt(II) pincer-Type material with selective absorptive and emissive responses to methanol and water. The yellow anhydrous form converts reversibly on a subsecond timescale to a red hydrate in the presence of parts-per-Thousand levels of atmospheric water vapour. Exposure to methanol induces a similarly-rapid and reversible colour change to a blue methanol solvate. Stable smart coatings on glass demonstrate robust switching over 10 4 cycles, and flexible microporous polymer membranes incorporating microcrystals of the complex showmore » identical vapochromic behaviour. The rapid vapochromic response can be rationalised from the crystal structure, and in combination with quantum-chemical modelling, we provide a complete microscopic picture of the switching mechanism. We discuss how this multiscale design approach can be used to obtain new compounds with tailored VOC selectivity and spectral responses.« less

A rapidly-reversible absorptive and emissive vapochromic Pt(II) pincer-based chemical sensor

DOE PAGES

Bryant, M. J.; Skelton, J. M.; Hatcher, L. E.; ...

2017-11-27

Selective, robust and cost-effective chemical sensors for detecting small volatile-organic compounds (VOCs) have widespread applications in industry, healthcare and environmental monitoring. Here we design a Pt(II) pincer-Type material with selective absorptive and emissive responses to methanol and water. The yellow anhydrous form converts reversibly on a subsecond timescale to a red hydrate in the presence of parts-per-Thousand levels of atmospheric water vapour. Exposure to methanol induces a similarly-rapid and reversible colour change to a blue methanol solvate. Stable smart coatings on glass demonstrate robust switching over 10 4 cycles, and flexible microporous polymer membranes incorporating microcrystals of the complex showmore » identical vapochromic behaviour. The rapid vapochromic response can be rationalised from the crystal structure, and in combination with quantum-chemical modelling, we provide a complete microscopic picture of the switching mechanism. We discuss how this multiscale design approach can be used to obtain new compounds with tailored VOC selectivity and spectral responses.« less

Quantum-mechanical parameters for the risk assessment of multi-walled carbon-nanotubes: A study using adsorption of probe compounds and its application to biomolecules.

PubMed

Chayawan; Vikas

2016-11-01

This work forwards new insights into the risk-assessment of multi-walled carbon-nanotubes (MWCNTs) while analysing the role of quantum-mechanical interactions between the electrons in the adsorption of probe compounds and biomolecules by MWCNTs. For this, the quantitative models are developed using quantum-chemical descriptors and their electron-correlation contribution. The major quantum-chemical factors contributing to the adsorption are found to be mean polarizability, electron-correlation energy, and electron-correlation contribution to the absolute electronegativity and LUMO energy. The proposed models, based on only three quantum-chemical factors, are found to be even more robust and predictive than the previously known five or four factors based linear free-energy and solvation-energy relationships. The proposed models are employed to predict the adsorption of biomolecules including steroid hormones and DNA bases. The steroid hormones are predicted to be strongly adsorbed by the MWCNTs, with the order: hydrocortisone > aldosterone > progesterone > ethinyl-oestradiol > testosterone > oestradiol, whereas the DNA bases are found to be relatively less adsorbed but follow the order as: guanine > adenine > thymine > cytosine > uracil. Besides these, the developed electron-correlation based models predict several insecticides, pesticides, herbicides, fungicides, plasticizers and antimicrobial agents in cosmetics, to be strongly adsorbed by the carbon-nanotubes. The present study proposes that the instantaneous inter-electronic interactions may be quite significant in various physico-chemical processes involving MWCNTs, and can be used as a reliable predictor for their risk assessment. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed

Jenkins, H Donald Brooke; Glasser, Leslie

2004-12-08

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

Predicting solvation free energies and thermodynamics in polar solvents and mixtures using a solvation-layer interface condition

PubMed Central

Goossens, Spencer; Mehdizadeh Rahimi, Ali

2017-01-01

We demonstrate that with two small modifications, the popular dielectric continuum model is capable of predicting, with high accuracy, ion solvation thermodynamics (Gibbs free energies, entropies, and heat capacities) in numerous polar solvents. We are also able to predict ion solvation free energies in water–co-solvent mixtures over available concentration series. The first modification to the classical dielectric Poisson model is a perturbation of the macroscopic dielectric-flux interface condition at the solute–solvent interface: we add a nonlinear function of the local electric field, giving what we have called a solvation-layer interface condition (SLIC). The second modification is including the microscopic interface potential (static potential) in our model. We show that the resulting model exhibits high accuracy without the need for fitting solute atom radii in a state-dependent fashion. Compared to experimental results in nine water–co-solvent mixtures, SLIC predicts transfer free energies to within 2.5 kJ/mol. The co-solvents include both protic and aprotic species, as well as biologically relevant denaturants such as urea and dimethylformamide. Furthermore, our results indicate that the interface potential is essential to reproduce entropies and heat capacities. These and previous tests of the SLIC model indicate that it is a promising dielectric continuum model for accurate predictions in a wide range of conditions.

Predicting solvation free energies and thermodynamics in polar solvents and mixtures using a solvation-layer interface condition

NASA Astrophysics Data System (ADS)

Molavi Tabrizi, Amirhossein; Goossens, Spencer; Mehdizadeh Rahimi, Ali; Knepley, Matthew; Bardhan, Jaydeep P.

2017-03-01

We demonstrate that with two small modifications, the popular dielectric continuum model is capable of predicting, with high accuracy, ion solvation thermodynamics (Gibbs free energies, entropies, and heat capacities) in numerous polar solvents. We are also able to predict ion solvation free energies in water-co-solvent mixtures over available concentration series. The first modification to the classical dielectric Poisson model is a perturbation of the macroscopic dielectric-flux interface condition at the solute-solvent interface: we add a nonlinear function of the local electric field, giving what we have called a solvation-layer interface condition (SLIC). The second modification is including the microscopic interface potential (static potential) in our model. We show that the resulting model exhibits high accuracy without the need for fitting solute atom radii in a state-dependent fashion. Compared to experimental results in nine water-co-solvent mixtures, SLIC predicts transfer free energies to within 2.5 kJ/mol. The co-solvents include both protic and aprotic species, as well as biologically relevant denaturants such as urea and dimethylformamide. Furthermore, our results indicate that the interface potential is essential to reproduce entropies and heat capacities. These and previous tests of the SLIC model indicate that it is a promising dielectric continuum model for accurate predictions in a wide range of conditions.

Cluster Quantum Chemical Study of the Grignard Reagent Formation

NASA Astrophysics Data System (ADS)

Tulub, A. V.; Porsev, V. V.

The main stages of the Grignard reagent formation are described in a framework of quantum chemical cluster model. We have established two kinds of the adsorption of CH3Hal on Mgn clusters, one of which leads to radical formation and the second is responsible for radical free dissociate adsorption. The charge redistribution in cluster CH3MgnHal result to the strong electrostatic interaction with ether and Grignard reagent formation without any activation barrier.

Lighting up micromotors with quantum dots for smart chemical sensing.

PubMed

Jurado-Sánchez, B; Escarpa, A; Wang, J

2015-09-25

A new "on-the-fly" chemical optical detection strategy based on the incorporation of fluorescence CdTe quantum dots (QDs) on the surface of self-propelled tubular micromotors is presented. The motion-accelerated binding of trace Hg to the QDs selectively quenches the fluorescence emission and leads to an effective discrimination between different mercury species and other co-existing ions.

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

PubMed

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

2018-04-26

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

Solvation Thermodynamic Properties of Hydrogen Sulfide in [C4mim][PF6], [C4mim][BF4], and [C4mim][Cl] Ionic Liquids, Determined by Molecular Simulations.

PubMed

Sánchez-Badillo, Joel; Gallo, Marco; Alvarado, Sandra; Glossman-Mitnik, Daniel

2015-08-20

Removal of hydrogen sulfide (H2S) and acid gases from natural gas is accomplished by absorption processes using a solvent. The gas solubility in a liquid can be used to measure the degree of removal of the gas and is quantified by the Henry's constant, the free energy of solvation at infinite dilution, or the excess chemical potential. In this work, Henry's constants and thermodynamic properties of solvation of H2S were calculated in three ionic liquids: [C4mim][PF6], [C4mim][BF4], and [C4mim][Cl] ([C4mim], 1-butyl-3-methyl imidazolium). The first step in this work was the evaluation of the force fields for the gas and condensed phases in order to obtain accurate values for the excess chemical potential for H2S on each ionic liquid using free energy perturbation techniques. In the H2S-[C4mim][PF6] and H2S-[C4mim][BF4] systems, the results obtained by molecular simulation agree with the experimental values reported in the literature. However, the solvation free energy calculated for the H2S-[C4mim][Cl] system can be considered predictive because of the lack of experimental data at the simulated conditions. Based on these results, the best solvent for removing H2S is [C4mim][Cl] because it has the highest affinity for this species (lowest value of the Henry's constant). Also, solvation thermodynamic properties such as enthalpy and entropy were calculated in order to evaluate their contribution to the free energy of solvation.

Constructing simple yet accurate potentials for describing the solvation of HCl/water clusters in bulk helium and nanodroplets.

PubMed

Boese, A Daniel; Forbert, Harald; Masia, Marco; Tekin, Adem; Marx, Dominik; Jansen, Georg

2011-08-28

The infrared spectroscopy of molecules, complexes, and molecular aggregates dissolved in superfluid helium clusters, commonly called HElium NanoDroplet Isolation (HENDI) spectroscopy, is an established, powerful experimental technique for extracting high resolution ro-vibrational spectra at ultra-low temperatures. Realistic quantum simulations of such systems, in particular in cases where the solute is undergoing a chemical reaction, require accurate solute-helium potentials which are also simple enough to be efficiently evaluated over the vast number of steps required in typical Monte Carlo or molecular dynamics sampling. This precludes using global potential energy surfaces as often parameterized for small complexes in the realm of high-resolution spectroscopic investigations that, in view of the computational effort imposed, are focused on the intermolecular interaction of rigid molecules with helium. Simple Lennard-Jones-like pair potentials, on the other hand, fall short in providing the required flexibility and accuracy in order to account for chemical reactions of the solute molecule. Here, a general scheme of constructing sufficiently accurate site-site potentials for use in typical quantum simulations is presented. This scheme employs atom-based grids, accounts for local and global minima, and is applied to the special case of a HCl(H(2)O)(4) cluster solvated by helium. As a first step, accurate interaction energies of a helium atom with a set of representative configurations sampled from a trajectory following the dissociation of the HCl(H(2)O)(4) cluster were computed using an efficient combination of density functional theory and symmetry-adapted perturbation theory, i.e. the DFT-SAPT approach. For each of the sampled cluster configurations, a helium atom was placed at several hundred positions distributed in space, leading to an overall number of about 400,000 such quantum chemical calculations. The resulting total interaction energies, decomposed into

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

PubMed

Sindhikara, Daniel J; Hirata, Fumio

2013-06-06

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

Quantum Chemical Studies of Actinides and Lanthanides: From Small Molecules to Nanoclusters

NASA Astrophysics Data System (ADS)

Vlaisavljevich, Bess

Research into actinides is of high interest because of their potential applications as an energy source and for the environmental implications therein. Global concern has arisen since the development of the actinide concept in the 1940s led to the industrial scale use of the commercial nuclear energy cycle and nuclear weapons production. Large quantities of waste have been generated from these processes inspiring efforts to address fundamental questions in actinide science. In this regard, the objective of this work is to use theory to provide insight and predictions into actinide chemistry, where experimental work is extremely challenging because of the intrinsic difficulties of the experiments themselves and the safety issues associated with this type of chemistry. This thesis is a collection of theoretical studies of actinide chemistry falling into three categories: quantum chemical and matrix isolation studies of small molecules, the electronic structure of organoactinide systems, and uranyl peroxide nanoclusters and other solid state actinide compounds. The work herein not only spans a wide range of systems size but also investigates a range of chemical problems. Various quantum chemical approaches have been employed. Wave function-based methods have been used to study the electronic structure of actinide containing molecules of small to middle-size. Among these methods, the complete active space self consistent field (CASSCF) approach with corrections from second-order perturbation theory (CASPT2), the generalized active space SCF (GASSCF) approach, and Moller-Plesset second-order perturbation theory (MP2) have been employed. Likewise, density functional theory (DFT) has been used along with analysis tools like bond energy decomposition, bond orders, and Bader's Atoms in Molecules. From these quantum chemical results, comparison with experimentally obtained structures and spectra are made.

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

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

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

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

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Quantum chemical modeling of enzymatic reactions: the case of 4-oxalocrotonate tautomerase.

PubMed

Sevastik, Robin; Himo, Fahmi

2007-12-01

The reaction mechanism of 4-oxalocrotonate tautomerase (4-OT) is studied using the density functional theory method B3LYP. This enzyme catalyzes the isomerisation of unconjugated alpha-keto acids to their conjugated isomers. Two different quantum chemical models of the active site are devised and the potential energy curves for the reaction are computed. The calculations support the proposed reaction mechanism in which Pro-1 acts as a base to shuttle a proton from the C3 to the C5 position of the substrate. The first step (proton transfer from C3 to proline) is shown to be the rate-limiting step. The energy of the charge-separated intermediate (protonated proline-deprotonated substrate) is calculated to be quite low, in accordance with measured pKa values. The results of the two models are used to evaluate the methodology employed in modeling enzyme active sites using quantum chemical cluster models.

A quantum mechanical strategy to investigate the structure of liquids: the cases of acetonitrile, formamide, and their mixture.

PubMed

Mennucci, Benedetta; da Silva, Clarissa O

2008-06-05

A computational strategy based on quantum mechanical (QM) calculations and continuum solvation models is used to investigate the structure of liquids (either neat liquids or mixtures). The strategy is based on the comparison of calculated and experimental spectroscopic properties (IR-Raman vibrational frequencies and Raman intensities). In particular, neat formamide, neat acetonitrile, and their equimolar mixture are studied comparing isolated and solvated clusters of different nature and size. In all cases, the study seems to indicate that liquids, even when strongly associated, can be effectively modeled in terms of a shell-like system in which clusters of strongly interacting molecules (the microenvironments) are solvated by a polarizable macroenvironment represented by the rest of the molecules. Only taking into proper account both these effects can a correct picture of the liquid structure be achieved.

Spectroscopic and chemical reactivity analysis of D-Myo-Inositol using quantum chemical approach and its experimental verification

NASA Astrophysics Data System (ADS)

Mishra, Devendra P.; Srivastava, Anchal; Shukla, R. K.

2017-07-01

This paper describes the spectroscopic (^1H and ^{13}C NMR, FT-IR and UV-Visible), chemical, nonlinear optical and thermodynamic properties of D-Myo-Inositol using quantum chemical technique and its experimental verification. The structural parameters of the compound are determined from the optimized geometry by B3LYP method with 6 {-}311{+}{+}G(d,p) basis set. It was found that the optimized parameters thus obtained are almost in agreement with the experimental ones. A detailed interpretation of the infrared spectra of D-Myo-Inositol is also reported in the present work. After optimization, the proton and carbon NMR chemical shifts of the studied compound are calculated using GIAO and 6 {-}311{+}{+}G(d,p) basis set. The search of organic materials with improved charge transfer properties requires precise quantum chemical calculations of space-charge density distribution, state and transition dipole moments and HOMO-LUMO states. The nature of the transitions in the observed UV-Visible spectrum of the compound has been studied by the time-dependent density functional theory (TD-DFT). The global reactivity descriptors like chemical potential, electronegativity, hardness, softness and electrophilicity index, have been calculated using DFT. The thermodynamic calculation related to the title compound was also performed at B3LYP/ 6 {-}311{+}{+}G(d,p) level of theory. The standard statistical thermodynamic functions like heat capacity at constant pressure, entropy and enthalpy change were obtained from the theoretical harmonic frequencies of the optimized molecule. It is observed that the values of heat capacity, entropy and enthalpy increase with increase in temperature from 100 to 1000 K, which is attributed to the enhancement of molecular vibration with the increase in temperature.

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

PubMed

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

2013-09-12

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

High-dimensional neural network potentials for solvation: The case of protonated water clusters in helium.

PubMed

Schran, Christoph; Uhl, Felix; Behler, Jörg; Marx, Dominik

2018-03-14

The design of accurate helium-solute interaction potentials for the simulation of chemically complex molecules solvated in superfluid helium has long been a cumbersome task due to the rather weak but strongly anisotropic nature of the interactions. We show that this challenge can be met by using a combination of an effective pair potential for the He-He interactions and a flexible high-dimensional neural network potential (NNP) for describing the complex interaction between helium and the solute in a pairwise additive manner. This approach yields an excellent agreement with a mean absolute deviation as small as 0.04 kJ mol -1 for the interaction energy between helium and both hydronium and Zundel cations compared with coupled cluster reference calculations with an energetically converged basis set. The construction and improvement of the potential can be performed in a highly automated way, which opens the door for applications to a variety of reactive molecules to study the effect of solvation on the solute as well as the solute-induced structuring of the solvent. Furthermore, we show that this NNP approach yields very convincing agreement with the coupled cluster reference for properties like many-body spatial and radial distribution functions. This holds for the microsolvation of the protonated water monomer and dimer by a few helium atoms up to their solvation in bulk helium as obtained from path integral simulations at about 1 K.

High-dimensional neural network potentials for solvation: The case of protonated water clusters in helium

NASA Astrophysics Data System (ADS)

Schran, Christoph; Uhl, Felix; Behler, Jörg; Marx, Dominik

2018-03-01

The design of accurate helium-solute interaction potentials for the simulation of chemically complex molecules solvated in superfluid helium has long been a cumbersome task due to the rather weak but strongly anisotropic nature of the interactions. We show that this challenge can be met by using a combination of an effective pair potential for the He-He interactions and a flexible high-dimensional neural network potential (NNP) for describing the complex interaction between helium and the solute in a pairwise additive manner. This approach yields an excellent agreement with a mean absolute deviation as small as 0.04 kJ mol-1 for the interaction energy between helium and both hydronium and Zundel cations compared with coupled cluster reference calculations with an energetically converged basis set. The construction and improvement of the potential can be performed in a highly automated way, which opens the door for applications to a variety of reactive molecules to study the effect of solvation on the solute as well as the solute-induced structuring of the solvent. Furthermore, we show that this NNP approach yields very convincing agreement with the coupled cluster reference for properties like many-body spatial and radial distribution functions. This holds for the microsolvation of the protonated water monomer and dimer by a few helium atoms up to their solvation in bulk helium as obtained from path integral simulations at about 1 K.

Tuning electronic properties in graphene quantum dots by chemical functionalization: Density functional theory calculations

NASA Astrophysics Data System (ADS)

Abdelsalam, Hazem; Elhaes, Hanan; Ibrahim, Medhat A.

2018-03-01

The energy gap and dipole moment of chemically functionalized graphene quantum dots are investigated by density functional theory. The energy gap can be tuned through edge passivation by different elements or groups. Edge passivation by oxygen considerably decreases the energy gap in hexagonal nanodots. Edge states in triangular quantum dots can also be manipulated by passivation with fluorine. The dipole moment depends on: (a) shape and edge termination of the quantum dot, (b) attached group, and (c) position to which the groups are attached. Depending on the position of attached groups, the total dipole can be increased, decreased, or eliminated.

Rhorix: An interface between quantum chemical topology and the 3D graphics program blender

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

Mills, Matthew J. L.; Sale, Kenneth L.; Simmons, Blake A.

Journal of Computational Chemistry Published by Wiley Periodicals, Inc. Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter-free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition ofmore » mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python “Add-On” named Rhorix for the state-of-the-art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. Finally, a number of examples are discussed..« less

Rhorix: An interface between quantum chemical topology and the 3D graphics program blender

PubMed Central

Sale, Kenneth L.; Simmons, Blake A.; Popelier, Paul L. A.

2017-01-01

Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter‐free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition of mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python “Add‐On” named Rhorix for the state‐of‐the‐art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. A number of examples are discussed. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:28857244

Rhorix: An interface between quantum chemical topology and the 3D graphics program blender

DOE PAGES

Mills, Matthew J. L.; Sale, Kenneth L.; Simmons, Blake A.; ...

2017-08-31

Journal of Computational Chemistry Published by Wiley Periodicals, Inc. Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter-free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition ofmore » mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python “Add-On” named Rhorix for the state-of-the-art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. Finally, a number of examples are discussed..« less

Prediction of solvation enthalpy of gaseous organic compounds in propanol

NASA Astrophysics Data System (ADS)

Golmohammadi, Hassan; Dashtbozorgi, Zahra

2016-09-01

The purpose of this paper is to present a novel way for developing quantitative structure-property relationship (QSPR) models to predict the gas-to-propanol solvation enthalpy (Δ H solv) of 95 organic compounds. Different kinds of descriptors were calculated for each compound using the Dragon software package. The variable selection technique of replacement method (RM) was employed to select the optimal subset of solute descriptors. Our investigation reveals that the dependence of physical chemistry properties of solution on solvation enthalpy is nonlinear and that the RM method is unable to model the solvation enthalpy accurately. The results established that the calculated Δ H solv values by SVM were in good agreement with the experimental ones, and the performances of the SVM models were superior to those obtained by RM model.

Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy

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

Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy, E-mail: ramamoor@umich.edu

2015-10-14

Proton NMR spectroscopy in the solid state has recently attracted much attention owing to the significant enhancement in spectral resolution afforded by the remarkable advances in ultrafast magic angle spinning (MAS) capabilities. In particular, proton chemical shift anisotropy (CSA) has become an important tool for obtaining specific insights into inter/intra-molecular hydrogen bonding. However, even at the highest currently feasible spinning frequencies (110–120 kHz), {sup 1}H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong {sup 1}H–{sup 1}H homonuclear dipolar couplings and narrow {sup 1}H chemical shift (CS) ranges, which rendermore » it difficult to determine the CSA of specific proton sites in the standard CSA/single-quantum (SQ) chemical shift correlation experiment. Herein, we propose a three-dimensional (3D) {sup 1}H double-quantum (DQ) chemical shift/CSA/SQ chemical shift correlation experiment to extract the CS tensors of proton sites whose signals are not well resolved along the single-quantum chemical shift dimension. As extracted from the 3D spectrum, the F1/F3 (DQ/SQ) projection provides valuable information about {sup 1}H–{sup 1}H proximities, which might also reveal the hydrogen-bonding connectivities. In addition, the F2/F3 (CSA/SQ) correlation spectrum, which is similar to the regular 2D CSA/SQ correlation experiment, yields chemical shift anisotropic line shapes at different isotropic chemical shifts. More importantly, since the F2/F1 (CSA/DQ) spectrum correlates the CSA with the DQ signal induced by two neighboring proton sites, the CSA spectrum sliced at a specific DQ chemical shift position contains the CSA information of two neighboring spins indicated by the DQ chemical shift. If these two spins have different CS tensors, both tensors can be extracted by numerical fitting. We believe that this robust and elegant single-channel proton-based 3D experiment provides useful

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

PubMed Central

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

2016-01-01

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

Atomic Radius and Charge Parameter Uncertainty in Biomolecular Solvation Energy Calculations

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

Yang, Xiu; Lei, Huan; Gao, Peiyuan

Atomic radii and charges are two major parameters used in implicit solvent electrostatics and energy calculations. The optimization problem for charges and radii is under-determined, leading to uncertainty in the values of these parameters and in the results of solvation energy calculations using these parameters. This paper presents a method for quantifying this uncertainty in solvation energies using surrogate models based on generalized polynomial chaos (gPC) expansions. There are relatively few atom types used to specify radii parameters in implicit solvation calculations; therefore, surrogate models for these low-dimensional spaces could be constructed using least-squares fitting. However, there are many moremore » types of atomic charges; therefore, construction of surrogate models for the charge parameter space required compressed sensing combined with an iterative rotation method to enhance problem sparsity. We present results for the uncertainty in small molecule solvation energies based on these approaches. Additionally, we explore the correlation between uncertainties due to radii and charges which motivates the need for future work in uncertainty quantification methods for high-dimensional parameter spaces.« less

Quantum Effects on the Capacitance of Graphene-Based Electrodes

DOE PAGES

Zhan, Cheng; Neal, Justin; Wu, Jianzhong; ...

2015-09-08

We recently measured quantum capacitance for electric double layers (EDL) at electrolyte/graphene interfaces. However, the importance of quantum capacitance in realistic carbon electrodes is not clear. Toward understanding that from a theoretical perspective, here we studied the quantum capacitance and total capacitance of graphene electrodes as a function of the number of graphene layers. The quantum capacitance was obtained from electronic density functional theory based on fixed band approximation with an implicit solvation model, while the EDL capacitances were from classical density functional theory. We found that quantum capacitance plays a dominant role in total capacitance of the single-layer graphenemore » both in aqueous and ionic-liquid electrolytes but the contribution decreases as the number of graphene layers increases. Moreover, the total integral capacitance roughly levels off and is dominated by the EDL capacitance beyond about four graphene layers. Finally, because many porous carbons have nanopores with stacked graphene layers at the surface, this research provides a good estimate of the effect of quantum capacitance on their electrochemical performance.« less

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

NASA Technical Reports Server (NTRS)

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

2017-01-01

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

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

PubMed

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

2017-04-06

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

Recent Trends in Quantum Chemical Modeling of Enzymatic Reactions.

PubMed

Himo, Fahmi

2017-05-24

The quantum chemical cluster approach is a powerful method for investigating enzymatic reactions. Over the past two decades, a large number of highly diverse systems have been studied and a great wealth of mechanistic insight has been developed using this technique. This Perspective reviews the current status of the methodology. The latest technical developments are highlighted, and challenges are discussed. Some recent applications are presented to illustrate the capabilities and progress of this approach, and likely future directions are outlined.

The Radical Pair Mechanism and the Avian Chemical Compass: Quantum Coherence and Entanglement

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

Zhang, Yiteng; Kais, Sabre; Berman, Gennady Petrovich

2015-02-02

We review the spin radical pair mechanism which is a promising explanation of avian navigation. This mechanism is based on the dependence of product yields on 1) the hyperfine interaction involving electron spins and neighboring nuclear spins and 2) the intensity and orientation of the geomagnetic field. One surprising result is that even at ambient conditions quantum entanglement of electron spins can play an important role in avian magnetoreception. This review describes the general scheme of chemical reactions involving radical pairs generated from singlet and triplet precursors; the spin dynamics of the radical pairs; and the magnetic field dependence ofmore » product yields caused by the radical pair mechanism. The main part of the review includes a description of the chemical compass in birds. We review: the general properties of the avian compass; the basic scheme of the radical pair mechanism; the reaction kinetics in cryptochrome; quantum coherence and entanglement in the avian compass; and the effects of noise. We believe that the quantum avian compass can play an important role in avian navigation and can also provide the foundation for a new generation of sensitive and selective magnetic-sensing nano-devices.« less

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

PubMed Central

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

2008-01-01

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

In silico insights into the solvation characteristics of the ionic liquid 1-methyltriethoxy-3-ethylimidazolium acetate for cellulosic biomass.

PubMed

Schutt, Timothy C; Bharadwaj, Vivek S; Hegde, Govind A; Johns, Adam J; Mark Maupin, C

2016-09-14

Lignocellulosic biomass is a domestically grown, sustainable, and potentially carbon-neutral feedstock for the production of liquid fuels and other value added chemicals. This underutilized renewable feedstock has the potential to alleviate some of the current socio-economic dependence on foreign petroleum supplies while stimulating rural economies. Unfortunately, the potential of biomass has largely been underdeveloped due to the recalcitrant nature of lignocellulosic materials. Task-specific ionic liquids (ILs) have shown considerable promise as an alternative non-aqueous solvent for solvation and deconstruction of lignocellulose in the presence of metal chloride catalyst or enzymes. Recently it has been hypothesized that adding oxygen atoms to the tail of an imidazolium cation would alleviate some of the negative characteristics of the ILs by increasing mass transport properties, and decreasing IL deactivation of enzymes, while at the same time retaining favorable solvation characteristics for lignocellulose. Reported here are fully atomistic molecular dynamic simulations of 1-methyltriethoxy-3-ethylimidazolium acetate ([Me-(OEt)3-Et-IM(+)] [OAc(-)]) that elucidate promising molecular-level details pertaining to the solvation characteristics of model compounds of cellulose, and IL-induced side-chain and ring puckering conformations. It is found that the anion interactions with the saccharide induce alternate ring puckering conformations from those seen in aqueous environments (i.e.(1)C4), while the cation interactions are found to influence the conformation of the ω dihedral. These perturbations in saccharide structures are discussed in the context of their contribution to the disruption of hydrogen bonding in cellulosic architecture and their role in solvation.

Quantum Chemical Mass Spectrometry: Verification and Extension of the Mobile Proton Model for Histidine

NASA Astrophysics Data System (ADS)

Cautereels, Julie; Blockhuys, Frank

2017-06-01

The quantum chemical mass spectrometry for materials science (QCMS2) method is used to verify the proposed mechanism for proton transfer - the Mobile Proton Model (MPM) - by histidine for ten XHS tripeptides, based on quantum chemical calculations at the DFT/B3LYP/6-311+G* level of theory. The fragmentations of the different intermediate structures in the MPM mechanism are studied within the QCMS2 framework, and the energetics of the proposed mechanism itself and those of the fragmentations of the intermediate structures are compared, leading to the computational confirmation of the MPM. In addition, the calculations suggest that the mechanism should be extended from considering only the formation of five-membered ring intermediates to include larger-ring intermediates. [Figure not available: see fulltext.

Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility.

PubMed

Drake, Justin A; Harris, Robert C; Pettitt, B Montgomery

2016-08-23

Oligoglycine is a backbone mimic for all proteins and is prevalent in the sequences of intrinsically disordered proteins. We have computed the absolute chemical potential of glycine oligomers at infinite dilution by simulation with the CHARMM36 and Amber ff12SB force fields. We performed a thermodynamic decomposition of the solvation free energy (ΔG(sol)) of Gly2-5 into enthalpic (ΔH(sol)) and entropic (ΔS(sol)) components as well as their van der Waals and electrostatic contributions. Gly2-5 was either constrained to a rigid/extended conformation or allowed to be completely flexible during simulations to assess the effects of flexibility on these thermodynamic quantities. For both rigid and flexible oligoglycine models, the decrease in ΔG(sol) with chain length is enthalpically driven with only weak entropic compensation. However, the apparent rates of decrease of ΔG(sol), ΔH(sol), ΔS(sol), and their elec and vdw components differ for the rigid and flexible models. Thus, we find solvation entropy does not drive aggregation for this system and may not explain the collapse of long oligoglycines. Additionally, both force fields yield very similar thermodynamic scaling relationships with respect to chain length despite both force fields generating different conformational ensembles of various oligoglycine chains. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Picosecond solvation dynamics—A potential viewer of DMSO—Water binary mixtures

NASA Astrophysics Data System (ADS)

Banik, Debasis; Kundu, Niloy; Kuchlyan, Jagannath; Roy, Arpita; Banerjee, Chiranjib; Ghosh, Surajit; Sarkar, Nilmoni

2015-02-01

In this work, we have investigated the composition dependent anomalous behavior of dimethyl sulfoxide (DMSO)-water binary mixture by collecting the ultrafast solvent relaxation response around a well known solvation probe Coumarin 480 (C480) by using a femtosecond fluorescence up-conversion spectrometer. Recent molecular dynamics simulations have predicted two anomalous regions of DMSO-water binary mixture. Particularly, these studies encourage us to investigate the anomalies from experimental background. DMSO-water binary mixture has repeatedly given evidences of its dual anomalous nature in front of our systematic investigation through steady-state and time-resolved measurements. We have calculated average solvation times of C480 by two individual well-known methods, among them first one is spectral-reconstruction method and another one is single-wavelength measurement method. The results of both the methods roughly indicate that solvation time of C480 reaches maxima in the mole fraction of DMSO XD = 0.12-0.17 and XD = 0.27-0.35, respectively. Among them, the second region (XD = 0.27-0.35) is very common as most of the thermodynamic properties exhibit deviation in this range. Most probably, the anomalous solvation trend in this region is fully guided by the shear viscosity of the medium. However, the first region is the most interesting one. In this region due to formation of strongly hydrogen bonded 1DMSO:2H2O complexes, hydration around the probe C480 decreases, as a result of which solvation time increases.

