KECSA-Movable Type Implicit Solvation Model (KMTISM)

PubMed Central

2015-01-01

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

Accelerating Molecular Dynamic Simulation on Graphics Processing Units

PubMed Central

Friedrichs, Mark S.; Eastman, Peter; Vaidyanathan, Vishal; Houston, Mike; Legrand, Scott; Beberg, Adam L.; Ensign, Daniel L.; Bruns, Christopher M.; Pande, Vijay S.

2009-01-01

We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core. PMID:19191337

Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent

NASA Astrophysics Data System (ADS)

Wu, Johnny; Zhen, Xia; Shen, Hujun; Li, Guohui; Ren, Pengyu

2011-10-01

A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into "alpha helix" and "beta sheet" structures. The 5-residue polyalanine displays a substantial increase in the "beta strand" fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling.

COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids.

PubMed

Andrews, Casey T; Elcock, Adrian H

2014-11-11

We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions-which we term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)-quantitatively reproduced all of the "target" MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concentrated amino acid solutions; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concentrations that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic ( PLoS Comput. Biol. 2014 , 5 , e1003638). The anomalously strong intermolecular interactions seen in the MD study were reproduced in the COFFDROP simulations; a simple scaling of COFFDROP's nonbonded parameters, however, produced results in better accordance with experiment. Overall, our results suggest that potential functions derived from simulations of pairwise amino acid interactions might be of quite broad applicability, with COFFDROP likely to be especially useful for modeling unfolded or intrinsically disordered proteins.

COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids

PubMed Central

2015-01-01

We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions—which we term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)—quantitatively reproduced all of the “target” MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concentrated amino acid solutions; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concentrations that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic (PLoS Comput. Biol.2014, 5, e1003638). The anomalously strong intermolecular interactions seen in the MD study were reproduced in the COFFDROP simulations; a simple scaling of COFFDROP’s nonbonded parameters, however, produced results in better accordance with experiment. Overall, our results suggest that potential functions derived from simulations of pairwise amino acid interactions might be of quite broad applicability, with COFFDROP likely to be especially useful for modeling unfolded or intrinsically disordered proteins. PMID:25400526

Can a continuum solvent model reproduce the free energy landscape of a -hairpin folding in water?

NASA Astrophysics Data System (ADS)

Zhou, Ruhong; Berne, Bruce J.

2002-10-01

The folding free energy landscape of the C-terminal -hairpin of protein G is explored using the surface-generalized Born (SGB) implicit solvent model, and the results are compared with the landscape from an earlier study with explicit solvent model. The OPLSAA force field is used for the -hairpin in both implicit and explicit solvent simulations, and the conformational space sampling is carried out with a highly parallel replica-exchange method. Surprisingly, we find from exhaustive conformation space sampling that the free energy landscape from the implicit solvent model is quite different from that of the explicit solvent model. In the implicit solvent model some nonnative states are heavily overweighted, and more importantly, the lowest free energy state is no longer the native -strand structure. An overly strong salt-bridge effect between charged residues (E42, D46, D47, E56, and K50) is found to be responsible for this behavior in the implicit solvent model. Despite this, we find that the OPLSAA/SGB energies of all the nonnative structures are higher than that of the native structure; thus the OPLSAA/SGB energy is still a good scoring function for structure prediction for this -hairpin. Furthermore, the -hairpin population at 282 K is found to be less than 40% from the implicit solvent model, which is much smaller than the 72% from the explicit solvent model and 80% from experiment. On the other hand, both implicit and explicit solvent simulations with the OPLSAA force field exhibit no meaningful helical content during the folding process, which is in contrast to some very recent studies using other force fields.

Can a continuum solvent model reproduce the free energy landscape of a β-hairpin folding in water?

PubMed Central

Zhou, Ruhong; Berne, Bruce J.

2002-01-01

The folding free energy landscape of the C-terminal β-hairpin of protein G is explored using the surface-generalized Born (SGB) implicit solvent model, and the results are compared with the landscape from an earlier study with explicit solvent model. The OPLSAA force field is used for the β-hairpin in both implicit and explicit solvent simulations, and the conformational space sampling is carried out with a highly parallel replica-exchange method. Surprisingly, we find from exhaustive conformation space sampling that the free energy landscape from the implicit solvent model is quite different from that of the explicit solvent model. In the implicit solvent model some nonnative states are heavily overweighted, and more importantly, the lowest free energy state is no longer the native β-strand structure. An overly strong salt-bridge effect between charged residues (E42, D46, D47, E56, and K50) is found to be responsible for this behavior in the implicit solvent model. Despite this, we find that the OPLSAA/SGB energies of all the nonnative structures are higher than that of the native structure; thus the OPLSAA/SGB energy is still a good scoring function for structure prediction for this β-hairpin. Furthermore, the β-hairpin population at 282 K is found to be less than 40% from the implicit solvent model, which is much smaller than the 72% from the explicit solvent model and ≈80% from experiment. On the other hand, both implicit and explicit solvent simulations with the OPLSAA force field exhibit no meaningful helical content during the folding process, which is in contrast to some very recent studies using other force fields. PMID:12242327

Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

PubMed

Zhou, Ruhong; Berne, Bruce J

2002-10-01

The folding free energy landscape of the C-terminal beta-hairpin of protein G is explored using the surface-generalized Born (SGB) implicit solvent model, and the results are compared with the landscape from an earlier study with explicit solvent model. The OPLSAA force field is used for the beta-hairpin in both implicit and explicit solvent simulations, and the conformational space sampling is carried out with a highly parallel replica-exchange method. Surprisingly, we find from exhaustive conformation space sampling that the free energy landscape from the implicit solvent model is quite different from that of the explicit solvent model. In the implicit solvent model some nonnative states are heavily overweighted, and more importantly, the lowest free energy state is no longer the native beta-strand structure. An overly strong salt-bridge effect between charged residues (E42, D46, D47, E56, and K50) is found to be responsible for this behavior in the implicit solvent model. Despite this, we find that the OPLSAA/SGB energies of all the nonnative structures are higher than that of the native structure; thus the OPLSAA/SGB energy is still a good scoring function for structure prediction for this beta-hairpin. Furthermore, the beta-hairpin population at 282 K is found to be less than 40% from the implicit solvent model, which is much smaller than the 72% from the explicit solvent model and approximately equal 80% from experiment. On the other hand, both implicit and explicit solvent simulations with the OPLSAA force field exhibit no meaningful helical content during the folding process, which is in contrast to some very recent studies using other force fields.

Gay-Berne and electrostatic multipole based coarse-grain potential in implicit solvent

PubMed Central

Wu, Johnny; Zhen, Xia; Shen, Hujun; Li, Guohui; Ren, Pengyu

2011-01-01

A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is described by the Generalized Kirkwood theory. The CG model is calibrated using the results of all-atom simulations of model compounds in solution. Instead of matching the overall effective forces produced by atomic models, the fundamental intermolecular forces such as electrostatic, repulsion-dispersion, and solvation are represented explicitly at a CG level. We demonstrate that the CG alanine dipeptide model is able to reproduce quantitatively the conformational energy of all-atom force fields in both gas and solution phases, including the electrostatic and solvation components. Replica exchange molecular dynamics and microsecond dynamic simulations of polyalanine of 5 and 12 residues reveal that the CG polyalanines fold into “alpha helix” and “beta sheet” structures. The 5-residue polyalanine displays a substantial increase in the “beta strand” fraction relative to the 12-residue polyalanine. The detailed conformational distribution is compared with those reported from recent all-atom simulations and experiments. The results suggest that the new coarse-graining approach presented in this study has the potential to offer both accuracy and efficiency for biomolecular modeling. PMID:22029338

Anomalous Protein-Protein Interactions in Multivalent Salt Solution.

PubMed

Pasquier, Coralie; Vazdar, Mario; Forsman, Jan; Jungwirth, Pavel; Lund, Mikael

2017-04-13

The stability of aqueous protein solutions is strongly affected by multivalent ions, which induce ion-ion correlations beyond the scope of classical mean-field theory. Using all-atom molecular dynamics (MD) and coarse grained Monte Carlo (MC) simulations, we investigate the interaction between a pair of protein molecules in 3:1 electrolyte solution. In agreement with available experimental findings of "reentrant protein condensation", we observe an anomalous trend in the protein-protein potential of mean force with increasing electrolyte concentration in the order: (i) double-layer repulsion, (ii) ion-ion correlation attraction, (iii) overcharge repulsion, and in excess of 1:1 salt, (iv) non Coulombic attraction. To efficiently sample configurational space we explore hybrid continuum solvent models, applicable to many-protein systems, where weakly coupled ions are treated implicitly, while strongly coupled ones are treated explicitly. Good agreement is found with the primitive model of electrolytes, as well as with atomic models of protein and solvent.

Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes.

PubMed

Gkionis, Konstantinos; Kruse, Holger; Šponer, Jiří

2016-04-12

Modern dispersion-corrected DFT methods have made it possible to perform reliable QM studies on complete nucleic acid (NA) building blocks having hundreds of atoms. Such calculations, although still limited to investigations of potential energy surfaces, enhance the portfolio of computational methods applicable to NAs and offer considerably more accurate intrinsic descriptions of NAs than standard MM. However, in practice such calculations are hampered by the use of implicit solvent environments and truncation of the systems. Conventional QM optimizations are spoiled by spurious intramolecular interactions and severe structural deformations. Here we compare two approaches designed to suppress such artifacts: partially restrained continuum solvent QM and explicit solvent QM/MM optimizations. We report geometry relaxations of a set of diverse double-quartet guanine quadruplex (GQ) DNA stems. Both methods provide neat structures without major artifacts. However, each one also has distinct weaknesses. In restrained optimizations, all errors in the target geometries (i.e., low-resolution X-ray and NMR structures) are transferred to the optimized geometries. In QM/MM, the initial solvent configuration causes some heterogeneity in the geometries. Nevertheless, both approaches represent a decisive step forward compared to conventional optimizations. We refine earlier computations that revealed sizable differences in the relative energies of GQ stems computed with AMBER MM and QM. We also explore the dependence of the QM/MM results on the applied computational protocol.

Free energy landscape of protein folding in water: explicit vs. implicit solvent.

PubMed

Zhou, Ruhong

2003-11-01

The Generalized Born (GB) continuum solvent model is arguably the most widely used implicit solvent model in protein folding and protein structure prediction simulations; however, it still remains an open question on how well the model behaves in these large-scale simulations. The current study uses the beta-hairpin from C-terminus of protein G as an example to explore the folding free energy landscape with various GB models, and the results are compared to the explicit solvent simulations and experiments. All free energy landscapes are obtained from extensive conformation space sampling with a highly parallel replica exchange method. Because solvation model parameters are strongly coupled with force fields, five different force field/solvation model combinations are examined and compared in this study, namely the explicit solvent model: OPLSAA/SPC model, and the implicit solvent models: OPLSAA/SGB (Surface GB), AMBER94/GBSA (GB with Solvent Accessible Surface Area), AMBER96/GBSA, and AMBER99/GBSA. Surprisingly, we find that the free energy landscapes from implicit solvent models are quite different from that of the explicit solvent model. Except for AMBER96/GBSA, all other implicit solvent models find the lowest free energy state not the native state. All implicit solvent models show erroneous salt-bridge effects between charged residues, particularly in OPLSAA/SGB model, where the overly strong salt-bridge effect results in an overweighting of a non-native structure with one hydrophobic residue F52 expelled from the hydrophobic core in order to make better salt bridges. On the other hand, both AMBER94/GBSA and AMBER99/GBSA models turn the beta-hairpin in to an alpha-helix, and the alpha-helical content is much higher than the previously reported alpha-helices in an explicit solvent simulation with AMBER94 (AMBER94/TIP3P). Only AMBER96/GBSA shows a reasonable free energy landscape with the lowest free energy structure the native one despite an erroneous salt-bridge between D47 and K50. Detailed results on free energy contour maps, lowest free energy structures, distribution of native contacts, alpha-helical content during the folding process, NOE comparison with NMR, and temperature dependences are reported and discussed for all five models. Copyright 2003 Wiley-Liss, Inc.

Quantum dynamics in continuum for proton transport II: Variational solvent-solute interface.

PubMed

Chen, Duan; Chen, Zhan; Wei, Guo-Wei

2012-01-01

Proton transport plays an important role in biological energy transduction and sensory systems. Therefore, it has attracted much attention in biological science and biomedical engineering in the past few decades. The present work proposes a multiscale/multiphysics model for the understanding of the molecular mechanism of proton transport in transmembrane proteins involving continuum, atomic, and quantum descriptions, assisted with the evolution, formation, and visualization of membrane channel surfaces. We describe proton dynamics quantum mechanically via a new density functional theory based on the Boltzmann statistics, while implicitly model numerous solvent molecules as a dielectric continuum to reduce the number of degrees of freedom. The density of all other ions in the solvent is assumed to obey the Boltzmann distribution in a dynamic manner. The impact of protein molecular structure and its charge polarization on the proton transport is considered explicitly at the atomic scale. A variational solute-solvent interface is designed to separate the explicit molecule and implicit solvent regions. We formulate a total free-energy functional to put proton kinetic and potential energies, the free energy of all other ions, and the polar and nonpolar energies of the whole system on an equal footing. The variational principle is employed to derive coupled governing equations for the proton transport system. Generalized Laplace-Beltrami equation, generalized Poisson-Boltzmann equation, and generalized Kohn-Sham equation are obtained from the present variational framework. The variational solvent-solute interface is generated and visualized to facilitate the multiscale discrete/continuum/quantum descriptions. Theoretical formulations for the proton density and conductance are constructed based on fundamental laws of physics. A number of mathematical algorithms, including the Dirichlet-to-Neumann mapping, matched interface and boundary method, Gummel iteration, and Krylov space techniques are utilized to implement the proposed model in a computationally efficient manner. The gramicidin A channel is used to validate the performance of the proposed proton transport model and demonstrate the efficiency of the proposed mathematical algorithms. The proton channel conductances are studied over a number of applied voltages and reference concentrations. A comparison with experimental data verifies the present model predictions and confirms the proposed model. Copyright © 2011 John Wiley & Sons, Ltd.

Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

PubMed Central

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

2018-01-01

Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the solvent can turn out to be too expensive in large biomolecular systems, most implicit solvent methods fail to capture “dewetting” effects and heterogeneous hydration by relying on a pre-established (i.e., guessed) solvation interface. Here we focus on the Variational Implicit Solvent Method, an implicit solvent method that adds water “plasticity” back to the picture by formulating the solvation free energy as a functional of all possible solvation interfaces. We survey VISM's applications to the problem of molecular recognition and report some of the most recent efforts to tailor VISM for more challenging scenarios, with the ultimate goal of including thermal fluctuations into the framework. The advances reported herein pave the way to make VISM a uniquely successful approach to characterize complex solvation properties in the recognition and binding of large-scale biomolecular complexes. PMID:29484300

Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.

PubMed

Frembgen-Kesner, Tamara; Andrews, Casey T; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A; Jain, Aakash; Olayiwola, Oluwatoni J; Weishaar, Mitch R; Elcock, Adrian H

2015-05-12

Recently, we reported the parametrization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral, and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral, and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downward in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multidomain proteins connected by flexible linkers.

Simulations of fluorescence solvatochromism in substituted PPV oligomers from excited state molecular dynamics with implicit solvent

DOE PAGES

Bjorgaard, J. A.; Nelson, T.; Kalinin, K.; ...

2015-04-28

In this study, an efficient method of treating solvent effects in excited state molecular dynamics (ESMD) is implemented and tested by exploring the solvatochromic effects in substituted p-phenylene vinylene oligomers. A continuum solvent model is used which has very little computational overhead. This allows simulations of ESMD with solvent effects on the scale of hundreds of picoseconds for systems of up to hundreds of atoms. At these time scales, solvatochromic shifts in fluoresence spectra can be described. Solvatochromic shifts in absorption and fluorescence spectra from ESMD are compared with time-dependent density functional theory calculations and experiments.

Computational insights into the photocyclization of diclofenac in solution: effects of halogen and hydrogen bonding.

PubMed

Bani-Yaseen, Abdulilah Dawoud

2016-08-21

The effects of noncovalent interactions, namely halogen and hydrogen bonding, on the photochemical conversion of the photosensitizing drug diclofenac (DCF) in solution were investigated computationally. Both explicit and implicit solvent effects were qualitatively and quantitatively assessed employing the DFT/6-31+G(d) and SQM(PM7) levels of theory. Full geometry optimizations were performed in solution for the reactant DCF, hypothesized radical-based intermediates, and the main product at both levels of theories. Notably, in good agreement with previous experimental results concerning the intermolecular halogen bonding of DCF, the SQM(PM7) method revealed different values for d(ClO, Å) and ∠(C-ClO, °) for the two chlorine-substituents of DCF, with values of 2.63 Å/162° and 3.13 Å/142° for the trans and cis orientations, respectively. Employing the DFT/6-31+G(d) method with implicit solvent effects was not conclusive; however, explicit solvent effects confirmed the key contribution of hydrogen and halogen bonding in stabilizing/destabilizing the reactant and hypothesized intermediates. Interestingly, the obtained results revealed that a protic solvent such as water can increase the rate of photocyclization of DCF not only through hydrogen bonding effects, but also through halogen bonding. Furthermore, the atomic charges of atoms majorly involved in the photocyclization of DCF were calculated using different methods, namely Mulliken, Hirshfeld, and natural bond orbital (NBO). The obtained results revealed that in all cases there is a notable nonequivalency in the noncovalent intermolecular interactions of the two chlorine substituents of DCF and the radical intermediates with the solvent, which in turn may account for the discrepancy of their reactivity in different media. These computational results provide insight into the importance of halogen and hydrogen bonding throughout the progression of the photochemical conversion of DCF in solution.

Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

PubMed Central

2016-01-01

We present the AMBER ff15ipq force field for proteins, the second-generation force field developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized atomic charges in the presence of explicit solvent. The ff15ipq force field is a complete rederivation including more than 300 unique atomic charges, 900 unique torsion terms, 60 new angle parameters, and new atomic radii for polar hydrogens. The atomic charges were derived in the context of the SPC/Eb water model, which yields more-accurate rotational diffusion of proteins and enables direct calculation of nuclear magnetic resonance (NMR) relaxation parameters from molecular dynamics simulations. The atomic radii improve the accuracy of modeling salt bridge interactions relative to contemporary fixed-charge force fields, rectifying a limitation of ff14ipq that resulted from its use of pair-specific Lennard-Jones radii. In addition, ff15ipq reproduces penta-alanine J-coupling constants exceptionally well, gives reasonable agreement with NMR relaxation rates, and maintains the expected conformational propensities of structured proteins/peptides, as well as disordered peptides—all on the microsecond (μs) time scale, which is a critical regime for drug design applications. These encouraging results demonstrate the power and robustness of our automated methods for deriving new force fields. All parameters described here and the mdgx program used to fit them are included in the AmberTools16 distribution. PMID:27399642

Parameterization of backbone flexibility in a coarse-grained force field for proteins (COFFDROP) derived from all-atom explicit-solvent molecular dynamics simulations of all possible two-residue peptides

PubMed Central

Frembgen-Kesner, Tamara; Andrews, Casey T.; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A.; Jain, Aakash; Olayiwola, Oluwatoni; Weishaar, Mitch R.; Elcock, Adrian H.

2015-01-01

Recently, we reported the parameterization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs, and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downwards in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multi-domain proteins connected by flexible linkers. PMID:26574429

Structure and dynamics of human vimentin intermediate filament dimer and tetramer in explicit and implicit solvent models.

PubMed

Qin, Zhao; Buehler, Markus J

2011-01-01

Intermediate filaments, in addition to microtubules and microfilaments, are one of the three major components of the cytoskeleton in eukaryotic cells, and play an important role in mechanotransduction as well as in providing mechanical stability to cells at large stretch. The molecular structures, mechanical and dynamical properties of the intermediate filament basic building blocks, the dimer and the tetramer, however, have remained elusive due to persistent experimental challenges owing to the large size and fibrillar geometry of this protein. We have recently reported an atomistic-level model of the human vimentin dimer and tetramer, obtained through a bottom-up approach based on structural optimization via molecular simulation based on an implicit solvent model (Qin et al. in PLoS ONE 2009 4(10):e7294, 9). Here we present extensive simulations and structural analyses of the model based on ultra large-scale atomistic-level simulations in an explicit solvent model, with system sizes exceeding 500,000 atoms and simulations carried out at 20 ns time-scales. We report a detailed comparison of the structural and dynamical behavior of this large biomolecular model with implicit and explicit solvent models. Our simulations confirm the stability of the molecular model and provide insight into the dynamical properties of the dimer and tetramer. Specifically, our simulations reveal a heterogeneous distribution of the bending stiffness along the molecular axis with the formation of rather soft and highly flexible hinge-like regions defined by non-alpha-helical linker domains. We report a comparison of Ramachandran maps and the solvent accessible surface area between implicit and explicit solvent models, and compute the persistence length of the dimer and tetramer structure of vimentin intermediate filaments for various subdomains of the protein. Our simulations provide detailed insight into the dynamical properties of the vimentin dimer and tetramer intermediate filament building blocks, which may guide the development of novel coarse-grained models of intermediate filaments, and could also help in understanding assembly mechanisms.

Design and application of implicit solvent models in biomolecular simulations.

PubMed

Kleinjung, Jens; Fraternali, Franca

2014-04-01

We review implicit solvent models and their parametrisation by introducing the concepts and recent devlopments of the most popular models with a focus on parametrisation via force matching. An overview of recent applications of the solvation energy term in protein dynamics, modelling, design and prediction is given to illustrate the usability and versatility of implicit solvation in reproducing the physical behaviour of biomolecular systems. Limitations of implicit modes are discussed through the example of more challenging systems like nucleic acids and membranes. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges.

PubMed

Lara, A; Riquelme, M; Vöhringer-Martinez, E

2018-05-11

Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have also been used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study, atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in a vacuum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases, the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account, and when the energy needed to polarize the electron density of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogs. Comparison of the two partitioning methods, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS), revealed some deficiencies in the Hirshfeld-I method related to the unstable isolated anionic nitrogen pro-atom used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

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.

Efficient minimization of multipole electrostatic potentials in torsion space

PubMed Central

Bodmer, Nicholas K.

2018-01-01

The development of models of macromolecular electrostatics capable of delivering improved fidelity to quantum mechanical calculations is an active field of research in computational chemistry. Most molecular force field development takes place in the context of models with full Cartesian coordinate degrees of freedom. Nevertheless, a number of macromolecular modeling programs use a reduced set of conformational variables limited to rotatable bonds. Efficient algorithms for minimizing the energies of macromolecular systems with torsional degrees of freedom have been developed with the assumption that all atom-atom interaction potentials are isotropic. We describe novel modifications to address the anisotropy of higher order multipole terms while retaining the efficiency of these approaches. In addition, we present a treatment for obtaining derivatives of atom-centered tensors with respect to torsional degrees of freedom. We apply these results to enable minimization of the Amoeba multipole electrostatics potential in a system with torsional degrees of freedom, and validate the correctness of the gradients by comparison to finite difference approximations. In the interest of enabling a complete model of electrostatics with implicit treatment of solvent-mediated effects, we also derive expressions for the derivative of solvent accessible surface area with respect to torsional degrees of freedom. PMID:29641557

Probing the free energy landscape of the FBP28WW domain using multiple techniques.

PubMed

Periole, Xavier; Allen, Lucy R; Tamiola, Kamil; Mark, Alan E; Paci, Emanuele

2009-05-01

The free-energy landscape of a small protein, the FBP 28 WW domain, has been explored using molecular dynamics (MD) simulations with alternative descriptions of the molecule. The molecular models used range from coarse-grained to all-atom with either an implicit or explicit treatment of the solvent. Sampling of conformation space was performed using both conventional and temperature-replica exchange MD simulations. Experimental chemical shifts and NOEs were used to validate the simulations, and experimental phi values both for validation and as restraints. This combination of different approaches has provided insight into the free energy landscape and barriers encountered by the protein during folding and enabled the characterization of native, denatured and transition states which are compatible with the available experimental data. All the molecular models used stabilize well defined native and denatured basins; however, the degree of agreement with the available experimental data varies. While the most detailed, explicit solvent model predicts the data reasonably accurately, it does not fold despite a simulation time 10 times that of the experimental folding time. The less detailed models performed poorly relative to the explicit solvent model: an implicit solvent model stabilizes a ground state which differs from the experimental native state, and a structure-based model underestimates the size of the barrier between the two states. The use of experimental phi values both as restraints, and to extract structures from unfolding simulations, result in conformations which, although not necessarily true transition states, appear to share the geometrical characteristics of transition state structures. In addition to characterizing the native, transition and denatured states of this particular system in this work, the advantages and limitations of using varying levels of representation are discussed. 2008 Wiley Periodicals, Inc.

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

Testing the Use of Implicit Solvent in the Molecular Dynamics Modelling of DNA Flexibility

NASA Astrophysics Data System (ADS)

Mitchell, J.; Harris, S.

DNA flexibility controls packaging, looping and in some cases sequence specific protein binding. Molecular dynamics simulations carried out with a computationally efficient implicit solvent model are potentially a powerful tool for studying larger DNA molecules than can be currently simulated when water and counterions are represented explicitly. In this work we compare DNA flexibility at the base pair step level modelled using an implicit solvent model to that previously determined from explicit solvent simulations and database analysis. Although much of the sequence dependent behaviour is preserved in implicit solvent, the DNA is considerably more flexible when the approximate model is used. In addition we test the ability of the implicit solvent to model stress induced DNA disruptions by simulating a series of DNA minicircle topoisomers which vary in size and superhelical density. When compared with previously run explicit solvent simulations, we find that while the levels of DNA denaturation are similar using both computational methodologies, the specific structural form of the disruptions is different.

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

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

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

2014-01-21

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

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

PubMed Central

Knight, Jennifer L.

2011-01-01

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

Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.

PubMed

Vorobjev, Y N; Almagro, J C; Hermans, J

1998-09-01

A new method for calculating the total conformational free energy of proteins in water solvent is presented. The method consists of a relatively brief simulation by molecular dynamics with explicit solvent (ES) molecules to produce a set of microstates of the macroscopic conformation. Conformational energy and entropy are obtained from the simulation, the latter in the quasi-harmonic approximation by analysis of the covariance matrix. The implicit solvent (IS) dielectric continuum model is used to calculate the average solvation free energy as the sum of the free energies of creating the solute-size hydrophobic cavity, of the van der Waals solute-solvent interactions, and of the polarization of water solvent by the solute's charges. The reliability of the solvation free energy depends on a number of factors: the details of arrangement of the protein's charges, especially those near the surface; the definition of the molecular surface; and the method chosen for solving the Poisson equation. Molecular dynamics simulation in explicit solvent relaxes the protein's conformation and allows polar surface groups to assume conformations compatible with interaction with solvent, while averaging of internal energy and solvation free energy tend to enhance the precision. Two recently developed methods--SIMS, for calculation of a smooth invariant molecular surface, and FAMBE, for solution of the Poisson equation via a fast adaptive multigrid boundary element--have been employed. The SIMS and FAMBE programs scale linearly with the number of atoms. SIMS is superior to Connolly's MS (molecular surface) program: it is faster, more accurate, and more stable, and it smooths singularities of the molecular surface. Solvation free energies calculated with these two programs do not depend on molecular position or orientation and are stable along a molecular dynamics trajectory. We have applied this method to calculate the conformational free energy of native and intentionally misfolded globular conformations of proteins (the EMBL set of deliberately misfolded proteins) and have obtained good discrimination in favor of the native conformations in all instances.

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.

A coarse-grained DNA model for the prediction of current signals in DNA translocation experiments

NASA Astrophysics Data System (ADS)

Weik, Florian; Kesselheim, Stefan; Holm, Christian

2016-11-01

We present an implicit solvent coarse-grained double-stranded DNA (dsDNA) model confined to an infinite cylindrical pore that reproduces the experimentally observed current modulations of a KaCl solution at various concentrations. Our model extends previous coarse-grained and mean-field approaches by incorporating a position dependent friction term on the ions, which Kesselheim et al. [Phys. Rev. Lett. 112, 018101 (2014)] identified as an essential ingredient to correctly reproduce the experimental data of Smeets et al. [Nano Lett. 6, 89 (2006)]. Our approach reduces the computational effort by orders of magnitude compared with all-atom simulations and serves as a promising starting point for modeling the entire translocation process of dsDNA. We achieve a consistent description of the system's electrokinetics by using explicitly parameterized ions, a friction term between the DNA beads and the ions, and a lattice-Boltzmann model for the solvent.

Conformation of ionizable poly Para phenylene ethynylene in dilute solutions

DOE PAGES

Wijesinghe, Sidath; Maskey, Sabina; Perahia, Dvora; ...

2015-11-03

The conformation of dinonyl poly para phenylene ethynylenes (PPEs) with carboxylate side chains, equilibrated in solvents of different quality is studied using molecular dynamics simulations. PPEs are of interest because of their tunable electro-optical properties, chemical diversity, and functionality which are essential in wide range of applications. The polymer conformation determines the conjugation length and their assembly mode and affects electro-optical properties which are critical in their current and potential uses. The current study investigates the effect of carboxylate fraction on PPEs side chains on the conformation of chains in the dilute limit, in solvents of different quality. The dinonylmore » PPE chains are modeled atomistically, where the solvents are modeled both implicitly and explicitly. Dinonyl PPEs maintained a stretched out conformation up to a carboxylate fraction f of 0.7 in all solvents studied. The nonyl side chains are extended and oriented away from the PPE backbone in toluene and in implicit good solvent whereas in water and implicit poor solvent, the nonyl side chains are collapsed towards the PPE backbone. Thus, rotation around the aromatic ring is fast and no long range correlations are seen within the backbone.« less

Conformation of ionizable poly Para phenylene ethynylene in dilute solutions

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

Wijesinghe, Sidath; Maskey, Sabina; Perahia, Dvora

The conformation of dinonyl poly para phenylene ethynylenes (PPEs) with carboxylate side chains, equilibrated in solvents of different quality is studied using molecular dynamics simulations. PPEs are of interest because of their tunable electro-optical properties, chemical diversity, and functionality which are essential in wide range of applications. The polymer conformation determines the conjugation length and their assembly mode and affects electro-optical properties which are critical in their current and potential uses. The current study investigates the effect of carboxylate fraction on PPEs side chains on the conformation of chains in the dilute limit, in solvents of different quality. The dinonylmore » PPE chains are modeled atomistically, where the solvents are modeled both implicitly and explicitly. Dinonyl PPEs maintained a stretched out conformation up to a carboxylate fraction f of 0.7 in all solvents studied. The nonyl side chains are extended and oriented away from the PPE backbone in toluene and in implicit good solvent whereas in water and implicit poor solvent, the nonyl side chains are collapsed towards the PPE backbone. Thus, rotation around the aromatic ring is fast and no long range correlations are seen within the backbone.« less

Treecode-based generalized Born method

NASA Astrophysics Data System (ADS)

Xu, Zhenli; Cheng, Xiaolin; Yang, Haizhao

2011-02-01

We have developed a treecode-based O(Nlog N) algorithm for the generalized Born (GB) implicit solvation model. Our treecode-based GB (tGB) is based on the GBr6 [J. Phys. Chem. B 111, 3055 (2007)], an analytical GB method with a pairwise descreening approximation for the R6 volume integral expression. The algorithm is composed of a cutoff scheme for the effective Born radii calculation, and a treecode implementation of the GB charge-charge pair interactions. Test results demonstrate that the tGB algorithm can reproduce the vdW surface based Poisson solvation energy with an average relative error less than 0.6% while providing an almost linear-scaling calculation for a representative set of 25 proteins with different sizes (from 2815 atoms to 65456 atoms). For a typical system of 10k atoms, the tGB calculation is three times faster than the direct summation as implemented in the original GBr6 model. Thus, our tGB method provides an efficient way for performing implicit solvent GB simulations of larger biomolecular systems at longer time scales.

A Coarse-Grained Protein Model in a Water-like Solvent

NASA Astrophysics Data System (ADS)

Sharma, Sumit; Kumar, Sanat K.; Buldyrev, Sergey V.; Debenedetti, Pablo G.; Rossky, Peter J.; Stanley, H. Eugene

2013-05-01

Simulations employing an explicit atom description of proteins in solvent can be computationally expensive. On the other hand, coarse-grained protein models in implicit solvent miss essential features of the hydrophobic effect, especially its temperature dependence, and have limited ability to capture the kinetics of protein folding. We propose a free space two-letter protein (``H-P'') model in a simple, but qualitatively accurate description for water, the Jagla model, which coarse-grains water into an isotropically interacting sphere. Using Monte Carlo simulations, we design protein-like sequences that can undergo a collapse, exposing the ``Jagla-philic'' monomers to the solvent, while maintaining a ``hydrophobic'' core. This protein-like model manifests heat and cold denaturation in a manner that is reminiscent of proteins. While this protein-like model lacks the details that would introduce secondary structure formation, we believe that these ideas represent a first step in developing a useful, but computationally expedient, means of modeling proteins.

Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations.

PubMed

Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro

2018-01-01

Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms. More recently outstanding advancement in both implicit solvent models and in entropy calculations are making the goal of free energy estimation from end-point simulations more feasible than ever before. We review briefly the basic theory and discuss the advancements in light of practical applications.

Structure and Dynamics of End-to-End Loop Formation of the Penta-Peptide Cys-Ala-Gly-Gln-Trp in Implicit Solvents

DTIC Science & Technology

2009-01-01

implicit solvents on peptide structure and dynamics , we performed extensive molecular dynamics simulations on the penta-peptide Cys-Ala-Gly-Gln-Trp. Two...end-to-end distances and dihedral angles obtained from molecular dynamics simulations with implicit solvent models were in a good agreement with those...to maintain the temperature of the systems. Introduction Molecular dynamics (MD) simulation techniques are widely used to study structure and

Solvent induced conformational fluctuation of alanine dipeptide studied by using vibrational probes

NASA Astrophysics Data System (ADS)

Cai, Kaicong; Du, Fenfen; Liu, Jia; Su, Tingting

2015-02-01

The solvation effect on the three dimensional structure and the vibrational feature of alanine dipeptide (ALAD) was evaluated by applying the implicit solvents from polarizable continuum solvent model (PCM) through ab initio calculations, by using molecular dynamic (MD) simulations with explicit solvents, and by combining these two approaches. The implicit solvent induced potential energy fluctuations of ALAD in CHCl3, DMSO and H2O are revealed by means of ab initio calculations, and a global view of conformational and solvation environmental dependence of amide I frequencies is achieved. The results from MD simulations with explicit solvents show that ALAD trends to form PPII, αL, αR, and C5 in water, PPII and C5 in DMSO, and C5 in CHCl3, ordered by population, and the demonstration of the solvated structure, the solute-solvent interaction and hydrogen bonding is therefore enhanced. Representative ALAD-solvent clusters were sampled from MD trajectories and undergone ab initio calculations. The explicit solvents reveal the hydrogen bonding between ALAD and solvents, and the correlation between amide I frequencies and the Cdbnd O bond length is built. The implicit solvents applied to the ALAD-solvent clusters further compensate the solvation effect from the bulk, and thus enlarge the degree of structural distortion and the amide I frequency red shift. The combination of explicit solvent in the first hydration shell and implicit solvent in the bulk is helpful for our understanding about the conformational fluctuation of solvated polypeptides through vibrational probes.

Refinement of NMR structures using implicit solvent and advanced sampling techniques.

PubMed

Chen, Jianhan; Im, Wonpil; Brooks, Charles L

2004-12-15

NMR biomolecular structure calculations exploit simulated annealing methods for conformational sampling and require a relatively high level of redundancy in the experimental restraints to determine quality three-dimensional structures. Recent advances in generalized Born (GB) implicit solvent models should make it possible to combine information from both experimental measurements and accurate empirical force fields to improve the quality of NMR-derived structures. In this paper, we study the influence of implicit solvent on the refinement of protein NMR structures and identify an optimal protocol of utilizing these improved force fields. To do so, we carry out structure refinement experiments for model proteins with published NMR structures using full NMR restraints and subsets of them. We also investigate the application of advanced sampling techniques to NMR structure refinement. Similar to the observations of Xia et al. (J.Biomol. NMR 2002, 22, 317-331), we find that the impact of implicit solvent is rather small when there is a sufficient number of experimental restraints (such as in the final stage of NMR structure determination), whether implicit solvent is used throughout the calculation or only in the final refinement step. The application of advanced sampling techniques also seems to have minimal impact in this case. However, when the experimental data are limited, we demonstrate that refinement with implicit solvent can substantially improve the quality of the structures. In particular, when combined with an advanced sampling technique, the replica exchange (REX) method, near-native structures can be rapidly moved toward the native basin. The REX method provides both enhanced sampling and automatic selection of the most native-like (lowest energy) structures. An optimal protocol based on our studies first generates an ensemble of initial structures that maximally satisfy the available experimental data with conventional NMR software using a simplified force field and then refines these structures with implicit solvent using the REX method. We systematically examine the reliability and efficacy of this protocol using four proteins of various sizes ranging from the 56-residue B1 domain of Streptococcal protein G to the 370-residue Maltose-binding protein. Significant improvement in the structures was observed in all cases when refinement was based on low-redundancy restraint data. The proposed protocol is anticipated to be particularly useful in early stages of NMR structure determination where a reliable estimate of the native fold from limited data can significantly expedite the overall process. This refinement procedure is also expected to be useful when redundant experimental data are not readily available, such as for large multidomain biomolecules and in solid-state NMR structure determination.

Investigating the Effect of Charge Hydration Asymmetry and Incorporating it in Continuum Solvation Framework

NASA Astrophysics Data System (ADS)

Mukhopadhyay, Abhishek

One of the essential requirements of biomolecular modeling is an accurate description of water as a solvent. The challenge is to make this description computationally facile - reasonably fast, simple, robust and easy to incorporate into existing software packages, yet accurate. The most rigorous procedure to model the effect of aqueous solvent is to explicitly model every water molecule in the system. For many practical applications, this approach is computationally too intense, as the number of required water atoms is on an average at least one order of magnitude larger than the number of atoms of the molecule of interest. Implicit solvent models, in which solvent molecules are replaced by a continuous dielectric, have become a popular alternative to explicit solvent methods. However, implicit solvation models often lack various microscopic details which are crucial for accuracy. One such missing effect that is currently missing from popular implicit models is the so called effect of charge hydration asymmetry (CHA). The missing effect of charge hydration asymmetry - the asymmetric response of water upon the sign of solute charge - manifests a characteristic, strong dependence of solvation free energies on the sign of solute charge. Here, we incorporate this missing effect into the continuum solvation framework via the conceptually simplest Born equation and also in the generalized Born model. We identify the key electric multipole moments of model water molecules critical for the various degrees of CHA effect observed in studies based on molecular dynamics simulations using different rigid water models. We then use this gained insight to incorporate this effect first into the Born model and then into the generalized Born model. The proposed framework significantly improves accuracy of the hydration free energy estimates tested on a comprehensive set of varied molecular solutes - monovalent and divalent ions, small drug-like molecules, charged and uncharged amino acid dipeptides, and small proteins. We finally develop a methodology to resolve the issue with unacceptably large uncertainty that stems from a variety of fundamental and technical difficulties in experimental quantification of CHA from charged solutes. Using the proposed corrections in the continuum framework, we untangle the charge-asymmetric response of water from its symmetric response, and further circumvent the difficulties by extracting accurate estimate propensity of water to cause CHA from accurate experimental hydration free energies of neutral polar molecules. We show that the asymmetry in water's response is strong, about 50% of the symmetric response.

Ab initio folding of mixed-fold FSD-EY protein using formula-based polarizable hydrogen bond (PHB) charge model

NASA Astrophysics Data System (ADS)

Zhang, Dawei; Lazim, Raudah; Mun Yip, Yew

2017-09-01

We conducted an all-atom ab initio folding of FSD-EY, a protein with a ββα configuration using non-polarizable (AMBER) and polarizable force fields (PHB designed by Gao et al.) in implicit solvent. The effect of reducing the polarization effect integrated into the force field by the PHB model, termed the PHB0.7 was also examined in the folding of FSD-EY. This model incorporates into the force field 70% of the original polarization effect to minimize the likelihood of over-stabilizing the backbone hydrogen bonds. Precise folding of the β-sheet of FSD-EY was further achieved by relaxing the REMD structure obtained in explicit water.

Sampling of Protein Folding Transitions: Multicanonical Versus Replica Exchange Molecular Dynamics.

PubMed

Jiang, Ping; Yaşar, Fatih; Hansmann, Ulrich H E

2013-08-13

We compare the efficiency of multicanonical and replica exchange molecular dynamics for the sampling of folding/unfolding events in simulations of proteins with end-to-end β -sheet. In Go-model simulations of the 75-residue MNK6, we observe improvement factors of 30 in the number of folding/unfolding events of multicanonical molecular dynamics over replica exchange molecular dynamics. As an application, we use this enhanced sampling to study the folding landscape of the 36-residue DS119 with an all-atom physical force field and implicit solvent. Here, we find that the rate-limiting step is the formation of the central helix that then provides a scaffold for the parallel β -sheet formed by the two chain ends.

Ab initio calculation of the deprotonation constants of an atomistically defined nanometer-sized, aluminium hydroxide oligomer

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

Wander, Matthew C. F.; Shuford, Kevin L.; Rustad, James R.

Aluminium possesses significant and diverse chemistry. Numerous compounds have been defined, and the elucidation of their chemistry is of significant geochemical interest. In this paper, a brucite-like, eight-aluminium aqueous cluster is modelled with density functional theory to identify its primary site of deprotonation and the associated pK(a) constant using both explicit (a full first solvent shell) and implicit solvent. Two methods for calculating the pK(a) are compared. We found that a bond density approach is better than a direct energy calculation for ions with large charge and high symmetry. The terminal aluminium atoms have equatorial ligated waters that in solventmore » have one long O-H bond. This site is more reactive than any of the other protons on the particle. Insights into the experimental crystal structure and Bader's Atoms in Molecules density analysis are presented as routes to reduce the computational time required for the identification of protonation sites.« less

Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations

PubMed Central

Zhou, Shenggao; Sun, Hui; Cheng, Li-Tien; Dzubiella, Joachim; McCammon, J. Andrew

2016-01-01

Recent years have seen the initial success of a variational implicit-solvent model (VISM), implemented with a robust level-set method, in capturing efficiently different hydration states and providing quantitatively good estimation of solvation free energies of biomolecules. The level-set minimization of the VISM solvation free-energy functional of all possible solute-solvent interfaces or dielectric boundaries predicts an equilibrium biomolecular conformation that is often close to an initial guess. In this work, we develop a theory in the form of Langevin geometrical flow to incorporate solute-solvent interfacial fluctuations into the VISM. Such fluctuations are crucial to biomolecular conformational changes and binding process. We also develop a stochastic level-set method to numerically implement such a theory. We describe the interfacial fluctuation through the “normal velocity” that is the solute-solvent interfacial force, derive the corresponding stochastic level-set equation in the sense of Stratonovich so that the surface representation is independent of the choice of implicit function, and develop numerical techniques for solving such an equation and processing the numerical data. We apply our computational method to study the dewetting transition in the system of two hydrophobic plates and a hydrophobic cavity of a synthetic host molecule cucurbit[7]uril. Numerical simulations demonstrate that our approach can describe an underlying system jumping out of a local minimum of the free-energy functional and can capture dewetting transitions of hydrophobic systems. In the case of two hydrophobic plates, we find that the wavelength of interfacial fluctuations has a strong influence to the dewetting transition. In addition, we find that the estimated energy barrier of the dewetting transition scales quadratically with the inter-plate distance, agreeing well with existing studies of molecular dynamics simulations. Our work is a first step toward the inclusion of fluctuations into the VISM and understanding the impact of interfacial fluctuations on biomolecular solvation with an implicit-solvent approach. PMID:27497546

Free energy landscapes of small peptides in an implicit solvent model determined by force-biased multicanonical molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Watanabe, Yukihisa S.; Kim, Jae Gil; Fukunishi, Yoshifumi; Nakamura, Haruki

2004-12-01

In order to investigate whether the implicit solvent (GB/SA) model could reproduce the free energy landscapes of peptides, the potential of mean forces (PMFs) of eight tripeptides was examined and compared with the PMFs of the explicit water model. The force-biased multicanonical molecular dynamics method was used for the enhanced conformational sampling. Consequently, the GB/SA model reproduced almost all the global and local minima in the PMFs observed with the explicit water model. However, the GB/SA model overestimated frequencies of the structures that are stabilized by intra-peptide hydrogen bonds.

Functionally relevant protein motions: Extracting basin-specific collective coordinates from molecular dynamics trajectories

NASA Astrophysics Data System (ADS)

Pan, Patricia Wang; Dickson, Russell J.; Gordon, Heather L.; Rothstein, Stuart M.; Tanaka, Shigenori

2005-01-01

Functionally relevant motion of proteins has been associated with a number of atoms moving in a concerted fashion along so-called "collective coordinates." We present an approach to extract collective coordinates from conformations obtained from molecular dynamics simulations. The power of this technique for differentiating local structural fuctuations between classes of conformers obtained by clustering is illustrated by analyzing nanosecond-long trajectories for the response regulator protein Spo0F of Bacillus subtilis, generated both in vacuo and using an implicit-solvent representation. Conformational clustering is performed using automated histogram filtering of the inter-Cα distances. Orthogonal (varimax) rotation of the vectors obtained by principal component analysis of these interresidue distances for the members of individual clusters is key to the interpretation of collective coordinates dominating each conformational class. The rotated loadings plots isolate significant variation in interresidue distances, and these are associated with entire mobile secondary structure elements. From this we infer concerted motions of these structural elements. For the Spo0F simulations employing an implicit-solvent representation, collective coordinates obtained in this fashion are consistent with the location of the protein's known active sites and experimentally determined mobile regions.

CHARMM: The Biomolecular Simulation Program

PubMed Central

Brooks, B.R.; Brooks, C.L.; MacKerell, A.D.; Nilsson, L.; Petrella, R.J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A.R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R.W.; Post, C.B.; Pu, J.Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D.M.; Karplus, M.

2009-01-01

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. In addition, the CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This paper provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM paper in 1983. PMID:19444816

Folding and stability of helical bundle proteins from coarse-grained models.

PubMed

Kapoor, Abhijeet; Travesset, Alex

2013-07-01

We develop a coarse-grained model where solvent is considered implicitly, electrostatics are included as short-range interactions, and side-chains are coarse-grained to a single bead. The model depends on three main parameters: hydrophobic, electrostatic, and side-chain hydrogen bond strength. The parameters are determined by considering three level of approximations and characterizing the folding for three selected proteins (training set). Nine additional proteins (containing up to 126 residues) as well as mutated versions (test set) are folded with the given parameters. In all folding simulations, the initial state is a random coil configuration. Besides the native state, some proteins fold into an additional state differing in the topology (structure of the helical bundle). We discuss the stability of the native states, and compare the dynamics of our model to all atom molecular dynamics simulations as well as some general properties on the interactions governing folding dynamics. Copyright © 2013 Wiley Periodicals, Inc.

Explicit ions/implicit water generalized Born model for nucleic acids

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

Tolokh, Igor S.; Thomas, Dennis G.; Onufriev, Alexey V.

Ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure and interactions. Here we utilized the implicit solvent framework to develop a model for the explicit treatment of ions interacting with nucleic acid molecules. The proposed explicit ions/implicit water model is based on a significantly modified generalized Born (GB) model, and utilizes a non-standard approach to defining the solute/solvent dielectric boundary. Specifically, the model includes modifications to the GB interaction terms for the case of multiple interacting solutes – disconnected dielectric boundary around the solute-ion or ion-ion pairs. Fully analytical description of all energymore » components for charge-charge interactions is provided. The effectiveness of the approach is demonstrated by calculating the potential of mean force (PMF) for Na+-Cl− ion pair and by carrying out a set of Monte Carlo (MC) simulations of mono- and trivalent ions interacting with DNA and RNA duplexes. The monovalent (Na+) and trivalent (CoHex3+) counterion distributions predicted by the model are in close quantitative agreement with all-atom explicit water molecular dynamics simulations used as reference. Expressed in the units of energy, the maximum deviations of local ion concentrations from the reference are within kBT. The proposed explicit ions/implicit water GB model is able to resolve subtle features and differences of CoHex distributions around DNA and RNA duplexes. These features include preferential CoHex binding inside the major groove of RNA duplex, in contrast to CoHex biding at the "external" surface of the sugar-phosphate backbone of DNA duplex; these differences in the counterion binding patters were shown earlier to be responsible for the observed drastic differences in condensation propensities between short DNA and RNA duplexes. MC simulations of CoHex ions interacting with homopolymeric poly(dA·dT) DNA duplex with modified (de-methylated) and native Thymine bases are used to explore the physics behind CoHex-Thymine interactions. The simulations suggest that the ion desolvation penalty due to proximity to the low dielectric volume of the methyl group can contribute significantly to CoHex-Thymine interactions. Compared to the steric repulsion between the ion and the methyl group, the desolvation penalty interaction has a longer range, and may be important to consider in the context of methylation effects on DNA condensation.« less

Explicit ions/implicit water generalized Born model for nucleic acids

NASA Astrophysics Data System (ADS)

Tolokh, Igor S.; Thomas, Dennis G.; Onufriev, Alexey V.

2018-05-01

The ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure, and interactions. Here we utilized the implicit solvent framework to develop a model for the explicit treatment of ions interacting with nucleic acid molecules. The proposed explicit ions/implicit water model is based on a significantly modified generalized Born (GB) model and utilizes a non-standard approach to define the solute/solvent dielectric boundary. Specifically, the model includes modifications to the GB interaction terms for the case of multiple interacting solutes—disconnected dielectric boundary around the solute-ion or ion-ion pairs. A fully analytical description of all energy components for charge-charge interactions is provided. The effectiveness of the approach is demonstrated by calculating the potential of mean force for Na+-Cl- ion pair and by carrying out a set of Monte Carlo (MC) simulations of mono- and trivalent ions interacting with DNA and RNA duplexes. The monovalent (Na+) and trivalent (CoHex3+) counterion distributions predicted by the model are in close quantitative agreement with all-atom explicit water molecular dynamics simulations used as reference. Expressed in the units of energy, the maximum deviations of local ion concentrations from the reference are within kBT. The proposed explicit ions/implicit water GB model is able to resolve subtle features and differences of CoHex distributions around DNA and RNA duplexes. These features include preferential CoHex binding inside the major groove of the RNA duplex, in contrast to CoHex biding at the "external" surface of the sugar-phosphate backbone of the DNA duplex; these differences in the counterion binding patters were earlier shown to be responsible for the observed drastic differences in condensation propensities between short DNA and RNA duplexes. MC simulations of CoHex ions interacting with the homopolymeric poly(dA.dT) DNA duplex with modified (de-methylated) and native thymine bases are used to explore the physics behind CoHex-thymine interactions. The simulations suggest that the ion desolvation penalty due to proximity to the low dielectric volume of the methyl group can contribute significantly to CoHex-thymine interactions. Compared to the steric repulsion between the ion and the methyl group, the desolvation penalty interaction has a longer range and may be important to consider in the context of methylation effects on DNA condensation.

Improving the Efficiency of Non-equilibrium Sampling in the Aqueous Environment via Implicit-Solvent Simulations.

PubMed

Liu, Hui; Chen, Fu; Sun, Huiyong; Li, Dan; Hou, Tingjun

2017-04-11

By means of estimators based on non-equilibrium work, equilibrium free energy differences or potentials of mean force (PMFs) of a system of interest can be computed from biased molecular dynamics (MD) simulations. The approach, however, is often plagued by slow conformational sampling and poor convergence, especially when the solvent effects are taken into account. Here, as a possible way to alleviate the problem, several widely used implicit-solvent models, which are derived from the analytic generalized Born (GB) equation and implemented in the AMBER suite of programs, were employed in free energy calculations based on non-equilibrium work and evaluated for their abilities to emulate explicit water. As a test case, pulling MD simulations were carried out on an alanine polypeptide with different solvent models and protocols, followed by comparisons of the reconstructed PMF profiles along the unfolding coordinate. The results show that when employing the non-equilibrium work method, sampling with an implicit-solvent model is several times faster and, more importantly, converges more rapidly than that with explicit water due to reduction of dissipation. Among the assessed GB models, the Neck variants outperform the OBC and HCT variants in terms of accuracy, whereas their computational costs are comparable. In addition, for the best-performing models, the impact of the solvent-accessible surface area (SASA) dependent nonpolar solvation term was also examined. The present study highlights the advantages of implicit-solvent models for non-equilibrium sampling.

Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations.

PubMed

Godschalk, Frithjof; Genheden, Samuel; Söderhjelm, Pär; Ryde, Ulf

2013-05-28

Molecular mechanics with generalised Born and surface area solvation (MM/GBSA) is a popular method to calculate the free energy of the binding of ligands to proteins. It involves molecular dynamics (MD) simulations with an explicit solvent of the protein-ligand complex to give a set of snapshots for which energies are calculated with an implicit solvent. This change in the solvation method (explicit → implicit) would strictly require that the energies are reweighted with the implicit-solvent energies, which is normally not done. In this paper we calculate MM/GBSA energies with two generalised Born models for snapshots generated by the same methods or by explicit-solvent simulations for five synthetic N-acetyllactosamine derivatives binding to galectin-3. We show that the resulting energies are very different both in absolute and relative terms, showing that the change in the solvent model is far from innocent and that standard MM/GBSA is not a consistent method. The ensembles generated with the various solvent models are quite different with root-mean-square deviations of 1.2-1.4 Å. The ensembles can be converted to each other by performing short MD simulations with the new method, but the convergence is slow, showing mean absolute differences in the calculated energies of 6-7 kJ mol(-1) after 2 ps simulations. Minimisations show even slower convergence and there are strong indications that the energies obtained from minimised structures are different from those obtained by MD.

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.

PubMed

Wallace, Jason A; Shen, Jana K

2012-11-14

Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pK(a) values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future.

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH

PubMed Central

Wallace, Jason A.; Shen, Jana K.

2012-01-01

Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pKa values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future. PMID:23163362

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

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

PubMed Central

2012-01-01

We present an implementation of generalized Born implicit solvent all-atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA enabled NVIDIA graphics processing units (GPUs). We discuss the algorithms that are used to exploit the processing power of the GPUs and show the performance that can be achieved in comparison to simulations on conventional CPU clusters. The implementation supports three different precision models in which the contributions to the forces are calculated in single precision floating point arithmetic but accumulated in double precision (SPDP), or everything is computed in single precision (SPSP) or double precision (DPDP). In addition to performance, we have focused on understanding the implications of the different precision models on the outcome of implicit solvent MD simulations. We show results for a range of tests including the accuracy of single point force evaluations and energy conservation as well as structural properties pertainining to protein dynamics. The numerical noise due to rounding errors within the SPSP precision model is sufficiently large to lead to an accumulation of errors which can result in unphysical trajectories for long time scale simulations. We recommend the use of the mixed-precision SPDP model since the numerical results obtained are comparable with those of the full double precision DPDP model and the reference double precision CPU implementation but at significantly reduced computational cost. Our implementation provides performance for GB simulations on a single desktop that is on par with, and in some cases exceeds, that of traditional supercomputers. PMID:22582031

Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy

PubMed Central

Snow, Christopher D.; Qiu, Linlin; Du, Deguo; Gai, Feng; Hagen, Stephen J.; Pande, Vijay S.

2004-01-01

We studied the microsecond folding dynamics of three β hairpins (Trp zippers 1–3, TZ1–TZ3) by using temperature-jump fluorescence and atomistic molecular dynamics in implicit solvent. In addition, we studied TZ2 by using time-resolved IR spectroscopy. By using distributed computing, we obtained an aggregate simulation time of 22 ms. The simulations included 150, 212, and 48 folding events at room temperature for TZ1, TZ2, and TZ3, respectively. The all-atom optimized potentials for liquid simulations (OPLSaa) potential set predicted TZ1 and TZ2 properties well; the estimated folding rates agreed with the experimentally determined folding rates and native conformations were the global potential-energy minimum. The simulations also predicted reasonable unfolding activation enthalpies. This work, directly comparing large simulated folding ensembles with multiple spectroscopic probes, revealed both the surprising predictive ability of current models as well as their shortcomings. Specifically, for TZ1–TZ3, OPLS for united atom models had a nonnative free-energy minimum, and the folding rate for OPLSaa TZ3 was sensitive to the initial conformation. Finally, we characterized the transition state; all TZs fold by means of similar, native-like transition-state conformations. PMID:15020773

Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy

NASA Astrophysics Data System (ADS)

Snow, Christopher D.; Qiu, Linlin; Du, Deguo; Gai, Feng; Hagen, Stephen J.; Pande, Vijay S.

2004-03-01

We studied the microsecond folding dynamics of three hairpins (Trp zippers 1-3, TZ1-TZ3) by using temperature-jump fluorescence and atomistic molecular dynamics in implicit solvent. In addition, we studied TZ2 by using time-resolved IR spectroscopy. By using distributed computing, we obtained an aggregate simulation time of 22 ms. The simulations included 150, 212, and 48 folding events at room temperature for TZ1, TZ2, and TZ3, respectively. The all-atom optimized potentials for liquid simulations (OPLSaa) potential set predicted TZ1 and TZ2 properties well; the estimated folding rates agreed with the experimentally determined folding rates and native conformations were the global potential-energy minimum. The simulations also predicted reasonable unfolding activation enthalpies. This work, directly comparing large simulated folding ensembles with multiple spectroscopic probes, revealed both the surprising predictive ability of current models as well as their shortcomings. Specifically, for TZ1-TZ3, OPLS for united atom models had a nonnative free-energy minimum, and the folding rate for OPLSaa TZ3 was sensitive to the initial conformation. Finally, we characterized the transition state; all TZs fold by means of similar, native-like transition-state conformations.

Computational study of the free energy landscape of the miniprotein CLN025 in explicit and implicit solvent.

PubMed

Rodriguez, Alex; Mokoema, Pol; Corcho, Francesc; Bisetty, Khrisna; Perez, Juan J

2011-02-17

The prediction capabilities of atomistic simulations of peptides are hampered by different difficulties, including the reliability of force fields, the treatment of the solvent or the adequate sampling of the conformational space. In this work, we have studied the conformational profile of the 10 residue miniprotein CLN025 known to exhibit a β-hairpin in its native state to understand the limitations of implicit methods to describe solvent effects and how these may be compensated by using different force fields. For this purpose, we carried out a thorough sampling of the conformational space of CLN025 in explicit solvent using the replica exchange molecular dynamics method as a sampling technique and compared the results with simulations of the system modeled using the analytical linearized Poisson-Boltzmann (ALPB) method with three different AMBER force fields: parm94, parm96, and parm99SB. The results show the peptide to exhibit a funnel-like free energy landscape with two minima in explicit solvent. In contrast, the higher minimum nearly disappears from the energy surface when the system is studied with an implicit representation of the solvent. Moreover, the different force fields used in combination with the ALPB method do not describe the system in the same manner. The results of this work suggest that the balance between intra- and intermolecular interactions is the cause of the differences between implicit and explicit solvent simulations in this system, stressing the role of the environment to define properly the conformational profile of a peptide in solution.

Level-Set Variational Implicit-Solvent Modeling of Biomolecules with the Coulomb-Field Approximation

PubMed Central

2011-01-01

Central in the variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett.2006, 96, 087802 and J. Chem. Phys.2006, 124, 084905] of molecular solvation is a mean-field free-energy functional of all possible solute–solvent interfaces or dielectric boundaries. Such a functional can be minimized numerically by a level-set method to determine stable equilibrium conformations and solvation free energies. Applications to nonpolar systems have shown that the level-set VISM is efficient and leads to qualitatively and often quantitatively correct results. In particular, it is capable of capturing capillary evaporation in hydrophobic confinement and corresponding multiple equilibrium states as found in molecular dynamics (MD) simulations. In this work, we introduce into the VISM the Coulomb-field approximation of the electrostatic free energy. Such an approximation is a volume integral over an arbitrary shaped solvent region, requiring no solutions to any partial differential equations. With this approximation, we obtain the effective boundary force and use it as the “normal velocity” in the level-set relaxation. We test the new approach by calculating solvation free energies and potentials of mean force for small and large molecules, including the two-domain protein BphC. Our results reveal the importance of coupling polar and nonpolar interactions in the underlying molecular systems. In particular, dehydration near the domain interface of BphC subunits is found to be highly sensitive to local electrostatic potentials as seen in previous MD simulations. This is a first step toward capturing the complex protein dehydration process by an implicit-solvent approach. PMID:22346739

Combining the ensemble and Franck-Condon approaches for calculating spectral shapes of molecules in solution

NASA Astrophysics Data System (ADS)

Zuehlsdorff, T. J.; Isborn, C. M.

2018-01-01

The correct treatment of vibronic effects is vital for the modeling of absorption spectra of many solvated dyes. Vibronic spectra for small dyes in solution can be easily computed within the Franck-Condon approximation using an implicit solvent model. However, implicit solvent models neglect specific solute-solvent interactions on the electronic excited state. On the other hand, a straightforward way to account for solute-solvent interactions and temperature-dependent broadening is by computing vertical excitation energies obtained from an ensemble of solute-solvent conformations. Ensemble approaches usually do not account for vibronic transitions and thus often produce spectral shapes in poor agreement with experiment. We address these shortcomings by combining zero-temperature vibronic fine structure with vertical excitations computed for a room-temperature ensemble of solute-solvent configurations. In this combined approach, all temperature-dependent broadening is treated classically through the sampling of configurations and quantum mechanical vibronic contributions are included as a zero-temperature correction to each vertical transition. In our calculation of the vertical excitations, significant regions of the solvent environment are treated fully quantum mechanically to account for solute-solvent polarization and charge-transfer. For the Franck-Condon calculations, a small amount of frozen explicit solvent is considered in order to capture solvent effects on the vibronic shape function. We test the proposed method by comparing calculated and experimental absorption spectra of Nile red and the green fluorescent protein chromophore in polar and non-polar solvents. For systems with strong solute-solvent interactions, the combined approach yields significant improvements over the ensemble approach. For systems with weak to moderate solute-solvent interactions, both the high-energy vibronic tail and the width of the spectra are in excellent agreement with experiments.

Mapping conformational dynamics of proteins using torsional dynamics simulations.

PubMed

Gangupomu, Vamshi K; Wagner, Jeffrey R; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan

2013-05-07

All-atom molecular dynamics simulations are widely used to study the flexibility of protein conformations. However, enhanced sampling techniques are required for simulating protein dynamics that occur on the millisecond timescale. In this work, we show that torsional molecular dynamics simulations enhance protein conformational sampling by performing conformational search in the low-frequency torsional degrees of freedom. In this article, we use our recently developed torsional-dynamics method called Generalized Newton-Euler Inverse Mass Operator (GNEIMO) to study the conformational dynamics of four proteins. We investigate the use of the GNEIMO method in simulations of the conformationally flexible proteins fasciculin and calmodulin, as well as the less flexible crambin and bovine pancreatic trypsin inhibitor. For the latter two proteins, the GNEIMO simulations with an implicit-solvent model reproduced the average protein structural fluctuations and sample conformations similar to those from Cartesian simulations with explicit solvent. The application of GNEIMO with replica exchange to the study of fasciculin conformational dynamics produced sampling of two of this protein's experimentally established conformational substates. Conformational transition of calmodulin from the Ca(2+)-bound to the Ca(2+)-free conformation occurred readily with GNEIMO simulations. Moreover, the GNEIMO method generated an ensemble of conformations that satisfy about half of both short- and long-range interresidue distances obtained from NMR structures of holo to apo transitions in calmodulin. Although unconstrained all-atom Cartesian simulations have failed to sample transitions between the substates of fasciculin and calmodulin, GNEIMO simulations show the transitions in both systems. The relatively short simulation times required to capture these long-timescale conformational dynamics indicate that GNEIMO is a promising molecular-dynamics technique for studying domain motion in proteins. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2013-07-01

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

Differential geometry based solvation model. III. Quantum formulation

PubMed Central

Chen, Zhan; Wei, Guo-Wei

2011-01-01

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

Modeling the Hydration Layer around Proteins: Applications to Small- and Wide-Angle X-Ray Scattering

PubMed Central

Virtanen, Jouko Juhani; Makowski, Lee; Sosnick, Tobin R.; Freed, Karl F.

2011-01-01

Small-/wide-angle x-ray scattering (SWAXS) experiments can aid in determining the structures of proteins and protein complexes, but success requires accurate computational treatment of solvation. We compare two methods by which to calculate SWAXS patterns. The first approach uses all-atom explicit-solvent molecular dynamics (MD) simulations. The second, far less computationally expensive method involves prediction of the hydration density around a protein using our new HyPred solvation model, which is applied without the need for additional MD simulations. The SWAXS patterns obtained from the HyPred model compare well to both experimental data and the patterns predicted by the MD simulations. Both approaches exhibit advantages over existing methods for analyzing SWAXS data. The close correspondence between calculated and observed SWAXS patterns provides strong experimental support for the description of hydration implicit in the HyPred model. PMID:22004761

CHARMM-GUI 10 Years for Biomolecular Modeling and Simulation

PubMed Central

Jo, Sunhwan; Cheng, Xi; Lee, Jumin; Kim, Seonghoon; Park, Sang-Jun; Patel, Dhilon S.; Beaven, Andrew H.; Lee, Kyu Il; Rui, Huan; Roux, Benoît; MacKerell, Alexander D.; Klauda, Jeffrey B.; Qi, Yifei

2017-01-01

CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface that prepares complex biomolecular systems for molecular simulations. CHARMM-GUI creates input files for a number of programs including CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of simulations: (1) PDB Reader & Manipulator, Glycan Reader, and Ligand Reader & Modeler for reading and modifying molecules; (2) Quick MD Simulator, Membrane Builder, Nanodisc Builder, HMMM Builder, Monolayer Builder, Micelle Builder, and Hex Phase Builder for building all-atom simulation systems in various environments; (3) PACE CG Builder and Martini Maker for building coarse-grained simulation systems; (4) DEER Facilitator and MDFF/xMDFF Utilizer for experimentally guided simulations; (5) Implicit Solvent Modeler, PBEQ-Solver, and GCMC/BD Ion Simulator for implicit solvent related calculations; (6) Ligand Binder for ligand solvation and binding free energy simulations; and (7) Drude Prepper for preparation of simulations with the CHARMM Drude polarizable force field. Recently, new modules have been integrated into CHARMM-GUI, such as Glycolipid Modeler for generation of various glycolipid structures, and LPS Modeler for generation of lipopolysaccharide structures from various Gram-negative bacteria. These new features together with existing modules are expected to facilitate advanced molecular modeling and simulation thereby leading to an improved understanding of the molecular details of the structure and dynamics of complex biomolecular systems. Here, we briefly review these capabilities and discuss potential future directions in the CHARMM-GUI development project. PMID:27862047

CHARMM-GUI 10 years for biomolecular modeling and simulation.

PubMed

Jo, Sunhwan; Cheng, Xi; Lee, Jumin; Kim, Seonghoon; Park, Sang-Jun; Patel, Dhilon S; Beaven, Andrew H; Lee, Kyu Il; Rui, Huan; Park, Soohyung; Lee, Hui Sun; Roux, Benoît; MacKerell, Alexander D; Klauda, Jeffrey B; Qi, Yifei; Im, Wonpil

2017-06-05

CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface that prepares complex biomolecular systems for molecular simulations. CHARMM-GUI creates input files for a number of programs including CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of simulations: (1) PDB Reader & Manipulator, Glycan Reader, and Ligand Reader & Modeler for reading and modifying molecules; (2) Quick MD Simulator, Membrane Builder, Nanodisc Builder, HMMM Builder, Monolayer Builder, Micelle Builder, and Hex Phase Builder for building all-atom simulation systems in various environments; (3) PACE CG Builder and Martini Maker for building coarse-grained simulation systems; (4) DEER Facilitator and MDFF/xMDFF Utilizer for experimentally guided simulations; (5) Implicit Solvent Modeler, PBEQ-Solver, and GCMC/BD Ion Simulator for implicit solvent related calculations; (6) Ligand Binder for ligand solvation and binding free energy simulations; and (7) Drude Prepper for preparation of simulations with the CHARMM Drude polarizable force field. Recently, new modules have been integrated into CHARMM-GUI, such as Glycolipid Modeler for generation of various glycolipid structures, and LPS Modeler for generation of lipopolysaccharide structures from various Gram-negative bacteria. These new features together with existing modules are expected to facilitate advanced molecular modeling and simulation thereby leading to an improved understanding of the structure and dynamics of complex biomolecular systems. Here, we briefly review these capabilities and discuss potential future directions in the CHARMM-GUI development project. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Comparison of volume and surface area nonpolar solvation free energy terms for implicit solvent simulations.

PubMed

Lee, Michael S; Olson, Mark A

2013-07-28

Implicit solvent models for molecular dynamics simulations are often composed of polar and nonpolar terms. Typically, the nonpolar solvation free energy is approximated by the solvent-accessible-surface area times a constant factor. More sophisticated approaches incorporate an estimate of the attractive dispersion forces of the solvent and∕or a solvent-accessible volume cavitation term. In this work, we confirm that a single volume-based nonpolar term most closely fits the dispersion and cavitation forces obtained from benchmark explicit solvent simulations of fixed protein conformations. Next, we incorporated the volume term into molecular dynamics simulations and find the term is not universally suitable for folding up small proteins. We surmise that while mean-field cavitation terms such as volume and SASA often tilt the energy landscape towards native-like folds, they also may sporadically introduce bottlenecks into the folding pathway that hinder the progression towards the native state.

Comparison of volume and surface area nonpolar solvation free energy terms for implicit solvent simulations

NASA Astrophysics Data System (ADS)

Lee, Michael S.; Olson, Mark A.

2013-07-01

Implicit solvent models for molecular dynamics simulations are often composed of polar and nonpolar terms. Typically, the nonpolar solvation free energy is approximated by the solvent-accessible-surface area times a constant factor. More sophisticated approaches incorporate an estimate of the attractive dispersion forces of the solvent and/or a solvent-accessible volume cavitation term. In this work, we confirm that a single volume-based nonpolar term most closely fits the dispersion and cavitation forces obtained from benchmark explicit solvent simulations of fixed protein conformations. Next, we incorporated the volume term into molecular dynamics simulations and find the term is not universally suitable for folding up small proteins. We surmise that while mean-field cavitation terms such as volume and SASA often tilt the energy landscape towards native-like folds, they also may sporadically introduce bottlenecks into the folding pathway that hinder the progression towards the native state.

Mapping Conformational Dynamics of Proteins Using Torsional Dynamics Simulations

PubMed Central

Gangupomu, Vamshi K.; Wagner, Jeffrey R.; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan

2013-01-01

All-atom molecular dynamics simulations are widely used to study the flexibility of protein conformations. However, enhanced sampling techniques are required for simulating protein dynamics that occur on the millisecond timescale. In this work, we show that torsional molecular dynamics simulations enhance protein conformational sampling by performing conformational search in the low-frequency torsional degrees of freedom. In this article, we use our recently developed torsional-dynamics method called Generalized Newton-Euler Inverse Mass Operator (GNEIMO) to study the conformational dynamics of four proteins. We investigate the use of the GNEIMO method in simulations of the conformationally flexible proteins fasciculin and calmodulin, as well as the less flexible crambin and bovine pancreatic trypsin inhibitor. For the latter two proteins, the GNEIMO simulations with an implicit-solvent model reproduced the average protein structural fluctuations and sample conformations similar to those from Cartesian simulations with explicit solvent. The application of GNEIMO with replica exchange to the study of fasciculin conformational dynamics produced sampling of two of this protein’s experimentally established conformational substates. Conformational transition of calmodulin from the Ca2+-bound to the Ca2+-free conformation occurred readily with GNEIMO simulations. Moreover, the GNEIMO method generated an ensemble of conformations that satisfy about half of both short- and long-range interresidue distances obtained from NMR structures of holo to apo transitions in calmodulin. Although unconstrained all-atom Cartesian simulations have failed to sample transitions between the substates of fasciculin and calmodulin, GNEIMO simulations show the transitions in both systems. The relatively short simulation times required to capture these long-timescale conformational dynamics indicate that GNEIMO is a promising molecular-dynamics technique for studying domain motion in proteins. PMID:23663843

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

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

PubMed

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

2015-12-28

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

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

PubMed Central

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

2015-01-01

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

Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes.

PubMed

Chen, Fu; Sun, Huiyong; Wang, Junmei; Zhu, Feng; Liu, Hui; Wang, Zhe; Lei, Tailong; Li, Youyong; Hou, Tingjun

2018-06-21

Molecular docking provides a computationally efficient way to predict the atomic structural details of protein-RNA interactions (PRI), but accurate prediction of the three-dimensional structures and binding affinities for PRI is still notoriously difficult, partly due to the unreliability of the existing scoring functions for PRI. MM/PBSA and MM/GBSA are more theoretically rigorous than most scoring functions for protein-RNA docking, but their prediction performance for protein-RNA systems remains unclear. Here, we systemically evaluated the capability of MM/PBSA and MM/GBSA to predict the binding affinities and recognize the near-native binding structures for protein-RNA systems with different solvent models and interior dielectric constants (ϵ in ). For predicting the binding affinities, the predictions given by MM/GBSA based on the minimized structures in explicit solvent and the GBGBn1 model with ϵ in = 2 yielded the highest correlation with the experimental data. Moreover, the MM/GBSA calculations based on the minimized structures in implicit solvent and the GBGBn1 model distinguished the near-native binding structures within the top 10 decoys for 118 out of the 149 protein-RNA systems (79.2%). This performance is better than all docking scoring functions studied here. Therefore, the MM/GBSA rescoring is an efficient way to improve the prediction capability of scoring functions for protein-RNA systems. Published by Cold Spring Harbor Laboratory Press for the RNA Society.

VoroMQA: Assessment of protein structure quality using interatomic contact areas.

PubMed

Olechnovič, Kliment; Venclovas, Česlovas

2017-06-01

In the absence of experimentally determined protein structure many biological questions can be addressed using computational structural models. However, the utility of protein structural models depends on their quality. Therefore, the estimation of the quality of predicted structures is an important problem. One of the approaches to this problem is the use of knowledge-based statistical potentials. Such methods typically rely on the statistics of distances and angles of residue-residue or atom-atom interactions collected from experimentally determined structures. Here, we present VoroMQA (Voronoi tessellation-based Model Quality Assessment), a new method for the estimation of protein structure quality. Our method combines the idea of statistical potentials with the use of interatomic contact areas instead of distances. Contact areas, derived using Voronoi tessellation of protein structure, are used to describe and seamlessly integrate both explicit interactions between protein atoms and implicit interactions of protein atoms with solvent. VoroMQA produces scores at atomic, residue, and global levels, all in the fixed range from 0 to 1. The method was tested on the CASP data and compared to several other single-model quality assessment methods. VoroMQA showed strong performance in the recognition of the native structure and in the structural model selection tests, thus demonstrating the efficacy of interatomic contact areas in estimating protein structure quality. The software implementation of VoroMQA is freely available as a standalone application and as a web server at http://bioinformatics.lt/software/voromqa. Proteins 2017; 85:1131-1145. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides

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

None, None

Synthetic oligopeptides containing π-conjugated cores self-assemble novel materials with attractive electronic and photophysical properties. All-atom, explicit solvent molecular dynamics simulations of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp peptides were used to parameterize an implicit solvent model to simulate early-stage self-assembly. Under low-pH conditions, peptides assemble into β-sheet-like stacks with strongly favorable monomer association free energies of ΔF ≈ -25kBT. Aggregation at high-pH produces disordered aggregates destabilized by Coulombic repulsion between negatively charged Asp termini (ΔF ≈ -5kBT). In simulations of hundreds of monomers over 70 ns we observe the spontaneous formation of up to undecameric aggregates under low-pH conditions. Modeling assembly as a continuous-time Markovmore » process, we infer transition rates between different aggregate sizes and microsecond relaxation times for early-stage assembly. Our data suggests a hierarchical model of assembly in which peptides coalesce into small clusters over tens of nanoseconds followed by structural ripening and diffusion limited aggregation on longer time scales. This work provides new molecular-level understanding of early-stage assembly, and a means to study the impact of peptide sequence and aromatic core chemistry upon the thermodynamics, assembly kinetics, and morphology of the supramolecular aggregates.« less

Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides

DOE PAGES

None, None

2016-03-22

Synthetic oligopeptides containing π-conjugated cores self-assemble novel materials with attractive electronic and photophysical properties. All-atom, explicit solvent molecular dynamics simulations of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp peptides were used to parameterize an implicit solvent model to simulate early-stage self-assembly. Under low-pH conditions, peptides assemble into β-sheet-like stacks with strongly favorable monomer association free energies of ΔF ≈ -25kBT. Aggregation at high-pH produces disordered aggregates destabilized by Coulombic repulsion between negatively charged Asp termini (ΔF ≈ -5kBT). In simulations of hundreds of monomers over 70 ns we observe the spontaneous formation of up to undecameric aggregates under low-pH conditions. Modeling assembly as a continuous-time Markovmore » process, we infer transition rates between different aggregate sizes and microsecond relaxation times for early-stage assembly. Our data suggests a hierarchical model of assembly in which peptides coalesce into small clusters over tens of nanoseconds followed by structural ripening and diffusion limited aggregation on longer time scales. This work provides new molecular-level understanding of early-stage assembly, and a means to study the impact of peptide sequence and aromatic core chemistry upon the thermodynamics, assembly kinetics, and morphology of the supramolecular aggregates.« less

Photoisomers of Azobenzene Star with a Flat Core: Theoretical Insights into Multiple States from DFT and MD Perspective.

PubMed

Koch, Markus; Saphiannikova, Marina; Santer, Svetlana; Guskova, Olga

2017-09-21

This study focuses on comparing physical properties of photoisomers of an azobenzene star with benzene-1,3,5-tricarboxamide core. Three azobenzene arms of the molecule undergo a reversible trans-cis isomerization upon UV-vis light illumination giving rise to multiple states from the planar all-trans one, via two mixed states to the kinked all-cis isomer. Employing density functional theory, we characterize the structural and photophysical properties of each state indicating a role the planar core plays in the coupling between azobenzene chromophores. To characterize the light-triggered switching of solvophilicity/solvophobicity of the star, the difference in solvation free energy is calculated for the transfer of an azobenzene star from its gas phase to implicit or explicit solvents. For the latter case, classical all-atom molecular dynamics simulations of aqueous solutions of azobenzene star are performed employing the polymer consistent force field to shed light on the thermodynamics of explicit hydration as a function of the isomerization state and on the structuring of water around the star. From the analysis of two contributions to the free energy of hydration, the nonpolar van der Waals and the electrostatic terms, it is concluded that isomerization specificity largely determines the polarity of the molecule and the solute-solvent electrostatic interactions. This convertible hydrophilicity/hydrophobicity together with readjustable occupied volume and the surface area accessible to water, affects the self-assembly/disassembly of the azobenzene star with a flat core triggered by light.

Constant pH Molecular Dynamics of Proteins in Explicit Solvent with Proton Tautomerism

PubMed Central

Goh, Garrett B.; Hulbert, Benjamin S.; Zhou, Huiqing; Brooks, Charles L.

2015-01-01

pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMDMSλD). In the CPHMDMSλD framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMDMSλD simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMDMSλD framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules – proteins and nucleic acids is now possible. PMID:24375620

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

Zhou, Shenggao, E-mail: sgzhou@suda.edu.cn, E-mail: bli@math.ucsd.edu; Sun, Hui; Cheng, Li-Tien

Recent years have seen the initial success of a variational implicit-solvent model (VISM), implemented with a robust level-set method, in capturing efficiently different hydration states and providing quantitatively good estimation of solvation free energies of biomolecules. The level-set minimization of the VISM solvation free-energy functional of all possible solute-solvent interfaces or dielectric boundaries predicts an equilibrium biomolecular conformation that is often close to an initial guess. In this work, we develop a theory in the form of Langevin geometrical flow to incorporate solute-solvent interfacial fluctuations into the VISM. Such fluctuations are crucial to biomolecular conformational changes and binding process. Wemore » also develop a stochastic level-set method to numerically implement such a theory. We describe the interfacial fluctuation through the “normal velocity” that is the solute-solvent interfacial force, derive the corresponding stochastic level-set equation in the sense of Stratonovich so that the surface representation is independent of the choice of implicit function, and develop numerical techniques for solving such an equation and processing the numerical data. We apply our computational method to study the dewetting transition in the system of two hydrophobic plates and a hydrophobic cavity of a synthetic host molecule cucurbit[7]uril. Numerical simulations demonstrate that our approach can describe an underlying system jumping out of a local minimum of the free-energy functional and can capture dewetting transitions of hydrophobic systems. In the case of two hydrophobic plates, we find that the wavelength of interfacial fluctuations has a strong influence to the dewetting transition. In addition, we find that the estimated energy barrier of the dewetting transition scales quadratically with the inter-plate distance, agreeing well with existing studies of molecular dynamics simulations. Our work is a first step toward the inclusion of fluctuations into the VISM and understanding the impact of interfacial fluctuations on biomolecular solvation with an implicit-solvent approach.« less

Optimization of the GBMV2 implicit solvent force field for accurate simulation of protein conformational equilibria.

PubMed

Lee, Kuo Hao; Chen, Jianhan

2017-06-15

Accurate treatment of solvent environment is critical for reliable simulations of protein conformational equilibria. Implicit treatment of solvation, such as using the generalized Born (GB) class of models arguably provides an optimal balance between computational efficiency and physical accuracy. Yet, GB models are frequently plagued by a tendency to generate overly compact structures. The physical origins of this drawback are relatively well understood, and the key to a balanced implicit solvent protein force field is careful optimization of physical parameters to achieve a sufficient level of cancellation of errors. The latter has been hampered by the difficulty of generating converged conformational ensembles of non-trivial model proteins using the popular replica exchange sampling technique. Here, we leverage improved sampling efficiency of a newly developed multi-scale enhanced sampling technique to re-optimize the generalized-Born with molecular volume (GBMV2) implicit solvent model with the CHARMM36 protein force field. Recursive optimization of key GBMV2 parameters (such as input radii) and protein torsion profiles (via the CMAP torsion cross terms) has led to a more balanced GBMV2 protein force field that recapitulates the structures and stabilities of both helical and β-hairpin model peptides. Importantly, this force field appears to be free of the over-compaction bias, and can generate structural ensembles of several intrinsically disordered proteins of various lengths that seem highly consistent with available experimental data. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

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

PubMed

Ritchie, Andrew W; Webb, Lauren J

2014-07-17

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

FT-IR study and solvent-implicit and explicit effect on stepwise tautomerism of Guanylurea: M06-2X as a case of study

NASA Astrophysics Data System (ADS)

Karimzadeh, Morteza; Manouchehri, Neda; Saberi, Dariush; Niknam, Khodabakhsh

2018-06-01

All 66 conformers of guanylurea were optimized and frequency calculations were performed at M06-2X/6-311++G(d,p) level of theory. Theses conformers were categorized into five tautomers, and the most stable conformer of each tautomer were found. Geometrical parameters indicated that these tautomers have almost planar structure. Complete stepwise tautomerism were studied through both intramolecular proton transfer routs and internal rotations. Results indicated that the proton transfer routs involving four-membered heterocyclic structures were rate-determining steps. Also, intramolecular proton movement having six-membered transition state structures had very low energy barrier comparable to the transition states of internal rotation routs. Differentiation of studied tautomers could easily be done through their FT-IR spectra in the range of 3200 to 3900 cm-1 by comparing absorption bands and intensity of peaks. Solvent-implicit effects on the stability of tautomers were also studied through re-optimization and frequency calculation in four solvents. Water, DMSO, acetone and toluene had stabilization effect on all considered tautomers, but the order of stabilization effect was as follows: water > DMSO > acetone > toluene. Finally, solvent-explicit, base-explicit and acid-explicit effect were also studied by taking place of studied tautomer nearside of acid, base or solvent and optimization of them. Frequency calculation for proton movement by contribution of explicit effect showed that formic acid had a very strong effect on proton transfer from tautomer A1 to tautomer D8 by lowering the energy barrier from 42.57 to 0.8 kcal/mol. In addition, ammonia-explicit effect was found to lower the barrier from 42.57 to 22.46 kcal/mol, but this effect is lower than that of water and methanol-explicit effect.

Probing energetics of Abeta fibril elongation by molecular dynamics simulations.

PubMed

Takeda, Takako; Klimov, Dmitri K

2009-06-03

Using replica exchange molecular dynamics simulations and an all-atom implicit solvent model, we probed the energetics of Abeta(10-40) fibril growth. The analysis of the interactions between incoming Abeta peptides and the fibril led us to two conclusions. First, considerable variations in fibril binding propensities are observed along the Abeta sequence. The peptides in the fibril and those binding to its edge interact primarily through their N-termini. Therefore, the mutations affecting the Abeta positions 10-23 are expected to have the largest impact on fibril elongation compared with those occurring in the C-terminus and turn. Second, we performed weak perturbations of the binding free energy landscape by scanning partial deletions of side-chain interactions at various Abeta sequence positions. The results imply that strong side-chain interactions--in particular, hydrophobic contacts--impede fibril growth by favoring disordered docking of incoming peptides. Therefore, fibril elongation may be promoted by moderate reduction of Abeta hydrophobicity. The comparison with available experimental data is presented.

Modeling the absorption spectrum of the permanganate ion in vacuum and in aqueous solution

NASA Astrophysics Data System (ADS)

Olsen, Jógvan Magnus Haugaard; Hedegård, Erik Donovan

The absorption spectrum of the MnO$_{4}$$^{-}$ ion has been a test-bed for quantum-chemical methods over the last decades. Its correct description requires highly-correlated multiconfigurational methods, which are incompatible with the inclusion of finite-temperature and solvent effects due to their high computational demands. Therefore, implicit solvent models are usually employed. Here we show that implicit solvent models are not sufficiently accurate to model the solvent shift of MnO$_{4}$$^{-}$, and we analyze the origins of their failure. We obtain the correct solvent shift for MnO$_{4}$$^{-}$ in aqueous solution by employing the polarizable embedding (PE) model combined with a range-separated complete active space short-range density functional theory method (CAS-srDFT). Finite-temperature effects are taken into account by averaging over structures obtained from ab initio molecular dynamics simulations. The explicit treatment of finite-temperature and solvent effects facilitates the interpretation of the bands in the low-energy region of the MnO$_{4}$$^{-}$ absorption spectrum, whose assignment has been elusive.

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.

Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.

PubMed

Goh, Garrett B; Hulbert, Benjamin S; Zhou, Huiqing; Brooks, Charles L

2014-07-01

pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMD(MSλD)). In the CPHMD(MSλD) framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMD(MSλD) simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal protein L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMD(MSλD) framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules-proteins and nucleic acids is now possible. © 2013 Wiley Periodicals, Inc.

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

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

NASA Astrophysics Data System (ADS)

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

2014-03-01

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

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.

Explicit treatment of active-site waters enhances quantum mechanical/implicit solvent scoring: Inhibition of CDK2 by new pyrazolo[1,5-a]pyrimidines.

PubMed

Hylsová, Michaela; Carbain, Benoit; Fanfrlík, Jindřich; Musilová, Lenka; Haldar, Susanta; Köprülüoğlu, Cemal; Ajani, Haresh; Brahmkshatriya, Pathik S; Jorda, Radek; Kryštof, Vladimír; Hobza, Pavel; Echalier, Aude; Paruch, Kamil; Lepšík, Martin

2017-01-27

We present comprehensive testing of solvent representation in quantum mechanics (QM)-based scoring of protein-ligand affinities. To this aim, we prepared 21 new inhibitors of cyclin-dependent kinase 2 (CDK2) with the pyrazolo[1,5-a]pyrimidine core, whose activities spanned three orders of magnitude. The crystal structure of a potent inhibitor bound to the active CDK2/cyclin A complex revealed that the biphenyl substituent at position 5 of the pyrazolo[1,5-a]pyrimidine scaffold was located in a previously unexplored pocket and that six water molecules resided in the active site. Using molecular dynamics, protein-ligand interactions and active-site water H-bond networks as well as thermodynamics were probed. Thereafter, all the inhibitors were scored by the QM approach utilizing the COSMO implicit solvent model. Such a standard treatment failed to produce a correlation with the experiment (R 2  = 0.49). However, the addition of the active-site waters resulted in significant improvement (R 2  = 0.68). The activities of the compounds could thus be interpreted by taking into account their specific noncovalent interactions with CDK2 and the active-site waters. In summary, using a combination of several experimental and theoretical approaches we demonstrate that the inclusion of explicit solvent effects enhance QM/COSMO scoring to produce a reliable structure-activity relationship with physical insights. More generally, this approach is envisioned to contribute to increased accuracy of the computational design of novel inhibitors. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

FT-IR study and solvent-implicit and explicit effect on stepwise tautomerism of Guanylurea: M06-2X as a case of study.

PubMed

Karimzadeh, Morteza; Manouchehri, Neda; Saberi, Dariush; Niknam, Khodabakhsh

2018-06-15

All 66 conformers of guanylurea were optimized and frequency calculations were performed at M06-2X/6-311++G(d,p) level of theory. Theses conformers were categorized into five tautomers, and the most stable conformer of each tautomer were found. Geometrical parameters indicated that these tautomers have almost planar structure. Complete stepwise tautomerism were studied through both intramolecular proton transfer routs and internal rotations. Results indicated that the proton transfer routs involving four-membered heterocyclic structures were rate-determining steps. Also, intramolecular proton movement having six-membered transition state structures had very low energy barrier comparable to the transition states of internal rotation routs. Differentiation of studied tautomers could easily be done through their FT-IR spectra in the range of 3200 to 3900cm -1 by comparing absorption bands and intensity of peaks. Solvent-implicit effects on the stability of tautomers were also studied through re-optimization and frequency calculation in four solvents. Water, DMSO, acetone and toluene had stabilization effect on all considered tautomers, but the order of stabilization effect was as follows: water>DMSO>acetone>toluene. Finally, solvent-explicit, base-explicit and acid-explicit effect were also studied by taking place of studied tautomer nearside of acid, base or solvent and optimization of them. Frequency calculation for proton movement by contribution of explicit effect showed that formic acid had a very strong effect on proton transfer from tautomer A1 to tautomer D8 by lowering the energy barrier from 42.57 to 0.8kcal/mol. In addition, ammonia-explicit effect was found to lower the barrier from 42.57 to 22.46kcal/mol, but this effect is lower than that of water and methanol-explicit effect. Copyright © 2018 Elsevier B.V. All rights reserved.

Virtual screening using molecular simulations.

PubMed

Yang, Tianyi; Wu, Johnny C; Yan, Chunli; Wang, Yuanfeng; Luo, Ray; Gonzales, Michael B; Dalby, Kevin N; Ren, Pengyu

2011-06-01

Effective virtual screening relies on our ability to make accurate prediction of protein-ligand binding, which remains a great challenge. In this work, utilizing the molecular-mechanics Poisson-Boltzmann (or Generalized Born) surface area approach, we have evaluated the binding affinity of a set of 156 ligands to seven families of proteins, trypsin β, thrombin α, cyclin-dependent kinase (CDK), cAMP-dependent kinase (PKA), urokinase-type plasminogen activator, β-glucosidase A, and coagulation factor Xa. The effect of protein dielectric constant in the implicit-solvent model on the binding free energy calculation is shown to be important. The statistical correlations between the binding energy calculated from the implicit-solvent approach and experimental free energy are in the range of 0.56-0.79 across all the families. This performance is better than that of typical docking programs especially given that the latter is directly trained using known binding data whereas the molecular mechanics is based on general physical parameters. Estimation of entropic contribution remains the barrier to accurate free energy calculation. We show that the traditional rigid rotor harmonic oscillator approximation is unable to improve the binding free energy prediction. Inclusion of conformational restriction seems to be promising but requires further investigation. On the other hand, our preliminary study suggests that implicit-solvent based alchemical perturbation, which offers explicit sampling of configuration entropy, can be a viable approach to significantly improve the prediction of binding free energy. Overall, the molecular mechanics approach has the potential for medium to high-throughput computational drug discovery. Copyright © 2011 Wiley-Liss, Inc.

Thermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils.

PubMed

O'Brien, Edward P; Okamoto, Yuko; Straub, John E; Brooks, Bernard R; Thirumalai, D

2009-10-29

The mechanism of addition of a soluble unstructured monomer to a preformed ordered amyloid fibril is a complex process. On the basis of the kinetics of monomer disassociation of Abeta(1-40) from the amyloid fibril, it has been suggested that deposition is a multistep process involving a rapid reversible association of the unstructured monomer to the fibril surface (docking) followed by a slower conformational rearrangement leading to the incorporation onto the underlying fibril lattice (locking). By exploiting the vast time scale separation between the dock and lock processes and using molecular dynamics simulation of deposition of the disordered peptide fragment (35)MVGGVV(40) from the Abeta peptide onto the fibril with known crystal structure, we provide a thermodynamic basis for the dock-lock mechanism of fibril growth. Free energy profiles, computed using implicit solvent model and enhanced sampling methods with the distance (delta(C)) between the center of mass of the peptide and the fibril surface as the order parameter, show three distinct basins of attraction. When delta(C) is large, the monomer is compact and unstructured and the favorable interactions with the fibril results in stretching of the peptide at delta(C) approximately 13 A. As delta(C) is further decreased, the peptide docks onto the fibril surface with a structure that is determined by a balance between intrapeptide and peptide fibril interactions. At delta(C) approximately 4 A, a value that is commensurate with the spacing between beta-strands in the fibril, the monomer expands and locks onto the fibril. Using simulations with implicit solvent model and all atom molecular dynamics in explicit water, we show that the locked monomer, which interacts with the underlying fibril, undergoes substantial conformational fluctuations and is not stable. The cosolutes urea and TMAO destabilize the unbound phase and stabilize the docked phase. Interestingly, small crowding particles enhance the stability of the fibril-bound monomer only marginally. We predict that the experimentally measurable critical monomer concentration, C(R), at which the soluble unbound monomer is in equilibrium with the ordered fibril, increases sharply as temperature is increased under all solution conditions.

Surface Passivation in Empirical Tight Binding

NASA Astrophysics Data System (ADS)

He, Yu; Tan, Yaohua; Jiang, Zhengping; Povolotskyi, Michael; Klimeck, Gerhard; Kubis, Tillmann

2016-03-01

Empirical Tight Binding (TB) methods are widely used in atomistic device simulations. Existing TB methods to passivate dangling bonds fall into two categories: 1) Method that explicitly includes passivation atoms is limited to passivation with atoms and small molecules only. 2) Method that implicitly incorporates passivation does not distinguish passivation atom types. This work introduces an implicit passivation method that is applicable to any passivation scenario with appropriate parameters. This method is applied to a Si quantum well and a Si ultra-thin body transistor oxidized with SiO2 in several oxidation configurations. Comparison with ab-initio results and experiments verifies the presented method. Oxidation configurations that severely hamper the transistor performance are identified. It is also shown that the commonly used implicit H atom passivation overestimates the transistor performance.

Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies.

PubMed

Bardhan, Jaydeep P; Jungwirth, Pavel; Makowski, Lee

2012-09-28

Two mechanisms have been proposed to drive asymmetric solvent response to a solute charge: a static potential contribution similar to the liquid-vapor potential, and a steric contribution associated with a water molecule's structure and charge distribution. In this work, we use free-energy perturbation molecular-dynamics calculations in explicit water to show that these mechanisms act in complementary regimes; the large static potential (∼44 kJ/mol/e) dominates asymmetric response for deeply buried charges, and the steric contribution dominates for charges near the solute-solvent interface. Therefore, both mechanisms must be included in order to fully account for asymmetric solvation in general. Our calculations suggest that the steric contribution leads to a remarkable deviation from the popular "linear response" model in which the reaction potential changes linearly as a function of charge. In fact, the potential varies in a piecewise-linear fashion, i.e., with different proportionality constants depending on the sign of the charge. This discrepancy is significant even when the charge is completely buried, and holds for solutes larger than single atoms. Together, these mechanisms suggest that implicit-solvent models can be improved using a combination of affine response (an offset due to the static potential) and piecewise-linear response (due to the steric contribution).

Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies

PubMed Central

Bardhan, Jaydeep P.; Jungwirth, Pavel; Makowski, Lee

2012-01-01

Two mechanisms have been proposed to drive asymmetric solvent response to a solute charge: a static potential contribution similar to the liquid-vapor potential, and a steric contribution associated with a water molecule's structure and charge distribution. In this work, we use free-energy perturbation molecular-dynamics calculations in explicit water to show that these mechanisms act in complementary regimes; the large static potential (∼44 kJ/mol/e) dominates asymmetric response for deeply buried charges, and the steric contribution dominates for charges near the solute-solvent interface. Therefore, both mechanisms must be included in order to fully account for asymmetric solvation in general. Our calculations suggest that the steric contribution leads to a remarkable deviation from the popular “linear response” model in which the reaction potential changes linearly as a function of charge. In fact, the potential varies in a piecewise-linear fashion, i.e., with different proportionality constants depending on the sign of the charge. This discrepancy is significant even when the charge is completely buried, and holds for solutes larger than single atoms. Together, these mechanisms suggest that implicit-solvent models can be improved using a combination of affine response (an offset due to the static potential) and piecewise-linear response (due to the steric contribution). PMID:23020318

An ellipsoid-chain model for conjugated polymer solutions

NASA Astrophysics Data System (ADS)

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

2012-02-01

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

Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation

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

Yu, Yuqi; Wang, Jinan; Shao, Qiang, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn

2015-03-28

The application of temperature replica exchange molecular dynamics (REMD) simulation on protein motion is limited by its huge requirement of computational resource, particularly when explicit solvent model is implemented. In the previous study, we developed a velocity-scaling optimized hybrid explicit/implicit solvent REMD method with the hope to reduce the temperature (replica) number on the premise of maintaining high sampling efficiency. In this study, we utilized this method to characterize and energetically identify the conformational transition pathway of a protein model, the N-terminal domain of calmodulin. In comparison to the standard explicit solvent REMD simulation, the hybrid REMD is much lessmore » computationally expensive but, meanwhile, gives accurate evaluation of the structural and thermodynamic properties of the conformational transition which are in well agreement with the standard REMD simulation. Therefore, the hybrid REMD could highly increase the computational efficiency and thus expand the application of REMD simulation to larger-size protein systems.« less

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.

Structure-wise discrimination of adenine and guanine by proteins on the basis of their nonbonded interactions.

PubMed

Usha, S; Selvaraj, S

2015-01-01

We have analyzed the nonbonded interactions of the structurally similar moieties, adenine and guanine forming complexes with proteins. The results comprise (a) the amino acid-ligand atom preferences, (b) solvent accessibility of ligand atoms before and after complex formation with proteins, and (c) preferred amino acid residue atoms involved in the interactions. We have observed that the amino acid preferences involved in the hydrogen bonding interactions vary for adenine and guanine. The structural variation between the purine atoms is clearly reflected by their burial tendency in the solvent environment. Correlation of the mean amino acid preference values show the variation that exists between adenine and guanine preferences of all the amino acid residues. All our observations provide evidence for the discriminating nature of the proteins in recognizing adenine and guanine.

All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water.

PubMed

Huang, Yandong; Chen, Wei; Wallace, Jason A; Shen, Jana

2016-11-08

Development of a pH stat to properly control solution pH in biomolecular simulations has been a long-standing goal in the community. Toward this goal recent years have witnessed the emergence of the so-called constant pH molecular dynamics methods. However, the accuracy and generality of these methods have been hampered by the use of implicit-solvent models or truncation-based electrostatic schemes. Here we report the implementation of the particle mesh Ewald (PME) scheme into the all-atom continuous constant pH molecular dynamics (CpHMD) method, enabling CpHMD to be performed with a standard MD engine at a fractional added computational cost. We demonstrate the performance using pH replica-exchange CpHMD simulations with titratable water for a stringent test set of proteins, HP36, BBL, HEWL, and SNase. With the sampling time of 10 ns per replica, most pK a 's are converged, yielding the average absolute and root-mean-square deviations of 0.61 and 0.77, respectively, from experiment. Linear regression of the calculated vs experimental pK a shifts gives a correlation coefficient of 0.79, a slope of 1, and an intercept near 0. Analysis reveals inadequate sampling of structure relaxation accompanying a protonation-state switch as a major source of the remaining errors, which are reduced as simulation prolongs. These data suggest PME-based CpHMD can be used as a general tool for pH-controlled simulations of macromolecular systems in various environments, enabling atomic insights into pH-dependent phenomena involving not only soluble proteins but also transmembrane proteins, nucleic acids, surfactants, and polysaccharides.

Modeling the thermal unfolding 2DIR spectra of a β-hairpin peptide based on the implicit solvent MD simulation.

PubMed

Wu, Tianmin; Yang, Lijiang; Zhang, Ruiting; Shao, Qiang; Zhuang, Wei

2013-07-25

We simulated the equilibrium isotope-edited FTIR and 2DIR spectra of a β-hairpin peptide trpzip2 at a series of temperatures. The simulation was based on the configuration distributions generated using the GB(OBC) implicit solvent model and the integrated tempering sampling (ITS) technique. A soaking procedure was adapted to generate the peptide in explicit solvent configurations for the spectroscopy calculations. The nonlinear exciton propagation (NEP) method was then used to calculate the spectra. Agreeing with the experiments, the intensities and ellipticities of the isotope-shifted peaks in our simulated signals have the site-specific temperature dependences, which suggest the inhomogeneous local thermal stabilities along the peptide chain. Our simulation thus proposes a cost-effective means to understand a peptide's conformational change and related IR spectra across its thermal unfolding transition.

Search for Length Dependent Stable Structures of Polyglutamaine Proteins with Replica Exchange Molecular Dynamic

NASA Astrophysics Data System (ADS)

Kluber, Alexander; Hayre, Robert; Cox, Daniel

2012-02-01

Motivated by the need to find beta-structure aggregation nuclei for the polyQ diseases such as Huntington's, we have undertaken a search for length dependent structure in model polyglutamine proteins. We use the Onufriev-Bashford-Case (OBC) generalized Born implicit solvent GPU based AMBER11 molecular dynamics with the parm96 force field coupled with a replica exchange method to characterize monomeric strands of polyglutamine as a function of chain length and temperature. This force field and solvation method has been shown among other methods to accurately reproduce folded metastability in certain small peptides, and to yield accurately de novo folded structures in a millisecond time-scale protein. Using GPU molecular dynamics we can sample out into the microsecond range. Additionally, explicit solvent runs will be used to verify results from the implicit solvent runs. We will assess order using measures of secondary structure and hydrogen bond content.

Solvent effects on the properties of hyperbranched polythiophenes.

PubMed

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

2016-09-21

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

Quantum Dynamics in Continuum for Proton Transport I: Basic Formulation.

PubMed

Chen, Duan; Wei, Guo-Wei

2013-01-01

Proton transport is one of the most important and interesting phenomena in living cells. The present work proposes a multiscale/multiphysics model for the understanding of the molecular mechanism of proton transport in transmembrane proteins. We describe proton dynamics quantum mechanically via a density functional approach while implicitly model other solvent ions as a dielectric continuum to reduce the number of degrees of freedom. The densities of all other ions in the solvent are assumed to obey the Boltzmann distribution. The impact of protein molecular structure and its charge polarization on the proton transport is considered explicitly at the atomic level. We formulate a total free energy functional to put proton kinetic and potential energies as well as electrostatic energy of all ions on an equal footing. The variational principle is employed to derive nonlinear governing equations for the proton transport system. Generalized Poisson-Boltzmann equation and Kohn-Sham equation are obtained from the variational framework. Theoretical formulations for the proton density and proton conductance are constructed based on fundamental principles. The molecular surface of the channel protein is utilized to split the discrete protein domain and the continuum solvent domain, and facilitate the multiscale discrete/continuum/quantum descriptions. A number of mathematical algorithms, including the Dirichlet to Neumann mapping, matched interface and boundary method, Gummel iteration, and Krylov space techniques are utilized to implement the proposed model in a computationally efficient manner. The Gramicidin A (GA) channel is used to demonstrate the performance of the proposed proton transport model and validate the efficiency of proposed mathematical algorithms. The electrostatic characteristics of the GA channel is analyzed with a wide range of model parameters. The proton conductances are studied over a number of applied voltages and reference concentrations. A comparison with experimental data verifies the present model predictions and validates the proposed model.

Interactions between Nanoparticles and Polymer Brushes: Molecular Dynamics Simulations and Self-consistent Field Theory Calculations

NASA Astrophysics Data System (ADS)

Cheng, Shengfeng; Wen, Chengyuan; Egorov, Sergei

2015-03-01

Molecular dynamics simulations and self-consistent field theory calculations are employed to study the interactions between a nanoparticle and a polymer brush at various densities of chains grafted to a plane. Simulations with both implicit and explicit solvent are performed. In either case the nanoparticle is loaded to the brush at a constant velocity. Then a series of simulations are performed to compute the force exerted on the nanoparticle that is fixed at various distances from the grafting plane. The potential of mean force is calculated and compared to the prediction based on a self-consistent field theory. Our simulations show that the explicit solvent leads to effects that are not captured in simulations with implicit solvent, indicating the importance of including explicit solvent in molecular simulations of such systems. Our results also demonstrate an interesting correlation between the force on the nanoparticle and the density profile of the brush. We gratefully acknowledge the support of NVIDIA Corporation with the donation of the Tesla K40 GPU used for this research.

A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water

PubMed Central

Wu, Xiongwu; Brooks, Bernard R.

2015-01-01

Chemical and thermodynamic equilibrium of multiple states is a fundamental phenomenon in biology systems and has been the focus of many experimental and computational studies. This work presents a simulation method to directly study the equilibrium of multiple states. This method constructs a virtual mixture of multiple states (VMMS) to sample the conformational space of all chemical states simultaneously. The VMMS system consists of multiple subsystems, one for each state. The subsystem contains a solute and a solvent environment. The solute molecules in all subsystems share the same conformation but have their own solvent environments. Transition between states is implicated by the change of their molar fractions. Simulation of a VMMS system allows efficient calculation of relative free energies of all states, which in turn determine their equilibrium molar fractions. For systems with a large number of state transition sites, an implicit site approximation is introduced to minimize the cost of simulation. A direct application of the VMMS method is for constant pH simulation to study protonation equilibrium. Applying the VMMS method to a heptapeptide of 3 ionizable residues, we calculated the pKas of those residues both with all explicit states and with implicit sites and obtained consistent results. For mouse epidermal growth factor of 9 ionizable groups, our VMMS simulations with implicit sites produced pKas of all 9 ionizable groups and the results agree qualitatively with NMR measurement. This example demonstrates the VMMS method can be applied to systems of a large number of ionizable groups and the computational cost scales linearly with the number of ionizable groups. For one of the most challenging systems in constant pH calculation, SNase Δ+PHS/V66K, our VMMS simulation shows that it is the state-dependent water penetration that causes the large deviation in lysine66’s pKa. PMID:26506245

A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water.

PubMed

Wu, Xiongwu; Brooks, Bernard R

2015-10-01

Chemical and thermodynamic equilibrium of multiple states is a fundamental phenomenon in biology systems and has been the focus of many experimental and computational studies. This work presents a simulation method to directly study the equilibrium of multiple states. This method constructs a virtual mixture of multiple states (VMMS) to sample the conformational space of all chemical states simultaneously. The VMMS system consists of multiple subsystems, one for each state. The subsystem contains a solute and a solvent environment. The solute molecules in all subsystems share the same conformation but have their own solvent environments. Transition between states is implicated by the change of their molar fractions. Simulation of a VMMS system allows efficient calculation of relative free energies of all states, which in turn determine their equilibrium molar fractions. For systems with a large number of state transition sites, an implicit site approximation is introduced to minimize the cost of simulation. A direct application of the VMMS method is for constant pH simulation to study protonation equilibrium. Applying the VMMS method to a heptapeptide of 3 ionizable residues, we calculated the pKas of those residues both with all explicit states and with implicit sites and obtained consistent results. For mouse epidermal growth factor of 9 ionizable groups, our VMMS simulations with implicit sites produced pKas of all 9 ionizable groups and the results agree qualitatively with NMR measurement. This example demonstrates the VMMS method can be applied to systems of a large number of ionizable groups and the computational cost scales linearly with the number of ionizable groups. For one of the most challenging systems in constant pH calculation, SNase Δ+PHS/V66K, our VMMS simulation shows that it is the state-dependent water penetration that causes the large deviation in lysine66's pKa.

DIFFUSED SOLUTE-SOLVENT INTERFACE WITH POISSON-BOLTZMANN ELECTROSTATICS: FREE-ENERGY VARIATION AND SHARP-INTERFACE LIMIT.

PubMed

Li, B O; Liu, Yuan

A phase-field free-energy functional for the solvation of charged molecules (e.g., proteins) in aqueous solvent (i.e., water or salted water) is constructed. The functional consists of the solute volumetric and solute-solvent interfacial energies, the solute-solvent van der Waals interaction energy, and the continuum electrostatic free energy described by the Poisson-Boltzmann theory. All these are expressed in terms of phase fields that, for low free-energy conformations, are close to one value in the solute phase and another in the solvent phase. A key property of the model is that the phase-field interpolation of dielectric coefficient has the vanishing derivative at both solute and solvent phases. The first variation of such an effective free-energy functional is derived. Matched asymptotic analysis is carried out for the resulting relaxation dynamics of the diffused solute-solvent interface. It is shown that the sharp-interface limit is exactly the variational implicit-solvent model that has successfully captured capillary evaporation in hydrophobic confinement and corresponding multiple equilibrium states of underlying biomolecular systems as found in experiment and molecular dynamics simulations. Our phase-field approach and analysis can be used to possibly couple the description of interfacial fluctuations for efficient numerical computations of biomolecular interactions.

SAMPL5: 3D-RISM partition coefficient calculations with partial molar volume corrections and solute conformational sampling.

PubMed

Luchko, Tyler; Blinov, Nikolay; Limon, Garrett C; Joyce, Kevin P; Kovalenko, Andriy

2016-11-01

Implicit solvent methods for classical molecular modeling are frequently used to provide fast, physics-based hydration free energies of macromolecules. Less commonly considered is the transferability of these methods to other solvents. The Statistical Assessment of Modeling of Proteins and Ligands 5 (SAMPL5) distribution coefficient dataset and the accompanying explicit solvent partition coefficient reference calculations provide a direct test of solvent model transferability. Here we use the 3D reference interaction site model (3D-RISM) statistical-mechanical solvation theory, with a well tested water model and a new united atom cyclohexane model, to calculate partition coefficients for the SAMPL5 dataset. The cyclohexane model performed well in training and testing ([Formula: see text] for amino acid neutral side chain analogues) but only if a parameterized solvation free energy correction was used. In contrast, the same protocol, using single solute conformations, performed poorly on the SAMPL5 dataset, obtaining [Formula: see text] compared to the reference partition coefficients, likely due to the much larger solute sizes. Including solute conformational sampling through molecular dynamics coupled with 3D-RISM (MD/3D-RISM) improved agreement with the reference calculation to [Formula: see text]. Since our initial calculations only considered partition coefficients and not distribution coefficients, solute sampling provided little benefit comparing against experiment, where ionized and tautomer states are more important. Applying a simple [Formula: see text] correction improved agreement with experiment from [Formula: see text] to [Formula: see text], despite a small number of outliers. Better agreement is possible by accounting for tautomers and improving the ionization correction.

SAMPL5: 3D-RISM partition coefficient calculations with partial molar volume corrections and solute conformational sampling

NASA Astrophysics Data System (ADS)

Luchko, Tyler; Blinov, Nikolay; Limon, Garrett C.; Joyce, Kevin P.; Kovalenko, Andriy

2016-11-01

Implicit solvent methods for classical molecular modeling are frequently used to provide fast, physics-based hydration free energies of macromolecules. Less commonly considered is the transferability of these methods to other solvents. The Statistical Assessment of Modeling of Proteins and Ligands 5 (SAMPL5) distribution coefficient dataset and the accompanying explicit solvent partition coefficient reference calculations provide a direct test of solvent model transferability. Here we use the 3D reference interaction site model (3D-RISM) statistical-mechanical solvation theory, with a well tested water model and a new united atom cyclohexane model, to calculate partition coefficients for the SAMPL5 dataset. The cyclohexane model performed well in training and testing (R=0.98 for amino acid neutral side chain analogues) but only if a parameterized solvation free energy correction was used. In contrast, the same protocol, using single solute conformations, performed poorly on the SAMPL5 dataset, obtaining R=0.73 compared to the reference partition coefficients, likely due to the much larger solute sizes. Including solute conformational sampling through molecular dynamics coupled with 3D-RISM (MD/3D-RISM) improved agreement with the reference calculation to R=0.93. Since our initial calculations only considered partition coefficients and not distribution coefficients, solute sampling provided little benefit comparing against experiment, where ionized and tautomer states are more important. Applying a simple pK_{ {a}} correction improved agreement with experiment from R=0.54 to R=0.66, despite a small number of outliers. Better agreement is possible by accounting for tautomers and improving the ionization correction.

Contribution of Charged Groups to the Enthalpic Stabilization of the Folded States of Globular Proteins

PubMed Central

Dadarlat, Voichita M.; Post, Carol Beth

2016-01-01

In this paper we use the results from all atom MD simulations of proteins and peptides to assess individual contribution of charged atomic groups to the enthalpic stability of the native state of globular proteins and investigate how the distribution of charged atomic groups in terms of solvent accessibility relates to protein enthalpic stability. The contributions of charged groups is calculated using a comparison of nonbonded interaction energy terms from equilibrium simulations of charged amino acid dipeptides in water (the “unfolded state”) and charged amino acids in globular proteins (the “folded state”). Contrary to expectation, the analysis shows that many buried, charged atomic groups contribute favorably to protein enthalpic stability. The strongest enthalpic contributions favoring the folded state come from the carboxylate (COO−) groups of either Glu or Asp. The contributions from Arg guanidinium groups are generally somewhat stabilizing, while NH3+ groups from Lys contribute little toward stabilizing the folded state. The average enthalpic gain due to the transfer of a methyl group in an apolar amino acid from solution to the protein interior is described for comparison. Notably, charged groups that are less exposed to solvent contribute more favorably to protein native-state enthalpic stability than charged groups that are solvent exposed. While solvent reorganization/release has favorable contributions to folding for all charged atomic groups, the variation in folded state stability among proteins comes mainly from the change in the nonbonded interaction energy of charged groups between the unfolded and folded states. A key outcome is that the calculated enthalpic stabilization is found to be inversely proportional to the excess charge density on the surface, in support of an hypothesis proposed previously. PMID:18303881

The Utility of Implicit Learning in the Teaching of Rules

ERIC Educational Resources Information Center

Saetrevik, Bjorn; Reber, Rolf; Sannum, Petter

2006-01-01

The potential impact of implicit learning on education has been repeatedly stressed, though little research has examined this connection directly. The current paper describes two experiments that, inspired by artificial grammar learning experiments, examine the utility of implicit learning as a method for teaching atomic bonding rules to 11-12…

Predicting hydration free energies with a hybrid QM/MM approach

PubMed Central

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

2014-01-01

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

A semi-implicit augmented IIM for Navier–Stokes equations with open, traction, or free boundary conditions

PubMed Central

Li, Zhilin; Xiao, Li; Cai, Qin; Zhao, Hongkai; Luo, Ray

2016-01-01

In this paper, a new Navier–Stokes solver based on a finite difference approximation is proposed to solve incompressible flows on irregular domains with open, traction, and free boundary conditions, which can be applied to simulations of fluid structure interaction, implicit solvent model for biomolecular applications and other free boundary or interface problems. For some problems of this type, the projection method and the augmented immersed interface method (IIM) do not work well or does not work at all. The proposed new Navier–Stokes solver is based on the local pressure boundary method, and a semi-implicit augmented IIM. A fast Poisson solver can be used in our algorithm which gives us the potential for developing fast overall solvers in the future. The time discretization is based on a second order multi-step method. Numerical tests with exact solutions are presented to validate the accuracy of the method. Application to fluid structure interaction between an incompressible fluid and a compressible gas bubble is also presented. PMID:27087702

A semi-implicit augmented IIM for Navier-Stokes equations with open, traction, or free boundary conditions.

PubMed

Li, Zhilin; Xiao, Li; Cai, Qin; Zhao, Hongkai; Luo, Ray

2015-08-15

In this paper, a new Navier-Stokes solver based on a finite difference approximation is proposed to solve incompressible flows on irregular domains with open, traction, and free boundary conditions, which can be applied to simulations of fluid structure interaction, implicit solvent model for biomolecular applications and other free boundary or interface problems. For some problems of this type, the projection method and the augmented immersed interface method (IIM) do not work well or does not work at all. The proposed new Navier-Stokes solver is based on the local pressure boundary method, and a semi-implicit augmented IIM. A fast Poisson solver can be used in our algorithm which gives us the potential for developing fast overall solvers in the future. The time discretization is based on a second order multi-step method. Numerical tests with exact solutions are presented to validate the accuracy of the method. Application to fluid structure interaction between an incompressible fluid and a compressible gas bubble is also presented.

Temperature-Dependent Implicit-Solvent Model of Polyethylene Glycol in Aqueous Solution.

PubMed

Chudoba, Richard; Heyda, Jan; Dzubiella, Joachim

2017-12-12

A temperature (T)-dependent coarse-grained (CG) Hamiltonian of polyethylene glycol/oxide (PEG/PEO) in aqueous solution is reported to be used in implicit-solvent material models in a wide temperature (i.e., solvent quality) range. The T-dependent nonbonded CG interactions are derived from a combined "bottom-up" and "top-down" approach. The pair potentials calculated from atomistic replica-exchange molecular dynamics simulations in combination with the iterative Boltzmann inversion are postrefined by benchmarking to experimental data of the radius of gyration. For better handling and a fully continuous transferability in T-space, the pair potentials are conveniently truncated and mapped to an analytic formula with three structural parameters expressed as explicit continuous functions of T. It is then demonstrated that this model without further adjustments successfully reproduces other experimentally known key thermodynamic properties of semidilute PEG solutions such as the full equation of state (i.e., T-dependent osmotic pressure) for various chain lengths as well as their cloud point (or collapse) temperature.

Accelerating NLTE radiative transfer by means of the Forth-and-Back Implicit Lambda Iteration: A two-level atom line formation in 2D Cartesian coordinates

NASA Astrophysics Data System (ADS)

Milić, Ivan; Atanacković, Olga

2014-10-01

State-of-the-art methods in multidimensional NLTE radiative transfer are based on the use of local approximate lambda operator within either Jacobi or Gauss-Seidel iterative schemes. Here we propose another approach to the solution of 2D NLTE RT problems, Forth-and-Back Implicit Lambda Iteration (FBILI), developed earlier for 1D geometry. In order to present the method and examine its convergence properties we use the well-known instance of the two-level atom line formation with complete frequency redistribution. In the formal solution of the RT equation we employ short characteristics with two-point algorithm. Using an implicit representation of the source function in the computation of the specific intensities, we compute and store the coefficients of the linear relations J=a+bS between the mean intensity J and the corresponding source function S. The use of iteration factors in the ‘local’ coefficients of these implicit relations in two ‘inward’ sweeps of 2D grid, along with the update of the source function in other two ‘outward’ sweeps leads to four times faster solution than the Jacobi’s one. Moreover, the update made in all four consecutive sweeps of the grid leads to an acceleration by a factor of 6-7 compared to the Jacobi iterative scheme.

Lid opening and conformational stability of T1 Lipase is mediated by increasing chain length polar solvents

PubMed Central

Mohamad Ali, Mohd Shukuri; Salleh, Abu Bakar; Rahman, Raja Noor Zaliha Raja Abd; Normi, Yahaya M.; Mohd Shariff, Fairolniza

2017-01-01

The dynamics and conformational landscape of proteins in organic solvents are events of potential interest in nonaqueous process catalysis. Conformational changes, folding transitions, and stability often correspond to structural rearrangements that alter contacts between solvent molecules and amino acid residues. However, in nonaqueous enzymology, organic solvents limit stability and further application of proteins. In the present study, molecular dynamics (MD) of a thermostable Geobacillus zalihae T1 lipase was performed in different chain length polar organic solvents (methanol, ethanol, propanol, butanol, and pentanol) and water mixture systems to a concentration of 50%. On the basis of the MD results, the structural deviations of the backbone atoms elucidated the dynamic effects of water/organic solvent mixtures on the equilibrium state of the protein simulations in decreasing solvent polarity. The results show that the solvent mixture gives rise to deviations in enzyme structure from the native one simulated in water. The drop in the flexibility in H2O, MtOH, EtOH and PrOH simulation mixtures shows that greater motions of residues were influenced in BtOH and PtOH simulation mixtures. Comparing the root mean square fluctuations value with the accessible solvent area (SASA) for every residue showed an almost correspondingly high SASA value of residues to high flexibility and low SASA value to low flexibility. The study further revealed that the organic solvents influenced the formation of more hydrogen bonds in MtOH, EtOH and PrOH and thus, it is assumed that increased intraprotein hydrogen bonding is ultimately correlated to the stability of the protein. However, the solvent accessibility analysis showed that in all solvent systems, hydrophobic residues were exposed and polar residues tended to be buried away from the solvent. Distance variation of the tetrahedral intermediate packing of the active pocket was not conserved in organic solvent systems, which could lead to weaknesses in the catalytic H-bond network and most likely a drop in catalytic activity. The conformational variation of the lid domain caused by the solvent molecules influenced its gradual opening. Formation of additional hydrogen bonds and hydrophobic interactions indicates that the contribution of the cooperative network of interactions could retain the stability of the protein in some solvent systems. Time-correlated atomic motions were used to characterize the correlations between the motions of the atoms from atomic coordinates. The resulting cross-correlation map revealed that the organic solvent mixtures performed functional, concerted, correlated motions in regions of residues of the lid domain to other residues. These observations suggest that varying lengths of polar organic solvents play a significant role in introducing dynamic conformational diversity in proteins in a decreasing order of polarity. PMID:28533982

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

NASA Astrophysics Data System (ADS)

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

2011-10-01

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

The Role of Histone Tails in the Nucleosome: A Computational Study

PubMed Central

Erler, Jochen; Zhang, Ruihan; Petridis, Loukas; Cheng, Xiaolin; Smith, Jeremy C.; Langowski, Jörg

2014-01-01

Histone tails play an important role in gene transcription and expression. We present here a systematic computational study of the role of histone tails in the nucleosome, using replica exchange molecular dynamics simulations with an implicit solvent model and different well-established force fields. We performed simulations for all four histone tails, H4, H3, H2A, and H2B, isolated and with inclusion of the nucleosome. The results confirm predictions of previous theoretical studies for the secondary structure of the isolated tails but show a strong dependence on the force field used. In the presence of the entire nucleosome for all force fields, the secondary structure of the histone tails is destabilized. Specific contacts are found between charged lysine and arginine residues and DNA phosphate groups and other binding sites in the minor and major DNA grooves. Using cluster analysis, we found a single dominant configuration of binding to DNA for the H4 and H2A histone tails, whereas H3 and H2B show multiple binding configurations with an equal probability. The leading stabilizing contribution for those binding configurations is the attractive interaction between the positively charged lysine and arginine residues and the negatively charged phosphate groups, and thus the resulting charge neutralization. Finally, we present results of molecular dynamics simulations in explicit solvent to confirm our conclusions. Results from both implicit and explicit solvent models show that large portions of the histone tails are not bound to DNA, supporting the complex role of these tails in gene transcription and expression and making them possible candidates for binding sites of transcription factors, enzymes, and other proteins. PMID:25517156

Free energy component analysis for drug design: a case study of HIV-1 protease-inhibitor binding.

PubMed

Kalra, P; Reddy, T V; Jayaram, B

2001-12-06

A theoretically rigorous and computationally tractable methodology for the prediction of the free energies of binding of protein-ligand complexes is presented. The method formulated involves developing molecular dynamics trajectories of the enzyme, the inhibitor, and the complex, followed by a free energy component analysis that conveys information on the physicochemical forces driving the protein-ligand complex formation and enables an elucidation of drug design principles for a given receptor from a thermodynamic perspective. The complexes of HIV-1 protease with two peptidomimetic inhibitors were taken as illustrative cases. Four-nanosecond-level all-atom molecular dynamics simulations using explicit solvent without any restraints were carried out on the protease-inhibitor complexes and the free proteases, and the trajectories were analyzed via a thermodynamic cycle to calculate the binding free energies. The computed free energies were seen to be in good accord with the reported data. It was noted that the net van der Waals and hydrophobic contributions were favorable to binding while the net electrostatics, entropies, and adaptation expense were unfavorable in these protease-inhibitor complexes. The hydrogen bond between the CH2OH group of the inhibitor at the scissile position and the catalytic aspartate was found to be favorable to binding. Various implicit solvent models were also considered and their shortcomings discussed. In addition, some plausible modifications to the inhibitor residues were attempted, which led to better binding affinities. The generality of the method and the transferability of the protocol with essentially no changes to any other protein-ligand system are emphasized.

Maintenance of electrostatic stabilization in altered tubulin lateral contacts may facilitate formation of helical filaments in foraminifera.

PubMed

Bassen, David M; Hou, Yubo; Bowser, Samuel S; Banavali, Nilesh K

2016-08-19

Microtubules in foraminiferan protists (forams) can convert into helical filament structures, in which longitudinal intraprotofilament interactions between tubulin heterodimers are thought to be lost, while lateral contacts across protofilaments are still maintained. The coarse geometric features of helical filaments are known through low-resolution negative stain electron microscopy (EM). In this study, geometric restraints derived from these experimental data were used to generate an average atomic-scale helical filament model, which anticipated a modest reorientation in the lateral tubulin heterodimer interface. Restrained molecular dynamics (MD) simulations of the nearest neighbor interactions combined with a Genalized Born implicit solvent model were used to assess the lateral, longitudinal, and seam contacts in 13-3 microtubules and the reoriented lateral contacts in the helical filament model. This electrostatic analysis suggests that the change in the lateral interface in the helical filament does not greatly diminish the lateral electrostatic interaction. After longitudinal dissociation, the 13-3 seam interaction is much weaker than the reoriented lateral interface in the helical filament model, providing a plausible atomic-detail explanation for seam-to-lateral contact transition that enables the transition to a helical filament structure.

Maintenance of electrostatic stabilization in altered tubulin lateral contacts may facilitate formation of helical filaments in foraminifera

NASA Astrophysics Data System (ADS)

Bassen, David M.; Hou, Yubo; Bowser, Samuel S.; Banavali, Nilesh K.

2016-08-01

Microtubules in foraminiferan protists (forams) can convert into helical filament structures, in which longitudinal intraprotofilament interactions between tubulin heterodimers are thought to be lost, while lateral contacts across protofilaments are still maintained. The coarse geometric features of helical filaments are known through low-resolution negative stain electron microscopy (EM). In this study, geometric restraints derived from these experimental data were used to generate an average atomic-scale helical filament model, which anticipated a modest reorientation in the lateral tubulin heterodimer interface. Restrained molecular dynamics (MD) simulations of the nearest neighbor interactions combined with a Genalized Born implicit solvent model were used to assess the lateral, longitudinal, and seam contacts in 13-3 microtubules and the reoriented lateral contacts in the helical filament model. This electrostatic analysis suggests that the change in the lateral interface in the helical filament does not greatly diminish the lateral electrostatic interaction. After longitudinal dissociation, the 13-3 seam interaction is much weaker than the reoriented lateral interface in the helical filament model, providing a plausible atomic-detail explanation for seam-to-lateral contact transition that enables the transition to a helical filament structure.