Radiation and quantum chemical studies of chalcone derivatives.

PubMed

Gaikwad, P; Priyadarsini, K I; Naumov, S; Rao, B S M

2010-08-05

The reactions of oxidizing radicals ((*)OH, Br(2)(*-), and SO(4)(*-)) with -OH-, -CH(3)-, or -NH(2)-substituted indole chalcones and hydroxy benzenoid chalcones were studied by radiation and quantum chemical methods. The (*)OH radical was found to react by addition at diffusion-controlled rates (k = 1.1-1.7 x 10(10) dm(3) mol(-1) s(-1)), but Br(2)(*-) radical reacted by 2 orders of magnitude lower. Quantum chemical calculations at the B3LYP/6-31+G(d,p) level of theory have shown that the (C2-OH)(*), (C11-OH)(*), and (C10-OH)(*) adducts of the indole chalcones and the (C7-OH)(*) and (C8-OH)(*) adducts of the hydroxy benzenoid chalcones are more stable with DeltaH = -39 to -28 kcal mol(-1) and DeltaG = -32 to -19 kcal mol(-1). This suggests that (*)OH addition to the alpha,beta-unsaturated bond is a major reaction channel in both types of chalcones and is barrierless. The stability and lack of dehydration of the (*)OH adducts arise from two factors: strong frontier orbital interaction due to the low energy gap between interacting orbitals and the negligible Coulombic repulsion due to small absolute values of Mulliken charges. The transient absorption spectrum measured in the (*)OH radical reaction with all the indole chalcone derivatives exhibited a maximum at 390 nm, which is in excellent agreement with the computed value (394 nm). The formation of three phenolic products under steady-state radiolysis is in line with the three stable (*)OH adducts predicted by theory. Independent of the substituent, identical spectra (lambda(max) = 330-360 and approximately 580 nm) were obtained on one-electron oxidation of the three indole chalcones. MO calculations predict the deprotonation from the -NH group is more efficient than from the substituent due to the larger electron density on the N1 atom forming the chalcone indolyl radical. Its reduction potential was determined to be 0.56 V from the ABTS(*-)/ABTS(2-) couple. In benzenoid chalcones, the (*)OH adduct spectrum is

Benzonitrile: Electron affinity, excited states, and anion solvation

NASA Astrophysics Data System (ADS)

Dixon, Andrew R.; Khuseynov, Dmitry; Sanov, Andrei

2015-10-01

We report a negative-ion photoelectron imaging study of benzonitrile and several of its hydrated, oxygenated, and homo-molecularly solvated cluster anions. The photodetachment from the unsolvated benzonitrile anion to the X ˜ 1 A 1 state of the neutral peaks at 58 ± 5 meV. This value is assigned as the vertical detachment energy (VDE) of the valence anion and the upper bound of adiabatic electron affinity (EA) of benzonitrile. The EA of the lowest excited electronic state of benzonitrile, a ˜ 3 A 1 , is determined as 3.41 ± 0.01 eV, corresponding to a 3.35 eV lower bound for the singlet-triplet splitting. The next excited state, the open-shell singlet A ˜ 1 A 1 , is found about an electron-volt above the triplet, with a VDE of 4.45 ± 0.01 eV. These results are in good agreement with ab initio calculations for neutral benzonitrile and its valence anion but do not preclude the existence of a dipole-bound state of similar energy and geometry. The step-wise and cumulative solvation energies of benzonitrile anions by several types of species were determined, including homo-molecular solvation by benzonitrile, hydration by 1-3 waters, oxygenation by 1-3 oxygen molecules, and mixed solvation by various combinations of O2, H2O, and benzonitrile. The plausible structures of the dimer anion of benzonitrile were examined using density functional theory and compared to the experimental observations. It is predicted that the dimer anion favors a stacked geometry capitalizing on the π-π interactions between the two partially charged benzonitrile moieties.

Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation

NASA Astrophysics Data System (ADS)

Carnevale, V.; Raugei, S.

2009-12-01

Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

Protein structure refinement using a quantum mechanics-based chemical shielding predictor.

PubMed

Bratholm, Lars A; Jensen, Jan H

2017-03-01

The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ , 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1-0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural

A gold cyano complex in nitromethane: MD simulation and X-ray diffraction.

PubMed

Probst, Michael; Injan, Natcha; Megyes, Tünde; Bako, Imre; Balint, Szabolcz; Limtrakul, Jumras; Nazmutdinov, Renat; Mitev, Pavlin D; Hermansson, Kersti

2012-06-29

The solvation structure around the dicyanoaurate(I) anion (Au(CN) 2 - ) in a dilute nitromethane (CH 3 NO 2 ) solution is presented from X-ray diffraction measurements and molecular dynamics simulation (NVT ensemble, 460 nitromethane molecules at room temperature). The simulations are based on a new solute-solvent force-field fitted to a training set of quantum-chemically derived interaction energies. Radial distribution functions from experiment and simulation are in good agreement. The solvation structure has been further elucidated from MD data. Several shells can be identified. We obtain a solvation number of 13-17 nitromethane molecules with a strong preference to be oriented with their methyl groups towards the solute.

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

PubMed

Pliego, Josefredo R; Miguel, Elizabeth L M

2013-05-02

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

Solvation of Cr 3+ cation in water-acetonitrile mixture studied by IR spectroscopy: molecular penetration into the solvation shells

NASA Astrophysics Data System (ADS)

Jamróz, Dorota; Wójcik, Marek; Lindgren, Jan

2000-09-01

Infrared spectra of mixtures of water and deuteroacetonitrile containing the Cr 3+ cation have been studied as a function of concentration, time and temperature. The CN stretching vibration of CD 3CN molecules has been used as a probe of the structural environments. The CN band in the spectra of the solutions is a superposition of four subbands, which may be attributed to CD 3CN bound in the first, second, and third solvation shells of the cation and to non-bound CD 3CN. The character of changes of the integral intensities of the subbands with time for various H 2O:Cr 3+ molar ratios are explained by suggesting mechanisms of molecular replacement within the solvation shells of Cr 3+.

Quantum chemical methods for the investigation of photoinitiated processes in biological systems: theory and applications.

PubMed

Dreuw, Andreas

2006-11-13

With the advent of modern computers and advances in the development of efficient quantum chemical computer codes, the meaningful computation of large molecular systems at a quantum mechanical level became feasible. Recent experimental effort to understand photoinitiated processes in biological systems, for instance photosynthesis or vision, at a molecular level also triggered theoretical investigations in this field. In this Minireview, standard quantum chemical methods are presented that are applicable and recently used for the calculation of excited states of photoinitiated processes in biological molecular systems. These methods comprise configuration interaction singles, the complete active space self-consistent field method, and time-dependent density functional theory and its variants. Semiempirical approaches are also covered. Their basic theoretical concepts and mathematical equations are briefly outlined, and their properties and limitations are discussed. Recent successful applications of the methods to photoinitiated processes in biological systems are described and theoretical tools for the analysis of excited states are presented.

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

NASA Astrophysics Data System (ADS)

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

2014-02-01

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

Revealing electronic open quantum systems with subsystem TDDFT.

PubMed

Krishtal, Alisa; Pavanello, Michele

2016-03-28

Open quantum systems (OQSs) are perhaps the most realistic systems one can approach through simulations. In recent years, describing OQSs with Density Functional Theory (DFT) has been a prominent avenue of research with most approaches based on a density matrix partitioning in conjunction with an ad-hoc description of system-bath interactions. We propose a different theoretical approach to OQSs based on partitioning of the electron density. Employing the machinery of subsystem DFT (and its time-dependent extension), we provide a novel way of isolating and analyzing the various terms contributing to the coupling between the system and the surrounding bath. To illustrate the theory, we provide numerical simulations on a toy system (a molecular dimer) and on a condensed phase system (solvated excimer). The simulations show that non-Markovian dynamics in the electronic system-bath interactions are important in chemical applications. For instance, we show that the superexchange mechanism of transport in donor-bridge-acceptor systems is a non-Markovian interaction between the donor-acceptor (OQS) with the bridge (bath) which is fully characterized by real-time subsystem time-dependent DFT.

Revealing electronic open quantum systems with subsystem TDDFT

NASA Astrophysics Data System (ADS)

Krishtal, Alisa; Pavanello, Michele

2016-03-01

Open quantum systems (OQSs) are perhaps the most realistic systems one can approach through simulations. In recent years, describing OQSs with Density Functional Theory (DFT) has been a prominent avenue of research with most approaches based on a density matrix partitioning in conjunction with an ad-hoc description of system-bath interactions. We propose a different theoretical approach to OQSs based on partitioning of the electron density. Employing the machinery of subsystem DFT (and its time-dependent extension), we provide a novel way of isolating and analyzing the various terms contributing to the coupling between the system and the surrounding bath. To illustrate the theory, we provide numerical simulations on a toy system (a molecular dimer) and on a condensed phase system (solvated excimer). The simulations show that non-Markovian dynamics in the electronic system-bath interactions are important in chemical applications. For instance, we show that the superexchange mechanism of transport in donor-bridge-acceptor systems is a non-Markovian interaction between the donor-acceptor (OQS) with the bridge (bath) which is fully characterized by real-time subsystem time-dependent DFT.

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

PubMed

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

2015-01-29

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

Influence of temperature and molecular structure on ionic liquid solvation layers.

PubMed

Wakeham, Deborah; Hayes, Robert; Warr, Gregory G; Atkin, Rob

2009-04-30

Atomic force microscopy (AFM) force profiling is used to investigate the structure of adsorbed and solvation layers formed on a mica surface by various room temperature ionic liquids (ILs) ethylammonium nitrate (EAN), ethanolammonium nitrate (EtAN), ethylammonium formate (EAF), propylammonium formate (PAF), ethylmethylammonium formate (EMAF), and dimethylethylammonium formate (DMEAF). At least seven layers are observed for EAN at 14 degrees C (melting point 13 degrees C), decreasing as the temperature is increased to 30 degrees C due to thermal energy disrupting solvophobic forces that lead to segregation of cation alkyl tails from the charged ammonium and nitrate moieties. The number and properties of the solvation layers can also be controlled by introducing an alcohol moiety to the cation's alkyl tail (EtAN), or by replacing the nitrate anion with formate (EAF and PAF), even leading to the detection of distinct cation and anion sublayers. Substitution of primary by secondary or tertiary ammonium cations reduces the number of solvation layers formed, and also weakens the cation layer adsorbed onto mica. The observed solvation and adsorbed layer structures are discussed in terms of the intermolecular cohesive forces within the ILs.

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

Differential geometry based solvation model I: Eulerian formulation

NASA Astrophysics Data System (ADS)

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

2010-11-01

This paper presents a differential geometry based model for the analysis and computation of the equilibrium property of solvation. Differential geometry theory of surfaces is utilized to define and construct smooth interfaces with good stability and differentiability for use in characterizing the solvent-solute boundaries and in generating continuous dielectric functions across the computational domain. A total free energy functional is constructed to couple polar and nonpolar contributions to the solvation process. Geometric measure theory is employed to rigorously convert a Lagrangian formulation of the surface energy into an Eulerian formulation so as to bring all energy terms into an equal footing. By optimizing the total free energy functional, we derive coupled generalized Poisson-Boltzmann equation (GPBE) and generalized geometric flow equation (GGFE) for the electrostatic potential and the construction of realistic solvent-solute boundaries, respectively. By solving the coupled GPBE and GGFE, we obtain the electrostatic potential, the solvent-solute boundary profile, and the smooth dielectric function, and thereby improve the accuracy and stability of implicit solvation calculations. We also design efficient second-order numerical schemes for the solution of the GPBE and GGFE. Matrix resulted from the discretization of the GPBE is accelerated with appropriate preconditioners. An alternative direct implicit (ADI) scheme is designed to improve the stability of solving the GGFE. Two iterative approaches are designed to solve the coupled system of nonlinear partial differential equations. Extensive numerical experiments are designed to validate the present theoretical model, test computational methods, and optimize numerical algorithms. Example solvation analysis of both small compounds and proteins are carried out to further demonstrate the accuracy, stability, efficiency and robustness of the present new model and numerical approaches. Comparison is given to

Quantum chemical study of a derivative of 3-substituted dithiocarbamic flavanone

NASA Astrophysics Data System (ADS)

Gosav, Steluta; Paduraru, Nicoleta; Maftei, Dan; Birsa, Mihail Lucian; Praisler, Mirela

2017-02-01

The aim of this work is to characterize a quite novel 3-dithiocarbamic flavonoid by vibrational spectroscopy in conjunction with Density Functional Theory (DFT) calculations. Quantum mechanics calculations of energies, geometries and vibrational wavenumbers in the ground state were carried out by using hybrid functional B3LYP with 6-311G(d,p) as basis set. The results indicate a remarkable agreement between the calculated molecular geometries, as well as vibrational frequencies, and the corresponding experimental data. In addition, a complete assignment of all the absorption bands present in the vibrational spectrum has been performed. In order to assess its chemical potential, quantum molecular descriptors characterizing the interactions between the 3-dithiocarbamic flavonoid and its biological receptors have been computed. The frontier molecular orbitals and the HOMO-LUMO energy gap have been used in order to explain the way in which the new molecule can interact with other species and to characterize its molecular chemical stability/reactivity. The molecular electrostatic potential (MEP) map, computed in order to identify the sites of the studied flavonoid that are most likely to interact with electrophilic and nucleophilic species, is discussed.

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

PubMed

Nguyen, Duc D; Wei, Guo-Wei

2017-01-05

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

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.

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.

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

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

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

2016-03-21

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

Strong Stretching of Poly(ethylene glycol) Brushes Mediated by Ionic Liquid Solvation.

PubMed

Han, Mengwei; Espinosa-Marzal, Rosa M

2017-09-07

We have measured forces between mica surfaces coated with a poly(ethylene glycol) (PEG) brush solvated by a vacuum-dry ionic liquid, 1-ethyl-3-methyl imidazolium bis(trifluoromethylsulfonyl)imide, with a surface forces apparatus. At high grafting density, the solvation mediated by the ionic liquid causes the brush to stretch twice as much as in water. Modeling of the steric repulsion indicates that PEG behaves as a polyelectrolyte; the hydrogen bonding between ethylene glycol and the imidazolium cation seems to effectively charge the polymer brush, which justifies the strong stretching. Importantly, under strong polymer compression, solvation layers are squeezed out at a higher rate than for the neat ionic liquid. We propose that the thermal fluctuations of the PEG chains, larger in the brush than in the mushroom configuration, maintain the fluidity of the ionic liquid under strong compression, in contrast to the solid-like squeezing-out behavior of the neat ionic liquid. This is the first experimental study of the behavior of a polymer brush solvated by an ionic liquid under nanoconfinement.

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

DOE PAGES

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

2014-12-19

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

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.

Reaction Rate Theory in Coordination Number Space: An Application to Ion Solvation

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

Roy, Santanu; Baer, Marcel D.; Mundy, Christopher J.

2016-04-14

Understanding reaction mechanisms in many chemical and biological processes require application of rare event theories. In these theories, an effective choice of a reaction coordinate to describe a reaction pathway is essential. To this end, we study ion solvation in water using molecular dynamics simulations and explore the utility of coordination number (n = number of water molecules in the first solvation shell) as the reaction coordinate. Here we compute the potential of mean force (W(n)) using umbrella sampling, predicting multiple metastable n-states for both cations and anions. We find with increasing ionic size, these states become more stable andmore » structured for cations when compared to anions. We have extended transition state theory (TST) to calculate transition rates between n-states. TST overestimates the rate constant due to solvent-induced barrier recrossings that are not accounted for. We correct the TST rates by calculating transmission coefficients using the reactive flux method. This approach enables a new way of understanding rare events involving coordination complexes. We gratefully acknowledge Liem Dang and Panos Stinis for useful discussion. This research used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. SR, CJM, and GKS were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative, a Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL). PNNL is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy.« less

The Excess Chemical Potential of Water at the Interface with a Protein from End Point Simulations.

PubMed

Zhang, Bin W; Cui, Di; Matubayasi, Nobuyuki; Levy, Ronald M

2018-05-03

We use end point simulations to estimate the excess chemical potential of water in the homogeneous liquid and at the interface with a protein in solution. When the pure liquid is taken as the reference, the excess chemical potential of interfacial water is the difference between the solvation free energy of a water molecule at the interface and in the bulk. Using the homogeneous liquid as an example, we show that the solvation free energy for growing a water molecule can be estimated by applying UWHAM to the simulation data generated from the initial and final states (i.e., "the end points") instead of multistate free energy perturbation simulations because of the possible overlaps of the configurations sampled at the end points. Then end point simulations are used to estimate the solvation free energy of water at the interface with a protein in solution. The estimate of the solvation free energy at the interface from two simulations at the end points agrees with the benchmark using 32 states within a 95% confidence interval for most interfacial locations. The ability to accurately estimate the excess chemical potential of water from end point simulations facilitates the statistical thermodynamic analysis of diverse interfacial phenomena. Our focus is on analyzing the excess chemical potential of water at protein receptor binding sites with the goal of using this information to assist in the design of tight binding ligands.

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

PubMed

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

2017-01-13

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

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

PubMed

Martins, Silvia A; Sousa, Sergio F

2013-06-05

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

Computing UV/vis spectra using a combined molecular dynamics and quantum chemistry approach: bis-triazin-pyridine (BTP) ligands studied in solution.

PubMed

Höfener, Sebastian; Trumm, Michael; Koke, Carsten; Heuser, Johannes; Ekström, Ulf; Skerencak-Frech, Andrej; Schimmelpfennig, Bernd; Panak, Petra J

2016-03-21

We report a combined computational and experimental study to investigate the UV/vis spectra of 2,6-bis(5,6-dialkyl-1,2,4-triazin-3-yl)pyridine (BTP) ligands in solution. In order to study molecules in solution using theoretical methods, force-field parameters for the ligand-water interaction are adjusted to ab initio quantum chemical calculations. Based on these parameters, molecular dynamics (MD) simulations are carried out from which snapshots are extracted as input to quantum chemical excitation-energy calculations to obtain UV/vis spectra of BTP ligands in solution using time-dependent density functional theory (TDDFT) employing the Tamm-Dancoff approximation (TDA). The range-separated CAM-B3LYP functional is used to avoid large errors for charge-transfer states occurring in the electronic spectra. In order to study environment effects with theoretical methods, the frozen-density embedding scheme is applied. This computational procedure allows to obtain electronic spectra calculated at the (range-separated) DFT level of theory in solution, revealing solvatochromic shifts upon solvation of up to about 0.6 eV. Comparison to experimental data shows a significantly improved agreement compared to vacuum calculations and enables the analysis of relevant excitations for the line shape in solution.

QSTR of the toxicity of some organophosphorus compounds by using the quantum chemical and topological descriptors.

PubMed

Senior, Samir A; Madbouly, Magdy D; El massry, Abdel-Moneim

2011-09-01

Quantum chemical and topological descriptors of some organophosphorus compounds (OP) were correlated with their toxicity LD(50) as a dermal. The quantum chemical parameters were obtained using B3LYP/LANL2DZdp-ECP optimization. Using linear regression analysis, equations were derived to calculate the theoretical LD(50) of the studied compounds. The inclusion of quantum parameters, having both charge indices and topological indices, affects the toxicity of the studied compounds resulting in high correlation coefficient factors for the obtained equations. Two of the new four firstly supposed descriptors give higher correlation coefficients namely the Heteroatom Corrected Extended Connectivity Randic index ((1)X(HCEC)) and the Density Randic index ((1)X(Den)). The obtained linear equations were applied to predict the toxicity of some related structures. It was found that the sulfur atoms in these compounds must be replaced by oxygen atoms to achieve improved toxicity. Copyright © 2011 Elsevier Ltd. All rights reserved.

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.

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

PubMed

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

2017-07-13

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

A gold cyano complex in nitromethane: MD simulation and X-ray diffraction

PubMed Central

Probst, Michael; Injan, Natcha; Megyes, Tünde; Bako, Imre; Balint, Szabolcz; Limtrakul, Jumras; Nazmutdinov, Renat; Mitev, Pavlin D.; Hermansson, Kersti

2012-01-01

The solvation structure around the dicyanoaurate(I) anion (Au(CN)2−) in a dilute nitromethane (CH3NO2) solution is presented from X-ray diffraction measurements and molecular dynamics simulation (NVT ensemble, 460 nitromethane molecules at room temperature). The simulations are based on a new solute–solvent force-field fitted to a training set of quantum-chemically derived interaction energies. Radial distribution functions from experiment and simulation are in good agreement. The solvation structure has been further elucidated from MD data. Several shells can be identified. We obtain a solvation number of 13–17 nitromethane molecules with a strong preference to be oriented with their methyl groups towards the solute. PMID:25540462

Residue length and solvation model dependency of elastinlike polypeptides

NASA Astrophysics Data System (ADS)

Bilsel, Mustafa; Arkin, Handan

2010-05-01

We have performed exhaustive multicanonical Monte Carlo simulations of elastinlike polypeptides with a chain including amino acids (valine-proline-glycine-valine-glycine)n or in short (VPGVG)n , where n changes from 1 to 4, in order to investigate the thermodynamic and structural properties. To predict the characteristic secondary structure motifs of the molecules, Ramachandran plots were prepared and analyzed as well. In these studies, we utilized a realistic model where the interactions between all types of atoms were taken into account. Effects of solvation were also simulated by using an implicit-solvent model with two commonly used solvation parameter sets and compared with the vacuum case.

Understanding Lithium Solvation and Diffusion through Topological Analysis of First-Principles Molecular Dynamics

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

Bhatia, Harsh; Gyulassy, Attila; Ong, Mitchell

2016-09-27

The performance of lithium-ion batteries is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact, both, the solvation and diffusivity of Li ions. In this work, we present our application of the topological techniques to extract and predict such behavior in the data generated by the first-principles molecular dynamics simulation of Li ions in an important organic solvent -ethylene carbonate. More specifically, we use the scalar topology of the electron charge density field tomore » analyze the evolution of the solvation structures. This allows us to derive a parameter-free bond definition for lithium-oxygen bonds, to provide a quantitative measure for bond strength, and to understand the regions of influence of each atom in the simulation. This has provided new insights into how and under what conditions certain bonds may form and break. As a result, we can identify and, more importantly, predict, unstable configurations in solvation structures. This can be very useful in understanding when small changes to the atoms' movements can cause significantly different bond structures to evolve. Ultimately, this promises to allow scientists to explore lithium ion solvation and diffusion more systematically, with the aim of new insights and potentially accelerating the calculations themselves.« less

Supramolecular polymerization of benzene-1,3,5-tricarboxamide: a molecular dynamics simulation study.

PubMed

Bejagam, Karteek K; Fiorin, Giacomo; Klein, Michael L; Balasubramanian, Sundaram

2014-05-15

Supramolecular polymerization in the family of benzene-1,3,5-tricarboxamide (BTA) has been investigated using atomistic molecular dynamics (MD) simulations. Gas phase calculations using a nonpolarizable force field reproduce the cooperativity in binding energy and intermolecular structure seen in quantum chemical calculations. Both quantum chemical and force field based calculations suggest that the ground state structure of the BTA dimer contains two donor hydrogen bonds and one acceptor hydrogen bond rather than the conjectured three-donor and zero-acceptor hydrogen-bonded state. MD simulations of BTA molecules in a realistic solvent, n-nonane, demonstrate the self-assembly process. The free energy (FE) of dimerization and of solvation has been determined. The solvated dimer of BTA with hexyl tails is more stable than two monomers by about 13 kcal/mol. Furthermore, the FE of association of a BTA molecule to an oligomer exhibits a dependence on the oligomer size, which is a robust signature of cooperative self-assembly.

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

Surface emitting ring quantum cascade lasers for chemical sensing

NASA Astrophysics Data System (ADS)

Szedlak, Rolf; Hayden, Jakob; Martín-Mateos, Pedro; Holzbauer, Martin; Harrer, Andreas; Schwarz, Benedikt; Hinkov, Borislav; MacFarland, Donald; Zederbauer, Tobias; Detz, Hermann; Andrews, Aaron Maxwell; Schrenk, Werner; Acedo, Pablo; Lendl, Bernhard; Strasser, Gottfried

2018-01-01

We review recent advances in chemical sensing applications based on surface emitting ring quantum cascade lasers (QCLs). Such lasers can be implemented in monolithically integrated on-chip laser/detector devices forming compact gas sensors, which are based on direct absorption spectroscopy according to the Beer-Lambert law. Furthermore, we present experimental results on radio frequency modulation up to 150 MHz of surface emitting ring QCLs. This technique provides detailed insight into the modulation characteristics of such lasers. The gained knowledge facilitates the utilization of ring QCLs in combination with spectroscopic techniques, such as heterodyne phase-sensitive dispersion spectroscopy for gas detection and analysis.

Reactions of Solvated Ions Final Report

DOE R&D Accomplishments Database

Taube, H.

1962-09-24

Brief summaries are presented on isotopic dilution studies on salts dissolved in CH{sub 3}OH, studies on metal and metal salts in solvents of the amine type, and studies on phosphato complexes of the pentammine Co(III) series. A list of papers published on reactions of solvated ions is included. (N.W.R.)

Generalized Born Models of Macromolecular Solvation Effects

NASA Astrophysics Data System (ADS)

Bashford, Donald; Case, David A.

2000-10-01

It would often be useful in computer simulations to use a simple description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation, and approximations to such models that avoid the need to solve the Poisson equation are attractive because of their computational efficiency. Here we give an overview of one such approximation, the generalized Born model, which is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids. We discuss its strengths and weaknesses, both for its fidelity to the underlying continuum model and for its ability to replace explicit consideration of solvent molecules in macromolecular simulations. We focus particularly on versions of the generalized Born model that have a pair-wise analytical form, and therefore fit most naturally into conventional molecular mechanics calculations.

Enthalpy-entropy compensation: the role of solvation.

PubMed

Dragan, Anatoliy I; Read, Christopher M; Crane-Robinson, Colyn

2017-05-01

Structural modifications to interacting systems frequently lead to changes in both the enthalpy (heat) and entropy of the process that compensate each other, so that the Gibbs free energy is little changed: a major barrier to the development of lead compounds in drug discovery. The conventional explanation for such enthalpy-entropy compensation (EEC) is that tighter contacts lead to a more negative enthalpy but increased molecular constraints, i.e., a compensating conformational entropy reduction. Changes in solvation can also contribute to EEC but this contribution is infrequently discussed. We review long-established and recent cases of EEC and conclude that the large fluctuations in enthalpy and entropy observed are too great to be a result of only conformational changes and must result, to a considerable degree, from variations in the amounts of water immobilized or released on forming complexes. Two systems exhibiting EEC show a correlation between calorimetric entropies and local mobilities, interpreted to mean conformational control of the binding entropy/free energy. However, a substantial contribution from solvation gives the same effect, as a consequence of a structural link between the amount of bound water and the protein flexibility. Only by assuming substantial changes in solvation-an intrinsically compensatory process-can a more complete understanding of EEC be obtained. Faced with such large, and compensating, changes in the enthalpies and entropies of binding, the best approach to engineering elevated affinities must be through the addition of ionic links, as they generate increased entropy without affecting the enthalpy.

Simulating chemistry using quantum computers.

PubMed

Kassal, Ivan; Whitfield, James D; Perdomo-Ortiz, Alejandro; Yung, Man-Hong; Aspuru-Guzik, Alán

2011-01-01

The difficulty of simulating quantum systems, well known to quantum chemists, prompted the idea of quantum computation. One can avoid the steep scaling associated with the exact simulation of increasingly large quantum systems on conventional computers, by mapping the quantum system to another, more controllable one. In this review, we discuss to what extent the ideas in quantum computation, now a well-established field, have been applied to chemical problems. We describe algorithms that achieve significant advantages for the electronic-structure problem, the simulation of chemical dynamics, protein folding, and other tasks. Although theory is still ahead of experiment, we outline recent advances that have led to the first chemical calculations on small quantum information processors.

Self-consistent continuum solvation for optical absorption of complex molecular systems in solution

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

Timrov, Iurii; Biancardi, Alessandro; Andreussi, Oliviero

2015-01-21

We introduce a new method to compute the optical absorption spectra of complex molecular systems in solution, based on the Liouville approach to time-dependent density-functional perturbation theory and the revised self-consistent continuum solvation model. The former allows one to obtain the absorption spectrum over a whole wide frequency range, using a recently proposed Lanczos-based technique, or selected excitation energies, using the Casida equation, without having to ever compute any unoccupied molecular orbitals. The latter is conceptually similar to the polarizable continuum model and offers the further advantages of allowing an easy computation of atomic forces via the Hellmann-Feynman theorem andmore » a ready implementation in periodic-boundary conditions. The new method has been implemented using pseudopotentials and plane-wave basis sets, benchmarked against polarizable continuum model calculations on 4-aminophthalimide, alizarin, and cyanin and made available through the QUANTUM ESPRESSO distribution of open-source codes.« less

Optimized multi-step NMR-crystallography approach for structural characterization of a stable quercetin solvate.

PubMed

Filip, Xenia; Miclaus, Maria; Martin, Flavia; Filip, Claudiu; Grosu, Ioana Georgeta

2017-05-10

Herein we report the preparation and solid state structural investigation of the 1,4-dioxane-quercetin solvate. NMR crystallography methods were employed for crystal structure determination of the solvate from microcrystalline powder. The stability of the compound relative to other reported quercetin solvates is discussed and found to be in perfect agreement with the hydrogen bonding networks/supra-molecular architectures formed in each case. It is also clearly shown that NMR crystallography represents an ideal analytical tool in such cases when hydrogen-bonding networks are required to be constrained at a high accuracy level. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantum chemical approaches to [NiFe] hydrogenase.

PubMed

Vaissier, Valerie; Van Voorhis, Troy

2017-05-09

The mechanism by which [NiFe] hydrogenase catalyses the oxidation of molecular hydrogen is a significant yet challenging topic in bioinorganic chemistry. With far-reaching applications in renewable energy and carbon mitigation, significant effort has been invested in the study of these complexes. In particular, computational approaches offer a unique perspective on how this enzyme functions at an electronic and atomistic level. In this article, we discuss state-of-the art quantum chemical methods and how they have helped deepen our comprehension of [NiFe] hydrogenase. We outline the key strategies that can be used to compute the (i) geometry, (ii) electronic structure, (iii) thermodynamics and (iv) kinetic properties associated with the enzymatic activity of [NiFe] hydrogenase and other bioinorganic complexes. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Reassigning the Structures of Natural Products Using NMR Chemical Shifts Computed with Quantum Mechanics: A Laboratory Exercise

ERIC Educational Resources Information Center

Palazzo, Teresa A.; Truong, Tiana T.; Wong, Shirley M. T.; Mack, Emma T.; Lodewyk, Michael W.; Harrison, Jason G.; Gamage, R. Alan; Siegel, Justin B.; Kurth, Mark J.; Tantillo, Dean J.

2015-01-01

An applied computational chemistry laboratory exercise is described in which students use modern quantum chemical calculations of chemical shifts to assign the structure of a recently isolated natural product. A pre/post assessment was used to measure student learning gains and verify that students demonstrated proficiency of key learning…

Spectroscopic, quantum chemical calculation and molecular docking of dipfluzine

NASA Astrophysics Data System (ADS)

Srivastava, Karnica; Srivastava, Anubha; Tandon, Poonam; Sinha, Kirti; Wang, Jing

2016-12-01

Molecular structure and vibrational analysis of dipfluzine (C27H29FN2O) were presented using FT-IR and FT-Raman spectroscopy and quantum chemical calculations. The theoretical ground state geometry and electronic structure of dipfluzine are optimized by the DFT/B3LYP/6-311++G (d,p) method and compared with those of the crystal data. The 1D potential energy scan was performed by varying the dihedral angle using B3LYP functional at 6-31G(d,p) level of theory and thus the most stable conformer of the compound were determined. Molecular electrostatic potential surface (MEPS), frontier orbital analysis and electronic reactivity descriptor were used to predict the chemical reactivity of molecule. Energies of intra- and inter-molecular hydrogen bonds in molecule and their electronic aspects were investigated by natural bond orbital (NBO). To find out the anti-apoptotic activity of the title compound molecular docking studies have been performed against protein Fas.

Include dispersion in quantum chemical modeling of enzymatic reactions: the case of isoaspartyl dipeptidase.

PubMed

Zhang, Hai-Mei; Chen, Shi-Lu

2015-06-09

The lack of dispersion in the B3LYP functional has been proposed to be the main origin of big errors in quantum chemical modeling of a few enzymes and transition metal complexes. In this work, the essential dispersion effects that affect quantum chemical modeling are investigated. With binuclear zinc isoaspartyl dipeptidase (IAD) as an example, dispersion is included in the modeling of enzymatic reactions by two different procedures, i.e., (i) geometry optimizations followed by single-point calculations of dispersion (approach I) and (ii) the inclusion of dispersion throughout geometry optimization and energy evaluation (approach II). Based on a 169-atom chemical model, the calculations show a qualitative consistency between approaches I and II in energetics and most key geometries, demonstrating that both approaches are available with the latter preferential since both geometry and energy are dispersion-corrected in approach II. When a smaller model without Arg233 (147 atoms) was used, an inconsistency was observed, indicating that the missing dispersion interactions are essentially responsible for determining equilibrium geometries. Other technical issues and mechanistic characteristics of IAD are also discussed, in particular with respect to the effects of Arg233.

Water-enhanced solvation of organic solutes in ketone and ester solvents

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

Lee, J.H.; Brunt, V. van; King, C.J.

1994-05-01

Previous research has shown that the solubilities of dicarboxylic acids in certain electron-donor solvents are substantially increased in the presence of water. Information on solubilities, liquid-liquid equilibria and maximum-boiling ternary azeotropes was screened so as to identify other systems where codissolved water appears to enhance solvation of organic solutes in solvents. Several carboxylic acids, an alcohol, diols, and phenols were selected for examination as solutes in ketone and ester solvents. Effects of water upon solute solubilities and volatilities were measured. Results showed that water-enhanced solvation is greatest for carboxylic acids. Solute activity coefficients decreased by factors of 2--3, 6--8, andmore » 7--10 due to the presence of water for mono-, di and tricarboxylic acids, respectively. Activity coefficients decreased by a factor of about 1.5 for ethanol and 1,2-propanediol as solutes. Water-enhanced solvation of phenols is small, when existent.« less

Angle-Resolved Photoemission of Solvated Electrons in Sodium-Doped Clusters.

PubMed

West, Adam H C; Yoder, Bruce L; Luckhaus, David; Saak, Clara-Magdalena; Doppelbauer, Maximilian; Signorell, Ruth

2015-04-16

Angle-resolved photoelectron spectroscopy of the unpaired electron in sodium-doped water, methanol, ammonia, and dimethyl ether clusters is presented. The experimental observations and the complementary calculations are consistent with surface electrons for the cluster size range studied. Evidence against internally solvated electrons is provided by the photoelectron angular distribution. The trends in the ionization energies seem to be mainly determined by the degree of hydrogen bonding in the solvent and the solvation of the ion core. The onset ionization energies of water and methanol clusters do not level off at small cluster sizes but decrease slightly with increasing cluster size.

Hydroxide Solvation and Transport in Anion Exchange Membranes.

PubMed

Chen, Chen; Tse, Ying-Lung Steve; Lindberg, Gerrick E; Knight, Chris; Voth, Gregory A

2016-01-27

Understanding hydroxide solvation and transport in anion exchange membranes (AEMs) can provide important insight into the design principles of these new membranes. To accurately model hydroxide solvation and transport, we developed a new multiscale reactive molecular dynamics model for hydroxide in aqueous solution, which was then subsequently modified for an AEM material. With this model, we investigated the hydroxide solvation structure and transport mechanism in the membrane. We found that a relatively even separation of the rigid side chains produces a continuous overlapping region for hydroxide transport that is made up of the first hydration shell of the tethered cationic groups. Our results show that hydroxide has a significant preference for this overlapping region, transporting through it and between the AEM side chains with substantial contributions from both vehicular (standard diffusion) and Grotthuss (proton hopping) mechanisms. Comparison of the AEM with common proton exchange membranes (PEMs) showed that the excess charge is less delocalized in the AEM than the PEMs, which is correlated with a higher free energy barrier for proton transfer reactions. The vehicular mechanism also contributes considerably more than the Grotthuss mechanism for hydroxide transport in the AEM, while our previous studies of PEM systems showed a larger contribution from the Grotthuss mechanism than the vehicular mechanism for proton transport. The activation energy barrier for hydroxide diffusion in the AEM is greater than that for proton diffusion in PEMs, implying a more significant enhancement of ion transport in the AEM at elevated temperatures.

Structural and vibrational spectral investigations of melaminium maleate monohydrate by FTIR, FT-Raman and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Arjunan, V.; Kalaivani, M.; Marchewka, M. K.; Mohan, S.

2013-04-01

The structural investigations of the molecular complex of melamine with maleic acid, namely melaminium maleate monohydrate have been carried out by quantum chemical methods in addition to FTIR, FT-Raman and far-infrared spectral studies. The quantum chemical studies were performed with DFT (B3LYP) method using 6-31G**, cc-pVDZ and 6-311++G** basis sets to determine the energy, structural and thermodynamic parameters of melaminium maleate monohydrate. The hydrogen atom from maleic acid was transferred to the melamine molecule giving the singly protonated melaminium cation. The ability of ions to form spontaneous three-dimensional structure through weak Osbnd H⋯O and Nsbnd H⋯O hydrogen bonds shows notable vibrational effects.

Revealing electronic open quantum systems with subsystem TDDFT

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

Krishtal, Alisa, E-mail: alisa.krishtal@rutgers.edu; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu

2016-03-28

Open quantum systems (OQSs) are perhaps the most realistic systems one can approach through simulations. In recent years, describing OQSs with Density Functional Theory (DFT) has been a prominent avenue of research with most approaches based on a density matrix partitioning in conjunction with an ad-hoc description of system-bath interactions. We propose a different theoretical approach to OQSs based on partitioning of the electron density. Employing the machinery of subsystem DFT (and its time-dependent extension), we provide a novel way of isolating and analyzing the various terms contributing to the coupling between the system and the surrounding bath. To illustratemore » the theory, we provide numerical simulations on a toy system (a molecular dimer) and on a condensed phase system (solvated excimer). The simulations show that non-Markovian dynamics in the electronic system-bath interactions are important in chemical applications. For instance, we show that the superexchange mechanism of transport in donor-bridge-acceptor systems is a non-Markovian interaction between the donor-acceptor (OQS) with the bridge (bath) which is fully characterized by real-time subsystem time-dependent DFT.« less

Modeling Free Energies of Solvation in Olive Oil

PubMed Central

Chamberlin, Adam C.; Levitt, David G.; Cramer, Christopher J.; Truhlar, Donald G.

2009-01-01

Olive oil partition coefficients are useful for modeling the bioavailability of drug-like compounds. We have recently developed an accurate solvation model called SM8 for aqueous and organic solvents (Marenich, A. V.; Olson, R. M.; Kelly, C. P.; Cramer, C. J.; Truhlar, D. G. J. Chem. Theory Comput. 2007, 3, 2011) and a temperature-dependent solvation model called SM8T for aqueous solution (Chamberlin, A. C.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. B 2008, 112, 3024). Here we describe an extension of SM8T to predict air–olive oil and water–olive oil partitioning for drug-like solutes as functions of temperature. We also describe the database of experimental partition coefficients used to parameterize the model; this database includes 371 entries for 304 compounds spanning the 291–310 K temperature range. PMID:19434923

The Influence of Solvent on the Structural Properties of trans-(NHC)PtI2Py Complex: A Platinum-Based Anticancer Drug

NASA Astrophysics Data System (ADS)

Sadigh Vishkaee, Teherh; Fazaeli, Reza

2018-06-01

Quantum chemical calculations using MPW1PW91 method were applied to analyze the solvent effect on the structural, spectral, and thermochemical parameters for a platinum-based anticancer drug trans-(NHC)PtI2Py complex. The solvent effects were examined by the self-consistent reaction field theory (SCRF) based on Polarizable Continuum Model (PCM). The linear correlations between the solvation energies, HOMO-LUMO gaps, IR-active stretching vibration of Pt-N bonds and N-H of NHC ligand with dielectric constants of solvents were studied. The wave numbers of these IR-active stretching vibrations in different solvents were correlated with the Kirkwood-Bauer-Magat equation (KBM). The thermodynamic activation parameter such free energy of solvation, enthalpy of solvation were also calculated.

Crystal structure and physicochemical characterization of ambazone monohydrate, anhydrous, and acetate salt solvate.

PubMed

Muresan-Pop, Marieta; Braga, Dario; Pop, Mihaela M; Borodi, Gheorghe; Kacso, Irina; Maini, Lucia

2014-11-01

The crystal structures of the monohydrate and anhydrous forms of ambazone were determined by single-crystal X-ray diffraction (SC-XRD). Ambazone monohydrate is characterized by an infinite three-dimensional network involving the water molecules, whereas anhydrous ambazone forms a two-dimensional network via hydrogen bonds. The reversible transformation between the monohydrate and anhydrous forms of ambazone was evidenced by thermal analysis, temperature-dependent X-ray powder diffraction and accelerated stability at elevated temperature, and relative humidity (RH). Additionally, a novel ambazone acetate salt solvate form was obtained and its nature was elucidated by SC-XRD. Powder dissolution measurements revealed a substantial solubility and dissolution rate improvement of acetate salt solvated form in water and physiological media compared with ambazone forms. Also, the acetate salt solvate displayed good thermal and solution stability but it transformed to the monohydrate on storage at elevated temperature and RH. Our study shows that despite the requirement for controlled storage conditions, the acetate salt solvated form could be an alternative to ambazone when solubility and bioavailability improvement is critical for the clinical efficacy of the drug product. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Thin Metallic Films from Solvated Metal Atoms.

DTIC Science & Technology

1987-07-14

platinium , and especially indium are discussed. N, ; ,, -- !, : N) By Dist , , . N S f1 -- ~~r, 821-19 C[ Thin metallic films from solvated metal atoms...metallic films. Cold, palladium, platinium , and especially indium are discussed. 1- INTRQDUCTION In the field of chemistry an active and broad area of

Predicting allergic contact dermatitis: a hierarchical structure activity relationship (SAR) approach to chemical classification using topological and quantum chemical descriptors

NASA Astrophysics Data System (ADS)

Basak, Subhash C.; Mills, Denise; Hawkins, Douglas M.

2008-06-01

A hierarchical classification study was carried out based on a set of 70 chemicals—35 which produce allergic contact dermatitis (ACD) and 35 which do not. This approach was implemented using a regular ridge regression computer code, followed by conversion of regression output to binary data values. The hierarchical descriptor classes used in the modeling include topostructural (TS), topochemical (TC), and quantum chemical (QC), all of which are based solely on chemical structure. The concordance, sensitivity, and specificity are reported. The model based on the TC descriptors was found to be the best, while the TS model was extremely poor.

High Color-Purity Green, Orange, and Red Light-Emitting Didoes Based on Chemically Functionalized Graphene Quantum Dots

NASA Astrophysics Data System (ADS)

Kwon, Woosung; Kim, Young-Hoon; Kim, Ji-Hee; Lee, Taehyung; Do, Sungan; Park, Yoonsang; Jeong, Mun Seok; Lee, Tae-Woo; Rhee, Shi-Woo

2016-04-01

Chemically derived graphene quantum dots (GQDs) to date have showed very broad emission linewidth due to many kinds of chemical bondings with different energy levels, which significantly degrades the color purity and color tunability. Here, we show that use of aniline derivatives to chemically functionalize GQDs generates new extrinsic energy levels that lead to photoluminescence of very narrow linewidths. We use transient absorption and time-resolved photoluminescence spectroscopies to study the electronic structures and related electronic transitions of our GQDs, which reveals that their underlying carrier dynamics is strongly related to the chemical properties of aniline derivatives. Using these functionalized GQDs as lumophores, we fabricate light-emitting didoes (LEDs) that exhibit green, orange, and red electroluminescence that has high color purity. The maximum current efficiency of 3.47 cd A-1 and external quantum efficiency of 1.28% are recorded with our LEDs; these are the highest values ever reported for LEDs based on carbon-nanoparticle phosphors. This functionalization of GQDs with aniline derivatives represents a new method to fabricate LEDs that produce natural color.

Preferential Solvation of Silver (I) Bromate in Methanol-Dimethylsulfoxide Mixtures

NASA Astrophysics Data System (ADS)

Janardhanan, S.; Kalidas, C.

1984-06-01

The solubiltiy of silver bromate, the Gibbs transfer energy of Ag+ and BrO3- and the solvent transport number in methanol-dimethyl sulfoxide mixtures are reported. The solubility of silver bromate increases with addition of DMSO. The Gibbs energy of transfer of the silver ion (based on the ferrocene reference method) decreases, while that of the bromate ion becomes slightly negative with the addition of DMSO. The solvent transport number A passes through a maximum (⊿ = 1.0 at XDMSO = 0.65. From these results, it is concluded that the silver ion is preferentially solvated by DMSO whereas the bromate ion shows no preferential solvation.

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

NASA Astrophysics Data System (ADS)

Chong, Song-Ho; Ham, Sihyun

2011-07-01

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

Characterization of heterocyclic rings through quantum chemical topology.

PubMed

Griffiths, Mark Z; Popelier, Paul L A

2013-07-22

Five-membered rings are found in a myriad of molecules important in a wide range of areas such as catalysis, nutrition, and drug and agrochemical design. Systematic insight into their largely unexplored chemical space benefits from first principle calculations presented here. This study comprehensively investigates a grand total of 764 different rings, all geometry optimized at the B3LYP/6-311+G(2d,p) level, from the perspective of Quantum Chemical Topology (QCT). For the first time, a 3D space of local topological properties was introduced, in order to characterize rings compactly. This space is called RCP space, after the so-called ring critical point. This space is analogous to BCP space, named after the bond critical point, which compactly and successfully characterizes a chemical bond. The relative positions of the rings in RCP space are determined by the nature of the ring scaffold, such as the heteroatoms within the ring or the number of π-bonds. The summed atomic QCT charges of the five ring atoms revealed five features (number and type of heteroatom, number of π-bonds, substituent and substitution site) that dictate a ring's net charge. Each feature independently contributes toward a ring's net charge. Each substituent has its own distinct and systematic effect on the ring's net charge, irrespective of the ring scaffold. Therefore, this work proves the possibility of designing a ring with specific properties by fine-tuning it through manipulation of these five features.

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

NASA Astrophysics Data System (ADS)

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

2010-09-01

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

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

PubMed Central

2017-01-01

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

Towards quantum chemistry on a quantum computer.

PubMed

Lanyon, B P; Whitfield, J D; Gillett, G G; Goggin, M E; Almeida, M P; Kassal, I; Biamonte, J D; Mohseni, M; Powell, B J; Barbieri, M; Aspuru-Guzik, A; White, A G

2010-02-01

Exact first-principles calculations of molecular properties are currently intractable because their computational cost grows exponentially with both the number of atoms and basis set size. A solution is to move to a radically different model of computing by building a quantum computer, which is a device that uses quantum systems themselves to store and process data. Here we report the application of the latest photonic quantum computer technology to calculate properties of the smallest molecular system: the hydrogen molecule in a minimal basis. We calculate the complete energy spectrum to 20 bits of precision and discuss how the technique can be expanded to solve large-scale chemical problems that lie beyond the reach of modern supercomputers. These results represent an early practical step toward a powerful tool with a broad range of quantum-chemical applications.

Chemical and explosive detections using photo-acoustic effect and quantum cascade lasers

NASA Astrophysics Data System (ADS)

Choa, Fow-Sen

2013-12-01

Photoacoustic (PA) effect is a sensitive spectroscopic technique for chemical sensing. In recent years, with the development of quantum cascade lasers (QCLs), significant progress has been achieved for PA sensing applications. Using high-power, tunable mid-IR QCLs as laser sources, PA chemical sensor systems have demonstrated parts-pertrillion- level detection sensitivity. Many of these high sensitivity measurements were demonstrated locally in PA cells. Recently, we have demonstrated standoff PA detection of isopropanol vapor for more than 41 feet distance using a quantum cascade laser and a microphone with acoustic reflectors. We also further demonstrated solid phase TNT detections at a standoff distance of 8 feet. To further calibrate the detection sensitivity, we use nerve gas simulants that were generated and calibrated by a commercial vapor generator. Standoff detection of gas samples with calibrated concentration of 2.3 ppm was achieved at a detection distance of more than 2 feet. An extended detection distance up to 14 feet was observed for a higher gas concentration of 13.9 ppm. For field operations, array of microphones and microphone-reflector pairs can be utilized to achieve noise rejection and signal enhancement. We have experimentally demonstrated that the signal and noise spectra of the 4 microphone/4 reflector system with a combined SNR of 12.48 dB. For the 16-microphone and one reflector case, an SNR of 17.82 was achieved. These successful chemical sensing demonstrations will likely create new demands for widely tunable QCLs with ultralow threshold (for local fire-alarm size detection systems) and high-power (for standoff detection systems) performances.

Structural and vibrational spectral investigations of melaminium maleate monohydrate by FTIR, FT-Raman and quantum chemical calculations.

PubMed

Arjunan, V; Kalaivani, M; Marchewka, M K; Mohan, S

2013-04-15

The structural investigations of the molecular complex of melamine with maleic acid, namely melaminium maleate monohydrate have been carried out by quantum chemical methods in addition to FTIR, FT-Raman and far-infrared spectral studies. The quantum chemical studies were performed with DFT (B3LYP) method using 6-31G(**), cc-pVDZ and 6-311++G(**) basis sets to determine the energy, structural and thermodynamic parameters of melaminium maleate monohydrate. The hydrogen atom from maleic acid was transferred to the melamine molecule giving the singly protonated melaminium cation. The ability of ions to form spontaneous three-dimensional structure through weak OH···O and NH···O hydrogen bonds shows notable vibrational effects. Copyright © 2013 Elsevier B.V. All rights reserved.

The influence of structural factors on the composition, spectral-luminescent properties and thermal stability of zinc(II) bis(dipyrromethenate)s crystal solvates with amines

NASA Astrophysics Data System (ADS)

Guseva, G. B.; Ksenofontov, A. A.; Antina, E. V.

2017-02-01

It was found that 3,3‧-, 2,3‧- and 2,2‧-zinc(II) bis(dipyrromethenate)s ([Zn2L2]) form stable supramolecular complexes with aromatic and aliphatic amines (X - pyridine (Py), N,N-dimethylmethanamide (DMF), diethylamine (DEA) and triethylamine (TEA)) of the composition [Zn2L2(X)n]. Composition, stability and spectral-luminescent properties of the [Zn2L2(X)n] crystal solvates were studied by means of FTIR, PXRD, thermal, mass spectral, absorption, and fluorescence analyses. Spectroscopic studies showed that the quantum yield (φ) of [Zn2L2(Х)n] in cyclohexane is much lower (to ∼ 1.4-4.0 times) than φ for the [Zn2L2]. Crystal solvates are stable up to a temperature ∼367.35-427.55 K. It is demonstrated, that the high interactions energies (Znsbnd N) in [Zn2L2(X)n] supramolecular complexes are the main cause of the fluorescence quenching of [Zn2L2] luminophores in the presence of electron-donor molecules. The obtained results are of interest for the development on the basis of [Zn2L2] of a new fluorescent sensors of the electron donor molecules.

Hydroxide Solvation and Transport in Anion Exchange Membranes

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

Chen, Chen; Tse, Ying-Lung Steve; Lindberg, Gerrick E.

Understanding hydroxide solvation and transport in anion exchange membranes (AEMs) can provide important insight into the design principles of these new membranes. To accurately model hydroxide solvation and transport, we developed a new multiscale reactive molecular dynamics model for hydroxide in aqueous solution, which was then subsequently modified for an AEM material. With this model, we investigated the hydroxide solvation structure and transport mechanism in the membrane. We found that a relatively even separation of the rigid side chains produces a continuous overlapping region for hydroxide transport that is made up of the first hydration shell of the tethered cationicmore » groups. Our results show that hydroxide has a significant preference for this overlapping region, transporting through it and between the AEM side chains with substantial contributions from both vehicular (standard diffusion) and Grotthuss (proton hopping) mechanisms. Comparison of the AEM with common proton exchange membranes (PEMs) showed that the excess charge is less delocalized in the AEM than the PEMs, which is correlated with a higher free energy barrier for proton transfer reactions. The vehicular mechanism also contributes considerably more than the Grotthuss mechanism for hydroxide transport in the AEM, while our previous studies of PEM systems showed a larger contribution from the Grotthuss mechanism than the vehicular mechanism for proton transport. The activation energy barrier for hydroxide diffusion in the AEM is greater than that for proton diffusion in PEMs, implying a more significant enhancement of ion transport in the AEM at elevated temperatures.« less

Reactions of solvated electrons initiated by sodium atom ionization at the vacuum-liquid interface.

PubMed

Alexander, William A; Wiens, Justin P; Minton, Timothy K; Nathanson, Gilbert M

2012-03-02

Solvated electrons are powerful reagents in the liquid phase that break chemical bonds and thereby create additional reactive species, including hydrogen atoms. We explored the distinct chemistry that ensues when electrons are liberated near the liquid surface rather than within the bulk. Specifically, we detected the products resulting from exposure of liquid glycerol to a beam of sodium atoms. The Na atoms ionized in the surface region, generating electrons that reacted with deuterated glycerol, C(3)D(5)(OD)(3), to produce D atoms, D(2), D(2)O, and glycerol fragments. Surprisingly, 43 ± 4% of the D atoms traversed the interfacial region and desorbed into vacuum before attacking C-D bonds to produce D(2).

Ultrafast fluxional exchange dynamics in electrolyte solvation sheath of lithium ion battery

NASA Astrophysics Data System (ADS)

Lee, Kyung-Koo; Park, Kwanghee; Lee, Hochan; Noh, Yohan; Kossowska, Dorota; Kwak, Kyungwon; Cho, Minhaeng

2017-03-01

Lithium cation is the charge carrier in lithium-ion battery. Electrolyte solution in lithium-ion battery is usually based on mixed solvents consisting of polar carbonates with different aliphatic chains. Despite various experimental evidences indicating that lithium ion forms a rigid and stable solvation sheath through electrostatic interactions with polar carbonates, both the lithium solvation structure and more importantly fluctuation dynamics and functional role of carbonate solvent molecules have not been fully elucidated yet with femtosecond vibrational spectroscopic methods. Here we investigate the ultrafast carbonate solvent exchange dynamics around lithium ions in electrolyte solutions with coherent two-dimensional infrared spectroscopy and find that the time constants of the formation and dissociation of lithium-ion...carbonate complex in solvation sheaths are on a picosecond timescale. We anticipate that such ultrafast microscopic fluxional processes in lithium-solvent complexes could provide an important clue to understanding macroscopic mobility of lithium cation in lithium-ion battery on a molecular level.

Ultrafast fluxional exchange dynamics in electrolyte solvation sheath of lithium ion battery

PubMed Central

Lee, Kyung-Koo; Park, Kwanghee; Lee, Hochan; Noh, Yohan; Kossowska, Dorota; Kwak, Kyungwon; Cho, Minhaeng

2017-01-01

Lithium cation is the charge carrier in lithium-ion battery. Electrolyte solution in lithium-ion battery is usually based on mixed solvents consisting of polar carbonates with different aliphatic chains. Despite various experimental evidences indicating that lithium ion forms a rigid and stable solvation sheath through electrostatic interactions with polar carbonates, both the lithium solvation structure and more importantly fluctuation dynamics and functional role of carbonate solvent molecules have not been fully elucidated yet with femtosecond vibrational spectroscopic methods. Here we investigate the ultrafast carbonate solvent exchange dynamics around lithium ions in electrolyte solutions with coherent two-dimensional infrared spectroscopy and find that the time constants of the formation and dissociation of lithium-ion···carbonate complex in solvation sheaths are on a picosecond timescale. We anticipate that such ultrafast microscopic fluxional processes in lithium-solvent complexes could provide an important clue to understanding macroscopic mobility of lithium cation in lithium-ion battery on a molecular level. PMID:28272396

Ultrafast fluxional exchange dynamics in electrolyte solvation sheath of lithium ion battery.

PubMed

Lee, Kyung-Koo; Park, Kwanghee; Lee, Hochan; Noh, Yohan; Kossowska, Dorota; Kwak, Kyungwon; Cho, Minhaeng

2017-03-08

Lithium cation is the charge carrier in lithium-ion battery. Electrolyte solution in lithium-ion battery is usually based on mixed solvents consisting of polar carbonates with different aliphatic chains. Despite various experimental evidences indicating that lithium ion forms a rigid and stable solvation sheath through electrostatic interactions with polar carbonates, both the lithium solvation structure and more importantly fluctuation dynamics and functional role of carbonate solvent molecules have not been fully elucidated yet with femtosecond vibrational spectroscopic methods. Here we investigate the ultrafast carbonate solvent exchange dynamics around lithium ions in electrolyte solutions with coherent two-dimensional infrared spectroscopy and find that the time constants of the formation and dissociation of lithium-ion···carbonate complex in solvation sheaths are on a picosecond timescale. We anticipate that such ultrafast microscopic fluxional processes in lithium-solvent complexes could provide an important clue to understanding macroscopic mobility of lithium cation in lithium-ion battery on a molecular level.

Atomistic characterization of the active-site solvation dynamics of a model photocatalyst

DOE PAGES

van Driel, Tim B.; Kjær, Kasper S.; Hartsock, Robert W.; ...

2016-11-28

The interactions between the reactive excited state of molecular photocatalysts and surrounding solvent dictate reaction mechanisms and pathways, but are not readily accessible to conventional optical spectroscopic techniques. Here we report an investigation of the structural and solvation dynamics following excitation of a model photocatalytic molecular system [Ir 2(dimen) 4] 2+, where dimen is para-diisocyanomenthane. The time-dependent structural changes in this model photocatalyst, as well as the changes in the solvation shell structure, have been measured with ultrafast diffuse X-ray scattering and simulated with Born-Oppenheimer Molecular Dynamics. Both methods provide direct access to the solute–solvent pair distribution function, enabling themore » solvation dynamics around the catalytically active iridium sites to be robustly characterized. Our results provide evidence for the coordination of the iridium atoms by the acetonitrile solvent and demonstrate the viability of using diffuse X-ray scattering at free-electron laser sources for studying the dynamics of photocatalysis.« less

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

PubMed

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

2016-12-21

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

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

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.

Prediction of contaminant persistence in aqueous phase: a quantum chemical approach.

PubMed

Blotevogel, Jens; Mayeno, Arthur N; Sale, Tom C; Borch, Thomas

2011-03-15

At contaminated field sites where active remediation measures are not feasible, monitored natural attenuation is sometimes the only alternative for surface water or groundwater decontamination. However, due to slow degradation rates of some contaminants under natural conditions, attenuation processes and their performance assessment can take several years to decades to complete. Here, we apply quantum chemical calculations to predict contaminant persistence in the aqueous phase. For the test compound hexamethylphosphoramide (HMPA), P-N bond hydrolysis is the only thermodynamically favorable reaction that may lead to its degradation under reducing conditions. Through calculation of aqueous Gibbs free energies of activation for all potential reaction mechanisms, it is predicted that HMPA hydrolyzes via an acid-catalyzed mechanism at pH < 8.2, and an uncatalyzed mechanism at pH 8.2-8.5. The estimated half-lives of thousands to hundreds of thousands of years over the groundwater-typical pH range of 6.0 to 8.5 indicate that HMPA will be persistent in the absence of suitable oxidants. At pH 0, where the hydrolysis reaction is rapid enough to enable measurement, the experimentally determined rate constant and half-life are in excellent agreement with the predicted values. Since the quantum chemical methodology described herein can be applied to virtually any contaminant or reaction of interest, it is especially valuable for the prediction of persistence when slow reaction rates impede experimental investigations and appropriate QSARs are unavailable.

Biomimetic, Mild Chemical Synthesis of CdTe-GSH Quantum Dots with Improved Biocompatibility

PubMed Central

Pérez-Donoso, José M.; Monrás, Juan P.; Bravo, Denisse; Aguirre, Adam; Quest, Andrew F.; Osorio-Román, Igor O.; Aroca, Ricardo F.; Chasteen, Thomas G.; Vásquez, Claudio C.

2012-01-01

Multiple applications of nanotechnology, especially those involving highly fluorescent nanoparticles (NPs) or quantum dots (QDs) have stimulated the research to develop simple, rapid and environmentally friendly protocols for synthesizing NPs exhibiting novel properties and increased biocompatibility. In this study, a simple protocol for the chemical synthesis of glutathione (GSH)-capped CdTe QDs (CdTe-GSH) resembling conditions found in biological systems is described. Using only CdCl2, K2TeO3 and GSH, highly fluorescent QDs were obtained under pH, temperature, buffer and oxygen conditions that allow microorganisms growth. These CdTe-GSH NPs displayed similar size, chemical composition, absorbance and fluorescence spectra and quantum yields as QDs synthesized using more complicated and expensive methods. CdTe QDs were not freely incorporated into eukaryotic cells thus favoring their biocompatibility and potential applications in biomedicine. In addition, NPs entry was facilitated by lipofectamine, resulting in intracellular fluorescence and a slight increase in cell death by necrosis. Toxicity of the as prepared CdTe QDs was lower than that observed with QDs produced by other chemical methods, probably as consequence of decreased levels of Cd+2 and higher amounts of GSH. We present here the simplest, fast and economical method for CdTe QDs synthesis described to date. Also, this biomimetic protocol favors NPs biocompatibility and helps to establish the basis for the development of new, “greener” methods to synthesize cadmium-containing QDs. PMID:22292028

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.

Exploiting Locality in Quantum Computation for Quantum Chemistry.

PubMed

McClean, Jarrod R; Babbush, Ryan; Love, Peter J; Aspuru-Guzik, Alán

2014-12-18

Accurate prediction of chemical and material properties from first-principles quantum chemistry is a challenging task on traditional computers. Recent developments in quantum computation offer a route toward highly accurate solutions with polynomial cost; however, this solution still carries a large overhead. In this Perspective, we aim to bring together known results about the locality of physical interactions from quantum chemistry with ideas from quantum computation. We show that the utilization of spatial locality combined with the Bravyi-Kitaev transformation offers an improvement in the scaling of known quantum algorithms for quantum chemistry and provides numerical examples to help illustrate this point. We combine these developments to improve the outlook for the future of quantum chemistry on quantum computers.

Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies.

PubMed

Sodt, Alexander J; Mei, Ye; König, Gerhard; Tao, Peng; Steele, Ryan P; Brooks, Bernard R; Shao, Yihan

2015-03-05

In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton-Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. They produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin-luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy.