Dielectric relaxation of ethylene carbonate and propylene carbonate from molecular dynamics simulations

DOE PAGES

Chaudhari, Mangesh I.; You, Xinli; Pratt, Lawrence R.; ...

2015-11-24

Ethylene carbonate (EC) and propylene carbonate (PC) are widely used solvents in lithium (Li)-ion batteries and supercapacitors. Ion dissolution and diffusion in those media are correlated with solvent dielectric responses. Here, we use all-atom molecular dynamics simulations of the pure solvents to calculate dielectric constants and relaxation times, and molecular mobilities. The computed results are compared with limited available experiments to assist more exhaustive studies of these important characteristics. As a result, the observed agreement is encouraging and provides guidance for further validation of force-field simulation models for EC and PC solvents.

Solvatochromic Effects on the Absorption Spectrum of 2-Thiocytosine

PubMed Central

2017-01-01

The solvatochromic effects of six different solvents on the UV absorption spectrum of 2-thiocytosine have been studied by a combination of experimental and theoretical techniques. The steady-state absorption spectra show significant shifts of the absorption bands, where in more polar solvents the first absorption maximum shifts to higher transition energies and the second maximum to lower energies. The observed solvatochromic shifts have been rationalized using three popular solvatochromic scales and with high-level multireference quantum chemistry calculations including implicit and explicit solvent effects. It has been found that the dipole moments of the excited states account for some general shifts in the excitation energies, whereas the explicit solvent interactions explain the differences in the spectra recorded in the different solvents. PMID:28452483

Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units.

PubMed

Zhang, Baofeng; Kilburg, Denise; Eastman, Peter; Pande, Vijay S; Gallicchio, Emilio

2017-04-15

We present an algorithm to efficiently compute accurate volumes and surface areas of macromolecules on graphical processing unit (GPU) devices using an analytic model which represents atomic volumes by continuous Gaussian densities. The volume of the molecule is expressed by means of the inclusion-exclusion formula, which is based on the summation of overlap integrals among multiple atomic densities. The surface area of the molecule is obtained by differentiation of the molecular volume with respect to atomic radii. The many-body nature of the model makes a port to GPU devices challenging. To our knowledge, this is the first reported full implementation of this model on GPU hardware. To accomplish this, we have used recursive strategies to construct the tree of overlaps and to accumulate volumes and their gradients on the tree data structures so as to minimize memory contention. The algorithm is used in the formulation of a surface area-based non-polar implicit solvent model implemented as an open source plug-in (named GaussVol) for the popular OpenMM library for molecular mechanics modeling. GaussVol is 50 to 100 times faster than our best optimized implementation for the CPUs, achieving speeds in excess of 100 ns/day with 1 fs time-step for protein-sized systems on commodity GPUs. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Effect of Destined High-Pressure Torsion on the Structure and Mechanical Properties of Rare Earth-Based Metallic Glasses

NASA Astrophysics Data System (ADS)

Zhao, W.; Cheng, H.; Jiang, X.; Wu, M. L.; Li, G.

2018-03-01

Changes in the atomic structure and mechanical properties of rare earth-based metallic glasses caused by destined high-pressure torsion (HPT) were studied by X-ray diffraction synchrotron radiation and nanoindentation. Results showed that destined HPT improved nanohardness and wear resistance, which indicated the significant contributions of this technique. The diffraction patterns showed that the contents of pairs between solvent and solute atoms with a large negative mixing enthalpy increased, whereas those of pairs between solvent atoms and between solute atoms decreased after destined HPT. Thus, the process was improved by increasing the proportion of high-intensity pairs between solvent and solute atoms.

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

PubMed

Nguyen, Bao Linh; Pettitt, B Montgomery

2015-04-14

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

Determination of gold, indium, tellurium and thallium in the same sample digest of geological materials by atomic-absorption spectroscopy and two-step solvent extraction

USGS Publications Warehouse

Hubert, A.E.; Chao, T.T.

1985-01-01

A rock, soil, or stream-sediment sample is decomposed with hydrofluoric acid, aqua regia, and hydrobromic acid-bromine solution. Gold, thallium, indium and tellurium are separated and concentrated from the sample digest by a two-step MIBK extraction at two concentrations of hydrobromic add. Gold and thallium are first extracted from 0.1M hydrobromic acid medium, then indium and tellurium are extracted from 3M hydrobromic acid in the presence of ascorbic acid to eliminate iron interference. The elements are then determined by flame atomic-absorption spectrophotometry. The two-step solvent extraction can also be used in conjunction with electrothermal atomic-absorption methods to lower the detection limits for all four metals in geological materials. ?? 1985.

Conformational analysis of glutamic acid: a density functional approach using implicit continuum solvent model.

PubMed

Turan, Başak; Selçuki, Cenk

2014-09-01

Amino acids are constituents of proteins and enzymes which take part almost in all metabolic reactions. Glutamic acid, with an ability to form a negatively charged side chain, plays a major role in intra and intermolecular interactions of proteins, peptides, and enzymes. An exhaustive conformational analysis has been performed for all eight possible forms at B3LYP/cc-pVTZ level. All possible neutral, zwitterionic, protonated, and deprotonated forms of glutamic acid structures have been investigated in solution by using polarizable continuum model mimicking water as the solvent. Nine families based on the dihedral angles have been classified for eight glutamic acid forms. The electrostatic effects included in the solvent model usually stabilize the charged forms more. However, the stability of the zwitterionic form has been underestimated due to the lack of hydrogen bonding between the solute and solvent; therefore, it is observed that compact neutral glutamic acid structures are more stable in solution than they are in vacuum. Our calculations have shown that among all eight possible forms, some are not stable in solution and are immediately converted to other more stable forms. Comparison of isoelectronic glutamic acid forms indicated that one of the structures among possible zwitterionic and anionic forms may dominate over the other possible forms. Additional investigations using explicit solvent models are necessary to determine the stability of charged forms of glutamic acid in solution as our results clearly indicate that hydrogen bonding and its type have a major role in the structure and energy of conformers.

SEPARATION OF PLUTONIUM FROM ELEMENTS HAVING AN ATOMIC NUMBER NOT LESS THAN 92

DOEpatents

Fitch, F.T.; Russell, D.S.

1958-09-16

other elements having atomic numbers nnt less than 92, It has been proposed in the past to so separate plutonium by solvent extraction iato an organic solvent using triglycoldichlcride as the organic solvent. The improvement lies in the discovery that triglycoldichloride performs far more efflciently as an extractant, wher certain second organie compounds are added to it. Mentioned as satisfactory additive compounds are benzaldehyde, saturated aliphatic aldehydes containtng at least twc carbon atoms, and certain polyhydric phenols.

Revisiting the Dielectric Constant Effect on the Nucleophile and Leaving Group of Prototypical Backside Sn2 Reactions: a Reaction Force and Atomic Contribution Analysis.

PubMed

Pedraza-González, Laura Milena; Galindo, Johan Fabian; Gonzalez, Ronald; Reyes, Andrés

2016-10-09

The solvent effect on the nucleophile and leaving group atoms of the prototypical F - + CH 3 Cl → CH 3 F + Cl - backside bimolecular nucleophilic substitution reaction (S N 2) is analyzed employing the reaction force and the atomic contributions methods on the intrinsic reaction coordinate (IRC). Solvent effects were accounted for using the polarizable continuum solvent model. Calculations were performed employing eleven dielectric constants, ε, ranging from 1.0 to 78.5, to cover a wide spectrum of solvents. The reaction force data reveals that the solvent mainly influences the region of the IRC preceding the energy barrier, where the structural rearrangement to reach the transition state occurs. A detailed analysis of the atomic role in the reaction as a function of ε reveals that the nucleophile and the carbon atom are the ones that contribute the most to the energy barrier. In addition, we investigated the effect of the choice of nucleophile and leaving group on the ΔE 0 and ΔE ↕ of Y - + CH 3 X → YCH 3 + X - (X,Y= F, Cl, Br, I) in aqueous solution. Our analysis allowed us to find relationships between the atomic contributions to the activation energy and leaving group ability and nucleophilicity.

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

NASA Astrophysics Data System (ADS)

Chung, Kee-Choo; Park, Hwangseo

2016-11-01

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

Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations.

PubMed

Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep

2015-06-15

In this study, we examine the temperature dependence of free energetics of nanotube association using graphical processing unit-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion, and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intratube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and interpretations of hydrophobicity in terms of alternative but parallel signatures such as interfacial fluctuations, dewetting transitions, and enhanced fluctuation probabilities at interfaces. © 2015 Wiley Periodicals, Inc.

Free energy landscapes of a highly structured β-hairpin peptide and its single mutant

NASA Astrophysics Data System (ADS)

Kim, Eunae; Yang, Changwon; Jang, Soonmin; Pak, Youngshang

2008-10-01

We investigated the free energy landscapes of a highly structured β-hairpin peptide (MBH12) and a less structured peptide with a single mutation of Tyr6 to Asp6 (MBH10). For the free energy mapping, starting from an extended conformation, the replica exchange molecular dynamic simulations for two β-hairpins were performed using a modified version of an all-atom force field employing an implicit solvation (param99MOD5/GBSA). With the present simulation approach, we demonstrated that detailed stability changes associated with the sequence modification from MBH12 to MBH10 are quantitatively well predicted at the all-atom level.

Universal calculational recipe for solvent-mediated potential: based on a combination of integral equation theory and density functional theory

NASA Astrophysics Data System (ADS)

Zhou, Shiqi

2004-07-01

A universal formalism, which enables calculation of solvent-mediated potential (SMP) between two equal or non-equal solute particles with any shape immersed in solvent reservior consisting of atomic particle and/or polymer chain or their mixture, is proposed by importing a density functional theory externally into OZ equation systems. Only if size asymmetry of the solvent bath components is moderate, the present formalism can calculate the SMP in any complex fluids at the present development stage of statistical mechanics, and therefore avoids all of limitations of previous approaches for SMP. Preliminary calculation indicates the reliability of the present formalism.

Influence of solvents on the conformation of benzoin.

PubMed

Pawełka, Z; Czarnik-Matusewicz, B; Zeegers-Huyskens, Th

2010-01-01

The conformation of benzoin in several organic solvents is investigated by infrared spectrometry and dipolometry. The frequencies, intensities, and band shapes of the nu(OH), nu(C=O), and aromatic ring vibrations indicate that in solvents of low proton acceptor ability, the cis conformer with intramolecular OH...O hydrogen bonding is preserved. In solvents of large proton acceptor ability there is equilibrium between the cis and trans conformers. The dipole moments are less sensitive to conformational changes, but indicate the same trends. The results are discussed as a function of the specific solvation of the O atoms or OH groups of benzoin. Copyright 2009 Elsevier B.V. All rights reserved.

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

PubMed Central

Nguyen, Bao Linh; Pettitt, B. Montgomery

2015-01-01

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

On-the-fly Numerical Surface Integration for Finite-Difference Poisson-Boltzmann Methods.

PubMed

Cai, Qin; Ye, Xiang; Wang, Jun; Luo, Ray

2011-11-01

Most implicit solvation models require the definition of a molecular surface as the interface that separates the solute in atomic detail from the solvent approximated as a continuous medium. Commonly used surface definitions include the solvent accessible surface (SAS), the solvent excluded surface (SES), and the van der Waals surface. In this study, we present an efficient numerical algorithm to compute the SES and SAS areas to facilitate the applications of finite-difference Poisson-Boltzmann methods in biomolecular simulations. Different from previous numerical approaches, our algorithm is physics-inspired and intimately coupled to the finite-difference Poisson-Boltzmann methods to fully take advantage of its existing data structures. Our analysis shows that the algorithm can achieve very good agreement with the analytical method in the calculation of the SES and SAS areas. Specifically, in our comprehensive test of 1,555 molecules, the average unsigned relative error is 0.27% in the SES area calculations and 1.05% in the SAS area calculations at the grid spacing of 1/2Å. In addition, a systematic correction analysis can be used to improve the accuracy for the coarse-grid SES area calculations, with the average unsigned relative error in the SES areas reduced to 0.13%. These validation studies indicate that the proposed algorithm can be applied to biomolecules over a broad range of sizes and structures. Finally, the numerical algorithm can also be adapted to evaluate the surface integral of either a vector field or a scalar field defined on the molecular surface for additional solvation energetics and force calculations.

Water Dynamics at Protein-Protein Interfaces: Molecular Dynamics Study of Virus-Host Receptor Complexes.

PubMed

Dutta, Priyanka; Botlani, Mohsen; Varma, Sameer

2014-12-26

The dynamical properties of water at protein-water interfaces are unlike those in the bulk. Here we utilize molecular dynamics simulations to study water dynamics in interstitial regions between two proteins. We consider two natural protein-protein complexes, one in which the Nipah virus G protein binds to cellular ephrin B2 and the other in which the same G protein binds to ephrin B3. While the two complexes are structurally similar, the two ephrins share only a modest sequence identity of ∼50%. X-ray crystallography also suggests that these interfaces are fairly extensive and contain exceptionally large amounts of waters. We find that while the interstitial waters tend to occupy crystallographic sites, almost all waters exhibit residence times of less than hundred picoseconds in the interstitial region. We also find that while the differences in the sequence of the two ephrins result in quantitative differences in the dynamics of interstitial waters, the trends in the shifts with respect to bulk values are similar. Despite the high wetness of the protein-protein interfaces, the dynamics of interstitial waters are considerably slower compared to the bulk-the interstitial waters diffuse an order of magnitude slower and have 2-3 fold longer hydrogen bond lifetimes and 2-1000 fold slower dipole relaxation rates. To understand the role of interstitial waters, we examine how implicit solvent models compare against explicit solvent models in producing ephrin-induced shifts in the G conformational density. Ephrin-induced shifts in the G conformational density are critical to the allosteric activation of another viral protein that mediates fusion. We find that in comparison with the explicit solvent model, the implicit solvent model predicts a more compact G-B2 interface, presumably because of the absence of discrete waters at the G-B2 interface. Simultaneously, we find that the two models yield strikingly different induced changes in the G conformational density, even for those residues whose conformational densities in the apo state are unaffected by the treatment of the bulk solvent. Together, these results show that the explicit treatment of interstitial water molecules is necessary for a proper description of allosteric transitions.

A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein-protein interaction with an all-atom model in explicit solvent

NASA Astrophysics Data System (ADS)

Higo, Junichi; Umezawa, Koji; Nakamura, Haruki

2013-05-01

We propose a novel generalized ensemble method, a virtual-system coupled multicanonical molecular dynamics (V-McMD), to enhance conformational sampling of biomolecules expressed by an all-atom model in an explicit solvent. In this method, a virtual system, of which physical quantities can be set arbitrarily, is coupled with the biomolecular system, which is the target to be studied. This method was applied to a system of an Endothelin-1 derivative, KR-CSH-ET1, known to form an antisymmetric homodimer at room temperature. V-McMD was performed starting from a configuration in which two KR-CSH-ET1 molecules were mutually distant in an explicit solvent. The lowest free-energy state (the most thermally stable state) at room temperature coincides with the experimentally determined native complex structure. This state was separated to other non-native minor clusters by a free-energy barrier, although the barrier disappeared with elevated temperature. V-McMD produced a canonical ensemble faster than a conventional McMD method.

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

PubMed

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

2016-06-05

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

Thermodynamic of cellulose solvation in novel solvent mixtures

NASA Astrophysics Data System (ADS)

Das, Ritankar; Chu, Jhih-Wei

2013-04-01

Biomass contains abundant amounts of cellulose as crystalline microfibrils. A limiting step to using cellulose as an alternative energy source, however, is the hydrolysis of the biomass and subsequent transformation into fuels. Cellulose is insoluble in most solvents including organic solvents and water, but it is soluble in some ionic liquids like BMIM-Cl. This project aims to find alternative solvents that are less expensive and are more environmentally benign than the ionic liquids. All-atom molecular dynamics simulations were performed on dissociated glucan chains separated by multiple (4-5) solvation shells, in the presence of several novel solvents and solvent mixtures. The solubility of the chains in each solvent was indicated by contacts calculations after the equilibration of the molecular dynamics. It was discovered that pyridine and imidazole acted as the best solvents because their aromatic electronic structure was able to effectively disrupt the inter-sheet interactions among the glucan chains in the axial direction, and because perturbation of the solvent interactions in the presence of glucan chains was minimal.

Thermodynamic of cellulose solvation in novel solvent mixtures

NASA Astrophysics Data System (ADS)

Das, Ritankar

2013-03-01

Biomass contains abundant amounts of cellulose as crystalline microfibrils. A limiting step to using cellulose as an alternative energy source, however, is the hydrolysis of the biomass and subsequent transformation into fuels. Cellulose is insoluble in most solvents including organic solvents and water, but it is soluble in some ionic liquids like BMIM-Cl. This project aims to find alternative solvents that are less expensive and are more environmentally benign than the ionic liquids. All-atom molecular dynamics simulations were performed on dissociated glucan chains separated by multiple (4-5) solvation shells, in the presence of several novel solvents and solvent mixtures. The solubility of the chains in each solvent was indicated by contacts calculations after the equilibration of the molecular dynamics. It was discovered that pyridine and imidazole acted as the best solvents because their aromatic electronic structure was able to effectively disrupt the inter-sheet interactions among the glucan chains in the axial direction, and because perturbation of the solvent interactions in the presence of glucan chains was minimal.

Thermodynamics of cellulose solvation in novel solvent mixtures

NASA Astrophysics Data System (ADS)

Das, Ritankar; Chu, Jhih-Wei

2012-10-01

Biomass contains abundant amounts of cellulose as crystalline microfibrils. A limiting step to using cellulose as an alternative energy source, however, is the hydrolysis of the biomass and subsequent transformation into fuels. Cellulose is insoluble in most solvents including organic solvents and water, but it is soluble in some ionic liquids like BMIM-Cl. This project aims to find alternative solvents that are less expensive and are more environmentally benign than the ionic liquids. All-atom molecular dynamics simulations were performed on dissociated glucan chains separated by multiple (4-5) solvation shells, in the presence of several novel solvents and solvent mixtures. The solubility of the chains in each solvent was indicated by contacts calculations after the equilibration of the molecular dynamics. It was discovered that pyridine and imidazole acted as the best solvents because their aromatic electronic structure was able to effectively disrupt the inter-sheet interactions among the glucan chains in the axial direction, and because perturbation of the solvent interactions in the presence of glucan chains was minimal.

Thermodynamic of cellulose solvation in novel solvent mixtures

NASA Astrophysics Data System (ADS)

Das, Ritankar

2012-11-01

Biomass contains abundant amounts of cellulose as crystalline microfibrils. A limiting step to using cellulose as an alternative energy source, however, is the hydrolysis of the biomass and subsequent transformation into fuels. Cellulose is insoluble in most solvents including organic solvents and water, but it is soluble in some ionic liquids like BMIM-Cl. This project aims to find alternative solvents that are less expensive and are more environmentally benign than the ionic liquids. All-atom molecular dynamics simulations were performed on dissociated glucan chains separated by multiple (4-5) solvation shells, in the presence of several novel solvents and solvent mixtures. The solubility of the chains in each solvent was indicated by contacts calculations after the equilibration of the molecular dynamics. It was discovered that pyridine and imidazole acted as the best solvents because their aromatic electronic structure was able to effectively disrupt the inter-sheet interactions among the glucan chains in the axial direction, and because perturbation of the solvent interactions in the presence of glucan chains was minimal.

Replica Exchange Simulations of the Thermodynamics of Aβ Fibril Growth

PubMed Central

Takeda, Takako; Klimov, Dmitri K.

2009-01-01

Abstract Replica exchange molecular dynamics and an all-atom implicit solvent model are used to probe the thermodynamics of deposition of Alzheimer's Aβ monomers on preformed amyloid fibrils. Consistent with the experiments, two deposition stages have been identified. The docking stage occurs over a wide temperature range, starting with the formation of the first peptide-fibril interactions at 500 K. Docking is completed when a peptide fully adsorbs on the fibril edge at the temperature of 380 K. The docking transition appears to be continuous, and occurs without free energy barriers or intermediates. During docking, incoming Aβ monomer adopts a disordered structure on the fibril edge. The locking stage occurs at the temperature of ≈360 K and is characterized by the rugged free energy landscape. Locking takes place when incoming Aβ peptide forms a parallel β-sheet structure on the fibril edge. Because the β-sheets formed by locked Aβ peptides are typically off-registry, the structure of the locked phase differs from the structure of the fibril interior. The study also reports that binding affinities of two distinct fibril edges with respect to incoming Aβ peptides are different. The peptides bound to the concave edge have significantly lower free energy compared to those bound on the convex edge. Comparison with the available experimental data is discussed. PMID:19167295

Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units

PubMed Central

Mamonov, Artem B.; Lettieri, Steven; Ding, Ying; Sarver, Jessica L.; Palli, Rohith; Cunningham, Timothy F.; Saxena, Sunil; Zuckerman, Daniel M.

2012-01-01

Building on our recently introduced library-based Monte Carlo (LBMC) approach, we describe a flexible protocol for mixed coarse-grained (CG)/all-atom (AA) simulation of proteins and ligands. In the present implementation of LBMC, protein side chain configurations are pre-calculated and stored in libraries, while bonded interactions along the backbone are treated explicitly. Because the AA side chain coordinates are maintained at minimal run-time cost, arbitrary sites and interaction terms can be turned on to create mixed-resolution models. For example, an AA region of interest such as a binding site can be coupled to a CG model for the rest of the protein. We have additionally developed a hybrid implementation of the generalized Born/surface area (GBSA) implicit solvent model suitable for mixed-resolution models, which in turn was ported to a graphics processing unit (GPU) for faster calculation. The new software was applied to study two systems: (i) the behavior of spin labels on the B1 domain of protein G (GB1) and (ii) docking of randomly initialized estradiol configurations to the ligand binding domain of the estrogen receptor (ERα). The performance of the GPU version of the code was also benchmarked in a number of additional systems. PMID:23162384

Naproxen Interferes with the Assembly of Aβ Oligomers Implicated in Alzheimer's Disease

PubMed Central

Kim, Seongwon; Chang, Wenling E.; Kumar, Rashmi; Klimov, Dmitri K.

2011-01-01

Experimental and epidemiological studies have shown that the nonsteroidal antiinflammatory drug naproxen may be useful in the treatment of Alzheimer's disease. To investigate the interactions of naproxen with Aβ dimers, which are the smallest cytotoxic aggregated Aβ peptide species, we use united atom implicit solvent model and exhaustive replica exchange molecular dynamics. We show that naproxen ligands bind to Aβ dimer and penetrate its volume interfering with the interpeptide interactions. As a result naproxen induces a destabilizing effect on Aβ dimer. By comparing the free-energy landscapes of naproxen interactions with Aβ dimers and fibrils, we conclude that this ligand has stronger antiaggregation potential against Aβ fibrils rather than against dimers. The analysis of naproxen binding energetics shows that the location of ligand binding sites in Aβ dimer is dictated by the Aβ amino acid sequence. Comparison of the in silico findings with experimental observations reveals potential limitations of naproxen as an effective therapeutic agent in the treatment of Alzheimer's disease. PMID:21504739

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 both experimental and theoretical results in the literature.

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 both experimental and theoretical results in the literature. PMID:20938489

Parallel Tempering of Dark Matter from the Ebola Virus Proteome: Comparison of CHARMM36m and CHARMM22 Force Fields with Implicit Solvent and Coarse Grained Model

DTIC Science & Technology

2017-08-10

simulation models the conformational plasticity along the helix-forming reaction coordinate was limited by free - energy barriers. By comparison the coarse...revealed. The latter becomes evident in comparing the energy Z-score landscapes , where CHARMM22 simulation shows a manifold of shuttling...solvent simulations of calculating the charging free energy of protein conformations.33 Deviation to the protocol by modification of Born radii

Treatment of geometric singularities in implicit solvent models

NASA Astrophysics Data System (ADS)

Yu, Sining; Geng, Weihua; Wei, G. W.

2007-06-01

Geometric singularities, such as cusps and self-intersecting surfaces, are major obstacles to the accuracy, convergence, and stability of the numerical solution of the Poisson-Boltzmann (PB) equation. In earlier work, an interface technique based PB solver was developed using the matched interface and boundary (MIB) method, which explicitly enforces the flux jump condition at the solvent-solute interfaces and leads to highly accurate biomolecular electrostatics in continuum electric environments. However, such a PB solver, denoted as MIBPB-I, cannot maintain the designed second order convergence whenever there are geometric singularities, such as cusps and self-intersecting surfaces. Moreover, the matrix of the MIBPB-I is not optimally symmetrical, resulting in the convergence difficulty. The present work presents a new interface method based PB solver, denoted as MIBPB-II, to address the aforementioned problems. The present MIBPB-II solver is systematical and robust in treating geometric singularities and delivers second order convergence for arbitrarily complex molecular surfaces of proteins. A new procedure is introduced to make the MIBPB-II matrix optimally symmetrical and diagonally dominant. The MIBPB-II solver is extensively validated by the molecular surfaces of few-atom systems and a set of 24 proteins. Converged electrostatic potentials and solvation free energies are obtained at a coarse grid spacing of 0.5Å and are considerably more accurate than those obtained by the PBEQ and the APBS at finer grid spacings.

Thermodynamic description of cellulose chain collapse using coarse grain modeling

NASA Astrophysics Data System (ADS)

Das, Ritankar; Chu, Jhih-Wei

2012-11-01

Biomass contains abundant amounts of cellulose as crystalline microfibrils. A limiting step to using cellulose as an alternative energy source, however, is the hydrolysis of the biomass and subsequent transformation into fuels. Cellulose is insoluble in most solvents including organic solvents and water, but it is soluble in some ionic liquids like BMIM-Cl. This project aims to find alternative solvents that are less expensive and are more environmentally benign than the ionic liquids. All-atom molecular dynamics simulations were performed on dissociated glucan chains separated by multiple (4-5) solvation shells, in the presence of several novel solvents and solvent mixtures. The solubility of the chains in each solvent was indicated by contacts calculations after the equilibration of the molecular dynamics. It was discovered that pyridine and imidazole acted as the best solvents because their aromatic electronic structure was able to effectively disrupt the inter-sheet interactions among the glucan chains in the axial direction, and because perturbation of the solvent interactions in the presence of glucan chains was minimal.

The theoretical investigation of solvent effects on the relative stability and 15N NMR shielding of antidepressant heterocyclic drug

NASA Astrophysics Data System (ADS)

Tahan, Arezoo; Khojandi, Mahya; Salari, Ali Akbar

2016-01-01

The density functional theory (DFT) and Tomasi's polarized continuum model (PCM) were used for the investigation of solvent polarity and its dielectric constant effects on the relative stability and NMR shielding tensors of antidepressant mirtazapine (MIR). The obtained results indicated that the relative stability in the polar solvents is higher than that in non-polar solvents and the most stable structure was observed in the water at the B3LYP/6-311++G ( d, p) level of theory. Also, natural bond orbital (NBO) interpretation demonstrated that by increase of solvent dielectric constant, negative charge on nitrogen atoms of heterocycles and resonance energy for LP(N10) → σ* and π* delocalization of the structure's azepine ring increase and the highest values of them were observed in water. On the other hand, NMR calculations showed that with an increase in negative charge of nitrogen atoms, isotropic chemical shielding (σiso) around them increase and nitrogen of piperazine ring (N19) has the highest values of negative charge and σiso among nitrogen atoms. NMR calculations also represented that direct solvent effect on nitrogen of pyridine ring (N15) is more than other nitrogens, while its effect on N19 is less than other ones. Based on NMR data and NBO interpretation, it can be deduced that with a decrease in the negative charge on nitrogen atoms, the intramolecular effects on them decrease, while direct solvent effect increases.

Nafion®-catalyzed microwave-assisted Ritter reaction: An atom-economic solvent-free synthesis of amides

EPA Science Inventory

An atom-economic solvent-free synthesis of amides by the Ritter reaction of alcohols and nitriles under microwave irradiation is reported. This green protocol is catalyzed by solid supported Nafion®NR50 with improved efficiency and reduced waste production.

Solvent-driven reductive activation of carbon dioxide by gold anions.

PubMed

Knurr, Benjamin J; Weber, J Mathias

2012-11-14

Catalytic activation and electrochemical reduction of CO(2) for the formation of chemically usable feedstock and fuel are central goals for establishing a carbon neutral fuel cycle. The role of solvent molecules in catalytic processes is little understood, although solvent-solute interactions can strongly influence activated intermediate species. We use vibrational spectroscopy of mass-selected Au(CO(2))(n)(-) cluster ions to probe the solvation of AuCO(2)(-) as a model for a reactive intermediate in the reductive activation of a CO(2) ligand by a single-atom catalyst. For the first few solvent molecules, solvation of the complex preferentially occurs at the CO(2) moiety, enhancing reductive activation through polarization of the excess charge onto the partially reduced ligand. At higher levels of solvation, direct interaction of additional solvent molecules with the Au atom diminishes reduction. The results show how the solvation environment can enhance or diminish the effects of a catalyst, offering design criteria for single-atom catalyst engineering.

Polder maps: Improving OMIT maps by excluding bulk solvent

DOE PAGES

Liebschner, Dorothee; Afonine, Pavel V.; Moriarty, Nigel W.; ...

2017-02-01

The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factorsmore » and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk-solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit-cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk-solvent model may obscure it further. A possible solution to this problem is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. As a result, the tools described in this manuscript have been implemented and are available in PHENIX.« less

Computer simulations of a liquid crystalline dendrimer in liquid crystalline solvents

NASA Astrophysics Data System (ADS)

Wilson, Mark R.; Ilnytskyi, Jaroslav M.; Stimson, Lorna M.

2003-08-01

Molecular dynamics simulations have been carried out to study the structure of a model liquid crystalline dendrimer (LCDr) in solution. A simplified model is used for a third generation carbosilane LCDr in which united atom Lennard-Jones sites are used to represent all heavy atoms in the dendrimer with the exception of the terminal mesogenic groups, which are represented by Gay-Berne potentials. The model dendrimer is immersed in a mesogenic solvent composed of Gay-Berne particles, which can form nematic and smectic-A phases in addition to the isotropic liquid. Markedly different behavior results from simulations in the different phases, with the dendrimer changing shape from spherical to rodlike in moving from isotropic to nematic solvents. In the smectic-A phase the terminal mesogenic units are able to occupy five separate smectic layers. The change in structure of the dendrimer is mediated by conformational changes in the flexible chains, which link the terminal mesogenic moieties to the dendrimer core.

Structure refinement of membrane proteins via molecular dynamics simulations.

PubMed

Dutagaci, Bercem; Heo, Lim; Feig, Michael

2018-07-01

A refinement protocol based on physics-based techniques established for water soluble proteins is tested for membrane protein structures. Initial structures were generated by homology modeling and sampled via molecular dynamics simulations in explicit lipid bilayer and aqueous solvent systems. Snapshots from the simulations were selected based on scoring with either knowledge-based or implicit membrane-based scoring functions and averaged to obtain refined models. The protocol resulted in consistent and significant refinement of the membrane protein structures similar to the performance of refinement methods for soluble proteins. Refinement success was similar between sampling in the presence of lipid bilayers and aqueous solvent but the presence of lipid bilayers may benefit the improvement of lipid-facing residues. Scoring with knowledge-based functions (DFIRE and RWplus) was found to be as good as scoring using implicit membrane-based scoring functions suggesting that differences in internal packing is more important than orientations relative to the membrane during the refinement of membrane protein homology models. © 2018 Wiley Periodicals, Inc.

The origin of consistent protein structure refinement from structural averaging.

PubMed

Park, Hahnbeom; DiMaio, Frank; Baker, David

2015-06-02

Recent studies have shown that explicit solvent molecular dynamics (MD) simulation followed by structural averaging can consistently improve protein structure models. We find that improvement upon averaging is not limited to explicit water MD simulation, as consistent improvements are also observed for more efficient implicit solvent MD or Monte Carlo minimization simulations. To determine the origin of these improvements, we examine the changes in model accuracy brought about by averaging at the individual residue level. We find that the improvement in model quality from averaging results from the superposition of two effects: a dampening of deviations from the correct structure in the least well modeled regions, and a reinforcement of consistent movements towards the correct structure in better modeled regions. These observations are consistent with an energy landscape model in which the magnitude of the energy gradient toward the native structure decreases with increasing distance from the native state. Copyright © 2015 Elsevier Ltd. All rights reserved.

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.

Long Dynamics Simulations of Proteins Using Atomistic Force Fields and a Continuum Representation of Solvent Effects: Calculation of Structural and Dynamic Properties

PubMed Central

Li, Xianfeng; Hassan, Sergio A.; Mehler, Ernest L.

2006-01-01

Long dynamics simulations were carried out on the B1 immunoglobulin-binding domain of streptococcal protein G (ProtG) and bovine pancreatic trypsin inhibitor (BPTI) using atomistic descriptions of the proteins and a continuum representation of solvent effects. To mimic frictional and random collision effects, Langevin dynamics (LD) were used. The main goal of the calculations was to explore the stability of tens-of-nanosecond trajectories as generated by this molecular mechanics approximation and to analyze in detail structural and dynamical properties. Conformational fluctuations, order parameters, cross correlation matrices, residue solvent accessibilities, pKa values of titratable groups, and hydrogen-bonding (HB) patterns were calculated from all of the trajectories and compared with available experimental data. The simulations comprised over 40 ns per trajectory for ProtG and over 30 ns per trajectory for BPTI. For comparison, explicit water molecular dynamics simulations (EW/MD) of 3 ns and 4 ns, respectively, were also carried out. Two continuum simulations were performed on each protein using the CHARMM program, one with the all-atom PAR22 representation of the protein force field (here referred to as PAR22/LD simulations) and the other with the modifications introduced by the recently developed CMAP potential (CMAP/LD simulations). The explicit solvent simulations were performed with PAR22 only. Solvent effects are described by a continuum model based on screened Coulomb potentials (SCP) reported earlier, i.e., the SCP-based implicit solvent model (SCP–ISM). For ProtG, both the PAR22/LD and the CMAP/LD 40-ns trajectories were stable, yielding Cα root mean square deviations (RMSD) of about 1.0 and 0.8 Å respectively along the entire simulation time, compared to 0.8 Å for the EW/MD simulation. For BPTI, only the CMAP/LD trajectory was stable for the entire 30-ns simulation, with a Cα RMSD of ≈ 1.4 Å, while the PAR22/LD trajectory became unstable early in the simulation, reaching a Cα RMSD of about 2.7 Å and remaining at this value until the end of the simulation; the Cα RMSD of the EW/MD simulation was about 1.5 Å. The source of the instabilities of the BPTI trajectories in the PAR22/LD simulations was explored by an analysis of the backbone torsion angles. To further validate the findings from this analysis of BPTI, a 35-ns SCP–ISM simulation of Ubiquitin (Ubq) was carried out. For this protein, the CMAP/LD simulation was stable for the entire simulation time (Cα RMSD of ≈1.0 Å), while the PAR22/LD trajectory showed a trend similar to that in BPTI, reaching a Cα RMSD of ≈1.5 Å at 7 ns. All the calculated properties were found to be in agreement with the corresponding experimental values, although local deviations were also observed. HB patterns were also well reproduced by all the continuum solvent simulations with the exception of solvent-exposed side chain–side chain (sc–sc) HB in ProtG, where several of the HB interactions observed in the crystal structure and in the EW/MD simulation were lost. The overall analysis reported in this work suggests that the combination of an atomistic representation of a protein with a CMAP/CHARMM force field and a continuum representation of solvent effects such as the SCP–ISM provides a good description of structural and dynamic properties obtained from long computer simulations. Although the SCP–ISM simulations (CMAP/LD) reported here were shown to be stable and the properties well reproduced, further refinement is needed to attain a level of accuracy suitable for more challenging biological applications, particularly the study of protein–protein interactions. PMID:15959866

Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): time-resolved fluorescence measurements and all-atom molecular dynamics simulations.

PubMed

Das, Anuradha; Das, Suman; Biswas, Ranjit

2015-01-21

Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

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

Das, Anuradha; Das, Suman; Biswas, Ranjit, E-mail: ranjit@bose.res.in

2015-01-21

Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH{sub 3}CONH{sub 2}) and urea (NH{sub 2}CONH{sub 2}) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH{sub 3}CONH{sub 2} + (1 − f)NH{sub 2}CONH{sub 2}] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probemore » solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α{sub 2}) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.« less

Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Das, Anuradha; Das, Suman; Biswas, Ranjit

2015-01-01

Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH3CONH2) and urea (NH2CONH2) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH3CONH2 + (1 - f)NH2CONH2] have been studied in a temperature range of 328-353 K which is ˜120-145 K above the measured glass transition temperatures (˜207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (˜70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α2) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

Orientation-dependent potential of mean force for protein folding

NASA Astrophysics Data System (ADS)

Mukherjee, Arnab; Bhimalapuram, Prabhakar; Bagchi, Biman

2005-07-01

We present a solvent-implicit minimalistic model potential among the amino acid residues of proteins, obtained by using the known native structures [deposited in the Protein Data Bank (PDB)]. In this model, the amino acid side chains are represented by a single ellipsoidal site, defined by the group of atoms about the center of mass of the side chain. These ellipsoidal sites interact with other sites through an orientation-dependent interaction potential which we construct in the following fashion. First, the site-site potential of mean force (PMF) between heavy atoms is calculated [following F. Melo and E. Feytsman, J. Mol. Biol. 267, 207 (1997)] from statistics of their distance separation obtained from crystal structures. These site-site potentials are then used to calculate the distance and the orientation-dependent potential between side chains of all the amino acid residues (AAR). The distance and orientation dependencies show several interesting results. For example, we find that the PMF between two hydrophobic AARs, such as phenylalanine, is strongly attractive at short distances (after the obvious repulsive region at very short separation) and is characterized by a deep minimum, for specific orientations. For the interaction between two hydrophilic AARs, such a deep minimum is absent and in addition, the potential interestingly reveals the combined effect of polar (charge) and hydrophobic interactions among some of these AARs. The effectiveness of our potential has been tested by calculating the Z-scores for a large set of proteins. The calculated Z-scores show high negative values for most of them, signifying the success of the potential to identify the native structure from among a large number of its decoy states.

Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force Field.

PubMed

Aguayo, Daniel; González-Nilo, Fernando D; Chipot, Christophe

2012-05-08

Simulation of three models of cardiolipin (CL) containing membranes using a new set of parameters for tetramyristoyl and tetraoleoyl CLs has been developed in the framework of the united-atom CHARMM27-UA and the all-atom CHARMM36 force fields with the aim of performing molecular dynamics (MD) simulations of cardiolipin-containing mixed-lipid membranes. The new parameters use a hybrid representation of all-atom head groups in conjunction with implicit-hydrogen united-atom (UA) to describe the oleoyl and myristoyl chains of the CLs, in lieu of the fully atomistic description, thereby allowing longer simulations to be undertaken. The physicochemical properties of the bilayers were determined and compared with previously reported data. Furthermore, using tetramyristoyl CL mixed with POPG and POPE lipids, a mitochondrial membrane was simulated. The results presented here show the different behavior of the bilayers as a result of the lipid composition, where the length of the acyl chain and the conformation of the headgroup can be associated with the mitochondrial membrane properties. The new hybrid CL parameters prove to be well suited for the simulation of the molecular structure of CL-containing bilayers and can be extended to other lipid bilayers composed of CLs with different acyl chains or alternate head groups.

Carbonyl Activation by Borane Lewis Acid Complexation: Transition States of H2 Splitting at the Activated Carbonyl Carbon Atom in a Lewis Basic Solvent and the Proton-Transfer Dynamics of the Boroalkoxide Intermediate.

PubMed

Heshmat, Mojgan; Privalov, Timofei

2017-07-06

By using transition-state (TS) calculations, we examined how Lewis acid (LA) complexation activates carbonyl compounds in the context of hydrogenation of carbonyl compounds by H 2 in Lewis basic (ethereal) solvents containing borane LAs of the type (C 6 F 5 ) 3 B. According to our calculations, LA complexation does not activate a ketone sufficiently enough for the direct addition of H 2 to the O=C unsaturated bond; but, calculations indicate a possibly facile heterolytic cleavage of H 2 at the activated and thus sufficiently Lewis acidic carbonyl carbon atom with the assistance of the Lewis basic solvent (i.e., 1,4-dioxane or THF). For the solvent-assisted H 2 splitting at the carbonyl carbon atom of (C 6 F 5 ) 3 B adducts with different ketones, a number of TSs are computed and the obtained results are related to insights from experiment. By using the Born-Oppenheimer molecular dynamics with the DFT for electronic structure calculations, the evolution of the (C 6 F 5 ) 3 B-alkoxide ionic intermediate and the proton transfer to the alkoxide oxygen atom were investigated. The results indicate a plausible hydrogenation mechanism with a LA, that is, (C 6 F 5 ) 3 B, as a catalyst, namely, 1) the step of H 2 cleavage that involves a Lewis basic solvent molecule plus the carbonyl carbon atom of thermodynamically stable and experimentally identifiable (C 6 F 5 ) 3 B-ketone adducts in which (C 6 F 5 ) 3 B is the "Lewis acid promoter", 2) the transfer of the solvent-bound proton to the oxygen atom of the (C 6 F 5 ) 3 B-alkoxide intermediate giving the (C 6 F 5 ) 3 B-alcohol adduct, and 3) the S N 2-style displacement of the alcohol by a ketone or a Lewis basic solvent molecule. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Geometric measures of large biomolecules: surface, volume, and pockets.

PubMed

Mach, Paul; Koehl, Patrice

2011-11-15

Geometry plays a major role in our attempts to understand the activity of large molecules. For example, surface area and volume are used to quantify the interactions between these molecules and the water surrounding them in implicit solvent models. In addition, the detection of pockets serves as a starting point for predictive studies of biomolecule-ligand interactions. The alpha shape theory provides an exact and robust method for computing these geometric measures. Several implementations of this theory are currently available. We show however that these implementations fail on very large macromolecular systems. We show that these difficulties are not theoretical; rather, they are related to the architecture of current computers that rely on the use of cache memory to speed up calculation. By rewriting the algorithms that implement the different steps of the alpha shape theory such that we enforce locality, we show that we can remediate these cache problems; the corresponding code, UnionBall has an apparent O(n) behavior over a large range of values of n (up to tens of millions), where n is the number of atoms. As an example, it takes 136 sec with UnionBall to compute the contribution of each atom to the surface area and volume of a viral capsid with more than five million atoms on a commodity PC. UnionBall includes functions for computing analytically the surface area and volume of the intersection of two, three and four spheres that are fully detailed in an appendix. UnionBall is available as an OpenSource software. Copyright © 2011 Wiley Periodicals, Inc.

Geometric Measures of Large Biomolecules: Surface, Volume and Pockets

PubMed Central

Mach, Paul; Koehl, Patrice

2011-01-01

Geometry plays a major role in our attempt to understand the activity of large molecules. For example, surface area and volume are used to quantify the interactions between these molecules and the water surrounding them in implicit solvent models. In addition, the detection of pockets serves as a starting point for predictive studies of biomolecule-ligand interactions. The alpha shape theory provides an exact and robust method for computing these geometric measures. Several implementations of this theory are currently available. We show however that these implementations fail on very large macromolecular systems. We show that these difficulties are not theoretical; rather, they are related to the architecture of current computers that rely on the use of cache memory to speed up calculation. By rewriting the algorithms that implement the different steps of the alpha shape theory such that we enforce locality, we show that we can remediate these cache problems; the corresponding code, UnionBall has an apparent (n) behavior over a large range of values of n (up to tens of millions), where n is the number of atoms. As an example, it takes 136 seconds with UnionBall to compute the contribution of each atom to the surface area and volume of a viral capsid with more than five million atoms on a commodity PC. UnionBall includes functions for computing the surface area and volume of the intersection of two, three and four spheres that are fully detailed in an appendix. UnionBall is available as an OpenSource software. PMID:21823134

Molecular Origins of Internal Friction Effects on Protein Folding Rates

PubMed Central

Sirur, Anshul

2014-01-01

Recent experiments on protein folding dynamics have revealed strong evidence for internal friction effects. That is, observed relaxation times are not simply proportional to the solvent viscosity as might be expected if the solvent were the only source of friction. However, a molecular interpretation of this remarkable phenomenon is currently lacking. Here, we use all-atom simulations of peptide and protein folding in explicit solvent, to probe the origin of the unusual viscosity dependence. We find that an important contribution to this effect, explaining the viscosity dependence of helix formation and the folding of a helix-containing protein, is the insensitivity of torsion angle isomerization to solvent friction. The influence of this landscape roughness can, in turn, be quantitatively explained by a rate theory including memory friction. This insensitivity of local barrier crossing to solvent friction is expected to contribute to the viscosity dependence of folding rates in larger proteins. PMID:24986114

Molecular origins of internal friction effects on protein-folding rates.

PubMed

de Sancho, David; Sirur, Anshul; Best, Robert B

2014-07-02

Recent experiments on protein-folding dynamics have revealed strong evidence for internal friction effects. That is, observed relaxation times are not simply proportional to the solvent viscosity as might be expected if the solvent were the only source of friction. However, a molecular interpretation of this remarkable phenomenon is currently lacking. Here, we use all-atom simulations of peptide and protein folding in explicit solvent, to probe the origin of the unusual viscosity dependence. We find that an important contribution to this effect, explaining the viscosity dependence of helix formation and the folding of a helix-containing protein, is the insensitivity of torsion angle isomerization to solvent friction. The influence of this landscape roughness can, in turn, be quantitatively explained by a rate theory including memory friction. This insensitivity of local barrier crossing to solvent friction is expected to contribute to the viscosity dependence of folding rates in larger proteins.

Influence of different amino substituents in position 1 and 4 on spectroscopic and acid base properties of 9,10-anthraquinone moiety.

PubMed

Wcisło, Anna; Niedziałkowski, Paweł; Wnuk, Elżbieta; Zarzeczańska, Dorota; Ossowski, Tadeusz

2013-05-01

A series of novel 1-amino and 1,4-diamino-9,10-anthraquinones, substituted with different alkyl groups, were synthesized as the result of alkylation with amino substituents. All the obtained aminoanthraquinone derivatives were characterized by NMR, IR spectroscopy and mass spectrometry. The spectroscopic properties of these compounds were determined by using UV-Vis spectroscopy in acetonitrile, and in the mixture of acetonitrile and methanol at different pH ranges. The effects of various substituents present in the newly developed anthraquinone derivatives and their ability to form hydrogen bonds between the carbonyl oxygen atom of anthraquinone moiety and nitrogen atom of N-H group in 1-aminoanthraquinone (1-AAQ) and 1,4-diaminoanthraquinone (1,4-DAAQ) were studied. Additionally, the effects of hydrogen bond formation between O-H group in hydroxyethylamino substituent and the carbonyl oxygen atom of anthraquinone were investigated. The spectroscopic behavior of the studied derivatives strongly depended on the solvent-solute interactions and the nature of solvent. The values of pKa for the new anthraquinones were determined by the combined potentiometric and spectrophotometric titration methods. Copyright © 2013 Elsevier B.V. All rights reserved.

Effects of liquid chromatography mobile phases and buffer salts on phosphorus inductively coupled plasma atomic emission and mass spectrometries utilizing ultrasonic nebulization and membrane desolvation.

PubMed

Carr, John E; Kwok, Kaho; Webster, Gregory K; Carnahan, Jon W

2006-01-23

Atomic spectrometry, specifically inductively coupled plasma atomic emission spectrometry (ICP-AES) and mass spectrometry (ICP-MS) show promise for heteroatom-based detection of pharmaceutical compounds. The combination of ultrasonic nebulization (USN) with membrane desolvation (MD) greatly enhances detection limits with these approaches. Because pharmaceutical analyses often incorporate liquid chromatography, the study herein was performed to examine the effects of solvent composition on the analytical behaviors of these approaches. The target analyte was phosphorus, introduced as phosphomycin. AES response was examined at the 253.7 nm atom line and mass 31 ions were monitored for the MS experiments. With pure aqueous solutions, detection limits of 5 ppb (0.5 ng in 0.1 mL injection volumes) were obtained with ICP-MS. The ICP-AES detection limit was 150 ppb. Solvent compositions were varied from 0 to 80% organic (acetonitrile and methanol) with nine buffers at concentrations typically used in liquid chromatography. In general, solvents and buffers had statistically significant, albeit small, effects on ICP-AES sensitivities. A few exceptions occurred in cases where typical liquid chromatography buffer concentrations produced higher mass loadings on the plasma. Indications are that isocratic separations can be reliably performed. Within reasonable accuracy tolerances, it appears that gradient chromatography can be performed without the need for signal response normalization. Organic solvent and buffer effects were more significant with ICP-MS. Sensitivities varied significantly with different buffers and organic solvent content. In these cases, gradient chromatography will require careful analytical calibration as solvent and buffer content is varied. However, for most buffer and solvent combinations, signal and detection limits are only moderately affected. Isocratic separations and detection are feasible.

Synthesis of substantially monodispersed colloids

NASA Technical Reports Server (NTRS)

Stoeva, Savka (Inventor); Klabunde, Kenneth J. (Inventor); Sorensen, Christopher (Inventor)

2003-01-01

A method of forming ligated nanoparticles of the formula Y(Z).sub.x where Y is a nanoparticle selected from the group consisting of elemental metals having atomic numbers ranging from 21-34, 39-52, 57-83 and 89-102, all inclusive, the halides, oxides and sulfides of such metals, and the alkali metal and alkaline earth metal halides, and Z represents ligand moieties such as the alkyl thiols. In the method, a first colloidal dispersion is formed made up of nanoparticles solvated in a molar excess of a first solvent (preferably a ketone such as acetone), a second solvent different than the first solvent (preferably an organic aryl solvent such as toluene) and a quantity of ligand moieties; the first solvent is then removed under vacuum and the ligand moieties ligate to the nanoparticles to give a second colloidal dispersion of the ligated nanoparticles solvated in the second solvent. If substantially monodispersed nanoparticles are desired, the second dispersion is subjected to a digestive ripening process. Upon drying, the ligated nanoparticles may form a three-dimensional superlattice structure.

Effect of solvent volume on the physical properties of aluminium doped nanocrystalline zinc oxide thin films deposited using a simplified spray pyrolysis technique

NASA Astrophysics Data System (ADS)

Jabena Begum, N.; Mohan, R.; Ravichandran, K.

2013-01-01

Aluminium doped zinc oxide (AZO) thin films were deposited by employing a low cost and simplified spray technique using a perfume atomizer from starting solutions having different volumes (10, 20, … , 50 mL) of solvent. The effect of solvent volume on the structural, electrical, optical, photoluminescence (PL) and surface morphological properties was studied. The electrical resistivity of the AZO films is remarkably influenced by the variation in the solvent volume. The X-ray diffraction profiles clearly showed that all the films have preferential orientation along the (0 0 2) plane irrespective of the solvent volume. The crystallite size was found to be in the nano range of 35-46 nm. The optical transmittance in the visible region is desirably high (>85%). The AFM images show columnar morphology with varying grain size. The PL studies revealed that the AZO film deposited from 50 mL of solvent volume has good quality with lesser defect density.

Nebulization reflux concentrator

NASA Technical Reports Server (NTRS)

Collins, V. G.; Cofer, W. R., III

1986-01-01

A nebulization reflux concentrator for removing trace gas contaminants from a sample gas is described. Sample gas from a gas supply is drawn by a suction source into a vessel. The gas enters the vessel through an atomizing nozzle, thereby atomizing and entraining a scrubbing liquid solvent drawn through a siphon tube from a scrubbing liquid reservoir. The gas and entrained liquid rise through a concentrator and impinge upon a solvent phobic filter, whereby purified gas exits through the filter housing and contaminated liquid coalesces on the solvent phobic filter and falls into the reservoir.

Reduced atomic pair-interaction design (RAPID) model for simulations of proteins.

PubMed

Ni, Boris; Baumketner, Andrij

2013-02-14

Increasingly, theoretical studies of proteins focus on large systems. This trend demands the development of computational models that are fast, to overcome the growing complexity, and accurate, to capture the physically relevant features. To address this demand, we introduce a protein model that uses all-atom architecture to ensure the highest level of chemical detail while employing effective pair potentials to represent the effect of solvent to achieve the maximum speed. The effective potentials are derived for amino acid residues based on the condition that the solvent-free model matches the relevant pair-distribution functions observed in explicit solvent simulations. As a test, the model is applied to alanine polypeptides. For the chain with 10 amino acid residues, the model is found to reproduce properly the native state and its population. Small discrepancies are observed for other folding properties and can be attributed to the approximations inherent in the model. The transferability of the generated effective potentials is investigated in simulations of a longer peptide with 25 residues. A minimal set of potentials is identified that leads to qualitatively correct results in comparison with the explicit solvent simulations. Further tests, conducted for multiple peptide chains, show that the transferable model correctly reproduces the experimentally observed tendency of polyalanines to aggregate into β-sheets more strongly with the growing length of the peptide chain. Taken together, the reported results suggest that the proposed model could be used to succesfully simulate folding and aggregation of small peptides in atomic detail. Further tests are needed to assess the strengths and limitations of the model more thoroughly.

Computational Elucidation of a Role That Brønsted Acidification of the Lewis Acid-Bound Water Might Play in the Hydrogenation of Carbonyl Compounds with H2 in Lewis Basic Solvents.

PubMed

Heshmat, Mojgan; Privalov, Timofei

2017-08-25

Brønsted acidification of water by Lewis acid (LA) complexation is one of the fundamental principles in chemistry. Using transition-state calculations (TS), herein we investigate the role that Brønsted acidification of the LA-bound water might play in the mechanism of the hydrogenation of carbonyl compounds in Lewis basic solvents under non-anhydrous conditions. The potential energy scans and TS calculations were carried out with a series of eight borane LAs as well as the commonly known strong LA AlCl 3 in 1,4-dioxane or THF as Lewis basic solvents. Our molecular model consists of the dative LA-water adduct with hydrogen bonds to acetone and a solvent molecule plus one additional solvent molecule that participates is the TS structure describing the cleavage of H 2 at acetone's carbonyl carbon atom. In all the molecular models applied here, acetone (O=CMe 2 ) is the archetypical carbonyl substrate. We demonstrate that Brønsted acidification of the LA-bound water can indeed lower the barrier height of the solvent-involving H 2 -cleavage at the acetone's carbonyl carbon atom. This is significant because at present it is believed that the mechanism of the herein considered reaction is described by the same mechanism regardless of whether the reaction conditions are strictly anhydrous or non-anhydrous. Our results offer an alternative to this belief that warrants consideration and further study. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Gas separation by composite solvent-swollen membranes

DOEpatents

Matson, S.L.; Lee, E.K.L.; Friesen, D.T.; Kelly, D.J.

1989-04-25

There is disclosed a composite immobilized liquid membrane of a solvent-swollen polymer and a microporous organic or inorganic support, the solvent being at least one highly polar solvent containing at least one nitrogen, oxygen, phosphorus or sulfur atom, and having a boiling point of at least 100 C and a specified solubility parameter. The solvent or solvent mixture is homogeneously distributed through the solvent-swollen polymer from 20% to 95% by weight. The membrane is suitable for acid gas scrubbing and oxygen/nitrogen separation. 3 figs.

Gas separation by composite solvent-swollen membranes

DOEpatents

Matson, Stephen L.; Lee, Eric K. L.; Friesen, Dwayne T.; Kelly, Donald J.

1989-01-01

There is disclosed a composite immobulized liquid membrane of a solvent-swollen polymer and a microporous organic or inorganic support, the solvent being at least one highly polar solvent containing at least one nitrogen, oxygen, phosphorous or sulfur atom, and having a boiling point of at least 100.degree. C. and a specified solubility parameter. The solvent or solvent mixture is homogeneously distributed through the solvent-swollen polymer from 20% to 95% by weight. The membrane is suitable for acid gas scrubbing and oxygen/nitrogen separation.

Modeling the temperature-dependent peptide vibrational spectra based on implicit-solvent model and enhance sampling technique

NASA Astrophysics Data System (ADS)

Tianmin, Wu; Tianjun, Wang; Xian, Chen; Bin, Fang; Ruiting, Zhang; Wei, Zhuang

2016-01-01

We herein review our studies on simulating the thermal unfolding Fourier transform infrared and two-dimensional infrared spectra of peptides. The peptide-water configuration ensembles, required forspectrum modeling, aregenerated at a series of temperatures using the GBOBC implicit solvent model and the integrated tempering sampling technique. The fluctuating vibrational Hamiltonians of the amide I vibrational band are constructed using the Frenkel exciton model. The signals are calculated using nonlinear exciton propagation. The simulated spectral features such as the intensity and ellipticity are consistent with the experimental observations. Comparing the signals for two beta-hairpin polypeptides with similar structures suggests that this technique is sensitive to peptide folding landscapes. Project supported by the National Natural Science Foundation of China (Grant No. 21203178), the National Natural Science Foundation of China (Grant No. 21373201), the National Natural Science Foundation of China (Grant No. 21433014), the Science and Technological Ministry of China (Grant No. 2011YQ09000505), and “Strategic Priority Research Program” of the Chinese Academy of Sciences (Grant Nos. XDB10040304 and XDB100202002).

Applications of MMPBSA to Membrane Proteins I: Efficient Numerical Solutions of Periodic Poisson-Boltzmann Equation

PubMed Central

Botello-Smith, Wesley M.; Luo, Ray

2016-01-01

Continuum solvent models have been widely used in biomolecular modeling applications. Recently much attention has been given to inclusion of implicit membrane into existing continuum Poisson-Boltzmann solvent models to extend their applications to membrane systems. Inclusion of an implicit membrane complicates numerical solutions of the underlining Poisson-Boltzmann equation due to the dielectric inhomogeneity on the boundary surfaces of a computation grid. This can be alleviated by the use of the periodic boundary condition, a common practice in electrostatic computations in particle simulations. The conjugate gradient and successive over-relaxation methods are relatively straightforward to be adapted to periodic calculations, but their convergence rates are quite low, limiting their applications to free energy simulations that require a large number of conformations to be processed. To accelerate convergence, the Incomplete Cholesky preconditioning and the geometric multi-grid methods have been extended to incorporate periodicity for biomolecular applications. Impressive convergence behaviors were found as in the previous applications of these numerical methods to tested biomolecules and MMPBSA calculations. PMID:26389966

Flory-type theories of polymer chains under different external stimuli

NASA Astrophysics Data System (ADS)

Budkov, Yu A.; Kiselev, M. G.

2018-01-01

In this Review, we present a critical analysis of various applications of the Flory-type theories to a theoretical description of the conformational behavior of single polymer chains in dilute polymer solutions under a few external stimuli. Different theoretical models of flexible polymer chains in the supercritical fluid are discussed and analysed. Different points of view on the conformational behavior of the polymer chain near the liquid-gas transition critical point of the solvent are presented. A theoretical description of the co-solvent-induced coil-globule transitions within the implicit-solvent-explicit-co-solvent models is discussed. Several explicit-solvent-explicit-co-solvent theoretical models of the coil-to-globule-to-coil transition of the polymer chain in a mixture of good solvents (co-nonsolvency) are analysed and compared with each other. Finally, a new theoretical model of the conformational behavior of the dielectric polymer chain under the external constant electric field in the dilute polymer solution with an explicit account for the many-body dipole correlations is discussed. The polymer chain collapse induced by many-body dipole correlations of monomers in the context of statistical thermodynamics of dielectric polymers is analysed.

Process for making ultra-fine ceramic particles

DOEpatents

Stangle, Gregory C.; Venkatachari, Koththavasal R.; Ostrander, Steven P.; Schulze, Walter A.

1995-01-01

A process for producing ultra-fine ceramic particles in which droplets are formed from a ceramic precursor mixture containing a metal cation, a nitrogen-containing fuel, a solvent, and an anion capable of participating in an anionic oxidation-reduction reaction with the nitrogen containing fuel. The nitrogen-containing fuel contains at least three nitrogen atoms, at least one oxygen atom, and at least one carbon atom. The ceramic precursor mixture is dried to remove at least 85 weight percent of the solvent, and the dried mixture is then ignited to form a combusted powder.

Dendrimer Interactions with Lipid Bilayer: Comparison of Force Field and Effect of Implicit vs Explicit Solvation.

PubMed

Kanchi, Subbarao; Gosika, Mounika; Ayappa, K G; Maiti, Prabal K

2018-06-13

The understanding of dendrimer interactions with cell membranes has great importance in drug/gene delivery based therapeutics. Although molecular simulations have been used to understand the nature of dendrimer interactions with lipid membranes, its dependency on available force field parameters is poorly understood. In this study, we have carried out fully atomistic molecular dynamics (MD) simulations of a protonated G3 poly(amido amine) (PAMAM) dendrimer-dimyristoylphosphatidylcholine (DMPC) lipid bilayer complex using three different force fields (FFs) namely, CHARMM, GAFF, and GROMOS in the presence of explicit water to understand the structure of the lipid-dendrimer complex and nature of their interaction. CHARMM and GAFF dendrimers initially in contact with the lipid head groups were found to move away from the lipid bilayer during the course of simulation; however, the dendrimer remained strongly bound to the lipid head groups with the GROMOS FF. Potential of the mean force (PMF) computations of the dendrimer along the bilayer normal showed a repulsive barrier (∼20 kcal/mol) between dendrimer and lipid bilayer in the case of CHARMM and GAFF force fields. In contrast, an attractive interaction (∼40 kcal/mol) is obtained with the GROMOS force field, consistent with experimental observations of membrane binding observed with lower generation G3 PAMAM dendrimers. This difference with the GROMOS dendrimer is attributed to the strong dendrimer-lipid interaction and lowered surface hydration of the dendrimer. Assessing the role of solvent, we find that the CHARMM and GAFF dendrimers strongly bind to the lipid bilayer with an implicit solvent (Generalized Born) model, whereas binding is not observed with explicit water (TIP3P). The opposing nature of dendrimer-membrane interactions in the presence of explicit and implicit solvents demonstrates that hydration effects play an important role in modulating the dendrimer-lipid interaction warranting a case for refinement of the existing dendrimer/lipid force fields.

RECOVERY OF METAL VALUES FROM AQUEOUS SOLUTIONS BY SOLVENT EXTRACTION

DOEpatents

Moore, R.L.

1959-09-01

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

The effect of macromolecular crowding on the electrostatic component of barnase-barstar binding: a computational, implicit solvent-based study.

PubMed

Qi, Helena W; Nakka, Priyanka; Chen, Connie; Radhakrishnan, Mala L

2014-01-01

Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder-protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein-protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase-barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders), this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered "effective" solvent dielectric to account for crowding, although the "best" effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the electrostatic component of protein binding, and it provides an initial framework for future analyses.

The Effect of Macromolecular Crowding on the Electrostatic Component of Barnase–Barstar Binding: A Computational, Implicit Solvent-Based Study

PubMed Central

Qi, Helena W.; Nakka, Priyanka; Chen, Connie; Radhakrishnan, Mala L.