Incorporation of Mn2+ into CdSe quantum dots by chemical bath co-deposition method for photovoltaic enhancement of quantum dot-sensitized solar cells

NASA Astrophysics Data System (ADS)

Zhang, Chenguang; Liu, Shaowen; Liu, Xingwei; Deng, Fei; Xiong, Yan; Tsai, Fang-Chang

2018-03-01

A photoelectric conversion efficiency (PCE) of 4.9% was obtained under 100 mW cm-2 illumination by quantum-dot-sensitized solar cells (QDSSCs) using a CdS/Mn : CdSe sensitizer. CdS quantum dots (QDs) were deposited on a TiO2 mesoporous oxide film by successive ionic layer absorption and reaction. Mn2+ doping into CdSe QDs is an innovative and simple method-chemical bath co-deposition, that is, mixing the Mn ion source with CdSe precursor solution for Mn : CdSe QD deposition. Compared with the CdS/CdSe sensitizer without Mn2+ incorporation, the PCE was increased from 3.4% to 4.9%. The effects of Mn2+ doping on the chemical, physical and photovoltaic properties of the QDSSCs were investigated by energy dispersive spectrometry, absorption spectroscopy, photocurrent density-voltage characteristics and electrochemical impedance spectroscopy. Mn-doped CdSe QDs in QDSSCs can obtain superior light absorption, faster electron transport and slower charge recombination than CdSe QDs.

Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces

DOE PAGES

Herron, Jeffrey A.; Morikawa, Yoshitada; Mavrikakis, Manos

2016-08-08

Using ab initio molecular dynamics (as implemented in periodic, self-consistent (GGA-PBE) density functional theory (DFT) we investigated the mechanism of methanol electro-oxidation on Pt(111). We investigated the role of solvation and electrode potential on the energetics of the first proton transfer step, methanol electro-oxidation to methoxy (CH 3O) or hydroxymethyl (CH 2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), while the binding energy of methanol and hydroxymethyl are not significantly affected. The free energies of activation for breaking the C-H and O-H bonds in methanol were calculated through a Blue Moon Ensemble using constrainedmore » ab initio molecular dynamics. Calculated barriers for these elementary steps on unsolvated, uncharged Pt(111) are similar to results for climbing-image nudged elastic band calculations from the literature. Solvation reduces the barrier for both C-H and O-H bond activation steps with respect to their vapor phase values, though the effect is more pronounced for C-H bond activation due to less disruption of the hydrogen-bond network. The calculated activation energy barriers show that breaking the C-H bond of methanol is more facile than the O-H bond on solvated negatively biased, or uncharged Pt(111). Furthermore, with positive bias, O-H bond activation is enhanced, becoming slightly more facile than C-H bond activation.« less

Empirical, thermodynamic and quantum-chemical investigations of inclusion complexation between flavanones and (2-hydroxypropyl)-cyclodextrins.

PubMed

Liu, Benguo; Li, Wei; Nguyen, Tien An; Zhao, Jian

2012-09-15

The inclusion complexation of (2-hydroxypropyl)-cyclodextrins with flavanones was investigated by phase solubility measurements, as well as thermodynamic and quantum chemical methods. Inclusion complexes were formed between (2-hydroxypropyl)-α-cyclodextrin (HP-α-CD), (2-hydroxypropyl)-β-cyclodextrin (HP-β-CD), (2-hydroxypropyl)-γ-cyclodextrin (HP-γ-CD) and β-cyclodextrin (β-CD) and four flavanones (naringenin, naringin, hesperetin and dihydromyricetin) in aqueous solutions and their phase solubility was determined. For all the flavanones, the stability constants of their complexes formed with different CDs followed the rank order: HP-β-CD (MW 1540)>HP-β-CD (MW 1460)>HP-β-CD (MW 1380)>β-CD>HP-γ-CD>HP-α-CD. Experimental results and quantum chemical calculations showed that the ability of flavanones to form inclusion complex with (2-hydroxypropyl)-cyclodextrins was determined by both the steric effect and hydrophobicity of the flavanones. For flavanones that have similar molecular volumes, the hydrophobicity of the molecule was the main determining factor of its ability to form inclusion complexes with HP-β-CD, and the hydrophobicity parameter Log P is highly correlated with the stability constant of the complexes. Results of thermodynamic study demonstrated that hydrophobic interaction is the main driving force for the formation process of the flavanone-CD inclusion complexes. Quantum chemical analysis of the most active hydroxyl groups and HOMO (the highest occupied molecular orbital) showed that the B ring of the flavanones was most likely involved in hydrogen bonding with the side groups in the cavity of the CDs, through which the inclusion complex was stabilised. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

DOE PAGES

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

2017-09-18

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

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

PubMed

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

2011-06-06

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

Quantum Dot and Polymer Composite Cross-Reactive Array for Chemical Vapor Detection.

PubMed

Bright, Collin J; Nallon, Eric C; Polcha, Michael P; Schnee, Vincent P

2015-12-15

A cross-reactive chemical sensing array was made from CdSe Quantum Dots (QDs) and five different organic polymers by inkjet printing to create segmented fluorescent composite regions on quartz substrates. The sensor array was challenged with exposures from two sets of analytes, including one set of 14 different functionalized benzenes and one set of 14 compounds related to security concerns, including the explosives trinitrotoluene (TNT) and ammonium nitrate. The array was broadly responsive to analytes with different chemical functionalities due to the multiple sensing mechanisms that altered the QDs' fluorescence. The sensor array displayed excellent discrimination between members within both sets. Classification accuracy of more than 93% was achieved, including the complete discrimination of very similar dinitrobenzene isomers and three halogenated, substituted benzene compounds. The simple fabrication, broad responsivity, and high discrimination capacity of this type of cross-reactive array are ideal qualities for the development of sensors with excellent sensitivity to chemical and explosive threats while maintaining low false alarm rates.

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

PubMed

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

2008-06-26

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

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

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

Role of Quantum Vibrations on the Structural, Electronic, and Optical Properties of 9-Methylguanine.

PubMed

Law, Yu Kay; Hassanali, Ali A

2015-11-05

In this work, we report theoretical predictions of the UV-absorption spectra of 9-methylguanine using time dependent density functional theory (TDDFT). Molecular dynamics simulations of the hydrated DNA base are peformed using an empirical force field, Born-Oppenheimer ab initio molecular dynamics (AIMD), and finally path-integral AIMD to understand the role of the underlying electronic potential, solvation, and nuclear quantum vibrations on the absorption spectra. It is shown that the conformational distributions, including hydrogen bonding interactions, are perturbed by the inclusion of nuclear quantum effects, leading to significant changes in the total charge and dipole fluctuations of the DNA base. The calculated absorption spectra using the different sampling protocols shows that the inclusion of nuclear quantum effects causes a significant broadening and red shift of the spectra bringing it into closer agreement with experiments.

Quantum-chemical calculations and electron diffraction study of the equilibrium molecular structure of vitamin K3

NASA Astrophysics Data System (ADS)

Khaikin, L. S.; Tikhonov, D. S.; Grikina, O. E.; Rykov, A. N.; Stepanov, N. F.

2014-05-01

The equilibrium molecular structure of 2-methyl-1,4-naphthoquinone (vitamin K3) having C s symmetry is experimentally characterized for the first time by means of gas-phase electron diffraction using quantum-chemical calculations and data on the vibrational spectra of related compounds.

Chemical potentials and thermodynamic characteristics of ideal Bose- and Fermi-gases in the region of quantum degeneracy

NASA Astrophysics Data System (ADS)

Sotnikov, A. G.; Sereda, K. V.; Slyusarenko, Yu. V.

2017-01-01

Calculations of chemical potentials for ideal monatomic gases with Bose-Einstein and Fermi-Dirac statistics as functions of temperature, across the temperature region that is typical for the collective quantum degeneracy effect, are presented. Numerical calculations are performed without any additional approximations, and explicit dependences of the chemical potentials on temperature are constructed at a fixed density of gas particles. Approximate polynomial dependences of chemical potentials on temperature are obtained that allow for the results to be used in further studies without re-applying the involved numerical methods. The ease of using the obtained representations is demonstrated on examples of deformation of distribution for a population of energy states at low temperatures, and on the impact of quantum statistics (exchange interaction) on the equations of state for ideal gases and some of the thermodynamic properties thereof. The results of this study essentially unify two opposite limiting cases in an intermediate region that are used to describe the equilibrium states of ideal gases, which are well known from university courses on statistical physics, thus adding value from an educational point of view.

Quantum cascade transmitters for ultrasensitive chemical agent and explosives detection

NASA Astrophysics Data System (ADS)

Schultz, John F.; Taubman, Matthew S.; Harper, Warren W.; Williams, Richard M.; Myers, Tanya L.; Cannon, Bret D.; Sheen, David M.; Anheier, Norman C., Jr.; Allen, Paul J.; Sundaram, S. K.; Johnson, Bradley R.; Aker, Pamela M.; Wu, Ming C.; Lau, Erwin K.

2003-07-01

The small size, high power, promise of access to any wavelength between 3.5 and 16 microns, substantial tuning range about a chosen center wavelength, and general robustness of quantum cascade (QC) lasers provide opportunities for new approaches to ultra-sensitive chemical detection and other applications in the mid-wave infrared. PNNL is developing novel remote and sampling chemical sensing systems based on QC lasers, using QC lasers loaned by Lucent Technologies. In recent months laboratory cavity-enhanced sensing experiments have achieved absorption sensitivities of 8.5 x 10-11 cm-1 Hz-1/2, and the PNNL team has begun monostatic and bi-static frequency modulated, differential absorption lidar (FM DIAL) experiments at ranges of up to 2.5 kilometers. In related work, PNNL and UCLA are developing miniature QC laser transmitters with the multiplexed tunable wavelengths, frequency and amplitude stability, modulation characteristics, and power levels needed for chemical sensing and other applications. Current miniaturization concepts envision coupling QC oscillators, QC amplifiers, frequency references, and detectors with miniature waveguides and waveguide-based modulators, isolators, and other devices formed from chalcogenide or other types of glass. Significant progress has been made on QC laser stabilization and amplification, and on development and characterization of high-purity chalcogenide glasses, waveguide writing techniques, and waveguide metrology.

Photoinduced electron transfer and solvation in iodide-doped acetonitrile clusters.

PubMed

Ehrler, Oli T; Griffin, Graham B; Young, Ryan M; Neumark, Daniel M

2009-04-02

We have used ultrafast time-resolved photoelectron imaging to measure charge transfer dynamics in iodide-doped acetonitrile clusters I(-)(CH(3)CN)(n) with n = 5-10. Strong modulations of vertical detachment energies were observed following charge transfer from the halide, allowing interpretation of the ongoing dynamics. We observe a sharp drop in the vertical detachment energy (VDE) within 300-400 fs, followed by a biexponential increase that is complete by approximately 10 ps. Comparison to theory suggests that the iodide is internally solvated and that photodetachment results in formation of a diffuse electron cloud in a confined cavity. We interpret the initial drop in VDE as a combination of expansion of the cavity and localization of the excess electron on one or two solvent molecules. The subsequent increase in VDE is attributed to a combination of the I atom leaving the cavity and rearrangement of the acetonitrile molecules to solvate the electron. The n = 5-8 clusters then show a drop in VDE of around 50 meV on a much longer time scale. The long-time VDEs are consistent with those of (CH(3)CN)(n)(-) clusters with internally solvated electrons. Although the excited-state created by the pump pulse decays by emission of a slow electron, no such decay is seen by 200 ps.

Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

PubMed Central

2012-01-01

Implicit solvation is a mean force approach to model solvent forces acting on a solute molecule. It is frequently used in molecular simulations to reduce the computational cost of solvent treatment. In the first instance, the free energy of solvation and the associated solvent–solute forces can be approximated by a function of the solvent-accessible surface area (SASA) of the solute and differentiated by an atom–specific solvation parameter σiSASA. A procedure for the determination of values for the σiSASA parameters through matching of explicit and implicit solvation forces is proposed. Using the results of Molecular Dynamics simulations of 188 topologically diverse protein structures in water and in implicit solvent, values for the σiSASA parameters for atom types i of the standard amino acids in the GROMOS force field have been determined. A simplified representation based on groups of atom types σgSASA was obtained via partitioning of the atom–type σiSASA distributions by dynamic programming. Three groups of atom types with well separated parameter ranges were obtained, and their performance in implicit versus explicit simulations was assessed. The solvent forces are available at http://mathbio.nimr.mrc.ac.uk/wiki/Solvent_Forces. PMID:23180979

Solvation of the fluorine containing anions and their lithium salts in propylene carbonate and dimethoxyethane.

PubMed

Chaban, Vitaly

2015-07-01

Electrolyte solutions based on the propylene carbonate (PC)-dimethoxyethane (DME) mixtures are of significant importance and urgency due to emergence of lithium-ion batteries. Solvation and coordination of the lithium cation in these systems have been recently attended in detail. However, analogous information concerning anions (tetrafluoroborate, hexafluorophosphate) is still missed. This work reports PM7-MD simulations (electronic-structure level of description) to include finite-temperature effects on the anion solvation regularities in the PC-DME mixture. The reported result evidences that the anions appear weakly solvated. This observation is linked to the absence of suitable coordination sites in the solvent molecules. In the concentrated electrolyte solutions, both BF4(-) and PF6(-) prefer to exist as neutral ion pairs (LiBF4, LiPF6).

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

PubMed

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

2016-01-07

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

Solvation of decane and benzene in mixtures of 1-octanol and N, N-dimethylformamide

NASA Astrophysics Data System (ADS)

Kustov, A. V.; Smirnova, N. L.

2016-09-01

The heats of dissolution of decane and benzene in a model system of octanol-1 (OctOH) and N, N-dimethylformamide (DMF) at 308 K are measured using a variable temperature calorimeter equipped with an isothermal shell. Standard enthalpies are determined and standard heat capacities of dissolution in the temperature range of 298-318 K are calculated using data obtained in [1, 2]. The state of hydrocarbon molecules in a binary mixture is studied in terms of the enhanced coordination model (ECM). Benzene is shown to be preferentially solvated by DMF over the range of physiological temperatures. The solvation shell of decane is found to be strongly enriched with 1-octanol. It is obvious that although both hydrocarbons are nonpolar, the presence of the aromatic π-system in benzene leads to drastic differences in their solvation in a lipid-protein medium.

Quantum Chemical and Docking Insights into Bioavailability Enhancement of Curcumin by Piperine in Pepper.

PubMed

Patil, Vaishali M; Das, Sukanya; Balasubramanian, Krishnan

2016-05-26

We combine quantum chemical and molecular docking techniques to provide new insights into how piperine molecule in various forms of pepper enhances bioavailability of a number of drugs including curcumin in turmeric for which it increases its bioavailability by a 20-fold. We have carried out docking studies of quantum chemically optimized piperine structure binding to curcumin, CYP3A4 in cytochrome P450, p-Glycoprotein and UDP-glucuronosyltransferase (UGT), the enzyme responsible for glucuronosylation, which increases the solubility of curcumin. All of these studies establish that piperine binds to multiple sites on the enzymes and also intercalates with curcumin forming a hydrogen bonded complex with curcumin. The conjugated network of double bonds and the presence of multiple charge centers of piperine offer optimal binding sites for piperine to bind to enzymes such as UDP-GDH, UGT, and CYP3A4. Piperine competes for curcumin's intermolecular hydrogen bonding and its stacking propensity by hydrogen bonding with enolic proton of curcumin. This facilitates its metabolic transport, thereby increasing its bioavailability both through intercalation into curcumin layers through intermolecular hydrogen bonding, and by inhibiting enzymes that cause glucuronosylation of curcumin.

An investigation into the effective surface passivation of quantum dots by a photo-assisted chemical method

NASA Astrophysics Data System (ADS)

Joo, So-Yeong; Park, Hyun-Su; Kim, Do-yeon; Kim, Bum-Sung; Lee, Chan Gi; Kim, Woo-Byoung

2018-01-01

In this study, we have developed an effective amino passivation process for quantum dots (QDs) at room temperature and have investigated a passivation mechanism using a photo-assisted chemical method. As a result of the reverse reaction of the H2O molecules, the etching kinetics of the photo-assisted chemical method increased upon increasing the 3-amino-1-propanol (APOL)/H2O ratio of the etching solution. Photon-excited electron-hole pairs lead to strong bonding between the organic and surface atoms of the QDs, and results in an increase of the quantum yield (QY%). This passivation method is also applicable to CdSe/ZnSe core/shell structures of QDs, due to the passivation of mid-gap defects states at the interface. The QY% of the as-synthesized CdSe QDs is dramatically enhanced by the amino passivation from 37% to 75% and the QY% of the CdSe/ZnSe core/shell QDs is also improved by ˜28%.

Quantum mechanical model for the anticarcinogenic effect of extremely-low-frequency electromagnetic fields on early chemical hepatocarcinogenesis

NASA Astrophysics Data System (ADS)

Godina-Nava, Juan José; Torres-Vega, Gabino; López-Riquelme, Germán Octavio; López-Sandoval, Eduardo; Samana, Arturo Rodolfo; García Velasco, Fermín; Hernández-Aguilar, Claudia; Domínguez-Pacheco, Arturo

2017-02-01

Using the conventional Haberkorn approach, it is evaluated the recombination of the radical pair (RP) singlet spin state to study theoretically the cytoprotective effect of an extremely-low-frequency electromagnetic field (ELF-EMF) on early stages of hepatic cancer chemically induced in rats. The proposal is that ELF-EMF modulates the interconversion rate of singlet and triplet spin states of the RP populations modifying the products from the metabolization of carcinogens. Previously, we found that the daily treatment with ELF-EMF 120 Hz inhibited the number and area of preneoplastic lesions in chemical carcinogenesis. The singlet spin population is evaluated diagonalizing the spin density matrix through the Lanczos method in a radical pair mechanism (RPM). Using four values of the interchange energy, we have studied the variations over the singlet population. The low magnetic field effect as a test of the influence over the enzymatic chemical reaction is evaluated calculating the quantum yield. Through a bootstrap technique the range is found for the singlet decay rate for the process. Applying the quantum measurements concept, we addressed the impact toward hepatic cells. The result contributes to improving our understanding of the chemical carcinogenesis process affected by charged particles that damage the DNA.

Preferential solvatation of human serum albumin in dimethylsulfoxide-H2O binary solution

NASA Astrophysics Data System (ADS)

Grigoryan, K. R.

2009-12-01

The preferential solvatation of human serum albumin (HSA) in dimethylsulfoxide (DMSO) aqueous solutions were studied using the densitometry method. It has been shown that at DMSO low concentrations HSA undergoes to preferential hydration, but at DMSO higher concentrations preferential binding of DMSO molecules to protein occurs. It has been estimated that DMSO exhibits stabilizing/destabilizing effect on HSA structure which is explained in terms of hydration/solvatation of protein, on the one hand, and the medium structure enhancement/disruption around the protein molecule, on the other hand.

Quantum chemical study of the inhibition of the corrosion of mild steel in H2SO4 by some antibiotics.

PubMed

Eddy, Nnabuk O; Ibok, Udo J; Ebenso, Eno E; El Nemr, Ahmed; El Ashry, El Sayed H

2009-09-01

The inhibition efficiency of some antibiotics against mild steel corrosion was studied using weight loss and quantum chemical techniques. Values of inhibition efficiency obtained from weight loss measurements correlated strongly with theoretical values obtained through semi empirical calculations. High correlation coefficients were also obtained between inhibition efficiency of the antibiotics and some quantum chemical parameters, including frontier orbital (E (HOMO) and E (LUMO)), dipole moment, log P, TNC and LSER parameters (critical volume and dipolar-polarisability factor), which indicated that these parameters affect the inhibition efficiency of the compounds. It was also found that quantitative structure activity relation can be used to adequately predict the inhibition effectiveness of these compounds.

Signatures of Solvation Thermodynamics in Spectra of Intermolecular Vibrations

PubMed Central

2017-01-01

This study explores the thermodynamic and vibrational properties of water in the three-dimensional environment of solvated ions and small molecules using molecular simulations. The spectrum of intermolecular vibrations in liquid solvents provides detailed information on the shape of the local potential energy surface, which in turn determines local thermodynamic properties such as the entropy. Here, we extract this information using a spatially resolved extension of the two-phase thermodynamics method to estimate hydration water entropies based on the local vibrational density of states (3D-2PT). Combined with an analysis of solute–water and water–water interaction energies, this allows us to resolve local contributions to the solvation enthalpy, entropy, and free energy. We use this approach to study effects of ions on their surrounding water hydrogen bond network, its spectrum of intermolecular vibrations, and resulting thermodynamic properties. In the three-dimensional environment of polar and nonpolar functional groups of molecular solutes, we identify distinct hydration water species and classify them by their characteristic vibrational density of states and molecular entropies. In each case, we are able to assign variations in local hydration water entropies to specific changes in the spectrum of intermolecular vibrations. This provides an important link for the thermodynamic interpretation of vibrational spectra that are accessible to far-infrared absorption and Raman spectroscopy experiments. Our analysis provides unique microscopic details regarding the hydration of hydrophobic and hydrophilic functional groups, which enable us to identify interactions and molecular degrees of freedom that determine relevant contributions to the solvation entropy and consequently the free energy. PMID:28783431

Quantum chemical modeling of zeolite-catalyzed methylation reactions: toward chemical accuracy for barriers.

PubMed

Svelle, Stian; Tuma, Christian; Rozanska, Xavier; Kerber, Torsten; Sauer, Joachim

2009-01-21

The methylation of ethene, propene, and t-2-butene by methanol over the acidic microporous H-ZSM-5 catalyst has been investigated by a range of computational methods. Density functional theory (DFT) with periodic boundary conditions (PBE functional) fails to describe the experimentally determined decrease of apparent energy barriers with the alkene size due to inadequate description of dispersion forces. Adding a damped dispersion term expressed as a parametrized sum over atom pair C(6) contributions leads to uniformly underestimated barriers due to self-interaction errors. A hybrid MP2:DFT scheme is presented that combines MP2 energy calculations on a series of cluster models of increasing size with periodic DFT calculations, which allows extrapolation to the periodic MP2 limit. Additionally, errors caused by the use of finite basis sets, contributions of higher order correlation effects, zero-point vibrational energy, and thermal contributions to the enthalpy were evaluated and added to the "periodic" MP2 estimate. This multistep approach leads to enthalpy barriers at 623 K of 104, 77, and 48 kJ/mol for ethene, propene, and t-2-butene, respectively, which deviate from the experimentally measured values by 0, +13, and +8 kJ/mol. Hence, enthalpy barriers can be calculated with near chemical accuracy, which constitutes significant progress in the quantum chemical modeling of reactions in heterogeneous catalysis in general and microporous zeolites in particular.

Differential geometry based solvation model I: Eulerian formulation

PubMed Central

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

2010-01-01

This paper presents a differential geometry based model for the analysis and computation of the equilibrium property of solvation. Differential geometry theory of surfaces is utilized to define and construct smooth interfaces with good stability and differentiability for use in characterizing the solvent-solute boundaries and in generating continuous dielectric functions across the computational domain. A total free energy functional is constructed to couple polar and nonpolar contributions to the salvation process. Geometric measure theory is employed to rigorously convert a Lagrangian formulation of the surface energy into an Eulerian formulation so as to bring all energy terms into an equal footing. By minimizing the total free energy functional, we derive coupled generalized Poisson-Boltzmann equation (GPBE) and generalized geometric flow equation (GGFE) for the electrostatic potential and the construction of realistic solvent-solute boundaries, respectively. By solving the coupled GPBE and GGFE, we obtain the electrostatic potential, the solvent-solute boundary profile, and the smooth dielectric function, and thereby improve the accuracy and stability of implicit solvation calculations. We also design efficient second order numerical schemes for the solution of the GPBE and GGFE. Matrix resulted from the discretization of the GPBE is accelerated with appropriate preconditioners. An alternative direct implicit (ADI) scheme is designed to improve the stability of solving the GGFE. Two iterative approaches are designed to solve the coupled system of nonlinear partial differential equations. Extensive numerical experiments are designed to validate the present theoretical model, test computational methods, and optimize numerical algorithms. Example solvation analysis of both small compounds and proteins are carried out to further demonstrate the accuracy, stability, efficiency and robustness of the present new model and numerical approaches. Comparison is given to

Highly Stable Lithium Metal Batteries Enabled by Regulating the Solvation of Lithium Ions in Nonaqueous Electrolytes.

PubMed

Zhang, Xue-Qiang; Chen, Xiang; Cheng, Xin-Bing; Li, Bo-Quan; Shen, Xin; Yan, Chong; Huang, Jia-Qi; Zhang, Qiang

2018-05-04

Safe and rechargeable lithium metal batteries have been difficult to achieve because of the formation of lithium dendrites. Herein an emerging electrolyte based on a simple solvation strategy is proposed for highly stable lithium metal anodes in both coin and pouch cells. Fluoroethylene carbonate (FEC) and lithium nitrate (LiNO 3 ) were concurrently introduced into an electrolyte, thus altering the solvation sheath of lithium ions, and forming a uniform solid electrolyte interphase (SEI), with an abundance of LiF and LiN x O y on a working lithium metal anode with dendrite-free lithium deposition. Ultrahigh Coulombic efficiency (99.96 %) and long lifespans (1000 cycles) were achieved when the FEC/LiNO 3 electrolyte was applied in working batteries. The solvation chemistry of electrolyte was further explored by molecular dynamics simulations and first-principles calculations. This work provides insight into understanding the critical role of the solvation of lithium ions in forming the SEI and delivering an effective route to optimize electrolytes for safe lithium metal batteries. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Graphene-based quantum Hall resistance standards grown by chemical vapor deposition on silicon carbide

NASA Astrophysics Data System (ADS)

Ribeiro-Palau, Rebeca; Lafont, Fabien; Kazazis, Dimitris; Michon, Adrien; Couturaud, Olivier; Consejo, Christophe; Jouault, Benoit; Poirier, Wilfrid; Schopfer, Felicien

2015-03-01

Replace GaAs-based quantum Hall resistance standards (GaAs-QHRS) by a more convenient one, based on graphene (Gr-QHRS), is an ongoing goal in metrology. The new Gr-QHRS are expected to work in less demanding experimental conditions than GaAs ones. It will open the way to a broad dissemination of quantum standards, potentially towards industrial end-users, and it will support the implementation of a new International System of Units based on fixed fundamental constants. Here, we present accurate quantum Hall resistance measurements in large graphene Hall bars, grown by the hybrid scalable technique of propane/hydrogen chemical vapor deposition (CVD) on silicon carbide (SiC). This new Gr-QHRS shows a relative accuracy of 1 ×10-9 of the Hall resistance under the lowest magnetic field ever achieved in graphene. These experimental conditions surpass those of the most wildely used GaAs-QHRS. These results confirm the promises of graphene for resistance metrology applications and emphasizes the quality of the graphene produced by the CVD on SiC for applications as demanding as the resistance metrology.

Incorporation of Mn2+ into CdSe quantum dots by chemical bath co-deposition method for photovoltaic enhancement of quantum dot-sensitized solar cells.

PubMed

Zhang, Chenguang; Liu, Shaowen; Liu, Xingwei; Deng, Fei; Xiong, Yan; Tsai, Fang-Chang

2018-03-01

A photoelectric conversion efficiency (PCE) of 4.9% was obtained under 100 mW cm -2 illumination by quantum-dot-sensitized solar cells (QDSSCs) using a CdS/Mn : CdSe sensitizer. CdS quantum dots (QDs) were deposited on a TiO 2 mesoporous oxide film by successive ionic layer absorption and reaction. Mn 2+ doping into CdSe QDs is an innovative and simple method-chemical bath co-deposition, that is, mixing the Mn ion source with CdSe precursor solution for Mn : CdSe QD deposition. Compared with the CdS/CdSe sensitizer without Mn 2+ incorporation, the PCE was increased from 3.4% to 4.9%. The effects of Mn 2+ doping on the chemical, physical and photovoltaic properties of the QDSSCs were investigated by energy dispersive spectrometry, absorption spectroscopy, photocurrent density-voltage characteristics and electrochemical impedance spectroscopy. Mn-doped CdSe QDs in QDSSCs can obtain superior light absorption, faster electron transport and slower charge recombination than CdSe QDs.

Incorporation of Mn2+ into CdSe quantum dots by chemical bath co-deposition method for photovoltaic enhancement of quantum dot-sensitized solar cells

PubMed Central

Zhang, Chenguang; Liu, Shaowen; Liu, Xingwei; Deng, Fei

2018-01-01

A photoelectric conversion efficiency (PCE) of 4.9% was obtained under 100 mW cm−2 illumination by quantum-dot-sensitized solar cells (QDSSCs) using a CdS/Mn : CdSe sensitizer. CdS quantum dots (QDs) were deposited on a TiO2 mesoporous oxide film by successive ionic layer absorption and reaction. Mn2+ doping into CdSe QDs is an innovative and simple method—chemical bath co-deposition, that is, mixing the Mn ion source with CdSe precursor solution for Mn : CdSe QD deposition. Compared with the CdS/CdSe sensitizer without Mn2+ incorporation, the PCE was increased from 3.4% to 4.9%. The effects of Mn2+ doping on the chemical, physical and photovoltaic properties of the QDSSCs were investigated by energy dispersive spectrometry, absorption spectroscopy, photocurrent density–voltage characteristics and electrochemical impedance spectroscopy. Mn-doped CdSe QDs in QDSSCs can obtain superior light absorption, faster electron transport and slower charge recombination than CdSe QDs. PMID:29657776

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

Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software.

PubMed

Riniker, Sereina; Christ, Clara D; Hansen, Halvor S; Hünenberger, Philippe H; Oostenbrink, Chris; Steiner, Denise; van Gunsteren, Wilfred F

2011-11-24

The calculation of the relative free energies of ligand-protein binding, of solvation for different compounds, and of different conformational states of a polypeptide is of considerable interest in the design or selection of potential enzyme inhibitors. Since such processes in aqueous solution generally comprise energetic and entropic contributions from many molecular configurations, adequate sampling of the relevant parts of configurational space is required and can be achieved through molecular dynamics simulations. Various techniques to obtain converged ensemble averages and their implementation in the GROMOS software for biomolecular simulation are discussed, and examples of their application to biomolecules in aqueous solution are given. © 2011 American Chemical Society

Quantum Chemical Prediction of Equilibrium Acidities of Ureas, Deltamides, Squaramides, and Croconamides.

PubMed

Ho, Junming; Zwicker, Vincent E; Yuen, Karen K Y; Jolliffe, Katrina A

2017-10-06

Robust quantum chemical methods are employed to predict the pK a 's of several families of dual hydrogen-bonding organocatalysts/anion receptors, including deltamides and croconamides as well as their thio derivatives. The average accuracy of these predictions is ∼1 pK a unit and allows for a comparison of the acidity between classes of receptors and for quantitative studies of substituent effects. These computational insights further explain the relationship between pK a and chloride anion affinity of these receptors that will be important for designing future anion receptors and organocatalysts.

Replacement solvents for use in chemical synthesis

DOEpatents

Molnar, Linda K.; Hatton, T. Alan; Buchwald, Stephen L.

2001-05-15

Replacement solvents for use in chemical synthesis include polymer-immobilized solvents having a flexible polymer backbone and a plurality of pendant groups attached onto the polymer backbone, the pendant groups comprising a flexible linking unit bound to the polymer backbone and to a terminal solvating moiety. The polymer-immobilized solvent may be dissolved in a benign medium. Replacement solvents for chemical reactions for which tetrahydrofuran or diethyl may be a solvent include substituted tetrahydrofurfuryl ethers and substituted tetrahydro-3-furan ethers. The replacement solvents may be readily recovered from the reaction train using conventional methods.