2014-01-01

Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder–protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein–protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase–barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders), this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered “effective” solvent dielectric to account for crowding, although the “best” effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the electrostatic component of protein binding, and it provides an initial framework for future analyses. PMID:24915485

Solvent effect in implicit/explicit model on FT-IR, 1H, 13C and 19F NMR, UV-vis and fluorescence spectra, linear, second- and third-nonlinear optical parameters of 2-(trifluoromethyl)benzoic acid: Experimental and computational study

NASA Astrophysics Data System (ADS)

Avcı, Davut; Altürk, Sümeyye; Tamer, Ömer; Kuşbazoğlu, Mustafa; Atalay, Yusuf

2017-09-01

FT-IR, 1H, 13C and 19F NMR, UV-vis and fluorescence spectra for 2-(trifluoromethyl)benzoic acid (2-TFMBA) were recorded. DFT//B3LYP/6-31++G(d,p) calculations were used to determine the optimized molecular geometry, vibrational frequencies, 1H, 13C and 19F GIAO-NMR chemical shifts of 2-TFMBA. The detailed assignments of vibrational frequencies were carried out on the basis of potential energy distribution (PED) by using VEDA program. TD-DFT/B3LYP/6-31++G(d,p) calculations with the PCM (polarizable continuum model) in ethanol and DMSO solvents based on implicit/explicit model and gas phase in the excited state were employed to investigate UV-vis absorption and fluorescence emission wavelengths. The UV-vis and emission spectra were given in ethanol and DMSO solvents, and the major contributions to the electronic transitions were obtained. In addition, the NLO parameters (β, γ and χ(3)) and frontier molecular orbital energies of 2-TFMBA were calculated by using B3LYP/6-31++G(d,p) level. The NLO parameters of 2-TFMBA were compared with that of para-Nitroaniline (pNA) and urea which are the typical NLO materials. The refractive index (n) is calculated by using the Lorentz-Lorenz equation to observe polarization behavior of 2-TFMBA in DMSO and ethanol solvents. In order to investigate intramolecular and hydrogen bonding interactions, NBO calculations were also performed by the same level. To sum up, considering the well-known biological role, photochemical properties of 2-TFMBA were discussed.

Modeling the antisymmetric and symmetric stretching vibrational modes of aqueous carboxylate anions

NASA Astrophysics Data System (ADS)

Sutton, Catherine C. R.; Franks, George V.; da Silva, Gabriel

2015-01-01

The infrared spectra of six aqueous carboxylate anions have been calculated at the M05-2X/cc-pVTZ level of theory with the SMD solvent model, and validated against experimental data from the literature over the region of 1700 cm-1 to 1250 cm-1; this region corresponds to the stretching modes of the carboxylate group, and is often interrogated when probing bonding of carboxylates to other species and surfaces. The anions studied here were formate, acetate, oxalate, succinate, glutarate and citrate. For the lowest energy conformer of each anion, the carboxylate moiety antisymmetric stretching peak was predicted with a mean signed error of only 4 cm-1 using the SMD solvent model, while the symmetric peak was slightly overestimated. Performing calculations in vacuum and scaling was found to generally over-predict the antisymmetric vibrational frequencies and under predict the symmetric peak. Different conformers of the same anion were found to have only slightly different spectra in the studied region and the inclusion of explicit water molecules was not found to significantly change the calculated spectra when the implicit solvent model is used. Overall, the use of density functional theory in conjunction with an implicit solvent model was found to result in infra-red spectra that are the best reproduction of the features found experimentally for the aqueous carboxylate ions in the important 1700 cm-1 to 1250 cm-1 region. The development of validated model chemistries for simulating the stretching modes of aqueous carboxylate ions will be valuable for future studies that investigate how carboxylate anions complex with multivalent metal cations and related species in solution.

An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions

NASA Astrophysics Data System (ADS)

Lin, Yuchun; Baumketner, Andrij; Deng, Shaozhong; Xu, Zhenli; Jacobs, Donald; Cai, Wei

2009-10-01

In this paper, a new solvation model is proposed for simulations of biomolecules in aqueous solutions that combines the strengths of explicit and implicit solvent representations. Solute molecules are placed in a spherical cavity filled with explicit water, thus providing microscopic detail where it is most needed. Solvent outside of the cavity is modeled as a dielectric continuum whose effect on the solute is treated through the reaction field corrections. With this explicit/implicit model, the electrostatic potential represents a solute molecule in an infinite bath of solvent, thus avoiding unphysical interactions between periodic images of the solute commonly used in the lattice-sum explicit solvent simulations. For improved computational efficiency, our model employs an accurate and efficient multiple-image charge method to compute reaction fields together with the fast multipole method for the direct Coulomb interactions. To minimize the surface effects, periodic boundary conditions are employed for nonelectrostatic interactions. The proposed model is applied to study liquid water. The effect of model parameters, which include the size of the cavity, the number of image charges used to compute reaction field, and the thickness of the buffer layer, is investigated in comparison with the particle-mesh Ewald simulations as a reference. An optimal set of parameters is obtained that allows for a faithful representation of many structural, dielectric, and dynamic properties of the simulated water, while maintaining manageable computational cost. With controlled and adjustable accuracy of the multiple-image charge representation of the reaction field, it is concluded that the employed model achieves convergence with only one image charge in the case of pure water. Future applications to pKa calculations, conformational sampling of solvated biomolecules and electrolyte solutions are briefly discussed.

Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.

PubMed

Marenich, Aleksandr V; Cramer, Christopher J; Truhlar, Donald G

2009-05-07

We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the "D" stands for "density" to denote that the full solute electron density is used without defining partial atomic charges. "Continuum" denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute-solvent boundary. SMD is a universal solvation model, where "universal" denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which a few key descriptors are known (in particular, dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the solution of the nonhomogeneous Poisson equation for electrostatics in terms of the integral-equation-formalism polarizable continuum model (IEF-PCM). The cavities for the bulk electrostatic calculation are defined by superpositions of nuclear-centered spheres. The second component is called the cavity-dispersion-solvent-structure term and is the contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell. This contribution is a sum of terms that are proportional (with geometry-dependent proportionality constants called atomic surface tensions) to the solvent-accessible surface areas of the individual atoms of the solute. The SMD model has been parametrized with a training set of 2821 solvation data including 112 aqueous ionic solvation free energies, 220 solvation free energies for 166 ions in acetonitrile, methanol, and dimethyl sulfoxide, 2346 solvation free energies for 318 neutral solutes in 91 solvents (90 nonaqueous organic solvents and water), and 143 transfer free energies for 93 neutral solutes between water and 15 organic solvents. The elements present in the solutes are H, C, N, O, F, Si, P, S, Cl, and Br. The SMD model employs a single set of parameters (intrinsic atomic Coulomb radii and atomic surface tension coefficients) optimized over six electronic structure methods: M05-2X/MIDI!6D, M05-2X/6-31G, M05-2X/6-31+G, M05-2X/cc-pVTZ, B3LYP/6-31G, and HF/6-31G. Although the SMD model has been parametrized using the IEF-PCM protocol for bulk electrostatics, it may also be employed with other algorithms for solving the nonhomogeneous Poisson equation for continuum solvation calculations in which the solute is represented by its electron density in real space. This includes, for example, the conductor-like screening algorithm. With the 6-31G basis set, the SMD model achieves mean unsigned errors of 0.6-1.0 kcal/mol in the solvation free energies of tested neutrals and mean unsigned errors of 4 kcal/mol on average for ions with either Gaussian03 or GAMESS.

Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions

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

Marenich, Aleksandr; Cramer, Christopher J; Truhlar, Donald G

2009-04-30

We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the “D” stands for “density” to denote that the full solute electron density is used without defining partial atomic charges. “Continuum” denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute-solvent boundary. SMD is a universal solvation model, where “universal” denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which amore » few key descriptors are known (in particular, dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the solution of the nonhomogeneous Poisson equation for electrostatics in terms of the integral-equation-formalism polarizable continuum model (IEF-PCM). The cavities for the bulk electrostatic calculation are defined by superpositions of nuclear-centered spheres. The second component is called the cavity-dispersion-solvent-structure term and is the contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell. This contribution is a sum of terms that are proportional (with geometry-dependent proportionality constants called atomic surface tensions) to the solvent-accessible surface areas of the individual atoms of the solute. The SMD model has been parametrized with a training set of 2821 solvation data including 112 aqueous ionic solvation free energies, 220 solvation free energies for 166 ions in acetonitrile, methanol, and dimethyl sulfoxide, 2346 solvation free energies for 318 neutral solutes in 91 solvents (90 nonaqueous organic solvents and water), and 143 transfer free energies for 93 neutral solutes between water and 15 organic solvents. The elements present in the solutes are H, C, N, O, F, Si, P, S, Cl, and Br. The SMD model employs a single set of parameters (intrinsic atomic Coulomb radii and atomic surface tension coefficients) optimized over six electronic structure methods: M05-2X/MIDI!6D, M05-2X/6-31G*, M05-2X/6-31+G**, M05-2X/cc-pVTZ, B3LYP/6-31G*, and HF/6-31G*. Although the SMD model has been parametrized using the IEF-PCM protocol for bulk electrostatics, it may also be employed with other algorithms for solving the nonhomogeneous Poisson equation for continuum solvation calculations in which the solute is represented by its electron density in real space. This includes, for example, the conductor-like screening algorithm. With the 6-31G* basis set, the SMD model achieves mean unsigned errors of 0.6-1.0 kcal/mol in the solvation free energies of tested neutrals and mean unsigned errors of 4 kcal/mol on average for ions with either Gaussian03 or GAMESS.« less

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

PubMed

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

2017-03-23

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

Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling

PubMed Central

Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

2014-01-01

Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES) simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape. PMID:25340714

Regulation of substituent groups on morphologies and self-assembly of organogels based on some azobenzene imide derivatives

NASA Astrophysics Data System (ADS)

Jiao, Tifeng; Wang, Yujin; Zhang, Qingrui; Zhou, Jingxin; Gao, Faming

2013-04-01

In this paper, new azobenzene imide derivatives with different substituent groups were designed and synthesized. Their gelation behaviors in 21 solvents were tested as novel low-molecular-mass organic gelators. It was shown that the alkyl substituent chains and headgroups of azobenzene residues in gelators played a crucial role in the gelation behavior of all compounds in various organic solvents. More alkyl chains in molecular skeletons in present gelators are favorable for the gelation of organic solvents. Scanning electron microscopy and atomic force microscopy observations revealed that the gelator molecules self-assemble into different aggregates, from wrinkle, lamella, and belt to fiber with the change of solvents. Spectral studies indicated that there existed different H-bond formations between amide groups and conformations of methyl chains. The present work may give some insight to the design and character of new organogelators and soft materials with special molecular structures.

Regulation of substituent groups on morphologies and self-assembly of organogels based on some azobenzene imide derivatives

PubMed Central

2013-01-01

In this paper, new azobenzene imide derivatives with different substituent groups were designed and synthesized. Their gelation behaviors in 21 solvents were tested as novel low-molecular-mass organic gelators. It was shown that the alkyl substituent chains and headgroups of azobenzene residues in gelators played a crucial role in the gelation behavior of all compounds in various organic solvents. More alkyl chains in molecular skeletons in present gelators are favorable for the gelation of organic solvents. Scanning electron microscopy and atomic force microscopy observations revealed that the gelator molecules self-assemble into different aggregates, from wrinkle, lamella, and belt to fiber with the change of solvents. Spectral studies indicated that there existed different H-bond formations between amide groups and conformations of methyl chains. The present work may give some insight to the design and character of new organogelators and soft materials with special molecular structures. PMID:23566628

Rapid calculation of accurate atomic charges for proteins via the electronegativity equalization method.

PubMed

Ionescu, Crina-Maria; Geidl, Stanislav; Svobodová Vařeková, Radka; Koča, Jaroslav

2013-10-28

We focused on the parametrization and evaluation of empirical models for fast and accurate calculation of conformationally dependent atomic charges in proteins. The models were based on the electronegativity equalization method (EEM), and the parametrization procedure was tailored to proteins. We used large protein fragments as reference structures and fitted the EEM model parameters using atomic charges computed by three population analyses (Mulliken, Natural, iterative Hirshfeld), at the Hartree-Fock level with two basis sets (6-31G*, 6-31G**) and in two environments (gas phase, implicit solvation). We parametrized and successfully validated 24 EEM models. When tested on insulin and ubiquitin, all models reproduced quantum mechanics level charges well and were consistent with respect to population analysis and basis set. Specifically, the models showed on average a correlation of 0.961, RMSD 0.097 e, and average absolute error per atom 0.072 e. The EEM models can be used with the freely available EEM implementation EEM_SOLVER.

A rapid solvent accessible surface area estimator for coarse grained molecular simulations.

PubMed

Wei, Shuai; Brooks, Charles L; Frank, Aaron T

2017-06-05

The rapid and accurate calculation of solvent accessible surface area (SASA) is extremely useful in the energetic analysis of biomolecules. For example, SASA models can be used to estimate the transfer free energy associated with biophysical processes, and when combined with coarse-grained simulations, can be particularly useful for accounting for solvation effects within the framework of implicit solvent models. In such cases, a fast and accurate, residue-wise SASA predictor is highly desirable. Here, we develop a predictive model that estimates SASAs based on Cα-only protein structures. Through an extensive comparison between this method and a comparable method, POPS-R, we demonstrate that our new method, Protein-C α Solvent Accessibilities or PCASA, shows better performance, especially for unfolded conformations of proteins. We anticipate that this model will be quite useful in the efficient inclusion of SASA-based solvent free energy estimations in coarse-grained protein folding simulations. PCASA is made freely available to the academic community at https://github.com/atfrank/PCASA. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Molecular dynamics simulations of β2-microglobulin interaction with hydrophobic surfaces.

PubMed

Dongmo Foumthuim, Cedrix J; Corazza, Alessandra; Esposito, Gennaro; Fogolari, Federico

2017-11-21

Hydrophobic surfaces are known to adsorb and unfold proteins, a process that has been studied only for a few proteins. Here we address the interaction of β2-microglobulin, a paradigmatic protein for the study of amyloidogenesis, with hydrophobic surfaces. A system with 27 copies of the protein surrounded by a model cubic hydrophobic box is studied by implicit solvent molecular dynamics simulations. Most proteins adsorb on the walls of the box without major distortions in local geometry, whereas free molecules maintain proper structures and fluctuations as observed in explicit solvent molecular dynamics simulations. The major conclusions from the simulations are as follows: (i) the adopted implicit solvent model is adequate to describe protein dynamics and thermodynamics; (ii) adsorption occurs readily and is irreversible on the simulated timescale; (iii) the regions most involved in molecular encounters and stable interactions with the walls are the same as those that are important in protein-protein and protein-nanoparticle interactions; (iv) unfolding following adsorption occurs at regions found to be flexible by both experiments and simulations; (v) thermodynamic analysis suggests a very large contribution from van der Waals interactions, whereas unfavorable electrostatic interactions are not found to contribute much to adsorption energy. Surfaces with different degrees of hydrophobicity may occur in vivo. Our simulations show that adsorption is a fast and irreversible process which is accompanied by partial unfolding. The results and the thermodynamic analysis presented here are consistent with and rationalize previous experimental work.

[Supercomputer investigation of the protein-ligand system low-energy minima].

PubMed

Oferkin, I V; Sulimov, A V; Katkova, E V; Kutov, D K; Grigoriev, F V; Kondakova, O A; Sulimov, V B

2015-01-01

The accuracy of the protein-ligand binding energy calculations and ligand positioning is strongly influenced by the choice of the docking target function. This work demonstrates the evaluation of the five different target functions used in docking: functions based on MMFF94 force field and functions based on PM7 quantum-chemical method accounting or without accounting the implicit solvent model (PCM, COSMO or SGB). For these purposes the ligand positions corresponding to the minima of the target function and the experimentally known ligand positions in the protein active site (crystal ligand positions) were compared. Each function was examined on the same test-set of 16 protein-ligand complexes. The new parallelized docking program FLM based on Monte Carlo search algorithm was developed to perform the comprehensive low-energy minima search and to calculate the protein-ligand binding energy. This study demonstrates that the docking target function based on the MMFF94 force field can be used to detect the crystal or near crystal positions of the ligand by the finding the low-energy local minima spectrum of the target function. The importance of solvent accounting in the docking process for the accurate ligand positioning is also shown. The accuracy of the ligand positioning as well as the correlation between the calculated and experimentally determined protein-ligand binding energies are improved when the MMFF94 force field is substituted by the new PM7 method with implicit solvent accounting.

Density functional theory of freezing of a system of highly elongated ellipsoidal oligomer solutions

NASA Astrophysics Data System (ADS)

Dwivedi, Shikha; Mishra, Pankaj

2017-05-01

We have used the density functional theory of freezing to study the liquid crystalline phase behavior of a system of highly elongated ellipsoidal conjugated oligomers dispersed in three different solvents namely chloroform, toluene and their equimolar mixture. The molecules are assumed to interact via solvent-implicit coarse-grained Gay-Berne potential. Pair correlation functions needed as input in the density functional theory have been calculated using the Percus-Yevick (PY) integral equation theory. Considering the isotropic and nematic phases, we have calculated the isotropic-nematic phase transition parameters and presented the temperature-density and pressure-temperature phase diagrams. Different solvent conditions are found not only to affect the transition parameters but also determine the capability of oligomers to form nematic phase in various thermodynamic conditions. In principle, our results are verifiable through computer simulations.

Sampling the multiple folding mechanisms of Trp-cage in explicit solvent

PubMed Central

Juraszek, J.; Bolhuis, P. G.

2006-01-01

We investigate the kinetic pathways of folding and unfolding of the designed miniprotein Trp- cage in explicit solvent. Straightforward molecular dynamics and replica exchange methods both have severe convergence problems, whereas transition path sampling allows us to sample unbiased dynamical pathways between folded and unfolded states and leads to deeper understanding of the mechanisms of (un)folding. In contrast to previous predictions employing an implicit solvent, we find that Trp-cage folds primarily (80% of the paths) via a pathway forming the tertiary contacts and the salt bridge, before helix formation. The remaining 20% of the paths occur in the opposite order, by first forming the helix. The transition states of the rate-limiting steps are solvated native-like structures. Water expulsion is found to be the last step upon folding for each route. Committor analysis suggests that the dynamics of the solvent is not part of the reaction coordinate. Nevertheless, during the transition, specific water molecules are strongly bound and can play a structural role in the folding. PMID:17035504

Allosteric effects of gold nanoparticles on human serum albumin.

PubMed

Shao, Qing; Hall, Carol K

2017-01-07

The ability of nanoparticles to alter protein structure and dynamics plays an important role in their medical and biological applications. We investigate allosteric effects of gold nanoparticles on human serum albumin protein using molecular simulations. The extent to which bound nanoparticles influence the structure and dynamics of residues distant from the binding site is analyzed. The root mean square deviation, root mean square fluctuation and variation in the secondary structure of individual residues on a human serum albumin protein are calculated for four protein-gold nanoparticle binding complexes. The complexes are identified in a brute-force search process using an implicit-solvent coarse-grained model for proteins and nanoparticles. They are then converted to atomic resolution and their structural and dynamic properties are investigated using explicit-solvent atomistic molecular dynamics simulations. The results show that even though the albumin protein remains in a folded structure, the presence of a gold nanoparticle can cause more than 50% of the residues to decrease their flexibility significantly, and approximately 10% of the residues to change their secondary structure. These affected residues are distributed on the whole protein, even on regions that are distant from the nanoparticle. We analyze the changes in structure and flexibility of amino acid residues on a variety of binding sites on albumin and confirm that nanoparticles could allosterically affect the ability of albumin to bind fatty acids, thyroxin and metals. Our simulations suggest that allosteric effects must be considered when designing and deploying nanoparticles in medical and biological applications that depend on protein-nanoparticle interactions.

Effects of solvent evaporation conditions on solvent vapor annealed cylinder-forming block polymer thin films

NASA Astrophysics Data System (ADS)

Grant, Meagan; Jakubowski, William; Nelson, Gunnar; Drapes, Chloe; Baruth, A.

Solvent vapor annealing is a less time and energy intensive method compared to thermal annealing, to direct the self-assembly of block polymer thin films. Periodic nanostructures have applications in ultrafiltration, magnetic arrays, or other structures with nanometer dimensions, driving its continued interest. Our goal is to create thin films with hexagonally packed, perpendicular aligned cylinders of poly(lactide) in a poly(styrene) matrix that span the thickness of the film with low anneal times and low defect densities, all with high reproducibility, where the latter is paramount. Through the use of our computer-controlled, pneumatically-actuated, purpose-built solvent vapor annealing chamber, we have the ability to monitor and control vapor pressure, solvent concentration within the film, and solvent evaporation rate with unprecedented precision and reliability. Focusing on evaporation, we report on two previously unexplored areas, chamber pressure during solvent evaporation and the flow rate of purging gas aiding the evaporation. We will report our exhaustive results following atomic force microscopy analysis of films exposed to a wide range of pressures and flow rates. Reliably achieving well-ordered films, while occurring within a large section of this parameter space, was correlated with high-flow evaporation rates and low chamber pressures. These results have significant implications on other methods of solvent annealing, including ``jar'' techniques.

Alcohols as hydrogen-donor solvents for treatment of coal

DOEpatents

Ross, David S.; Blessing, James E.

1981-01-01

A method for the hydroconversion of coal by solvent treatment at elevated temperatures and pressure wherein an alcohol having an .alpha.-hydrogen atom, particularly a secondary alcohol such as isopropanol, is utilized as a hydrogen donor solvent. In a particular embodiment, a base capable of providing a catalytically effective amount of the corresponding alcoholate anion under the solvent treatment conditions is added to catalyze the alcohol-coal reaction.

Uncovering Implicit Assumptions: A Large-Scale Study on Students' Mental Models of Diffusion

ERIC Educational Resources Information Center

Stains, Marilyne; Sevian, Hannah

2015-01-01

Students' mental models of diffusion in a gas phase solution were studied through the use of the Structure and Motion of Matter (SAMM) survey. This survey permits identification of categories of ways students think about the structure of the gaseous solute and solvent, the origin of motion of gas particles, and trajectories of solute particles in…

"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.

Identification of protein-ligand binding sites by the level-set variational implicit-solvent approach.

PubMed

Guo, Zuojun; Li, Bo; Cheng, Li-Tien; Zhou, Shenggao; McCammon, J Andrew; Che, Jianwei

2015-02-10

Protein–ligand binding is a key biological process at the molecular level. The identification and characterization of small-molecule binding sites on therapeutically relevant proteins have tremendous implications for target evaluation and rational drug design. In this work, we used the recently developed level-set variational implicit-solvent model (VISM) with the Coulomb field approximation (CFA) to locate and characterize potential protein–small-molecule binding sites. We applied our method to a data set of 515 protein–ligand complexes and found that 96.9% of the cocrystallized ligands bind to the VISM-CFA-identified pockets and that 71.8% of the identified pockets are occupied by cocrystallized ligands. For 228 tight-binding protein–ligand complexes (i.e, complexes with experimental pKd values larger than 6), 99.1% of the cocrystallized ligands are in the VISM-CFA-identified pockets. In addition, it was found that the ligand binding orientations are consistent with the hydrophilic and hydrophobic descriptions provided by VISM. Quantitative characterization of binding pockets with topological and physicochemical parameters was used to assess the “ligandability” of the pockets. The results illustrate the key interactions between ligands and receptors and can be very informative for rational drug design.

Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER.

PubMed

Voelz, Vincent A; Dill, Ken A; Chorny, Ilya

2011-01-01

To test the accuracy of existing AMBER force field models in predicting peptoid conformation and dynamics, we simulated a set of model peptoid molecules recently examined by Butterfoss et al. (JACS 2009, 131, 16798-16807) using QM methods as well as three peptoid sequences with experimentally determined structures. We found that AMBER force fields, when used with a Generalized Born/Surface Area (GBSA) implicit solvation model, could accurately reproduce the peptoid torsional landscape as well as the major conformers of known peptoid structures. Enhanced sampling by replica exchange molecular dynamics (REMD) using temperatures from 300 to 800 K was used to sample over cis-trans isomerization barriers. Compared to (Nrch)5 and cyclo-octasarcosyl, the free energy of N-(2-nitro-3-hydroxyl phenyl)glycine-N-(phenyl)glycine has the most "foldable" free energy landscape, due to deep trans-amide minima dictated by N-aryl sidechains. For peptoids with (S)-N (1-phenylethyl) (Nspe) side chains, we observe a discrepancy in backbone dihedral propensities between molecular simulations and QM calculations, which may be due to force field effects or the inability to capture n --> n* interactions. For these residues, an empirical phi-angle biasing potential can "rescue" the backbone propensities seen in QM. This approach can serve as a general strategy for addressing force fields without resorting to a complete reparameterization. Overall, this study demonstrates the utility of implicit-solvent REMD simulations for efficient sampling to predict peptoid conformational landscapes, providing a potential tool for first-principles design of sequences with specific folding properties.

Solvent effect on the vibrational spectra of Carvedilol.

PubMed

Billes, Ferenc; Pataki, Hajnalka; Unsalan, Ozan; Mikosch, Hans; Vajna, Balázs; Marosi, György

2012-09-01

Carvedilol (CRV) is an important medicament for heart arrhythmia. The aim of this work was the interpretation of its vibrational spectra with consideration on the solvent effect. Infrared and Raman spectra were recorded in solid state as well in solution. The experimental spectra were evaluated using DFT quantum chemical calculations computing the optimized structure, atomic net charges, vibrational frequencies and force constants. The same calculations were done for the molecule in DMSO and aqueous solutions applying the PCM method. The calculated force constants were scaled to the experimentally observed solid state frequencies. The characters of the vibrational modes were determined by their potential energy distributions. Solvent effects on the molecular properties were interpreted. Based on these results vibrational spectra were simulated. Copyright © 2012 Elsevier B.V. All rights reserved.

Electric current-producing device having sulfone-based electrolyte

DOEpatents

Angell, Charles Austen; Sun, Xiao-Guang

2010-11-16

Electrolytic solvents and applications of such solvents including electric current-producing devices. For example, a solvent can include a sulfone compound of R1--SO2--R2, with R1 being an alkyl group and R2 a partially oxygenated alkyl group, to exhibit high chemical and thermal stability and high oxidation resistance. For another example, a battery can include, between an anode and a cathode, an electrolyte which includes ionic electrolyte salts and a non-aqueous electrolyte solvent which includes a non-symmetrical, non-cyclic sulfone. The sulfone has a formula of R1--SO2--R2, wherein R1 is a linear or branched alkyl or partially or fully fluorinated linear or branched alkyl group having 1 to 7 carbon atoms, and R2 is a linear or branched or partially or fully fluorinated linear or branched oxygen containing alkyl group having 1 to 7 carbon atoms. The electrolyte can include an electrolyte co-solvent and an electrolyte additive for protective layer formation.

Complexation of nicotinic acid with first generation poly(amidoamine) dendrimers: A microscopic view from density functional theory

NASA Astrophysics Data System (ADS)

Badalkhani-Khamseh, Farideh; Bahrami, Aidin; Ebrahim-Habibi, Azadeh; Hadipour, Nasser L.

2017-09-01

This study explains some electronic and structural parameters of niacin (NA) encapsulation into PAMAM-G1 dendrimer using DFT calculations. Optimized structural geometries, interaction energies, NMR, NBO, and AIM analyses, in accordance with experiment, revealed that the stability of G1@NA complex can be attributed to the five intermolecular hydrogen bonds formed between the functional groups of G1 and NA. Because of nearing to the experimental results, all the calculations repeated again using a self-consistent reaction field (SCRF) and the polarizable continuum model (PCM) to address the implicit solvent effects and the obtained results were in line with the calculations in gas phase.

Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

PubMed Central

Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; Koliński, Andrzej

2013-01-01

We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems. PMID:23665897

Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm.

PubMed

Zhang, Qing; Beard, Daniel A; Schlick, Tamar

2003-12-01

Salt-mediated electrostatics interactions play an essential role in biomolecular structures and dynamics. Because macromolecular systems modeled at atomic resolution contain thousands of solute atoms, the electrostatic computations constitute an expensive part of the force and energy calculations. Implicit solvent models are one way to simplify the model and associated calculations, but they are generally used in combination with standard atomic models for the solute. To approximate electrostatics interactions in models on the polymer level (e.g., supercoiled DNA) that are simulated over long times (e.g., milliseconds) using Brownian dynamics, Beard and Schlick have developed the DiSCO (Discrete Surface Charge Optimization) algorithm. DiSCO represents a macromolecular complex by a few hundred discrete charges on a surface enclosing the system modeled by the Debye-Hückel (screened Coulombic) approximation to the Poisson-Boltzmann equation, and treats the salt solution as continuum solvation. DiSCO can represent the nucleosome core particle (>12,000 atoms), for example, by 353 discrete surface charges distributed on the surfaces of a large disk for the nucleosome core particle and a slender cylinder for the histone tail; the charges are optimized with respect to the Poisson-Boltzmann solution for the electric field, yielding a approximately 5.5% residual. Because regular surfaces enclosing macromolecules are not sufficiently general and may be suboptimal for certain systems, we develop a general method to construct irregular models tailored to the geometry of macromolecules. We also compare charge optimization based on both the electric field and electrostatic potential refinement. Results indicate that irregular surfaces can lead to a more accurate approximation (lower residuals), and the refinement in terms of the electric field is more robust. We also show that surface smoothing for irregular models is important, that the charge optimization (by the TNPACK minimizer) is efficient and does not depend on the initial assigned values, and that the residual is acceptable when the distance to the model surface is close to, or larger than, the Debye length. We illustrate applications of DiSCO's model-building procedure to chromatin folding and supercoiled DNA bound to Hin and Fis proteins. DiSCO is generally applicable to other interesting macromolecular systems for which mesoscale models are appropriate, to yield a resolution between the all-atom representative and the polymer level. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 2063-2074, 2003

Modeling DNA bubble formation at the atomic scale

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

Beleva, V; Rasmussen, K. O.; Garcia, A. E.

We describe the fluctuations of double stranded DNA molecules using a minimalist Go model over a wide range of temperatures. Minimalist models allow us to describe, at the atomic level, the opening and formation of bubbles in DNA double helices. This model includes all the geometrical constraints in helix melting imposed by the 3D structure of the molecule. The DNA forms melted bubbles within double helices. These bubbles form and break as a function of time. The equilibrium average number of broken base pairs shows a sharp change as a function of T. We observe a temperature profile of sequencemore » dependent bubble formation similar to those measured by Zeng et al. Long nuclei acid molecules melt partially through the formations of bubbles. It is known that CG rich sequences melt at higher temperatures than AT rich sequences. The melting temperature, however, is not solely determined by the CG content, but by the sequence through base stacking and solvent interactions. Recently, models that incorporate the sequence and nonlinear dynamics of DNA double strands have shown that DNA exhibits a very rich dynamics. Recent extensions of the Bishop-Peyrard model show that fluctuations in the DNA structure lead to opening in localized regions, and that these regions in the DNA are associated with transcription initiation sites. 1D and 2D models of DNA may contain enough information about stacking and base pairing interactions, but lack the coupling between twisting, bending and base pair opening imposed by the double helical structure of DNA that all atom models easily describe. However, the complexity of the energy function used in all atom simulations (including solvent, ions, etc) does not allow for the description of DNA folding/unfolding events that occur in the microsecond time scale.« less

SOLVENT EXTRACTION OF URANIUM VALUES

DOEpatents

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

1959-02-01

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

A new method for calculating time-dependent atomic level populations

NASA Technical Reports Server (NTRS)

Kastner, S. O.

1981-01-01

A method is described for reducing the number of levels to be dealt with in calculating time-dependent populations of atoms or ions in plasmas. The procedure effectively extends the collisional-radiative model to consecutive stages of ionization, treating ground and metastable levels explicitly and excited levels implicitly. Direct comparisons of full and simulated systems are carried out for five-level models.

Sensitized and heavy atom induced production of acenaphthylene triplet: A laser flash photolysis study

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

Samanta, A.; Fessenden, R.W.

1989-07-27

The triplet state of acenaphthylene has been examined by nanosecond laser flash photolysis using sensitization and heavy atom perturbation techniques. Although acenaphthylene does not form any observable triplet upon direct flash excitation, a transient with microsecond lifetime ({lambda}{sub max} = 315 nm) is observable when a solution of the sample is excited by sensitizers (benzophenone, thioxanthone, benzil). This transient is ascribed to the triplet of acenaphthylene on the basis of its quenching behavior toward oxygen, ferrocene, azulene, and {beta}-carotene. Quantitative data concerning the triplet-triplet absorption and quenching constants are presented. The triplet energy is estimated to lie between 46 andmore » 47 kcal/mol. The triplet can also be produced by direct excitation in solvents containing heavy atoms (ethyl bromide, ethyl iodide). The triplet yield is found to increase with an increase of the amount of the heavy atom containing solvent. No saturation limit is obtained. These facts together with the effect of heavy atoms on the T{sub 1} {yields} S{sub 0} process allow the differing behavior of ethyl bromide and ethyl iodide on the photodimerization process of acenaphthylene to be explained. Triplet-state parameters (extinction coefficient and triplet yield) have been estimated in these solvents by the energy-transfer technique and actinometry.« less

Application of discrete solvent reaction field model with self-consistent atomic charges and atomic polarizabilities to calculate the χ(1) and χ(2) of organic molecular crystals

NASA Astrophysics Data System (ADS)

Lu, Shih-I.

2018-01-01

We use the discrete solvent reaction field model to evaluate the linear and second-order nonlinear optical susceptibilities of 3-methyl-4-nitropyridine-1-oxyde crystal. In this approach, crystal environment is created by supercell architecture. A self-consistent procedure is used to obtain charges and polarizabilities for environmental atoms. Impact of atomic polarizabilities on the properties of interest is highlighted. This approach is shown to give the second-order nonlinear optical susceptibilities within error bar of experiment as well as the linear optical susceptibilities in the same order as experiment. Similar quality of calculations are also applied to both 4-N,N-dimethylamino-3-acetamidonitrobenzene and 2-methyl-4-nitroaniline crystals.

The effect of denaturant on protein stability: a Monte Carlo lattice simulation

NASA Astrophysics Data System (ADS)

Choi, Ho Sup; Huh, June; Jo, Won Ho

2003-03-01

Denaturants are the reagents that decrease protein stability by interacting with both nonpolar and polar surfaces of protein when added to the aqueous solvent. However, the physical nature of these interactions has not been clearly understood. It is not easy to elucidate the nature of denaturant theoretically or experimentally. Even in computer simulation, the denaturant atoms are unable to be dealt explicitly due to computationally enormous costs. We have used a lattice model of protein and denaturant. By varying concentration of denaturant and interaction energy between protein and denaturant, we have measured the change of stability of the protein. This simple model reflects the experimental observation that the free energy of unfolding is a linear function of denaturant concentration in the transition range. We have also performed a simulation under isotropic perturbation. In this case, denaturant molecules are not included and a biasing potential is introduced in order to increase the radius of gyration of protein, which incorporates the effect of denaturant implicitly. The calculated free energy landscape and conformational ensembles sampled under this condition is very close to those of simulation using denaturant molecules interacting with protein. We have applied this simple approach for simulating the effect of denaturant to real proteins.

Influence of different amino substituents in position 1 and 4 on spectroscopic and acid base properties of 9,10-anthraquinone moiety

NASA Astrophysics Data System (ADS)

Wcisło, Anna; Niedziałkowski, Paweł; Wnuk, Elżbieta; Zarzeczańska, Dorota; Ossowski, Tadeusz

2013-05-01

A series of novel 1-amino and 1,4-diamino-9,10-anthraquinones, substituted with different alkyl groups, were synthesized as the result of alkylation with amino substituents. All the obtained aminoanthraquinone derivatives were characterized by NMR, IR spectroscopy and mass spectrometry. The spectroscopic properties of these compounds were determined by using UV-Vis spectroscopy in acetonitrile, and in the mixture of acetonitrile and methanol at different pH ranges. The effects of various substituents present in the newly developed anthraquinone derivatives and their ability to form hydrogen bonds between the carbonyl oxygen atom of anthraquinone moiety and nitrogen atom of N-H group in 1-aminoanthraquinone (1-AAQ) and 1,4-diaminoanthraquinone (1,4-DAAQ) were studied. Additionally, the effects of hydrogen bond formation between O-H group in hydroxyethylamino substituent and the carbonyl oxygen atom of anthraquinone were investigated. The spectroscopic behavior of the studied derivatives strongly depended on the solvent-solute interactions and the nature of solvent. The values of pKa for the new anthraquinones were determined by the combined potentiometric and spectrophotometric titration methods.

Understanding the impact of the central atom on the ionic liquid behavior: phosphonium vs ammonium cations.

PubMed

Carvalho, Pedro J; Ventura, Sónia P M; Batista, Marta L S; Schröder, Bernd; Gonçalves, Fernando; Esperança, José; Mutelet, Fabrice; Coutinho, João A P

2014-02-14

The influence of the cation's central atom in the behavior of pairs of ammonium- and phosphonium-based ionic liquids was investigated through the measurement of densities, viscosities, melting temperatures, activity coefficients at infinite dilution, refractive indices, and toxicity against Vibrio fischeri. All the properties investigated are affected by the cation's central atom nature, with ammonium-based ionic liquids presenting higher densities, viscosities, melting temperatures, and enthalpies. Activity coefficients at infinite dilution show the ammonium-based ionic liquids to present slightly higher infinite dilution activity coefficients for non-polar solvents, becoming slightly lower for polar solvents, suggesting that the ammonium-based ionic liquids present somewhat higher polarities. In good agreement these compounds present lower toxicities than the phosphonium congeners. To explain this behavior quantum chemical gas phase DFT calculations were performed on isolated ion pairs at the BP-TZVP level of theory. Electronic density results were used to derive electrostatic potentials of the identified minimum conformers. Electrostatic potential-derived CHelpG and Natural Population Analysis charges show the P atom of the tetraalkylphosphonium-based ionic liquids cation to be more positively charged than the N atom in the tetraalkylammonium-based analogous IL cation, and a noticeable charge delocalization occurring in the tetraalkylammonium cation, when compared with the respective phosphonium congener. It is argued that this charge delocalization is responsible for the enhanced polarity observed on the ammonium based ionic liquids explaining the changes in the thermophysical properties observed.

Understanding the impact of the central atom on the ionic liquid behavior: Phosphonium vs ammonium cations

NASA Astrophysics Data System (ADS)

Carvalho, Pedro J.; Ventura, Sónia P. M.; Batista, Marta L. S.; Schröder, Bernd; Gonçalves, Fernando; Esperança, José; Mutelet, Fabrice; Coutinho, João A. P.

2014-02-01

The influence of the cation's central atom in the behavior of pairs of ammonium- and phosphonium-based ionic liquids was investigated through the measurement of densities, viscosities, melting temperatures, activity coefficients at infinite dilution, refractive indices, and toxicity against Vibrio fischeri. All the properties investigated are affected by the cation's central atom nature, with ammonium-based ionic liquids presenting higher densities, viscosities, melting temperatures, and enthalpies. Activity coefficients at infinite dilution show the ammonium-based ionic liquids to present slightly higher infinite dilution activity coefficients for non-polar solvents, becoming slightly lower for polar solvents, suggesting that the ammonium-based ionic liquids present somewhat higher polarities. In good agreement these compounds present lower toxicities than the phosphonium congeners. To explain this behavior quantum chemical gas phase DFT calculations were performed on isolated ion pairs at the BP-TZVP level of theory. Electronic density results were used to derive electrostatic potentials of the identified minimum conformers. Electrostatic potential-derived CHelpG and Natural Population Analysis charges show the P atom of the tetraalkylphosphonium-based ionic liquids cation to be more positively charged than the N atom in the tetraalkylammonium-based analogous IL cation, and a noticeable charge delocalization occurring in the tetraalkylammonium cation, when compared with the respective phosphonium congener. It is argued that this charge delocalization is responsible for the enhanced polarity observed on the ammonium based ionic liquids explaining the changes in the thermophysical properties observed.

Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Perilla, Juan R.; Schulten, Klaus

2017-07-01

Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of ~1,300 proteins with altogether 4 million atoms. Although the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical-physical properties of an empty HIV-1 capsid, including its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. The simulations reveal critical details about the capsid with implications to biological function.

Determination of traces of silicone defoamer in fruit juices by solvent extraction/atomic absorption spectroscopy.

PubMed

Gooch, E G

1993-01-01

Silicone defoamers are used to control foam during the processing of fruit juices. Residual silicones in fruit juices can be separated from the naturally occurring siliceous materials in fruit products and selectively recovered by solvent extraction, after suitable pretreatment. The recovered silicone is measured by atomic absorption spectroscopy. Silicone concentrations as low as about 1 ppm can be measured. The juices are accurately spiked for recovery studies by the addition of silicone dispersed in D-sorbitol.

EPR parameters of L-α-alanine radicals in aqueous solution: a first-principles study

NASA Astrophysics Data System (ADS)

Janbazi, Mehdi; T. Azar, Yavar; Ziaie, Farhood

2018-07-01

EPR (electron paramagnetic resonance) response for a wide range of possible alanine radicals has been analysed employing quantum chemical methods. The strong correlation between geometry and EPR parameter structure of these radicals has been shown in this research work. Significant solvent effect on EPR parameters has been shown employing both explicit and implicit solvent models. In a relatively good agreement with the experiment, stable conformation of these radicals in acidic and basic conditions was determined, and a new conformation was suggested based on possible proton transfer in the intermediate pH range. The employed methodology along with experimental results may be used for the characterisation of different radiation-induced amino acid radicals.

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

PubMed

Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N

2009-05-01

Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function.

An All-atom Structure-Based Potential for Proteins: Bridging Minimal Models with All-atom Empirical Forcefields

PubMed Central

Whitford, Paul C.; Noel, Jeffrey K.; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y.; Onuchic, José N.

2012-01-01

Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Gō) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a Cα structure-based model and an all-atom empirical forcefield. Key findings include 1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature 2) folding mechanisms are robust to variations of the energetic parameters 3) protein folding free energy barriers can be manipulated through parametric modifications 4) the global folding mechanisms in a Cα model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model 5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Since this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035

Design, construction, and testing a purpose-built climate-controlled solvent vapor annealing chamber for guided self-assembly of block polymer thin films

NASA Astrophysics Data System (ADS)

Gnabasik, Ryan; Haase, Rustin; Baruth, Andrew

2014-03-01

Despite its efficacy to produce well-ordered, periodic nanostructures, the intricate role multiple parameters play in solvent vapor annealing has not been fully established. In solvent vapor annealing a thin polymer film is exposed to the vapors of a solvent(s) thus forming a swollen and mobile layer to direct the self-assembly process at the nanoscale. Recent developments in both theory and experiment have directly identified critical parameters, but controlling them in any systematic way has proven non-trivial. These identified parameters include vapor pressure, solvent concentration in the film, and, critically, the solvent evaporation rate. To explore their role, a purpose-built solvent vapor annealing chamber was designed and constructed. The all-metal chamber is inert to solvent exposure and pneumatically actuated valves allow for precision timing in the introduction and withdrawal of solvent vapor. Furthermore, the mass flow controlled inlet, chamber pressure gauges, in situ spectral reflectance-based thickness monitoring, and high precision micrometer relief valve, give real-time monitoring and control during the annealing and evaporation phases. Using atomic force microscopy to image the annealed films, we are able to map out the parameter space for a series of polystyrene- b-polylactide (Mn = 75 kg/mol and fPLA = 0.28) block polymer thin films with an intrinsic cylindrical morphology and identify their role in directed assembly. Funded by Creighton University Summer Research Grant.

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

PubMed Central

Topgaard, Daniel; Sparr, Emma

2017-01-01

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

Predicting solvatochromic shifts and colours of a solvated organic dye: The example of nile red

NASA Astrophysics Data System (ADS)

Zuehlsdorff, T. J.; Haynes, P. D.; Payne, M. C.; Hine, N. D. M.

2017-03-01

The solvatochromic shift, as well as the change in colour of the simple organic dye nile red, is studied in two polar and two non-polar solvents in the context of large-scale time-dependent density-functional theory (TDDFT) calculations treating large parts of the solvent environment from first principles. We show that an explicit solvent representation is vital to resolve absorption peak shifts between nile red in n-hexane and toluene, as well as acetone and ethanol. The origin of the failure of implicit solvent models for these solvents is identified as being due to the strong solute-solvent interactions in form of π-stacking and hydrogen bonding in the case of toluene and ethanol. We furthermore demonstrate that the failures of the computationally inexpensive Perdew-Burke-Ernzerhof (PBE) functional in describing some features of the excited state potential energy surface of the S1 state of nile red can be corrected for in a straightforward fashion, relying only on a small number of calculations making use of more sophisticated range-separated hybrid functionals. The resulting solvatochromic shifts and predicted colours are in excellent agreement with experiment, showing the computational approach outlined in this work to yield very robust predictions of optical properties of dyes in solution.

Flexible binding simulation by a novel and improved version of virtual-system coupled adaptive umbrella sampling

NASA Astrophysics Data System (ADS)

Dasgupta, Bhaskar; Nakamura, Haruki; Higo, Junichi

2016-10-01

Virtual-system coupled adaptive umbrella sampling (VAUS) enhances sampling along a reaction coordinate by using a virtual degree of freedom. However, VAUS and regular adaptive umbrella sampling (AUS) methods are yet computationally expensive. To decrease the computational burden further, improvements of VAUS for all-atom explicit solvent simulation are presented here. The improvements include probability distribution calculation by a Markov approximation; parameterization of biasing forces by iterative polynomial fitting; and force scaling. These when applied to study Ala-pentapeptide dimerization in explicit solvent showed advantage over regular AUS. By using improved VAUS larger biological systems are amenable.

Novel Fischer-Tropsch catalysts

DOEpatents

Vollhardt, Kurt P. C.; Perkins, Patrick

1981-01-01

Novel polymer-supported metal complexes of the formula PS -R Me(CO).sub.n H.sub.m where: PS represents a divinylbenzene crosslinked polystyrene in which the divinylbenzene crosslinking is greater than 1% and less than about 18%; R represents a cycloalkadienyl radical of 4 through 6 carbon atoms; Me represents a Group VIII metal; CO represents a carbonyl radical; H represents hydrogen; n represents an integer varying from 0 through 3; m represents an integer varying from 0 through 2 inclusively with the further provision that 2n+m must total 18 when added to the electrons in R and Me, or n+m must total 0; are prepared by: brominating PS -H by treating same with bromine in the presence of a thallium salt in a partially or fully halogenated solvent to form PS -Br; treating said PS -Br so produced with a lithium alkyl of 1 through 12 carbon atoms in an aromatic solvent to produce PS -Li; substituting said PS - Li so produced by reaction with a 2-cycloalkenone of 4 to 6 carbon atoms in the presence of an ether solvent and using a water work-up to form a cycloalkenylalcohol-substituted PS ; dehydrating said alcohol so produced by heating under a vacuum to produce a cycloalkadienyl-substituted PS ; reacting the cycloalkadienyl-substituted PS with metal carbonyl in the presence of a partially or fully halogenated hydrocarbon, aromatic hydrocarbon of 6 through 8 carbon atoms, ethers, or esters of 4 through 10 carbon atoms as a solvent to produce a polystyrene-supported cycloalkadienyl metal carbonyl. The novel compounds are used as improved Fischer-Tropsch catalysts particularly for the conversion of CO+H.sub.2 to gaseous and liquid hydrocarbons at milder conditions than with prior catalysts.

Novel Fischer-Tropsch catalysts

DOEpatents

Vollhardt, Kurt P. C.; Perkins, Patrick

1980-01-01

Novel polymer-supported metal complexes of the formula: PS --R Me(CO).sub.n H.sub.m where: PS represents a divinylbenzene crosslinked polystyrene in which the divinylbenzene crosslinking is greater than 1% and less than about 18%; R represents a cycloalkadienyl radical of 4 through 6 carbon atoms; Me represents a Group VIII metal; CO represents a carbonyl radical; H represents hydrogen; n represents an integer varying from 0 through 3; m represents an integer varying from 0 through 2 inclusively with the further provision that 2n+m must total 18 when added to the electrons in R and Me, or n+m must total 0; are prepared by: brominating PS --H by treating same with bromine in the presence of a thallium salt in a partially or fully halogenated solvent to form PS --Br; treating said PS --Br so produced with a lithium alkyl of 1 through 12 carbon atoms in an aromatic solvent to produce PS --Li; substituting said PS-- Li so produced by reaction with a 2-cycloalkenone of 4 to 6 carbon atoms in the presence of an ether solvent and using a water work-up to form a cycloalkenylalcohol-substituted PS ; dehydrating said alcohol so produced by heating under a vacuum to produce a cycloalkadienyl-substituted PS ; reacting the cycloalkadienyl-substituted PS with metal carbonyl in the presence of a partially or fully halogenated hydrocarbon, aromatic hydrocarbon of 6 through 8 carbon atoms, ethers, or esters of 4 through 10 carbon atoms as a solvent to produce a polystyrene-supported cycloalkadienyl metal carbonyl. The novel compounds are used as improved Fischer-Tropsch catalysts particularly for the conversion of CO+H.sub.2 to gaseous and liquid hydrocarbons at milder conditions than with prior catalysts.

Novel Fischer-Tropsch catalysts

DOEpatents

Vollhardt, Kurt P. C.; Perkins, Patrick

1981-01-01

Novel polymer-supported metal complexes of the formula: PS --R Me(CO).sub.n H.sub.m where: PS represents a divinylbenzene crosslinked polystyrene in which the divinylbenzene crosslinking is greater than 1% and less than about 18%; R represents a cycloalkadienyl radical of 4 through 6 carbon atoms; Me represents a Group VIII metal; CO represents a carbonyl radical; H represents hydrogen; n represents an integer varying from 0 through 3; m represents an integer varying from 0 through 2 inclusively with the further provision that 2n+m must total 18 when added to the electrons in R and Me, or n+m must total 0; are prepared by: brominating PS --H by treating same with bromine in the presence of a thallium salt in a partially or fully halogenated solvent to form PS --Br; treating said PS --Br so produced with a lithium alkyl of 1 through 12 carbon atoms in an aromatic solvent to produce PS --Li; substituting said PS-- Li so produced by reaction with a 2-cycloalkenone of 4 to 6 carbon atoms in the presence of an ether solvent and using a water work-up to form a cycloalkenylalcohol-substituted PS ; dehydrating said alcohol so produced by heating under a vacuum to produce a cycloalkadienyl-substituted PS ; reacting the cycloalkadienyl-substituted PS with metal carbonyl in the presence of a partially or fully halogenated hydrocarbon, aromatic hydrocarbon of 6 through 8 carbon atoms, ethers, or esters of 4 through 10 carbon atoms as a solvent to produce a polystyrene-supported cycloalkadienyl metal carbonyl. The novel compounds are used as improved Fischer-Tropsch catalysts particularly for the conversion of CO+H.sub.2 to gaseous and liquid hydrocarbons at milder conditions than with prior catalysts.

Acid gas scrubbing by composite solvent-swollen membranes

DOEpatents

Matson, Stephen L.; Lee, Eric K. L.; Friesen, Dwayne T.; Kelly, Donald J.

1988-01-01

A composite immobilized liquid membrane suitable for acid gas scrubbing is disclosed. The membrane is a solvent-swollen polymer and a microporous polymeric support, the solvent being selected from a class of highly polar solvents containing at least one atom selected from nitrogen, oxygen, phosphorous and sulfur, and having a boiling point of at least 100.degree. C. and a solubility parameter of from about 7.5 to about 13.5 (cal/cm.sup.3 -atm).sup.1/2. Such solvents are homogeneously distributed through the solvent-swollen polymer from 20% to 95% by weight. Also disclosed are methods of acid gas scrubbing of high- and low-Btu gas effluents with such solvent-swollen membranes.

Acid gas scrubbing by composite solvent-swollen membranes

DOEpatents

Matson, S.L.; Lee, E.K.L.; Friesen, D.T.; Kelly, D.J.

1988-04-12

A composite immobilized liquid membrane suitable for acid gas scrubbing is disclosed. The membrane is a solvent-swollen polymer and a microporous polymeric support, the solvent being selected from a class of highly polar solvents containing at least one atom selected from nitrogen, oxygen, phosphorus and sulfur, and having a boiling point of at least 100 C and a solubility parameter of from about 7.5 to about 13.5 (cal/cm[sup 3]-atm)[sup 1/2]. Such solvents are homogeneously distributed through the solvent-swollen polymer from 20% to 95% by weight. Also disclosed are methods of acid gas scrubbing of high- and low-Btu gas effluents with such solvent-swollen membranes. 3 figs.

The interaction between ketamine and some crown ethers in common organic solvents studied by NMR: The effect of donating atoms and ligand structure

NASA Astrophysics Data System (ADS)

Chekin, Fereshteh; Bordbar, Maryam; Fathollahi, Yaghoub; Alizadeh, Naader

2006-02-01

1H NMR spectroscopy was used to investigate the stoichiometry and stability of the drug ketamine cation complexes with some crown ethers, such as 15-crown-5 (15C5), aza-15-crown-5 (A15C5), 18-crown-6 (18C6), aza-18-crown-6 (A18C6), diaza-18-crown-6 (DA18C6), dibenzyl-diaza-18-crown-6 (DBzDA18C6) and cryptant [2,2,2] (C222) in acetonitrile (AN), dimethylsulfoxide (DMSO) and methanol (MeOH) at 27 °C. In order to evaluate the formation constants of the ketamine cation complexes, the CH 3 protons chemical shift (on the nitrogen atom of ketamine) was measured as function of ligand/ketamine mole ratio. The formation constant of resulting complexes were calculated by the computer fitting of chemical shift versus mole ratio data to appropriate equations. A significant chemical shift variation was not observed for 15C5 and 18C6. The stoichiometry of the mono aza and diaza ligands are 1:1 and 1:2 (ligand/ketamine), respectively. In all of the solvents studied, DA18C6 formed more stable complexes than other ligands. The solvent effect on the stability of these complexes is discussed.

Overview of the SAMPL5 host–guest challenge: Are we doing better?

PubMed Central

Yin, Jian; Henriksen, Niel M.; Slochower, David R.; Shirts, Michael R.; Chiu, Michael W.; Mobley, David L.; Gilson, Michael K.

2016-01-01

The ability to computationally predict protein-small molecule binding affinities with high accuracy would accelerate drug discovery and reduce its cost by eliminating rounds of trial-and-error synthesis and experimental evaluation of candidate ligands. As academic and industrial groups work toward this capability, there is an ongoing need for datasets that can be used to rigorously test new computational methods. Although protein–ligand data are clearly important for this purpose, their size and complexity make it difficult to obtain well-converged results and to troubleshoot computational methods. Host–guest systems offer a valuable alternative class of test cases, as they exemplify noncovalent molecular recognition but are far smaller and simpler. As a consequence, host–guest systems have been part of the prior two rounds of SAMPL prediction exercises, and they also figure in the present SAMPL5 round. In addition to being blinded, and thus avoiding biases that may arise in retrospective studies, the SAMPL challenges have the merit of focusing multiple researchers on a common set of molecular systems, so that methods may be compared and ideas exchanged. The present paper provides an overview of the host–guest component of SAMPL5, which centers on three different hosts, two octa-acids and a glycoluril-based molecular clip, and two different sets of guest molecules, in aqueous solution. A range of methods were applied, including electronic structure calculations with implicit solvent models; methods that combine empirical force fields with implicit solvent models; and explicit solvent free energy simulations. The most reliable methods tend to fall in the latter class, consistent with results in prior SAMPL rounds, but the level of accuracy is still below that sought for reliable computer-aided drug design. Advances in force field accuracy, modeling of protonation equilibria, electronic structure methods, and solvent models, hold promise for future improvements. PMID:27658802

Overview of the SAMPL5 host-guest challenge: Are we doing better?

PubMed

Yin, Jian; Henriksen, Niel M; Slochower, David R; Shirts, Michael R; Chiu, Michael W; Mobley, David L; Gilson, Michael K

2017-01-01

The ability to computationally predict protein-small molecule binding affinities with high accuracy would accelerate drug discovery and reduce its cost by eliminating rounds of trial-and-error synthesis and experimental evaluation of candidate ligands. As academic and industrial groups work toward this capability, there is an ongoing need for datasets that can be used to rigorously test new computational methods. Although protein-ligand data are clearly important for this purpose, their size and complexity make it difficult to obtain well-converged results and to troubleshoot computational methods. Host-guest systems offer a valuable alternative class of test cases, as they exemplify noncovalent molecular recognition but are far smaller and simpler. As a consequence, host-guest systems have been part of the prior two rounds of SAMPL prediction exercises, and they also figure in the present SAMPL5 round. In addition to being blinded, and thus avoiding biases that may arise in retrospective studies, the SAMPL challenges have the merit of focusing multiple researchers on a common set of molecular systems, so that methods may be compared and ideas exchanged. The present paper provides an overview of the host-guest component of SAMPL5, which centers on three different hosts, two octa-acids and a glycoluril-based molecular clip, and two different sets of guest molecules, in aqueous solution. A range of methods were applied, including electronic structure calculations with implicit solvent models; methods that combine empirical force fields with implicit solvent models; and explicit solvent free energy simulations. The most reliable methods tend to fall in the latter class, consistent with results in prior SAMPL rounds, but the level of accuracy is still below that sought for reliable computer-aided drug design. Advances in force field accuracy, modeling of protonation equilibria, electronic structure methods, and solvent models, hold promise for future improvements.

Correlation of atomic packing with the boson peak in amorphous alloys

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

Yang, W. M.; Key Laboratory of Magnetic Materials and Devices, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201; School of Materials Science and Engineering, Southeast University, Nanjing 211189

2014-09-28

Boson peaks (BP) have been observed from phonon specific heats in 10 studied amorphous alloys. Two Einstein-type vibration modes were proposed in this work and all data can be fitted well. By measuring and analyzing local atomic structures of studied amorphous alloys and 56 reported amorphous alloys, it is found that (a) the BP originates from local harmonic vibration modes associated with the lengths of short-range order (SRO) and medium-range order (MRO) in amorphous alloys, and (b) the atomic packing in amorphous alloys follows a universal scaling law, i.e., the ratios of SRO and MRO lengths to solvent atomic diametermore » are 3 and 7, respectively, which exact match with length ratios of BP vibration frequencies to Debye frequency for the studied amorphous alloys. This finding provides a new perspective for atomic packing in amorphous materials, and has significant implications for quantitative description of the local atomic orders and understanding the structure-property relationship.« less

Standard atomic volumes in double-stranded DNA and packing in protein–DNA interfaces

PubMed Central

Nadassy, Katalin; Tomás-Oliveira, Isabel; Alberts, Ian; Janin, Joël; Wodak, Shoshana J.

2001-01-01

Standard volumes for atoms in double-stranded B-DNA are derived using high resolution crystal structures from the Nucleic Acid Database (NDB) and compared with corresponding values derived from crystal structures of small organic compounds in the Cambridge Structural Database (CSD). Two different methods are used to compute these volumes: the classical Voronoi method, which does not depend on the size of atoms, and the related Radical Planes method which does. Results show that atomic groups buried in the interior of double-stranded DNA are, on average, more tightly packed than in related small molecules in the CSD. The packing efficiency of DNA atoms at the interfaces of 25 high resolution protein–DNA complexes is determined by computing the ratios between the volumes of interfacial DNA atoms and the corresponding standard volumes. These ratios are found to be close to unity, indicating that the DNA atoms at protein–DNA interfaces are as closely packed as in crystals of B-DNA. Analogous volume ratios, computed for buried protein atoms, are also near unity, confirming our earlier conclusions that the packing efficiency of these atoms is similar to that in the protein interior. In addition, we examine the number, volume and solvent occupation of cavities located at the protein–DNA interfaces and compared them with those in the protein interior. Cavities are found to be ubiquitous in the interfaces as well as inside the protein moieties. The frequency of solvent occupation of cavities is however higher in the interfaces, indicating that those are more hydrated than protein interiors. Lastly, we compare our results with those obtained using two different measures of shape complementarity of the analysed interfaces, and find that the correlation between our volume ratios and these measures, as well as between the measures themselves, is weak. Our results indicate that a tightly packed environment made up of DNA, protein and solvent atoms plays a significant role in protein–DNA recognition. PMID:11504874

Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions.

PubMed

Olson, Mark A; Feig, Michael; Brooks, Charles L

2008-04-15

This article examines ab initio methods for the prediction of protein loops by a computational strategy of multiscale conformational sampling and physical energy scoring functions. Our approach consists of initial sampling of loop conformations from lattice-based low-resolution models followed by refinement using all-atom simulations. To allow enhanced conformational sampling, the replica exchange method was implemented. Physical energy functions based on CHARMM19 and CHARMM22 parameterizations with generalized Born (GB) solvent models were applied in scoring loop conformations extracted from the lattice simulations and, in the case of all-atom simulations, the ensemble of conformations were generated and scored with these models. Predictions are reported for 25 loop segments, each eight residues long and taken from a diverse set of 22 protein structures. We find that the simulations generally sampled conformations with low global root-mean-square-deviation (RMSD) for loop backbone coordinates from the known structures, whereas clustering conformations in RMSD space and scoring detected less favorable loop structures. Specifically, the lattice simulations sampled basins that exhibited an average global RMSD of 2.21 +/- 1.42 A, whereas clustering and scoring the loop conformations determined an RMSD of 3.72 +/- 1.91 A. Using CHARMM19/GB to refine the lattice conformations improved the sampling RMSD to 1.57 +/- 0.98 A and detection to 2.58 +/- 1.48 A. We found that further improvement could be gained from extending the upper temperature in the all-atom refinement from 400 to 800 K, where the results typically yield a reduction of approximately 1 A or greater in the RMSD of the detected loop. Overall, CHARMM19 with a simple pairwise GB solvent model is more efficient at sampling low-RMSD loop basins than CHARMM22 with a higher-resolution modified analytical GB model; however, the latter simulation method provides a more accurate description of the all-atom energy surface, yet demands a much greater computational cost. (c) 2007 Wiley Periodicals, Inc.

Solvent selection for explaining the morphology of nitroguanidine crystal by molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Song, Liang; Chen, Lizhen; Cao, Duanlin; Wang, Jianlong

2018-02-01

In this article, a method was performed to predict the morphology of needle-shaped crystals by analyzing the growth mechanisms for the various crystal faces. As an example, the crystal morphology of a nitroguanidine (NQ) was investigated via molecular dynamics simulations. The modified attachment energy (MEA) model was constructed by introducing surface chemistry terms and the relevant morphology of the habit crystal faces. The results indicate that the growth morphology of NQ in vacuum is dominated by {2 2 0}, {0 4 0}, {1 1 1}, {1 3 1} and {3 1 1} faces. The {2 2 0} and {0 4 0} faces are parallel to the elongation direction of the crystal, while the other faces are at the needle tips direction. The atoms or atomic groups exposed in crystal surface were used to analyze the relationship between structure and morphology. Compared to the surrounding faces, the needle tip faces have a large number of polar atoms or atomic groups. The needle tip faces have a high electronegativity on N, O atoms via molecular electrostatic potential (ESP) analysis. Furthermore, the protic solvent was used to reduce the attachment energy of the tip surfaces for achieving the purpose of inhibiting the growth of needle tips. Gamma-butyrolactone as the selected solvent inhibited effectively the growth of the needle tip faces. The predicted result is serviceable for the formation design.

Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

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

Perilla, Juan R.; Schulten, Klaus

Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of B 1,300 proteins with altogether 4 million atoms. Though the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical–physical properties of an empty HIV-1 capsid, includingmore » its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. Furthermore, the simulations reveal critical details about the capsid with implications to biological function.« less

Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

DOE PAGES

Perilla, Juan R.; Schulten, Klaus

2017-07-19

Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of B 1,300 proteins with altogether 4 million atoms. Though the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical–physical properties of an empty HIV-1 capsid, includingmore » its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. Furthermore, the simulations reveal critical details about the capsid with implications to biological function.« less

“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

Implicit membrane treatment of buried charged groups: application to peptide translocation across lipid bilayers.

PubMed

Lazaridis, Themis; Leveritt, John M; PeBenito, Leo

2014-09-01

The energetic cost of burying charged groups in the hydrophobic core of lipid bilayers has been controversial, with simulations giving higher estimates than certain experiments. Implicit membrane approaches are usually deemed too simplistic for this problem. Here we challenge this view. The free energy of transfer of amino acid side chains from water to the membrane center predicted by IMM1 is reasonably close to all-atom free energy calculations. The shape of the free energy profile, however, for the charged side chains needs to be modified to reflect the all-atom simulation findings (IMM1-LF). Membrane thinning is treated by combining simulations at different membrane widths with an estimate of membrane deformation free energy from elasticity theory. This approach is first tested on the voltage sensor and the isolated S4 helix of potassium channels. The voltage sensor is stably inserted in a transmembrane orientation for both the original and the modified model. The transmembrane orientation of the isolated S4 helix is unstable in the original model, but a stable local minimum in IMM1-LF, slightly higher in energy than the interfacial orientation. Peptide translocation is addressed by mapping the effective energy of the peptide as a function of vertical position and tilt angle, which allows identification of minimum energy pathways and transition states. The barriers computed for the S4 helix and other experimentally studied peptides are low enough for an observable rate. Thus, computational results and experimental studies on the membrane burial of peptide charged groups appear to be consistent. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova. Copyright © 2014 Elsevier B.V. All rights reserved.

Dielectric Boundary Force in Molecular Solvation with the Poisson–Boltzmann Free Energy: A Shape Derivative Approach

PubMed Central

Li, Bo; Cheng, Xiaoliang; Zhang, Zhengfang

2013-01-01

In an implicit-solvent description of molecular solvation, the electrostatic free energy is given through the electrostatic potential. This potential solves a boundary-value problem of the Poisson–Boltzmann equation in which the dielectric coefficient changes across the solute-solvent interface—the dielectric boundary. The dielectric boundary force acting on such a boundary is the negative first variation of the electrostatic free energy with respect to the location change of the boundary. In this work, the concept of shape derivative is used to define such variations and formulas of the dielectric boundary force are derived. It is shown that such a force is always in the direction toward the charged solute molecules. PMID:24058212

LIGAMENT-CONTROLLED EFFERVESCENT ATOMIZATION

EPA Science Inventory

The operating principles and performance of a new type of spray nozzle are presented. This nozzle, termed a "ligament-controlled effervescent atomizer," was developed to allow consumer product manufacturers to replace volatile organic compound (VOC) solvents with water and hydroc...

Selective determination of arsenic(III) and arsenic(V) with ammonium pyrrolidinedithiocarbamate, sodium diethyldithiocarbamate and dithizone by means of flameless atomic-absorption spectrophotometry with a carbon-tube atomizer.

PubMed

Kamada, T

The extraction behaviour of arsenic(III) and arsenic(V) with ammonium pyrrolidinedithiocarbamate, sodium diethyldithiocarbamate and dithizone in organic solvents has been investigated by means of nameless atomic-absorption spectrophotometry with a carbon-tube atomizer. The selective extraction of arsenic(III) and differential determination of arsenic(III) and arsenic(V) have been developed. With ammonium pyrrolidinedithiocarbamate and methyl isobutyl ketone or nitrobenzene, when the aqueous phase/solvent volume ratio is 5 and the injection volume in the carbon tube is 20 mul, the sensitivities for 1% absorption are 0.4 and 0.5 part per milliard of arsenic, respectively. The relative standard deviations are ca. 3%. Interference by many metal ions can be prevented by masking with EDTA. The proposed methods are applied satisfactorily for determination of As(III) and As(V) in various types of water.

Effect of solvent volume on the physical properties of undoped and fluorine doped tin oxide films deposited using a low-cost spray technique

NASA Astrophysics Data System (ADS)

Muruganantham, G.; Ravichandran, K.; Saravanakumar, K.; Ravichandran, A. T.; Sakthivel, B.

2011-12-01

Undoped and fluorine doped tin oxide films were deposited from starting solutions having different values of solvent volume (10-50 ml) by employing a low cost and simplified spray technique using perfume atomizer. X-ray diffraction studies showed that there was a change in the preferential orientation from (2 1 1) plane to (1 1 0) plane as the volume of the solvent was increased. The sheet resistance ( Rsh) of undoped SnO 2 film was found to be minimum (13.58 KΩ/□) when the solvent volume was lesser (10 ml) and there was a sharp increase in Rsh for higher values of solvent volume. Interestingly, it was observed that while the Rsh increases sharply with the increase in solvent volume for undoped SnO 2 films, it decreases gradually in the case of fluorine doped SnO 2 films. The quantitative analysis of EDAX confirmed that the electrical resistivity of the sprayed tin oxide film was mainly governed by the number of oxygen vacancies and the interstitial incorporation of Sn atoms which in turn was governed by the impinging flux on the hot substrate. The films were found to have good optical characteristics suitable for opto-electronic devices.

Molecular dynamics analysis of the aggregation propensity of polyglutamine segments

PubMed Central

Wen, Jingran; Scoles, Daniel R.

2017-01-01

Protein misfolding and aggregation is a pathogenic feature shared among at least ten polyglutamine (polyQ) neurodegenerative diseases. While solvent-solution interaction is a key factor driving protein folding and aggregation, the solvation properties of expanded polyQ tracts are not well understood. By using GPU-enabled all-atom molecular dynamics simulations of polyQ monomers in an explicit solvent environment, this study shows that solvent-polyQ interaction propensity decreases as the lengths of polyQ tract increases. This study finds a predominance in long-distance interactions between residues far apart in polyQ sequences with longer polyQ segments, that leads to significant conformational differences. This study also indicates that large loops, comprised of parallel β-structures, appear in long polyQ tracts and present new aggregation building blocks with aggregation driven by long-distance intra-polyQ interactions. Finally, consistent with previous observations using coarse-grain simulations, this study demonstrates that there is a gain in the aggregation propensity with increased polyQ length, and that this gain is correlated with decreasing ability of solvent-polyQ interaction. These results suggest the modulation of solvent-polyQ interactions as a possible therapeutic strategy for treating polyQ diseases. PMID:28542401

Molecular simulations of self-assembly processes in metal-organic frameworks: Model dependence

NASA Astrophysics Data System (ADS)

Biswal, Debasmita; Kusalik, Peter G.

2017-07-01

Molecular simulation is a powerful tool for investigating microscopic behavior in various chemical systems, where the use of suitable models is critical to successfully reproduce the structural and dynamic properties of the real systems of interest. In this context, molecular dynamics simulation studies of self-assembly processes in metal-organic frameworks (MOFs), a well-known class of porous materials with interesting chemical and physical properties, are relatively challenging, where a reasonably accurate representation of metal-ligand interactions is anticipated to play an important role. In the current study, we both investigate the performance of some existing models and introduce and test new models to help explore the self-assembly in an archetypal Zn-carboxylate MOF system. To this end, the behavior of six different Zn-ion models, three solvent models, and two ligand models was examined and validated against key experimental structural parameters. To explore longer time scale ordering events during MOF self-assembly via explicit solvent simulations, it is necessary to identify a suitable combination of simplified model components representing metal ions, organic ligands, and solvent molecules. It was observed that an extended cationic dummy atom (ECDA) Zn-ion model combined with an all-atom carboxylate ligand model and a simple dipolar solvent model can reproduce characteristic experimental structures for the archetypal MOF system. The successful use of these models in extensive sets of molecular simulations, which provide key insights into the self-assembly mechanism of this archetypal MOF system occurring during the early stages of this process, has been very recently reported.

Free Enthalpy Differences between α-, π-, and 310-Helices of an Atomic Level Fine-Grained Alanine Deca-Peptide Solvated in Supramolecular Coarse-Grained Water.

PubMed

Lin, Zhixiong; Riniker, Sereina; van Gunsteren, Wilfred F

2013-03-12

Atomistic molecular dynamics simulations of peptides or proteins in aqueous solution are still limited to the multi-nanosecond time scale and multi-nanometer range by computational cost. Combining atomic solutes with a supramolecular solvent model in hybrid fine-grained/coarse-grained (FG/CG) simulations allows atomic detail in the region of interest while being computationally more efficient. We used enveloping distribution sampling (EDS) to calculate the free enthalpy differences between different helical conformations, i.e., α-, π-, and 310-helices, of an atomic level FG alanine deca-peptide solvated in a supramolecular CG water solvent. The free enthalpy differences obtained show that by replacing the FG solvent by the CG solvent, the π-helix is destabilized with respect to the α-helix by about 2.5 kJ mol(-1), and the 310-helix is stabilized with respect to the α-helix by about 9 kJ mol(-1). In addition, the dynamics of the peptide becomes faster. By introducing a FG water layer of 0.8 nm around the peptide, both thermodynamic and dynamic properties are recovered, while the hybrid FG/CG simulations are still four times more efficient than the atomistic simulations, even when the cutoff radius for the nonbonded interactions is increased from 1.4 to 2.0 nm. Hence, the hybrid FG/CG model, which yields an appropriate balance between reduced accuracy and enhanced computational speed, is very suitable for molecular dynamics simulation investigations of biomolecules.

Solvated molecular dynamics of LiCN isomerization: All-atom argon solvent versus a generalized Langevin bath.

PubMed

Junginger, Andrej; Garcia-Muller, Pablo L; Borondo, F; Benito, R M; Hernandez, Rigoberto

2016-01-14

The reaction rate rises and falls with increasing density or friction when a molecule is activated by collisions with the solvent particles. This so-called Kramers turnover has recently been observed in the isomerization reaction of LiCN in an argon bath. In this paper, we demonstrate by direct comparison with those results that a reduced-dimensional (generalized) Langevin description gives rise to similar reaction dynamics as the corresponding (computationally expensive) full molecular dynamics calculations. We show that the density distributions within the Langevin description are in direct agreement with the full molecular dynamics results and that the turnover in the reaction rates is reproduced qualitatively and quantitatively at different temperatures.

Simulating Ru L 3 -Edge X-ray Absorption Spectroscopy with Time-Dependent Density Functional Theory: Model Complexes and Electron Localization in Mixed-Valence Metal Dimers

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

Van Kuiken, Benjamin E.; Valiev, Marat; Daifuku, Stephanie L.

2013-05-30

Ruthenium L3-edge X-ray absorption (XA) spectroscopy probes unoccupied 4d orbitals of the metal atom and is increasingly being used to investigate the local electronic structure in ground and excited electronic states of Ru complexes. The simultaneous development of computational tools for simulating Ru L3-edge spectra is crucial for interpreting the spectral features at a molecular level. This study demonstrates that time-dependent density functional theory (TDDFT) is a viable and predictive tool for simulating ruthenium L3-edge XA spectroscopy. We systematically investigate the effects of exchange correlation functional and implicit and explicit solvent interactions on a series of RuII and RuIII complexesmore » in their ground and electronic excited states. The TDDFT simulations reproduce all of the experimentally observed features in Ru L3-edge XA spectra within the experimental resolution (0.4 eV). Our simulations identify ligand-specific charge transfer features in complicated Ru L3-edge spectra of [Ru(CN)6]4- and RuII polypyridyl complexes illustrating the advantage of using TDDFT in complex systems. We conclude that the B3LYP functional most accurately predicts the transition energies of charge transfer features in these systems. We use our TDDFT approach to simulate experimental Ru L3-edge XA spectra of transition metal mixed-valence dimers of the form [(NC)5MII-CN-RuIII(NH3)5] (where M = Fe or Ru) dissolved in water. Our study determines the spectral signatures of electron delocalization in Ru L3-edge XA spectra. We find that the inclusion of explicit solvent molecules is necessary for reproducing the spectral features and the experimentally determined valencies in these mixed-valence complexes. This study validates the use of TDDFT for simulating Ru 2p excitations using popular quantum chemistry codes and providing a powerful interpretive tool for equilibrium and ultrafast Ru L3-edge XA spectroscopy.« less

Traceable atomic force microscopy of high-quality solvent-free crystals of [6,6]-phenyl-C61-butyric acid methyl ester

NASA Astrophysics Data System (ADS)

Lazzerini, Giovanni Mattia; Paternò, Giuseppe Maria; Tregnago, Giulia; Treat, Neil; Stingelin, Natalie; Yacoot, Andrew; Cacialli, Franco

2016-02-01

We report high-resolution, traceable atomic force microscopy measurements of high-quality, solvent-free single crystals of [6,6]-phenyl-C61-butyric acid methyl ester (PCBM). These were grown by drop-casting PCBM solutions onto the spectrosil substrates and by removing the residual solvent in a vacuum. A home-built atomic force microscope featuring a plane mirror differential optical interferometer, fiber-fed from a frequency-stabilized laser (emitting at 632.8 nm), was used to measure the crystals' height. The optical interferometer together with the stabilized laser provides traceability (via the laser wavelength) of the vertical measurements made with the atomic force microscope. We find that the crystals can conform to the surface topography, thanks to their height being significantly smaller compared to their lateral dimensions (namely, heights between about 50 nm and 140 nm, for the crystals analysed, vs. several tens of microns lateral dimensions). The vast majority of the crystals are flat, but an isolated, non-flat crystal provides insights into the growth mechanism and allows identification of "molecular terraces" whose height corresponds to one of the lattice constants of the single PCBM crystal (1.4 nm) as measured with X-ray diffraction.

Traceable atomic force microscopy of high-quality solvent-free crystals of [6,6]-phenyl-C{sub 61}-butyric acid methyl ester

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

Lazzerini, Giovanni Mattia; Yacoot, Andrew; Paternò, Giuseppe Maria

2016-02-01

We report high-resolution, traceable atomic force microscopy measurements of high-quality, solvent-free single crystals of [6,6]-phenyl-C61-butyric acid methyl ester (PCBM). These were grown by drop-casting PCBM solutions onto the spectrosil substrates and by removing the residual solvent in a vacuum. A home-built atomic force microscope featuring a plane mirror differential optical interferometer, fiber-fed from a frequency-stabilized laser (emitting at 632.8 nm), was used to measure the crystals' height. The optical interferometer together with the stabilized laser provides traceability (via the laser wavelength) of the vertical measurements made with the atomic force microscope. We find that the crystals can conform to the surfacemore » topography, thanks to their height being significantly smaller compared to their lateral dimensions (namely, heights between about 50 nm and 140 nm, for the crystals analysed, vs. several tens of microns lateral dimensions). The vast majority of the crystals are flat, but an isolated, non-flat crystal provides insights into the growth mechanism and allows identification of “molecular terraces” whose height corresponds to one of the lattice constants of the single PCBM crystal (1.4 nm) as measured with X-ray diffraction.« less

Ultrathin Hydrophobic Coatings Obtained on Polyethylene Terephthalate Materials in Supercritical Carbon Dioxide with Co-Solvents

NASA Astrophysics Data System (ADS)

Kumeeva, T. Yu.; Prorokova, N. P.

2018-02-01

The surface properties of ultradisperse polytetrafluoroethylene coatings on polyethylene terephthalate materials modified in a supercritical carbon dioxide medium with co-solvent additions (aliphatic alcohols) were analyzed. An atomic force microscopy study revealed the peculiarities of the morphology of the hydrophobic coatings formed in the presence of co-solvents. The contribution of the co-solvents to the formation of the surface layer with a low surface energy was evaluated from the surface energy components of the modified polyester material. The stability of the coatings against dry friction was analyzed.

Algorithm For Hypersonic Flow In Chemical Equilibrium

NASA Technical Reports Server (NTRS)

Palmer, Grant

1989-01-01

Implicit, finite-difference, shock-capturing algorithm calculates inviscid, hypersonic flows in chemical equilibrium. Implicit formulation chosen because overcomes limitation on mathematical stability encountered in explicit formulations. For dynamical portion of problem, Euler equations written in conservation-law form in Cartesian coordinate system for two-dimensional or axisymmetric flow. For chemical portion of problem, equilibrium state of gas at each point in computational grid determined by minimizing local Gibbs free energy, subject to local conservation of molecules, atoms, ions, and total enthalpy. Major advantage: resulting algorithm naturally stable and captures strong shocks without help of artificial-dissipation terms to damp out spurious numerical oscillations.

Self-assembly of organogels via new luminol imide derivatives: diverse nanostructures and substituent chain effect

PubMed Central

2013-01-01

Luminol is considered as an efficient sycpstem in electrochemiluminescence (ECL) measurements for the detection of hydrogen peroxide. In this paper, new luminol imide derivatives with different alkyl substituent chains were designed and synthesized. Their gelation behaviors in 26 solvents were tested as novel low molecular mass organic gelators. It was shown that the length and number of alkyl substituent chains linked to a benzene ring in gelators played a crucial role in the gelation behavior of all compounds in various organic solvents. Longer alkyl chains in molecular skeletons in present gelators are favorable for the gelation of organic solvents. Scanning electron microscope and atomic force microscope observations revealed that the gelator molecules self-assemble into different micro/nanoscale aggregates from a dot, flower, belt, rod, and lamella to wrinkle with change of solvents. Spectral studies indicated that there existed different H-bond formations and hydrophobic forces, depending on the alkyl substituent chains in molecular skeletons. The present work may give some insight to the design and characteristic of new versatile soft materials and potential ECL biosensors with special molecular structures. PMID:23758979

Self-assembly of organogels via new luminol imide derivatives: diverse nanostructures and substituent chain effect

NASA Astrophysics Data System (ADS)

Jiao, Tifeng; Huang, Qinqin; Zhang, Qingrui; Xiao, Debao; Zhou, Jingxin; Gao, Faming

2013-06-01

Luminol is considered as an efficient sycpstem in electrochemiluminescence (ECL) measurements for the detection of hydrogen peroxide. In this paper, new luminol imide derivatives with different alkyl substituent chains were designed and synthesized. Their gelation behaviors in 26 solvents were tested as novel low molecular mass organic gelators. It was shown that the length and number of alkyl substituent chains linked to a benzene ring in gelators played a crucial role in the gelation behavior of all compounds in various organic solvents. Longer alkyl chains in molecular skeletons in present gelators are favorable for the gelation of organic solvents. Scanning electron microscope and atomic force microscope observations revealed that the gelator molecules self-assemble into different micro/nanoscale aggregates from a dot, flower, belt, rod, and lamella to wrinkle with change of solvents. Spectral studies indicated that there existed different H-bond formations and hydrophobic forces, depending on the alkyl substituent chains in molecular skeletons. The present work may give some insight to the design and characteristic of new versatile soft materials and potential ECL biosensors with special molecular structures.

Alkyl hydrogen atom abstraction reactions of the CN radical with ethanol

NASA Astrophysics Data System (ADS)

Athokpam, Bijyalaxmi; Ramesh, Sai G.

2018-04-01

We present a study of the abstraction of alkyl hydrogen atoms from the β and α positions of ethanol by the CN radical in solution using the Empirical Valence Bond (EVB) method. We have built separate 2 × 2 EVB models for the Hβ and Hα reactions, where the atom transfer is parameterized using ab initio calculations. The intra- and intermolecular potentials of the reactant and product molecules were modelled with the General AMBER Force Field, with some modifications. We have carried out the dynamics in water and chloroform, which are solvents of contrasting polarity. We have computed the potential of mean force for both abstractions in each of the solvents. They are found to have a small and early barrier along the reaction coordinate with a large energy release. Analyzing the solvent structure around the reaction system, we have found two solvents to have little effect on either reaction. Simulating the dynamics from the transition state, we also study the fate of the energies in the HCN vibrational modes. The HCN molecule is born vibrationally hot in the CH stretch in both reactions and additionally in the HCN bends for the Hα abstraction reaction. In the early stage of the dynamics, we find that the CN stretch mode gains energy at the expense of the energy in CH stretch mode.

The structural study of acetohydroxamic and oxalodihydroxamic acids in DMSO solution based on the DFT calculations of NMR spectra

NASA Astrophysics Data System (ADS)

Kaczor, Agnieszka; Proniewicz, Leonard M.

2004-10-01

The 1H and 13C NMR spectra of acetohydroxamic (aha) and oxalodihydroxamic (oxha) acids were measured in DMSO- d6 solution. The atoms chemical shifts of chosen stable entgegen and zusammen conformers of monomeric acids were computed along with some clusters of the compounds with the solvent molecules [B3LYP/6-311++G(d,p), GIAO]. The latter were proposed to explain the differences between the theoretical and experimental resonances of the protons of the N-H and O-H groups. The computed chemical shifts of aha-(DMSO) 2 and oxha-(DMSO) 2 models are in good agreement with experimental data proving that the compounds existing in solution form aggregates with DMSO. The acids are H-bonded via all the labile protons to the oxygen atoms of the solvent molecules. aha exists in the zusammen and entgegen (relative to C-N bond) forms with the relative intensities of 8:1 while the sole z, E, z-conformers (notation refers to C-N, C-C and C-N bonds, respectively) were found for oxha.

Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules

PubMed Central

2014-01-01

Background Brownian dynamics (BD) simulations can be used to study very large molecular systems, such as models of the intracellular environment, using atomic-detail structures. Such simulations require strategies to contain the computational costs, especially for the computation of interaction forces and energies. A common approach is to compute interaction forces between macromolecules by precomputing their interaction potentials on three-dimensional discretized grids. For long-range interactions, such as electrostatics, grid-based methods are subject to finite size errors. We describe here the implementation of a Debye-Hückel correction to the grid-based electrostatic potential used in the SDA BD simulation software that was applied to simulate solutions of bovine serum albumin and of hen egg white lysozyme. Results We found that the inclusion of the long-range electrostatic correction increased the accuracy of both the protein-protein interaction profiles and the protein diffusion coefficients at low ionic strength. Conclusions An advantage of this method is the low additional computational cost required to treat long-range electrostatic interactions in large biomacromolecular systems. Moreover, the implementation described here for BD simulations of protein solutions can also be applied in implicit solvent molecular dynamics simulations that make use of gridded interaction potentials. PMID:25045516

Insights into the mechanism of C5aR inhibition by PMX53 via implicit solvent molecular dynamics simulations and docking

PubMed Central

2014-01-01

Background The complement protein C5a acts by primarily binding and activating the G-protein coupled C5a receptor C5aR (CD88), and is implicated in many inflammatory diseases. The cyclic hexapeptide PMX53 (sequence Ace-Phe-[Orn-Pro-dCha-Trp-Arg]) is a full C5aR antagonist of nanomolar potency, and is widely used to study C5aR function in disease. Results We construct for the first time molecular models for the C5aR:PMX53 complex without the a priori use of experimental constraints, via a computational framework of molecular dynamics (MD) simulations, docking, conformational clustering and free energy filtering. The models agree with experimental data, and are used to propose important intermolecular interactions contributing to binding, and to develop a hypothesis for the mechanism of PMX53 antagonism. Conclusion This work forms the basis for the design of improved C5aR antagonists, as well as for atomic-detail mechanistic studies of complement activation and function. Our computational framework can be widely used to develop GPCR-ligand structural models in membrane environments, peptidomimetics and other chemical compounds with potential clinical use. PMID:25170421

Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies.

PubMed

Forouzesh, Negin; Izadi, Saeed; Onufriev, Alexey V

2017-10-23

Fast and accurate calculation of solvation free energies is central to many applications, such as rational drug design. In this study, we present a grid-based molecular surface implementation of "R6" flavor of the generalized Born (GB) implicit solvent model, named GBNSR6. The speed, accuracy relative to numerical Poisson-Boltzmann treatment, and sensitivity to grid surface parameters are tested on a set of 15 small protein-ligand complexes and a set of biomolecules in the range of 268 to 25099 atoms. Our results demonstrate that the proposed model provides a relatively successful compromise between the speed and accuracy of computing polar components of the solvation free energies (ΔG pol ) and binding free energies (ΔΔG pol ). The model tolerates a relatively coarse grid size h = 0.5 Å, where the grid artifact error in computing ΔΔG pol remains in the range of k B T ∼ 0.6 kcal/mol. The estimated ΔΔG pol s are well correlated (r 2 = 0.97) with the numerical Poisson-Boltzmann reference, while showing virtually no systematic bias and RMSE = 1.43 kcal/mol. The grid-based GBNSR6 model is available in Amber (AmberTools) package of molecular simulation programs.

Effect of Atomic Charges on Octanol-Water Partition Coefficient Using Alchemical Free Energy Calculation.

PubMed

Ogata, Koji; Hatakeyama, Makoto; Nakamura, Shinichiro

2018-02-15

The octanol-water partition coefficient (log P ow ) is an important index for measuring solubility, membrane permeability, and bioavailability in the drug discovery field. In this paper, the log P ow values of 58 compounds were predicted by alchemical free energy calculation using molecular dynamics simulation. In free energy calculations, the atomic charges of the compounds are always fixed. However, they must be recalculated for each solvent. Therefore, three different sets of atomic charges were tested using quantum chemical calculations, taking into account vacuum, octanol, and water environments. The calculated atomic charges in the different environments do not necessarily influence the correlation between calculated and experimentally measured ∆ G water values. The largest correlation coefficient values of the solvation free energy in water and octanol were 0.93 and 0.90, respectively. On the other hand, the correlation coefficient of log P ow values calculated from free energies, the largest of which was 0.92, was sensitive to the combination of the solvation free energies calculated from the calculated atomic charges. These results reveal that the solvent assumed in the atomic charge calculation is an important factor determining the accuracy of predicted log P ow values.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Limiting assumptions in molecular modeling: electrostatics.

PubMed

Marshall, Garland R

2013-02-01

Molecular mechanics attempts to represent intermolecular interactions in terms of classical physics. Initial efforts assumed a point charge located at the atom center and coulombic interactions. It is been recognized over multiple decades that simply representing electrostatics with a charge on each atom failed to reproduce the electrostatic potential surrounding a molecule as estimated by quantum mechanics. Molecular orbitals are not spherically symmetrical, an implicit assumption of monopole electrostatics. This perspective reviews recent evidence that requires use of multipole electrostatics and polarizability in molecular modeling.

Solvent influence upon structure & throughput of poly vinyledene fluoride thin film nano-patterns by imprint lithography

NASA Astrophysics Data System (ADS)

Sankar, M. S. Ravi; Gangineni, R. B.

2018-04-01

This work aims at understanding the solvent influence upon the throughput and structure of poly vinyledene fluoride (PVDF)nano-patterned films. The PVDF thin films are deposited by spin coating method using Dimethylsulfoxide (DMSO), Tetrahydrofuran (THF) and 2-butanone solvents. The nano-patterns are realized by imprinting SONY 700 MB CD aluminum constructions on PVDF thin filmsusing imprint lithography technique under ambient annealing temperature and pressure. Surface morphology &imprint pattern transfer quality is evaluated with Atomic force microscopy (AFM). Raman spectroscopy is used for evaluating the structural evolutions with respect to solvent & patterning.

A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers.

PubMed

Cooper, Christopher D; Bardhan, Jaydeep P; Barba, L A

2014-03-01

The continuum theory applied to biomolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like solvent-filled cavities or ion-exclusion (Stern) layers, due to the added difficulty of treating multiple boundary surfaces. This has hindered meaningful comparisons with volume-based methods, and the effects on accuracy of including these features has remained unknown. This work presents a solver called PyGBe that uses a boundary-element formulation and can handle multiple interacting surfaces. It was used to study the effects of solvent-filled cavities and Stern layers on the accuracy of calculating solvation energy and binding energy of proteins, using the well-known apbs finite-difference code for comparison. The results suggest that if required accuracy for an application allows errors larger than about 2% in solvation energy, then the simpler, single-surface model can be used. When calculating binding energies, the need for a multi-surface model is problem-dependent, becoming more critical when ligand and receptor are of comparable size. Comparing with the apbs solver, the boundary-element solver is faster when the accuracy requirements are higher. The cross-over point for the PyGBe code is in the order of 1-2% error, when running on one gpu card (nvidia Tesla C2075), compared with apbs running on six Intel Xeon cpu cores. PyGBe achieves algorithmic acceleration of the boundary element method using a treecode, and hardware acceleration using gpus via PyCuda from a user-visible code that is all Python. The code is open-source under MIT license.

A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers

NASA Astrophysics Data System (ADS)

Cooper, Christopher D.; Bardhan, Jaydeep P.; Barba, L. A.

2014-03-01

The continuum theory applied to biomolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like solvent-filled cavities or ion-exclusion (Stern) layers, due to the added difficulty of treating multiple boundary surfaces. This has hindered meaningful comparisons with volume-based methods, and the effects on accuracy of including these features has remained unknown. This work presents a solver called PyGBe that uses a boundary-element formulation and can handle multiple interacting surfaces. It was used to study the effects of solvent-filled cavities and Stern layers on the accuracy of calculating solvation energy and binding energy of proteins, using the well-known APBS finite-difference code for comparison. The results suggest that if required accuracy for an application allows errors larger than about 2% in solvation energy, then the simpler, single-surface model can be used. When calculating binding energies, the need for a multi-surface model is problem-dependent, becoming more critical when ligand and receptor are of comparable size. Comparing with the APBS solver, the boundary-element solver is faster when the accuracy requirements are higher. The cross-over point for the PyGBe code is on the order of 1-2% error, when running on one GPU card (NVIDIA Tesla C2075), compared with APBS running on six Intel Xeon CPU cores. PyGBe achieves algorithmic acceleration of the boundary element method using a treecode, and hardware acceleration using GPUs via PyCuda from a user-visible code that is all Python. The code is open-source under MIT license.

Combined effect of cortical cytoskeleton and transmembrane proteins on domain formation in biomembranes

PubMed Central

Sikder, Md. Kabir Uddin; Stone, Kyle A.; Kumar, P. B. Sunil; Laradji, Mohamed

2014-01-01

We investigate the combined effects of transmembrane proteins and the subjacent cytoskeleton on the dynamics of phase separation in multicomponent lipid bilayers using computer simulations of a particle-based implicit solvent model for lipid membranes with soft-core interactions. We find that microphase separation can be achieved by the protein confinement by the cytoskeleton. Our results have relevance to the finite size of lipid rafts in the plasma membrane of mammalian cells. PMID:25106608

Prediction of Protein-Peptide Interactions: Application of the XPairIT to Anthrax Lethal Factor and Substrates

DTIC Science & Technology

2013-09-01

hydrogen bonds in Tyrosine-containing peptides. Dalkas et al[7] used docking and molecular dynamics simulations to study a variety of MAPKK-based... simulated using NAMD molecular dynamics and the CHARMM[20] forcefield at 300K and employing the Generalized Born Implicit Solvent (GBIS[21]) with the...which were reported in Section 2. Specifically, after a ~10ns molecular dynamics simulation in TIP3 explicit water, significant motion of domains III

Accurate representation of B-DNA double helical structure with implicit solvent and counterions.

PubMed Central

Wang, Lihua; Hingerty, Brian E; Srinivasan, A R; Olson, Wilma K; Broyde, Suse

2002-01-01

High-resolution nuclear magnetic resonance (NMR) and crystallographic data have been taken to refine the force field used in the torsion angle space nucleic acids molecular mechanics program DUPLEX. The population balance deduced from NMR studies of two carcinogen-modified DNA conformers in equilibrium was used to fine tune a sigmoidal, distance-dependent dielectric function so that reasonable relative energies could be obtained. In addition, the base-pair and backbone geometry from high-resolution crystal structures of the Dickerson-Drew dodecamer was used to re-evaluate the deoxyribose pseudorotation profile and the Lennard-Jones nonbonded energy terms. With a modified dielectric function that assumes a very steep distance-dependent form, a deoxyribose pseudorotation profile with reduced energy barriers between C2'- and C3'-endo minima, and a shift of the Lennard-Jones potential energy minimum to a distance approximately 0.4 A greater than the sum of the van der Waals' radii, the sequence-dependent conformational features of the Dickerson-Drew dodecamer in both the solid state and the aqueous liquid crystalline phase are well reproduced. The robust performance of the revised force field, in conjunction with its efficiency through implicit treatment of solvent and counterions, provides a valuable tool for elucidating conformations and structure-function relationships of DNA, including those of molecules modified by carcinogens and other ligands. PMID:12080128

The Determination of Lead in Gasoline by Atomic Absorption Spectrometry.

ERIC Educational Resources Information Center

Coleman, M. F. M.

1985-01-01

Describes an experiment that involves the extraction of lead from gasoline into an aqueous solvent using iodine monochloride reagent. This method (which avoids the aspiration of organic solvents) also illustrates the use of wavelengths other than the most sensitive wavelength and effects of flame stoichiometry and burner height upon absorbance.…

Role of solvent environments in single molecule conductance used insulator-modified mechanically controlled break junctions

NASA Astrophysics Data System (ADS)

Muthusubramanian, Nandini; Maity, Chandan; Galan Garcia, Elena; Eelkema, Rienk; Grozema, Ferdinand; van der Zant, Herre; Kavli Institute of Nanoscience Collaboration; Department of Chemical Engineering Collaboration

We present a method for studying the effects of polar solvents on charge transport through organic/biological single molecules by developing solvent-compatible mechanically controlled break junctions of gold coated with a thin layer of aluminium oxide using plasma enhanced atomic layer deposition (ALD). The optimal oxide thickness was experimentally determined to be 15 nm deposited at ALD operating temperature of 300°C which yielded atomically sharp electrodes and reproducible single-barrier tunnelling behaviour across a wide conductance range between 1 G0 and 10-7 G0. The insulator protected MCBJ devices were found to be effective in various solvents such as deionized water, phosphate buffered saline, methanol, acetonitrile and dichlorobenzene. The yield of molecular junctions using such insulated electrodes was tested by developing a chemical protocol for synthesizing an amphipathic form of oligo-phenylene ethynylene (OPE3-PEO) with thioacetate anchoring groups. This work has further applications in studying effects of solvation, dipole orientation and other thermodynamic interactions on charge transport. Eu Marie Curie Initial Training Network (ITN). MOLECULAR-SCALE ELECTRONICS: ``MOLESCO'' Project Number 606728.

Lurking systematics in dust-based estimates of galaxy ISM masses

NASA Astrophysics Data System (ADS)

Janowiecki, Steven; Cortese, Luca; Catinella, Barbara; Goodwin, Adelle

2018-01-01

We use galaxies from the Herschel Reference Survey to evaluate commonly used indirect predictors of cold gas masses. With observations of cold neutral atomic and molecular gas, we calibrate predictive relationships using infrared dust emission and gas depletion time methods. We derive a set of self-consistent predictions of cold gas masses with ~20% scatter, and the greatest accuracy for total cold gas mass. However, significant systematic residuals are found in all calibrations which depend strongly on the molecular-to-atomic hydrogen mass ratio, and they can over/under-predict gas masses by >0.5 dex. Extending these types of indirect predictions to high-z galaxies (e.g., using ALMA observations of dust continuum to determine gas masses) requires implicit assumptions about the conditions in their interstellar medium. Any scaling relations derived using predicted gas masses may be more closely related to the calibrations used than to the actual galaxies observed.

Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions

NASA Astrophysics Data System (ADS)

He, Jianbin; Zhang, Zhiyong; Shi, Yunyu; Liu, Haiyan

2003-08-01

We describe a method for efficient sampling of the energy landscape of a protein in atomic molecular dynamics simulations. A simulation is divided into alternatively occurring relaxation phases and excitation phases. In the relaxation phase (conventional simulation), we use a frequently updated reference structure and deviations from this reference structure to mark whether the system has been trapped in a local minimum. In that case, the simulation enters the excitation phase, during which a few slow collective modes of the system are coupled to a higher temperature bath. After the system has escaped from the minimum (also judged by deviations from the reference structure) the simulation reenters the relaxation phase. The collective modes are obtained from a coarse-grained Gaussian elastic network model. The scheme, which we call ACM-AME (amplified collective motion-assisted minimum escaping), is compared with conventional simulations as well as an alternative scheme that elevates the temperature of all degrees of freedom during the excitation phase (amplified overall motion-assisted minimum escaping, or AOM-AME). Comparison is made using simulations on four peptides starting from non-native extended or all helical structures. In terms of sampling low energy conformations and continuously sampling new conformations throughout a simulation, the ACM-AME scheme demonstrates very good performance while the AOM-AME scheme shows little improvement upon conventional simulations. Limited success is achieved in producing structures close to the native structures of the peptides: for an S-peptide analog, the ACM-AME approach is able to reproduce its native helical structure, and starting from an all-helical structure of the villin headpiece subdomain (HP-36) in implicit solvent, two out of three 150 ns ACM-AME runs are able to sample structures with 3-4 Å backbone root-mean-square deviations from the nuclear magnetic resonance structure of the protein.

Exploring O2 Diffusion in A-Type Cytochrome c Oxidases: Molecular Dynamics Simulations Uncover Two Alternative Channels towards the Binuclear Site

PubMed Central

Oliveira, A. Sofia F.; Damas, João M.; Baptista, António M.; Soares, Cláudio M.

2014-01-01

Cytochrome c oxidases (Ccoxs) are the terminal enzymes of the respiratory chain in mitochondria and most bacteria. These enzymes couple dioxygen (O2) reduction to the generation of a transmembrane electrochemical proton gradient. Despite decades of research and the availability of a large amount of structural and biochemical data available for the A-type Ccox family, little is known about the channel(s) used by O2 to travel from the solvent/membrane to the heme a3-CuB binuclear center (BNC). Moreover, the identification of all possible O2 channels as well as the atomic details of O2 diffusion is essential for the understanding of the working mechanisms of the A-type Ccox. In this work, we determined the O2 distribution within Ccox from Rhodobacter sphaeroides, in the fully reduced state, in order to identify and characterize all the putative O2 channels leading towards the BNC. For that, we use an integrated strategy combining atomistic molecular dynamics (MD) simulations (with and without explicit O2 molecules) and implicit ligand sampling (ILS) calculations. Based on the 3D free energy map for O2 inside Ccox, three channels were identified, all starting in the membrane hydrophobic region and connecting the surface of the protein to the BNC. One of these channels corresponds to the pathway inferred from the X-ray data available, whereas the other two are alternative routes for O2 to reach the BNC. Both alternative O2 channels start in the membrane spanning region and terminate close to Y288I. These channels are a combination of multiple transiently interconnected hydrophobic cavities, whose opening and closure is regulated by the thermal fluctuations of the lining residues. Furthermore, our results show that, in this Ccox, the most likely (energetically preferred) routes for O2 to reach the BNC are the alternative channels, rather than the X-ray inferred pathway. PMID:25474152

Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and their Complexes with Proteins

PubMed Central

Nguyen, Hai; Pérez, Alberto; Bermeo, Sherry; Simmerling, Carlos

2016-01-01

The Generalized Born (GB) implicit solvent model has undergone significant improvements in accuracy for modeling of proteins and small molecules. However, GB still remains a less widely explored option for nucleic acid simulations, in part because fast GB models are often unable to maintain stable nucleic acid structures, or they introduce structural bias in proteins, leading to difficulty in application of GB models in simulations of protein-nucleic acid complexes. Recently, GB-neck2 was developed to improve the behavior of protein simulations. In an effort to create a more accurate model for nucleic acids, a similar procedure to the development of GB-neck2 is described here for nucleic acids. The resulting parameter set significantly reduces absolute and relative energy error relative to Poisson Boltzmann for both nucleic acids and nucleic acid-protein complexes, when compared to its predecessor GB-neck model. This improvement in solvation energy calculation translates to increased structural stability for simulations of DNA and RNA duplexes, quadruplexes, and protein-nucleic acid complexes. The GB-neck2 model also enables successful folding of small DNA and RNA hairpins to near native structures as determined from comparison with experiment. The functional form and all required parameters are provided here and also implemented in the AMBER software. PMID:26574454

PROCESS FOR PRODUCING ALKYL ORTHOPHOSPHORIC ACID EXTRACTANTS

DOEpatents

Grinstead, R.R.

1962-01-23

A process is given for producing superior alkyl orthophosphoric acid extractants for use in solvent extraction methods to recover and purify various metals such as uranium and vanadium. The process comprises slurrying P/sub 2/O/ sub 5/ in a solvent diluent such as kerosene, benzene, isopropyl ether, and the like. An alipbatic alcohol having from nine to seventeen carbon atoms, and w- hcrein ihc OH group is situated inward of the terminal carbon atoms, is added to the slurry while the reaction temperature is mainiained below 60 deg C. The alcohol is added in the mole ratio of about 2 to l, alcohol to P/sub 2/O/sub 5/. A pyrophosphate reaotion product is formed in the slurry-alcohol mixture. Subsequently, the pyrophosphate reaction product is hydrolyzed with dilute mineral acid to produce the desired alkyl orthophosphoric aeid extractant. The extraetant may then be separated and utilized in metal-recovery, solvent- extraction processes. (AEC)

Poly(diiododiacetylene): A Potential Precursor for New All-Carbon Materials

NASA Astrophysics Data System (ADS)

Resch, Daniel Joseph

Poly(diiododiacetylene) (PIDA) is a polymer consisting entirely of carbon and iodine. The polymer is prepared by cocrystallizing a bis(nitrile) oxalamide host with the monomer diiodobutadiyne. These compounds are held together by a halogen bond and an ordered 1,4-topochemical polymerization occurs in the solid state. The formation of the monomer cocrystals was found to be highly solvent dependent. Acetonitrile was found to greatly improve the yield of cocrystals over solvents used in the past. Cocrystals could not be obtained from other solvents such as dimethoxyethane and acetone. THF did give some cocrystal but the yield was poor. The use of acetonitrile as a solvent now allows for PIDA cocrystals to be reliably prepared in excellent yield for detailed studies. The weak C-I bonds in PIDA can be broken under mild conditions with simple Lewis bases like pyrrolidine and iodide ion. Studies with small molecule models show that the mechanism of elimination is E2-like and highly solvent dependent. Polar aprotic solvents favor the reaction while non-polar solvents disfavor it. Reaction occurs in protic solvents, but the rate is much slower. Iodide was found to carry out the reaction in 1 hour d5-PhNO 2 while reaction with pyrrolidine did not reach completion in 15 hours. When PIDA is subjected to deiodination the product is an amorphous graphite-like material that contains non-carbon atoms. Depending on the reaction conditions, it is possible to incorporate sulfur or phosphorus into the final product. The source of these elements is the reducing agent that is typically added to sequester molecular iodine. Sequestering the iodine prevents it from reacting with the carbon species. New insights into the deiodination reaction have made PIDA more promising as a precursor to prepare all-carbon materials or heteroatom-functionalized carbon under mild conditions.

Cavities in molecular liquids and the theory of hydrophobic solubilities

NASA Technical Reports Server (NTRS)

Pohorille, A.; Pratt, L. R.; MacElroy, R. (Principal Investigator)

1990-01-01

Thermal configurational data on neat liquids are used to obtain the work of formation of hard spherical cavities of atomic size in six molecular solvents: n-hexane, n-dodecane, n-undecyl alcohol, chloroform, carbon tetrachloride, and water. These results are used to test a recent suggestion that the differences between nonaqueous solvents and liquid water in solvation of inert gases are not principally due to the hydrogen-bonded structure of liquid water but rather to the comparatively small size of the water molecule. The frequencies of occurrence of cavities in liquid water can be meaningfully distinguished from those in the organic solvents. Liquid water has a larger fractional free volume, but that free volume is distributed in smaller packets. With respect to cavity work, water is compared to a solvent of the same molecular density and composed of hard spheres of the same size as the water molecule. That comparison indicates that the hard-sphere liquid finds more ways to configure its free volume in order to accommodate an atomic solute of substantial size and thus, would be more favorable solvent for inert gases. The scaled particle model of inert gas solubility in liquid water predicts cavity works 20% below the numerical data for TIP4P water at 300 K and 1.0 g/cm3 for cavity radii near 2.0 angstroms. It is argued that the sign of this difference is just the sign that ought to be expected and that the magnitude of this difference measures structural differences between water and the directly comparable hard-sphere liquid. In conjunction with previous data, these results indicate that atomic sized cavities should be considered submacroscopic.

Implicit self-esteem decreases in adolescence: a cross-sectional study.

PubMed

Cai, Huajian; Wu, Mingzheng; Luo, Yu L L; Yang, Jing

2014-01-01

Implicit self-esteem has remained an active research topic in both the areas of implicit social cognition and self-esteem in recent decades. The purpose of this study is to explore the development of implicit self-esteem in adolescents. A total of 599 adolescents from junior and senior high schools in East China participated in the study. They ranged in age from 11 to 18 years with a mean age of 14.10 (SD = 2.16). The degree of implicit self-esteem was assessed using the Implicit Association Test (IAT) with the improved D score as the index. Participants also completed the Rosenberg Self-Esteem Scale (α = 0.77). For all surveyed ages, implicit self-esteem was positively biased, all ts>8.59, all ps<0.001. The simple correlation between implicit self-esteem and age was significant, r =  -.25, p = 1. 10(-10). A regression with implicit self-esteem as the criterion variable, and age, gender, and age × gender interaction as predictors further revealed the significant negative linear relationship between age and implicit self-esteem, β = -0.19, t = -3.20, p = 0.001. However, explicit self-esteem manifested a reverse "U" shape throughout adolescence. Implicit self-esteem in adolescence manifests a declining trend with increasing age, suggesting that it is sensitive to developmental or age-related changes. This finding enriches our understanding of the development of implicit social cognition.

Multiscale modeling and computation of nano-electronic transistors and transmembrane proton channels

NASA Astrophysics Data System (ADS)

Chen, Duan

The miniaturization of nano-scale electronic transistors, such as metal oxide semiconductor field effect transistors (MOSFETs), has given rise to a pressing demand in the new theoretical understanding and practical tactic for dealing with quantum mechanical effects in integrated circuits. In biology, proton dynamics and transport across membrane proteins are of paramount importance to the normal function of living cells. Similar physical characteristics are behind the two subjects, and model simulations share common mathematical interests/challenges. In this thesis work, multiscale and multiphysical models are proposed to study the mechanisms of nanotransistors and proton transport in transmembrane at the atomic level. For nano-electronic transistors, we introduce a unified two-scale energy functional to describe the electrons and the continuum electrostatic potential. This framework enables us to put microscopic and macroscopic descriptions on an equal footing at nano-scale. Additionally, this model includes layered structures and random doping effect of nano-transistors. For transmembrane proton channels, we describe proton dynamics quantum mechanically via a density functional approach while implicitly treat numerous solvent molecules as a dielectric continuum. The densities of all other ions in the solvent are assumed to obey the Boltzmann distribution. The impact of protein molecular structure and its charge polarization on the proton transport is considered in atomic details. We formulate a total free energy functional to include kinetic and potential energies of protons, as well as electrostatic energy of all other ions on an equal footing. For both nano-transistors and proton channels systems, the variational principle is employed to derive nonlinear governing equations. The Poisson-Kohn-Sham equations are derived for nano-transistors while the generalized Poisson-Boltzmann equation and Kohn-Sham equation are obtained for proton channels. Related numerical challenges in simulations are addressed: the matched interface and boundary (MIB) method, the Dirichlet-to-Neumann mapping (DNM) technique, and the Krylov subspace and preconditioner theory are introduced to improve the computational efficiency of the Poisson-type equation. The quantum transport theory is employed to solve the Kohn-Sham equation. The Gummel iteration and relaxation technique are utilized for overall self-consistent iterations. Finally, applications are considered and model validations are verified by realistic nano-transistors and transmembrane proteins. Two distinct device configurations, a double-gate MOSFET and a four-gate MOSFET, are considered in our threedimensional numerical simulations. For these devices, the current uctuation and voltage threshold lowering effect induced by discrete dopants are explored. For proton transport, a realistic channel protein, the Gramicidin A (GA) is used to demonstrate the performance of the proposed proton channel model and validate the efficiency of the proposed mathematical algorithms. The electrostatic characteristics of the GA channel is analyzed with a wide range of model parameters. Proton channel conductances are studied over a number of applied voltages and reference concentrations. Comparisons with experimental data are utilized to verify our model predictions.

Interaction-component analysis of the hydration and urea effects on cytochrome c

NASA Astrophysics Data System (ADS)

Yamamori, Yu; Ishizuka, Ryosuke; Karino, Yasuhito; Sakuraba, Shun; Matubayasi, Nobuyuki

2016-02-01

Energetics was analyzed for cytochrome c in pure-water solvent and in a urea-water mixed solvent to elucidate the solvation effect in the structural variation of the protein. The solvation free energy was computed through all-atom molecular dynamics simulation combined with the solution theory in the energy representation, and its correlations were examined over sets of protein structures against the electrostatic and van der Waals components in the average interaction energy of the protein with the solvent and the excluded-volume component in the solvation free energy. It was observed in pure-water solvent that the solvation free energy varies in parallel to the electrostatic component with minor roles played by the van der Waals and excluded-volume components. The effect of urea on protein structure was then investigated in terms of the free-energy change upon transfer of the protein solute from pure-water solvent to the urea-water mixed solvent. The decomposition of the transfer free energy into the contributions from urea and water showed that the urea contribution is partially canceled by the water contribution and governs the total free energy of transfer. When correlated against the change in the solute-solvent interaction energy upon transfer and the corresponding changes in the electrostatic, van der Waals, and excluded-volume components, the transfer free energy exhibited strong correlations with the total change in the solute-solvent energy and its van der Waals component. The solute-solvent energy was decomposed into the contributions from the protein backbone and side chain, furthermore, and neither of the contributions was seen to be decisive in the correlation to the transfer free energy.

Neutron Crystallography for the Study of Hydrogen Bonds in Macromolecules.

PubMed

Oksanen, Esko; Chen, Julian C-H; Fisher, Suzanne Zoë

2017-04-07

Abstract : The hydrogen bond (H bond) is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, the protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. This article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.

Neutron crystallography for the study of hydrogen bonds in macromolecules

DOE PAGES

Oksanen, Esko; Chen, Julian C.; Fisher, Zoe

2017-04-07

The hydrogen bond (H bond) is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, themore » protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. Finally, this article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.« less

Neutron crystallography for the study of hydrogen bonds in macromolecules

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

Oksanen, Esko; Chen, Julian C.; Fisher, Zoe

The hydrogen bond (H bond) is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, themore » protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. Finally, this article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.« less

Deep Eutectic Solvents as Convenient Media for Synthesis of Novel Coumarinyl Schiff Bases and Their QSAR Studies.

PubMed

Molnar, Maja; Komar, Mario; Brahmbhatt, Harshad; Babić, Jurislav; Jokić, Stela; Rastija, Vesna

2017-09-05

Deep eutectic solvents, as green and environmentally friendly media, were utilized in the synthesis of novel coumarinyl Schiff bases. Novel derivatives were synthesized from 2-((4-methyl-2-oxo-2 H -chromen-7-yl)oxy)acetohydrazide and corresponding aldehyde in choline chloride:malonic acid (1:1) based deep eutectic solvent. In these reactions, deep eutectic solvent acted as a solvent and catalyst as well. Novel Schiff bases were synthesized in high yields (65-75%) with no need for further purification, and their structures were confirmed by mass spectra, ¹H and 13 C NMR. Furthermore, their antioxidant activity was determined and compared to antioxidant activity of previously synthesized derivatives, thus investigating their structure-activity relationship utilizing quantitative structure-activity relationship QSAR studies. Calculation of molecular descriptors has been performed by DRAGON software. The best QSAR model ( R tr = 0.636; R ext = 0.709) obtained with three descriptors ( MATS3m , Mor22u , Hy ) implies that the pairs of atoms higher mass at the path length 3, three-dimensional arrangement of atoms at scattering parameter s = 21 Å - ¹, and higher number of hydrophilic groups (-OH, -NH) enhanced antioxidant activity. Electrostatic potential surface of the most active compounds showed possible regions for donation of electrons to 1,1-diphenyl-2-picryhydrazyl (DPPH) radicals.

X-ray diffraction measurement of cosolvent accessible volume in rhombohedral insulin crystals

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

Soares, Alexei S.; Caspar, Donald L. D.

We report x-ray crystallographic measurement of the number of solvent electrons in the unit cell of a protein crystal equilibrated with aqueous solutions of different densities provides information about preferential hydration in the crystalline state. Room temperature and cryo-cooled rhombohedral insulin crystals were equilibrated with 1.2 M trehalose to study the effect of lowered water activity. The native and trehalose soaked crystals were isomorphous and had similar structures. Including all the low resolution data, the amplitudes of the structure factors were put on an absolute scale (in units of electrons per asymmetric unit) by constraining the integrated number of electronsmore » inside the envelope of the calculated protein density map to equal the number deduced from the atomic model. This procedure defines the value of F(0 0 0), the amplitude at the origin of the Fourier transform, which is equal to the total number of electrons in the asymmetric unit (i.e. protein plus solvent). Comparison of the F(0 0 0) values for three isomorphous pairs of room temperature insulin crystals, three with trehalose and three without trehalose, indicates that 75 ± 12 electrons per asymmetric unit were added to the crystal solvent when soaked in 1.2 M trehalose. If all the water in the crystal were available as solvent for the trehalose, 304 electrons would have been added. Thus, the co-solvent accessible volume is one quarter of the total water in the crystal. Finally, determination of the total number of electrons in a protein crystal is an essential first step for mapping the average density distribution of the disordered solvent.« less

X-ray diffraction measurement of cosolvent accessible volume in rhombohedral insulin crystals

DOE PAGES

Soares, Alexei S.; Caspar, Donald L. D.

2017-08-31

We report x-ray crystallographic measurement of the number of solvent electrons in the unit cell of a protein crystal equilibrated with aqueous solutions of different densities provides information about preferential hydration in the crystalline state. Room temperature and cryo-cooled rhombohedral insulin crystals were equilibrated with 1.2 M trehalose to study the effect of lowered water activity. The native and trehalose soaked crystals were isomorphous and had similar structures. Including all the low resolution data, the amplitudes of the structure factors were put on an absolute scale (in units of electrons per asymmetric unit) by constraining the integrated number of electronsmore » inside the envelope of the calculated protein density map to equal the number deduced from the atomic model. This procedure defines the value of F(0 0 0), the amplitude at the origin of the Fourier transform, which is equal to the total number of electrons in the asymmetric unit (i.e. protein plus solvent). Comparison of the F(0 0 0) values for three isomorphous pairs of room temperature insulin crystals, three with trehalose and three without trehalose, indicates that 75 ± 12 electrons per asymmetric unit were added to the crystal solvent when soaked in 1.2 M trehalose. If all the water in the crystal were available as solvent for the trehalose, 304 electrons would have been added. Thus, the co-solvent accessible volume is one quarter of the total water in the crystal. Finally, determination of the total number of electrons in a protein crystal is an essential first step for mapping the average density distribution of the disordered solvent.« less

Cosolvent pretreatment in cellulosic biofuel production: Effect of tetrahydrofuran-water on lignin structure and dynamics

DOE PAGES

Smith, Micholas Dean; Mostofian, Barmak; Cheng, Xiaolin; ...

2015-10-05

The deconstruction of cellulose is an essential step in the production of ethanol from lignocellulosic biomass. However, the presence of lignin hinders this process. Recently, a novel cosolvent based biomass pretreatment method called CELF (Cosolvent Enhanced Lignocellulosic Fractionation) which employs tetrahydrofuran (THF) in a single phase mixture with water, was found to be highly effective at solubilizing and extracting lignin from lignocellulosic biomass and achieving high yields of fermentable sugars. Here, using all-atom molecular-dynamics simulation, we find that THF preferentially solvates lignin, and in doing so, shifts the equilibrium configurational distribution of the biopolymer from a crumpled globule to coil,more » independent of temperature. Whereas pure water is a bad solvent for lignin, the THF : water cosolvent acts as a "theta" solvent, in which solvent : lignin and lignin : lignin interactions are approximately equivalent in strength. Furthermore, under these conditions, polymers do not aggregate, thus providing a mechanism for the observed lignin solubilization that facilitates unfettered access of celluloytic enzymes to cellulose.« less

Investigation of the antioxidant and radical scavenging activities of some phenolic Schiff bases with different free radicals.

PubMed

Marković, Zoran; Đorović, Jelena; Petrović, Zorica D; Petrović, Vladimir P; Simijonović, Dušica

2015-11-01

The antioxidant properties of some phenolic Schiff bases in the presence of different reactive particles such as (•)OH, (•)OOH, (CH2=CH-O-O(•)), and (-•)O2 were investigated. The thermodynamic values, ΔH BDE, ΔH IP, and ΔH PA, were used for this purpose. Three possible mechanisms for transfer of hydrogen atom, concerted proton-electron transfer (CPET), single electron transfer followed by proton transfer (SET-PT), and sequential proton loss electron transfer (SPLET) were considered. These mechanisms were tested in solvents of different polarity. On the basis of the obtained results it was shown that SET-PT antioxidant mechanism can be the dominant mechanism when Schiff bases react with radical cation, while SPLET and CPET are competitive mechanisms for radical scavenging of hydroxy radical in all solvents under investigation. Examined Schiff bases react with the peroxy radicals via SPLET mechanism in polar and nonpolar solvents. The superoxide radical anion reacts with these Schiff bases very slowly.

Polymorphous Computing Architectures

DTIC Science & Technology

2007-12-12

provide a multiprocessor implementation. In this work, we introduce the Atomos transactional programming language, which is the first to include...implicit transactions, strong atomicity, and a scalable multiprocessor implementation [47]. Atomos is derived from Java, but replaces its synchronization...and conditional waiting constructs with transactional alternatives. The Atomos conditional waiting proposal is tailored to allow efficient

Calculation of Protein Heat Capacity from Replica-Exchange Molecular Dynamics Simulations with Different Implicit Solvent Models

DTIC Science & Technology

2008-10-30

rigorous Poisson-based methods generally apply a Lee-Richards mo- lecular surface.9 This surface is considered the de facto description for continuum...definition and calculation of the Born radii. To evaluate the Born radii, two approximations are invoked. The first is the Coulomb field approximation (CFA...energy term, and depending on the particular GB formulation, higher-order non- Coulomb correction terms may be added to the Born radii to account for the

Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations

PubMed Central

Wang, Junmei; Hou, Tingjun

2012-01-01

It is of great interest in modern drug design to accurately calculate the free energies of protein-ligand or nucleic acid-ligand binding. MM-PBSA (Molecular Mechanics-Poisson Boltzmann Surface Area) and MM-GBSA (Molecular Mechanics-Generalized Born Surface Area) have gained popularity in this field. For both methods, the conformational entropy, which is usually calculated through normal mode analysis (NMA), is needed to calculate the absolute binding free energies. Unfortunately, NMA is computationally demanding and becomes a bottleneck of the MM-PB/GBSA-NMA methods. In this work, we have developed a fast approach to estimate the conformational entropy based upon solvent accessible surface area calculations. In our approach, the conformational entropy of a molecule, S, can be obtained by summing up the contributions of all atoms, no matter they are buried or exposed. Each atom has two types of surface areas, solvent accessible surface area (SAS) and buried SAS (BSAS). The two types of surface areas are weighted to estimate the contribution of an atom to S. Atoms having the same atom type share the same weight and a general parameter k is applied to balance the contributions of the two types of surface areas. This entropy model was parameterized using a large set of small molecules for which their conformational entropies were calculated at the B3LYP/6-31G* level taking the solvent effect into account. The weighted solvent accessible surface area (WSAS) model was extensively evaluated in three tests. For the convenience, TS, the product of temperature T and conformational entropy S, were calculated in those tests. T was always set to 298.15 K through the text. First of all, good correlations were achieved between WSAS TS and NMA TS for 44 protein or nucleic acid systems sampled with molecular dynamics simulations (10 snapshots were collected for post-entropy calculations): the mean correlation coefficient squares (R2) was 0.56. As to the 20 complexes, the TS changes upon binding, TΔS, were also calculated and the mean R2 was 0.67 between NMA and WSAS. In the second test, TS were calculated for 12 proteins decoy sets (each set has 31 conformations) generated by the Rosetta software package. Again, good correlations were achieved for all decoy sets: the mean, maximum, minimum of R2 were 0.73, 0.89 and 0.55, respectively. Finally, binding free energies were calculated for 6 protein systems (the numbers of inhibitors range from 4 to 18) using four scoring functions. Compared to the measured binding free energies, the mean R2 of the six protein systems were 0.51, 0.47, 0.40 and 0.43 for MM-GBSA-WSAS, MM-GBSA-NMA, MM-PBSA-WSAS and MM-PBSA-NMA, respectively. The mean RMS errors of prediction were 1.19, 1.24, 1.41, 1.29 kcal/mol for the four scoring functions, correspondingly. Therefore, the two scoring functions employing WSAS achieved a comparable prediction performance to that of the scoring functions using NMA. It should be emphasized that no minimization was performed prior to the WSAS calculation in the last test. Although WSAS is not as rigorous as physical models such as quasi-harmonic analysis and thermodynamic integration (TI), it is computationally very efficient as only surface area calculation is involved and no structural minimization is required. Moreover, WSAS has achieved a comparable performance to normal mode analysis. We expect that this model could find its applications in the fields like high throughput screening (HTS), molecular docking and rational protein design. In those fields, efficiency is crucial since there are a large number of compounds, docking poses or protein models to be evaluated. A list of acronyms and abbreviations used in this work is provided for quick reference. PMID:22497310

Super-hydrophobic fluorine containing aerogels

DOEpatents

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

2007-05-01

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

Influence of solvents on the conformation of benzoin

NASA Astrophysics Data System (ADS)

Pawełka, Z.; Czarnik-Matusewicz, B.; Zeegers-Huyskens, Th.

2010-01-01

The conformation of benzoin in several organic solvents is investigated by infrared spectrometry and dipolometry. The frequencies, intensities, and band shapes of the ν(OH), ν(C dbnd O), and aromatic ring vibrations indicate that in solvents of low proton acceptor ability, the cis conformer with intramolecular OH···O hydrogen bonding is preserved. In solvents of large proton acceptor ability there is equilibrium between the cis and trans conformers. The dipole moments are less sensitive to conformational changes, but indicate the same trends. The results are discussed as a function of the specific solvation of the O atoms or OH groups of benzoin.

Implicit Self-Esteem Decreases in Adolescence: A Cross-Sectional Study

PubMed Central

Cai, Huajian; Wu, Mingzheng; Luo, Yu L. L.; Yang, Jing

2014-01-01

Implicit self-esteem has remained an active research topic in both the areas of implicit social cognition and self-esteem in recent decades. The purpose of this study is to explore the development of implicit self-esteem in adolescents. A total of 599 adolescents from junior and senior high schools in East China participated in the study. They ranged in age from 11 to 18 years with a mean age of 14.10 (SD = 2.16). The degree of implicit self-esteem was assessed using the Implicit Association Test (IAT) with the improved D score as the index. Participants also completed the Rosenberg Self-Esteem Scale (α = 0.77). For all surveyed ages, implicit self-esteem was positively biased, all ts>8.59, all ps<0.001. The simple correlation between implicit self-esteem and age was significant, r = −.25, p = 1.0×10−10. A regression with implicit self-esteem as the criterion variable, and age, gender, and age × gender interaction as predictors further revealed the significant negative linear relationship between age and implicit self-esteem, β = −0.19, t = −3.20, p = 0.001. However, explicit self-esteem manifested a reverse “U” shape throughout adolescence. Implicit self-esteem in adolescence manifests a declining trend with increasing age, suggesting that it is sensitive to developmental or age-related changes. This finding enriches our understanding of the development of implicit social cognition. PMID:24587169

A highly selective and sensitive ultrasonic assisted dispersive liquid phase microextraction based on deep eutectic solvent for determination of cadmium in food and water samples prior to electrothermal atomic absorption spectrometry.