Experimental and quantum-chemical studies on the three-particle fragmentation of neutral triatomic hydrogen

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

Galster, Ulrich; Baumgartner, Frank; Mueller, Ulrich

2005-12-15

Dissociation of well-defined H{sub 3} Rydberg states into three ground state hydrogen atoms reveals characteristic correlation patterns in the center-of-mass motion of the three fragments. We present an extensive experimental dataset of momentum correlation maps for all lower Rydberg states of H{sub 3} and D{sub 3}. In particular the states with principal quantum number n=2 feature simple correlation patterns with regular occurence of mutual affinities. Energetically higher-lying states typically show more complex patterns which are unique for each state. Quantum-chemical calculations on adiabatic potential energy surfaces of H{sub 3} Rydberg states are presented to illuminate the likely origin of thesemore » differences. We discuss the likely dissociation mechanisms and paths which are responsible for the observed continuum correlation.« less

Accurate Estimation of Solvation Free Energy Using Polynomial Fitting Techniques

PubMed Central

Shyu, Conrad; Ytreberg, F. Marty

2010-01-01

This report details an approach to improve the accuracy of free energy difference estimates using thermodynamic integration data (slope of the free energy with respect to the switching variable λ) and its application to calculating solvation free energy. The central idea is to utilize polynomial fitting schemes to approximate the thermodynamic integration data to improve the accuracy of the free energy difference estimates. Previously, we introduced the use of polynomial regression technique to fit thermodynamic integration data (Shyu and Ytreberg, J Comput Chem 30: 2297–2304, 2009). In this report we introduce polynomial and spline interpolation techniques. Two systems with analytically solvable relative free energies are used to test the accuracy of the interpolation approach. We also use both interpolation and regression methods to determine a small molecule solvation free energy. Our simulations show that, using such polynomial techniques and non-equidistant λ values, the solvation free energy can be estimated with high accuracy without using soft-core scaling and separate simulations for Lennard-Jones and partial charges. The results from our study suggest these polynomial techniques, especially with use of non-equidistant λ values, improve the accuracy for ΔF estimates without demanding additional simulations. We also provide general guidelines for use of polynomial fitting to estimate free energy. To allow researchers to immediately utilize these methods, free software and documentation is provided via http://www.phys.uidaho.edu/ytreberg/software. PMID:20623657

Interfacial ion solvation: Obtaining the thermodynamic limit from molecular simulations

NASA Astrophysics Data System (ADS)

Cox, Stephen J.; Geissler, Phillip L.

2018-06-01

Inferring properties of macroscopic solutions from molecular simulations is complicated by the limited size of systems that can be feasibly examined with a computer. When long-ranged electrostatic interactions are involved, the resulting finite size effects can be substantial and may attenuate very slowly with increasing system size, as shown by previous work on dilute ions in bulk aqueous solution. Here we examine corrections for such effects, with an emphasis on solvation near interfaces. Our central assumption follows the perspective of Hünenberger and McCammon [J. Chem. Phys. 110, 1856 (1999)]: Long-wavelength solvent response underlying finite size effects should be well described by reduced models like dielectric continuum theory, whose size dependence can be calculated straightforwardly. Applied to an ion in a periodic slab of liquid coexisting with vapor, this approach yields a finite size correction for solvation free energies that differs in important ways from results previously derived for bulk solution. For a model polar solvent, we show that this new correction quantitatively accounts for the variation of solvation free energy with volume and aspect ratio of the simulation cell. Correcting periodic slab results for an aqueous system requires an additional accounting for the solvent's intrinsic charge asymmetry, which shifts electric potentials in a size-dependent manner. The accuracy of these finite size corrections establishes a simple method for a posteriori extrapolation to the thermodynamic limit and also underscores the realism of dielectric continuum theory down to the nanometer scale.

Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Calculations. 1. Estimation of Polarization Energies

PubMed Central

2015-01-01

In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton–Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. They produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin–luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy. PMID:25321186

Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies

DOE PAGES

Sodt, Alexander J.; Mei, Ye; Konig, Gerhard; ...

2014-10-16

In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton–Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completelymore » avoided at each configuration. Here, they produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin–luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy.« less

Benchmarking quantum mechanical calculations with experimental NMR chemical shifts of 2-HADNT

NASA Astrophysics Data System (ADS)

Liu, Yuemin; Junk, Thomas; Liu, Yucheng; Tzeng, Nianfeng; Perkins, Richard

2015-04-01

In this study, both GIAO-DFT and GIAO-MP2 calculations of nuclear magnetic resonance (NMR) spectra were benchmarked with experimental chemical shifts. The experimental chemical shifts were determined experimentally for carbon-13 (C-13) of seven carbon atoms for the TNT degradation product 2-hydroxylamino-4,6-dinitrotoluene (2-HADNT). Quantum mechanics GIAO calculations were implemented using Becke-3-Lee-Yang-Parr (B3LYP) and other six hybrid DFT methods (Becke-1-Lee-Yang-Parr (B1LYP), Becke-half-and-half-Lee-Yang-Parr (BH and HLYP), Cohen-Handy-3-Lee-Yang-Parr (O3LYP), Coulomb-attenuating-B3LYP (CAM-B3LYP), modified-Perdew-Wang-91-Lee-Yang-Parr (mPW1LYP), and Xu-3-Lee-Yang-Parr (X3LYP)) which use the same correlation functional LYP. Calculation results showed that the GIAO-MP2 method gives the most accurate chemical shift values, and O3LYP method provides the best prediction of chemical shifts among the B3LYP and other five DFT methods. Three types of atomic partial charges, Mulliken (MK), electrostatic potential (ESP), and natural bond orbital (NBO), were also calculated using MP2/aug-cc-pVDZ method. A reasonable correlation was discovered between NBO partial charges and experimental chemical shifts of carbon-13 (C-13).

Quantum chemical determination of young?s modulus of lignin. Calculations on ß-O-4' model compound

Treesearch

Thomas Elder

2007-01-01

The calculation of Young?s modulus of lignin has been examined by subjecting a dimeric model compound to strain, coupled with the determination of energy and stress. The computational results, derived from quantum chemical calculations, are in agreement with available experimental results. Changes in geometry indicate that modifications in dihedral angles occur in...

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

PubMed Central

Vitalis, Andreas; Pappu, Rohit V.

2009-01-01

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

Quantum dissipation theory and applications to quantum transport and quantum measurement in mesoscopic systems

NASA Astrophysics Data System (ADS)

Cui, Ping

celebrated Marcus' inversion and Kramers' turnover behaviors, the new theory also shows some distinct quantum solvation effects that can alter the ET mechanism. Moreover, the present theory predicts further for the ET reaction thermodynamics, such as equilibrium Gibbs free-energy and entropy, some interesting solvent-dependent features that are calling for experimental verification. In Chapter 6, we discuss the constructed QDTs, in terms of their unified mathematical structure that supports a linear dynamics space, and thus facilitates their applications to various physical problems. The involving details are exemplified with the CODDE form of QDT. As the linear space is concerned, we identify the Schrodinger versus Heisenberg picture and the forward versus backward propagation of the reduced, dissipative Liouville dynamics. For applications we discuss the reduced linear response theory and the optimal control problems, in which the correlated effects of non-Markovian dissipation and field driving are shown to be important. In Chapter 7, we turn to quantum transport, i.e., electric current through molecular or mesoscopic systems under finite applied voltage. By viewing the nonequilibrium transport setup as a quantum open system, we develop a reduced-density-matrix approach to quantum transport. The resulting current is explicitly expressed in terms of the molecular reduced density matrix by tracing out the degrees of freedom of the electrodes at finite bias and temperature. We propose a conditional quantum master equation theory, which is an extension of the conventional (or unconditional) QDT by tracing out the well-defined bath subsets individually, instead of the entire bath degrees of freedom. Both the current and the noise spectrum can be conveniently analyzed in terms of the conditional reduced density matrix dynamics. By far, the QDT (including the conditional one) has only been exploited in second-order form. A self-consistent Born approximation for the system

New generation of docking programs: Supercomputer validation of force fields and quantum-chemical methods for docking.

PubMed

Sulimov, Alexey V; Kutov, Danil C; Katkova, Ekaterina V; Ilin, Ivan S; Sulimov, Vladimir B

2017-11-01

Discovery of new inhibitors of the protein associated with a given disease is the initial and most important stage of the whole process of the rational development of new pharmaceutical substances. New inhibitors block the active site of the target protein and the disease is cured. Computer-aided molecular modeling can considerably increase effectiveness of new inhibitors development. Reliable predictions of the target protein inhibition by a small molecule, ligand, is defined by the accuracy of docking programs. Such programs position a ligand in the target protein and estimate the protein-ligand binding energy. Positioning accuracy of modern docking programs is satisfactory. However, the accuracy of binding energy calculations is too low to predict good inhibitors. For effective application of docking programs to new inhibitors development the accuracy of binding energy calculations should be higher than 1kcal/mol. Reasons of limited accuracy of modern docking programs are discussed. One of the most important aspects limiting this accuracy is imperfection of protein-ligand energy calculations. Results of supercomputer validation of several force fields and quantum-chemical methods for docking are presented. The validation was performed by quasi-docking as follows. First, the low energy minima spectra of 16 protein-ligand complexes were found by exhaustive minima search in the MMFF94 force field. Second, energies of the lowest 8192 minima are recalculated with CHARMM force field and PM6-D3H4X and PM7 quantum-chemical methods for each complex. The analysis of minima energies reveals the docking positioning accuracies of the PM7 and PM6-D3H4X quantum-chemical methods and the CHARMM force field are close to one another and they are better than the positioning accuracy of the MMFF94 force field. Copyright © 2017 Elsevier Inc. All rights reserved.

Thermodynamics of DL-alanine solvation in water-dimethylsulfoxide mixtures at 298.15 K

NASA Astrophysics Data System (ADS)

Roy, S.; Mahali, K.; Mondal, S.; Dolui, B. K.

2015-04-01

In this study we mainly discuss the transfer Gibbs free energy Δ G {/t 0}( i) and Δ S {/t 0}( i)entropy of DL-alanine at 298.15 K and consequently the involved chemical transfer free energy (Δ G {/t,ch 0}( i)) and entropy ( TΔ S {/t,ch 0}( i)) in aqueous mixtures of dimethylsulfoxide are discussed to clarify the solvation chemistry of DL-alanine. For the evaluation of these energy terms, solubility of this amino acid has been measured by formol titrimetry at five equidistant temperatures i.e., from 288.15 to 308.15 K in different composition of this mixed solvent system. The various solvent parameters as well as thermodynamic parameters like molar volume, density, dipole moment and solvent diameter of this solvent system have also been reported here. The chemical effects of the transfer Gibbs energies (Δ G {/t,ch 0}( i)) and entropies of transfer ( TΔ S {/t,ch 0}( i)) have been obtained after elimination of cavity effect and dipole-dipole interaction effects from the total transfer energies. Here the chemical contribution of transfer energetics of DL-alanine is mainly guided by the composite effects of increased dispersion interaction, basicity effect and decreased acidity, hydrogen bonding effects, hydrophilic hydration and hydrophobic hydration of aqueous DMSO mixtures as compared to that of reference solvent, water.

Conformational, structural, vibrational and quantum chemical analysis on 4-aminobenzohydrazide and 4-hydroxybenzohydrazide--a comparative study.

PubMed

Arjunan, V; Jayaprakash, A; Carthigayan, K; Periandy, S; Mohan, S

2013-05-01

Experimental and theoretical quantum chemical studies were carried out on 4-hydroxybenzohydrazide (4HBH) and 4-aminobenzohydrazide (4ABH) using FTIR and FT-Raman spectral data. The structural characteristics and vibrational spectroscopic analysis were carried performed by quantum chemical methods with the hybrid exchange-correlation functional B3LYP using 6-31G(**), 6-311++G(**) and aug-cc-pVDZ basis sets. The most stable conformer of the title compounds have been determined from the analysis of potential energy surface. The stable molecular geometries, electronic and thermodynamic parameters, IR intensities, harmonic vibrational frequencies, depolarisation ratio and Raman intensities have been computed. Molecular electrostatic potential and frontier molecular orbitals were constructed to understand the electronic properties. The potential energy distributions (PEDs) were calculated to explain the mixing of fundamental modes. The theoretical geometrical parameters and the fundamental frequencies were compared with the experimental. The interactions of hydroxy and amino group substitutions on the characteristic vibrations of the ring and hydrazide group have been analysed. Copyright © 2013 Elsevier B.V. All rights reserved.

Recent developments of the quantum chemical cluster approach for modeling enzyme reactions.

PubMed

Siegbahn, Per E M; Himo, Fahmi

2009-06-01

The quantum chemical cluster approach for modeling enzyme reactions is reviewed. Recent applications have used cluster models much larger than before which have given new modeling insights. One important and rather surprising feature is the fast convergence with cluster size of the energetics of the reactions. Even for reactions with significant charge separation it has in some cases been possible to obtain full convergence in the sense that dielectric cavity effects from outside the cluster do not contribute to any significant extent. Direct comparisons between quantum mechanics (QM)-only and QM/molecular mechanics (MM) calculations for quite large clusters in a case where the results differ significantly have shown that care has to be taken when using the QM/MM approach where there is strong charge polarization. Insights from the methods used, generally hybrid density functional methods, have also led to possibilities to give reasonable error limits for the results. Examples are finally given from the most extensive study using the cluster model, the one of oxygen formation at the oxygen-evolving complex in photosystem II.

Solvent screening for a hard-to-dissolve molecular crystal.

PubMed

Maiti, A; Pagoria, P F; Gash, A E; Han, T Y; Orme, C A; Gee, R H; Fried, L E

2008-09-01

Materials with a high-degree of inter- and intra-molecular hydrogen bonding generally have limited solubility in conventional organic solvents. This presents a problem for the dissolution, manipulation and purification of these materials. Using a state-of-the-art density-functional-theory based quantum chemical solvation model we systematically evaluated solvents for a known hydrogen-bonded molecular crystal. This, coupled with direct solubility measurements, uncovered a class of ionic liquids involving fluoride anions that possess more than two orders of magnitude higher solvation power as compared with the best conventional solvents. The crystal structure of one such ionic liquid, determined by X-ray diffraction spectroscopy, indicates that F- ions are stabilized through H-bonded chains with water. The presence of coordinating water in such ionic liquids seems to facilitate the dissolution process by keeping the chemical activity of the F- ions in check.

Electrolytes in a nanometer slab-confinement: Ion-specific structure and solvation forces

NASA Astrophysics Data System (ADS)

Kalcher, Immanuel; Schulz, Julius C. F.; Dzubiella, Joachim

2010-10-01

We study the liquid structure and solvation forces of dense monovalent electrolytes (LiCl, NaCl, CsCl, and NaI) in a nanometer slab-confinement by explicit-water molecular dynamics (MD) simulations, implicit-water Monte Carlo (MC) simulations, and modified Poisson-Boltzmann (PB) theories. In order to consistently coarse-grain and to account for specific hydration effects in the implicit methods, realistic ion-ion and ion-surface pair potentials have been derived from infinite-dilution MD simulations. The electrolyte structure calculated from MC simulations is in good agreement with the corresponding MD simulations, thereby validating the coarse-graining approach. The agreement improves if a realistic, MD-derived dielectric constant is employed, which partially corrects for (water-mediated) many-body effects. Further analysis of the ionic structure and solvation pressure demonstrates that nonlocal extensions to PB (NPB) perform well for a wide parameter range when compared to MC simulations, whereas all local extensions mostly fail. A Barker-Henderson mapping of the ions onto a charged, asymmetric, and nonadditive binary hard-sphere mixture shows that the strength of structural correlations is strongly related to the magnitude and sign of the salt-specific nonadditivity. Furthermore, a grand canonical NPB analysis shows that the Donnan effect is dominated by steric correlations, whereas solvation forces and overcharging effects are mainly governed by ion-surface interactions. However, steric corrections to solvation forces are strongly repulsive for high concentrations and low surface charges, while overcharging can also be triggered by steric interactions in strongly correlated systems. Generally, we find that ion-surface and ion-ion correlations are strongly coupled and that coarse-grained methods should include both, the latter nonlocally and nonadditive (as given by our specific ionic diameters), when studying electrolytes in highly inhomogeneous situations.

Quantum chemistry simulation on quantum computers: theories and experiments.

PubMed

Lu, Dawei; Xu, Boruo; Xu, Nanyang; Li, Zhaokai; Chen, Hongwei; Peng, Xinhua; Xu, Ruixue; Du, Jiangfeng

2012-07-14

It has been claimed that quantum computers can mimic quantum systems efficiently in the polynomial scale. Traditionally, those simulations are carried out numerically on classical computers, which are inevitably confronted with the exponential growth of required resources, with the increasing size of quantum systems. Quantum computers avoid this problem, and thus provide a possible solution for large quantum systems. In this paper, we first discuss the ideas of quantum simulation, the background of quantum simulators, their categories, and the development in both theories and experiments. We then present a brief introduction to quantum chemistry evaluated via classical computers followed by typical procedures of quantum simulation towards quantum chemistry. Reviewed are not only theoretical proposals but also proof-of-principle experimental implementations, via a small quantum computer, which include the evaluation of the static molecular eigenenergy and the simulation of chemical reaction dynamics. Although the experimental development is still behind the theory, we give prospects and suggestions for future experiments. We anticipate that in the near future quantum simulation will become a powerful tool for quantum chemistry over classical computations.

Solvation of excess electrons trapped in charge pockets on molecular surfaces

NASA Astrophysics Data System (ADS)

Jalbout, Abraham F.

This work considers the ability of hydrogen fluoride (HF) to solvate excess electrons located on cyclic hydrocarbon surfaces. The principle applied involves the formation of systems in which excess electrons can be stabilized not only on concentrated molecular surface charge pockets but also by HF. Recent studies have shown that OH groups can form stable hydrogen-bonded networks on one side of a hydrocarbon surface (i.e. cyclohexane sheets), at the same time, the hydrogen atoms on the opposite side of this surface form a pocket of positive charge can attract the excess electron. This density can be further stabilized by the addition of an HF molecule that can form an 'anion with an internally solvated electron' (AISE) state. These systems are shown to be stable with respect to vertical electron detachment (VDE).

Variations of water's local-structure induced by solvation of NaCl

NASA Astrophysics Data System (ADS)

Gu, Bin; Zhang, Feng-Shou; Huang, Yu-Gai; Fang, Xia

2010-03-01

The researches on the structure of water and its changes induced by solutes are of enduring interests. The changes of the local structure of liquid water induced by NaCl solute under ambient conditions are studied and presented quantitatively with some order parameters and visualized with 2-body and 3-body correlation functions. The results show that, after the NaCl are solvated, the translational order t of water is decreased for the suppression of the second hydration shells around H2O molecules; the tetrahedral order (q) of water is also decreased and its favorite distribution peak moves from 0.76 to 0.5. In addition, the orientational freedom k and the diffusion coefficient D of water molecules are reduced because of new formed hydrogen-bonding structures between water and solvated ions.

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.

Hybrid quantum and classical methods for computing kinetic isotope effects of chemical reactions in solutions and in enzymes.

PubMed

Gao, Jiali; Major, Dan T; Fan, Yao; Lin, Yen-Lin; Ma, Shuhua; Wong, Kin-Yiu

2008-01-01

A method for incorporating quantum mechanics into enzyme kinetics modeling is presented. Three aspects are emphasized: 1) combined quantum mechanical and molecular mechanical methods are used to represent the potential energy surface for modeling bond forming and breaking processes, 2) instantaneous normal mode analyses are used to incorporate quantum vibrational free energies to the classical potential of mean force, and 3) multidimensional tunneling methods are used to estimate quantum effects on the reaction coordinate motion. Centroid path integral simulations are described to make quantum corrections to the classical potential of mean force. In this method, the nuclear quantum vibrational and tunneling contributions are not separable. An integrated centroid path integral-free energy perturbation and umbrella sampling (PI-FEP/UM) method along with a bisection sampling procedure was summarized, which provides an accurate, easily convergent method for computing kinetic isotope effects for chemical reactions in solution and in enzymes. In the ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT), these three aspects of quantum mechanical effects can be individually treated, providing useful insights into the mechanism of enzymatic reactions. These methods are illustrated by applications to a model process in the gas phase, the decarboxylation reaction of N-methyl picolinate in water, and the proton abstraction and reprotonation process catalyzed by alanine racemase. These examples show that the incorporation of quantum mechanical effects is essential for enzyme kinetics simulations.

Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics

PubMed Central

Christensen, Anders S.; Linnet, Troels E.; Borg, Mikael; Boomsma, Wouter; Lindorff-Larsen, Kresten; Hamelryck, Thomas; Jensen, Jan H.

2013-01-01

We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3 JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding. PMID:24391900

Exit channel dynamics in a micro-hydrated SN2 reaction of the hydroxyl anion.

PubMed

Otto, R; Brox, J; Trippel, S; Stei, M; Best, T; Wester, R

2013-08-29

We report on the reaction dynamics of the monosolvated SN2 reaction of cold OH(-)(H2O) with CH3I that have been studied using crossed beam ion imaging. Two SN2 reaction channels are possible for this reaction: Formation of unsolvated I(-) and of solvated I(-)(H2O) products. We find a strong preference for the formation of unsolvated I(-) reaction products with respect to the energetically favored reaction toward solvated I(-)(H2O). Angle differential cross section measurements reveal similar velocity and angular distributions for all solvated and parts of the unsolvated reaction products. We furthermore find that the contribution of these two products to the total product flux can be described by the same collision energy dependence. We interpret our findings in terms of a joint reaction mechanism in which a CH3OH(H2O)···I(-) complex is formed that decays into either solvated or unsolvated products. Quantum chemical calculation are used to support this assumption.

Water-enhanced solvation of organics

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

Lee, Jane H.

1993-07-01

Water-enhanced solvation (WES) was explored for Lewis acid solutes in Lewis base organic solvents, to develop cheap extract regeneration processes. WES for solid solutes was determined from ratios of solubilities of solutes in water-sat. and low-water solvent; both were determined from solid-liquid equilibrium. Vapor-headspace analysis was used to determine solute activity coefficients as function of organic phase water concentration. WES magnitudes of volatile solutes were normalized, set equal to slope of log γ s vs x w/x s curve. From graph shape Δ(log γ s) represents relative change in solute activity coefficient. Solutes investigated by vapor-headspace analysis were acetic acid,more » propionic acid, ethanol, 1,2-propylene glycol, 2,3-butylene glycol. Monocarboxylic acids had largest decrease in activity coefficient with water addition followed by glycols and alcohols. Propionic acid in cyclohexanone showed greatest water-enhancement Δ(log γ acid)/Δ(x w/x acid) = -0.25. In methylcyclohexanone, the decrease of the activity coefficient of propionic acid was -0.19. Activity coefficient of propionic acid in methylcyclohexanone stopped decreasing once the water reached a 2:1 water to acid mole ratio, implying a stoichiometric relation between water, ketone, and acid. Except for 2,3-butanediol, activity coefficients of the solutes studied decreased monotonically with water content. Activity coefficient curves of ethanol, 1,2-propanediol and 2,3-butanediol did not level off at large water/solute mole ratio. Solutes investigated by solid-liquid equilibrium were citric acid, gallic acid, phenol, xylenols, 2-naphthol. Saturation concentration of citric acid in anhydrous butyl acetate increased from 0.0009 to 0.087 mol/L after 1.3 % (g/g) water co-dissolved into organic phase. Effect of water-enhanced solvation for citric acid is very large but very small for phenol and its derivatives.« less

The quantum dynamics of electronically nonadiabatic chemical reactions

NASA Technical Reports Server (NTRS)

Truhlar, Donald G.

1993-01-01

Considerable progress was achieved on the quantum mechanical treatment of electronically nonadiabatic collisions involving energy transfer and chemical reaction in the collision of an electronically excited atom with a molecule. In the first step, a new diabatic representation for the coupled potential energy surfaces was created. A two-state diabatic representation was developed which was designed to realistically reproduce the two lowest adiabatic states of the valence bond model and also to have the following three desirable features: (1) it is more economical to evaluate; (2) it is more portable; and (3) all spline fits are replaced by analytic functions. The new representation consists of a set of two coupled diabatic potential energy surfaces plus a coupling surface. It is suitable for dynamics calculations on both the electronic quenching and reaction processes in collisions of Na(3p2p) with H2. The new two-state representation was obtained by a three-step process from a modified eight-state diatomics-in-molecules (DIM) representation of Blais. The second step required the development of new dynamical methods. A formalism was developed for treating reactions with very general basis functions including electronically excited states. Our formalism is based on the generalized Newton, scattered wave, and outgoing wave variational principles that were used previously for reactive collisions on a single potential energy surface, and it incorporates three new features: (1) the basis functions include electronic degrees of freedom, as required to treat reactions involving electronic excitation and two or more coupled potential energy surfaces; (2) the primitive electronic basis is assumed to be diabatic, and it is not assumed that it diagonalizes the electronic Hamiltonian even asymptotically; and (3) contracted basis functions for vibrational-rotational-orbital degrees of freedom are included in a very general way, similar to previous prescriptions for locally

Mechanistic insights into the decomposition of fructose to hydroxy methyl furfural in neutral and acidic environments using high-level quantum chemical methods.

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

Assary, R. S.; Redfern, P. C.; Greeley, J.

2011-03-28

Efficient catalytic chemical transformation of fructose to hydroxy methyl furfural (HMF) is one of the key steps for attaining industrial level conversion of biomass to useful chemicals. We report an investigation of the reaction mechanisms for the decomposition of fructose to HMF in both neutral and acidic environments at the Gaussian-4 level of theory including calculation of enthalpies, free energies, and effective solvation interactions. In neutral water solvent, the transformation of fructose to HMF involves a four step reaction sequence with four transition states. The effective activation energy relative to fructose in neutral water at 298 K is very large,more » about 74 kcal/mol, so that transformation in neutral media around this temperature is unlikely. In contrast, the computed potential energy surface is much more favorable for the transformation in acidic media at 498 K, as the effective activation barrier is about 39 kcal/mol. The transformation in acidic media is a much more complex mechanism involving dehydration and hydrogen transfer steps, which are more favorable when protonated intermediates are involved.« less

Mechanistic Insights into the Decomposition of Fructose to Hydroxy Methyl Furfural in Neutral and Acidic Environments Using High-Level Quantum Chemical Methods

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

Assary, Rajeev S.; Redfern, Paul C.; Greeley, Jeffrey P.

2011-04-21

Efficient catalytic chemical transformation of fructose to hydroxy methyl furfural (HMF) is one of the key steps for attaining industrial level conversion of biomass to useful chemicals. We report an investigation of the reaction mechanisms for the decomposition of fructose to HMF in both neutral and acidic environments at the Gaussian-4 level of theory including calculation of enthalpies, free energies, and effective solvation interactions. In neutral water solvent, the transformation of fructose to HMF involves a four step reaction sequence with four transition states. The effective activation energy relative to fructose in neutral water at 298 K is very large,more » about 74 kcal/mol, so that transformation in neutral media around this temperature is unlikely. In contrast, the computed potential energy surface is much more favorable for the transformation in acidic media at 498 K, as the effective activation barrier is about 39 kcal/mol. The transformation in acidic media is a much more complex mechanism involving dehydration and hydrogen transfer steps, which are more favorable when protonated intermediates are involved.« less

Mechanistic Insights into the Decomposition of Fructose to Hydroxy Methyl Furfural in Neutral and Acidic Environments Using High-Level Quantum Chemical Methods

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

Assary, Rajeev S.; Redfern, Paul C.; Greeley, Jeffrey

2011-03-28

Efficient catalytic chemical transformation of fructose to hydroxy methyl furfural (HMF) is one of the key steps for attaining industrial level conversion of biomass to useful chemicals. We report an investigation of the reaction mechanisms for the decomposition of fructose to HMF in both neutral and acidic environments at the Gaussian-4 level of theory including calculation of enthalpies, free energies, and effective solvation interactions. In neutral water solvent, the transformation of fructose to HMF involves a four step reaction sequence with four transition states. The effective activation energy relative to fructose in neutral water at 298 K is very large,more » about 74 kcal/mol, so that transformation in neutral media around this temperature is unlikely. In contrast, the computed potential energy surface is much more favorable for the transformation in acidic media at 498 K, as the effective activation barrier is about 39 kcal/mol. The transformation in acidic media is a much more complex mechanism involving dehydration and hydrogen transfer steps, which are more favorable when protonated intermediates are involved.« less

QSAR, DFT and quantum chemical studies on the inhibition potentials of some carbozones for the corrosion of mild steel in HCl.

PubMed

Eddy, Nnabuk O; Ita, Benedict I

2011-02-01

Experimental aspects of the inhibition of the corrosion of mild steel in HCl solutions by some carbozones were studied using gravimetric, thermometric and gasometric methods, while a theoretical study was carried out using density functional theory, a quantitative structure-activity relation, and quantum chemical principles. The results obtained indicated that the studied carbozones are good adsorption inhibitors for the corrosion of mild steel in HCl. The inhibition efficiencies of the studied carbozones were found to increase with increasing concentration of the respective inhibitor. A strong correlation was found between the average inhibition efficiency and some quantum chemical parameters, and also between the experimental and theoretical inhibition efficiencies (obtained from the quantitative structure-activity relation).

Spectroscopic studies and quantum chemical investigations of (3,4-dimethoxybenzylidene) propanedinitrile

NASA Astrophysics Data System (ADS)

Gupta, Ujval; Kumar, Vinay; Singh, Vivek K.; Kant, Rajni; Khajuria, Yugal

2015-04-01

The Fourier Transform Infrared (FTIR), Ultra-Violet Visible (UV-Vis) spectroscopy and Thermogravimetric (TG) analysis of (3,4-dimethoxybenzylidene) propanedinitrile have been carried out and investigated using quantum chemical calculations. The molecular geometry, harmonic vibrational frequencies, Mulliken charges, natural atomic charges and thermodynamic properties in the ground state have been investigated by using Hartree Fock Theory (HF) and Density Functional Theory (DFT) using B3LYP functional with 6-311G(d,p) basis set. Both HF and DFT methods yield good agreement with the experimental data. Vibrational modes are assigned with the help of Vibrational Energy Distribution Analysis (VEDA) program. UV-Visible spectrum was recorded in the spectral range of 190-800 nm and the results are compared with the calculated values using TD-DFT approach. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The results obtained from the studies of Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) are used to calculate molecular parameters like ionization potential, electron affinity, global hardness, electron chemical potential and global electrophilicity.

Terahertz Absorption and Circular Dichroism Spectroscopy of Solvated Biopolymers

NASA Astrophysics Data System (ADS)

Xu, Jing; Plaxco, Kevin; Allen, S. James

2006-03-01

Biopolymers are expected to exhibit broad spectral features in the terahertz frequency range, corresponding to their functionally relevant, global and sub-global collective vibrational modes with ˜ picosecond timescale. Recent advances in terahertz technology have stimulated researchers to employ terahertz absorption spectroscopy to directly probe these postulated collective modes. However, these pioneering studies have been limited to dry and, at best, moist samples. Successful isolation of low frequency vibrational activities of solvated biopolymers in their natural water environment has remained elusive, due to the overwhelming attenuation of the terahertz radiation by water. Here we have developed a terahertz absorption and circular dichroism spectrometer suitable for studying biopolymers in biologically relevant water solutions. We have precisely isolated, for the first time, the terahertz absorption of solvated prototypical proteins, Bovine Serum Albumin and Lysozyme, and made important direct comparison to the existing molecular dynamic simulations and normal mode calculations. We have also successfully demonstrated the magnetic circular dichroism in semiconductors, and placed upper bounds on the terahertz circular dichroism signatures of prototypical proteins in water solution.