PubMed

Zounr, Rizwan Ali; Tuzen, Mustafa; Deligonul, Nihal; Khuhawar, Muhammad Yar

2018-07-01

A simple, fast, green, sensitive and selective ultrasonic assisted deep eutectic solvent liquid-phase microextraction technique was used for preconcentration and extraction of cadmium (Cd) in water and food samples by electrothermal atomic absorption spectrometry (ETAAS). In this technique, a synthesized reagent (Z)-N-(3,5-diphenyl-1H-pyrrol-2-yl)-3,5-diphenyl-2H-pyrrol-2-imine (Azo) was used as a complexing agent for Cd. The main factors effecting the pre-concentration and extraction of Cd such as effect of pH, type and composition of deep eutectic solvent (DES), volume of DES, volume of complexing agent, volume of tetrahydrofuran (THF) and ultrasonication time have been examined in detail. At optimum conditions the value of pH and molar ratio of DES were found to be 6.0 and 1:4 (ChCl:Ph), respectively. The detection limit (LOD), limit of quantification (LOQ), relative standard deviation (RSD) and preconcentration factor (PF) were observed as 0.023 ng L -1 , 0.161 ng L -1 , 3.1% and 100, correspondingly. Validation of the developed technique was observed by extraction of Cd in certified reference materials (CRMs) and observed results were successfully compared with certified values. The developed procedure was practiced to various food, beverage and water samples. Copyright © 2018 Elsevier Ltd. All rights reserved.

Hierarchical atom type definitions and extensible all-atom force fields.

PubMed

Jin, Zhao; Yang, Chunwei; Cao, Fenglei; Li, Feng; Jing, Zhifeng; Chen, Long; Shen, Zhe; Xin, Liang; Tong, Sijia; Sun, Huai

2016-03-15

The extensibility of force field is a key to solve the missing parameter problem commonly found in force field applications. The extensibility of conventional force fields is traditionally managed in the parameterization procedure, which becomes impractical as the coverage of the force field increases above a threshold. A hierarchical atom-type definition (HAD) scheme is proposed to make extensible atom type definitions, which ensures that the force field developed based on the definitions are extensible. To demonstrate how HAD works and to prepare a foundation for future developments, two general force fields based on AMBER and DFF functional forms are parameterized for common organic molecules. The force field parameters are derived from the same set of quantum mechanical data and experimental liquid data using an automated parameterization tool, and validated by calculating molecular and liquid properties. The hydration free energies are calculated successfully by introducing a polarization scaling factor to the dispersion term between the solvent and solute molecules. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Effects of carbonization and solvent-extraction on change in fuel characteristics of sewage sludge.

PubMed

Park, Sang-Woo; Jang, Cheol-Hyeon

2011-09-01

Urban sewage sludge was carbonized at 300-500°C for 1h, and combustible components were extracted through the solvent-extraction process. N-methyl-2-pyrrolidinone (NMP) was used as the solvent for extraction, and the extraction temperature was fixed at 360°C. The atomic ratios of the solvent-extracted sludge of CS300 (ECS300) were shown to be 1.04 for H/C and 0.11 for O/C, which represented the characteristics of its coal band. Thus, its coal band was similar to that of a high-rank fuel such as bituminous coal. FT-IR analysis showed that the absorbance band of ECS300 was considerably different from that of dried sludge (RS) or the carbonized sludge at 300°C (CS300) but similar to that of coal, although the ash content absorbance band of 800-1200 cm(-1) was of very low intensity. The combustion profile showed that combustion of ESC300 occurred at a temperature higher than the ignition temperature (T(i)) or maximum weight loss rate (DTG(max)) of coal. Copyright © 2011 Elsevier Ltd. All rights reserved.

Influence of Solvent on the Drug-Loading Process of Amphiphilic Nanogel Star Polymers.

PubMed

Carr, Amber C; Piunova, Victoria A; Maarof, Hasmerya; Rice, Julia E; Swope, William C

2018-05-31

We present an all-atom molecular dynamics study of the effect of a range of organic solvents (dichloromethane, diethyl ether, toluene, methanol, dimethyl sulfoxide, and tetrahydrofuran) on the conformations of a nanogel star polymeric nanoparticle with solvophobic and solvophilic structural elements. These nanoparticles are of particular interest for drug delivery applications. As drug loading generally takes place in an organic solvent, this work serves to provide insight into the factors controlling the early steps of that process. Our work suggests that nanoparticle conformational structure is highly sensitive to the choice of solvent, providing avenues for further study as well as predictions for both computational and experimental explorations of the drug-loading process. Our findings suggest that when used in the drug-loading process, dichloromethane, tetrahydrofuran, and toluene allow for a more extensive and increased drug-loading into the interior of nanogel star polymers of the composition studied here. In contrast, methanol is more likely to support shallow or surface loading and, consequently, faster drug release rates. Finally, diethyl ether should not work in a formulation process since none of the regions of the nanogel star polymer appear to be sufficiently solvated by it.

Deep eutectic solvents: similia similibus solvuntur?

PubMed

Zahn, Stefan

2017-02-01

Deep eutectic solvents, mixtures of an organic compound and a salt with a deep eutectic melting point, are promising cheap and eco-friendly alternatives to ionic liquids. Ab initio molecular dynamics simulations of reline, a mixture consisting of urea and choline chloride, reveal that not solely hydrogen bonds allow similar interactions between both constituents. The chloride anion and the oxygen atom of urea also show a similar spatial distribution close to the cationic core of choline due to a similar charge located on both atoms. As a result of multiple similar interactions, clusters migrating together cannot be observed in reline which supports the hypothesis similia similibus solvuntur. In contrast to previous suggestions, the interaction of the hydroxyl group of choline with a hydrogen bond acceptor is overall rigid. Fast hydrogen bond acceptor dynamics is facilitated by the hydrogen atoms in the trans position to the carbonyl group of urea which contributes to the low melting point of reline.

Lead determination at ng/mL level by flame atomic absorption spectrometry using a tantalum coated slotted quartz tube atom trap.

PubMed

Demirtaş, İlknur; Bakırdere, Sezgin; Ataman, O Yavuz

2015-06-01

Flame atomic absorption spectrometry (FAAS) still keeps its importance despite the relatively low sensitivity; because it is a simple and economical technique for determination of metals. In recent years, atom traps have been developed to increase the sensitivity of FAAS. Although the detection limit of FAAS is only at the level of µg/mL, with the use of atom traps it can reach to ng/mL. Slotted quartz tube (SQT) is one of the atom traps used to improve sensitivity. In atom trapping mode of SQT, analyte is trapped on-line in SQT for few minutes using ordinary sample aspiration, followed by the introduction of a small volume of organic solvent to effect the revolatilization and atomization of analyte species resulting in a transient signal. This system is economical, commercially available and easy to use. In this study, a sensitive analytical method was developed for the determination of lead with the help of SQT atom trapping flame atomization (SQT-AT-FAAS). 574 Fold sensitivity enhancement was obtained at a sample suction rate of 3.9 mL/min for 5.0 min trapping period with respect to FAAS. Organic solvent was selected as 40 µL of methyl isobutyl ketone (MIBK). To obtain a further sensitivity enhancement inner surface of SQT was coated with several transition metals. The best sensitivity enhancement, 1650 fold enhancement, was obtained by the Ta-coated SQT-AT-FAAS. In addition, chemical nature of Pb species trapped on quartz and Ta surface, and the chemical nature of Ta on quartz surface were investigated by X-ray photoelectron spectroscopy (XPS) and Raman Spectroscopy. Raman spectrometric results indicate that tantalum is coated on SQT surface in the form of Ta2O5. XPS studies revealed that the oxidation state of Pb in species trapped on both bare and Ta coated SQT surfaces is +2. For the accuracy check, the analyses of standard reference material were performed by use of SCP SCIENCE EnviroMAT Low (EU-L-2) and results for Pb were to be in good agreement with the certified value using SQT-AT-FAAS and Ta coated-SQT. Copyright © 2015 Elsevier B.V. All rights reserved.

Ensemble-based characterization of unbound and bound states on protein energy landscape

PubMed Central

Ruvinsky, Anatoly M; Kirys, Tatsiana; Tuzikov, Alexander V; Vakser, Ilya A

2013-01-01

Physicochemical description of numerous cell processes is fundamentally based on the energy landscapes of protein molecules involved. Although the whole energy landscape is difficult to reconstruct, increased attention to particular targets has provided enough structures for mapping functionally important subspaces associated with the unbound and bound protein structures. The subspace mapping produces a discrete representation of the landscape, further called energy spectrum. We compiled and characterized ensembles of bound and unbound conformations of six small proteins and explored their spectra in implicit solvent. First, the analysis of the unbound-to-bound changes points to conformational selection as the binding mechanism for four proteins. Second, results show that bound and unbound spectra often significantly overlap. Moreover, the larger the overlap the smaller the root mean square deviation (RMSD) between the bound and unbound conformational ensembles. Third, the center of the unbound spectrum has a higher energy than the center of the corresponding bound spectrum of the dimeric and multimeric states for most of the proteins. This suggests that the unbound states often have larger entropy than the bound states. Fourth, the exhaustively long minimization, making small intrarotamer adjustments (all-atom RMSD ≤ 0.7 Å), dramatically reduces the distance between the centers of the bound and unbound spectra as well as the spectra extent. It condenses unbound and bound energy levels into a thin layer at the bottom of the energy landscape with the energy spacing that varies between 0.8–4.6 and 3.5–10.5 kcal/mol for the unbound and bound states correspondingly. Finally, the analysis of protein energy fluctuations showed that protein vibrations itself can excite the interstate transitions, including the unbound-to-bound ones. PMID:23526684

Bottom-up view of water network-mediated CO2 reduction using cryogenic cluster ion spectroscopy and direct dynamics simulations.

PubMed

Breen, Kristin J; DeBlase, Andrew F; Guasco, Timothy L; Voora, Vamsee K; Jordan, Kenneth D; Nagata, Takashi; Johnson, Mark A

2012-01-26

The transition states of a chemical reaction in solution are generally accessed through exchange of thermal energy between the solvent and the reactants. As such, an ensemble of reacting systems approaches the transition state configuration of reactant and surrounding solvent in an incoherent manner that does not lend itself to direct experimental observation. Here we describe how gas-phase cluster chemistry can provide a detailed picture of the microscopic mechanics at play when a network of six water molecules mediates the trapping of a highly reactive "hydrated electron" onto a neutral CO(2) molecule to form a radical anion. The exothermic reaction is triggered from a metastable intermediate by selective excitation of either the reactant CO(2) or the water network, which is evidenced by the evaporative decomposition of the product cluster. Ab initio molecular dynamics simulations of energized CO(2)·(H(2)O)(6)(-) clusters are used to elucidate the nature of the network deformations that mediate intracluster electron capture, thus revealing the detailed solvent fluctuations implicit in the Marcus theory for electron-transfer kinetics in solution.

Solvophobic and solvophilic contributions in the water-to-aqueous guanidinium chloride transfer free energy of model peptides

NASA Astrophysics Data System (ADS)

Tomar, Dheeraj S.; Ramesh, Niral; Asthagiri, D.

2018-06-01

We study the solvation free energy of two different conformations (helix and extended) of two different peptides (deca-alanine and deca-glycine) in two different solvents (water and aqueous guanidinium chloride, GdmCl). The free energies are obtained using the quasichemical organization of the potential distribution theorem, an approach that naturally provides the repulsive (solvophobic or cavity) and attractive (solvophilic) contributions to solvation. The solvophilic contribution is further parsed into a chemistry contribution arising from solute interaction with the solvent in the first solvation shell and a long-range contribution arising from non-specific interactions between the solute and the solvent beyond the first solvation shell. The cavity contribution is obtained for two different envelopes, ΣS E, which theory helps identify as the solvent excluded volume, and ΣG, a larger envelope beyond which solute-solvent interactions are Gaussian. The ΣS E envelope is independent of the solvent, as expected on the basis of the insensitivity to the solvent type of the distance of closest approach between protein heavy atoms and solvent heavy atoms, but contrary to the intuition based on treating solvent constituents as spheres of some effective radii. For both envelopes, the cavity contribution in water is proportional to the surface area of the envelope. The same does not hold for GdmCl(aq), revealing the limitation of using molecular area to assess solvation energetics. The ΣG-cavity contribution predicts that GdmCl(aq) should favor the more compact state, contrary to the role of GdmCl in unfolding proteins. The chemistry contribution attenuates this effect, but still the net local (chemistry plus ΣG-packing) contribution is inadequate in capturing the role of GdmCl. With the inclusion of the long-range contribution, which is dominated by van der Waals interaction, aqueous GdmCl favors the extended conformation over the compact conformation. Our finding emphasizes the importance of weak, but attractive, long-range dispersion interactions in protein solution thermodynamics.

Solvophobic and solvophilic contributions in the water-to-aqueous guanidinium chloride transfer free energy of model peptides.

PubMed

Tomar, Dheeraj S; Ramesh, Niral; Asthagiri, D

2018-06-14

We study the solvation free energy of two different conformations (helix and extended) of two different peptides (deca-alanine and deca-glycine) in two different solvents (water and aqueous guanidinium chloride, GdmCl). The free energies are obtained using the quasichemical organization of the potential distribution theorem, an approach that naturally provides the repulsive (solvophobic or cavity) and attractive (solvophilic) contributions to solvation. The solvophilic contribution is further parsed into a chemistry contribution arising from solute interaction with the solvent in the first solvation shell and a long-range contribution arising from non-specific interactions between the solute and the solvent beyond the first solvation shell. The cavity contribution is obtained for two different envelopes, Σ SE , which theory helps identify as the solvent excluded volume, and Σ G , a larger envelope beyond which solute-solvent interactions are Gaussian. The Σ SE envelope is independent of the solvent, as expected on the basis of the insensitivity to the solvent type of the distance of closest approach between protein heavy atoms and solvent heavy atoms, but contrary to the intuition based on treating solvent constituents as spheres of some effective radii. For both envelopes, the cavity contribution in water is proportional to the surface area of the envelope. The same does not hold for GdmCl(aq), revealing the limitation of using molecular area to assess solvation energetics. The Σ G -cavity contribution predicts that GdmCl(aq) should favor the more compact state, contrary to the role of GdmCl in unfolding proteins. The chemistry contribution attenuates this effect, but still the net local (chemistry plus Σ G -packing) contribution is inadequate in capturing the role of GdmCl. With the inclusion of the long-range contribution, which is dominated by van der Waals interaction, aqueous GdmCl favors the extended conformation over the compact conformation. Our finding emphasizes the importance of weak, but attractive, long-range dispersion interactions in protein solution thermodynamics.

iMODS: internal coordinates normal mode analysis server.

PubMed

López-Blanco, José Ramón; Aliaga, José I; Quintana-Ortí, Enrique S; Chacón, Pablo

2014-07-01

Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation improves the efficiency of NMA and extends its applicability while implicitly maintaining stereochemistry. Vibrational analysis, motion animations and morphing trajectories can be easily carried out at different resolution scales almost interactively. The server is versatile; non-specialists can rapidly characterize potential conformational changes, whereas advanced users can customize the model resolution with multiple coarse-grained atomic representations and elastic network potentials. iMODS supports advanced visualization capabilities for illustrating collective motions, including an improved affine-model-based arrow representation of domain dynamics. The generated all-heavy-atoms conformations can be used to introduce flexibility for more advanced modeling or sampling strategies. The server is free and open to all users with no login requirement at http://imods.chaconlab.org. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

Extending the Solvation-Layer Interface Condition Continum Electrostatic Model to a Linearized Poisson-Boltzmann Solvent.

PubMed

Molavi Tabrizi, Amirhossein; Goossens, Spencer; Mehdizadeh Rahimi, Ali; Cooper, Christopher D; Knepley, Matthew G; Bardhan, Jaydeep P

2017-06-13

We extend the linearized Poisson-Boltzmann (LPB) continuum electrostatic model for molecular solvation to address charge-hydration asymmetry. Our new solvation-layer interface condition (SLIC)/LPB corrects for first-shell response by perturbing the traditional continuum-theory interface conditions at the protein-solvent and the Stern-layer interfaces. We also present a GPU-accelerated treecode implementation capable of simulating large proteins, and our results demonstrate that the new model exhibits significant accuracy improvements over traditional LPB models, while reducing the number of fitting parameters from dozens (atomic radii) to just five parameters, which have physical meanings related to first-shell water behavior at an uncharged interface. In particular, atom radii in the SLIC model are not optimized but uniformly scaled from their Lennard-Jones radii. Compared to explicit-solvent free-energy calculations of individual atoms in small molecules, SLIC/LPB is significantly more accurate than standard parametrizations (RMS error 0.55 kcal/mol for SLIC, compared to RMS error of 3.05 kcal/mol for standard LPB). On parametrizing the electrostatic model with a simple nonpolar component for total molecular solvation free energies, our model predicts octanol/water transfer free energies with an RMS error 1.07 kcal/mol. A more detailed assessment illustrates that standard continuum electrostatic models reproduce total charging free energies via a compensation of significant errors in atomic self-energies; this finding offers a window into improving the accuracy of Generalized-Born theories and other coarse-grained models. Most remarkably, the SLIC model also reproduces positive charging free energies for atoms in hydrophobic groups, whereas standard PB models are unable to generate positive charging free energies regardless of the parametrized radii. The GPU-accelerated solver is freely available online, as is a MATLAB implementation.

Separation/preconcentration and determination of vanadium with dispersive liquid-liquid microextraction based on solidification of floating organic drop (DLLME-SFO) and electrothermal atomic absorption spectrometry.

PubMed

Asadollahi, Tahereh; Dadfarnia, Shayessteh; Shabani, Ali Mohammad Haji

2010-06-30

A novel dispersive liquid-liquid microextraction based on solidification of floating organic drop (DLLME-SFO) for separation/preconcentration of ultra trace amount of vanadium and its determination with the electrothermal atomic absorption spectrometry (ETAAS) was developed. The DLLME-SFO behavior of vanadium (V) using N-benzoyl-N-phenylhydroxylamine (BPHA) as complexing agent was systematically investigated. The factors influencing the complex formation and extraction by DLLME-SFO method were optimized. Under the optimized conditions: 100 microL, 200 microL and 25 mL of extraction solvent (1-undecanol), disperser solvent (acetone) and sample volume, respectively, an enrichment factor of 184, a detection limit (based on 3S(b)/m) of 7 ng L(-1) and a relative standard deviation of 4.6% (at 500 ng L(-1)) were obtained. The calibration graph using the preconcentration system for vanadium was linear from 20 to 1000 ng L(-1) with a correlation coefficient of 0.9996. The method was successfully applied for the determination of vanadium in water and parsley. Copyright 2010 Elsevier B.V. All rights reserved.

Role of solvent in metal-on-metal surface diffusion: A case for rational solvent selection for materials synthesis

NASA Astrophysics Data System (ADS)

Imandi, Venkataramana; Jagannath, Mantha Sai Pavan; Chatterjee, Abhijit

2018-09-01

The effect of solvent on diffusion at metal surfaces is poorly understood despite its importance to morphological evolution during materials processing, corrosion and catalysis. In this article, we probe the metal-solvent interfacial structure, effective nature of interactions and dynamics when a solvent is in contact with a metal using a novel accelerated molecular dynamics simulation technique called temperature programmed molecular dynamics (TPMD). TPMD simulations reveal that surface diffusion of metal-on-metal can be made to vary over orders-of-magnitude by tuning the metal-solvent interaction. Ultimately, the solvent can have an indirect effect on diffusion. As the solvent tugs at the metal surface the separation between the adsorbed metal atom (adatom) and the surface layer can be modulated via metal-solvent interactions. The resulting adatom-surface separation can cause stronger/weaker binding of the adatom to the metal surface, which in turn results in the observed slower/enhanced diffusion in the presence of solvent. We believe this effect is ubiquitous in pure metal and metal alloys and in principle one could rationally select solvent to control the material structural evolution. Implications on materials synthesis are discussed in the context of formation of nanoporous materials.

Analyzing For Light Elements By X-Ray Scattering

NASA Technical Reports Server (NTRS)

Ross, H. Richard

1993-01-01

Nondestructive method of determining concentrations of low-atomic-number elements in liquids and solids involves measurements of Compton and Rayleigh scattering of x rays. Applied in quantitative analysis of low-atomic-number constituents of alloys, of contaminants and corrosion products on surfaces of alloys, and of fractions of hydrogen in plastics, oils, and solvents.

First-Principles Molecular Dynamics Study of a Deep Eutectic Solvent: Choline Chloride/Urea and Its Mixture with Water

DOE PAGES

Fetisov, Evgenii O.; Harwood, David B.; Kuo, I-Feng William; ...

2017-12-07

First-principles molecular dynamics simulations in the canonical ensemble at temperatures of 333 and 363 K and at the corresponding experimental densities are carried out to investigate the behavior of the 1:2 choline chloride/urea (reline) deep eutectic solvent and its equimolar mixture with water. Analysis of atom–atom radial and spatial distribution functions and of the H-bond network reveals the microheterogeneous structure of these complex liquid mixtures. In neat reline, the structure is governed by strong H-bonds of the trans- and cis-H atoms of urea to the chloride ion. In hydrous reline, water competes for the anions, and the H atoms ofmore » urea have similar propensities to bond to the chloride ions and the O atoms of urea and water. Finally, the vibrational spectra exhibit relatively broad peaks reflecting the heterogeneity of the environment. Although the 100 ps trajectories allow only for a qualitative assessment of transport properties, the simulations indicate that water is more mobile than the other species and its addition also fosters faster motion of urea.« less

Atomic Charge Parameters for the Finite Difference Poisson-Boltzmann Method Using Electronegativity Neutralization.

PubMed

Yang, Qingyi; Sharp, Kim A

2006-07-01

An optimization of Rappe and Goddard's charge equilibration (QEq) method of assigning atomic partial charges is described. This optimization is designed for fast and accurate calculation of solvation free energies using the finite difference Poisson-Boltzmann (FDPB) method. The optimization is performed against experimental small molecule solvation free energies using the FDPB method and adjusting Rappe and Goddard's atomic electronegativity values. Using a test set of compounds for which experimental solvation energies are available and a rather small number of parameters, very good agreement was obtained with experiment, with a mean unsigned error of about 0.5 kcal/mol. The QEq atomic partial charge assignment method can reflect the effects of the conformational changes and solvent induction on charge distribution in molecules. In the second section of the paper we examined this feature with a study of the alanine dipeptide conformations in water solvent. The different contributions to the energy surface of the dipeptide were examined and compared with the results from fixed CHARMm charge potential, which is widely used for molecular dynamics studies.

Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations

PubMed Central

Im, Wonpil; Brooks, Charles L.

2005-01-01

The mechanism of interfacial folding and membrane insertion of designed peptides is explored by using an implicit membrane generalized Born model and replica-exchange molecular dynamics. Folding/insertion simulations initiated from fully extended peptide conformations in the aqueous phase, at least 28 Å away from the membrane interface, demonstrate a general mechanism for structure formation and insertion (when it occurs). The predominately hydrophobic peptides from the synthetic WALP and TMX series first become localized at the membrane-solvent interface where they form significant helical secondary structure via a helix–turn–helix motif that inserts the central hydrophobic residues into the membrane interior, and then fluctuations occur that provide a persistent helical structure throughout the peptide and it inserts with its N-terminal end moving across the membrane. More specifically, we observed that: (i) the WALP peptides (WALP16, WALP19, and WALP23) spontaneously insert in the membrane as just noted; (ii) TMX-1 also inserts spontaneously after a similar mechanism and forms a transmembrane helix with a population of ≈50% at 300 K; and (iii) TMX-3 does not insert, but exists in a fluctuating membrane interface-bound form. These findings are in excellent agreement with available experimental data and demonstrate the potential for new implicit solvent/membrane models together with advanced simulation protocols to guide experimental programs in exploring the nature and mechanism of membrane-associated folding and insertion of biologically important peptides. PMID:15860587

On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase

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

Brokaw, Jason B.; Chu, Jhih-wei

2010-11-17

We characterized the conformational change of adenylate kinase (AK) between open and closed forms by conducting five all-atom molecular-dynamics simulations, each of 100 ns duration. Different initial structures and substrate binding configurations were used to probe the pathways of AK conformational change in explicit solvent, and no bias potential was applied. A complete closed-to-open and a partial open-to-closed transition were observed, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available x-ray structures and earlier worksmore » of coarse-grained modeling. The trajectories of the all-atom molecular-dynamics simulations revealed the complexity of protein dynamics and the coupling between different domains during conformational change. Calculations of solvent density and density fluctuations surrounding AK did not show prominent variation during the transition between closed and open forms. Finally, we characterized the effects of local unfolding of an important hinge near Pro177 on the closed-to-open transition of AK and identified a novel mechanism by which hinge unfolding modulates protein conformational change. The local unfolding of Pro177 hinge induces alternative tertiary contacts that stabilize the closed structure and prevent the opening transition.« less

The solvent component of macromolecular crystals

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

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

2015-04-30

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

The electrostatics of solvent and membrane interfaces and the role of electronic polarizability

NASA Astrophysics Data System (ADS)

Vorobyov, Igor; Allen, Toby W.

2010-05-01

The electrostatics of solvent and lipid bilayer interfaces are investigated with the aim of understanding the interaction of ions and charged peptides with biological membranes. We overcome the lacking dielectric response of hydrocarbon by carrying out atomistic molecular dynamics simulations using a polarizable model. For air-solvent or solvent-solvent interfaces, the effect of polarizability itself is small, yet changes in the fixed atomic charge distribution are responsible for substantial changes in the potential. However, when electrostatics is probed by finite solutes, a cancellation of dominant quadrupolar terms from the macroscopic and microscopic (solute-solvent) interfaces eliminates this dependence and leads to small net contributions to partitioning thermodynamics. In contrast, the membrane dipole potential exhibits considerable dependence on lipid electronic polarizability, due to its dominant dipolar contribution. We report the dipole potential for a polarizable lipid hydrocarbon membrane model of 480-610 mV, in better accord with experimental measurements.

Fluoro-alcohol phase modifiers and process for cesium solvent extraction

DOEpatents

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

2003-05-20

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

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

Kinetic Network Study of the Diversity and Temperature Dependence of Trp-Cage Folding Pathways: Combining Transition Path Theory with Stochastic Simulations

PubMed Central

Zheng, Weihua; Gallicchio, Emilio; Deng, Nanjie; Andrec, Michael; Levy, Ronald M.

2011-01-01

We present a new approach to study a multitude of folding pathways and different folding mechanisms for the 20-residue mini-protein Trp-Cage using the combined power of replica exchange molecular dynamics (REMD) simulations for conformational sampling, Transition Path Theory (TPT) for constructing folding pathways and stochastic simulations for sampling the pathways in a high dimensional structure space. REMD simulations of Trp-Cage with 16 replicas at temperatures between 270K and 566K are carried out with an all-atom force field (OPLSAA) and an implicit solvent model (AGBNP). The conformations sampled from all temperatures are collected. They form a discretized state space that can be used to model the folding process. The equilibrium population for each state at a target temperature can be calculated using the Weighted-Histogram-Analysis Method (WHAM). By connecting states with similar structures and creating edges satisfying detailed balance conditions, we construct a kinetic network that preserves the equilibrium population distribution of the state space. After defining the folded and unfolded macrostates, committor probabilities (Pfold) are calculated by solving a set of linear equations for each node in the network and pathways are extracted together with their fluxes using the TPT algorithm. By clustering the pathways into folding “tubes”, a more physically meaningful picture of the diversity of folding routes emerges. Stochastic simulations are carried out on the network and a procedure is developed to project sampled trajectories onto the folding tubes. The fluxes through the folding tubes calculated from the stochastic trajectories are in good agreement with the corresponding values obtained from the TPT analysis. The temperature dependence of the ensemble of Trp-Cage folding pathways is investigated. Above the folding temperature, a large number of diverse folding pathways with comparable fluxes flood the energy landscape. At low temperature, however, the folding transition is dominated by only a few localized pathways. PMID:21254767

Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations.

PubMed

Zheng, Weihua; Gallicchio, Emilio; Deng, Nanjie; Andrec, Michael; Levy, Ronald M

2011-02-17

We present a new approach to study a multitude of folding pathways and different folding mechanisms for the 20-residue mini-protein Trp-Cage using the combined power of replica exchange molecular dynamics (REMD) simulations for conformational sampling, transition path theory (TPT) for constructing folding pathways, and stochastic simulations for sampling the pathways in a high dimensional structure space. REMD simulations of Trp-Cage with 16 replicas at temperatures between 270 and 566 K are carried out with an all-atom force field (OPLSAA) and an implicit solvent model (AGBNP). The conformations sampled from all temperatures are collected. They form a discretized state space that can be used to model the folding process. The equilibrium population for each state at a target temperature can be calculated using the weighted-histogram-analysis method (WHAM). By connecting states with similar structures and creating edges satisfying detailed balance conditions, we construct a kinetic network that preserves the equilibrium population distribution of the state space. After defining the folded and unfolded macrostates, committor probabilities (P(fold)) are calculated by solving a set of linear equations for each node in the network and pathways are extracted together with their fluxes using the TPT algorithm. By clustering the pathways into folding "tubes", a more physically meaningful picture of the diversity of folding routes emerges. Stochastic simulations are carried out on the network, and a procedure is developed to project sampled trajectories onto the folding tubes. The fluxes through the folding tubes calculated from the stochastic trajectories are in good agreement with the corresponding values obtained from the TPT analysis. The temperature dependence of the ensemble of Trp-Cage folding pathways is investigated. Above the folding temperature, a large number of diverse folding pathways with comparable fluxes flood the energy landscape. At low temperature, however, the folding transition is dominated by only a few localized pathways.

Charged patchy particle models in explicit salt: Ion distributions, electrostatic potentials, and effective interactions.

PubMed

Yigit, Cemil; Heyda, Jan; Dzubiella, Joachim

2015-08-14

We introduce a set of charged patchy particle models (CPPMs) in order to systematically study the influence of electrostatic charge patchiness and multipolarity on macromolecular interactions by means of implicit-solvent, explicit-ion Langevin dynamics simulations employing the Gromacs software. We consider well-defined zero-, one-, and two-patched spherical globules each of the same net charge and (nanometer) size which are composed of discrete atoms. The studied mono- and multipole moments of the CPPMs are comparable to those of globular proteins with similar size. We first characterize ion distributions and electrostatic potentials around a single CPPM. Although angle-resolved radial distribution functions reveal the expected local accumulation and depletion of counter- and co-ions around the patches, respectively, the orientation-averaged electrostatic potential shows only a small variation among the various CPPMs due to space charge cancellations. Furthermore, we study the orientation-averaged potential of mean force (PMF), the number of accumulated ions on the patches, as well as the CPPM orientations along the center-to-center distance of a pair of CPPMs. We compare the PMFs to the classical Derjaguin-Verwey-Landau-Overbeek theory and previously introduced orientation-averaged Debye-Hückel pair potentials including dipolar interactions. Our simulations confirm the adequacy of the theories in their respective regimes of validity, while low salt concentrations and large multipolar interactions remain a challenge for tractable theoretical descriptions.

ALKYL PYROPHOSPHATE METAL SOLVENT EXTRACTANTS AND PROCESS

DOEpatents

Long, R.L.

1958-09-30

A process is presented for the recovery of uranium from aqueous mineral acidic solutions by solvent extraction. The extractant is a synmmetrical dialkyl pyrophosphate in which the alkyl substituents have a chain length of from 4 to 17 carbon atoms. Mentioned as a preferred extractant is dioctyl pyrophosphate. The uranium is precipitated irom the organic extractant phase with an agent such as HF, fluoride salts. alcohol, or ammonia.

Are implicit self-esteem measures valid for assessing individual and cultural differences?

PubMed

Falk, Carl F; Heine, Steven J; Takemura, Kosuke; Zhang, Cathy X J; Hsu, Chih-Wei

2015-02-01

Our research utilized two popular theoretical conceptualizations of implicit self-esteem: 1) implicit self-esteem as a global automatic reaction to the self; and 2) implicit self-esteem as a context/domain specific construct. Under this framework, we present an extensive search for implicit self-esteem measure validity among different cultural groups (Study 1) and under several experimental manipulations (Study 2). In Study 1, Euro-Canadians (N = 107), Asian-Canadians (N = 187), and Japanese (N = 112) completed a battery of implicit self-esteem, explicit self-esteem, and criterion measures. Included implicit self-esteem measures were either popular or provided methodological improvements upon older methods. Criterion measures were sampled from previous research on implicit self-esteem and included self-report and independent ratings. In Study 2, Americans (N = 582) completed a shorter battery of these same types of measures under either a control condition, an explicit prime meant to activate the self-concept in a particular context, or prime meant to activate self-competence related implicit attitudes. Across both studies, explicit self-esteem measures far outperformed implicit self-esteem measures in all cultural groups and under all experimental manipulations. Implicit self-esteem measures are not valid for individual or cross-cultural comparisons. We speculate that individuals may not form implicit associations with the self as an attitudinal object. © 2013 Wiley Periodicals, Inc.

Fast Computation of Solvation Free Energies with Molecular Density Functional Theory: Thermodynamic-Ensemble Partial Molar Volume Corrections.

PubMed

Sergiievskyi, Volodymyr P; Jeanmairet, Guillaume; Levesque, Maximilien; Borgis, Daniel

2014-06-05

Molecular density functional theory (MDFT) offers an efficient implicit-solvent method to estimate molecule solvation free-energies, whereas conserving a fully molecular representation of the solvent. Even within a second-order approximation for the free-energy functional, the so-called homogeneous reference fluid approximation, we show that the hydration free-energies computed for a data set of 500 organic compounds are of similar quality as those obtained from molecular dynamics free-energy perturbation simulations, with a computer cost reduced by 2-3 orders of magnitude. This requires to introduce the proper partial volume correction to transform the results from the grand canonical to the isobaric-isotherm ensemble that is pertinent to experiments. We show that this correction can be extended to 3D-RISM calculations, giving a sound theoretical justification to empirical partial molar volume corrections that have been proposed recently.

A simple method for the fast calculation of charge redistribution of solutes in an implicit solvent model

NASA Astrophysics Data System (ADS)

Dias, L. G.; Shimizu, K.; Farah, J. P. S.; Chaimovich, H.

2002-09-01

We propose and demonstrate the usefulness of a method, defined as generalized Born electronegativity equalization method (GBEEM) to estimate solvent-induced charge redistribution. The charges obtained by GBEEM, in a representative series of small organic molecules, were compared to PM3-CM1 charges in vacuum and in water. Linear regressions with appropriate correlation coefficients and standard deviations between GBEEM and PM3-CM1 methods were obtained ( R=0.94,SD=0.15, Ftest=234, N=32, in vacuum; R=0.94,SD=0.16, Ftest=218, N=29, in water). In order to test the GBEEM response when intermolecular interactions are involved we calculated a water dimer in dielectric water using both GBEEM and PM3-CM1 and the results were similar. Hence, the method developed here is comparable to established calculation methods.

New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics

NASA Astrophysics Data System (ADS)

Xie, Dexuan

2014-10-01

The Poisson-Boltzmann equation (PBE) is one widely-used implicit solvent continuum model in the calculation of electrostatic potential energy for biomolecules in ionic solvent, but its numerical solution remains a challenge due to its strong singularity and nonlinearity caused by its singular distribution source terms and exponential nonlinear terms. To effectively deal with such a challenge, in this paper, new solution decomposition and minimization schemes are proposed, together with a new PBE analysis on solution existence and uniqueness. Moreover, a PBE finite element program package is developed in Python based on the FEniCS program library and GAMer, a molecular surface and volumetric mesh generation program package. Numerical tests on proteins and a nonlinear Born ball model with an analytical solution validate the new solution decomposition and minimization schemes, and demonstrate the effectiveness and efficiency of the new PBE finite element program package.

Free-energy landscape of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics.

PubMed

Higo, Junichi; Umezawa, Koji

2014-01-01

We introduce computational studies on intrinsically disordered proteins (IDPs). Especially, we present our multicanonical molecular dynamics (McMD) simulations of two IDP-partner systems: NRSF-mSin3 and pKID-KIX. McMD is one of enhanced conformational sampling methods useful for conformational sampling of biomolecular systems. IDP adopts a specific tertiary structure upon binding to its partner molecule, although it is unstructured in the unbound state (i.e. the free state). This IDP-specific property is called "coupled folding and binding". The McMD simulation treats the biomolecules with an all-atom model immersed in an explicit solvent. In the initial configuration of simulation, IDP and its partner molecules are set to be distant from each other, and the IDP conformation is disordered. The computationally obtained free-energy landscape for coupled folding and binding has shown that native- and non-native-complex clusters distribute complicatedly in the conformational space. The all-atom simulation suggests that both of induced-folding and population-selection are coupled complicatedly in the coupled folding and binding. Further analyses have exemplified that the conformational fluctuations (dynamical flexibility) in the bound and unbound states are essentially important to characterize IDP functioning.

Ultrafast, 2 min synthesis of monolayer-protected gold nanoclusters (d < 2 nm)

NASA Astrophysics Data System (ADS)

Martin, Matthew N.; Li, Dawei; Dass, Amala; Eah, Sang-Kee

2012-06-01

An ultrafast synthesis method is presented for hexanethiolate-coated gold nanoclusters (d < 2 nm, <250 atoms per nanocluster), which takes only 2 min and can be easily reproduced. With two immiscible solvents, gold nanoclusters are separated from the reaction byproducts fast and easily without any need for post-synthesis cleaning.An ultrafast synthesis method is presented for hexanethiolate-coated gold nanoclusters (d < 2 nm, <250 atoms per nanocluster), which takes only 2 min and can be easily reproduced. With two immiscible solvents, gold nanoclusters are separated from the reaction byproducts fast and easily without any need for post-synthesis cleaning. Electronic supplementary information (ESI) available: Experimental details of gold nanocluster synthesis and mass-spectrometry. See DOI: 10.1039/c2nr30890h

Biomass Conversion Strategies and the Renewable Production of Hydrogen using Heterogeneous Metal Catalysts

NASA Astrophysics Data System (ADS)

Carrasquillo-Flores, Ronald

Biomass is a renewable carbon source that can be processed into fuels and chemicals in a biorefinery. However, there are a number of challenges that need to be overcome for biomass utilization to be viable. The work presented herein aims to address two existing challenges in biomass processing schemes, namely the efficient utilization of all fractions of lignocellulosic biomass and the renewable production of the hydrogen necessary to reduce the oxygen functionalities native in biomass. First, lignin was depolymerized to produce a renewable phenolic solvent mixture. Biphasic reactions with this solvent and aqueous solution of glucose or xylose produce 5-hydroxymethylfurfural (HMF) and furfural, respectively, at high yields. HMF and furfuryl alcohol could also be upgraded into levulinic acid at high yields. The yields are due to the capacity of the solvent to partition these molecules and prevent their degradation. Second, propyl guaiacol, a component of the phenolic solvent, was used for biphasic reactions where ball milled biomass substrates were used. These substrates are converted to furfural and HMF at high yields due to the partition of these molecules into the solvent and the on-demand production of glucose and xylose from the substrate, minimizing the formation of humins. A study of the water-gas shift reaction over Pt-based catalysts was conducted. Alloying Pt with Re was found to increase the catalytic activity and microkinetic modeling revealed Pt is a good representation of the active site and Re acts as a promoter slightly destabilizing CO binding. A study on formic acid decomposition over Au catalysts was performed. Experiments, density functional theory and microkinetic modeling results indicate the reaction proceeds completely on highly undercoordinated Au atoms with any high coordination atom being largely inert. Motivated by the results on Au catalysts, the metal-support interaction was investigated for the reverse water-gas shift reaction. Using a combination of infrared spectroscopy, Raman spectroscopy, x-ray absorption spectroscopy, electron microscopy and reaction kinetics measurements it was found that the deposition of an organometallic molybdenum compound occurs at the undercoordinated Au sites to produce interfacial sites that are an order of magnitude more active than Au sites and activate water.

Electrostatics of proteins in dielectric solvent continua. I. An accurate and efficient reaction field description

NASA Astrophysics Data System (ADS)

Bauer, Sebastian; Mathias, Gerald; Tavan, Paul

2014-03-01

We present a reaction field (RF) method which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of an electrostatics calculation with polarizable molecular mechanics (MM) force fields. The method combines an approach originally suggested by Egwolf and Tavan [J. Chem. Phys. 118, 2039 (2003)] with concepts generalizing the Born solution [Z. Phys. 1, 45 (1920)] for a solvated ion. First, we derive an exact representation according to which the sources of the RF potential and energy are inducible atomic anti-polarization densities and atomic shielding charge distributions. Modeling these atomic densities by Gaussians leads to an approximate representation. Here, the strengths of the Gaussian shielding charge distributions are directly given in terms of the static partial charges as defined, e.g., by standard MM force fields for the various atom types, whereas the strengths of the Gaussian anti-polarization densities are calculated by a self-consistency iteration. The atomic volumes are also described by Gaussians. To account for covalently overlapping atoms, their effective volumes are calculated by another self-consistency procedure, which guarantees that the dielectric function ɛ(r) is close to one everywhere inside the protein. The Gaussian widths σi of the atoms i are parameters of the RF approximation. The remarkable accuracy of the method is demonstrated by comparison with Kirkwood's analytical solution for a spherical protein [J. Chem. Phys. 2, 351 (1934)] and with computationally expensive grid-based numerical solutions for simple model systems in dielectric continua including a di-peptide (Ac-Ala-NHMe) as modeled by a standard MM force field. The latter example shows how weakly the RF conformational free energy landscape depends on the parameters σi. A summarizing discussion highlights the achievements of the new theory and of its approximate solution particularly by comparison with so-called generalized Born methods. A follow-up paper describes how the method enables Hamiltonian, efficient, and accurate MM molecular dynamics simulations of proteins in dielectric solvent continua.

Electrostatics of proteins in dielectric solvent continua. I. An accurate and efficient reaction field description.

PubMed

Bauer, Sebastian; Mathias, Gerald; Tavan, Paul

2014-03-14

We present a reaction field (RF) method which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of an electrostatics calculation with polarizable molecular mechanics (MM) force fields. The method combines an approach originally suggested by Egwolf and Tavan [J. Chem. Phys. 118, 2039 (2003)] with concepts generalizing the Born solution [Z. Phys. 1, 45 (1920)] for a solvated ion. First, we derive an exact representation according to which the sources of the RF potential and energy are inducible atomic anti-polarization densities and atomic shielding charge distributions. Modeling these atomic densities by Gaussians leads to an approximate representation. Here, the strengths of the Gaussian shielding charge distributions are directly given in terms of the static partial charges as defined, e.g., by standard MM force fields for the various atom types, whereas the strengths of the Gaussian anti-polarization densities are calculated by a self-consistency iteration. The atomic volumes are also described by Gaussians. To account for covalently overlapping atoms, their effective volumes are calculated by another self-consistency procedure, which guarantees that the dielectric function ε(r) is close to one everywhere inside the protein. The Gaussian widths σ(i) of the atoms i are parameters of the RF approximation. The remarkable accuracy of the method is demonstrated by comparison with Kirkwood's analytical solution for a spherical protein [J. Chem. Phys. 2, 351 (1934)] and with computationally expensive grid-based numerical solutions for simple model systems in dielectric continua including a di-peptide (Ac-Ala-NHMe) as modeled by a standard MM force field. The latter example shows how weakly the RF conformational free energy landscape depends on the parameters σ(i). A summarizing discussion highlights the achievements of the new theory and of its approximate solution particularly by comparison with so-called generalized Born methods. A follow-up paper describes how the method enables Hamiltonian, efficient, and accurate MM molecular dynamics simulations of proteins in dielectric solvent continua.

Large-Area Atomic Oxygen Facility Used to Clean Fire-Damaged Artwork

NASA Technical Reports Server (NTRS)

Rutledge, Sharon K.; Banks, Bruce A.; Steuber, Thomas J.; Sechkar, Edward A.

2000-01-01

In addition to completely destroying artwork, fires in museums and public buildings can soil a displayed artwork with so much accumulated soot that it can no longer be used for study or be enjoyed by the public. In situations where the surface has not undergone extensive charring or melting, restoration can be attempted. However, soot deposits can be very difficult to remove from some types of painted surfaces, particularly when the paint is fragile or flaking or when the top surface of the paint binder has been damaged. Restoration typically involves the use of organic solvents to clean the surface, but these solvents may cause the paint layers to swell or leach out. Also, immersion of the surface or swabbing during solvent cleaning may move or remove pigment through mechanical contact, especially if the fire damage extends into the paint binder. A noncontact technique of removing organic deposits from surfaces was developed out of NASA research on the effects of oxygen atoms on various materials. Atomic oxygen is present in the atmosphere surrounding the Earth at the altitudes where satellites typically orbit. It can react chemically with surface coatings or deposits that contain carbon. In the reaction, the carbon is converted to carbon monoxide and some carbon dioxide. Water vapor is also a byproduct of the reaction if the surface contains carbon-hydrogen bonds. To study this reaction, NASA developed Earth-based facilities to produce atomic oxygen for material exposure and testing. A vacuum facility designed and built by the Electro-Physics Branch of the NASA Glenn Research Center at Lewis Field to provide atomic oxygen over a large area for studying reactions in low Earth orbit has been used to successfully clean several full-size paintings. (This facility can accommodate paintings up to 1.5 by 2.1 m. The atomic oxygen plasma is produced between two large parallel aluminum plates using a radiofrequency power source operating at roughly 400 W. Atomic oxygen is generated uniformly over this area at an operating pressure of 1 to 5 mtorr.

iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinates.

PubMed

Lopéz-Blanco, José Ramón; Chacón, Pablo

2013-11-01

Here, we employed the collective motions extracted from Normal Mode Analysis (NMA) in internal coordinates (torsional space) for the flexible fitting of atomic-resolution structures into electron microscopy (EM) density maps. The proposed methodology was validated using a benchmark of simulated cases, highlighting its robustness over the full range of EM resolutions and even over coarse-grained representations. A systematic comparison with other methods further showcased the advantages of this proposed methodology, especially at medium to lower resolutions. Using this method, computational costs and potential overfitting problems are naturally reduced by constraining the search in low-frequency NMA space, where covalent geometry is implicitly maintained. This method also effectively captures the macromolecular changes of a representative set of experimental test cases. We believe that this novel approach will extend the currently available EM hybrid methods to the atomic-level interpretation of large conformational changes and their functional implications. Copyright © 2013 Elsevier Inc. All rights reserved.

Linearly scaling and almost Hamiltonian dielectric continuum molecular dynamics simulations through fast multipole expansions

NASA Astrophysics Data System (ADS)

Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul

2015-11-01

Hamiltonian Dielectric Solvent (HADES) is a recent method [S. Bauer et al., J. Chem. Phys. 140, 104103 (2014)] which enables atomistic Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric solvent continua. Such simulations become rapidly impractical for large proteins, because the computational effort of HADES scales quadratically with the number N of atoms. If one tries to achieve linear scaling by applying a fast multipole method (FMM) to the computation of the HADES electrostatics, the Hamiltonian character (conservation of total energy, linear, and angular momenta) may get lost. Here, we show that the Hamiltonian character of HADES can be almost completely preserved, if the structure-adapted fast multipole method (SAMM) as recently redesigned by Lorenzen et al. [J. Chem. Theory Comput. 10, 3244-3259 (2014)] is suitably extended and is chosen as the FMM module. By this extension, the HADES/SAMM forces become exact gradients of the HADES/SAMM energy. Their translational and rotational invariance then guarantees (within the limits of numerical accuracy) the exact conservation of the linear and angular momenta. Also, the total energy is essentially conserved—up to residual algorithmic noise, which is caused by the periodically repeated SAMM interaction list updates. These updates entail very small temporal discontinuities of the force description, because the employed SAMM approximations represent deliberately balanced compromises between accuracy and efficiency. The energy-gradient corrected version of SAMM can also be applied, of course, to MD simulations of all-atom solvent-solute systems enclosed by periodic boundary conditions. However, as we demonstrate in passing, this choice does not offer any serious advantages.

High-level expression and deuteration of sperm whale myoglobin: A study of its solvent structure by X-ray and neutron diffraction methods

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

Shu, F.; Ramakrishnan, V.; Schoenborn, B.P.

1994-12-31

Neutron diffraction has become one of the best ways to study light atoms, such as hydrogens. Hydrogen however has a negative coherent scattering factor, and a large incoherent scattering factor, while deuterium has virtually no incoherent scattering, but a large positive coherent scattering factor. Beside causing high background due to its incoherent scattering, the negative coherent scattering of hydrogen tends to cancel out the positive contribution from other atoms in a neutron density map. Therefore a fully deuterated sample will yield better diffraction data with stronger density in the hydrogen position. On this basis, a sperm whale myoglobin gene modifiedmore » to include part of the A cII protein gene has been cloned into the T7 expression system. Milligram amounts of fully deuterated holo-myoglobin have been obtained and used for crystallization. The synthetic sperm whale myoglobin crystallized in P2{sub 1} space group isomorphous with the native protein crystal. A complete X-ray diffraction dataset at 1.5{Angstrom} has been collected. This X-ray dataset, and a neutron data set collected previously on a protonated carbon-monoxymyoglobin crystal have been used for solvent structure studies. Both X-ray and neutron data have shown that there are ordered hydration layers around the protein surface. Solvent shell analysis on the neutron data further has shown that the first hydration layer behaves differently around polar and apolar regions of the protein surface. Finally, the structure of per-deuterated myoglobin has been refined using all reflections to a R factor of 17%.« less

All-Atom Structural Models of the Transmembrane Domains of Insulin and Type 1 Insulin-Like Growth Factor Receptors

PubMed Central

Mohammadiarani, Hossein; Vashisth, Harish

2016-01-01

The receptor tyrosine kinase superfamily comprises many cell-surface receptors including the insulin receptor (IR) and type 1 insulin-like growth factor receptor (IGF1R) that are constitutively homodimeric transmembrane glycoproteins. Therefore, these receptors require ligand-triggered domain rearrangements rather than receptor dimerization for activation. Specifically, binding of peptide ligands to receptor ectodomains transduces signals across the transmembrane domains for trans-autophosphorylation in cytoplasmic kinase domains. The molecular details of these processes are poorly understood in part due to the absence of structures of full-length receptors. Using MD simulations and enhanced conformational sampling algorithms, we present all-atom structural models of peptides containing 51 residues from the transmembrane and juxtamembrane regions of IR and IGF1R. In our models, the transmembrane regions of both receptors adopt helical conformations with kinks at Pro961 (IR) and Pro941 (IGF1R), but the C-terminal residues corresponding to the juxtamembrane region of each receptor adopt unfolded and flexible conformations in IR as opposed to a helix in IGF1R. We also observe that the N-terminal residues in IR form a kinked-helix sitting at the membrane–solvent interface, while homologous residues in IGF1R are unfolded and flexible. These conformational differences result in a larger tilt-angle of the membrane-embedded helix in IGF1R in comparison to IR to compensate for interactions with water molecules at the membrane–solvent interfaces. Our metastable/stable states for the transmembrane domain of IR, observed in a lipid bilayer, are consistent with a known NMR structure of this domain determined in detergent micelles, and similar states in IGF1R are consistent with a previously reported model of the dimerized transmembrane domains of IGF1R. Our all-atom structural models suggest potentially unique structural organization of kinase domains in each receptor. PMID:27379020

Theoretical investigation of the weak interaction between graphene and alcohol solvents

NASA Astrophysics Data System (ADS)

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

2017-05-01

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

Spectroscopic properties of vitamin E models in solution

NASA Astrophysics Data System (ADS)

Oliveira, L. B. A.; Colherinhas, G.; Fonseca, T. L.; Castro, M. A.

2015-05-01

We investigate the first absorption band and the 13C and 17O magnetic shieldings of vitamin E models in chloroform and in water using the S-MC/QM methodology in combination with the TD-DFT and GIAO approaches. The results show that the solvent effects on these spectroscopic properties are small but a proper description of the solvent shift for 17O magnetic shielding of the hydroxyl group in water requires the use of explicit solute-solvent hydrogen bonds. In addition, the effect of the replacement of hydrogen atoms by methyl groups in the vitamin E models only affects magnetic shieldings.

Unfolding of globular polymers by external force

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

Bell, Samuel; Terentjev, Eugene M., E-mail: emt1000@cam.ac.uk

2015-11-14

We examine the problem of a polymer chain, folded into a globule in poor solvent, subjected to a constant tensile force. Such a situation represents a Gibbs thermodynamic ensemble and is useful for analysing force-clamp atomic force microscopy measurements, now very common in molecular biophysics. Using a basic Flory mean-field theory, we account for surface interactions of monomers with solvent. Under an increasing tensile force, a first-order phase transition occurs from a compact globule to a fully extended chain, in an “all-or-nothing” unfolding event. This contrasts with the regime of imposed extension, first studied by Halperin and Zhulina [Europhys. Lett.more » 15, 417 (1991)], where there is a regime of coexistence of a partial globule with an extended chain segment. We relate the transition forces in this problem to the solvent quality and degree of polymerisation, and also find analytical expressions for the energy barriers present in the problem. Using these expressions, we analyse the kinetic problem of a force-ramp experiment and show that the force at which a globule ruptures depends on the rate of loading.« less

Determination of cadmium and lead at sub-ppt level in soft drinks: An efficient combination between dispersive liquid-liquid microextraction and graphite furnace atomic absorption spectrometry.

PubMed

Mandlate, Jaime S; Soares, Bruno M; Seeger, Tassia S; Vecchia, Paula Dalla; Mello, Paola A; Flores, Erico M M; Duarte, Fabio A

2017-04-15

A DLLME method for extraction and preconcentration of Cd and Pb from soft drinks and further determination by GF AAS was developed. Important parameters of DLLME such as the type and volume of dispersive and extraction solvents, concentration of DDTC (complexing agent) and pH were evaluated. Better results were obtained using 500μL of acetone for Cd and 700μL of acetonitrile for Pb as dispersive solvents, 60μL of CCl 4 as extraction solvent for both analytes and 500μL of 1.5% DDTC solution. Accuracy was evaluated by recovery assays and ranged from 91 to 113% for Cd and from 95 to 108% for Pb, with RSD below 10 and 7%, respectively. The LODs were 0.006 and 0.072ngL -1 for Cd and Pb, respectively. The optimized method was applied for the determination of Cd and Pb in soft drinks with different brands and flavours. Copyright © 2016 Elsevier Ltd. All rights reserved.

Direct comparison of four implicit memory tests.

PubMed

Rajaram, S; Roediger, H L

1993-07-01

Four verbal implicit memory tests, word identification, word stem completion, word fragment completion, and anagram solution, were directly compared in one experiment and were contrasted with free recall. On all implicit tests, priming was greatest from prior visual presentation of words, less (but significant) from auditory presentation, and least from pictorial presentations. Typefont did not affect priming. In free recall, pictures were recalled better than words. The four implicit tests all largely index perceptual (lexical) operations in recognizing words, or visual word form representations.

Electrostatics of proteins in dielectric solvent continua. II. Hamiltonian reaction field dynamics

NASA Astrophysics Data System (ADS)

Bauer, Sebastian; Tavan, Paul; Mathias, Gerald

2014-03-01

In Paper I of this work [S. Bauer, G. Mathias, and P. Tavan, J. Chem. Phys. 140, 104102 (2014)] we have presented a reaction field (RF) method, which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of polarizable molecular mechanics (MM) force fields. Building upon these results, here we suggest a method for linearly scaling Hamiltonian RF/MM molecular dynamics (MD) simulations, which we call "Hamiltonian dielectric solvent" (HADES). First, we derive analytical expressions for the RF forces acting on the solute atoms. These forces properly account for all those conditions, which have to be self-consistently fulfilled by RF quantities introduced in Paper I. Next we provide details on the implementation, i.e., we show how our RF approach is combined with a fast multipole method and how the self-consistency iterations are accelerated by the use of the so-called direct inversion in the iterative subspace. Finally we demonstrate that the method and its implementation enable Hamiltonian, i.e., energy and momentum conserving HADES-MD, and compare in a sample application on Ac-Ala-NHMe the HADES-MD free energy landscape at 300 K with that obtained in Paper I by scanning of configurations and with one obtained from an explicit solvent simulation.

A technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography.

PubMed

Chatake, Toshiyuki; Fujiwara, Satoru

2016-01-01

A difference in the neutron scattering length between hydrogen and deuterium leads to a high density contrast in neutron Fourier maps. In this study, a technique for determining the deuterium/hydrogen (D/H) contrast map in neutron macromolecular crystallography is developed and evaluated using ribonuclease A. The contrast map between the D2O-solvent and H2O-solvent crystals is calculated in real space, rather than in reciprocal space as performed in previous neutron D/H contrast crystallography. The present technique can thus utilize all of the amplitudes of the neutron structure factors for both D2O-solvent and H2O-solvent crystals. The neutron D/H contrast maps clearly demonstrate the powerful detectability of H/D exchange in proteins. In fact, alternative protonation states and alternative conformations of hydroxyl groups are observed at medium resolution (1.8 Å). Moreover, water molecules can be categorized into three types according to their tendency towards rotational disorder. These results directly indicate improvement in the neutron crystal structure analysis. This technique is suitable for incorporation into the standard structure-determination process used in neutron protein crystallography; consequently, more precise and efficient determination of the D-atom positions is possible using a combination of this D/H contrast technique and standard neutron structure-determination protocols.

The effect of solvent upon molecularly thin rotaxane film formation

NASA Astrophysics Data System (ADS)

Farrell, Alan A.; Kay, Euan R.; Bottari, Giovanni; Leigh, David A.; Jarvis, Suzanne P.

2007-05-01

We have investigated variations in molecularly thin rotaxane films deposited by solvent evaporation, using atomic force microscopy (AFM). Small changes in rotaxane structure result in significant differences in film morphology. The addition of exo-pyridyl moietes to the rotaxane macrocycle results in uniform domains having orientations corresponding to the underlying substrate lattice, while a larger, less symmetric molecule results in a greater lattice mismatch and smaller domain sizes. We have measured differences in film heights both as a function of the solvent of deposition and as a function of surface coverage of rotaxanes. Based on these observations we describe how the use of solvents with higher hydrogen-bond basicity results in films which are more likely to favour sub-molecular motion.

Solvent-free Hydrodeoxygenation of Bio-oil Model Compounds Cyclopentanone and Acetophenone over Flame-made Bimetallic Pt-Pd/ZrO2 Catalysts

PubMed Central

Jiang, Yijiao; Büchel, Robert; Huang, Jun; Krumeich, Frank; Pratsinis, Sotiris E.; Baiker, Alfons

2013-01-01

Bimetallic Pt-Pd/ZrO2 catalysts with different Pt/Pd atomic ratio and homogeneous dispersion of the metal nanoparticles were prepared in a single step by flame-spray pyrolysis. The catalysts show high activity and tuneable product selectivity for the solvent-free hydrodeoxygenation of the bio-oil model compounds cyclopentanone and acetophenone. PMID:22674738

Liquid Crystals of Dendron-like Pt Complexes Processable into Nanofilms

DTIC Science & Technology

2013-05-01

vermicular dendrimers of the phenyleneethynylene type, which resulted be very soluble in non-polar solvents such as CHCl3, THF, toluene. Their chemical... dendrimers of the phenyleneethynylene type, which resulted be very soluble in non-polar solvents such as CHCl3, THF, toluene. Their chemical...2012 and 2013, to synthesize the same above dendron like oligomers but without the platinum atom in order to give, for example, the dendrimers

Displacement-dispersive liquid-liquid microextraction based on solidification of floating organic drop of trace amounts of palladium in water and road dust samples prior to graphite furnace atomic absorption spectrometry determination.

PubMed

Ghanbarian, Maryam; Afzali, Daryoush; Mostafavi, Ali; Fathirad, Fariba

2013-01-01

A new displacement-dispersive liquid-liquid microextraction method based on the solidification of floating organic drop was developed for separation and preconcentration of Pd(ll) in road dust and aqueous samples. This method involves two steps of dispersive liquid-liquid microextraction based on solidification. In Step 1, Cu ions react with diethyldithiocarbamate (DDTC) to form Cu-DDTC complex, which is extracted by dispersive liquid-liquid microextraction based on a solidification procedure using 1-undecanol (extraction solvent) and ethanol (dispersive solvent). In Step 2, the extracted complex is first dispersed using ethanol in a sample solution containing Pd ions, then a dispersive liquid-liquid microextraction based on a solidification procedure is performed creating an organic drop. In this step, Pd(ll) replaces Cu(ll) from the pre-extracted Cu-DDTC complex and goes into the extraction solvent phase. Finally, the Pd(ll)-containing drop is introduced into a graphite furnace using a microsyringe, and Pd(ll) is determined using atomic absorption spectrometry. Several factors that influence the extraction efficiency of Pd and its subsequent determination, such as extraction and dispersive solvent type and volume, pH of sample solution, centrifugation time, and concentration of DDTC, are optimized.

Influence of Sulfur for Oxygen Substitution in the Solvolytic Reactions of Chloroformate Esters and Related Compounds

PubMed Central

D’Souza, Malcolm J.; Kevill, Dennis N.

2014-01-01

The replacement of oxygen within a chloroformate ester (ROCOCl) by sulfur can lead to a chlorothioformate (RSCOCl), a chlorothionoformate (ROCSCl), or a chlorodithioformate (RSCSCl). Phenyl chloroformate (PhOCOCl) reacts over the full range of solvents usually included in Grunwald-Winstein equation studies of solvolysis by an addition-elimination (A-E) pathway. At the other extreme, phenyl chlorodithioformate (PhSCSCl) reacts across the range by an ionization pathway. The phenyl chlorothioformate (PhSCOCl) and phenyl chlorothionoformate (PhOCSCl) react at remarkably similar rates in a given solvent and there is a dichotomy of behavior with the A-E pathway favored in solvents such as ethanol-water and the ionization mechanism favored in aqueous solvents rich in fluoroalcohol. Alkyl esters behave similarly but with increased tendency to ionization as the alkyl group goes from 1° to 2° to 3°. N,N-Disubstituted carbamoyl halides favor the ionization pathway as do also the considerably faster reacting thiocarbamoyl chlorides. The tendency towards ionization increases as, within the three contributing structures of the resonance hybrid for the formed cation, the atoms carrying positive charge (other than the central carbon) change from oxygen to sulfur to nitrogen, consistent with the relative stabilities of species with positive charge on these atoms. PMID:25310653

Using implicit association tests for the assessment of implicit personality self-concepts of extraversion and neuroticism in schizophrenia.

PubMed

Suslow, Thomas; Lindner, Christian; Kugel, Harald; Egloff, Boris; Schmukle, Stefan C

2014-08-30

There is evidence from research based on self-report personality measures that schizophrenia patients tend to be lower in extraversion and higher in neuroticism than healthy individuals. Self-report personality measures assess aspects of the explicit self-concept. The Implicit Association Test (IAT) has been developed to assess aspects of implicit cognition such as implicit attitudes and implicit personality traits. The present study was conducted to investigate the applicability and reliability of the IAT in schizophrenia patients and test whether they differ from healthy individuals on implicitly measured extraversion and neuroticism. The IAT and the NEO-FFI were administered as implicit and explicit measures of extraversion and neuroticism to 34 schizophrenia patients and 45 healthy subjects. For all IAT scores satisfactory to good reliabilities were observed in the patient sample. In both study groups, IAT scores were not related to NEO-FFI scores. Schizophrenia patients were lower in implicit and explicit extraversion and higher in implicit and explicit neuroticism than healthy individuals. Our data show that the IAT can be reliably applied to schizophrenia patients and suggest that they differ from healthy individuals not only in their conscious representation but also in their implicit representation of the self with regard to neuroticism and extraversion-related characteristics. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Electrostatics of proteins in dielectric solvent continua. I. Newton's third law marries qE forces

NASA Astrophysics Data System (ADS)

Stork, Martina; Tavan, Paul

2007-04-01

The authors reformulate and revise an electrostatic theory treating proteins surrounded by dielectric solvent continua [B. Egwolf and P. Tavan, J. Chem. Phys. 118, 2039 (2003)] to make the resulting reaction field (RF) forces compatible with Newton's third law. Such a compatibility is required for their use in molecular dynamics (MD) simulations, in which the proteins are modeled by all-atom molecular mechanics force fields. According to the original theory the RF forces, which are due to the electric field generated by the solvent polarization and act on the partial charges of a protein, i.e., the so-called qE forces, can be quite accurately computed from Gaussian RF dipoles localized at the protein atoms. Using a slightly different approximation scheme also the RF energies of given protein configurations are obtained. However, because the qE forces do not account for the dielectric boundary pressure exerted by the solvent continuum on the protein, they do not obey the principle that actio equals reactio as required by Newton's third law. Therefore, their use in MD simulations is severely hampered. An analysis of the original theory has led the authors now to a reformulation removing the main difficulties. By considering the RF energy, which represents the dominant electrostatic contribution to the free energy of solvation for a given protein configuration, they show that its negative configurational gradient yields mean RF forces obeying the reactio principle. Because the evaluation of these mean forces is computationally much more demanding than that of the qE forces, they derive a suggestion how the qE forces can be modified to obey Newton's third law. Various properties of the thus established theory, particularly issues of accuracy and of computational efficiency, are discussed. A sample application to a MD simulation of a peptide in solution is described in the following paper [M. Stork and P. Tavan, J. Chem. Phys., 126, 165106 (2007).