Negative ion photoelectron spectroscopy of solvated electron cluster anions, (H2O){/n -} and (NH3){/n -}

NASA Astrophysics Data System (ADS)

Lee, G. H.; Arnold, S. T.; Eaton, J. G.; Sarkas, H. W.; Bowen, K. H.; Ludewigt, C.; Haberland, H.

1991-03-01

The photodetachment spectra of (H2O){/n =2-69/-} and (NH3){/n =41-1100/-} have been recorded, and vertical detachment energies (VDEs) were obtained from the spectra. For both systems, the cluster anion VDEs increase smoothly with increasing sizes and most species plot linearly with n -1/3, extrapolating to a VDE ( n=∞) value which is very close to the photoelectric threshold energy for the corresponding condensed phase solvated electron system. The linear extrapolation of this data to the analogous condensed phase property suggests that these cluster anions are gas phase counterparts to solvated electrons, i.e. they are embryonic forms of hydrated and ammoniated electrons which mature with increasing cluster size toward condensed phase solvated electrons.

Concentrated Electrolyte for the Sodium-Oxygen Battery: Solvation Structure and Improved Cycle Life.

PubMed

He, Mingfu; Lau, Kah Chun; Ren, Xiaodi; Xiao, Neng; McCulloch, William D; Curtiss, Larry A; Wu, Yiying

2016-12-05

Alkali metal-oxygen batteries are of great interests for energy storage because of their unparalleled theoretical energy densities. Particularly attractive is the emerging Na-O 2 battery because of the formation of superoxide as the discharge product. Dimethyl sulfoxide (DMSO) is a promising solvent for this battery but its instability towards Na makes it impractical in the Na-O 2 battery. Herein we report the enhanced stability of Na in DMSO solutions containing concentrated sodium trifluoromethanesulfonimide (NaTFSI) salts (>3 mol kg -1 ). Raman spectra of NaTFSI/DMSO electrolytes and ab initio molecular dynamics simulation reveal the Na + solvation number in DMSO and the formation of Na(DMSO) 3 (TFSI)-like solvation structure. The majority of DMSO molecules solvating Na + in concentrated solutions reduces the available free DMSO molecules that can react with Na and renders the TFSI anion decomposition, which protects Na from reacting with the electrolyte. Using these concentrated electrolytes, Na-O 2 batteries can be cycled forming sodium superoxide (NaO 2 ) as the sole discharge product with improved long cycle life, highlighting the beneficial role of concentrated electrolytes for Na-based batteries. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Concentrated Electrolyte for the Sodium-Oxygen Battery: Solvation Structure and Improved Cycle Life

DOE PAGES

He, Mingfu; Lau, Kah Chun; Ren, Xiaodi; ...

2016-11-03

Alkali metal-oxygen batteries are of great interests for energy storage because of their unparalleled theoretical energy densities. Particularly attractive is the emerging Na-O 2 battery because of the formation of superoxide as the discharge product. Dimethyl sulfoxide (DMSO) is a promising solvent for this battery but its instability towards Na makes it impractical in the Na-O 2 battery. Here in this paper, we report the enhanced stability of Na in DMSO solutions containing concentrated sodium trifluoromethanesulfonimide (NaTFSI) salts (>3molkg -1). Raman spectra of NaTFSI/DMSO electrolytes and abinitio molecular dynamics simulation reveal the Na + solvation number in DMSO and themore » formation of Na(DMSO) 3(TFSI)-like solvation structure. The majority of DMSO molecules solvating Na + in concentrated solutions reduces the available free DMSO molecules that can react with Na and renders the TFSI anion decomposition, which protects Na from reacting with the electrolyte. Using these concentrated electrolytes, Na-O 2 batteries can be cycled forming sodium superoxide (NaO 2) as the sole discharge product with improved long cycle life, highlighting the beneficial role of concentrated electrolytes for Na-based batteries.« less

Accurate Theoretical Predictions of the Properties of Energetic Materials

DTIC Science & Technology

2008-09-18

decomposition, Monte Carlo, molecular dynamics, supercritical fluids, solvation and separation, quantum Monte Carlo, potential energy surfaces, RDX , TNAZ...labs, who are contributing to the theoretical efforts, providing data for testing of the models, or aiding in the transition of the methods, models...and results to DoD applications. The major goals of the project are: • Models that describe phase transitions and chemical reactions in

Ultrafast hydrogen bond dynamics and partial electron transfer after photoexcitation of diethyl ester of 7-(diethylamino)-coumarin-3-phosphonic acid and its benzoxaphosphorin analog.

PubMed

Wagner, M S; Ilieva, E D; Petkov, P St; Nikolova, R D; Kienberger, R; Iglev, H

2015-04-21

The solvation dynamics after optical excitation of two phosphono-substituted coumarin derivatives dissolved in various solutions are studied by fluorescence up-conversion spectroscopy and quantum chemical simulations. The Kamlet-Taft analysis of the conventional absorption and emission spectra suggests weakening of the solvent-solute H-bonds upon optical excitation, which is in contrast to the results gained by the quantum simulations and earlier studies reported for coumarin derivatives without phosphono groups. The simulations give evidence that the solvent reorganisation around the excited fluorophore leads to partial electron transfer to the first solvation shell. The process occurs on a timescale between 1 and 10 ps depending on the solvent polarity and leads to a fast decay of the time-resolved emission signal. Using the ultrafast spectral shift of the time-dependent fluorescence we estimated the relaxation time of the H-bonds in the electronically excited state to be about 0.6 ps in water, 1.5 ps in ethanol and 2.8 ps in formamide.

Structure and dynamics of solvated polyethylenimine chains

NASA Astrophysics Data System (ADS)

Beu, Titus A.; Farcaş, Alexandra

2017-12-01

Polimeric gene-delivery carriers have attracted great interest in recent years, owing to their applicability in gene therapy. In particular, cationic polymers represent the most promising delivery vectors for nucleic acids into the cells. This study presents extensive atomistic molecular dynamics simulations of linear polyethylenimine chains. The simulations show that the variation of the chain size and protonation fraction causes a substantial change of the diffusion coefficient. Examination of the solvated chains suggests the possibility of controlling the polymer diffusion mobility in solution.

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

NASA Astrophysics Data System (ADS)

Shao, Yihan; Gan, Zhengting; Epifanovsky, Evgeny; Gilbert, Andrew T. B.; Wormit, Michael; Kussmann, Joerg; Lange, Adrian W.; Behn, Andrew; Deng, Jia; Feng, Xintian; Ghosh, Debashree; Goldey, Matthew; Horn, Paul R.; Jacobson, Leif D.; Kaliman, Ilya; Khaliullin, Rustam Z.; Kuś, Tomasz; Landau, Arie; Liu, Jie; Proynov, Emil I.; Rhee, Young Min; Richard, Ryan M.; Rohrdanz, Mary A.; Steele, Ryan P.; Sundstrom, Eric J.; Woodcock, H. Lee, III; Zimmerman, Paul M.; Zuev, Dmitry; Albrecht, Ben; Alguire, Ethan; Austin, Brian; Beran, Gregory J. O.; Bernard, Yves A.; Berquist, Eric; Brandhorst, Kai; Bravaya, Ksenia B.; Brown, Shawn T.; Casanova, David; Chang, Chun-Min; Chen, Yunqing; Chien, Siu Hung; Closser, Kristina D.; Crittenden, Deborah L.; Diedenhofen, Michael; DiStasio, Robert A., Jr.; Do, Hainam; Dutoi, Anthony D.; Edgar, Richard G.; Fatehi, Shervin; Fusti-Molnar, Laszlo; Ghysels, An; Golubeva-Zadorozhnaya, Anna; Gomes, Joseph; Hanson-Heine, Magnus W. D.; Harbach, Philipp H. P.; Hauser, Andreas W.; Hohenstein, Edward G.; Holden, Zachary C.; Jagau, Thomas-C.; Ji, Hyunjun; Kaduk, Benjamin; Khistyaev, Kirill; Kim, Jaehoon; Kim, Jihan; King, Rollin A.; Klunzinger, Phil; Kosenkov, Dmytro; Kowalczyk, Tim; Krauter, Caroline M.; Lao, Ka Un; Laurent, Adèle D.; Lawler, Keith V.; Levchenko, Sergey V.; Lin, Ching Yeh; Liu, Fenglai; Livshits, Ester; Lochan, Rohini C.; Luenser, Arne; Manohar, Prashant; Manzer, Samuel F.; Mao, Shan-Ping; Mardirossian, Narbe; Marenich, Aleksandr V.; Maurer, Simon A.; Mayhall, Nicholas J.; Neuscamman, Eric; Oana, C. Melania; Olivares-Amaya, Roberto; O'Neill, Darragh P.; Parkhill, John A.; Perrine, Trilisa M.; Peverati, Roberto; Prociuk, Alexander; Rehn, Dirk R.; Rosta, Edina; Russ, Nicholas J.; Sharada, Shaama M.; Sharma, Sandeep; Small, David W.; Sodt, Alexander; Stein, Tamar; Stück, David; Su, Yu-Chuan; Thom, Alex J. W.; Tsuchimochi, Takashi; Vanovschi, Vitalii; Vogt, Leslie; Vydrov, Oleg; Wang, Tao; Watson, Mark A.; Wenzel, Jan; White, Alec; Williams, Christopher F.; Yang, Jun; Yeganeh, Sina; Yost, Shane R.; You, Zhi-Qiang; Zhang, Igor Ying; Zhang, Xing; Zhao, Yan; Brooks, Bernard R.; Chan, Garnet K. L.; Chipman, Daniel M.; Cramer, Christopher J.; Goddard, William A., III; Gordon, Mark S.; Hehre, Warren J.; Klamt, Andreas; Schaefer, Henry F., III; Schmidt, Michael W.; Sherrill, C. David; Truhlar, Donald G.; Warshel, Arieh; Xu, Xin; Aspuru-Guzik, Alán; Baer, Roi; Bell, Alexis T.; Besley, Nicholas A.; Chai, Jeng-Da; Dreuw, Andreas; Dunietz, Barry D.; Furlani, Thomas R.; Gwaltney, Steven R.; Hsu, Chao-Ping; Jung, Yousung; Kong, Jing; Lambrecht, Daniel S.; Liang, WanZhen; Ochsenfeld, Christian; Rassolov, Vitaly A.; Slipchenko, Lyudmila V.; Subotnik, Joseph E.; Van Voorhis, Troy; Herbert, John M.; Krylov, Anna I.; Gill, Peter M. W.; Head-Gordon, Martin

2015-01-01

A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms

PubMed Central

Wagoner, Jason A.; Baker, Nathan A.

2006-01-01

Continuum solvation models provide appealing alternatives to explicit solvent methods because of their ability to reproduce solvation effects while alleviating the need for expensive sampling. Our previous work has demonstrated that Poisson-Boltzmann methods are capable of faithfully reproducing polar explicit solvent forces for dilute protein systems; however, the popular solvent-accessible surface area model was shown to be incapable of accurately describing nonpolar solvation forces at atomic-length scales. Therefore, alternate continuum methods are needed to reproduce nonpolar interactions at the atomic scale. In the present work, we address this issue by supplementing the solvent-accessible surface area model with additional volume and dispersion integral terms suggested by scaled particle models and Weeks–Chandler–Andersen theory, respectively. This more complete nonpolar implicit solvent model shows very good agreement with explicit solvent results and suggests that, although often overlooked, the inclusion of appropriate dispersion and volume terms are essential for an accurate implicit solvent description of atomic-scale nonpolar forces. PMID:16709675

Tuning structure and mobility of solvation shells surrounding tracer additives.

PubMed

Carmer, James; Jain, Avni; Bollinger, Jonathan A; van Swol, Frank; Truskett, Thomas M

2015-03-28

Molecular dynamics simulations and a stochastic Fokker-Planck equation based approach are used to illuminate how position-dependent solvent mobility near one or more tracer particle(s) is affected when tracer-solvent interactions are rationally modified to affect corresponding solvation structure. For tracers in a dense hard-sphere fluid, we compare two types of tracer-solvent interactions: (1) a hard-sphere-like interaction, and (2) a soft repulsion extending beyond the hard core designed via statistical mechanical theory to enhance tracer mobility at infinite dilution by suppressing coordination-shell structure [Carmer et al., Soft Matter 8, 4083-4089 (2012)]. For the latter case, we show that the mobility of surrounding solvent particles is also increased by addition of the soft repulsive interaction, which helps to rationalize the mechanism underlying the tracer's enhanced diffusivity. However, if multiple tracer surfaces are in closer proximity (as at higher tracer concentrations), similar interactions that disrupt local solvation structure instead suppress the position-dependent solvent dynamics.

Fluorination, Defluorination, Derivatization and Solvation of Single-Wall Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Margrave, John L.

1999-10-01

Direct fluorination has been used to create fluoronanotubes which have active sites for derivatizing carbon nanotubes. A new technique using hydrazine and its derivatives has been used for defluorination of fluoronanotubes. The products include N2 and HF. Fluorinated species can be derivatized with R-Li or Grignard Reagents to form inorganic fluorides and derivatized products e.g., methyl, butyl or hexyl-nanotubes, (NH2)x-nanotubes, etc. Mass-spectra IR and Raman spectra along with electron microprobe analyses have been utilized, along with AFM, SEM and TEM to characterize the products. ``Fluorotubes" can be solvated as individual tubes in various alcohol solvents via ultrasonication. These solutions persist long enough (over a week) to permit solution phase chemistry to be carried out on the fluorotubes. For example, the solvated fluorotubes can be precipitated out of solution with hydrazine to yield normal, unfluorinated SWNTs or they can be reacted with sodium methoxide to yield methoxylated SWNTs.

Femtosecond spectroscopic study of the solvation of amphiphilic molecules by water

NASA Astrophysics Data System (ADS)

Rezus, Y. L. A.; Bakker, H. J.

2008-06-01

We use polarization-resolved mid-infrared pump-probe spectroscopy to study the aqueous solvation of proline and N-methylacetamide. These molecules serve as models to study the solvation of proteins. We monitor the orientational dynamics of partly deuterated water molecules (HDO) that are present at a low concentration in the water. We find that the OD vibration of HDO relaxes via an intermediate level, that is characterized by a hydrogen-bond that is stronger than in the ground state. With increasing concentration the lifetime of the excited state increases from 1.8 ps to 2.4 ps and the lifetime of the intermediate level from 0.6 ps to 1.0 ps. Regarding the orientational dynamics we observe biexponential behavior, which finds its origin in the presence of two classes of water molecules. There is a fraction of water molecules that has bulk-like orientational dynamics ( τrot = 2.5 ps) and a fraction of immobilized water molecules ( τrot > 10 ps). The relative abundance of the two fractions is determined by the nature and concentration of the solute. We find that the hydrophobic solute groups are responsible for the immobilization of water molecules. Every methyl group causes the immobilization of approximately 4 water OH groups. The hydrophilic solute groups, on the other hand, do not hinder the reorientation and the water molecules solvating them reorient with the same rate as in the bulk liquid.

Epitaxial Zn quantum dots coherently grown on Si(1 1 1): growth mechanism, nonlinear optical and chemical states analyses

NASA Astrophysics Data System (ADS)

Huang, Bo-Jia; Kao, Li-Chi; Brahma, Sanjaya; Jeng, Yu-En; Chiu, Shang-Jui; Ku, Ching-Shun; Lo, Kuang-Yao

2017-05-01

Oxide- and defect-free metal/semiconductor interface is important to improve Ohmic contact for the suppression of electron scattering and the avoidance of an extrinsic surface state in estimating the barrier of the Schottky contact at the nanodevice interface. This study reports the growth mechanism of Zn quantum dots coherently grown on Si(1 1 1) and the physical phenomena of the crystalline, nonlinear optics, and the chemical states of Zn quantum dots. Epitaxial Zn quantum dots were coherently formed on a non-oxide Si(1 1 1) surface through the liquid- to solid-phase transformation as a result of pattern matching between the Zn(0 0 2) and Si(1 1 1) surfaces. The growth mechanism of constrained Zn quantum dots grown through strategic magnetron radio frequency sputtering is complex. Some factors, such as substrate temperature, hydrogen gas flow, and negative DC bias, influence the configuration of epitaxial Zn quantum dots. In particular, hydrogen gas plays an important role in reducing the ZnO+ and native oxide that is bombarded by accelerated ions, thereby enhancing the Zn ion surface diffusion. The reduction reaction can be inspected by distinguishing the chemical states of ZnO/Zn quantum dots from natural oxidation or the states of Zn 3d through the analysis of x-ray absorption near the edge structure spectrum. The complex growth mechanism can be systematically understood by analyzing a noncancelled anisotropic 3 m dipole from reflective second harmonic generation and inspecting the evolution between the Zn(0 0 2) and Zn(1 1 1) peaks of the collective ZnO/Zn quantum dots in synchrotron XRD.

Use of external cavity quantum cascade laser compliance voltage in real-time trace gas sensing of multiple chemicals

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

Phillips, Mark C.; Taubman, Matthew S.; Kriesel, Jason M.

2015-02-08

We describe a prototype trace gas sensor designed for real-time detection of multiple chemicals. The sensor uses an external cavity quantum cascade laser (ECQCL) swept over its tuning range of 940-1075 cm-1 (9.30-10.7 µm) at a 10 Hz repetition rate.

Rotational spectroscopic study of carbonyl sulfide solvated with hydrogen molecules.

PubMed

Michaud, Julie M; Jäger, Wolfgang

2008-10-14

Rotational spectra of small-sized (H(2))(N)-OCS clusters with N = 2-7 were measured using a pulsed-jet Fourier transform microwave spectrometer. These include spectra of pure (para-H(2))(N)-OCS clusters, pure (ortho-H(2))(N)-OCS clusters, and mixed ortho-H(2) and para-H(2) containing clusters. The rotational lines of ortho-H(2) molecules containing clusters show proton spin-proton spin hyperfine structure, and the pattern evolves as the number of ortho-H(2) molecules in the cluster increases. Various isotopologues of the clusters were investigated, including those with O(13)CS, OC(33)S, OC(34)S, and O(13)C(34)S. Nuclear quadrupole hyperfine structures of rotational transitions were observed for (33)S (nuclear spin quantum number I = 3/2) containing isotopologues. The (33)S nuclear quadrupole coupling constants are compared to the corresponding constant of the OCS monomer and those of the He(N)-OCS clusters. The assignment of the number of solvating hydrogen molecules N is supported by the analyses of the proton spin-proton spin hyperfine structures of the mixed clusters, the dependence of line intensities on sample conditions (pressure and concentrations), and the agreement of the (para-H(2))(N)-OCS and (ortho-H(2))(N)-OCS rotational constants with those from a previous infrared study [J. Tang and A. R. W. McKellar, J. Chem. Phys. 121, 3087 (2004)].

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

PubMed

Fulfer, K D; Kuroda, D G

2017-09-20

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

Quantum chemical characterization of zwitterionic structures: Supramolecular complexes for modifying the wettability of oil-water-limestone system.

PubMed

Lopez-Chavez, Ernesto; Garcia-Quiroz, Alberto; Gonzalez-Garcia, Gerardo; Orozco-Duran, Gabriela E; Zamudio-Rivera, Luis S; Martinez-Magadan, José M; Buenrostro-Gonzalez, Eduardo; Hernandez-Altamirano, Raul

2014-06-01

In this work, we present a quantum chemical study pertaining to some supramolecular complexes acting as wettability modifiers of oil-water-limestone system. The complexes studied are derived from zwitterionic liquids of the types N'-alkyl-bis, N-alquenil, N-cycloalkyl, N-amyl-bis-beta amino acid or salts acting as sparkling agents. We studied two molecules of zwitterionic liquids (ZL10 and ZL13), HOMO and LUMO levels, and the energy gap between them, were calculated, as well as the electron affinity (EA) and ionization potential (IP), chemical potential, chemical hardness, chemical electrophilicity index and selectivity descriptors such Fukui indices. In this work, electrochemical comparison was realized with cocamidopropyl betaine (CPB), which is a structure zwitterionic liquid type, nowadays widely applied in enhanced recovery processes. Copyright © 2014 Elsevier Inc. All rights reserved.

Systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions

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

Cooks, Robert Graham; Li, Anyin; Luo, Qingjie

The invention generally relates to systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions. In certain aspects, the invention provides methods that involve providing a metal and a solvent. The methods additionally involve applying voltage to the solvated metal to thereby produce solvent droplets including ions of the metal containing compound, and directing the solvent droplets including the metal ions to a target. In certain embodiments, once at the target, the metal ions can react directly or catalyze reactions.

Systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions

DOEpatents

Cooks, Robert Graham; Li, Anyin; Luo, Qingjie

2017-01-24

The invention generally relates to systems and methods for producing metal clusters; functionalized surfaces; and droplets including solvated metal ions. In certain aspects, the invention provides methods that involve providing a metal and a solvent. The methods additionally involve applying voltage to the solvated metal to thereby produce solvent droplets including ions of the metal containing compound, and directing the solvent droplets including the metal ions to a target. In certain embodiments, once at the target, the metal ions can react directly or catalyze reactions.

Physical transformation of niclosamide solvates in pharmaceutical suspensions determined by DSC and TG analysis.

PubMed

de Villiers, M M; Mahlatji, M D; Malan, S F; van Tonder, E C; Liebenberg, W

2004-07-01

This study reports the preparation of four niclosamide solvates and the determination of the stability of the crystal forms in different suspension vehicles by DSC and TG analysis. Thermal analysis showed that the niclosamide solvates were extremely unstable in a PVP-vehicle and rapidly changed to monohydrated crystals. A suspension in propylene glycol was more stable and TG analysis showed that crystal transformation was less rapid. In this vehicle, the crystals transformed to the anhydrate, rather than the monohydrate, since the vehicle was non-aqueous. The TEG-hemisolvate was the most stable in suspension and offered the best possibility of commercial exploitation.

High-School Students' Conceptual Difficulties and Attempts at Conceptual Change: The Case of Basic Quantum Chemical Concepts

ERIC Educational Resources Information Center

Tsaparlis, Georgios; Papaphotis, Georgios

2009-01-01

This study tested for deep understanding and critical thinking about basic quantum chemical concepts taught at 12th grade (age 17-18). Our aim was to achieve conceptual change in students. A quantitative study was conducted first (n = 125), and following this 23 selected students took part in semi-structured interviews either individually or in…

Chemical Potential for the Interacting Classical Gas and the Ideal Quantum Gas Obeying a Generalized Exclusion Principle

ERIC Educational Resources Information Center

Sevilla, F. J.; Olivares-Quiroz, L.

2012-01-01

In this work, we address the concept of the chemical potential [mu] in classical and quantum gases towards the calculation of the equation of state [mu] = [mu](n, T) where n is the particle density and "T" the absolute temperature using the methods of equilibrium statistical mechanics. Two cases seldom discussed in elementary textbooks are…

Chemical potential and compressibility of quantum Hall bilayer excitons,.

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

Skinner, Brian

2016-02-25

I consider a system of two parallel quantum Hall layers with total filling factor 0 or 1. When the distance between the layers is small enough, electrons and holes in opposite layers can form inter-layer excitons, which have a finite effective mass and interact via a dipole-dipole potential. I present results for the chemical potential u of the resulting bosonic system as a function of the exciton concentration n and the interlayer separation d. I show that both u and the interlayer capacitance have an unusual nonmonotonic dependence on d, owing to the interplay between an increasing dipole moment andmore » an increasing effective mass with increasing d. Finally, I discuss the transition between the superfluid and Wigner crystal phases, which is shown to occur at d x n-1/10. Results are derived first via simple intuitive arguments, and then verified with more careful analytic derivations and numeric calculations.« less

Mapping the Free Energy of Lithium Solvation in the Protic Ionic Liquid Ethylammonuim Nitrate: A Metadynamics Study.

PubMed

Kachmar, Ali; Carignano, Marcelo; Laino, Teodoro; Iannuzzi, Marcella; Hutter, Jürg

2017-08-10

Understanding lithium solvation and transport in ionic liquids is important due to their possible application in electrochemical devices. Using first-principles simulations aided by a metadynamics approach we study the free-energy landscape for lithium ions at infinite dilution in ethylammonium nitrate, a protic ionic liquid. We analyze the local structure of the liquid around the lithium cation and obtain a quantitative picture in agreement with experimental findings. Our simulations show that the lowest two free energy minima correspond to conformations with the lithium ion being solvated either by three or four nitrate ions with a transition barrier between them of 0.2 eV. Other less probable conformations having different solvation pattern are also investigated. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Compensation effects in molecular interactions and the quantum chemical le Chatelier principle.

PubMed

Mezey, Paul G

2015-05-28

Components of molecular interactions and various changes in the components of total energy changes during molecular processes typically exhibit some degrees of compensation. This may be as prominent as the over 90% compensation of the electronic energy and nuclear repulsion energy components of the total energy in some conformational changes. Some of these compensations are enhanced by solvent effects. For various arrangements of ions in a solvent, however, not only compensation but also a formal, mutual enhancement between the electronic energy and nuclear repulsion energy components of the total energy may also occur, when the tools of nuclear charge variation are applied to establish quantum chemically rigorous energy inequalities.

Directing the Lithium-Sulfur Reaction Pathway via Sparingly Solvating Electrolytes for High Energy Density Batteries.

PubMed

Lee, Chang-Wook; Pang, Quan; Ha, Seungbum; Cheng, Lei; Han, Sang-Don; Zavadil, Kevin R; Gallagher, Kevin G; Nazar, Linda F; Balasubramanian, Mahalingam

2017-06-28

The lithium-sulfur battery has long been seen as a potential next generation battery chemistry for electric vehicles owing to the high theoretical specific energy and low cost of sulfur. However, even state-of-the-art lithium-sulfur batteries suffer from short lifetimes due to the migration of highly soluble polysulfide intermediates and exhibit less than desired energy density due to the required excess electrolyte. The use of sparingly solvating electrolytes in lithium-sulfur batteries is a promising approach to decouple electrolyte quantity from reaction mechanism, thus creating a pathway toward high energy density that deviates from the current catholyte approach. Herein, we demonstrate that sparingly solvating electrolytes based on compact, polar molecules with a 2:1 ratio of a functional group to lithium salt can fundamentally redirect the lithium-sulfur reaction pathway by inhibiting the traditional mechanism that is based on fully solvated intermediates. In contrast to the standard catholyte sulfur electrochemistry, sparingly solvating electrolytes promote intermediate- and short-chain polysulfide formation during the first third of discharge, before disproportionation results in crystalline lithium sulfide and a restricted fraction of soluble polysulfides which are further reduced during the remaining discharge. Moreover, operation at intermediate temperatures ca. 50 °C allows for minimal overpotentials and high utilization of sulfur at practical rates. This discovery opens the door to a new wave of scientific inquiry based on modifying the electrolyte local structure to tune and control the reaction pathway of many precipitation-dissolution chemistries, lithium-sulfur and beyond.

Dissecting ion-specific dielectric spectra of sodium-halide solutions into solvation water and ionic contributions.

PubMed

Rinne, Klaus F; Gekle, Stephan; Netz, Roland R

2014-12-07

Using extensive equilibrium molecular dynamics simulations we determine the dielectric spectra of aqueous solutions of NaF, NaCl, NaBr, and NaI. The ion-specific and concentration-dependent shifts of the static dielectric constants and the dielectric relaxation times match experimental results very well, which serves as a validation of the classical and non-polarizable ionic force fields used. The purely ionic contribution to the dielectric response is negligible, but determines the conductivity of the salt solutions. The ion-water cross correlation contribution is negative and reduces the total dielectric response by about 5%-10% for 1 M solutions. The dominating water dielectric response is decomposed into different water solvation shells and ion-pair configurations, by this the spectral blue shift and the dielectric decrement of salt solutions with increasing salt concentration is demonstrated to be primarily caused by first-solvation shell water. With rising salt concentration the simulated spectra show more pronounced deviations from a single-Debye form and can be well described by a Cole-Cole fit, in quantitative agreement with experiments. Our spectral decomposition into ionic and different water solvation shell contributions does not render the individual contributions more Debye-like, this suggests the non-Debye-like character of the dielectric spectra of salt solutions not to be due to the superposition of different elementary relaxation processes with different relaxation times. Rather, the non-Debye-like character is likely to be an inherent spectral signature of solvation water around ions.

Photo-illuminated diamond as a solid-state source of solvated electrons in water for nitrogen reduction.

PubMed

Zhu, Di; Zhang, Linghong; Ruther, Rose E; Hamers, Robert J

2013-09-01

The photocatalytic reduction of N₂ to NH₃ is typically hampered by poor binding of N₂ to catalytic materials and by the very high energy of the intermediates involved in this reaction. Solvated electrons directly introduced into the reactant solution can provide an alternative pathway to overcome such limitations. Here we demonstrate that illuminated hydrogen-terminated diamond yields facile electron emission into water, thus inducing reduction of N₂ to NH₃ at ambient temperature and pressure. Transient absorption measurements at 632 nm reveal the presence of solvated electrons adjacent to the diamond after photoexcitation. Experiments using inexpensive synthetic diamond samples and diamond powder show that photocatalytic activity is strongly dependent on the surface termination and correlates with the production of solvated electrons. The use of diamond to eject electrons into a reactant liquid represents a new paradigm for photocatalytic reduction, bringing electrons directly to reactants without requiring molecular adsorption to the surface.

Free-energy analysis of the electron-density fluctuation in the quantum-mechanical/molecular-mechanical simulation combined with the theory of energy representation.

PubMed

Matubayasi, Nobuyuki; Takahashi, Hideaki

2012-01-28

The relationship is investigated for QM/MM (quantum-mechanical/molecular-mechanical) systems between the fluctuations of the electronic state of the QM subsystem and of the solvation effect due to the QM-MM interaction. The free-energy change due to the electron-density fluctuation around its average is highlighted, and is evaluated through an approximate functional formulated in terms of distribution functions of the many-body coupling (pairwise non-additive) part of the QM-MM interaction energy. A set of QM/MM simulations are conducted in MM water solvent for QM water solute in ambient and supercritical conditions and for QM glycine solute in the neutral and zwitterionic forms. The variation of the electronic distortion energy of the QM solute in the course of QM/MM simulation is then shown to be compensated by the corresponding variation of the free energy of solvation. The solvation free energy conditioned by the electronic distortion energy is further analyzed with its components. It is found that the many-body contribution is essentially equal between the free energy and the average sum of solute-solvent interaction energy. © 2012 American Institute of Physics

Demonstration of a rapidly-swept external cavity quantum cascade laser for rapid and sensitive quantification of chemical mixtures

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

Brumfield, Brian E.; Taubman, Matthew S.; Phillips, Mark C.

2016-02-13

A rapidly-swept external cavity quantum cascade laser (ECQCL) system for fast open-path quantification of multiple chemicals and mixtures is presented. The ECQCL system is swept over its entire tuning range (>100 cm-1) at frequencies up to 200 Hz. At 200 Hz the wavelength tuning rate and spectral resolution are 2x104 cm-1/sec and < 0.2 cm-1, respectively. The capability of the current system to quantify changes in chemical concentrations on millesecond timescales is demonstrated at atmospheric pressure using an open-path multi-pass cell. The detection limits for chemicals ranged from ppb to ppm levels depending on the absorption cross-section.

The Nature of the Chemical Bond--1990.

ERIC Educational Resources Information Center

Ogilvie, J. F.

1990-01-01

Three aspects of quantum mechanics in modern chemistry are stressed: the fundamental structure of quantum mechanics as a basis of chemical applications, the relationship of quantum mechanics to atomic and molecular structure, and the consequent implications for chemical education. A list of 64 references is included. (CW)

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

PubMed

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

2007-02-22

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

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

PubMed

Zanith, Caroline C; Pliego, Josefredo R

2015-03-01

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

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

NASA Astrophysics Data System (ADS)

Zanith, Caroline C.; Pliego, Josefredo R.

2015-03-01

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

A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water

NASA Astrophysics Data System (ADS)

Schwörer, Magnus; Wichmann, Christoph; Tavan, Paul

2016-03-01

The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). For the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a "first-principles" DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.

A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water

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

Schwörer, Magnus; Wichmann, Christoph; Tavan, Paul, E-mail: tavan@physik.uni-muenchen.de

2016-03-21

The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). Formore » the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a “first-principles” DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.« less

Influence of Spin-Orbit Quenching on the Solvation of Indium in Helium Droplets

NASA Astrophysics Data System (ADS)

Meyer, Ralf; Pototschnig, Johann V.; Ernst, Wolfgang E.; Hauser, Andreas W.

2017-06-01

Recent experimental interest of the collaborating group of M. Koch on the dynamics of electronic excitations of indium in helium droplets triggered a series of computational studies on the group 13 elements Al, Ga and In and their indecisive behavior between wetting and non wetting when placed onto superfluid helium droplets. We employ a combination of multiconfigurational self consistent field calculations (MCSCF) and multireference configuration interaction (MRCI) to calculate the diatomic potentials. Particularly interesting is the case of indium with an Ancilotto parameter λ close to the threshold value of 1.9. As shown by Reho et al. the spin-orbit splitting of metal atoms solvated in helium droplets is subject to a quenching effect. This can drastically change the solvation behavior. In this work we extend the approach presented by Reho et al. to include distance dependent spin-orbit coupling. The resulting potential surfaces are used to calculate the solvation energy of the ground state and the first excited state with orbital-free helium density functional theory. F. Ancilotto, P. B. Lerner and M. W. Cole, Journal of Low Temperature Physics, 1995, 101, 1123-1146 J. H. Reho, U. Merker, M. R. Radcliff, K. K. Lehmann and G. Scoles, The Journal of Physical Chemistry A, 2000, 104, 3620-3626

Quantitative prediction of solvation free energy in octanol of organic compounds.

PubMed

Delgado, Eduardo J; Jaña, Gonzalo A

2009-03-01

The free energy of solvation, DeltaGS0, in octanol of organic compounds is quantitatively predicted from the molecular structure. The model, involving only three molecular descriptors, is obtained by multiple linear regression analysis from a data set of 147 compounds containing diverse organic functions, namely, halogenated and non-halogenated alkanes, alkenes, alkynes, aromatics, alcohols, aldehydes, ketones, amines, ethers and esters; covering a DeltaGS0 range from about -50 to 0 kJ.mol(-1). The model predicts the free energy of solvation with a squared correlation coefficient of 0.93 and a standard deviation, 2.4 kJ.mol(-1), just marginally larger than the generally accepted value of experimental uncertainty. The involved molecular descriptors have definite physical meaning corresponding to the different intermolecular interactions occurring in the bulk liquid phase. The model is validated with an external set of 36 compounds not included in the training set.

Explicit polarization: a quantum mechanical framework for developing next generation force fields.

PubMed

Gao, Jiali; Truhlar, Donald G; Wang, Yingjie; Mazack, Michael J M; Löffler, Patrick; Provorse, Makenzie R; Rehak, Pavel

2014-09-16

Conspectus Molecular mechanical force fields have been successfully used to model condensed-phase and biological systems for a half century. By means of careful parametrization, such classical force fields can be used to provide useful interpretations of experimental findings and predictions of certain properties. Yet, there is a need to further improve computational accuracy for the quantitative prediction of biomolecular interactions and to model properties that depend on the wave functions and not just the energy terms. A new strategy called explicit polarization (X-Pol) has been developed to construct the potential energy surface and wave functions for macromolecular and liquid-phase simulations on the basis of quantum mechanics rather than only using quantum mechanical results to fit analytic force fields. In this spirit, this approach is called a quantum mechanical force field (QMFF). X-Pol is a general fragment method for electronic structure calculations based on the partition of a condensed-phase or macromolecular system into subsystems ("fragments") to achieve computational efficiency. Here, intrafragment energy and the mutual electronic polarization of interfragment interactions are treated explicitly using quantum mechanics. X-Pol can be used as a general, multilevel electronic structure model for macromolecular systems, and it can also serve as a new-generation force field. As a quantum chemical model, a variational many-body (VMB) expansion approach is used to systematically improve interfragment interactions, including exchange repulsion, charge delocalization, dispersion, and other correlation energies. As a quantum mechanical force field, these energy terms are approximated by empirical functions in the spirit of conventional molecular mechanics. This Account first reviews the formulation of X-Pol, in the full variationally correct version, in the faster embedded version, and with systematic many-body improvements. We discuss illustrative examples

Structure and Dynamics of Solvated Polymers near a Silica Surface: On the Different Roles Played by Solvent.

PubMed

Perrin, Elsa; Schoen, Martin; Coudert, François-Xavier; Boutin, Anne

2018-04-26

Whereas it is experimentally known that the inclusion of nanoparticles in hydrogels can lead to a mechanical reinforcement, a detailed molecular understanding of the adhesion mechanism is still lacking. Here we use coarse-grained molecular dynamics simulations to investigate the nature of the interface between silica surfaces and solvated polymers. We show how differences in the nature of the polymer and the polymer-solvent interactions can lead to drastically different behavior of the polymer-surface adhesion. Comparing explicit and implicit solvent models, we conclude that this effect cannot be fully described in an implicit solvent. We highlight the crucial role of polymer solvation for the adsorption of the polymer chain on the silica surface, the significant dynamics of polymer chains on the surface, and details of the modifications in the structure solvated polymer close to the interface.

Polarons and Mobile Impurities Near a Quantum Phase Transition

NASA Astrophysics Data System (ADS)

Shadkhoo, Shahriar

This dissertation aims at improving the current understanding of the physics of mobile impurities in highly correlated liquid-like phases of matter. Impurity problems pose challenging and intricate questions in different realms of many-body physics. For instance, the problem of ''solvation'' of charged solutes in polar solvents, has been the subject of longstanding debates among chemical physicists. The significant role of quantum fluctuations of the solvent, as well as the break down of linear response theory, render the ordinary treatments intractable. Inspired by this complicated problem, we first attempt to understand the role of non-specific quantum fluctuations in the solvation process. To this end, we calculate the dynamic structure factor of a model polar liquid, using the classical Molecular Dynamics (MD) simulations. We verify the failure of linear response approximation in the vicinity of a hydrated electron, by comparing the outcomes of MD simulations with the predictions of linear response theory. This nonlinear behavior is associated with the pronounced peaks of the structure factor, which reflect the strong fluctuations of the local modes. A cavity picture is constructed based on heuristic arguments, which suggests that the electron, along with the surrounding polarization cloud, behave like a frozen sphere, for which the linear response theory is broken inside and valid outside. The inverse radius of the spherical region serves as a UV momentum cutoff for the linear response approximation to be applicable. The problem of mobile impurities in polar liquids can be also addressed in the framework of the ''polaron'' problem. Polaron is a quasiparticle that typically acquires an extended state at weak couplings, and crossovers to a self-trapped state at strong couplings. Using the analytical fits to the numerically obtained charge-charge structure factor, a phenomenological approach is proposed within the Leggett's influence functional formalism, which

Spectroscopic studies and quantum chemical investigations of (3,4-dimethoxybenzylidene) propanedinitrile.

PubMed

Gupta, Ujval; Kumar, Vinay; Singh, Vivek K; Kant, Rajni; Khajuria, Yugal

2015-04-05

The Fourier Transform Infrared (FTIR), Ultra-Violet Visible (UV-Vis) spectroscopy and Thermogravimetric (TG) analysis of (3,4-dimethoxybenzylidene) propanedinitrile have been carried out and investigated using quantum chemical calculations. The molecular geometry, harmonic vibrational frequencies, Mulliken charges, natural atomic charges and thermodynamic properties in the ground state have been investigated by using Hartree Fock Theory (HF) and Density Functional Theory (DFT) using B3LYP functional with 6-311G(d,p) basis set. Both HF and DFT methods yield good agreement with the experimental data. Vibrational modes are assigned with the help of Vibrational Energy Distribution Analysis (VEDA) program. UV-Visible spectrum was recorded in the spectral range of 190-800nm and the results are compared with the calculated values using TD-DFT approach. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The results obtained from the studies of Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) are used to calculate molecular parameters like ionization potential, electron affinity, global hardness, electron chemical potential and global electrophilicity. Copyright © 2014 Elsevier B.V. All rights reserved.

Solvation of carbonaceous molecules by para-H2 and ortho-D2 clusters. II. Fullerenes.

PubMed

Calvo, F; Yurtsever, E

2016-08-28

The coating of various fullerenes by para-hydrogen and ortho-deuterium molecules has been computationally studied as a function of the solvent amount. Rotationally averaged interaction potentials for structureless hydrogen molecules are employed to model their interaction with neutral or charged carbonaceous dopants containing between 20 and 240 atoms, occasionally comparing different fullerenes having the same size but different shapes. The solvation energy and the size of the first solvation shell obtained from path-integral molecular dynamics simulations at 2 K show only minor influence on the dopant charge and on the possible deuteration of the solvent, although the shell size is largest for ortho-D2 coating cationic fullerenes. Nontrivial finite size effects have been found with the shell size varying non-monotonically close to its completion limit. For fullerenes embedded in large hydrogen clusters, the shell size and solvation energy both follow linear scaling with the fullerene size. The shell sizes obtained for C60 (+) and C70 (+) are close to 49 and 51, respectively, and agree with mass spectrometry experiments.

Solvation of carbonaceous molecules by para-H2 and ortho-D2 clusters. II. Fullerenes

NASA Astrophysics Data System (ADS)

Calvo, F.; Yurtsever, E.

2016-08-01

The coating of various fullerenes by para-hydrogen and ortho-deuterium molecules has been computationally studied as a function of the solvent amount. Rotationally averaged interaction potentials for structureless hydrogen molecules are employed to model their interaction with neutral or charged carbonaceous dopants containing between 20 and 240 atoms, occasionally comparing different fullerenes having the same size but different shapes. The solvation energy and the size of the first solvation shell obtained from path-integral molecular dynamics simulations at 2 K show only minor influence on the dopant charge and on the possible deuteration of the solvent, although the shell size is largest for ortho-D2 coating cationic fullerenes. Nontrivial finite size effects have been found with the shell size varying non-monotonically close to its completion limit. For fullerenes embedded in large hydrogen clusters, the shell size and solvation energy both follow linear scaling with the fullerene size. The shell sizes obtained for C 60+ and C 70+ are close to 49 and 51, respectively, and agree with mass spectrometry experiments.

Chemical processing of three-dimensional graphene networks on transparent conducting electrodes for depleted-heterojunction quantum dot solar cells.

PubMed

Tavakoli, Mohammad Mahdi; Simchi, Abdolreza; Fan, Zhiyong; Aashuri, Hossein

2016-01-07

We present a novel chemical procedure to prepare three-dimensional graphene networks (3DGNs) as a transparent conductive film to enhance the photovoltaic performance of PbS quantum-dot (QD) solar cells. It is shown that 3DGN electrodes enhance electron extraction, yielding a 30% improvement in performance compared with the conventional device.

Quantum mechanics/molecular mechanics modeling of photoelectron spectra: the carbon 1s core-electron binding energies of ethanol-water solutions.

PubMed

Löytynoja, T; Niskanen, J; Jänkälä, K; Vahtras, O; Rinkevicius, Z; Ågren, H

2014-11-20

Using ethanol-water solutions as illustration, we demonstrate the capability of the hybrid quantum mechanics/molecular mechanics (QM/MM) paradigm to simulate core photoelectron spectroscopy: the binding energies and the chemical shifts. An integrated approach with QM/MM binding energy calculations coupled to preceding molecular dynamics sampling is adopted to generate binding energies averaged over the solute-solvent configurations available at a particular temperature and pressure and thus allowing for a statistical assessment with confidence levels for the final binding energies. The results are analyzed in terms of the contributions in the molecular mechanics model-electrostatic, polarization, and van der Waals-with atom or bond granulation of the corresponding MM charge and polarizability force-fields. The role of extramolecular charge transfer screening of the core-hole and explicit hydrogen bonding is studied by extending the QM core to cover the first solvation shell. The results are compared to those obtained from pure electrostatic and polarizable continuum models. Particularly, the dependence of the carbon 1s binding energies with respect to the ethanol concentration is studied. Our results indicate that QM/MM can be used as an all-encompassing model to study photoelectron binding energies and chemical shifts in solvent environments.

Local protein solvation drives direct down-conversion in phycobiliprotein PC645 via incoherent vibronic transport

PubMed Central

Blau, Samuel M.; Bennett, Doran I. G.; Kreisbeck, Christoph; Scholes, Gregory D.; Aspuru-Guzik, Alán

2018-01-01

The mechanisms controlling excitation energy transport (EET) in light-harvesting complexes remain controversial. Following the observation of long-lived beats in 2D electronic spectroscopy of PC645, vibronic coherence, the delocalization of excited states between pigments supported by a resonant vibration, has been proposed to enable direct excitation transport from the highest-energy to the lowest-energy pigments, bypassing a collection of intermediate states. Here, we instead show that for phycobiliprotein PC645 an incoherent vibronic transport mechanism is at play. We quantify the solvation dynamics of individual pigments using ab initio quantum mechanics/molecular mechanics (QM/MM) nuclear dynamics. Our atomistic spectral densities reproduce experimental observations ranging from absorption and fluorescence spectra to the timescales and selectivity of down-conversion observed in transient absorption measurements. We construct a general model for vibronic dimers and establish the parameter regimes of coherent and incoherent vibronic transport. We demonstrate that direct down-conversion in PC645 proceeds incoherently, enhanced by large reorganization energies and a broad collection of high-frequency vibrations. We suggest that a similar incoherent mechanism is appropriate across phycobiliproteins and represents a potential design principle for nanoscale control of EET. PMID:29588417

Tuning structure and mobility of solvation shells surrounding tracer additives

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

Carmer, James; Jain, Avni; Bollinger, Jonathan A.

2015-03-28

Molecular dynamics simulations and a stochastic Fokker-Planck equation based approach are used to illuminate how position-dependent solvent mobility near one or more tracer particle(s) is affected when tracer-solvent interactions are rationally modified to affect corresponding solvation structure. For tracers in a dense hard-sphere fluid, we compare two types of tracer-solvent interactions: (1) a hard-sphere-like interaction, and (2) a soft repulsion extending beyond the hard core designed via statistical mechanical theory to enhance tracer mobility at infinite dilution by suppressing coordination-shell structure [Carmer et al., Soft Matter 8, 4083–4089 (2012)]. For the latter case, we show that the mobility of surroundingmore » solvent particles is also increased by addition of the soft repulsive interaction, which helps to rationalize the mechanism underlying the tracer’s enhanced diffusivity. However, if multiple tracer surfaces are in closer proximity (as at higher tracer concentrations), similar interactions that disrupt local solvation structure instead suppress the position-dependent solvent dynamics.« less

Directing the Lithium–Sulfur Reaction Pathway via Sparingly Solvating Electrolytes for High Energy Density Batteries

PubMed Central

2017-01-01

The lithium–sulfur battery has long been seen as a potential next generation battery chemistry for electric vehicles owing to the high theoretical specific energy and low cost of sulfur. However, even state-of-the-art lithium–sulfur batteries suffer from short lifetimes due to the migration of highly soluble polysulfide intermediates and exhibit less than desired energy density due to the required excess electrolyte. The use of sparingly solvating electrolytes in lithium–sulfur batteries is a promising approach to decouple electrolyte quantity from reaction mechanism, thus creating a pathway toward high energy density that deviates from the current catholyte approach. Herein, we demonstrate that sparingly solvating electrolytes based on compact, polar molecules with a 2:1 ratio of a functional group to lithium salt can fundamentally redirect the lithium–sulfur reaction pathway by inhibiting the traditional mechanism that is based on fully solvated intermediates. In contrast to the standard catholyte sulfur electrochemistry, sparingly solvating electrolytes promote intermediate- and short-chain polysulfide formation during the first third of discharge, before disproportionation results in crystalline lithium sulfide and a restricted fraction of soluble polysulfides which are further reduced during the remaining discharge. Moreover, operation at intermediate temperatures ca. 50 °C allows for minimal overpotentials and high utilization of sulfur at practical rates. This discovery opens the door to a new wave of scientific inquiry based on modifying the electrolyte local structure to tune and control the reaction pathway of many precipitation–dissolution chemistries, lithium–sulfur and beyond. PMID:28691072

Dissecting ion-specific dielectric spectra of sodium-halide solutions into solvation water and ionic contributions

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

Rinne, Klaus F.; Netz, Roland R.; Gekle, Stephan

2014-12-07

Using extensive equilibrium molecular dynamics simulations we determine the dielectric spectra of aqueous solutions of NaF, NaCl, NaBr, and NaI. The ion-specific and concentration-dependent shifts of the static dielectric constants and the dielectric relaxation times match experimental results very well, which serves as a validation of the classical and non-polarizable ionic force fields used. The purely ionic contribution to the dielectric response is negligible, but determines the conductivity of the salt solutions. The ion-water cross correlation contribution is negative and reduces the total dielectric response by about 5%-10% for 1 M solutions. The dominating water dielectric response is decomposed into differentmore » water solvation shells and ion-pair configurations, by this the spectral blue shift and the dielectric decrement of salt solutions with increasing salt concentration is demonstrated to be primarily caused by first-solvation shell water. With rising salt concentration the simulated spectra show more pronounced deviations from a single-Debye form and can be well described by a Cole-Cole fit, in quantitative agreement with experiments. Our spectral decomposition into ionic and different water solvation shell contributions does not render the individual contributions more Debye-like, this suggests the non-Debye-like character of the dielectric spectra of salt solutions not to be due to the superposition of different elementary relaxation processes with different relaxation times. Rather, the non-Debye-like character is likely to be an inherent spectral signature of solvation water around ions.« less

Directing the lithium–sulfur reaction pathway via sparingly solvating electrolytes for high energy density batteries

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

Lee, Chang -Wook; Pang, Quan; Ha, Seungbum

The lithium–sulfur battery has long been seen as a potential next generation battery chemistry for electric vehicles owing to the high theoretical specific energy and low cost of sulfur. However, even state-of-the-art lithium–sulfur batteries suffer from short lifetimes due to the migration of highly soluble polysulfide intermediates and exhibit less than desired energy density due to the required excess electrolyte. The use of sparingly solvating electrolytes in lithium–sulfur batteries is a promising approach to decouple electrolyte quantity from reaction mechanism, thus creating a pathway toward high energy density that deviates from the current catholyte approach. Herein, we demonstrate that sparinglymore » solvating electrolytes based on compact, polar molecules with a 2:1 ratio of a functional group to lithium salt can fundamentally redirect the lithium–sulfur reaction pathway by inhibiting the traditional mechanism that is based on fully solvated intermediates. In contrast to the standard catholyte sulfur electrochemistry, sparingly solvating electrolytes promote intermediate- and short-chain polysulfide formation during the first third of discharge, before disproportionation results in crystalline lithium sulfide and a restricted fraction of soluble polysulfides which are further reduced during the remaining discharge. Moreover, operation at intermediate temperatures ca. 50 °C allows for minimal overpotentials and high utilization of sulfur at practical rates. Finally, this discovery opens the door to a new wave of scientific inquiry based on modifying the electrolyte local structure to tune and control the reaction pathway of many precipitation–dissolution chemistries, lithium–sulfur and beyond.« less

Directing the lithium–sulfur reaction pathway via sparingly solvating electrolytes for high energy density batteries

DOE PAGES

Lee, Chang -Wook; Pang, Quan; Ha, Seungbum; ...

2017-05-25

The lithium–sulfur battery has long been seen as a potential next generation battery chemistry for electric vehicles owing to the high theoretical specific energy and low cost of sulfur. However, even state-of-the-art lithium–sulfur batteries suffer from short lifetimes due to the migration of highly soluble polysulfide intermediates and exhibit less than desired energy density due to the required excess electrolyte. The use of sparingly solvating electrolytes in lithium–sulfur batteries is a promising approach to decouple electrolyte quantity from reaction mechanism, thus creating a pathway toward high energy density that deviates from the current catholyte approach. Herein, we demonstrate that sparinglymore » solvating electrolytes based on compact, polar molecules with a 2:1 ratio of a functional group to lithium salt can fundamentally redirect the lithium–sulfur reaction pathway by inhibiting the traditional mechanism that is based on fully solvated intermediates. In contrast to the standard catholyte sulfur electrochemistry, sparingly solvating electrolytes promote intermediate- and short-chain polysulfide formation during the first third of discharge, before disproportionation results in crystalline lithium sulfide and a restricted fraction of soluble polysulfides which are further reduced during the remaining discharge. Moreover, operation at intermediate temperatures ca. 50 °C allows for minimal overpotentials and high utilization of sulfur at practical rates. Finally, this discovery opens the door to a new wave of scientific inquiry based on modifying the electrolyte local structure to tune and control the reaction pathway of many precipitation–dissolution chemistries, lithium–sulfur and beyond.« less

Advances in Quantum Mechanochemistry: Electronic Structure Methods and Force Analysis.

PubMed

Stauch, Tim; Dreuw, Andreas

2016-11-23

In quantum mechanochemistry, quantum chemical methods are used to describe molecules under the influence of an external force. The calculation of geometries, energies, transition states, reaction rates, and spectroscopic properties of molecules on the force-modified potential energy surfaces is the key to gain an in-depth understanding of mechanochemical processes at the molecular level. In this review, we present recent advances in the field of quantum mechanochemistry and introduce the quantum chemical methods used to calculate the properties of molecules under an external force. We place special emphasis on quantum chemical force analysis tools, which can be used to identify the mechanochemically relevant degrees of freedom in a deformed molecule, and spotlight selected applications of quantum mechanochemical methods to point out their synergistic relationship with experiments.

Rapid prediction of chemical metabolism by human UDP-glucuronosyltransferase isoforms using quantum chemical descriptors derived with the electronegativity equalization method.

PubMed

Sorich, Michael J; McKinnon, Ross A; Miners, John O; Winkler, David A; Smith, Paul A

2004-10-07

This study aimed to evaluate in silico models based on quantum chemical (QC) descriptors derived using the electronegativity equalization method (EEM) and to assess the use of QC properties to predict chemical metabolism by human UDP-glucuronosyltransferase (UGT) isoforms. Various EEM-derived QC molecular descriptors were calculated for known UGT substrates and nonsubstrates. Classification models were developed using support vector machine and partial least squares discriminant analysis. In general, the most predictive models were generated with the support vector machine. Combining QC and 2D descriptors (from previous work) using a consensus approach resulted in a statistically significant improvement in predictivity (to 84%) over both the QC and 2D models and the other methods of combining the descriptors. EEM-derived QC descriptors were shown to be both highly predictive and computationally efficient. It is likely that EEM-derived QC properties will be generally useful for predicting ADMET and physicochemical properties during drug discovery.

The Alexandria library, a quantum-chemical database of molecular properties for force field development.

PubMed

Ghahremanpour, Mohammad M; van Maaren, Paul J; van der Spoel, David

2018-04-10

Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.

The Alexandria library, a quantum-chemical database of molecular properties for force field development

NASA Astrophysics Data System (ADS)

Ghahremanpour, Mohammad M.; van Maaren, Paul J.; van der Spoel, David

2018-04-01

Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.

Structure activity studies of an analgesic drug tapentadol hydrochloride by spectroscopic and quantum chemical methods

NASA Astrophysics Data System (ADS)

Arjunan, V.; Santhanam, R.; Marchewka, M. K.; Mohan, S.; Yang, Haifeng

2015-11-01

Tapentadol is a novel opioid pain reliever drug with a dual mechanism of action, having potency between morphine and tramadol. Quantum chemical calculations have been carried out for tapentadol hydrochloride (TAP.Cl) to determine the properties. The geometry is optimised and the structural properties of the compound were determined from the optimised geometry by B3LYP method using 6-311++G(d,p), 6-31G(d,p) and cc-pVDZ basis sets. FT-IR and FT-Raman spectra are recorded in the solid phase in the region of 4000-400 and 4000-100 cm-1, respectively. Frontier molecular orbital energies, LUMO-HOMO energy gap, ionisation potential, electron affinity, electronegativity, hardness and chemical potential are also calculated. The stability of the molecule arising from hyperconjugative interactions and charge delocalisation has been analysed using NBO analysis. The 1H and 13C nuclear magnetic resonance chemical shifts of the molecule are analysed.

Improved pKa Prediction of Substituted Alcohols, Phenols, and Hydroperoxides in Aqueous Medium Using Density Functional Theory and a Cluster-Continuum Solvation Model.

PubMed

Thapa, Bishnu; Schlegel, H Bernhard

2017-06-22

Acid dissociation constants (pK a 's) are key physicochemical properties that are needed to understand the structure and reactivity of molecules in solution. Theoretical pK a 's have been calculated for a set of 72 organic compounds with -OH and -OOH groups (48 with known experimental pK a 's). This test set includes 17 aliphatic alcohols, 25 substituted phenols, and 30 hydroperoxides. Calculations in aqueous medium have been carried out with SMD implicit solvation and three hybrid DFT functionals (B3LYP, ωB97XD, and M06-2X) with two basis sets (6-31+G(d,p) and 6-311++G(d,p)). The effect of explicit water molecules on calculated pK a 's was assessed by including up to three water molecules. pK a 's calculated with only SMD implicit solvation are found to have average errors greater than 6 pK a units. Including one explicit water reduces the error by about 3 pK a units, but the error is still far from chemical accuracy. With B3LYP/6-311++G(d,p) and three explicit water molecules in SMD solvation, the mean signed error and standard deviation are only -0.02 ± 0.55; a linear fit with zero intercept has a slope of 1.005 and R 2 = 0.97. Thus, this level of theory can be used to calculate pK a 's directly without the need for linear correlations or thermodynamic cycles. Estimated pK a values are reported for 24 hydroperoxides that have not yet been determined experimentally.

Quantitative Prediction of Solvation Free Energy in Octanol of Organic Compounds

PubMed Central

Delgado, Eduardo J.; Jaña, Gonzalo A.

2009-01-01

The free energy of solvation, ΔGS0, in octanol of organic compunds is quantitatively predicted from the molecular structure. The model, involving only three molecular descriptors, is obtained by multiple linear regression analysis from a data set of 147 compounds containing diverse organic functions, namely, halogenated and non-halogenated alkanes, alkenes, alkynes, aromatics, alcohols, aldehydes, ketones, amines, ethers and esters; covering a ΔGS0 range from about −50 to 0 kJ·mol−1. The model predicts the free energy of solvation with a squared correlation coefficient of 0.93 and a standard deviation, 2.4 kJ·mol−1, just marginally larger than the generally accepted value of experimental uncertainty. The involved molecular descriptors have definite physical meaning corresponding to the different intermolecular interactions occurring in the bulk liquid phase. The model is validated with an external set of 36 compounds not included in the training set. PMID:19399236

Importance of polar solvation and configurational entropy for design of antiretroviral drugs targeting HIV-1 protease.

PubMed

Kar, Parimal; Lipowsky, Reinhard; Knecht, Volker

2013-05-16

Both KNI-10033 and KNI-10075 are high affinity preclinical HIV-1 protease (PR) inhibitors with affinities in the picomolar range. In this work, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method has been used to investigate the potency of these two HIV-1 PR inhibitors against the wild-type and mutated proteases assuming that potency correlates with the affinity of the drugs for the target protein. The decomposition of the binding free energy reveals the origin of binding affinities or mutation-induced affinity changes. Our calculations indicate that the mutation I50V causes drug resistance against both inhibitors. On the other hand, we predict that the mutant I84V causes drug resistance against KNI-10075 while KNI-10033 is more potent against the I84V mutant compared to wild-type protease. Drug resistance arises mainly from unfavorable shifts in van der Waals interactions and configurational entropy. The latter indicates that neglecting changes in configurational entropy in the computation of relative binding affinities as often done is not appropriate in general. For the bound complex PR(I50V)-KNI-10075, an increased polar solvation free energy also contributes to the drug resistance. The importance of polar solvation free energies is revealed when interactions governing the binding of KNI-10033 or KNI-10075 to the wild-type protease are compared to the inhibitors darunavir or GRL-06579A. Although the contributions from intermolecular electrostatic and van der Waals interactions as well as the nonpolar component of the solvation free energy are more favorable for PR-KNI-10033 or PR-KNI-10075 compared to PR-DRV or PR-GRL-06579A, both KNI-10033 and KNI-10075 show a similar affinity as darunavir and a lower binding affinity relative to GRL-06579A. This is because of the polar solvation free energy which is less unfavorable for darunavir or GRL-06579A relative to KNI-10033 or KNI-10075. The importance of the polar solvation as revealed here

Incorporation of the TIP4P water model into a continuum solvent for computing solvation free energy

NASA Astrophysics Data System (ADS)

Yang, Pei-Kun

2014-10-01

The continuum solvent model is one of the commonly used strategies to compute solvation free energy especially for large-scale conformational transitions such as protein folding or to calculate the binding affinity of protein-protein/ligand interactions. However, the dielectric polarization for computing solvation free energy from the continuum solvent is different than that obtained from molecular dynamic simulations. To mimic the dielectric polarization surrounding a solute in molecular dynamic simulations, the first-shell water molecules was modeled using a charge distribution of TIP4P in a hard sphere; the time-averaged charge distribution from the first-shell water molecules were estimated based on the coordination number of the solute, and the orientation distribution of the first-shell waters and the intermediate water molecules were treated as that of a bulk solvent. Based on this strategy, an equation describing the solvation free energy of ions was derived.

Solvation of o-hydroxybenzoic acid in pure and modified supercritical carbon dioxide, according to numerical modeling data

NASA Astrophysics Data System (ADS)

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

2015-08-01

The dissolution of an elementary fragment of crystal structure (an o-hydroxybenzoic acid ( o-HBA) dimer) in both pure and modified supercritical (SC) carbon dioxide by adding methanol (molar fraction, 0.035) at T = 318 K, ρ = 0.7 g/cm3 is simulated. Features of the solvation mechanism in each solvent are revealed. The solvation of o-HBA in pure SC CO2 is shown to occur via electron donor-acceptor interactions. o-HBA forms a solvate complex in modified SC CO2 through hydrogen bonds between the carboxyl group and methanol. The hydroxyl group of o-HBA participates in the formation of an intramolecular hydrogen bond, and not in interactions with the solvent. It is concluded that the o-HBA-methanol complex is a stable molecular structure, and its lifetime is one order of magnitude higher than those of other hydrogen bonds in fluids.

Solvent effect on the self-assembly of salt solvates of an antihypertensive drug azilsartan and 2-methylimidazole

NASA Astrophysics Data System (ADS)

Zhang, Xian-Rui; Zhang, Lei

2017-06-01

Three salt solvates of azilsartan (AZ) with 2-methylimidazole (2MI) (namely AZ-2MI-H2O, AZ-2MI-ACE and AZ-2MI-THF) and one azilsartan solvate (AZ-DIO, ACE = acetone, THF = tetrahydrofuran, and DIO = 1,4-dioxane) were manufactured by solvent-controlled self-assembly in aqueous-organic solutions. The experimental result of AZ-DIO shows that AZ is high affinity to DIO molecule, which has a unique ability to prevent salt formation between AZ and 2MI. Thermal studies of three salt solvates exhibit poor thermodynamic stability in environmental conditions. Solubility experiments show that AZ-2MI-ACE and AZ-2MI-THF are unstable and convert to AZ-2MI-H2O in aqueous solution, and that AZ-2MI-H2O exhibits increased solubility and retention stability in an aqueous medium compared with the commercial AZ-A crystalline form.