Free Energy Perturbation Calculations of the Thermodynamics of Protein Side-Chain Mutations.

PubMed

Steinbrecher, Thomas; Abel, Robert; Clark, Anthony; Friesner, Richard

2017-04-07

Protein side-chain mutation is fundamental both to natural evolutionary processes and to the engineering of protein therapeutics, which constitute an increasing fraction of important medications. Molecular simulation enables the prediction of the effects of mutation on properties such as binding affinity, secondary and tertiary structure, conformational dynamics, and thermal stability. A number of widely differing approaches have been applied to these predictions, including sequence-based algorithms, knowledge-based potential functions, and all-atom molecular mechanics calculations. Free energy perturbation theory, employing all-atom and explicit-solvent molecular dynamics simulations, is a rigorous physics-based approach for calculating thermodynamic effects of, for example, protein side-chain mutations. Over the past several years, we have initiated an investigation of the ability of our most recent free energy perturbation methodology to model the thermodynamics of protein mutation for two specific problems: protein-protein binding affinities and protein thermal stability. We highlight recent advances in the field and outline current and future challenges. Copyright © 2017 Elsevier Ltd. All rights reserved.

GRIFFIN: A versatile methodology for optimization of protein-lipid interfaces for membrane protein simulations

PubMed Central

Staritzbichler, René; Anselmi, Claudio; Forrest, Lucy R.; Faraldo-Gómez, José D.

2014-01-01

As new atomic structures of membrane proteins are resolved, they reveal increasingly complex transmembrane topologies, and highly irregular surfaces with crevices and pores. In many cases, specific interactions formed with the lipid membrane are functionally crucial, as is the overall lipid composition. Compounded with increasing protein size, these characteristics pose a challenge for the construction of simulation models of membrane proteins in lipid environments; clearly, that these models are sufficiently realistic bears upon the reliability of simulation-based studies of these systems. Here, we introduce GRIFFIN, which uses a versatile framework to automate and improve a widely-used membrane-embedding protocol. Initially, GRIFFIN carves out lipid and water molecules from a volume equivalent to that of the protein, so as to conserve the system density. In the subsequent optimization phase GRIFFIN adds an implicit grid-based protein force-field to a molecular dynamics simulation of the pre-carved membrane. In this force-field, atoms inside the implicit protein volume experience an outward force that will expel them from that volume, whereas those outside are subject to electrostatic and van-der-Waals interactions with the implicit protein. At each step of the simulation, these forces are updated by GRIFFIN and combined with the intermolecular forces of the explicit lipid-water system. This procedure enables the construction of realistic and reproducible starting configurations of the protein-membrane interface within a reasonable timeframe and with minimal intervention. GRIFFIN is a standalone tool designed to work alongside any existing molecular dynamics package, such as NAMD or GROMACS. PMID:24707227

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

PubMed

Tahan, A; Monajjemi, M

2011-12-01

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

Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences.

PubMed

Best, Robert B; Mittal, Jeetain

2011-04-01

Although it is now possible to fold peptides and miniproteins in molecular dynamics simulations, it is well appreciated that force fields are not all transferable to different proteins. Here, we investigate the influence of the protein force field and the solvent model on the folding energy landscape of a prototypical two-state folder, the GB1 hairpin. We use extensive replica-exchange molecular dynamics simulations to characterize the free-energy surface as a function of temperature. Most of these force fields appear similar at a global level, giving a fraction folded at 300 K between 0.2 and 0.8 in all cases, which is a difference in stability of 2.8 kT, and are generally consistent with experimental data at this temperature. The most significant differences appear in the unfolded state, where there are different residual secondary structures which are populated, and the overall dimensions of the unfolded states, which in most of the force fields are too collapsed relative to experimental Förster Resonance Energy Transfer (FRET) data.

Synthesis and Properties of N7O+ (PREPRINT)

DTIC Science & Technology

2009-11-23

isolated by pumping off the solvent and gaseous products at low temperature. With an excess of HN3, replacement of the second fluorine atom started to...was analyzed and involves the electrophilic attack of the terminal gamma-N atom of one azide ligand on the electron rich alpha-N atom of the second...Chem. Soc. 1995, 117, 6136. (8) Christe, K. O., Wilson, W. W., Schack, C. J., J. Fluorine . Chem. 1978, 11, 71. (9) Moller, C., Plesset, M. S., Phys

A decade of studying implicit racial/ethnic bias in healthcare providers using the implicit association test.

PubMed

Maina, Ivy W; Belton, Tanisha D; Ginzberg, Sara; Singh, Ajit; Johnson, Tiffani J

2018-02-01

Disparities in the care and outcomes of US racial/ethnic minorities are well documented. Research suggests that provider bias plays a role in these disparities. The implicit association test enables measurement of implicit bias via tests of automatic associations between concepts. Hundreds of studies have examined implicit bias in various settings, but relatively few have been conducted in healthcare. The aim of this systematic review is to synthesize the current knowledge on the role of implicit bias in healthcare disparities. A comprehensive literature search of several databases between May 2015 and September 2016 identified 37 qualifying studies. Of these, 31 found evidence of pro-White or light-skin/anti-Black, Hispanic, American Indian or dark-skin bias among a variety of HCPs across multiple levels of training and disciplines. Fourteen studies examined the association between implicit bias and healthcare outcomes using clinical vignettes or simulated patients. Eight found no statistically significant association between implicit bias and patient care while six studies found that higher implicit bias was associated with disparities in treatment recommendations, expectations of therapeutic bonds, pain management, and empathy. All seven studies that examined the impact of implicit provider bias on real-world patient-provider interaction found that providers with stronger implicit bias demonstrated poorer patient-provider communication. Two studies examined the effect of implicit bias on real-world clinical outcomes. One found an association and the other did not. Two studies tested interventions aimed at reducing bias, but only one found a post-intervention reduction in implicit bias. This review reveals a need for more research exploring implicit bias in real-world patient care, potential modifiers and confounders of the effect of implicit bias on care, and strategies aimed at reducing implicit bias and improving patient-provider communication. Future studies have the opportunity to build on this current body of research, and in doing so will enable us to achieve equity in healthcare and outcomes. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular structure, FT IR, NMR, UV, NBO and HOMO-LUMO of 1-(3-(dimethylamino)propyl)-1-(4-fluorophenyl)-1,3-dihydroisobenzofuran-5-carbonitrile by DFT/B3LYP and PBEPBE methods with LanL2DZ and 6-311++G(d,2p) basis sets.

PubMed

Khajehzadeh, Mostafa; Moghadam, Majid

2017-06-05

Structural and molecular properties of antidepressants 1-(3-(dimethylamino)propyl)-1-(4-fluorophenyl)-1,3-dihydroisobenzofuran-5-carbonitrile were examined using quantum mechanics of Density Functional Theory (DFT)/B3LYP and PBEPBE methods with 6-311++G(d,2p) and LanL2DZ basis sets to study the therapeutic properties of the drug. For this, the structure of desired material was optimized by the computer calculation method and with the use of powerful Gaussian 09 software. Then the lowest energy value and the bond length, bond angle and dihedral angle between its constituent atoms in the crystal structure of the desired material were measured from the optimized values. Then the amount of positive and negative charges, polarizability and dipole moment of its atoms using Mulliken charge and Natural atomic charges, DFT/B3LYP and PBEPBE methods with 6-311++G(d,2p) and LanL2DZ basis sets were determined and the results were compared with each other for individual atoms and by mentioned methods. Also the type of stretching vibrations and bending vibrations between the constituent atoms of the molecule were specified using mentioned computational methods and FT IR vibrational spectra. The experimental spectrum of this material was taken to determine the functional groups and the computational and experimental values were compared to each other and Nuclear Magnetic Resonance (NMR) was used to specify the isomer shift between the carbons and protons in the presence of polar and nonpolar solvents. Also Natural Bond Orbital (NBO) was used to determine the type of electron transfers in σ→σ∗ and π→π∗ and LP(1)→σ∗ and LP(2)→σ∗ and the amount of hardness and softness in molecule was determined using the difference between ionization energy and electron affinity energy in constituent atoms of that molecule in the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and in the presence of solvents H 2 O, CH 3 CN and C 6 H 12 . UV-Vis spectrum of the drug was taken using DFT/B3LYP and PBEPBE methods with 6-311++G(d,2p) and LanL2DZ basis sets as well as solvents H 2 O, CH 3 CN and C 6 H 12 and the associated transmissions were examined. Copyright © 2017 Elsevier B.V. All rights reserved.

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

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

Wu, Qin; Zaikowski, Lori; Kaur, Parmeet

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

Molecular simulations of self-assembly processes of amphiphiles in dilute solutions: the challenge for quantitative modelling

NASA Astrophysics Data System (ADS)

Jusufi, Arben

2013-11-01

We report on two recent developments in molecular simulations of self-assembly processes of amphiphilic solutions. We focus on the determination of micelle formation of ionic surfactants which exhibit the archetype of self-assembling compounds in solution. The first approach is centred on the challenge in predicting micellisation properties through explicit solvent molecular dynamics simulations. Even with a coarse-grained (CG) approach and the use of highly optimised software packages run on graphics processing unit hardware, it remains in many cases computationally infeasible to directly extract the critical micelle concentration (cmc). However, combined with a recently presented theoretical mean-field model this task becomes resolved. An alternative approach to study self-assembly is through implicit solvent modelling of the surfactants. Here we review some latest results and present new ones regarding capabilities of such a modelling approach in determining the cmc, and the aggregate structures in the dilute regime, that is currently not accessible through explicit solvent simulations, neither through atomistic nor through CG approaches. A special focus is put on surfactant concentration effects and surfactant correlations quantified by scattering intensities that are compared to recently published small-angle X-ray scattering data.

Can implicit appraisal concepts produce emotion-specific effects? A focus on unfairness and anger.

PubMed

Tong, Eddie M W; Tan, Deborah H; Tan, Yan Lin

2013-06-01

This research examined whether the non-conscious activation of an implicit appraisal concept could affect responses associated with the corresponding emotion as predicted by appraisal theories. Explicit and implicit emotional responses were examined. We focused on implicit unfairness and its effect on anger. The results show that subliminal activation of implicit unfairness affected implicit anger responses (anger facial expression and latency responses to anger words) but not explicit anger feelings (i.e., reported anger). The non-conscious effect of implicit unfairness was specific to anger, as no effect on sadness, fear, and guilt was found. Copyright © 2013 Elsevier Inc. All rights reserved.

Interactions of nanobubbles with bovine serum albumin and papain films on gold surfaces.

PubMed

Kolivoska, Viliam; Gál, Miroslav; Hromadová, Magdaléna; Lachmanová, Stepánka; Pospísil, Lubomír

2011-12-01

Nanobubbles formed on monocrystalline gold/water interface by means of the ethanol-to-water solvent exchange were exposed to the solutions of either bovine serum albumin or papain proteins. Both proteins do not change the position of nanobubbles in water, as observed by in situ tapping mode atomic force microscopy imaging before and after the introduction of the protein. The aqueous environment was subsequently replaced by ethanol. While all nanobubbles were found to dissolve in ethanol in the presence of bovine serum albumin, most of them survived when papain was employed. The protective ability of papain was ascribed to its resistance towards the protein denaturation in aqueous solutions of ethanol. The authors employed in situ atomic force nanolithography to investigate the nanomorphology of the papain/nanobubble assemblies in ethanol.

High-yield exfoliation of tungsten disulphide nanosheets by rational mixing of low-boiling-point solvents

NASA Astrophysics Data System (ADS)

Sajedi-Moghaddam, Ali; Saievar-Iranizad, Esmaiel

2018-01-01

Developing high-throughput, reliable, and facile approaches for producing atomically thin sheets of transition metal dichalcogenides is of great importance to pave the way for their use in real applications. Here, we report a highly promising route for exfoliating two-dimensional tungsten disulphide sheets by using binary combination of low-boiling-point solvents. Experimental results show significant dependence of exfoliation yield on the type of solvents as well as relative volume fraction of each solvent. The highest yield was found for appropriate combination of isopropanol/water (20 vol% isopropanol and 80 vol% water) which is approximately 7 times higher than that in pure isopropanol and 4 times higher than that in pure water. The dramatic increase in exfoliation yield can be attributed to perfect match between the surface tension of tungsten disulphide and binary solvent system. Furthermore, solvent molecular size also has a profound impact on the exfoliation efficiency, due to the steric repulsion.

PREPARATION OF ALKYL PYROPHOSPHATE EXTRACTANTS

DOEpatents

Levine, C.A.; Skiens, W.E.; Moore, G.R.

1960-08-01

A process for providing superior solvent extractants for metal recovery processes is given wherein the extractant comprises an alkyl pyrophosphoric acid ester dissolved in an organic solvent diluent. Finely divided solid P/sub 2/O/ sub 5/ is slurried in an organic solvent-diluent selected from organic solvents such as kerosene, benzene, chlorobenzene, toluene, etc. An alcohol selected from the higher alcohols having 4 to 17 carbon atoms. e.g.. hexanol-1. heptanol-3, octanol-1. 2.6-dimethyl-heptanol-4, and decanol-1, is rapidly added to the P/sub 2/O/sub 5/ slurry in the amount of about 2 moles of alcohol to 1 mole of P/sub 2/ O/sub 5/. The temperature is maintained below about 110 deg C during the course of the P/sub 2/O/sub 5/-alcohol reaction. An alkyl pyrophosphate extractant compound is formed as a consequence of the reaction process. The alkyl pyrophosphate solvent-diluent extractant phase is useful in solvent extraction metal recovery processes.

Fabrication and characterization of poly(L-lactic acid) gels induced by fibrous complex crystallization with solvents

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

Matsuda, Yasuhiro; Fukatsu, Akinobu; Wang, Yangyang

2014-01-01

Complex crystal induced gelation of poly(L-lactic acid) (PLLA) solutions was studied for a series of solvents, including N,N-dimethylformamide (DMF). By cooling the solutions prepared at elevated temperatures, PLLA gels were produced in solvents that induced complex crystals ( -crystals) with PLLA. Fibrous structure of PLLA in the gel with DMF was observed by polarizing optical microscopy, field emission electron microscopy, and atomic force microscopy. Upon heating, the crystal form of PLLA in the DMF gel changed from -crystal to a-crystal, the major crystal form in common untreated PLLA films, but the morphology and high elastic modulus of the gel remainedmore » until the a-crystal dissolved at higher temperature. In addition, a solvent exchanging method was developed, which allowed PLLA gels to be prepared in other useful solvents that do not induce -crystals without losing the morphology and mechanical properties.« less

Effect of solvents on the optical and morphological properties of MEH-PPV: PC70BM nanocomposites

NASA Astrophysics Data System (ADS)

Mhamdi, Asya; Ltaief, Adnen; Bouazizi, Abdelaziz

2017-10-01

Focused on phase separation and morphologies of polymer poly [2-methoxy-5-(2'-ethyl) hexoxy-1,4-phenylenevinylene] (MEH-PPV) and [6,6]-phenylC71-butyric acid methyl ester (PC70BM) nanocomposite, we studied the effect of organic solvent on the optical and morphological properties of these blends. The MEH-PPV: PC70BM films was prepared using three different solvent; Tetrahydrofuran (THF), Chlorobenzene (CB) and Toluene. On the other hand, the effect of 1-8 octanedithiol additives is also studied with the same different solvents. These blend films are characterized by photoluminescence spectroscopy, UV-Vis absorption spectroscopy and atomic force microscopy (AFM). The photoluminescence results show that the THF solvent provide the better charge transfer. In a morphological view point, the phase segregation was clearly appearing by the addition of the additive on the surface of the blend films.

Determination of the critical micelle concentration in simulations of surfactant systems

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

Santos, Andrew P.; Panagiotopoulos, Athanassios Z., E-mail: azp@princeton.edu

Alternative methods for determining the critical micelle concentration (cmc) are investigated using canonical and grand canonical Monte Carlo simulations of a lattice surfactant model. A common measure of the cmc is the “free” (unassociated) surfactant concentration in the presence of micellar aggregates. Many prior simulations of micellizing systems have observed a decrease in the free surfactant concentration with overall surfactant loading for both ionic and nonionic surfactants, contrary to theoretical expectations from mass-action models of aggregation. In the present study, we investigate a simple lattice nonionic surfactant model in implicit solvent, for which highly reproducible simulations are possible in bothmore » the canonical (NVT) and grand canonical (μVT) ensembles. We confirm the previously observed decrease of free surfactant concentration at higher overall loadings and propose an algorithm for the precise calculation of the excluded volume and effective concentration of unassociated surfactant molecules in the accessible volume of the solution. We find that the cmc can be obtained by correcting the free surfactant concentration for volume exclusion effects resulting from the presence of micellar aggregates. We also develop an improved method for determination of the cmc based on the maximum in curvature for the osmotic pressure curve determined from μVT simulations. Excellent agreement in cmc and other micellar properties between NVT and μVT simulations of different system sizes is observed. The methodological developments in this work are broadly applicable to simulations of aggregating systems using any type of surfactant model (atomistic/coarse grained) or solvent description (explicit/implicit)« less

Atomistic details of the disordered states of KID and pKID. Implications in coupled binding and folding.

PubMed

Ganguly, Debabani; Chen, Jianhan

2009-04-15

Intrinsically disordered proteins (IDPs) are a newly recognized class of functional proteins for which a lack of stable tertiary fold is required for function. Because of the heterogeneous and dynamical nature, molecular modeling is necessary to provide the missing details of disordered states of IDP that are crucial for understanding their functions. In particular, generalized Born (GB) implicit solvent, combined with replica exchange (REX), might offer an optimal balance between accuracy and efficiency for modeling IDPs. We carried out extensive REX simulations in an optimized GB force field to characterize the disordered states of a regulatory IDP, KID domain of transcription factor CREB, and its phosphorylated form, pKID. The results revealed that both KID and pKID, though highly disordered on the tertiary level, are compact and mainly occupy a small number of helical substates. Interestingly, although phosphorylation of KID Ser133 leads only to marginal changes in average helicities on the ensemble level, underlying conformational substates differ significantly. In particular, pSer133 appears to restrict the accessible conformational space of the loop region and thus reduces the entropic cost of KID folding upon binding to the KIX domain of CREB-binding protein. Such an expanded role of phosphorylation in the KID:KIX recognition was not previously recognized because of a lack of substantial conformational changes on the ensemble level and inaccessibility of the structural details from experiments. The results also suggest that an implicit solvent-based modeling framework, despite various existing limitations, might be feasible for accurate atomistic simulation of small IDPs in general.

Effect of fullerenol surface chemistry on nanoparticle binding-induced protein misfolding

NASA Astrophysics Data System (ADS)

Radic, Slaven; Nedumpully-Govindan, Praveen; Chen, Ran; Salonen, Emppu; Brown, Jared M.; Ke, Pu Chun; Ding, Feng

2014-06-01

Fullerene and its derivatives with different surface chemistry have great potential in biomedical applications. Accordingly, it is important to delineate the impact of these carbon-based nanoparticles on protein structure, dynamics, and subsequently function. Here, we focused on the effect of hydroxylation -- a common strategy for solubilizing and functionalizing fullerene -- on protein-nanoparticle interactions using a model protein, ubiquitin. We applied a set of complementary computational modeling methods, including docking and molecular dynamics simulations with both explicit and implicit solvent, to illustrate the impact of hydroxylated fullerenes on the structure and dynamics of ubiquitin. We found that all derivatives bound to the model protein. Specifically, the more hydrophilic nanoparticles with a higher number of hydroxyl groups bound to the surface of the protein via hydrogen bonds, which stabilized the protein without inducing large conformational changes in the protein structure. In contrast, fullerene derivatives with a smaller number of hydroxyl groups buried their hydrophobic surface inside the protein, thereby causing protein denaturation. Overall, our results revealed a distinct role of surface chemistry on nanoparticle-protein binding and binding-induced protein misfolding.Fullerene and its derivatives with different surface chemistry have great potential in biomedical applications. Accordingly, it is important to delineate the impact of these carbon-based nanoparticles on protein structure, dynamics, and subsequently function. Here, we focused on the effect of hydroxylation -- a common strategy for solubilizing and functionalizing fullerene -- on protein-nanoparticle interactions using a model protein, ubiquitin. We applied a set of complementary computational modeling methods, including docking and molecular dynamics simulations with both explicit and implicit solvent, to illustrate the impact of hydroxylated fullerenes on the structure and dynamics of ubiquitin. We found that all derivatives bound to the model protein. Specifically, the more hydrophilic nanoparticles with a higher number of hydroxyl groups bound to the surface of the protein via hydrogen bonds, which stabilized the protein without inducing large conformational changes in the protein structure. In contrast, fullerene derivatives with a smaller number of hydroxyl groups buried their hydrophobic surface inside the protein, thereby causing protein denaturation. Overall, our results revealed a distinct role of surface chemistry on nanoparticle-protein binding and binding-induced protein misfolding. Electronic supplementary information (ESI) is available: Fluorescence spectra, ITC, CD spectra and other data as described in the text. See DOI: 10.1039/c4nr01544d

Facile synthesis of analogous graphene quantum dots with sp(2) hybridized carbon atom dominant structures and their photovoltaic application.

PubMed

Huang, Zhengcheng; Shen, Yongtao; Li, Yu; Zheng, Wenjun; Xue, Yunjia; Qin, Chengqun; Zhang, Bo; Hao, Jingxiang; Feng, Wei

2014-11-07

Graphene quantum dot (GQD) is an emerging class of zero-dimensional nanocarbon material with many novel applications. It is of scientific importance to prepare GQDs with more perfect structures, that is, GQDs containing negligible oxygenous defects, for both optimizing their optical properties and helping in their photovoltaic applications. Herein, a new strategy for the facile preparation of "pristine" GQDs is reported. The method we presented is a combination of a bottom-up synthetic and a solvent-induced interface separation process, during which the target products with highly crystalline structure were selected by the organic solvent. The obtained organic soluble GQDs (O-GQDs) showed a significant difference in structure and composition compared with ordinary aqueous soluble GQDs, thus leading to a series of novel properties. Furthermore, O-GQDs were applied as electron-acceptors in a poly(3-hexylthiophene) (P3HT)-based organic photovoltaic device. The performance highlights that O-GQD has potential to be a novel electron-acceptor material due to the sp(2) hybridized carbon atom dominant structure and good solubility in organic solvents.

Counteraction of urea-induced protein denaturation by trimethylamine N-oxide: a chemical chaperone at atomic resolution.

PubMed

Bennion, Brian J; Daggett, Valerie

2004-04-27

Proteins are very sensitive to their solvent environments. Urea is a common chemical denaturant of proteins, yet some animals contain high concentrations of urea. These animals have evolved an interesting mechanism to counteract the effects of urea by using trimethylamine N-oxide (TMAO). The molecular basis for the ability of TMAO to act as a chemical chaperone remains unknown. Here, we describe molecular dynamics simulations of a small globular protein, chymotrypsin inhibitor 2, in 8 M urea and 4 M TMAO/8 M urea solutions, in addition to other control simulations, to investigate this effect at the atomic level. In 8 M urea, the protein unfolds, and urea acts in both a direct and indirect manner to achieve this effect. In contrast, introduction of 4 M TMAO counteracts the effect of urea and the protein remains well structured. TMAO makes few direct interactions with the protein. Instead, it prevents unfolding of the protein by structuring the solvent. In particular, TMAO orders the solvent and discourages it from competing with intraprotein H bonds and breaking up the hydrophobic core of the protein.

Ligandless dispersive liquid--liquid microextraction of iron in biological and foodstuff samples and its determination by Electrothermal atomic absorption spectrometry.

PubMed

Madadizadeh, Mohadeseh; Taher, Mohammad Ali; Ashkenani, Hamid

2013-01-01

A new, simple, and efficient method comprising ligandless dispersive liquid-liquid microextraction combined with electrothermal atomic absorption spectrometry is reported for the preconcentration and determination of ultratrace amounts of Fe(III). Carbon tetrachloride and acetone were used as the extraction and disperser solvents, respectively. Some effective parameters of the microextraction such as choice of extraction and disperser solvents, their volume, extraction time and temperature, salt and surfactant effect, and pH were optimized. Under the optimum conditions, the calibration curve was linear in the range of 0.02 to 0.46 microg/L of Fe(III), with LOD and LOQ of 5.2 and 17.4 ng/L, respectively. The RSD for seven replicated determinations of Fe(IIl) ion at 0.1 microg/L concentration level was 5.2%. Operational simplicity, rapidity, low cost, good repeatability, and low consumption of extraction solvent are the main advantages of the proposed method. The method was successfully applied to the determination of iron in biological, food, and certified reference samples.

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.

PubMed

Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V

2012-07-01

The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.

RNA and Its Ionic Cloud: Solution Scattering Experiments and Atomically Detailed Simulations

PubMed Central

Kirmizialtin, Serdal; Pabit, Suzette A.; Meisburger, Steve P.; Pollack, Lois; Elber, Ron

2012-01-01

RNA molecules play critical roles in many cellular processes. Traditionally viewed as genetic messengers, RNA molecules were recently discovered to have diverse functions related to gene regulation and expression. RNA also has great potential as a therapeutic and a tool for further investigation of gene regulation. Metal ions are an integral part of RNA structure and should be considered in any experimental or theoretical study of RNA. Here, we report a multidisciplinary approach that combines anomalous small-angle x-ray scattering and molecular-dynamics (MD) simulations with explicit solvent and ions around RNA. From experiment and simulation results, we find excellent agreement in the number and distribution of excess monovalent and divalent ions around a short RNA duplex. Although similar agreement can be obtained from a continuum description of the solvent and mobile ions (by solving the Poisson-Boltzmann equation and accounting for finite ion size), the use of MD is easily extended to flexible RNA systems with thermal fluctuations. Therefore, we also model a short RNA pseudoknot and find good agreement between the MD results and the experimentally derived solution structures. Surprisingly, both deviate from crystal structure predictions. These favorable comparisons of experiment and simulations encourage work on RNA in all-atom dynamic models. PMID:22385853

Using support vector machines to improve elemental ion identification in macromolecular crystal structures

DOE PAGES

Morshed, Nader; Echols, Nathaniel; Adams, Paul D.

2015-04-25

In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalousmore » diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.« less

Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes.

PubMed

Higo, Junichi; Ikebe, Jinzen; Kamiya, Narutoshi; Nakamura, Haruki

2012-03-01

Protein folding and protein-ligand docking have long persisted as important subjects in biophysics. Using multicanonical molecular dynamics (McMD) simulations with realistic expressions, i.e., all-atom protein models and an explicit solvent, free-energy landscapes have been computed for several systems, such as the folding of peptides/proteins composed of a few amino acids up to nearly 60 amino-acid residues, protein-ligand interactions, and coupled folding and binding of intrinsically disordered proteins. Recent progress in conformational sampling and its applications to biophysical systems are reviewed in this report, including descriptions of several outstanding studies. In addition, an algorithm and detailed procedures used for multicanonical sampling are presented along with the methodology of adaptive umbrella sampling. Both methods control the simulation so that low-probability regions along a reaction coordinate are sampled frequently. The reaction coordinate is the potential energy for multicanonical sampling and is a structural identifier for adaptive umbrella sampling. One might imagine that this probability control invariably enhances conformational transitions among distinct stable states, but this study examines the enhanced conformational sampling of a simple system and shows that reasonably well-controlled sampling slows the transitions. This slowing is induced by a rapid change of entropy along the reaction coordinate. We then provide a recipe to speed up the sampling by loosening the rapid change of entropy. Finally, we report all-atom McMD simulation results of various biophysical systems in an explicit solvent.

Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation

NASA Astrophysics Data System (ADS)

Sanyal, Tanmoy; Shell, M. Scott

2016-07-01

Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one at which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.

Determination of gold in geologic materials by solvent extraction and atomic-absorption spectrometry

USGS Publications Warehouse

Huffman, Claude; Mensik, J.D.; Riley, L.B.

1967-01-01

The two methods presented for the determination of traces of gold in geologic materials are the cyanide atomic-absorption method and the fire-assay atomic-absorption method. In the cyanide method gold is leached with a sodium-cyanide solution. The monovalent gold is then oxidized to the trivalent state and concentrated by extracting into methyl isobutyl ketone prior to estimation by atomic absorption. In the fire-assay atomic-absorption method, the gold-silver bead obtained from fire assay is dissolved in nitric and hydrochloric acids. Gold is then concentrated by extracting into methyl isobutyl ketone prior to determination by atomic absorption. By either method concentrations as low as 50 parts per billion of gold can be determined in a 15-gram sample.

On the radiation stability of crown ethers in ionic liquids.

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

Shkrob, I.; Marin, T.; Dietz, M.

2011-04-14

Crown ethers (CEs) are macrocyclic ionophores used for the separation of strontium-90 from acidic nuclear waste streams. Room temperature ionic liquids (ILs) are presently being considered as replacements for traditional molecular solvents employed in such separations. It is desirable that the extraction efficacy obtained with such solvents should not deteriorate in the strong radiation fields generated by decaying radionuclides. This deterioration will depend on the extent of radiation damage to both the IL solvent and the CE solute. While radiation damage to ILs has been extensively studied, the issue of the radiation stability of crown ethers, particularly in an ILmore » matrix, has not been adequately addressed. With this in mind, we have employed electron paramagnetic resonance (EPR) spectroscopy to study the formation of CE-related radicals in the radiolysis of selected CEs in ILs incorporating aromatic (imidazolium and pyridinium) cations. The crown ethers have been found to yield primarily hydrogen loss radicals, H atoms, and the formyl radical. In the low-dose regime, the relative yield of these radicals increases linearly with the mole fraction of the solute, suggesting negligible transfer of the excitation energy from the solvent to the solute; that is, the solvent has a 'radioprotective' effect. The damage to the CE in the loading region of practical interest is relatively low. Under such conditions, the main chemical pathway leading to decreased extraction performance is protonation of the macrocycle. At high radiation doses, sufficient to increase the acidity of the IL solvent significantly, such proton complexes compete with the solvent cations as electron traps. In this regime, the CEs will rapidly degrade as the result of H abstraction from the CE ring by the released H atoms. Thus, the radiation dose to which a CE/IL system is exposed must be maintained at a level sufficiently low to avoid this regime.« less

Formula for the Removal and Remediation of Polychlorinated Biphenyls in Painted Structures

NASA Technical Reports Server (NTRS)

Quinn, Jacqueline; Loftin, Kathleen; Geiger, Cherie

2010-01-01

An activated metal treatment system (AMTS) removes and destroys polychlorinated biphenyls (PCBs) found in painted structures or within the binding or caulking material on structures. It may be applied using a "paint-on and wipe-off" process that leaves the structure PCB-free and virtually unaltered in physical form. AMTS is used in conjunction with a solvent solution capable of donating hydrogen atoms. AMTS as a treatment technology has two functions: first, to extract PCBs from the material, and second, to degrade the extracted PCBs. The process for removing PCBs from structures is accomplished as an independent step to the degradation process. The goal is to extract the PCBs out of the paint, without destroying the paint, and to partition the PCBs into an environmentally friendly solvent. The research to date indicates this can be accomplished within the first 24 hours of AMTS contact with the paint. PCBs are extremely hydrophobic and prefer to be in the AMTS over the hardened paint or binder material. The solvent selected must be used to open, but not to destroy, the paint s polymeric lattice structure, allowing pathways for PCB movement out of the paint and into the solvent. A number of solvent systems were tested and are available for use within the AMTS. The second process of the AMTS is the degradation or dehalogenation of the PCBs. The solvent selection for this process is limited to solvents that are capable of donating a hydrogen atom to the PCB structure. Additional AMTS formulation properties that must be addressed for each site-specific application include viscosity and stability. The AMTS must be thick enough to remain where it is applied. Several thickening agents have been tested. Adding a stabilizing agent ensures that the AMTS will not evaporate and leave unprotected, activated metal exposed. During AMTS formulation testing, a number of reagents were evaluated to ensure the rate of dehalogenation was not inhibited by its addition to the system.

Halochromism, ionochromism, solvatochromism and density functional study of a synthesized copper(II) complex containing hemilabile amide derivative ligand.

PubMed

Golchoubian, Hamid; Moayyedi, Golasa; Reisi, Neda

2015-03-05

This study investigates chromotropism of newly synthesized 3,3'-(ethane-1,2-diylbis(benzylazanediyl))dipropanamide copper(II) perchlorate complex. The compound was structurally characterized by physico-chemical and spectroscopic methods. X-ray crystallography of the complex showed that the copper atom achieved a distorted square pyramidal environment through coordination of two amine N atoms and two O atoms of the amide moieties. The pH effect on the visible absorption spectrum of the complex was studied which functions as pH-induced "off-on-off" switches through protonation and deprotonation of amide moieties along with the CuO to CuN bond rearrangement at room temperature. The complex was also observed to show solvatochromism and ionochromism. The distinct solution color changes mainly associated with hemilability of the amide groups. The solvatochromism of the complex was investigated with different solvent parameter models using stepwise multiple linear regression method. The results suggested that the basicity power of the solvent has a dominant contribution to the shift of the d-d absorption band of the complex. Density functional theory, DFT calculations were performed in order to study the electronic structure of the complex, the relative stabilities of the CuN/CuO isomers, and to understand the nature of the halochromism processes taking place. DFT computational results buttressed the experimental observations indicating that in the natural pH (5.8) the CuO isomer is more stable than its linkage isomer and conversely in alkaline aqueous solution. Copyright © 2014 Elsevier B.V. All rights reserved.

Exact solution for the hydrogen atom confined by a dielectric continuum and the correct basis set to study many-electron atoms under similar confinements

NASA Astrophysics Data System (ADS)

Martínez-Sánchez, Michael-Adán; Aquino, Norberto; Vargas, Rubicelia; Garza, Jorge

2017-12-01

The Schrödinger equation associated to the hydrogen atom confined by a dielectric continuum is solved exactly and suggests the appropriate basis set to be used when an atom is immersed in a dielectric continuum. Exact results show that this kind of confinement spread the electron density, which is confirmed through the Shannon entropy. The basis set suggested by the exact results is similar to Slater type orbitals and it was applied on two-electron atoms, where the H- ion ejects one electron for moderate confinements for distances much larger than those commonly used to generate cavities in solvent models.

Solvent induced temperature dependencies of NMR parameters of hydrogen bonded anionic clusters

NASA Astrophysics Data System (ADS)

Golubev, Nikolai S.; Shenderovich, Ilja G.; Tolstoy, Peter M.; Shchepkin, Dmitry N.

2004-07-01

The solvent induced temperature dependence of NMR parameters (proton and fluorine chemical shifts, the two-bond scalar spin coupling constant across the hydrogen bridge, 2hJFF) for dihydrogen trifluoride anion, (FH) 2F -, in a polar aprotic solvent, CDF 3/CDF 2Cl, is reported and discussed. The results are interpreted in terms of a simple electrostatic model, accounting a decrease of electrostatic repulsion of two negatively charged fluorine atoms on placing into a dielectric medium. The conclusion is drawn that polar medium causes some contraction of hydrogen bonds in ionic clusters combined with a decrease of hydrogen bond asymmetry.

Theoretical study of structure and stability of small gadolinium carboxylate complexes in liquid scintillator solvents.

PubMed

Huang, Pin-Wen

2014-09-01

The structural properties of three small gadolinium carboxylate complexes in three liquid scintillator solvents (pseudocumene, linear alkylbenzene, and phenyl xylylethane) were theoretically investigated using density functional theory (B3LYP/LC-RECP) and polarizable continuum model (PCM). The average interaction energy between gadolinium atom and carboxylate ligand (E(int)) and the energy difference of the highest singly occupied molecular orbital and lowest unoccupied molecular orbital (Δ(SL)) were calculated to evaluate and compare the relative stability of these complexes in solvents. The calculation results show that the larger (with a longer alkyl chain) gadolinium carboxylate complex has greater stability than the smaller one, while these gadolinium carboxylates in linear alkylbenzene were found to have greater stability than those in the other two solvents.

Safe battery solvents

DOEpatents

Harrup, Mason K.; Delmastro, Joseph R.; Stewart, Frederick F.; Luther, Thomas A.

2007-10-23

An ion transporting solvent maintains very low vapor pressure, contains flame retarding elements, and is nontoxic. The solvent in combination with common battery electrolyte salts can be used to replace the current carbonate electrolyte solution, creating a safer battery. It can also be used in combination with polymer gels or solid polymer electrolytes to produce polymer batteries with enhanced conductivity characteristics. The solvents may comprise a class of cyclic and acyclic low molecular weight phosphazenes compounds, comprising repeating phosphorus and nitrogen units forming a core backbone and ion-carrying pendent groups bound to the phosphorus. In preferred embodiments, the cyclic phosphazene comprises at least 3 phosphorus and nitrogen units, and the pendent groups are polyethers, polythioethers, polyether/polythioethers or any combination thereof, and/or other groups preferably comprising other atoms from Group 6B of the periodic table of elements.

Spectroscopic (vibrational, NMR and UV-vis.) and quantum chemical investigations on 4-hexyloxy-3-methoxybenzaldehyde.

PubMed

Abbas, Ashgar; Gökce, Halil; Bahçeli, Semiha

2016-01-05

In this study, the 4-hexyloxy-3-methoxybenzaldehyde compound as one of the derivatives of vanillin which is a well known flavoring agent, C14H20O3, has been investigated by experimentally and extensively utilizing density functional theory (DFT) at the B3LYP/6-311++G(d,p) level. In this context, the optimized geometry, vibrational frequencies, (1)H and (13)C NMR chemical shifts, UV-vis. (in gas phase and in methanol solvent) spectra, HOMO-LUMO analysis, molecular electrostatic potential (MEP), thermodynamic parameters and atomic charges of 4-hexyloxy-3-methoxybenzaldehyde have been calculated. In addition, theoretically predicted IR, Raman and UV-vis. (in gas phase and in methanol solvent) spectra of the mentioned molecule have been constructed. The results calculated were compared with the experimental data. Copyright © 2015 Elsevier B.V. All rights reserved.

Mixed quantum-classical simulations of the vibrational relaxation of photolyzed carbon monoxide in a hemoprotein

NASA Astrophysics Data System (ADS)

Schubert, Alexander; Falvo, Cyril; Meier, Christoph

2016-08-01

We present mixed quantum-classical simulations on relaxation and dephasing of vibrationally excited carbon monoxide within a protein environment. The methodology is based on a vibrational surface hopping approach treating the vibrational states of CO quantum mechanically, while all remaining degrees of freedom are described by means of classical molecular dynamics. The CO vibrational states form the "surfaces" for the classical trajectories of protein and solvent atoms. In return, environmentally induced non-adiabatic couplings between these states cause transitions describing the vibrational relaxation from first principles. The molecular dynamics simulation yields a detailed atomistic picture of the energy relaxation pathways, taking the molecular structure and dynamics of the protein and its solvent fully into account. Using the ultrafast photolysis of CO in the hemoprotein FixL as an example, we study the relaxation of vibrationally excited CO and evaluate the role of each of the FixL residues forming the heme pocket.

Multiprobe Spectroscopic Inverstigation of Molecular-level Behavior within Aqueous 1-Butyl-3-methylimidazolium Tetrafluoroborate

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

Sarkar, Abhra; Ali, Maroof; Baker, Gary A

2009-01-01

In this work, an array of molecular-level solvent featuressincluding solute-solvent/solvent-solvent interactions, dipolarity, heterogeneity, dynamics, probe accessibility, and diffusionswere investigated across the entire composition of ambient mixtures containing the ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate, [bmim][BF4], and pH 7.0 phosphate buffer, based on results assembled for nine different molecular probes utilized in a range of spectroscopic modes. These studies uncovered interesting and unusual solvatochromic probe behavior within this benchmark mixture. Solvatochromic absorbance probessa watersoluble betaine dye (betaine dye 33), N,N-diethyl-4-nitroaniline, and 4-nitroanilineswere employed to determine ET (a blend of dipolarity/polarizability and hydrogen bond donor contributions) and the Kamlet-Taft indices * (dipolarity/polarizability), R (hydrogenmore » bond donor acidity), and (hydrogen bond acceptor basicity) characterizing the [bmim][BF4] + phosphate buffer system. These parameters each showed a marked deviation from ideality, suggesting selective solvation of the individual probe solutes by [bmim][BF4]. Similar conclusions were derived from the responses of the fluorescent polarity-sensitive probes pyrene and pyrene-1-carboxaldehyde. Importantly, the fluorescent microfluidity probe 1,3-bis(1-pyrenyl)propane senses a microviscosity within the mixture that significantly exceeds expectations derived from simple interpolation of the behavior in the neat solvents. On the basis of results from this probe, a correlation between microviscosity and bulk viscosity was established; pronounced solvent-solvent hydrogen-bonding interactions were implicit in this behavior. The greatest deviation from ideal additive behavior for the probes studied herein was consistently observed to occur in the buffer-rich regime. Nitromethane-based fluorescence quenching of pyrene within the [bmim][BF4] + phosphate buffer system showed unusual compliance with a sphere-of-action quenching model, a further manifestation of the microheterogeneity of the system. Fluorescence correlation spectroscopic results for both small (BODIPY FL) and macromolecular (Texas Red-10 kDa dextran conjugate) diffusional probes provide additional evidence in support of microphase segregation inherent to aqueous [bmim][BF4].« less

Consistent free energy landscapes and thermodynamic properties of small proteins based on a single all-atom force field employing an implicit solvation.

PubMed

Kim, Eunae; Jang, Soonmin; Pak, Youngshang

2007-10-14

We have attempted to improve the PARAM99 force field in conjunction with the generalized Born (GB) solvation model with a surface area correction for more consistent protein folding simulations. For this purpose, using an extended alphabeta training set of five well-studied molecules with various folds (alpha, beta, and betabetaalpha), a previously modified version of PARAM99/GBSA is further refined, such that all native states of the five training species correspond to their lowest free energy minimum states. The resulting modified force field (PARAM99MOD5/GBSA) clearly produces reasonably acceptable conformational free energy surfaces of the training set with correct identifications of their native states in the free energy minimum states. Moreover, due to its well-balanced nature, this new force field is expected to describe secondary structure propensities of diverse folds in a more consistent manner. Remarkably, temperature dependent behaviors simulated with the current force field are in good agreement with the experiment. This agreement is a significant improvement over the existing standard all-atom force fields. In addition, fundamentally important thermodynamic quantities, such as folding enthalpy (DeltaH) and entropy (DeltaS), agree reasonably well with the experimental data.

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

Mo, Alan K; Brown, Victoria L.; Rugg, Brandon K.

The adhesion of 100 nm thick electron-beam deposited Au and Pt and magnetron sputtered Au thin films onto poly(methyl methacrylate) (PMMA) substrates can be significantly enhanced to over 90% adhesion by either spin-casting or vapor-exposure to hydrohalocarbon solvents prior to metal deposition compared to samples that are either cleaned in isopropyl alcohol or pre-treated with a remote O2 plasma. X-ray photoelectron spectroscopy (XPS) and evolved gas Fourier transform infrared spectroscopy (EGA-FTIR) reveal the presence of residual halogenated solvent molecules at the PMMA surface which chemically activates the surface to produce a stable chemical interaction between the noble metal film andmore » the PMMA. Density functional theory (DFT) calculations show that the halogenated solvent molecules preferentially form a Lewis acid-base adduct with the oxygen atoms in the ester group in PMMA which is consistent with the measured enthalpy of desorption of chloroform (CHCl3) on PMMA determined by EGA-FTIR to be 36 kJ mol-1. The DFT model also supports the experimentally observed change in the high resolution XPS O 1s peak at 533.77 eV after metallization attributed to a change in the local bonding environment of the bridging O in the PMMA ester group. DFT also predicts that the deposited metal atom (M) inserts into the C-X bond where X is the halogen atom on either CHCl3 or bromoform (CHBr3) to form a O M X interaction that is observed by a M-X bond in the high resolution XPS Cl 2p3/2 peak at 198.03 eV and Br 3p3/2 peak at 182.06 eV. A range of solvents with differing polarities for PMMA pre-treatment have been used and it is proposed that non-complexing solvents result in significant metal adhesion improvement. The Gutmann acceptor number can be used to predict the effectiveness of solvent treatment for noble metal adhesion. A model is proposed in which the bond energy of the C-X bond of the solvent must be sufficiently low so that the C-X bond can be cleaved to form the M-X bond. Supporting this model, a negative control of vapor phase exposure to fluoroform (CHF3) is shown to have no effect on noble metal adhesion due to the higher bond dissociation energy of the C-F bond compared to the C-Cl and C-Br bond energy. The surface activation of vapor-phase exposed PMMA surfaces is technologically significant for the fabrication of polymer microdevices requiring Au or Pt metallization.« less

Toward Femtosecond Time-Resolved Studies of Solvent-Solute Energy Transfer in Doped Helium Nanodroplets

NASA Astrophysics Data System (ADS)

Bacellar, C.; Ziemkiewicz, M. P.; Leone, S. R.; Neumark, D. M.; Gessner, O.

2015-05-01

Superfluid helium nanodroplets provide a unique cryogenic matrix for high resolution spectroscopy and ultracold chemistry applications. With increasing photon energy and, in particular, in the increasingly important Extreme Ultraviolet (EUV) regime, the droplets become optically dense and, therefore, participate in the EUV-induced dynamics. Energy- and charge-transfer mechanisms between the host droplets and dopant atoms, however, are poorly understood. Static energy domain measurements of helium droplets doped with noble gas atoms (Xe, Kr) indicate that Penning ionization due to energy transfer from the excited droplet to dopant atoms may be a significant relaxation channel. We have set up a femtosecond time-resolved photoelectron imaging experiment to probe these dynamics directly in the time-domain. Droplets containing 104 to 106 helium atoms and a small percentage (<10-4) of dopant atoms (Xe, Kr, Ne) are excited to the 1s2p Rydberg band by 21.6 eV photons produced by high harmonic generation (HHG). Transiently populated states are probed by 1.6 eV photons, generating time-dependent photoelectron kinetic energy distributions, which are monitored by velocity map imaging (VMI). The results will provide new information about the dynamic timescales and the different relaxation channels, giving access to a more complete physical picture of solvent-solute interactions in the superfluid environment. Prospects and challenges of the novel experiment as well as preliminary experimental results will be discussed.

Implicit negotiation beliefs and performance: experimental and longitudinal evidence.

PubMed

Kray, Laura J; Haselhuhn, Michael P

2007-07-01

The authors argue that implicit negotiation beliefs, which speak to the expected malleability of negotiating ability, affect performance in dyadic negotiations. They expected negotiators who believe negotiating attributes are malleable (incremental theorists) to outperform negotiators who believe negotiating attributes are fixed (entity theorists). In Study 1, they gathered evidence of convergent and discriminant validity for the implicit negotiation belief construct. In Study 2, they examined the impact of implicit beliefs on the achievement goals that negotiators pursue. In Study 3, they explored the causal role of implicit beliefs on negotiation performance by manipulating negotiators' implicit beliefs within dyads. They also identified perceived ability as a moderator of the link between implicit negotiation beliefs and performance. In Study 4, they measured negotiators' beliefs in a classroom setting and examined how these beliefs affected negotiation performance and overall performance in the course 15 weeks later. Across all performance measures, incremental theorists outperformed entity theorists. Consistent with the authors' hypotheses, incremental theorists captured more of the bargaining surplus and were more integrative than their entity theorist counterparts, suggesting implicit theories are important determinants of how negotiators perform. Implications and future directions are discussed. Copyright 2007 APA, all rights reserved.

Development of a Charge-Implicit ReaxFF Potential for Hydrocarbon Systems.

PubMed

Kański, Michał; Maciążek, Dawid; Postawa, Zbigniew; Ashraf, Chowdhury M; van Duin, Adri C T; Garrison, Barbara J

2018-01-18

Molecular dynamics (MD) simulations continue to make important contributions to understanding chemical and physical processes. Concomitant with the growth of MD simulations is the need to have interaction potentials that both represent the chemistry of the system and are computationally efficient. We propose a modification to the ReaxFF potential for carbon and hydrogen that eliminates the time-consuming charge equilibration, eliminates the acknowledged flaws of the electronegativity equalization method, includes an expanded training set for condensed phases, has a repulsive wall for simulations of energetic particle bombardment, and is compatible with the LAMMPS code. This charge-implicit ReaxFF potential is five times faster than the conventional ReaxFF potential for a simulation of keV particle bombardment with a sample size of over 800 000 atoms.

Linearly scaling and almost Hamiltonian dielectric continuum molecular dynamics simulations through fast multipole expansions

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

Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul, E-mail: tavan@physik.uni-muenchen.de

2015-11-14

Hamiltonian Dielectric Solvent (HADES) is a recent method [S. Bauer et al., J. Chem. Phys. 140, 104103 (2014)] which enables atomistic Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric solvent continua. Such simulations become rapidly impractical for large proteins, because the computational effort of HADES scales quadratically with the number N of atoms. If one tries to achieve linear scaling by applying a fast multipole method (FMM) to the computation of the HADES electrostatics, the Hamiltonian character (conservation of total energy, linear, and angular momenta) may get lost. Here, we show that the Hamiltonian character of HADESmore » can be almost completely preserved, if the structure-adapted fast multipole method (SAMM) as recently redesigned by Lorenzen et al. [J. Chem. Theory Comput. 10, 3244-3259 (2014)] is suitably extended and is chosen as the FMM module. By this extension, the HADES/SAMM forces become exact gradients of the HADES/SAMM energy. Their translational and rotational invariance then guarantees (within the limits of numerical accuracy) the exact conservation of the linear and angular momenta. Also, the total energy is essentially conserved—up to residual algorithmic noise, which is caused by the periodically repeated SAMM interaction list updates. These updates entail very small temporal discontinuities of the force description, because the employed SAMM approximations represent deliberately balanced compromises between accuracy and efficiency. The energy-gradient corrected version of SAMM can also be applied, of course, to MD simulations of all-atom solvent-solute systems enclosed by periodic boundary conditions. However, as we demonstrate in passing, this choice does not offer any serious advantages.« less

Molecular Dynamics in Mixed Solvents Reveals Protein-Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions.

PubMed

Arcon, Juan Pablo; Defelipe, Lucas A; Modenutti, Carlos P; López, Elias D; Alvarez-Garcia, Daniel; Barril, Xavier; Turjanski, Adrián G; Martí, Marcelo A

2017-04-24

One of the most important biological processes at the molecular level is the formation of protein-ligand complexes. Therefore, determining their structure and underlying key interactions is of paramount relevance and has direct applications in drug development. Because of its low cost relative to its experimental sibling, molecular dynamics (MD) simulations in the presence of different solvent probes mimicking specific types of interactions have been increasingly used to analyze protein binding sites and reveal protein-ligand interaction hot spots. However, a systematic comparison of different probes and their real predictive power from a quantitative and thermodynamic point of view is still missing. In the present work, we have performed MD simulations of 18 different proteins in pure water as well as water mixtures of ethanol, acetamide, acetonitrile and methylammonium acetate, leading to a total of 5.4 μs simulation time. For each system, we determined the corresponding solvent sites, defined as space regions adjacent to the protein surface where the probability of finding a probe atom is higher than that in the bulk solvent. Finally, we compared the identified solvent sites with 121 different protein-ligand complexes and used them to perform molecular docking and ligand binding free energy estimates. Our results show that combining solely water and ethanol sites allows sampling over 70% of all possible protein-ligand interactions, especially those that coincide with ligand-based pharmacophoric points. Most important, we also show how the solvent sites can be used to significantly improve ligand docking in terms of both accuracy and precision, and that accurate predictions of ligand binding free energies, along with relative ranking of ligand affinity, can be performed.

Evaluating excited state atomic polarizabilities of chromophores† †Electronic supplementary information (ESI) available: Basis set dependence, definition of bond charges, Romberg differentiation, python script to calculate atomic polarizabilities, influence of the cavity radius, atomic polarizabilities of coumarin 153, all tables in atomic units. See DOI: 10.1039/c7cp08549d

PubMed Central

Heid, Esther

2018-01-01

Ground and excited state dipoles and polarizabilities of the chromophores N-methyl-6-oxyquinolinium betaine (MQ) and coumarin 153 (C153) in solution have been evaluated using time-dependent density functional theory (TD-DFT). A method for determining the atomic polarizabilities has been developed; the molecular dipole has been decomposed into atomic charge transfer and polarizability terms, and variation in the presence of an electric field has been used to evaluate atomic polarizabilities. On excitation, MQ undergoes very site-specific changes in polarizability while C153 shows significantly less variation. We also conclude that MQ cannot be adequately described by standard atomic polarizabilities based on atomic number and hybridization state. Changes in the molecular polarizability of MQ (on excitation) are not representative of the local site-specific changes in atomic polarizability, thus the overall molecular polarizability ratio does not provide a good approximation for local atom-specific polarizability changes on excitation. Accurate excited state force fields are needed for computer simulation of solvation dynamics. The chromophores considered in this study are often used as molecular probes. The methods and data reported here can be used for the construction of polarizable ground and excited state force fields. Atomic and molecular polarizabilities (ground and excited states) have been evaluated over a range of functionals and basis sets. Different mechanisms for including solvation effects have been examined; using a polarizable continuum model, explicit solvation and via sampling of clusters extracted from a MD simulation. A range of different solvents have also been considered. PMID:29542743

Alloy solution hardening with solute pairs

DOEpatents

Mitchell, John W.

1976-08-24

Solution hardened alloys are formed by using at least two solutes which form associated solute pairs in the solvent metal lattice. Copper containing equal atomic percentages of aluminum and palladium is an example.

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

SoftWAXS: a computational tool for modeling wide-angle X-ray solution scattering from biomolecules.

PubMed

Bardhan, Jaydeep; Park, Sanghyun; Makowski, Lee

2009-10-01

This paper describes a computational approach to estimating wide-angle X-ray solution scattering (WAXS) from proteins, which has been implemented in a computer program called SoftWAXS. The accuracy and efficiency of SoftWAXS are analyzed for analytically solvable model problems as well as for proteins. Key features of the approach include a numerical procedure for performing the required spherical averaging and explicit representation of the solute-solvent boundary and the surface of the hydration layer. These features allow the Fourier transform of the excluded volume and hydration layer to be computed directly and with high accuracy. This approach will allow future investigation of different treatments of the electron density in the hydration shell. Numerical results illustrate the differences between this approach to modeling the excluded volume and a widely used model that treats the excluded-volume function as a sum of Gaussians representing the individual atomic excluded volumes. Comparison of the results obtained here with those from explicit-solvent molecular dynamics clarifies shortcomings inherent to the representation of solvent as a time-averaged electron-density profile. In addition, an assessment is made of how the calculated scattering patterns depend on input parameters such as the solute-atom radii, the width of the hydration shell and the hydration-layer contrast. These results suggest that obtaining predictive calculations of high-resolution WAXS patterns may require sophisticated treatments of solvent.

Carbon based thirty six atom spheres

DOEpatents

Piskoti, Charles R.; Zettl, Alex K.; Cohen, Marvin L.; Cote, Michel; Grossman, Jeffrey C.; Louie, Steven G.

2005-09-06

A solid phase or form of carbon is based on fullerenes with thirty six carbon atoms (C.sub.36). The C.sub.36 structure with D.sub.6h symmetry is one of the two most energetically favorable, and is conducive to forming a periodic system. The lowest energy crystal is a highly bonded network of hexagonal planes of C.sub.36 subunits with AB stacking. The C.sub.36 solid is not a purely van der Waals solid, but has covalent-like bonding, leading to a solid with enhanced structural rigidity. The solid C.sub.36 material is made by synthesizing and selecting out C.sub.36 fullerenes in relatively large quantities. A C.sub.36 rich fullerene soot is produced in a helium environment arc discharge chamber by operating at an optimum helium pressure (400 torr). The C.sub.36 is separated from the soot by a two step process. The soot is first treated with a first solvent, e.g. toluene, to remove the higher order fullerenes but leave the C.sub.36. The soot is then treated with a second solvent, e.g. pyridine, which is more polarizable than the first solvent used for the larger fullerenes. The second solvent extracts the C.sub.36 from the soot. Thin films and powders can then be produced from the extracted C.sub.36. Other materials are based on C.sub.36 fullerenes, providing for different properties.

Atmospheric Chemistry of the Carbon Capture Solvent Monoethanolamine (MEA): A Theoretical Study

NASA Astrophysics Data System (ADS)

da Silva, G.

2012-12-01

The development of amine solvent technology for carbon capture and storage has the potential to create large new sources of amines to the atmosphere. The atmospheric chemistry of amines generally, and carbon capture solvents in particular, is not well understood. We have used quantum chemistry and master equation modelling to investigate the OH radical initiated oxidation of monoethanolamine (NH2CH2CH2OH), or MEA, the archetypal carbon capture solvent. The OH radical can abstract H atoms from either carbon atom in MEA, with negative reaction barriers. Treating these reactions with a two transition state model can reliably reproduce experimental rate constants and their temperature dependence. The products of the MEA + OH reaction, the NH2CHCH2OH and NH2CH2CHOH radicals, undergo subsequent reaction with O2, which has also been studied. In both cases chemically activated reactions that bypass peroxyl radical intermediates dominate, producing 2-iminoethanol + HO2 (from NH2CHCH2OH) or aminoacetaldehyde + HO2 (from NH2CH2CHOH), making the process HOx-neutral. The operation of chemically activated reaction mechanisms has implications for the ozone forming potential of MEA. The products of MEA photo-oxidation are proposed as important species in the formation of both organic and inorganic secondary aerosols, particularly through uptake of the imine 2-iminoethanol and subsequent hydrolysis to ammonia and glycolaldehyde.

Substituent and solvent effects on the UV-vis absorption spectrum of the photoactive yellow protein chromophore.

PubMed

García-Prieto, F Fernández; Aguilar, M A; Galván, I Fdez; Muñoz-Losa, A; Olivares del Valle, F J; Sánchez, M L; Martín, M E

2015-05-28

Solvent effects on the UV-vis absorption spectra and molecular properties of four models of the photoactive yellow protein (PYP) chromophore have been studied with ASEP/MD, a sequential quantum mechanics/molecular mechanics method. The anionic trans-p-coumaric acid (pCA(-)), thioacid (pCTA(-)), methyl ester (pCMe(-)), and methyl thioester (pCTMe(-)) derivatives have been studied in gas phase and in water solution. We analyze the modifications introduced by the substitution of sulfur by oxygen atoms and hydrogen by methyl in the coumaryl tail. We have found some differences in the absorption spectra of oxy and thio derivatives that could shed light on the different photoisomerization paths followed by these compounds. In solution, the spectrum substantially changes with respect to that obtained in the gas phase. The n → π1* state is destabilized by a polar solvent like water, and it becomes the third excited state in solution displaying an important blue shift. Now, the π → π1* and π → π2* states mix, and we find contributions from both transitions in S1 and S2. The presence of the sulfur atom modulates the solvent effect and the first two excited states become practically degenerate for pCA(-) and pCMe(-) but moderately well-separated for pCTA(-) and pCTMe(-).

Examining the origins of the hydration force between lipid bilayers using all-atom simulations.

PubMed

Gentilcore, Anastasia N; Michaud-Agrawal, Naveen; Crozier, Paul S; Stevens, Mark J; Woolf, Thomas B

2010-05-01

Using 237 all-atom double bilayer simulations, we examined the thermodynamic and structural changes that occur as a phosphatidylcholine lipid bilayer stack is dehydrated. The simulated system represents a micropatch of lipid multilayer systems that are studied experimentally using surface force apparatus, atomic force microscopy and osmotic pressure studies. In these experiments, the hydration level of the system is varied, changing the separation between the bilayers, in order to understand the forces that the bilayers feel as they are brought together. These studies have found a curious, strongly repulsive force when the bilayers are very close to each other, which has been termed the "hydration force," though the origins of this force are not clearly understood. We computationally reproduce this repulsive, relatively free energy change as bilayers come together and make qualitative conclusions as to the enthalpic and entropic origins of the free energy change. This analysis is supported by data showing structural changes in the waters, lipids and salts that have also been seen in experimental work. Increases in solvent ordering as the bilayers are dehydrated are found to be essential in causing the repulsion as the bilayers come together.

Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor.

PubMed Central

Guenot, J.; Kollman, P. A.

1992-01-01

Although aqueous simulations with periodic boundary conditions more accurately describe protein dynamics than in vacuo simulations, these are computationally intensive for most proteins. Trp repressor dynamic simulations with a small water shell surrounding the starting model yield protein trajectories that are markedly improved over gas phase, yet computationally efficient. Explicit water in molecular dynamics simulations maintains surface exposure of protein hydrophilic atoms and burial of hydrophobic atoms by opposing the otherwise asymmetric protein-protein forces. This properly orients protein surface side chains, reduces protein fluctuations, and lowers the overall root mean square deviation from the crystal structure. For simulations with crystallographic waters only, a linear or sigmoidal distance-dependent dielectric yields a much better trajectory than does a constant dielectric model. As more water is added to the starting model, the differences between using distance-dependent and constant dielectric models becomes smaller, although the linear distance-dependent dielectric yields an average structure closer to the crystal structure than does a constant dielectric model. Multiplicative constants greater than one, for the linear distance-dependent dielectric simulations, produced trajectories that are progressively worse in describing trp repressor dynamics. Simulations of bovine pancreatic trypsin were used to ensure that the trp repressor results were not protein dependent and to explore the effect of the nonbonded cutoff on the distance-dependent and constant dielectric simulation models. The nonbonded cutoff markedly affected the constant but not distance-dependent dielectric bovine pancreatic trypsin inhibitor simulations. As with trp repressor, the distance-dependent dielectric model with a shell of water surrounding the protein produced a trajectory in better agreement with the crystal structure than a constant dielectric model, and the physical properties of the trajectory average structure, both with and without a nonbonded cutoff, were comparable. PMID:1304396

The mechanism of water/ion exchange at a protein surface: a weakly bound chloride in Helicobacter pylori apoflavodoxin.

PubMed

Galano-Frutos, Juan J; Morón, M Carmen; Sancho, Javier

2015-11-21

Binding/unbinding of small ligands, such as ions, to/from proteins influences biochemical processes such as protein folding, enzyme catalysis or protein/ligand recognition. We have investigated the mechanism of chloride/water exchange at a protein surface (that of the apoflavodoxin from Helicobacter pylori) using classical all-atom molecular dynamics simulations. They reveal a variety of chloride exit routes and residence times; the latter is related to specific coordination modes of the anion. The role of solvent molecules in the mechanism of chloride unbinding has been studied in detail. We see no temporary increase in chloride coordination along the release process. Instead, the coordination of new water molecules takes place in most cases after the chloride/protein atom release event has begun. Moreover, the distribution function of water entrance events into the first chloride solvation shell peaks after chloride protein atom dissociation events. All these observations together seem to indicate that water molecules simply fill the vacancies left by the previously coordinating protein residues. We thus propose a step-by-step dissociation pathway in which protein/chloride interactions gradually break down before new water molecules progressively fill the vacant positions left by protein atoms. As observed for other systems, water molecules associated with bound chloride or with protein atoms have longer residence times than those bound to the free anion. The implications of the exchange mechanism proposed for the binding of the FMN (Flavin Mononucleotide) protein cofactor are discussed.