Prediction of Radical Scavenging Activities of Anthocyanins Applying Adaptive Neuro-Fuzzy Inference System (ANFIS) with Quantum Chemical Descriptors

PubMed Central

Jhin, Changho; Hwang, Keum Taek

2014-01-01

Radical scavenging activity of anthocyanins is well known, but only a few studies have been conducted by quantum chemical approach. The adaptive neuro-fuzzy inference system (ANFIS) is an effective technique for solving problems with uncertainty. The purpose of this study was to construct and evaluate quantitative structure-activity relationship (QSAR) models for predicting radical scavenging activities of anthocyanins with good prediction efficiency. ANFIS-applied QSAR models were developed by using quantum chemical descriptors of anthocyanins calculated by semi-empirical PM6 and PM7 methods. Electron affinity (A) and electronegativity (χ) of flavylium cation, and ionization potential (I) of quinoidal base were significantly correlated with radical scavenging activities of anthocyanins. These descriptors were used as independent variables for QSAR models. ANFIS models with two triangular-shaped input fuzzy functions for each independent variable were constructed and optimized by 100 learning epochs. The constructed models using descriptors calculated by both PM6 and PM7 had good prediction efficiency with Q-square of 0.82 and 0.86, respectively. PMID:25153627

Solvation-controlled lithium-ion complexes in a nonflammable solvent containing ethylene carbonate: structural and electrochemical aspects.

PubMed

Sogawa, Michiru; Kawanoue, Hikaru; Todorov, Yanko Marinov; Hirayama, Daisuke; Mimura, Hideyuki; Yoshimoto, Nobuko; Morita, Masayuki; Fujii, Kenta

2018-02-28

The structural and electrochemical properties of lithium-ion solvation complexes in a nonflammable organic solvent, tris(2,2,2-trifluoroethyl)phosphate (TFEP) containing ethylene carbonate (EC), were investigated using vibrational spectroscopic and electrochemical measurements. Based on quantitative Raman and infrared (IR) spectral analysis of the Li bis(trifluoromethanesulfonyl)amide (TFSA) salt in TFEP + EC electrolytes, we successfully evaluated the individual solvation numbers of EC (n EC ), TFEP (n TFEP ), and TFSA - (n TFSA ) in the first solvation sphere of the Li-ion. We found that the n EC value linearly increased with increasing EC mole fraction (x EC ), whereas the n TFEP and n TFSA values gradually decreased with increasing n EC . The ionic conductivity and viscosity (Walden plots) indicated that mainly Li + TFSA - ion pairs formed in neat TFEP (x EC = 0). This ion pair gradually dissociated into positively charged Li-ion complexes as x EC increased, which was consistent with the Raman/IR spectroscopy results. The redox reaction corresponding to an insertion/desertion of Li-ion into/from the graphite electrode occurred in the LiTFSA/TFEP + EC system at x EC ≥ 0.25. The same was not observed in the lower x EC cases. We discussed the relation between Li-ion solvation and electrode reaction behaviors at the molecular level and proposed that n EC plays a crucial role in the electrode reaction, particularly in terms of solid electrolyte interphase formation on the graphite electrode.

Studies on the Conformational Landscape of Tert-Butyl Acetate Using Microwave Spectroscopy and Quantum Chemical Calculations

NASA Astrophysics Data System (ADS)

Zhao, YueYue; Mouhib, Halima; Li, Guohua; Stahl, Wolfgang; Kleiner, Isabelle

2014-06-01

The tert-Butyl acetate molecule was studied using a combination of quantum chemical calculations and molecular beam Fourier transform microwave spectroscopy in the 9 to 14 GHz range. Due to its rather rigid frame, the molecule possesses only two different conformers: one of Cs and one of C1 symmetry. According to ab initio calculations, the Cs conformer is 46 kJ/mol lower in energy and is the one observed in the supersonic jet. We report on the structure and dynamics of the most abundant conformer of tert-butyl acetate, with accurate rotational and centrifugal distortion constants. Additionally, the barrier to internal rotation of the acetyl methyl group was determined. Splittings due to the internal rotation of the methyl group of up to 1.3 GHz were observed in the spectrum. Using the programs XIAM and BELGI-Cs, we determine the barrier height to be about 113 cm-1 and compare the molecular parameters obtained from these two codes. Additionally, the experimental rotational constants were used to validate numerous quantum chemical calculations. This study is part of a larger project which aims at determining the lowest energy conformers of organic esters and ketones which are of interest for flavor or perfume synthetic applications Project partly supported by the PHC PROCOPE 25059YB.

Portable open-path chemical sensor using a quantum cascade laser

NASA Astrophysics Data System (ADS)

Corrigan, Paul; Lwin, Maung; Huntley, Reuven; Chhabra, Amandeep; Moshary, Fred; Gross, Barry; Ahmed, Samir

2009-05-01

Remote sensing of enemy installations or their movements by trace gas detection is a critical but challenging military objective. Open path measurements over ranges of a few meters to many kilometers with sensitivity in the parts per million or billion regime are crucial in anticipating the presence of a threat. Previous approaches to detect ground level chemical plumes, explosive constituents, or combustion have relied on low-resolution, short range Fourier transform infrared spectrometer (FTIR), or low-sensitivity near-infrared differential optical absorption spectroscopy (DOAS). As mid-infrared quantum cascade laser (QCL) sources have improved in cost and performance, systems based on QCL's that can be tailored to monitor multiple chemical species in real time are becoming a viable alternative. We present the design of a portable, high-resolution, multi-kilometer open path trace gas sensor based on QCL technology. Using a tunable (1045-1047cm-1) QCL, a modeled atmosphere and link-budget analysis with commercial component specifications, we show that with this approach, accuracy in parts per billion ozone or ammonia can be obtained in seconds at path lengths up to 10 km. We have assembled an open-path QCL sensor based on this theoretical approach at City College of New York, and we present preliminary results demonstrating the potential of QCLs in open-path sensing applications.

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.

Quantum mechanical/molecular mechanical/continuum style solvation model: time-dependent density functional theory.

PubMed

Thellamurege, Nandun M; Cui, Fengchao; Li, Hui

2013-08-28

A combined quantum mechanical/molecular mechanical/continuum (QM/MMpol/C) style method is developed for time-dependent density functional theory (TDDFT, including long-range corrected TDDFT) method, induced dipole polarizable force field, and induced surface charge continuum model. Induced dipoles and induced charges are included in the TDDFT equations to solve for the transition energies, relaxed density, and transition density. Analytic gradient is derived and implemented for geometry optimization and molecular dynamics simulation. QM/MMpol/C style DFT and TDDFT methods are used to study the hydrogen bonding of the photoactive yellow protein chromopore in ground state and excited state.

POSSIBLE NATURE OF THE RADIATION-INDUCED SIGNAL IN NAILS: HIGH-FIELD EPR, CONFIRMING CHEMICAL SYNTHESIS, AND QUANTUM CHEMICAL CALCULATIONS

PubMed Central

Tipikin, Dmitriy S.; Swarts, Steven G.; Sidabras, Jason W.; Trompier, François; Swartz, Harold M.

2016-01-01

Exposure of finger- and toe-nails to ionizing radiation generates an Electron Paramagnetic Resonance (EPR) signal whose intensity is dose dependent and stable at room temperature for several days. The dependency of the radiation-induced signal (RIS) on the received dose may be used as the basis for retrospective dosimetry of an individual's fortuitous exposure to ionizing radiation. Two radiation-induced signals, a quasi-stable (RIS2) and stable signal (RIS5), have been identified in nails irradiated up to a dose of 50 Gy. Using X-band EPR, both RIS signals exhibit a singlet line shape with a line width around 1.0 mT and an apparent g-value of 2.0044. In this work, we seek information on the exact chemical nature of the radiation-induced free radicals underlying the signal. This knowledge may provide insights into the reason for the discrepancy in the stabilities of the two RIS signals and help develop strategies for stabilizing the radicals in nails or devising methods for restoring the radicals after decay. In this work an analysis of high field (94 GHz and 240 GHz) EPR spectra of the RIS using quantum chemical calculations, the oxidation–reduction properties and the pH dependence of the signal intensities are used to show that spectroscopic and chemical properties of the RIS are consistent with a semiquinone-type radical underlying the RIS. It has been suggested that semiquinone radicals formed on trace amounts of melanin in nails are the basis for the RIS signals. However, based on the quantum chemical calculations and chemical properties of the RIS, it is likely that the radicals underlying this signal are generated from the radiolysis of L-3,4-dihydroxyphenylalanine (DOPA) amino acids in the keratin proteins. These DOPA amino acids are likely formed from the exogenous oxidation of tyrosine in keratin by the oxygen from the air prior to irradiation. We show that these DOPA amino acids can work as radical traps, capturing the highly reactive and unstable

Chemical reaction CO+OH • → CO 2+H • autocatalyzed by carbon dioxide: Quantum chemical study of the potential energy surfaces

DOE PAGES

Masunov, Artem E.; Wait, Elizabeth; Vasu, Subith S.

2016-06-28

The supercritical carbon dioxide medium, used to increase efficiency in oxy combustion fossil energy technology, may drastically alter both rates and mechanisms of chemical reactions. Here we investigate potential energy surface of the second most important combustion reaction with quantum chemistry methods. Two types of effects are reported: formation of the covalent intermediates and formation of van der Waals complexes by spectator CO 2 molecule. While spectator molecule alter the activation barrier only slightly, the covalent bonding opens a new reaction pathway. The mechanism includes sequential covalent binding of CO 2 to OH radical and CO molecule, hydrogen transfer frommore » oxygen to carbon atoms, and CH bond dissociation. This reduces the activation barrier by 11 kcal/mol at the rate-determining step and is expected to accelerate the reaction rate. The finding of predicted catalytic effect is expected to play an important role not only in combustion but also in a broad array of chemical processes taking place in supercritical CO 2 medium. Furthermore, tt may open a new venue for controlling reaction rates for chemical manufacturing.« less

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models.

PubMed

Genheden, Samuel

2017-10-01

We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.

Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models

NASA Astrophysics Data System (ADS)

Genheden, Samuel

2017-10-01

We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.

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

PubMed

Qiao, Yu; Tu, Bin; Lu, Benzhuo

2014-05-07

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

Intramolecular hydrogen bonding in myricetin and myricitrin. Quantum chemical calculations and vibrational spectroscopy

NASA Astrophysics Data System (ADS)

Vojta, Danijela; Dominković, Katarina; Miljanić, Snežana; Spanget-Larsen, Jens

2017-03-01

The molecular structures of myricetin (3,3‧,4‧,5,5‧,7-hexahydroxyflavone; MCE) and myricitrin (myricetin 3-O-rhamnoside; MCI) are investigated by quantum chemical calculations (B3LYP/6-311G**). Two preferred molecular rotamers of MCI are predicted, corresponding to different conformations of the O-rhamnoside subunit. The rotamers are characterized by different hydrogen bonded cross-links between the hydroxy groups of the rhamnoside substituent and the parent MCE moiety. The predicted OH stretching frequencies are compared with vibrational spectra of MCE and MCI recorded for the sake of this investigation (IR and Raman). In addition, a reassignment of the Cdbnd O stretching bands is suggested.

Wavy carbon: A new series of carbon structures explored by quantum chemical calculations

NASA Astrophysics Data System (ADS)

Ohno, Koichi; Satoh, Hiroko; Iwamoto, Takeaki; Tokoyama, Hiroaki; Yamakado, Hideo

2015-10-01

A new carbon family adopting wavy structures has been found by quantum chemical calculations. The key motif of this family is a condensed four-membered ring. Periodically wavy-carbon sheets (wavy-Cn sheets, n = 2, 6, and 8) as well as wavy-C36 tube were found to be very similar to the previously reported prism-Cn carbon tubes (n = 5, 6, and 8) in several respects, including the relative energies per one carbon atom with respect to graphene, CC bond lengths, and CCC bond angles. Because of very high relative energies with respect to graphene (206-253 kJ mol-1), the wavy-carbons may behave as energy reserving materials.

Energetics of subdomain movements and fluorescence probe solvation environment change in ATP-bound myosin.

PubMed

Harris, Michael J; Woo, Hyung-June

2008-11-01

Energetics of conformational changes experienced by an ATP-bound myosin head detached from actin was studied by all-atom explicit water umbrella sampling simulations. The statistics of coupling between large scale domain movements and smaller scale structural features were examined, including the closing of the ATP binding pocket, and a number of key hydrogen bond formations shown to play roles in structural and biochemical studies. The statistics for the ATP binding pocket open/close transition show an evolution of the relative stability from the open state in the early stages of the recovery stroke to the stable closed state after the stroke. The change in solvation environment of the fluorescence probe Trp507 (scallop numbering; 501 in Dictyostelium discoideum) indicates that the probe faithfully reflects the closing of the binding pocket as previously shown in experimental studies, while being directly coupled to roughly the early half of the overall large scale conformational change of the converter domain rotation. The free energy change of this solvation environment change, in particular, is -1.3 kcal/mol, in close agreement with experimental estimates. In addition, our results provide direct molecular level data allowing for interpretations of the fluorescence experiments of myosin conformational change in terms of the de-solvation of Trp side chain.

SAMPL4, a blind challenge for computational solvation free energies: the compounds considered.

PubMed

Guthrie, J Peter

2014-03-01

For the fifth time I have provided a set of solvation energies (1 M gas to 1 M aqueous) for a SAMPL challenge. In this set there are 23 blind compounds and 30 supplementary compounds of related structure to one of the blind sets, but for which the solvation energy is readily available. The best current values of each compound are presented along with complete documentation of the experimental origins of the solvation energies. The calculations needed to go from reported data to solvation energies are presented, with particular attention to aspects which are new to this set. For some compounds the vapor pressures (VP) were reported for the liquid compound, which is solid at room temperature. To correct from VPsubcooled liquid to VPsublimation requires ΔSfusion, which is only known for mannitol. Estimated values were used for the others, all but one of which were benzene derivatives and expected to have very similar values. The final compound for which ΔSfusion was estimated was menthol, which melts at 42 °C so that modest errors in ΔSfusion will have little effect. It was also necessary to look into the effects of including estimated values of ΔCp on this correction. The approximate sizes of the effects of inclusion of ΔCp in the correction from VPsubcooled liquid to VPsublimation were estimated and it was noted that inclusion of ΔCp invariably makes ΔGS more positive. To extend the set of compounds for which the solvation energy could be calculated we explored the use of boiling point (b.p.) data from Reaxys/Beilstein as a substitute for studies of the VP as a function of temperature. B.p. data are not always reliable so it was necessary to develop a criterion for rejecting outliers. For two compounds (chlorinated guaiacols) it became clear that inclusion represented overreach; for each there were only two independent pressure, temperature points, which is too little for a trustworthy extrapolation. For a number of compounds the extrapolation from

SAMPL4, a blind challenge for computational solvation free energies: the compounds considered

NASA Astrophysics Data System (ADS)

Guthrie, J. Peter

2014-03-01

For the fifth time I have provided a set of solvation energies (1 M gas to 1 M aqueous) for a SAMPL challenge. In this set there are 23 blind compounds and 30 supplementary compounds of related structure to one of the blind sets, but for which the solvation energy is readily available. The best current values of each compound are presented along with complete documentation of the experimental origins of the solvation energies. The calculations needed to go from reported data to solvation energies are presented, with particular attention to aspects which are new to this set. For some compounds the vapor pressures (VP) were reported for the liquid compound, which is solid at room temperature. To correct from VPsubcooled liquid to VPsublimation requires ΔSfusion, which is only known for mannitol. Estimated values were used for the others, all but one of which were benzene derivatives and expected to have very similar values. The final compound for which ΔSfusion was estimated was menthol, which melts at 42 °C so that modest errors in ΔSfusion will have little effect. It was also necessary to look into the effects of including estimated values of ΔCp on this correction. The approximate sizes of the effects of inclusion of ΔCp in the correction from VPsubcooled liquid to VPsublimation were estimated and it was noted that inclusion of ΔCp invariably makes ΔGS more positive. To extend the set of compounds for which the solvation energy could be calculated we explored the use of boiling point (b.p.) data from Reaxys/Beilstein as a substitute for studies of the VP as a function of temperature. B.p. data are not always reliable so it was necessary to develop a criterion for rejecting outliers. For two compounds (chlorinated guaiacols) it became clear that inclusion represented overreach; for each there were only two independent pressure, temperature points, which is too little for a trustworthy extrapolation. For a number of compounds the extrapolation from lowest

Learning about Biomolecular Solvation from Water in Protein Crystals.

PubMed

Altan, Irem; Fusco, Diana; Afonine, Pavel V; Charbonneau, Patrick

2018-03-08

Water occupies typically 50% of a protein crystal and thus significantly contributes to the diffraction signal in crystallography experiments. Separating its contribution from that of the protein is, however, challenging because most water molecules are not localized and are thus difficult to assign to specific density peaks. The intricateness of the protein-water interface compounds this difficulty. This information has, therefore, not often been used to study biomolecular solvation. Here, we develop a methodology to surmount in part this difficulty. More specifically, we compare the solvent structure obtained from diffraction data for which experimental phasing is available to that obtained from constrained molecular dynamics (MD) simulations. The resulting spatial density maps show that commonly used MD water models are only partially successful at reproducing the structural features of biomolecular solvation. The radial distribution of water is captured with only slightly higher accuracy than its angular distribution, and only a fraction of the water molecules assigned with high reliability to the crystal structure is recovered. These differences are likely due to shortcomings of both the water models and the protein force fields. Despite these limitations, we manage to infer protonation states of some of the side chains utilizing MD-derived densities.

Characterization of solvated electrons in hydrogen cyanide clusters: (HCN)n- (n=3, 4)

NASA Astrophysics Data System (ADS)

Wu, Di; Li, Ying; Li, Zhuo; Chen, Wei; Li, Zhi-Ru; Sun, Chia-Chung

2006-02-01

Theoretical studies of the solvated electrons (HCN)n- (n =3, 4) reveal a variety of electron trapping possibilities in the (HCN)n (n =3, 4) clusters. Two isomers for (HCN)3- and four isomers for (HCN)4- are obtained at the MP2/aug -cc-pVDZ+dBF (diffusive bond functions) level of theory. In view of vertical electron detachment energies (VDEs) at the CCSD(T) level, the excess electron always "prefers" locating in the center of the system, i.e., the isomer with higher coordination number shows larger VDE value. However, the most stable isomers of the solvated electron state (HCN)3- and (HCN)4- are found to be the linear C∞ν and D∞h structures, respectively, but not the fullyl symmetric structures which have the largest VDE values.

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

DOE PAGES

Sornborger, Andrew Tyler; Stancil, Phillip; Geller, Michael R.

2018-03-22

Here, one of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputedmore » potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born–Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3–8 channels and circuit depths < 1000.« less

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

NASA Astrophysics Data System (ADS)

Sornborger, Andrew T.; Stancil, Phillip; Geller, Michael R.

2018-05-01

One of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputed potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born-Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈ 10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3-8 channels and circuit depths < 1000.

Toward prethreshold gate-based quantum simulation of chemical dynamics: using potential energy surfaces to simulate few-channel molecular collisions

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

Sornborger, Andrew Tyler; Stancil, Phillip; Geller, Michael R.

Here, one of the most promising applications of an error-corrected universal quantum computer is the efficient simulation of complex quantum systems such as large molecular systems. In this application, one is interested in both the electronic structure such as the ground state energy and dynamical properties such as the scattering cross section and chemical reaction rates. However, most theoretical work and experimental demonstrations have focused on the quantum computation of energies and energy surfaces. In this work, we attempt to make the prethreshold (not error-corrected) quantum simulation of dynamical properties practical as well. We show that the use of precomputedmore » potential energy surfaces and couplings enables the gate-based simulation of few-channel but otherwise realistic molecular collisions. Our approach is based on the widely used Born–Oppenheimer approximation for the structure problem coupled with a semiclassical method for the dynamics. In the latter the electrons are treated quantum mechanically but the nuclei are classical, which restricts the collisions to high energy or temperature (typically above ≈10 eV). By using operator splitting techniques optimized for the resulting time-dependent Hamiltonian simulation problem, we give several physically realistic collision examples, with 3–8 channels and circuit depths < 1000.« less

Quantum Hall resistance standards from graphene grown by chemical vapour deposition on silicon carbide

NASA Astrophysics Data System (ADS)

Lafont, F.; Ribeiro-Palau, R.; Kazazis, D.; Michon, A.; Couturaud, O.; Consejo, C.; Chassagne, T.; Zielinski, M.; Portail, M.; Jouault, B.; Schopfer, F.; Poirier, W.

2015-04-01

Replacing GaAs by graphene to realize more practical quantum Hall resistance standards (QHRS), accurate to within 10-9 in relative value, but operating at lower magnetic fields than 10 T, is an ongoing goal in metrology. To date, the required accuracy has been reported, only few times, in graphene grown on SiC by Si sublimation, under higher magnetic fields. Here, we report on a graphene device grown by chemical vapour deposition on SiC, which demonstrates such accuracies of the Hall resistance from 10 T up to 19 T at 1.4 K. This is explained by a quantum Hall effect with low dissipation, resulting from strongly localized bulk states at the magnetic length scale, over a wide magnetic field range. Our results show that graphene-based QHRS can replace their GaAs counterparts by operating in as-convenient cryomagnetic conditions, but over an extended magnetic field range. They rely on a promising hybrid and scalable growth method and a fabrication process achieving low-electron-density devices.

Quantum Hall resistance standards from graphene grown by chemical vapour deposition on silicon carbide

PubMed Central

Lafont, F.; Ribeiro-Palau, R.; Kazazis, D.; Michon, A.; Couturaud, O.; Consejo, C.; Chassagne, T.; Zielinski, M.; Portail, M.; Jouault, B.; Schopfer, F.; Poirier, W.

2015-01-01

Replacing GaAs by graphene to realize more practical quantum Hall resistance standards (QHRS), accurate to within 10−9 in relative value, but operating at lower magnetic fields than 10 T, is an ongoing goal in metrology. To date, the required accuracy has been reported, only few times, in graphene grown on SiC by Si sublimation, under higher magnetic fields. Here, we report on a graphene device grown by chemical vapour deposition on SiC, which demonstrates such accuracies of the Hall resistance from 10 T up to 19 T at 1.4 K. This is explained by a quantum Hall effect with low dissipation, resulting from strongly localized bulk states at the magnetic length scale, over a wide magnetic field range. Our results show that graphene-based QHRS can replace their GaAs counterparts by operating in as-convenient cryomagnetic conditions, but over an extended magnetic field range. They rely on a promising hybrid and scalable growth method and a fabrication process achieving low-electron-density devices. PMID:25891533

Computation of the free energy change associated with one-electron reduction of coenzyme immersed in water: a novel approach within the framework of the quantum mechanical/molecular mechanical method combined with the theory of energy representation.

PubMed

Takahashi, Hideaki; Ohno, Hajime; Kishi, Ryohei; Nakano, Masayoshi; Matubayasi, Nobuyuki

2008-11-28

The isoalloxazine ring (flavin ring) is a part of the coenzyme flavin adenine dinucleotide and acts as an active site in the oxidation of a substrate. We have computed the free energy change Deltamicro(red) associated with one-electron reduction of the flavin ring immersed in water by utilizing the quantum mechanical/molecular mechanical method combined with the theory of energy representation (QM/MM-ER method) recently developed. As a novel treatment in implementing the QM/MM-ER method, we have identified the excess charge to be attached on the flavin ring as a solute while the remaining molecules, i.e., flavin ring and surrounding water molecules, are treated as solvent species. Then, the reduction free energy can be decomposed into the contribution Deltamicro(red)(QM) due to the oxidant described quantum chemically and the free energy Deltamicro(red)(MM) due to the water molecules represented by a classical model. By the sum of these contributions, the total reduction free energy Deltamicro(red) has been given as -80.1 kcal/mol. To examine the accuracy and efficiency of this approach, we have also conducted the Deltamicro(red) calculation using the conventional scheme that Deltamicro(red) is constructed from the solvation free energies of the flavin rings at the oxidized and reduced states. The conventional scheme has been implemented with the QM/MM-ER method and the calculated Deltamicro(red) has been estimated as -81.0 kcal/mol, showing excellent agreement with the value given by the new approach. The present approach is efficient, in particular, to compute free energy change for the reaction occurring in a protein since it enables ones to circumvent the numerical problem brought about by subtracting the huge solvation free energies of the proteins in two states before and after the reduction.

Quantum Chemical Molecular Dynamics Simulations of 1,3-Dichloropropene Combustion.

PubMed

Ahubelem, Nwakamma; Shah, Kalpit; Moghtaderi, Behdad; Page, Alister J

2015-09-03

Oxidative decomposition of 1,3-dichloropropene was investigated using quantum chemical molecular dynamics (QM/MD) at 1500 and 3000 K. Thermal oxidation of 1,3-dichloropropene was initiated by (1) abstraction of allylic H/Cl by O2 and (2) intra-annular C-Cl bond scission and elimination of allylic Cl. A kinetic analysis shows that (2) is the more dominant initiation pathway, in agreement with QM/MD results. These QM/MD simulations reveal new routes to the formation of major products (H2O, CO, HCl, CO2), which are propagated primarily by the chloroperoxy (ClO2), OH, and 1,3-dichloropropene derived radicals. In particular, intra-annular C-C/C-H bond dissociation reactions of intermediate aldehydes/ketones are shown to play a dominant role in the formation of CO and CO2. Our simulations demonstrate that both combustion temperature and radical concentration can influence the product yield, however not the combustion mechanism.

Water Interfaces, Solvation, and Spectroscopy

NASA Astrophysics Data System (ADS)

Geissler, Phillip L.

2013-04-01

Liquid water consistently expands our appreciation of the rich statistical mechanics that can emerge from simple molecular constituents. Here I review several interrelated areas of recent work on aqueous systems that aim to explore and explain this richness by revealing molecular arrangements, their thermodynamic origins, and the timescales on which they change. Vibrational spectroscopy of OH stretching features prominently in these discussions, with an emphasis on efforts to establish connections between spectroscopic signals and statistics of intermolecular structure. For bulk solutions, the results of these efforts largely verify and enrich existing physical pictures of hydrogen-bond network connectivity, dynamics, and response. For water at interfaces, such pictures are still emerging. As an important example I discuss the solvation of small ions at the air-water interface, whose surface propensities challenge a basic understanding of how aqueous fluctuations accommodate solutes in heterogeneous environments.

Characterisation of different polymorphs of tris(8-hydroxyquinolinato)aluminium(III) using solid-state NMR and DFT calculations

PubMed Central

Goswami, Mithun; Nayak, Pabitra K; Periasamy, N; Madhu, PK

2009-01-01

Background Organic light emitting devices (OLED) are becoming important and characterisation of them, in terms of structure, charge distribution, and intermolecular interactions, is important. Tris(8-hydroxyquinolinato)-aluminium(III), known as Alq3, an organomettalic complex has become a reference material of great importance in OLED. It is important to elucidate the structural details of Alq3 in its various isomeric and solvated forms. Solid-state nuclear magnetic resonance (NMR) is a useful tool for this which can also complement the information obtained with X-ray diffraction studies. Results We report here 27Al one-dimensional (1D) and two-dimensional (2D) multiple-quantum magic-angle spinning (MQMAS) NMR studies of the meridional (α-phase) and the facial (δ-phase) isomeric forms of Alq3. Quadrupolar parameters are estimated from the 1D spectra under MAS and anisotropic slices of the 2D spectra and also calculated using DFT (density functional theory) quantum-chemical calculations. We have also studied solvated phase of Alq3 containing ethanol in its lattice. We show that both the XRD patterns and the quadrupolar parameters of the solvated phase are different from both the α-phase and the δ-phase, although the fluorescence emission shows no substantial difference between the α-phase and the solvated phase. Moreover, we have shown that after the removal of ethanol from the matrix the solvated Alq3 has similar XRD patterns and quadrupolar parameters to that of the α-phase. Conclusion The 2D MQMAS experiments have shown that all the different modifications of Alq3 have 27Al in single unique crystallographic site. The quadrupolar parameters predicted using the DFT calculation under the isodensity polarisable continuum model resemble closely the experimentally obtained values. The solvated phase of Alq3 containing ethanol has structural difference from the α-phase of Alq3 (containing meridional isomer) from the solid-state NMR studies. Solid-state NMR can

Characterisation of different polymorphs of tris(8-hydroxyquinolinato)aluminium(III) using solid-state NMR and DFT calculations.

PubMed

Goswami, Mithun; Nayak, Pabitra K; Periasamy, N; Madhu, P K

2009-11-09

Organic light emitting devices (OLED) are becoming important and characterisation of them, in terms of structure, charge distribution, and intermolecular interactions, is important. Tris(8-hydroxyquinolinato)-aluminium(III), known as Alq3, an organomettalic complex has become a reference material of great importance in OLED. It is important to elucidate the structural details of Alq3 in its various isomeric and solvated forms. Solid-state nuclear magnetic resonance (NMR) is a useful tool for this which can also complement the information obtained with X-ray diffraction studies. We report here 27Al one-dimensional (1D) and two-dimensional (2D) multiple-quantum magic-angle spinning (MQMAS) NMR studies of the meridional (alpha-phase) and the facial (delta-phase) isomeric forms of Alq3. Quadrupolar parameters are estimated from the 1D spectra under MAS and anisotropic slices of the 2D spectra and also calculated using DFT (density functional theory) quantum-chemical calculations. We have also studied solvated phase of Alq3 containing ethanol in its lattice. We show that both the XRD patterns and the quadrupolar parameters of the solvated phase are different from both the alpha-phase and the delta-phase, although the fluorescence emission shows no substantial difference between the alpha-phase and the solvated phase. Moreover, we have shown that after the removal of ethanol from the matrix the solvated Alq3 has similar XRD patterns and quadrupolar parameters to that of the alpha-phase. The 2D MQMAS experiments have shown that all the different modifications of Alq3 have 27Al in single unique crystallographic site. The quadrupolar parameters predicted using the DFT calculation under the isodensity polarisable continuum model resemble closely the experimentally obtained values. The solvated phase of Alq3 containing ethanol has structural difference from the alpha-phase of Alq3 (containing meridional isomer) from the solid-state NMR studies. Solid-state NMR can hence be

Effect of Solvation on Electron Detachment and Excitation Energies of a Green Fluorescent Protein Chromophore Variant.

PubMed

Bose, Samik; Chakrabarty, Suman; Ghosh, Debashree

2016-05-19

Hybrid quantum mechanics/molecular mechanics (QM/MM) is applied to the fluorinated green fluorescent protein (GFP) chromophore (DFHBDI) in its deprotonated form to understand the solvatochromic shifts in its vertical detachment energy (VDE) and vertical excitation energy (VEE). This variant of the GFP chromophore becomes fluorescent in an RNA environment and has a wide range of applications in biomedical and biochemical fields. From microsolvation studies, we benchmark (with respect to full QM) the accuracy of our QM/MM calculations with effective fragment potential (EFP) as the MM method of choice. We show that while the solvatochromic shift in the VEE is minimal (0.1 eV blue shift) and its polarization component is only 0.03 eV, the effect of the solvent on the VDE is quite large (3.85 eV). We also show by accurate calculations on the solvatochromic shift of the VDE that polarization accounts for ∼0.23 eV and therefore cannot be neglected. The effect of the counterions on the VDE of the deprotonated chromophore in solvation is studied in detail, and a charge-smearing scheme is suggested for charged chromophores.