NEOS AB3000

EPA Pesticide Factsheets

Technical product bulletin: this hydrocarbon solvent based dispersant used in oil spill cleanups can be sprayed neat on the oil slick in atomized form. Effective with crude and residual heavy oil, and also at controlling volatile emissions.

Model of twelve properties of a set of organic solvents with graph-theoretical and/or experimental parameters.

PubMed

Pogliani, Lionello

2010-01-30

Twelve properties of a highly heterogeneous class of organic solvents have been modeled with a graph-theoretical molecular connectivity modified (MC) method, which allows to encode the core electrons and the hydrogen atoms. The graph-theoretical method uses the concepts of simple, general, and complete graphs, where these last types of graphs are used to encode the core electrons. The hydrogen atoms have been encoded by the aid of a graph-theoretical perturbation parameter, which contributes to the definition of the valence delta, delta(v), a key parameter in molecular connectivity studies. The model of the twelve properties done with a stepwise search algorithm is always satisfactory, and it allows to check the influence of the hydrogen content of the solvent molecules on the choice of the type of descriptor. A similar argument holds for the influence of the halogen atoms on the type of core electron representation. In some cases the molar mass, and in a minor way, special "ad hoc" parameters have been used to improve the model. A very good model of the surface tension could be obtained by the aid of five experimental parameters. A mixed model method based on experimental parameters plus molecular connectivity indices achieved, instead, to consistently improve the model quality of five properties. To underline is the importance of the boiling point temperatures as descriptors in these last two model methodologies. Copyright 2009 Wiley Periodicals, Inc.

Gold in natural water: A method of determination by solvent extraction and electrothermal atomization

USGS Publications Warehouse

McHugh, J.B.

1984-01-01

A method has been developed using electrothermal atomization to effectively determine the amount of gold in natural water within the nanogram range. The method has four basic steps: (1) evaporating a 1-L sample; (2) putting it in hydrobromic acid-bromine solution; (3) extracting the sample with methyl-isobutyl-ketone; and (4) determining the amount of gold using an atomic absorption spectrophotometer. The limit of detection is 0.001 ??g gold per liter. Results from three studies indicate, respectively, that the method is precise, effective, and free of interference. Specifically, a precision study indicates that the method has a relative standard deviation of 16-18%; a recovery study indicates that the method recovers gold at an average of 93%; and an interference study indicates that the interference effects are eliminated with solvent extraction and background correction techniques. Application of the method to water samples collected from 41 sites throughout the Western United States and Alaska shows a gold concentration range of < 0.001 to 0.036 ??g gold per liter, with an average of 0.005 ??g/L. ?? 1984.

Bis(2-{2-[2-(benzyl­carbamo­yl)phen­oxy]acetamido}­eth­yl)ammonium nitrate ethanol disolvate

PubMed Central

Liu, Jiaji; Tang, Xiaoliang; Lu, Zhengdan; Zhang, Guolin; Liu, Weisheng

2011-01-01

In the title compound, C36H40N5O6 +·NO3 −·2C2H5OH, the nitrate anion is disordered over the two orientations of equal occupancy while the solvent mol­ecule reveals large displacement parameters. The cation is formed by protonation of the N atom of a secondary amine in the middle of the flexible chain and the whole compound has crystallographically imposed C-2 symmetry with the crystallographic b axis. An O atom of the nitrate anion links the acidic H atoms of the cation via N—H⋯O hydrogen bonding. In addition, neighbouring cations are connected by inter­molecular N—H⋯O hydrogen bonds and π–π inter­actions between the benzamide groups of the cations [centroid–centroid distance = 4.000 (3) Å], forming a chain along [001]. The ethanol solvent mol­ecules are arranged on the side of the chain through O—H⋯O hydrogen bonds. PMID:21522705

All-atom ab initio native structure prediction of a mixed fold (1FME): A comparison of structural and folding characteristics of various ββα miniproteins

NASA Astrophysics Data System (ADS)

Kim, Eunae; Jang, Soonmin; Pak, Youngshang

2009-11-01

We performed an all-atom ab initio native structure prediction of 1FME, which is one of the computationally challenging mixed fold ββα miniproteins, by combining a novel conformational search algorithm (multiplexed Q-replica exchange molecular dynamics scheme) with a well-balanced all-atom force field employing a generalized Born implicit solvation model (param99MOD5/GBSA). The nativelike structure of 1FME was identified from the lowest free energy minimum state and in excellent agreement with the NMR structure. Based on the interpretation of the free energy landscape, the structural properties as well as the folding behaviors of 1FME were compared with other ββα miniproteins (1FSD, 1PSV, and BBA5) that we have previously studied with the same force field. Our simulation showed that the 28-residue ββα miniproteins (1FME, 1FSD, and 1PSV) share a common feature of the free energy topography and exhibit the three local minimum states on each computed free energy map, but the 23-residue miniprotein (BBA5) follows a downhill folding with a single minimum state. Also, the structure and stability changes resulting from the two point mutation (Gln1→Glu1 and Ile7→Tyr7) of 1FSD were investigated in details for direct comparison with the experiment. The comparison shows that upon mutation, the experimentally observed turn type switch from an irregular turn (1FSD) to type I' turn (1FME) was well reproduced with the present simulation.

Liquid-phase microextraction combined with graphite furnace atomic absorption spectrometry: A review.

PubMed

de la Calle, Inmaculada; Pena-Pereira, Francisco; Lavilla, Isela; Bendicho, Carlos

2016-09-14

An overview of the combination of liquid-phase microextraction (LPME) techniques with graphite furnace atomic absorption spectrometry (GFAAS) is reported herein. The high sensitivity of GFAAS is significantly enhanced by its association with a variety of miniaturized solvent extraction approaches. LPME-GFAAS thus represents a powerful combination for determination of metals, metalloids and organometallic compounds at (ultra)trace level. Different LPME modes used with GFAAS are briefly described, and the experimental parameters that show an impact in those microextraction processes are discussed. Special attention is paid to those parameters affecting GFAAS analysis. Main issues found when coupling LPME and GFAAS, as well as those strategies reported in the literature to solve them, are summarized. Relevant applications published on the topic so far are included. Copyright © 2016 Elsevier B.V. All rights reserved.

Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes

PubMed Central

2015-01-01

The reliability of free energy simulations (FES) is limited by two factors: (a) the need for correct sampling and (b) the accuracy of the computational method employed. Classical methods (e.g., force fields) are typically used for FES and present a myriad of challenges, with parametrization being a principle one. On the other hand, parameter-free quantum mechanical (QM) methods tend to be too computationally expensive for adequate sampling. One widely used approach is a combination of methods, where the free energy difference between the two end states is computed by, e.g., molecular mechanics (MM), and the end states are corrected by more accurate methods, such as QM or hybrid QM/MM techniques. Here we report two new approaches that significantly improve the aforementioned scheme; with a focus on how to compute corrections between, e.g., the MM and the more accurate QM calculations. First, a molecular dynamics trajectory that properly samples relevant conformational degrees of freedom is generated. Next, potential energies of each trajectory frame are generated with a QM or QM/MM Hamiltonian. Free energy differences are then calculated based on the QM or QM/MM energies using either a non-Boltzmann Bennett approach (QM-NBB) or non-Boltzmann free energy perturbation (NB-FEP). Both approaches are applied to calculate relative and absolute solvation free energies in explicit and implicit solvent environments. Solvation free energy differences (relative and absolute) between ethane and methanol in explicit solvent are used as the initial test case for QM-NBB. Next, implicit solvent methods are employed in conjunction with both QM-NBB and NB-FEP to compute absolute solvation free energies for 21 compounds. These compounds range from small molecules such as ethane and methanol to fairly large, flexible solutes, such as triacetyl glycerol. Several technical aspects were investigated. Ultimately some best practices are suggested for improving methods that seek to connect MM to QM (or QM/MM) levels of theory in FES. PMID:24803863

Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes.

PubMed

König, Gerhard; Hudson, Phillip S; Boresch, Stefan; Woodcock, H Lee

2014-04-08

THE RELIABILITY OF FREE ENERGY SIMULATIONS (FES) IS LIMITED BY TWO FACTORS: (a) the need for correct sampling and (b) the accuracy of the computational method employed. Classical methods (e.g., force fields) are typically used for FES and present a myriad of challenges, with parametrization being a principle one. On the other hand, parameter-free quantum mechanical (QM) methods tend to be too computationally expensive for adequate sampling. One widely used approach is a combination of methods, where the free energy difference between the two end states is computed by, e.g., molecular mechanics (MM), and the end states are corrected by more accurate methods, such as QM or hybrid QM/MM techniques. Here we report two new approaches that significantly improve the aforementioned scheme; with a focus on how to compute corrections between, e.g., the MM and the more accurate QM calculations. First, a molecular dynamics trajectory that properly samples relevant conformational degrees of freedom is generated. Next, potential energies of each trajectory frame are generated with a QM or QM/MM Hamiltonian. Free energy differences are then calculated based on the QM or QM/MM energies using either a non-Boltzmann Bennett approach (QM-NBB) or non-Boltzmann free energy perturbation (NB-FEP). Both approaches are applied to calculate relative and absolute solvation free energies in explicit and implicit solvent environments. Solvation free energy differences (relative and absolute) between ethane and methanol in explicit solvent are used as the initial test case for QM-NBB. Next, implicit solvent methods are employed in conjunction with both QM-NBB and NB-FEP to compute absolute solvation free energies for 21 compounds. These compounds range from small molecules such as ethane and methanol to fairly large, flexible solutes, such as triacetyl glycerol. Several technical aspects were investigated. Ultimately some best practices are suggested for improving methods that seek to connect MM to QM (or QM/MM) levels of theory in FES.

Solvent-free functionalization of silicone rubber and efficacy of PAAm brushes grafted from an amino-PPX layer against bacterial adhesion.

PubMed

Fundeanu, Irina; Klee, Doris; Schouten, Arend J; Busscher, Henk J; van der Mei, Henny C

2010-11-01

Silicone rubber is a frequently employed biomaterial that is prone to bacterial adhesion and biofilm formation. In this study, the surface of silicone rubber was solvent-free functionalized by chemical vapor deposition (CVD) of poly(o-amino-p-xylylene-co-p-xylylene (amino-PPX). Subsequently, the amino groups of the amino-PPX layer were used to introduce the initiator from a vapor phase for atom transfer radical polymerization of acrylamide to form polyacrylamide (PAAm) brushes. The modification steps were verified by means of X-ray photoelectron spectroscopy and attenuated total reflection-Fourier transform infrared spectroscopy. Adhesion of Staphylococcus aureus ATCC 12600 and Escherichia coli 3.14 to an amino-PPX-PAAm brush coating in a parallel plate flow chamber was strongly reduced with respect to non-coated silicone rubber - by 93% and 99%, respectively. For E. coli 3.14, this reduction is larger than that obtained for solvent functionalization of γ-aminopropyltriethoxysilane-PAAm brushes due to the higher density of amino groups introduced by the CVD of amino-PPX. Copyright © 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Quantitative structure-property relationships for octanol-water partition coefficients of polybrominated diphenyl ethers.

PubMed

Li, Linnan; Xie, Shaodong; Cai, Hao; Bai, Xuetao; Xue, Zhao

2008-08-01

Theoretical molecular descriptors were tested against logK(OW) values for polybrominated diphenyl ethers (PBDEs) using the Partial Least-Squares Regression method which can be used to analyze data with many variables and few observations. A quantitative structure-property relationship (QSPR) model was successfully developed with a high cross-validated value (Q(cum)(2)) of 0.961, indicating a good predictive ability and stability of the model. The predictive power of the QSPR model was further cross-validated. The values of logK(OW) for PBDEs are mainly governed by molecular surface area, energy of the lowest unoccupied molecular orbital and the net atomic charges on the oxygen atom. All these descriptors have been discussed to interpret the partitioning mechanism of PBDE chemicals. The bulk property of the molecules represented by molecular surface area is the leading factor, and K(OW) values increase with the increase of molecular surface area. Higher energy of the lowest unoccupied molecular orbital and higher net atomic charge on the oxygen atom of PBDEs result in smaller K(OW). The energy of the lowest unoccupied molecular orbital and the net atomic charge on PBDEs oxygen also play important roles in affecting the partition of PBDEs between octanol and water by influencing the interactions between PBDEs and solvent molecules.

Function-Space-Based Solution Scheme for the Size-Modified Poisson-Boltzmann Equation in Full-Potential DFT.

PubMed

Ringe, Stefan; Oberhofer, Harald; Hille, Christoph; Matera, Sebastian; Reuter, Karsten

2016-08-09

The size-modified Poisson-Boltzmann (MPB) equation is an efficient implicit solvation model which also captures electrolytic solvent effects. It combines an account of the dielectric solvent response with a mean-field description of solvated finite-sized ions. We present a general solution scheme for the MPB equation based on a fast function-space-oriented Newton method and a Green's function preconditioned iterative linear solver. In contrast to popular multigrid solvers, this approach allows us to fully exploit specialized integration grids and optimized integration schemes. We describe a corresponding numerically efficient implementation for the full-potential density-functional theory (DFT) code FHI-aims. We show that together with an additional Stern layer correction the DFT+MPB approach can describe the mean activity coefficient of a KCl aqueous solution over a wide range of concentrations. The high sensitivity of the calculated activity coefficient on the employed ionic parameters thereby suggests to use extensively tabulated experimental activity coefficients of salt solutions for a systematic parametrization protocol.

Simulating the control of molecular reactions via modulated light fields: from gas phase to solution

NASA Astrophysics Data System (ADS)

Thallmair, Sebastian; Keefer, Daniel; Rott, Florian; de Vivie-Riedle, Regina

2017-04-01

Over the past few years quantum control has proven to be very successful in steering molecular processes. By combining theory with experiment, even highly complex control aims were realized in the gas phase. In this topical review, we illustrate the past achievements on several examples in the molecular context. The next step for the quantum control of chemical processes is to translate the fruitful interplay between theory and experiment to the condensed phase and thus to the regime where chemical synthesis can be supported. On the theory side, increased efforts to include solvent effects in quantum control simulations were made recently. We discuss two major concepts, namely an implicit description of the environment via the density matrix algorithm and an explicit inclusion of solvent molecules. By application to chemical reactions, both concepts conclude that despite environmental perturbations leading to more complex control tasks, efficient quantum control in the condensed phase is still feasible.

Nanoscale Morphology of PTB7 Based Organic Photovoltaics as a Function of Fullerene Size

DOE PAGES

Roehling, John D.; Baran, Derya; Sit, Joseph; ...

2016-08-08

High efficiency polymer:fullerene photovoltaic device layers self-assemble with hierarchical features from ångströms to 100’s of nanometers. The feature size, shape, composition, orientation, and order all contribute to device efficiency and are simultaneously difficult to study due to poor contrast between carbon based materials. This study seeks to increase device efficiency and simplify morphology measurements by replacing the typical fullerene acceptor with endohedral fullerene Lu 3N@PC 80BEH. The metal atoms give excellent scattering contrast for electron beam and x-ray experiments. Additionally, Lu 3N@PC 80BEH has a lower electron affinity than standard fullerenes, which can raise the open circuit voltage of photovoltaicmore » devices. Electron microscopy techniques are used to produce a detailed account of morphology evolution in mixtures of Lu 3N@PC 80BEH with the record breaking donor polymer, PTB7 and coated using solvent mixtures. We demonstrate that common solvent additives like 1,8-diiodooctane or chloronapthalene do not improve the morphology of endohedral fullerene devices as expected. The poor device performance is attributed to the lack of mutual miscibility between this particular polymer:fullerene combination and to co-crystallization of Lu 3N@PC 80BEH with 1,8-diiodooctane. This negative result explains why solvent additives mixtures are not necessarily a morphology cure-all.« less

Nanoscale Morphology of PTB7 Based Organic Photovoltaics as a Function of Fullerene Size

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

Roehling, John D.; Baran, Derya; Sit, Joseph

High efficiency polymer:fullerene photovoltaic device layers self-assemble with hierarchical features from ångströms to 100’s of nanometers. The feature size, shape, composition, orientation, and order all contribute to device efficiency and are simultaneously difficult to study due to poor contrast between carbon based materials. This study seeks to increase device efficiency and simplify morphology measurements by replacing the typical fullerene acceptor with endohedral fullerene Lu 3N@PC 80BEH. The metal atoms give excellent scattering contrast for electron beam and x-ray experiments. Additionally, Lu 3N@PC 80BEH has a lower electron affinity than standard fullerenes, which can raise the open circuit voltage of photovoltaicmore » devices. Electron microscopy techniques are used to produce a detailed account of morphology evolution in mixtures of Lu 3N@PC 80BEH with the record breaking donor polymer, PTB7 and coated using solvent mixtures. We demonstrate that common solvent additives like 1,8-diiodooctane or chloronapthalene do not improve the morphology of endohedral fullerene devices as expected. The poor device performance is attributed to the lack of mutual miscibility between this particular polymer:fullerene combination and to co-crystallization of Lu 3N@PC 80BEH with 1,8-diiodooctane. This negative result explains why solvent additives mixtures are not necessarily a morphology cure-all.« less

Investigations on the role of mixed-solvent for improved efficiency in perovskite solar cell

NASA Astrophysics Data System (ADS)

Singh, Ranbir; Suranagi, Sanjaykumar R.; Kumar, Manish; Shukla, Vivek Kumar

2017-12-01

The morphology of the spin-coated photoactive layer is one of the major factors affecting the performance of perovskite solar cells. In this work, we have employed a mixed-solvent strategy to obtain a high quality MAPbI3 (MA = CH3NH3) perovskite film, without pinholes and reduced grain boundaries. Perovskite films formed with single and mixed-solvents are systematically characterized for their optical, structural, and morphological properties using UV-vis absorption, photoluminescence (PL), X-ray diffraction (XRD), atomic force microscopy (AFM), and scanning electron microscopy (SEM) tools. The power conversion efficiency (PCE) of the devices fabricated using the mixed-solvent showed better performance than the devices made using the single solvent. The best-optimized mixed-solvent perovskite film exhibited a PCE of 15.2% with uniform film coverage on the substrate, better charge generation, and a high hole mobility of 1.16 × 10-4cm2/V s. The disparities in photovoltaic properties have been analyzed with the intensity dependent current density-voltage (J-V), transient photovoltage (TPV), and relationship between photocurrent (Jph) and effective voltage (Veff).

To Keep or Not to Keep? The Question of Crystallographic Waters for Enzyme Simulations in Organic Solvent

PubMed Central

Dahanayake, Jayangika N.; Gautam, Devaki N.; Verma, Rajni; Mitchell-Koch, Katie R.

2016-01-01

The use of enzymes in non-aqueous solvents expands the use of biocatalysts to hydrophobic substrates, with the ability to tune selectivity of reactions through solvent selection. Non-aqueous enzymology also allows for fundamental studies on the role of water and other solvents in enzyme structure, dynamics, and function. Molecular dynamics simulations serve as a powerful tool in this area, providing detailed atomic information about the effect of solvents on enzyme properties. However, a common protocol for non-aqueous enzyme simulations does not exist. If you want to simulate enzymes in non-aqueous solutions, how many and which crystallographic waters do you keep? In the present work, this question is addressed by determining which crystallographic water molecules lead most quickly to an equilibrated protein structure. Five different methods of selecting and keeping crystallographic waters are used in order to discover which crystallographic waters lead the protein structure to reach an equilibrated structure more rapidly in organic solutions. It is found that buried waters contribute most to rapid equilibration in organic solvent, with slow-diffusing waters giving similar results. PMID:27403032

Improved electron transport properties of n-type naphthalenediimide polymers through refined molecular ordering and orientation induced by processing solvents.

PubMed

An, Yujin; Long, Dang Xuan; Kim, Yiho; Noh, Yong-Young; Yang, Changduk

2016-05-14

To determine the role played by the choice of processing solvents in governing the photophysics, microstructure, and charge carrier transport in naphthalenediimide (NDI)-based polymers, we have prepared two new NDI-bithiophene (T2)- and NDI-thienothiophene (TTh)-containing polymers with hybrid siloxane pentyl chains (SiC5) (P(NDI2SiC5-T2) and P(NDI2SiC5-TTh)). Among the various processing solvents studied here, the films prepared using chloroform exhibited far better electron mobilities (0.16 ± 0.1-0.21 ± 0.05 cm(2) V(-1) s(-1)) than the corresponding samples prepared from different solvents, exceeding one order of magnitude higher, indicating the significant influence of the processing solvent on the charge transport. Upon thin-film analysis using atomic force microscopy and grazing incidence X-ray diffraction, we discovered that molecular ordering and orientation are affected by the choice of the processing solvent, which is responsible for the change in the transport characteristics of this class of polymers.

Computational Studies of Solubilities of LiO 2 and Li 2O 2 in Aprotic Solvents

DOE PAGES

Cheng, Lei; Redfern, Paul; Lau, Kah Chun; ...

2017-08-12

Knowledge of the solubilities of Li 2O 2 and LiO 2 in aprotic solvents is important for insight into the discharge and charge processes of Li-O 2 batteries, but these quantities are not well known. In this contribution, the solvation free energies of molecular LiO 2 and Li 2O 2 in various organic solvents were calculated using various explicit and implicit solvent models, as well as ab initio molecular dynamics (AIMD) methods. Best estimates for the solvation energies from these calculations along with calculated lattice energies of Li 2O 2 and LiO 2 were used to determine the solubility ofmore » bulk LiO 2 and Li 2O 2. The computed solubility of LiO 2 (1.8 × 10 -2 M) is about 15 orders higher than that of Li 2O 2 (2.0 × 10 -17 M) due to a much less negative lattice energy of bulk LiO 2 compared to that of Li 2O 2. The difference in solubilities between LiO 2 and Li 2O 2 likely will affect the nucleation and growth mechanisms and resulting morphologies of the products formed during battery discharge, influencing the performance of the battery cell. In conclusion, the calculated LiO 2 and Li 2O 2 solubilities provide important information for fundamental studies of discharge and charge chemistries in Li-O 2 batteries.« less

Computational Studies of Solubilities of LiO 2 and Li 2O 2 in Aprotic Solvents

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

Cheng, Lei; Redfern, Paul; Lau, Kah Chun

Knowledge of the solubilities of Li 2O 2 and LiO 2 in aprotic solvents is important for insight into the discharge and charge processes of Li-O 2 batteries, but these quantities are not well known. In this contribution, the solvation free energies of molecular LiO 2 and Li 2O 2 in various organic solvents were calculated using various explicit and implicit solvent models, as well as ab initio molecular dynamics (AIMD) methods. Best estimates for the solvation energies from these calculations along with calculated lattice energies of Li 2O 2 and LiO 2 were used to determine the solubility ofmore » bulk LiO 2 and Li 2O 2. The computed solubility of LiO 2 (1.8 × 10 -2 M) is about 15 orders higher than that of Li 2O 2 (2.0 × 10 -17 M) due to a much less negative lattice energy of bulk LiO 2 compared to that of Li 2O 2. The difference in solubilities between LiO 2 and Li 2O 2 likely will affect the nucleation and growth mechanisms and resulting morphologies of the products formed during battery discharge, influencing the performance of the battery cell. In conclusion, the calculated LiO 2 and Li 2O 2 solubilities provide important information for fundamental studies of discharge and charge chemistries in Li-O 2 batteries.« less

Systems and methods for laser assisted sample transfer to solution for chemical analysis

DOEpatents

Van Berkel, Gary J.; Kertesz, Vilmos; Ovchinnikova, Olga S.

2014-06-03

Systems and methods are described for laser ablation of an analyte from a specimen and capturing of the analyte in a dispensed solvent to form a testing solution. A solvent dispensing and extraction system can form a liquid microjunction with the specimen. The solvent dispensing and extraction system can include a surface sampling probe. The laser beam can be directed through the surface sampling probe. The surface sampling probe can also serve as an atomic force microscopy probe. The surface sampling probe can form a seal with the specimen. The testing solution including the analyte can then be analyzed using an analytical instrument or undergo further processing.

Systems and methods for laser assisted sample transfer to solution for chemical analysis

DOEpatents

Van Berkel, Gary J.; Kertesz, Vilmos; Ovchinnikova, Olga S.

2015-09-29

Systems and methods are described for laser ablation of an analyte from a specimen and capturing of the analyte in a dispensed solvent to form a testing solution. A solvent dispensing and extraction system can form a liquid microjunction with the specimen. The solvent dispensing and extraction system can include a surface sampling probe. The laser beam can be directed through the surface sampling probe. The surface sampling probe can also serve as an atomic force microscopy probe. The surface sampling probe can form a seal with the specimen. The testing solution including the analyte can then be analyzed using an analytical instrument or undergo further processing.

Systems and methods for laser assisted sample transfer to solution for chemical analysis

DOEpatents

Van Berkel, Gary J; Kertesz, Vilmos; Ovchinnikova, Olga S

2013-08-27

Systems and methods are described for laser ablation of an analyte from a specimen and capturing of the analyte in a dispensed solvent to form a testing solution. A solvent dispensing and extraction system can form a liquid microjunction with the specimen. The solvent dispensing and extraction system can include a surface sampling probe. The laser beam can be directed through the surface sampling probe. The surface sampling probe can also serve as an atomic force microscopy probe. The surface sampling probe can form a seal with the specimen. The testing solution including the analyte can then be analyzed using an analytical instrument or undergo further processing.

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

PubMed

Setny, Piotr

2015-12-08

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

A Meta-Analysis Suggests Different Neural Correlates for Implicit and Explicit Learning.

PubMed

Loonis, Roman F; Brincat, Scott L; Antzoulatos, Evan G; Miller, Earl K

2017-10-11

A meta-analysis of non-human primates performing three different tasks (Object-Match, Category-Match, and Category-Saccade associations) revealed signatures of explicit and implicit learning. Performance improved equally following correct and error trials in the Match (explicit) tasks, but it improved more after correct trials in the Saccade (implicit) task, a signature of explicit versus implicit learning. Likewise, error-related negativity, a marker for error processing, was greater in the Match (explicit) tasks. All tasks showed an increase in alpha/beta (10-30 Hz) synchrony after correct choices. However, only the implicit task showed an increase in theta (3-7 Hz) synchrony after correct choices that decreased with learning. In contrast, in the explicit tasks, alpha/beta synchrony increased with learning and decreased thereafter. Our results suggest that explicit versus implicit learning engages different neural mechanisms that rely on different patterns of oscillatory synchrony. Copyright © 2017 Elsevier Inc. All rights reserved.

A specific implicit sequence learning deficit as an underlying cause of dyslexia? Investigating the role of attention in implicit learning tasks.

PubMed

Staels, Eva; Van den Broeck, Wim

2017-05-01

Recently, a general implicit sequence learning deficit was proposed as an underlying cause of dyslexia. This new hypothesis was investigated in the present study by including a number of methodological improvements, for example, the inclusion of appropriate control conditions. The second goal of the study was to explore the role of attentional functioning in implicit and explicit learning tasks. In a 2 × 2 within-subjects design 4 tasks were administered in 30 dyslexic and 38 control children: an implicit and explicit serial reaction time (RT) task and an implicit and explicit contextual cueing task. Attentional functioning was also administered. The entire learning curves of all tasks were analyzed using latent growth curve modeling in order to compare performances between groups and to examine the role of attentional functioning on the learning curves. The amount of implicit learning was similar for both groups. However, the dyslexic group showed slower RTs throughout the entire task. This group difference reduced and became nonsignificant after controlling for attentional functioning. Both implicit learning tasks, but none of the explicit learning tasks, were significantly affected by attentional functioning. Dyslexic children do not suffer from a specific implicit sequence learning deficit. The slower RTs of the dyslexic children throughout the entire implicit sequence learning process are caused by their comorbid attention problems and overall slowness. A key finding of the present study is that, in contrast to what was assumed for a long time, implicit learning relies on attentional resources, perhaps even more than explicit learning does. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Attitudes towards individuals with disabilities as measured by the implicit association test: a literature review.

PubMed

Wilson, Michelle Clare; Scior, Katrina

2014-02-01

Research investigating attitudes towards individuals with disabilities has largely focused on self-reported explicit attitudes. Given that factors such as social desirability may influence explicit attitudes, researchers have developed tools which instead assess less consciously controllable implicit attitudes. Considering research on implicit attitudes thus seems pertinent. A review of studies measuring implicit attitudes towards individuals with physical disabilities (visual, motor or hearing) or intellectual disabilities via the Implicit Association Test (IAT; Greenwald, McGhee, & Schwartz, 1998) was carried out. Systematic searches of PsycINFO, CINAHL, EMBASE, ERIC, MEDLINE, PUBMED, Scopus and Web of Science databases identified relevant articles published between January 2000 and September 2012. Seventeen articles (reporting on 18 studies that employed the IAT) were identified. These investigated implicit attitudes towards individuals with; physical disabilities (N=13), intellectual disabilities (N=3), both physical and intellectual disabilities (N=1), and 'unspecified disabilities' (N=1). Across all studies, moderate to strong negative implicit attitudes were found and there was little to no association between explicit and implicit attitudes. Individuals' beliefs about the controllability of their future, sensitivity to the concept of disease, and contact with individuals with disabilities appear to be associated with implicit attitudes. A consistent pattern of moderate to strong negative implicit attitudes towards individuals with disabilities was evident. These studies provide a starting point, but methodological issues related to sampling and the employed IATs limit the generalizability of these results. Further research investigating implicit attitudes towards specific disability types, with a wider subject pool are necessary as well as further investigation of factors that contribute to these attitudes. Copyright © 2013 Elsevier Ltd. All rights reserved.

Intact implicit learning in autism spectrum conditions.

PubMed

Brown, Jamie; Aczel, Balazs; Jiménez, Luis; Kaufman, Scott Barry; Grant, Kate Plaisted

2010-09-01

Individuals with autism spectrum condition (ASC) have diagnostic impairments in skills that are associated with an implicit acquisition; however, it is not clear whether ASC individuals show specific implicit learning deficits. We compared ASC and typically developing (TD) individuals matched for IQ on five learning tasks: four implicit learning tasks--contextual cueing, serial reaction time, artificial grammar learning, and probabilistic classification learning tasks--that used procedures expressly designed to minimize the use of explicit strategies, and one comparison explicit learning task, paired associates learning. We found implicit learning to be intact in ASC. Beyond no evidence of differences, there was evidence of statistical equivalence between the groups on all the implicit learning tasks. This was not a consequence of compensation by explicit learning ability or IQ. Furthermore, there was no evidence to relate implicit learning to ASC symptomatology. We conclude that implicit mechanisms are preserved in ASC and propose that it is disruption by other atypical processes that impact negatively on the development of skills associated with an implicit acquisition.

Crystal structure of tetra-kis-[μ2-2-(di-methyl-amino)-ethano-lato-κ(3) N,O:O]di-μ3-hydroxido-di-thio-cyanato-κ(2) N-dichromium(III)dilead(II) di-thio-cyanate aceto-nitrile monosolvate.

PubMed

Rusanova, Julia A; Semenaka, Valentyna V; Omelchenko, Irina V

2016-04-01

The tetra-nuclear complex cation of the title compound, [Cr2Pb2(NCS)2(OH)2(C4H10NO)4](SCN)2·CH3CN, lies on an inversion centre. The main structural feature of the cation is a distorted seco-norcubane Pb2Cr2O6 cage with a central four-membered Cr2O2 ring. The Cr(III) ion is coordinated in a distorted octa-hedron, which involves two N atoms of one bidentate ligand and one thio-cyanate anion, two μ2-O atoms of 2-(di-methyl-amino)-ethano-late ligands and two μ3-O atoms of hydroxide ions. The coordination geometry of the Pb(II) ion is a distorted disphenoid, which involves one N atom, two μ2-O atoms and one μ3-O atom. In addition, weak Pb⋯S inter-actions involving the coordinating and non-coordinating thio-cyanate anions are observed. In the crystal, the complex cations are linked through the thio-cyanate anions via the Pb⋯S inter-actions and O-H⋯N hydrogen bonds into chains along the c axis. The chains are further linked together via S⋯S contacts. The contribution of the disordered solvent aceto-nitrile mol-ecule was removed with the SQUEEZE [Spek (2015 ▸). Acta Cryst. C71, 9-18] procedure in PLATON. The solvent is included in the reported mol-ecular formula, weight and density.

Nonaqueous electrocatalytic water oxidation by a surface-bound Ru(bda)(L)₂ complex.

PubMed

Sheridan, Matthew V; Sherman, Benjamin D; Wee, Kyung-Ryang; Marquard, Seth L; Gold, Alexander S; Meyer, Thomas J

2016-04-21

The rate of electrocatalytic water oxidation by the heterogeneous water oxidation catalyst [Ru(bda)(4-O(CH2)3P(O3H2)2-pyr)2], , (pyr = pyridine; bda = 2,2'-bipyridine-6,6'-dicarboxylate) on metal oxide surfaces is greatly enhanced relative to water as the solvent. In these experiments with propylene carbonate (PC) as the nonaqueous solvent, water is the limiting reagent. Mechanistic studies point to atom proton transfer (APT) as the rate limiting step in water oxidation catalysis.

Quantifying the Molecular Origins of Opposite Solvent Effects on Protein-Protein Interactions

PubMed Central

Vagenende, Vincent; Han, Alvin X.; Pek, Han B.; Loo, Bernard L. W.

2013-01-01

Although the nature of solvent-protein interactions is generally weak and non-specific, addition of cosolvents such as denaturants and osmolytes strengthens protein-protein interactions for some proteins, whereas it weakens protein-protein interactions for others. This is exemplified by the puzzling observation that addition of glycerol oppositely affects the association constants of two antibodies, D1.3 and D44.1, with lysozyme. To resolve this conundrum, we develop a methodology based on the thermodynamic principles of preferential interaction theory and the quantitative characterization of local protein solvation from molecular dynamics simulations. We find that changes of preferential solvent interactions at the protein-protein interface quantitatively account for the opposite effects of glycerol on the antibody-antigen association constants. Detailed characterization of local protein solvation in the free and associated protein states reveals how opposite solvent effects on protein-protein interactions depend on the extent of dewetting of the protein-protein contact region and on structural changes that alter cooperative solvent-protein interactions at the periphery of the protein-protein interface. These results demonstrate the direct relationship between macroscopic solvent effects on protein-protein interactions and atom-scale solvent-protein interactions, and establish a general methodology for predicting and understanding solvent effects on protein-protein interactions in diverse biological environments. PMID:23696727

Quantifying the molecular origins of opposite solvent effects on protein-protein interactions.

PubMed

Vagenende, Vincent; Han, Alvin X; Pek, Han B; Loo, Bernard L W

2013-01-01

Although the nature of solvent-protein interactions is generally weak and non-specific, addition of cosolvents such as denaturants and osmolytes strengthens protein-protein interactions for some proteins, whereas it weakens protein-protein interactions for others. This is exemplified by the puzzling observation that addition of glycerol oppositely affects the association constants of two antibodies, D1.3 and D44.1, with lysozyme. To resolve this conundrum, we develop a methodology based on the thermodynamic principles of preferential interaction theory and the quantitative characterization of local protein solvation from molecular dynamics simulations. We find that changes of preferential solvent interactions at the protein-protein interface quantitatively account for the opposite effects of glycerol on the antibody-antigen association constants. Detailed characterization of local protein solvation in the free and associated protein states reveals how opposite solvent effects on protein-protein interactions depend on the extent of dewetting of the protein-protein contact region and on structural changes that alter cooperative solvent-protein interactions at the periphery of the protein-protein interface. These results demonstrate the direct relationship between macroscopic solvent effects on protein-protein interactions and atom-scale solvent-protein interactions, and establish a general methodology for predicting and understanding solvent effects on protein-protein interactions in diverse biological environments.

Analytical Debye-Huckel model for electrostatic potentials around dissolved DNA.

PubMed

Wagner, K; Keyes, E; Kephart, T W; Edwards, G

1997-07-01

We present an analytical, Green-function-based model for the electric potential of DNA in solution, treating the surrounding solvent with the Debye-Huckel approximation. The partial charge of each atom is accounted for by modeling DNA as linear distributions of atoms on concentric cylindrical surfaces. The condensed ions of the solvent are treated with the Debye-Huckel approximation. The resultant leading term of the potential is that of a continuous shielded line charge, and the higher order terms account for the helical structure. Within several angstroms of the surface there is sufficient information in the electric potential to distinguish features and symmetries of DNA. Plots of the potential and equipotential surfaces, dominated by the phosphate charges, reflect the structural differences between the A, B, and Z conformations and, to a smaller extent, the difference between base sequences. As the distances from the helices increase, the magnitudes of the potentials decrease. However, the bases and sugars account for a larger fraction of the double helix potential with increasing distance. We have found that when the solvent is treated with the Debye-Huckel approximation, the potential decays more rapidly in every direction from the surface than it did in the concentric dielectric cylinder approximation.

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

PubMed

Moncho, Salvador; Autschbach, Jochen

2010-01-12

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

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

Ghosh, H.N.; Pal, H.; Sapre, A.V.

Photoexcitation of complexes between fullerence C[sub 60] and organic amines in benzene solutions is known to result in charge separation (CS) and subsequent charge recombination (CR) reactions, which lead to varying yields of fullerence triplet formation. Picosecond flash photolysis studies are carried out on C[sub 60]-diphenylamine (DPA), C[sub 60]-triethylamine (TEA), C[sub 60]-diazabicyclooctane (DABCO), and C[sub 60]-triphenylamine (TPA) systems to find out mechanistic details of the triplet formation on CR by inducing heavy atom and polarity effects by using suitable solvents. It is found that in the case of C[sub 60]-DPA, C[sub 60]-TEA, and C[sub 60]-DABCO systems proton transfer from themore » amine cation to the C[sub 60] anion in the ion pair state dominates, leading to poor triplet yields, which improve in heavy atom containing solvents. In TPA, proton transfer is not possible and hence fullerene triplet yields are high. Increase of solvent polarity for this system results in decreased C[sub 60] triplet yields with a consequent increase in the ion dissociation yield. A suitable reaction scheme is proposed to explain the results obtained. 34 refs., 5 figs., 2 tabs.« less

Sub-μL measurements of the thermal conductivity and heat capacity of liquids.

PubMed

López-Bueno, C; Bugallo, D; Leborán, V; Rivadulla, F

2018-03-07

We present the analysis of the thermal conductivity, κ, and heat capacity, C p , of a wide variety of liquids, covering organic molecular solvents, ionic liquids and water-polymer mixtures. These data were obtained from ≈0.6 μL samples, using an experimental development based on the 3ω method, capable of the simultaneous measurement of κ and C p . In spite of the different type and strength of interactions, expected in a priori so different systems, the ratio of κ to the sound velocity is approximately constant for all of them. This is the consequence of a similar atomic density for all these liquids, notwithstanding their different molecular structures. This was corroborated experimentally by the observation of a C p /V ≈ 1.89 × 10 6 J K -1 m -3 (≈3R/2 per atom), for all liquids studied in this work. Finally, the very small volume of the sample required in this experimental method is an important advantage for the characterization of systems like nanofluids, in which having a large amount of the dispersed phase is sometimes extremely challenging.

Efficient implementation of constant pH molecular dynamics on modern graphics processors.

PubMed

Arthur, Evan J; Brooks, Charles L

2016-09-15

The treatment of pH sensitive ionization states for titratable residues in proteins is often omitted from molecular dynamics (MD) simulations. While static charge models can answer many questions regarding protein conformational equilibrium and protein-ligand interactions, pH-sensitive phenomena such as acid-activated chaperones and amyloidogenic protein aggregation are inaccessible to such models. Constant pH molecular dynamics (CPHMD) coupled with the Generalized Born with a Simple sWitching function (GBSW) implicit solvent model provide an accurate framework for simulating pH sensitive processes in biological systems. Although this combination has demonstrated success in predicting pKa values of protein structures, and in exploring dynamics of ionizable side-chains, its speed has been an impediment to routine application. The recent availability of low-cost graphics processing unit (GPU) chipsets with thousands of processing cores, together with the implementation of the accurate GBSW implicit solvent model on those chipsets (Arthur and Brooks, J. Comput. Chem. 2016, 37, 927), provide an opportunity to improve the speed of CPHMD and ionization modeling greatly. Here, we present a first implementation of GPU-enabled CPHMD within the CHARMM-OpenMM simulation package interface. Depending on the system size and nonbonded force cutoff parameters, we find speed increases of between one and three orders of magnitude. Additionally, the algorithm scales better with system size than the CPU-based algorithm, thus allowing for larger systems to be modeled in a cost effective manner. We anticipate that the improved performance of this methodology will open the door for broad-spread application of CPHMD in its modeling pH-mediated biological processes. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Implicit cognitive aggression among young male prisoners: Association with dispositional and current aggression.

PubMed

Ireland, Jane L; Adams, Christine

2015-01-01

The current study explores associations between implicit and explicit aggression in young adult male prisoners, seeking to apply the Reflection-Impulsive Model and indicate parity with elements of the General Aggression Model and social cognition. Implicit cognitive aggressive processing is not an area that has been examined among prisoners. Two hundred and sixty two prisoners completed an implicit cognitive aggression measure (Puzzle Test) and explicit aggression measures, covering current behaviour (DIPC-R) and aggression disposition (AQ). It was predicted that dispositional aggression would be predicted by implicit cognitive aggression, and that implicit cognitive aggression would predict current engagement in aggressive behaviour. It was also predicted that more impulsive implicit cognitive processing would associate with aggressive behaviour whereas cognitively effortful implicit cognitive processing would not. Implicit aggressive cognitive processing was associated with increased dispositional aggression but not current reports of aggressive behaviour. Impulsive implicit cognitive processing of an aggressive nature predicted increased dispositional aggression whereas more cognitively effortful implicit cognitive aggression did not. The article concludes by outlining the importance of accounting for implicit cognitive processing among prisoners and the need to separate such processing into facets (i.e. impulsive vs. cognitively effortful). Implications for future research and practice in this novel area of study are indicated. Copyright © 2015 Elsevier Ltd. All rights reserved.

Electrostatic Solvation Energy for Two Oppositely Charged Ions in a Solvated Protein System: Salt Bridges Can Stabilize Proteins

PubMed Central

Gong, Haipeng; Freed, Karl F.

2010-01-01

Abstract Born-type electrostatic continuum methods have been an indispensable ingredient in a variety of implicit-solvent methods that reduce computational effort by orders of magnitude compared to explicit-solvent MD simulations and thus enable treatment using larger systems and/or longer times. An analysis of the limitations and failures of the Born approaches serves as a guide for fundamental improvements without diminishing the importance of prior works. One of the major limitations of the Born theory is the lack of a liquidlike description of the response of solvent dipoles to the electrostatic field of the solute and the changes therein, a feature contained in the continuum Langevin-Debye (LD) model applied here to investigate how Coulombic interactions depend on the location of charges relative to the protein/water boundary. This physically more realistic LD model is applied to study the stability of salt bridges. When compared head to head using the same (independently measurable) physical parameters (radii, dielectric constants, etc.), the LD model is in good agreement with observations, whereas the Born model is grossly in error. Our calculations also suggest that a salt bridge on the protein's surface can be stabilizing when the charge separation is ≤4 Å. PMID:20141761

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Charge-transfer-to-solvent reactions from I{sup −} to water, methanol, and ethanol studied by time-resolved photoelectron spectroscopy of liquids

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

Okuyama, Haruki; Karashima, Shutaro; Suzuki, Toshinori, E-mail: suzuki@kuchem.kyoto-u.ac.jp

The charge-transfer-to-solvent (CTTS) reactions from iodide (I{sup −}) to H{sub 2}O, D{sub 2}O, methanol, and ethanol were studied by time-resolved photoelectron spectroscopy of liquid microjets using a magnetic bottle time-of-flight spectrometer with variable pass energy. Photoexcited iodide dissociates into a weak complex (a contact pair) of a solvated electron and an iodine atom in similar reaction times, 0.3 ps in H{sub 2}O and D{sub 2}O and 0.5 ps in methanol and ethanol, which are much shorter than their dielectric relaxation times. The results indicate that solvated electrons are formed with minimal solvent reorganization in the long-range solvent polarization field createdmore » for I{sup −}. The photoelectron spectra for CTTS in H{sub 2}O and D{sub 2}O—measured with higher accuracy than in our previous study [Y. I. Suzuki et al., Chem. Sci. 2, 1094 (2011)]—indicate that internal conversion yields from the photoexcited I{sup −*} (CTTS) state are less than 10%, while alcohols provide 2–3 times greater yields of internal conversion from I{sup −*}. The overall geminate recombination yields are found to be in the order of H{sub 2}O > D{sub 2}O > methanol > ethanol, which is opposite to the order of the mutual diffusion rates of an iodine atom and a solvated electron. This result is consistent with the transition state theory for an adiabatic outer-sphere electron transfer process, which predicts that the recombination reaction rate has a pre-exponential factor inversely proportional to a longitudinal solvent relaxation time.« less

Investigation of the dipole formation and growth behavior at In2O3|TiO2 heterojunctions using photoemission spectroscopy and atomic force microscopy

NASA Astrophysics Data System (ADS)

Schaefer, Michael; Halpegamage, Sandamali; Batzill, Matthias; Schlaf, Rudy

2016-02-01

This paper discusses the investigation of the dipole formation at In2O3|TiO2 heterojunctions depending on preparation conditions, i.e., cleaning methods. In2O3 films were deposited using atomic layer deposition (ALD) onto solvent and in situ cleaned anatase and rutile film substrates. The interface dipole strength and film thickness were evaluated by photoemission spectroscopy. Our results indicate the formation of a large intrinsic and film thickness dependent interface dipole that reaches its maximum strength at monolayer thick ALD films. In addition, it was observed that UV photoelectron spectroscopy measurements introduced UV induced surface hydroxylation, which resulted in dipole potentials of -0.70 eV and -0.50 eV on solvent cleaned anatase and rutile, respectively. The overlayers also introduced small amounts of band bending (˜0.10 eV) at the interfaces. Taking these effects into account, the total dipole strength at monolayer thick In2O3 films was determined to be -0.96 eV for solvent cleaned anatase and rutile and -0.81 eV for in situ cleaned rutile. The deposition of single ALD cycles on differently cleaned rutile substrates resulted in similar work function values, suggesting little influence of the sample preparation method prior to ALD deposition on the dipole formation. This was assigned to the fact that ALD oxides benefit from ambient water related contamination by integrating the molecules into the growing ALD layer. Highest initial growth was observed on solvent cleaned rutile, followed by in-situ cleaned rutile and solvent cleaned anatase. The In2O3 growth converged at 0.3 Å/c past the nucleation regime.

Formation of indomethacin-saccharin cocrystals using supercritical fluid technology.

PubMed

Padrela, Luis; Rodrigues, Miguel A; Velaga, Sitaram P; Matos, Henrique A; de Azevedo, Edmundo Gomes

2009-08-12

The main objective of the present work is to check the feasibility of supercritical fluid (SCF) technologies in the screening and design of cocrystals (novel crystalline solids). The cocrystal formation tendencies in three different SCF techniques, focusing on distinct supercritical fluid properties - solvent, anti-solvent and atomization enhancer - were investigated. The effect of processing parameters on the cocrystal formation behaviour and particle properties in these techniques was also studied. A recently reported indomethacin-saccharin (IND-SAC) cocrystalline system was our model system. A 1:1 molar ratio of indomethacin (gamma-form) and saccharin was used as a starting material. The SCF techniques employed in the study include the CSS technique (cocrystallization with supercritical solvent), the SAS technique (supercritical anti-solvent), and the AAS technique (atomization and anti-solvent). The resulting cocrystalline phase was identified using differential scanning calorimetry (DSC), powder X-ray diffraction (PXRD), and Fourier transform-Raman (FT-Raman). The particle morphologies and size distributions were determined using scanning electron microscopy (SEM) and aerosizer, respectively. The pure IND-SAC cocrystals were obtained from SAS and AAS processes, whilst partial to no cocrystal formation occurred in the CSS process. However, no remarkable differences were observed in terms of cocrystal formation at different processing conditions in SAS and AAS processes. Particles from CSS processes were agglomerated and large, whilst needle-to-block-shaped and spherical particles were obtained from SAS and AAS processes, respectively. The particle size distribution of these particles was 0.2-5microm. Particulate IND-SAC cocrystals with different morphologies and sizes (nano-to-micron) were produced using supercritical fluid techniques. This work demonstrates the potential of SCF technologies as screening methods for cocrystals with possibilities for particle engineering.

Proposed Test of Relative Phase as Hidden Variable in Quantum Mechanics

DTIC Science & Technology

2012-01-01

implicitly due to its ubiquity in quantum theory , but searches for dependence of measurement outcome on other parameters have been lacking. For a two -state...implemen- tation for the specific case of an atomic two -state system with laser-induced fluores- cence for measurement. Keywords Quantum measurement...Measurement postulate · Born rule 1 Introduction 1.1 Problems with Quantum Measurement Quantum theory prescribes probabilities for outcomes of measurements

Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation

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

Sanyal, Tanmoy; Shell, M. Scott, E-mail: shell@engineering.ucsb.edu

Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one atmore » which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.« less

The Determination of Trace Metals in Saline Waters and Biological Tissues Using the Heated Graphite Atomizer

NASA Technical Reports Server (NTRS)

Segar, D. A.

1971-01-01

A selective, volatalization technique utilizing the heated graphite atomizer atomic absorption technique has been developed for the analysis of iron in sea water. A similar technique may be used to determine vanadium, copper, nickel and cobalt in saline waters when their concentrations are higher than those normally encountered'in unpolluted sea waters. A preliminary solvent extraction using ammonium pyrolidine dithiocarbamate and methyl iso-butyl ketone permits the determination of a number of elements including iron, copper, zinc, nickel, cobalt and lead in sea water. The heated graphite atomized technique has also been applied to the determination of a range of trace transition elements in marine plant and animal tissues.

High School Students' Implicit Theories of What Facilitates Science Learning

ERIC Educational Resources Information Center

Parsons, Eileen Carlton; Miles, Rhea; Petersen, Michael

2011-01-01

Background: Research has primarily concentrated on adults' implicit theories about high quality science education for all students. Little work has considered the students' perspective. This study investigated high school students' implicit theories about what helped them learn science. Purpose: This study addressed (1) What characterizes high…

Multiscale modeling of a rectifying bipolar nanopore: explicit-water versus implicit-water simulations.

PubMed

Ható, Zoltán; Valiskó, Mónika; Kristóf, Tamás; Gillespie, Dirk; Boda, Dezsö

2017-07-21

In a multiscale modeling approach, we present computer simulation results for a rectifying bipolar nanopore at two modeling levels. In an all-atom model, we use explicit water to simulate ion transport directly with the molecular dynamics technique. In a reduced model, we use implicit water and apply the Local Equilibrium Monte Carlo method together with the Nernst-Planck transport equation. This hybrid method makes the fast calculation of ion transport possible at the price of lost details. We show that the implicit-water model is an appropriate representation of the explicit-water model when we look at the system at the device (i.e., input vs. output) level. The two models produce qualitatively similar behavior of the electrical current for different voltages and model parameters. Looking at the details of concentration and potential profiles, we find profound differences between the two models. These differences, however, do not influence the basic behavior of the model as a device because they do not influence the z-dependence of the concentration profiles which are the main determinants of current. These results then address an old paradox: how do reduced models, whose assumptions should break down in a nanoscale device, predict experimental data? Our simulations show that reduced models can still capture the overall device physics correctly, even though they get some important aspects of the molecular-scale physics quite wrong; reduced models work because they include the physics that is necessary from the point of view of device function. Therefore, reduced models can suffice for general device understanding and device design, but more detailed models might be needed for molecular level understanding.

Fluorescent aliphatic hyperbranched polyether: chromophore-free and without any N and P atoms.

PubMed

Miao, Xuepei; Liu, Tuan; Zhang, Chen; Geng, Xinxin; Meng, Yan; Li, Xiaoyu

2016-02-14

The strong fluorescence, in both the solution and the bulk state, of a chromophore-free aliphatic hyperbranched polyether which does not contain N and P atoms was reported for the first time. Effects of concentration and solvent solubility were measured. Its ethanol solution shows a strong blue-green fluorescence (Yu = 0.11-0.39), and its fluorescence shows a strong selective quenching with respect to Fe(3+).

Measuring implicit attitudes: A positive framing bias flaw in the Implicit Relational Assessment Procedure (IRAP).

PubMed

O'Shea, Brian; Watson, Derrick G; Brown, Gordon D A

2016-02-01

How can implicit attitudes best be measured? The Implicit Relational Assessment Procedure (IRAP), unlike the Implicit Association Test (IAT), claims to measure absolute, not just relative, implicit attitudes. In the IRAP, participants make congruent (Fat Person-Active: false; Fat Person-Unhealthy: true) or incongruent (Fat Person-Active: true; Fat Person-Unhealthy: false) responses in different blocks of trials. IRAP experiments have reported positive or neutral implicit attitudes (e.g., neutral attitudes toward fat people) in cases in which negative attitudes are normally found on explicit or other implicit measures. It was hypothesized that these results might reflect a positive framing bias (PFB) that occurs when participants complete the IRAP. Implicit attitudes toward categories with varying prior associations (nonwords, social systems, flowers and insects, thin and fat people) were measured. Three conditions (standard, positive framing, and negative framing) were used to measure whether framing influenced estimates of implicit attitudes. It was found that IRAP scores were influenced by how the task was framed to the participants, that the framing effect was modulated by the strength of prior stimulus associations, and that a default PFB led to an overestimation of positive implicit attitudes when measured by the IRAP. Overall, the findings question the validity of the IRAP as a tool for the measurement of absolute implicit attitudes. A new tool (Simple Implicit Procedure:SIP) for measuring absolute, not just relative, implicit attitudes is proposed. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Experimental Issues in Coherent Quantum-State Manipulation of Trapped Atomic Ions

PubMed Central

Wineland, D. J.; Monroe, C.; Itano, W. M.; Leibfried, D.; King, B. E.; Meekhof, D. M.

1998-01-01

Methods for, and limitations to, the generation of entangled states of trapped atomic ions are examined. As much as possible, state manipulations are described in terms of quantum logic operations since the conditional dynamics implicit in quantum logic is central to the creation of entanglement. Keeping with current interest, some experimental issues in the proposal for trappedion quantum computation by J. I. Cirac and P. Zoller (University of Innsbruck) are discussed. Several possible decoherence mechanisms are examined and what may be the more important of these are identified. Some potential applications for entangled states of trapped-ions which lie outside the immediate realm of quantum computation are also discussed. PMID:28009379

Ion-mediated interactions in suspensions of oppositely charged nanoparticles

NASA Astrophysics Data System (ADS)

Dahirel, Vincent; Hansen, Jean Pierre

2009-08-01

The structure of oppositely charged spherical nanoparticles (polyions), dispersed in ionic solutions with continuous solvent (primitive model), is investigated by Monte Carlo (MC) simulations, within explicit and implicit microion representations, over a range of polyion valences and densities, and microion concentrations. Systems with explicit microions are explored by semigrand canonical MC simulations, and allow density-dependent effective polyion pair potentials vαβeff(r ) to be extracted from measured partial pair distribution functions. Implicit microion MC simulations are based on pair potentials of mean force vαβ(2)(r ) computed by explicit microion simulations of two charged polyions, in the low density limit. In the vicinity of the liquid-gas separation expected for oppositely charged polyions, the implicit microion representation leads to an instability against density fluctuations for polyion valences |Z| significantly below those at which the instability sets in within the exact explicit microion representation. Far from this instability region, the vαβ(2)(r ) are found to be fairly close to but consistently more repulsive than the effective pair potentials vαβeff(r ). This is corroborated by additional calculations of three-body forces between polyion triplets, which are repulsive when one polyion is of opposite charge to the other two. The explicit microion MC data were exploited to determine the ratio of salt concentrations c and co within the dispersion and the reservoir (Donnan effect). c /co is found to first increase before finally decreasing as a function of the polyion packing fraction.

Unraveling cellulose microfibrils: a twisted tale.

PubMed

Hadden, Jodi A; French, Alfred D; Woods, Robert J

2013-10-01

Molecular dynamics (MD) simulations of cellulose microfibrils are pertinent to the paper, textile, and biofuels industries for their unique capacity to characterize dynamic behavior and atomic-level interactions with solvent molecules and cellulase enzymes. While high-resolution crystallographic data have established a solid basis for computational analysis of cellulose, previous work has demonstrated a tendency for modeled microfibrils to diverge from the linear experimental structure and adopt a twisted conformation. Here, we investigate the dependence of this twisting behavior on computational approximations and establish the theoretical basis for its occurrence. We examine the role of solvent, the effect of nonbonded force field parameters [partial charges and van der Waals (vdW) contributions], and the use of explicitly modeled oxygen lone pairs in both the solute and solvent. Findings suggest that microfibril twisting is favored by vdW interactions, and counteracted by both intrachain hydrogen bonds and solvent effects at the microfibril surface. Copyright © 2013 Wiley Periodicals, Inc.

Unraveling Cellulose Microfibrils: A Twisted Tale

PubMed Central

Hadden, Jodi A.; French, Alfred D.; Woods, Robert J.

2014-01-01

Molecular dynamics (MD) simulations of cellulose microfibrils are pertinent to the paper, textile, and biofuels industries for their unique capacity to characterize dynamic behavior and atomic-level interactions with solvent molecules and cellulase enzymes. While high-resolution crystallographic data have established a solid basis for computational analysis of cellulose, previous work has demonstrated a tendency for modeled microfibrils to diverge from the linear experimental structure and adopt a twisted conformation. Here, we investigate the dependence of this twisting behavior on computational approximations and establish the theoretical basis for its occurrence. We examine the role of solvent, the effect of nonbonded force field parameters [partial charges and van der Waals (vdW) contributions], and the use of explicitly modeled oxygen lone pairs in both the solute and solvent. Findings suggest that microfibril twisting is favored by vdW interactions, and counteracted by both intrachain hydrogen bonds and solvent effects at the microfibril surface. PMID:23681971

Nuclear magnetic resonance spectral analysis and molecular properties of berberine

NASA Astrophysics Data System (ADS)

Huang, Ming-Ju; Lee, Ken S.; Hurley, Sharon J.

An extensive theoretical study of berberine has been performed at the ab initio HF/6-31G**, HF/6-311G**, and B3LYP/6-311G** levels with and without solvent effects. The optimized structures are compared with X-ray data. We found that the optimized structures with solvent effects are in slightly better agreement with X-ray data than those without solvent effects. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of berberine were calculated by using the gauge-independent atomic orbital (GIAO) (with and without solvent effects), CSGT, and IGAIM methods. The calculated chemical shifts were compared with the two-dimensional NMR experimental data. Overall, the calculated chemical shifts show very good agreement with the experimental results. The harmonic vibrational frequencies for berberine were calculated at the B3LYP/6-311G** level.

Effects of Solvent Diols on the Synthesis of ZnFe2O4 Particles and Their Use as Heterogeneous Photo-Fenton Catalysts

PubMed Central

Anchieta, Chayene Gonçalves; Cancelier, Adriano; Mazutti, Marcio Antonio; Jahn, Sérgio Luiz; Kuhn, Raquel Cristine; Gündel, Andre; Chiavone-Filho, Osvaldo; Foletto, Edson Luiz

2014-01-01

A solvothermal method was used to prepare zinc ferrite spinel oxide (ZnFe2O4) using ethylene glycol and 1,4 butanediol as solvent diols, and the influence of diols on the physical properties of ZnFe2O4 particles was investigated. The produced particles were characterized by X-ray powder diffraction (XRD), atomic force microscopy (AFM), Fourier transform infrared spectroscopy (FTIR) and nitrogen adsorption isotherms, and the catalytic activity for the organic pollutant decomposition by heterogeneous photo-Fenton reaction was investigated. Both solvents produced particles with cubic spinel structure. Microporous and mesoporous structures were obtained when ethylene glycol and 1,4 butanediol were used as diols, respectively. A higher pore volume and surface area, as well as a higher catalytic activity for the pollutant degradation were found when 1,4 butanediol was used as solvent. PMID:28788191

Accurate pKa calculation of the conjugate acids of alkanolamines, alkaloids and nucleotide bases by quantum chemical methods.

PubMed

Gangarapu, Satesh; Marcelis, Antonius T M; Zuilhof, Han

2013-04-02

The pKa of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08-HX and M11-L) and ab initio methods (SCS-MP2, G3). Implicit solvent effects are included with a conductor-like polarizable continuum model (CPCM) and universal solvation models (SMD, SM8). G3, SCS-MP2 and M11-L methods coupled with SMD and SM8 solvation models perform well for alkanolamines with mean unsigned errors below 0.20 pKa units, in all cases. Extending this method to the pKa calculation of 35 nitrogen-containing compounds spanning 12 pKa units showed an excellent correlation between experimental and computational pKa values of these 35 amines with the computationally low-cost SM8/M11-L density functional approach. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Iron species determination by task-specific ionic liquid-based in situ solvent formation dispersive liquid-liquid microextraction combined with flame atomic absorption spectrometry.

PubMed

Sadeghi, Susan; Ashoori, Vahid

2017-10-01

The task-specific ionic liquid (TSIL) of 1-ethyl-3-methylimidazolium bromide functionalized with 8-hydroxyquinoline was used as a chelating agent and extracting solvent for dispersive liquid-liquid microextraction and subsequent determination of Fe(III) by flame atomic absorption spectrometry. The in situ solvent formation of TSIL using KPF 6 provided the desired water-immiscible ionic liquid. The total Fe concentration could be determined after pre-oxidation of Fe(II) to Fe(III). Various factors affecting the proposed extraction procedure were optimized. The proposed analytical conditions were: sample pH 5, TSIL amount 0.3% (w/v), KPF 6 amount 0.15% (w/v), anti-sticking 0.1% (w/v) and salt concentration 5% (w/v). Under optimal conditions, the linear dynamic ranges for Fe(III) and total Fe were 20-80 and 20-110 ng mL -1 , respectively, with a detection limit of 6.9 ng mL -1 for Fe(III) and relative standard deviation of 2.2%. The proposed method was successfully applied to the determination of trace Fe(III) in water (underground, tap, refined water and artificial sea water) and beverage (apple, tomato, and tea) samples. The developed method offers advantages such as simplicity, ease of operation, and extraction of Fe(III) from aqueous solutions without the use of organic solvent. It was successfully applied for iron speciation in different real samples. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Implicit visual learning and the expression of learning.

PubMed

Haider, Hilde; Eberhardt, Katharina; Kunde, Alexander; Rose, Michael

2013-03-01

Although the existence of implicit motor learning is now widely accepted, the findings concerning perceptual implicit learning are ambiguous. Some researchers have observed perceptual learning whereas other authors have not. The review of the literature provides different reasons to explain this ambiguous picture, such as differences in the underlying learning processes, selective attention, or differences in the difficulty to express this knowledge. In three experiments, we investigated implicit visual learning within the original serial reaction time task. We used different response devices (keyboard vs. mouse) in order to manipulate selective attention towards response dimensions. Results showed that visual and motor sequence learning differed in terms of RT-benefits, but not in terms of the amount of knowledge assessed after training. Furthermore, visual sequence learning was modulated by selective attention. However, the findings of all three experiments suggest that selective attention did not alter implicit but rather explicit learning processes. Copyright © 2012 Elsevier Inc. All rights reserved.